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IMP Reference Guide  2.23.0
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.3.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2025 IMP Inventors. All rights reserved.
10 
11 
12 
13 
14 from sys import version_info as _swig_python_version_info
15 import _IMP_atom
16 
17 try:
18  import builtins as __builtin__
19 except ImportError:
20  import __builtin__
21 
22 def _swig_repr(self):
23  try:
24  strthis = "proxy of " + self.this.__repr__()
25  except __builtin__.Exception:
26  strthis = ""
27  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
28 
29 
30 def _swig_setattr_nondynamic_instance_variable(set):
31  def set_instance_attr(self, name, value):
32  if name == "this":
33  set(self, name, value)
34  elif name == "thisown":
35  self.this.own(value)
36  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
37  set(self, name, value)
38  else:
39  raise AttributeError("You cannot add instance attributes to %s" % self)
40  return set_instance_attr
41 
42 
43 def _swig_setattr_nondynamic_class_variable(set):
44  def set_class_attr(cls, name, value):
45  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
46  set(cls, name, value)
47  else:
48  raise AttributeError("You cannot add class attributes to %s" % cls)
49  return set_class_attr
50 
51 
52 def _swig_add_metaclass(metaclass):
53  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
54  def wrapper(cls):
55  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
56  return wrapper
57 
58 
59 class _SwigNonDynamicMeta(type):
60  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
62 
63 
64 import weakref
65 
66 class IMP_ATOM_SwigPyIterator(object):
67  r"""Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
68 
69  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
70 
71  def __init__(self, *args, **kwargs):
72  raise AttributeError("No constructor defined - class is abstract")
73  __repr__ = _swig_repr
74  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
75 
76  def value(self):
77  r"""value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
78  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
79 
80  def incr(self, n=1):
81  r"""incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
82  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
83 
84  def decr(self, n=1):
85  r"""decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
86  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
87 
88  def distance(self, x):
89  r"""distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
90  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
91 
92  def equal(self, x):
93  r"""equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
94  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
95 
96  def copy(self):
97  r"""copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
98  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
99 
100  def next(self):
101  r"""next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
102  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
103 
104  def __next__(self):
105  r"""__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
106  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
107 
108  def previous(self):
109  r"""previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
110  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
111 
112  def advance(self, n):
113  r"""advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
114  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
115 
116  def __eq__(self, x):
117  r"""__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
118  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
119 
120  def __ne__(self, x):
121  r"""__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
122  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
123 
124  def __iadd__(self, n):
125  r"""__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
126  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
127 
128  def __isub__(self, n):
129  r"""__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
130  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
131 
132  def __add__(self, n):
133  r"""__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
134  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
135 
136  def __sub__(self, *args):
137  r"""
138  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
139  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
140  """
141  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
142  def __iter__(self):
143  return self
144 
145 # Register IMP_ATOM_SwigPyIterator in _IMP_atom:
146 _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
147 
148 _value_types=[]
149 _object_types=[]
150 _raii_types=[]
151 _plural_types=[]
152 
153 IMP_DEBUG = _IMP_atom.IMP_DEBUG
154 
155 IMP_RELEASE = _IMP_atom.IMP_RELEASE
156 
157 IMP_SILENT = _IMP_atom.IMP_SILENT
158 
159 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
160 
161 IMP_TERSE = _IMP_atom.IMP_TERSE
162 
163 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
164 
165 IMP_MEMORY = _IMP_atom.IMP_MEMORY
166 
167 IMP_NONE = _IMP_atom.IMP_NONE
168 
169 IMP_USAGE = _IMP_atom.IMP_USAGE
170 
171 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
172 
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
174 
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_atom.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
176 
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
178 
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_atom.IMP_COMPILER_HAS_RANDOM_SHUFFLE
180 
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_atom.IMP_COMPILER_HAS_THREE_WAY
182 
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
184 
185 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
186 
187 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
188 
189 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
192 
193 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
194 
195 
196 import sys
197 class _DirectorObjects:
198  """@internal Simple class to keep references to director objects
199  to prevent premature deletion."""
200  def __init__(self):
201  self._objects = []
202  def register(self, obj):
203  """Take a reference to a director object; will only work for
204  refcounted C++ classes"""
205  if hasattr(obj, 'get_ref_count'):
206  self._objects.append(obj)
207  def cleanup(self):
208  """Only drop our reference and allow cleanup by Python if no other
209  Python references exist (we hold 3 references: one in self._objects,
210  one in x, and one in the argument list for getrefcount) *and* no
211  other C++ references exist (the Python object always holds one)"""
212  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
213  or x.get_ref_count() > 1]
214 # Do in two steps so the references are kept until the end of the
215 # function (deleting references may trigger a fresh call to this method)
216  self._objects = objs
217  def get_object_count(self):
218  """Get number of director objects (useful for testing only)"""
219  return len(self._objects)
220 _director_objects = _DirectorObjects()
221 
222 class _ostream(object):
223  r"""Proxy of C++ std::ostream class."""
224 
225  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
226 
227  def __init__(self, *args, **kwargs):
228  raise AttributeError("No constructor defined")
229  __repr__ = _swig_repr
230 
231  def write(self, osa_buf):
232  r"""write(_ostream self, char const * osa_buf)"""
233  return _IMP_atom._ostream_write(self, osa_buf)
234 
235 # Register _ostream in _IMP_atom:
236 _IMP_atom._ostream_swigregister(_ostream)
237 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
238 
239 import IMP
240 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
241 
242 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
243 
244 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
245 
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
247 
248 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
249 
250 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
251 
252 import IMP.cgal
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
254 
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
256 
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
258 
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
260 
261 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
262 
263 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
264 
265 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
266 
267 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
268 
269 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
270 
271 import IMP.algebra
272 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
273 
274 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
275 
276 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
277 
278 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
279 
280 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
281 
282 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
283 
284 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
285 
286 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
287 
288 import IMP.display
289 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
292 
293 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
294 
295 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
296 
297 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
298 
299 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
300 
301 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
302 
303 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
304 
305 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
306 
307 import IMP.score_functor
308 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
309 
310 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
311 
312 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
313 
314 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
315 
316 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
317 
318 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
319 
320 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
321 
322 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
323 
324 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
325 
326 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
327 
328 import IMP.core
329 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
330 
331 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
332 
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
334 
335 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
336 
337 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
338 
339 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
340 
341 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
342 
343 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
344 
345 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
346 
347 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
348 
349 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
350 
351 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
352 
353 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
354 
355 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
356 
357 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
358 
359 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
360 
361 import IMP.container
362 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
363 
364 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
365 
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 
368 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
369 
370 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
371 
372 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
373 
374 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
375 
376 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
377 
378 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
379 
380 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
381 
382 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
383 
384 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
385 
386 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
387 
388 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
389 
390 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
391 
392 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
393 
395  r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex > class."""
396 
397  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
398  __repr__ = _swig_repr
399 
400  def __init__(self):
401  r"""__init__(HierarchyTree self) -> HierarchyTree"""
402  _IMP_atom.HierarchyTree_swiginit(self, _IMP_atom.new_HierarchyTree())
403 
404  def get_graph(self):
405  r"""get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
406  return _IMP_atom.HierarchyTree_get_graph(self)
407 
408  def get_vertices(self):
409  r"""get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
410  return _IMP_atom.HierarchyTree_get_vertices(self)
411 
412  def get_vertex_name(self, i):
413  r"""get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
414  return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
415 
416  def get_in_neighbors(self, v):
417  r"""get_in_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
418  return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
419 
420  def get_out_neighbors(self, v):
421  r"""get_out_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
422  return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
423 
424  def show_graphviz(self, *args):
425  r"""show_graphviz(HierarchyTree self, _ostream out=std::cout)"""
426  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
427 
428  def get_graphviz_string(self):
429  r"""get_graphviz_string(HierarchyTree self) -> std::string"""
430  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
431 
432  def add_edge(self, v0, v1):
433  r"""add_edge(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)"""
434  return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
435 
436  def add_vertex(self, l):
437  r"""add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
438  return _IMP_atom.HierarchyTree_add_vertex(self, l)
439 
440  def remove_vertex(self, l):
441  r"""remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
442  return _IMP_atom.HierarchyTree_remove_vertex(self, l)
443  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
444 
445 # Register HierarchyTree in _IMP_atom:
446 _IMP_atom.HierarchyTree_swigregister(HierarchyTree)
447 
448 _value_types.append("HierarchyTree")
449 
450 
451 PDBRecords=list
452 _plural_types.append("PDBRecords")
453 _value_types.append("PDBRecord")
454 
455 
456 _object_types.append("LennardJonesType")
457 
458 
459 def _object_cast_to_LennardJonesType(o):
460  r"""_object_cast_to_LennardJonesType(Object o) -> LennardJonesType"""
461  return _IMP_atom._object_cast_to_LennardJonesType(o)
462 
463 _object_types.append("PDBSelector")
464 
465 
466 def _object_cast_to_PDBSelector(o):
467  r"""_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
468  return _IMP_atom._object_cast_to_PDBSelector(o)
469 
470 def Angles(l=[]):
471  return [Angle(x) for x in l]
472 _plural_types.append("Angles")
473 
474 
475 _value_types.append("Angle")
476 
477 
478 def Atoms(l=[]):
479  return [Atom(x) for x in l]
480 _plural_types.append("Atoms")
481 
482 
483 _value_types.append("Atom")
484 
485 
486 def Bonds(l=[]):
487  return [Bond(x) for x in l]
488 _plural_types.append("Bonds")
489 
490 
491 _value_types.append("Bond")
492 
493 
494 def Bondeds(l=[]):
495  return [Bonded(x) for x in l]
496 _plural_types.append("Bondeds")
497 
498 
499 _value_types.append("Bonded")
500 
501 
502 def CHARMMAtomList(l=[]):
503  return [CHARMMAtom(x) for x in l]
504 _plural_types.append("CHARMMAtomList")
505 
506 
507 _value_types.append("CHARMMAtom")
508 
509 
510 def Chains(l=[]):
511  return [Chain(x) for x in l]
512 _plural_types.append("Chains")
513 
514 
515 _value_types.append("Chain")
516 
517 
518 def CenterOfMasses(l=[]):
519  return [CenterOfMass(x) for x in l]
520 _plural_types.append("CenterOfMasses")
521 
522 
523 _value_types.append("CenterOfMass")
524 
525 
526 def Chargeds(l=[]):
527  return [Charged(x) for x in l]
528 _plural_types.append("Chargeds")
529 
530 
531 _value_types.append("Charged")
532 
533 
534 def Diffusions(l=[]):
535  return [Diffusion(x) for x in l]
536 _plural_types.append("Diffusions")
537 
538 
539 _value_types.append("Diffusion")
540 
541 
542 def RigidBodyDiffusions(l=[]):
543  return [RigidBodyDiffusion(x) for x in l]
544 _plural_types.append("RigidBodyDiffusions")
545 
546 
547 _value_types.append("RigidBodyDiffusion")
548 
549 
550 def TAMDParticles(l=[]):
551  return [TAMDParticle(x) for x in l]
552 _plural_types.append("TAMDParticles")
553 
554 
555 _value_types.append("TAMDParticle")
556 
557 
558 def TAMDCentroids(l=[]):
559  return [TAMDCentroid(x) for x in l]
560 _plural_types.append("TAMDCentroids")
561 
562 
563 _value_types.append("TAMDCentroid")
564 
565 
566 def Dihedrals(l=[]):
567  return [Dihedral(x) for x in l]
568 _plural_types.append("Dihedrals")
569 
570 
571 _value_types.append("Dihedral")
572 
573 
574 def Domains(l=[]):
575  return [Domain(x) for x in l]
576 _plural_types.append("Domains")
577 
578 
579 _value_types.append("Domain")
580 
581 
582 def Fragments(l=[]):
583  return [Fragment(x) for x in l]
584 _plural_types.append("Fragments")
585 
586 
587 _value_types.append("Fragment")
588 
589 
590 def Hierarchies(l=[]):
591  return [Hierarchy(x) for x in l]
592 _plural_types.append("Hierarchies")
593 
594 
595 _value_types.append("Hierarchy")
596 
597 
598 def LennardJonesList(l=[]):
599  return [LennardJones(x) for x in l]
600 _plural_types.append("LennardJonesList")
601 
602 
603 _value_types.append("LennardJones")
604 
605 
606 def LennardJonesTypeds(l=[]):
607  return [LennardJonesTyped(x) for x in l]
608 _plural_types.append("LennardJonesTypeds")
609 
610 
611 _value_types.append("LennardJonesTyped")
612 
613 
614 def Masses(l=[]):
615  return [Mass(x) for x in l]
616 _plural_types.append("Masses")
617 
618 
619 _value_types.append("Mass")
620 
621 
622 def LinearVelocities(l=[]):
623  return [LinearVelocity(x) for x in l]
624 _plural_types.append("LinearVelocities")
625 
626 
627 _value_types.append("LinearVelocity")
628 
629 
630 def AngularVelocities(l=[]):
631  return [AngularVelocity(x) for x in l]
632 _plural_types.append("AngularVelocities")
633 
634 
635 _value_types.append("AngularVelocity")
636 
637 
638 def Molecules(l=[]):
639  return [Molecule(x) for x in l]
640 _plural_types.append("Molecules")
641 
642 
643 _value_types.append("Molecule")
644 
645 
646 def Residues(l=[]):
647  return [Residue(x) for x in l]
648 _plural_types.append("Residues")
649 
650 
651 _value_types.append("Residue")
652 
653 
654 def Representations(l=[]):
655  return [Representation(x) for x in l]
656 _plural_types.append("Representations")
657 
658 
659 _value_types.append("Representation")
660 
661 
662 def States(l=[]):
663  return [State(x) for x in l]
664 _plural_types.append("States")
665 
666 
667 _value_types.append("State")
668 
669 
670 def Copies(l=[]):
671  return [Copy(x) for x in l]
672 _plural_types.append("Copies")
673 
674 
675 _value_types.append("Copy")
676 
677 
678 def SecondaryStructureResidues(l=[]):
679  return [SecondaryStructureResidue(x) for x in l]
680 _plural_types.append("SecondaryStructureResidues")
681 
682 
683 _value_types.append("SecondaryStructureResidue")
684 
685 
686 def StructureSources(l=[]):
687  return [StructureSource(x) for x in l]
688 _plural_types.append("StructureSources")
689 
690 
691 _value_types.append("StructureSource")
692 
693 
694 _object_types.append("Simulator")
695 
696 
697 def _object_cast_to_Simulator(o):
698  r"""_object_cast_to_Simulator(Object o) -> Simulator"""
699  return _IMP_atom._object_cast_to_Simulator(o)
700 
701 _object_types.append("ATOMPDBSelector")
702 
703 
704 def _object_cast_to_ATOMPDBSelector(o):
705  r"""_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
706  return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
707 
708 _object_types.append("AllMol2Selector")
709 
710 
711 def _object_cast_to_AllMol2Selector(o):
712  r"""_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
713  return _IMP_atom._object_cast_to_AllMol2Selector(o)
714 
715 _object_types.append("AllPDBSelector")
716 
717 
718 def _object_cast_to_AllPDBSelector(o):
719  r"""_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
720  return _IMP_atom._object_cast_to_AllPDBSelector(o)
721 
722 _object_types.append("AndPDBSelector")
723 
724 
725 def _object_cast_to_AndPDBSelector(o):
726  r"""_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
727  return _IMP_atom._object_cast_to_AndPDBSelector(o)
728 
729 _object_types.append("XorPDBSelector")
730 
731 
732 def _object_cast_to_XorPDBSelector(o):
733  r"""_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
734  return _IMP_atom._object_cast_to_XorPDBSelector(o)
735 
736 _object_types.append("ResidueTypePDBSelector")
737 
738 
739 def _object_cast_to_ResidueTypePDBSelector(o):
740  r"""_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
741  return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
742 
743 _object_types.append("AtomTypePDBSelector")
744 
745 
746 def _object_cast_to_AtomTypePDBSelector(o):
747  r"""_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
748  return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
749 
750 _object_types.append("AngleSingletonScore")
751 
752 
753 def _object_cast_to_AngleSingletonScore(o):
754  r"""_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
755  return _IMP_atom._object_cast_to_AngleSingletonScore(o)
756 
757 _object_types.append("BondEndpointsRefiner")
758 
759 
760 def _object_cast_to_BondEndpointsRefiner(o):
761  r"""_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
762  return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
763 
764 _object_types.append("BondPairContainer")
765 
766 
767 def _object_cast_to_BondPairContainer(o):
768  r"""_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
769  return _IMP_atom._object_cast_to_BondPairContainer(o)
770 
771 _object_types.append("BondSingletonScore")
772 
773 
774 def _object_cast_to_BondSingletonScore(o):
775  r"""_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
776  return _IMP_atom._object_cast_to_BondSingletonScore(o)
777 
778 _object_types.append("BondedPairFilter")
779 
780 
781 def _object_cast_to_BondedPairFilter(o):
782  r"""_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
783  return _IMP_atom._object_cast_to_BondedPairFilter(o)
784 
785 _object_types.append("BrownianDynamics")
786 
787 
788 def _object_cast_to_BrownianDynamics(o):
789  r"""_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
790  return _IMP_atom._object_cast_to_BrownianDynamics(o)
791 
792 _object_types.append("BrownianDynamicsTAMD")
793 
794 
795 def _object_cast_to_BrownianDynamicsTAMD(o):
796  r"""_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
797  return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
798 
799 _object_types.append("CAlphaPDBSelector")
800 
801 
802 def _object_cast_to_CAlphaPDBSelector(o):
803  r"""_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
804  return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
805 
806 _object_types.append("CBetaPDBSelector")
807 
808 
809 def _object_cast_to_CBetaPDBSelector(o):
810  r"""_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
811  return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
812 
813 _object_types.append("BackbonePDBSelector")
814 
815 
816 def _object_cast_to_BackbonePDBSelector(o):
817  r"""_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
818  return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
819 
820 _object_types.append("CHARMMParameters")
821 
822 
823 def _object_cast_to_CHARMMParameters(o):
824  r"""_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
825  return _IMP_atom._object_cast_to_CHARMMParameters(o)
826 
827 _object_types.append("CHARMMResidueTopology")
828 
829 
830 def _object_cast_to_CHARMMResidueTopology(o):
831  r"""_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
832  return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
833 
834 _object_types.append("CHARMMSegmentTopology")
835 
836 
837 def _object_cast_to_CHARMMSegmentTopology(o):
838  r"""_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
839  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
840 
841 _object_types.append("CHARMMStereochemistryRestraint")
842 
843 
844 def _object_cast_to_CHARMMStereochemistryRestraint(o):
845  r"""_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
846  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
847 
848 _object_types.append("CHARMMTopology")
849 
850 
851 def _object_cast_to_CHARMMTopology(o):
852  r"""_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
853  return _IMP_atom._object_cast_to_CHARMMTopology(o)
854 
855 _object_types.append("CPDBSelector")
856 
857 
858 def _object_cast_to_CPDBSelector(o):
859  r"""_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
860  return _IMP_atom._object_cast_to_CPDBSelector(o)
861 
862 _object_types.append("ChainPDBSelector")
863 
864 
865 def _object_cast_to_ChainPDBSelector(o):
866  r"""_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
867  return _IMP_atom._object_cast_to_ChainPDBSelector(o)
868 
869 _object_types.append("CoulombPairScore")
870 
871 
872 def _object_cast_to_CoulombPairScore(o):
873  r"""_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
874  return _IMP_atom._object_cast_to_CoulombPairScore(o)
875 
876 _object_types.append("CoverBond")
877 
878 
879 def _object_cast_to_CoverBond(o):
880  r"""_object_cast_to_CoverBond(Object o) -> CoverBond"""
881  return _IMP_atom._object_cast_to_CoverBond(o)
882 
883 _object_types.append("DihedralSingletonScore")
884 
885 
886 def _object_cast_to_DihedralSingletonScore(o):
887  r"""_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
888  return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
889 
890 _object_types.append("DopePairScore")
891 
892 
893 def _object_cast_to_DopePairScore(o):
894  r"""_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
895  return _IMP_atom._object_cast_to_DopePairScore(o)
896 
897 _object_types.append("LoopStatisticalPairScore")
898 
899 
900 def _object_cast_to_LoopStatisticalPairScore(o):
901  r"""_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
902  return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
903 
904 _object_types.append("OrientedSoapPairScore")
905 
906 
907 def _object_cast_to_OrientedSoapPairScore(o):
908  r"""_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
909  return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
910 
911 _object_types.append("EzRestraint")
912 
913 
914 def _object_cast_to_EzRestraint(o):
915  r"""_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
916  return _IMP_atom._object_cast_to_EzRestraint(o)
917 
918 _object_types.append("ForceFieldParameters")
919 
920 
921 def _object_cast_to_ForceFieldParameters(o):
922  r"""_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
923  return _IMP_atom._object_cast_to_ForceFieldParameters(o)
924 
925 _object_types.append("ForceSwitch")
926 
927 
928 def _object_cast_to_ForceSwitch(o):
929  r"""_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
930  return _IMP_atom._object_cast_to_ForceSwitch(o)
931 
932 _object_types.append("HydrogenPDBSelector")
933 
934 
935 def _object_cast_to_HydrogenPDBSelector(o):
936  r"""_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
937  return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
938 
939 _object_types.append("ImproperSingletonScore")
940 
941 
942 def _object_cast_to_ImproperSingletonScore(o):
943  r"""_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
944  return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
945 
946 _object_types.append("LennardJonesPairScore")
947 
948 
949 def _object_cast_to_LennardJonesPairScore(o):
950  r"""_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
951  return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
952 
953 _object_types.append("_LennardJonesTypedPairScore")
954 
955 
956 def _object_cast_to__LennardJonesTypedPairScore(o):
957  r"""_object_cast_to__LennardJonesTypedPairScore(Object o) -> _LennardJonesTypedPairScore"""
958  return _IMP_atom._object_cast_to__LennardJonesTypedPairScore(o)
959 
960 _object_types.append("_SwitchedLennardJonesTypedPairScore")
961 
962 
963 def _object_cast_to__SwitchedLennardJonesTypedPairScore(o):
964  r"""_object_cast_to__SwitchedLennardJonesTypedPairScore(Object o) -> _SwitchedLennardJonesTypedPairScore"""
965  return _IMP_atom._object_cast_to__SwitchedLennardJonesTypedPairScore(o)
966 
967 _object_types.append("Mol2Selector")
968 
969 
970 def _object_cast_to_Mol2Selector(o):
971  r"""_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
972  return _IMP_atom._object_cast_to_Mol2Selector(o)
973 
974 _object_types.append("MolecularDynamics")
975 
976 
977 def _object_cast_to_MolecularDynamics(o):
978  r"""_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
979  return _IMP_atom._object_cast_to_MolecularDynamics(o)
980 
981 _object_types.append("NPDBSelector")
982 
983 
984 def _object_cast_to_NPDBSelector(o):
985  r"""_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
986  return _IMP_atom._object_cast_to_NPDBSelector(o)
987 
988 _object_types.append("NonAlternativePDBSelector")
989 
990 
991 def _object_cast_to_NonAlternativePDBSelector(o):
992  r"""_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
993  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
994 
995 _object_types.append("NonHydrogenMol2Selector")
996 
997 
998 def _object_cast_to_NonHydrogenMol2Selector(o):
999  r"""_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
1000  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
1001 
1002 _object_types.append("NonHydrogenPDBSelector")
1003 
1004 
1005 def _object_cast_to_NonHydrogenPDBSelector(o):
1006  r"""_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
1007  return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
1008 
1009 _object_types.append("NonWaterNonHydrogenPDBSelector")
1010 
1011 
1012 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
1013  r"""_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
1014  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
1015 
1016 _object_types.append("NonWaterPDBSelector")
1017 
1018 
1019 def _object_cast_to_NonWaterPDBSelector(o):
1020  r"""_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
1021  return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
1022 
1023 _object_types.append("NotPDBSelector")
1024 
1025 
1026 def _object_cast_to_NotPDBSelector(o):
1027  r"""_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1028  return _IMP_atom._object_cast_to_NotPDBSelector(o)
1029 
1030 _object_types.append("OrPDBSelector")
1031 
1032 
1033 def _object_cast_to_OrPDBSelector(o):
1034  r"""_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1035  return _IMP_atom._object_cast_to_OrPDBSelector(o)
1036 
1037 _object_types.append("PPDBSelector")
1038 
1039 
1040 def _object_cast_to_PPDBSelector(o):
1041  r"""_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1042  return _IMP_atom._object_cast_to_PPDBSelector(o)
1043 
1044 _object_types.append("ProteinLigandAtomPairScore")
1045 
1046 
1047 def _object_cast_to_ProteinLigandAtomPairScore(o):
1048  r"""_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1049  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1050 
1051 _object_types.append("ProteinLigandRestraint")
1052 
1053 
1054 def _object_cast_to_ProteinLigandRestraint(o):
1055  r"""_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1056  return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1057 
1058 _object_types.append("SameResiduePairFilter")
1059 
1060 
1061 def _object_cast_to_SameResiduePairFilter(o):
1062  r"""_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1063  return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1064 
1065 _object_types.append("SoapPairFilter")
1066 
1067 
1068 def _object_cast_to_SoapPairFilter(o):
1069  r"""_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1070  return _IMP_atom._object_cast_to_SoapPairFilter(o)
1071 
1072 _object_types.append("SmoothingFunction")
1073 
1074 
1075 def _object_cast_to_SmoothingFunction(o):
1076  r"""_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1077  return _IMP_atom._object_cast_to_SmoothingFunction(o)
1078 
1079 _object_types.append("StereochemistryPairFilter")
1080 
1081 
1082 def _object_cast_to_StereochemistryPairFilter(o):
1083  r"""_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1084  return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1085 
1086 _object_types.append("VelocityScalingOptimizerState")
1087 
1088 
1089 def _object_cast_to_VelocityScalingOptimizerState(o):
1090  r"""_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1091  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1092 
1093 _object_types.append("WaterPDBSelector")
1094 
1095 
1096 def _object_cast_to_WaterPDBSelector(o):
1097  r"""_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1098  return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1099 
1100 _object_types.append("WritePDBOptimizerState")
1101 
1102 
1103 def _object_cast_to_WritePDBOptimizerState(o):
1104  r"""_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1105  return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1106 
1107 AtomTypes=list
1108 _plural_types.append("AtomTypes")
1109 _value_types.append("AtomType")
1110 
1111 
1112 CHARMMAtomTopologies=list
1113 _plural_types.append("CHARMMAtomTopologies")
1114 _value_types.append("CHARMMAtomTopology")
1115 
1116 
1117 CHARMMBondEndpoints=list
1118 _plural_types.append("CHARMMBondEndpoints")
1119 _value_types.append("CHARMMBondEndpoint")
1120 
1121 
1122 CHARMMBondParametersList=list
1123 _plural_types.append("CHARMMBondParametersList")
1124 _value_types.append("CHARMMBondParameters")
1125 
1126 
1127 CHARMMDihedralParametersList=list
1128 _plural_types.append("CHARMMDihedralParametersList")
1129 _value_types.append("CHARMMDihedralParameters")
1130 
1131 
1132 _object_types.append("CHARMMIdealResidueTopology")
1133 
1134 
1135 def _object_cast_to_CHARMMIdealResidueTopology(o):
1136  r"""_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1137  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1138 
1139 CHARMMInternalCoordinates=list
1140 _plural_types.append("CHARMMInternalCoordinates")
1141 _value_types.append("CHARMMInternalCoordinate")
1142 
1143 
1144 _object_types.append("CHARMMPatch")
1145 
1146 
1147 def _object_cast_to_CHARMMPatch(o):
1148  r"""_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1149  return _IMP_atom._object_cast_to_CHARMMPatch(o)
1150 
1151 _object_types.append("CHARMMResidueTopologyBase")
1152 
1153 
1154 def _object_cast_to_CHARMMResidueTopologyBase(o):
1155  r"""_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1156  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1157 
1158 ResidueTypes=list
1159 _plural_types.append("ResidueTypes")
1160 _value_types.append("ResidueType")
1161 
1162 
1163 ChainTypes=list
1164 _plural_types.append("ChainTypes")
1165 _value_types.append("ChainType")
1166 
1167 
1168 Selections=list
1169 _plural_types.append("Selections")
1170 _value_types.append("Selection")
1171 
1172 
1173 _object_types.append("RemoveRigidMotionOptimizerState")
1174 
1175 
1176 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1177  r"""_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1178  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1179 
1180 _object_types.append("BerendsenThermostatOptimizerState")
1181 
1182 
1183 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1184  r"""_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1185  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1186 
1187 _object_types.append("LangevinThermostatOptimizerState")
1188 
1189 
1190 def _object_cast_to_LangevinThermostatOptimizerState(o):
1191  r"""_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1192  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1193 
1194 _object_types.append("SelectionGeometry")
1195 
1196 
1197 def _object_cast_to_SelectionGeometry(o):
1198  r"""_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1199  return _IMP_atom._object_cast_to_SelectionGeometry(o)
1200 
1201 _object_types.append("HierarchyGeometry")
1202 
1203 
1204 def _object_cast_to_HierarchyGeometry(o):
1205  r"""_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1206  return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1207 
1208 _object_types.append("HierarchiesGeometry")
1209 
1210 
1211 def _object_cast_to_HierarchiesGeometry(o):
1212  r"""_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1213  return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1214 
1215 _object_types.append("BondGeometry")
1216 
1217 
1218 def _object_cast_to_BondGeometry(o):
1219  r"""_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1220  return _IMP_atom._object_cast_to_BondGeometry(o)
1221 
1222 _object_types.append("BondsGeometry")
1223 
1224 
1225 def _object_cast_to_BondsGeometry(o):
1226  r"""_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1227  return _IMP_atom._object_cast_to_BondsGeometry(o)
1228 
1229 _object_types.append("CAAngleRestraint")
1230 
1231 
1232 def _object_cast_to_CAAngleRestraint(o):
1233  r"""_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1234  return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1235 
1236 _object_types.append("CADihedralRestraint")
1237 
1238 
1239 def _object_cast_to_CADihedralRestraint(o):
1240  r"""_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1241  return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1242 
1243 _object_types.append("HelixRestraint")
1244 
1245 
1246 def _object_cast_to_HelixRestraint(o):
1247  r"""_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1248  return _IMP_atom._object_cast_to_HelixRestraint(o)
1249 
1250 CHARMMDihedrals=list
1251 _plural_types.append("CHARMMDihedrals")
1252 _value_types.append("CHARMMDihedral")
1253 
1254 
1255 CHARMMBonds=list
1256 _plural_types.append("CHARMMBonds")
1257 _value_types.append("CHARMMBond")
1258 
1259 
1260 CHARMMAngles=list
1261 _plural_types.append("CHARMMAngles")
1262 _value_types.append("CHARMMAngle")
1263 
1264 class Bond(IMP.Decorator):
1265  r"""Proxy of C++ IMP::atom::Bond class."""
1266 
1267  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1268 
1269  def __init__(self, *args):
1270  r"""
1271  __init__(Bond self) -> Bond
1272  __init__(Bond self, Model m, ParticleIndex id) -> Bond
1273  __init__(Bond self, _ParticleAdaptor d) -> Bond
1274  """
1275  _IMP_atom.Bond_swiginit(self, _IMP_atom.new_Bond(*args))
1276 
1277  def show(self, *args):
1278  r"""show(Bond self, _ostream out=std::cout)"""
1279  return _IMP_atom.Bond_show(self, *args)
1280 
1281  @staticmethod
1282  def get_is_setup(*args):
1283  r"""
1284  get_is_setup(_ParticleAdaptor p) -> bool
1285  get_is_setup(Model m, ParticleIndex pi) -> bool
1286  """
1287  return _IMP_atom.Bond_get_is_setup(*args)
1288  UNKNOWN = _IMP_atom.Bond_UNKNOWN
1289 
1290  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1291 
1292  SINGLE = _IMP_atom.Bond_SINGLE
1293 
1294  DOUBLE = _IMP_atom.Bond_DOUBLE
1295 
1296  TRIPLE = _IMP_atom.Bond_TRIPLE
1297 
1298  HYDROGEN = _IMP_atom.Bond_HYDROGEN
1299 
1300  SALT = _IMP_atom.Bond_SALT
1301 
1302  PEPTIDE = _IMP_atom.Bond_PEPTIDE
1303 
1304  AMIDE = _IMP_atom.Bond_AMIDE
1305 
1306  AROMATIC = _IMP_atom.Bond_AROMATIC
1307 
1308 
1309  def get_bonded(self, i):
1310  r"""get_bonded(Bond self, unsigned int i) -> Bonded"""
1311  return _IMP_atom.Bond_get_bonded(self, i)
1312 
1313  def get_type(self):
1314  r"""get_type(Bond self) -> IMP::Int"""
1315  return _IMP_atom.Bond_get_type(self)
1316 
1317  def set_type(self, t):
1318  r"""set_type(Bond self, IMP::Int t)"""
1319  return _IMP_atom.Bond_set_type(self, t)
1320 
1321  def get_order(self):
1322  r"""get_order(Bond self) -> IMP::Int"""
1323  return _IMP_atom.Bond_get_order(self)
1324 
1325  def set_order(self, t):
1326  r"""set_order(Bond self, IMP::Int t)"""
1327  return _IMP_atom.Bond_set_order(self, t)
1328 
1329  def get_length(self):
1330  r"""get_length(Bond self) -> IMP::Float"""
1331  return _IMP_atom.Bond_get_length(self)
1332 
1333  def set_length(self, t):
1334  r"""set_length(Bond self, IMP::Float t)"""
1335  return _IMP_atom.Bond_set_length(self, t)
1336 
1337  def get_stiffness(self):
1338  r"""get_stiffness(Bond self) -> IMP::Float"""
1339  return _IMP_atom.Bond_get_stiffness(self)
1340 
1341  def set_stiffness(self, t):
1342  r"""set_stiffness(Bond self, IMP::Float t)"""
1343  return _IMP_atom.Bond_set_stiffness(self, t)
1344 
1345  @staticmethod
1346  def get_length_key():
1347  r"""get_length_key() -> FloatKey"""
1348  return _IMP_atom.Bond_get_length_key()
1349 
1350  def add_attribute(self, *args):
1351  r"""
1352  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1353  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1354  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1355  add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1356  add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1357  add_attribute(Bond self, StringKey a0, IMP::String a1)
1358  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1359  add_attribute(Bond self, ObjectKey a0, Object a1)
1360  add_attribute(Bond self, SparseFloatKey a0, IMP::Float a1)
1361  add_attribute(Bond self, SparseIntKey a0, IMP::Int a1)
1362  add_attribute(Bond self, SparseStringKey a0, IMP::String a1)
1363  add_attribute(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1364  """
1365  return _IMP_atom.Bond_add_attribute(self, *args)
1366 
1367  def get_value(self, *args):
1368  r"""
1369  get_value(Bond self, FloatKey a0) -> IMP::Float
1370  get_value(Bond self, IntKey a0) -> IMP::Int
1371  get_value(Bond self, FloatsKey a0) -> IMP::Floats
1372  get_value(Bond self, IntsKey a0) -> IMP::Ints
1373  get_value(Bond self, StringKey a0) -> IMP::String
1374  get_value(Bond self, ParticleIndexKey a0) -> Particle
1375  get_value(Bond self, ObjectKey a0) -> Object
1376  get_value(Bond self, SparseFloatKey a0) -> IMP::Float
1377  get_value(Bond self, SparseIntKey a0) -> IMP::Int
1378  get_value(Bond self, SparseStringKey a0) -> IMP::String
1379  get_value(Bond self, SparseParticleIndexKey a0) -> ParticleIndex
1380  """
1381  return _IMP_atom.Bond_get_value(self, *args)
1382 
1383  def set_value(self, *args):
1384  r"""
1385  set_value(Bond self, FloatKey a0, IMP::Float a1)
1386  set_value(Bond self, IntKey a0, IMP::Int a1)
1387  set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1388  set_value(Bond self, IntsKey a0, IMP::Ints a1)
1389  set_value(Bond self, StringKey a0, IMP::String a1)
1390  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1391  set_value(Bond self, ObjectKey a0, Object a1)
1392  set_value(Bond self, SparseFloatKey a0, IMP::Float a1)
1393  set_value(Bond self, SparseIntKey a0, IMP::Int a1)
1394  set_value(Bond self, SparseStringKey a0, IMP::String a1)
1395  set_value(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1396  """
1397  return _IMP_atom.Bond_set_value(self, *args)
1398 
1399  def remove_attribute(self, *args):
1400  r"""
1401  remove_attribute(Bond self, FloatKey a0)
1402  remove_attribute(Bond self, IntKey a0)
1403  remove_attribute(Bond self, FloatsKey a0)
1404  remove_attribute(Bond self, IntsKey a0)
1405  remove_attribute(Bond self, StringKey a0)
1406  remove_attribute(Bond self, ParticleIndexKey a0)
1407  remove_attribute(Bond self, ObjectKey a0)
1408  remove_attribute(Bond self, SparseFloatKey a0)
1409  remove_attribute(Bond self, SparseIntKey a0)
1410  remove_attribute(Bond self, SparseStringKey a0)
1411  remove_attribute(Bond self, SparseParticleIndexKey a0)
1412  """
1413  return _IMP_atom.Bond_remove_attribute(self, *args)
1414 
1415  def has_attribute(self, *args):
1416  r"""
1417  has_attribute(Bond self, FloatKey a0) -> bool
1418  has_attribute(Bond self, IntKey a0) -> bool
1419  has_attribute(Bond self, FloatsKey a0) -> bool
1420  has_attribute(Bond self, IntsKey a0) -> bool
1421  has_attribute(Bond self, StringKey a0) -> bool
1422  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1423  has_attribute(Bond self, ObjectKey a0) -> bool
1424  has_attribute(Bond self, SparseFloatKey a0) -> bool
1425  has_attribute(Bond self, SparseIntKey a0) -> bool
1426  has_attribute(Bond self, SparseStringKey a0) -> bool
1427  has_attribute(Bond self, SparseParticleIndexKey a0) -> bool
1428  """
1429  return _IMP_atom.Bond_has_attribute(self, *args)
1430 
1431  def get_derivative(self, a0):
1432  r"""get_derivative(Bond self, FloatKey a0) -> double"""
1433  return _IMP_atom.Bond_get_derivative(self, a0)
1434 
1435  def get_name(self):
1436  r"""get_name(Bond self) -> std::string"""
1437  return _IMP_atom.Bond_get_name(self)
1438 
1439  def clear_caches(self):
1440  r"""clear_caches(Bond self)"""
1441  return _IMP_atom.Bond_clear_caches(self)
1442 
1443  def set_name(self, a0):
1444  r"""set_name(Bond self, std::string a0)"""
1445  return _IMP_atom.Bond_set_name(self, a0)
1446 
1447  def set_check_level(self, a0):
1448  r"""set_check_level(Bond self, IMP::CheckLevel a0)"""
1449  return _IMP_atom.Bond_set_check_level(self, a0)
1450 
1451  def add_to_derivative(self, a0, a1, a2):
1452  r"""add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1453  return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1454 
1455  def set_is_optimized(self, a0, a1):
1456  r"""set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1457  return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1458 
1459  def get_is_optimized(self, a0):
1460  r"""get_is_optimized(Bond self, FloatKey a0) -> bool"""
1461  return _IMP_atom.Bond_get_is_optimized(self, a0)
1462 
1463  def get_check_level(self):
1464  r"""get_check_level(Bond self) -> IMP::CheckLevel"""
1465  return _IMP_atom.Bond_get_check_level(self)
1466 
1467  def __eq__(self, *args):
1468  r"""
1469  __eq__(Bond self, Bond o) -> bool
1470  __eq__(Bond self, Particle d) -> bool
1471  """
1472  return _IMP_atom.Bond___eq__(self, *args)
1473 
1474  def __ne__(self, *args):
1475  r"""
1476  __ne__(Bond self, Bond o) -> bool
1477  __ne__(Bond self, Particle d) -> bool
1478  """
1479  return _IMP_atom.Bond___ne__(self, *args)
1480 
1481  def __le__(self, *args):
1482  r"""
1483  __le__(Bond self, Bond o) -> bool
1484  __le__(Bond self, Particle d) -> bool
1485  """
1486  return _IMP_atom.Bond___le__(self, *args)
1487 
1488  def __lt__(self, *args):
1489  r"""
1490  __lt__(Bond self, Bond o) -> bool
1491  __lt__(Bond self, Particle d) -> bool
1492  """
1493  return _IMP_atom.Bond___lt__(self, *args)
1494 
1495  def __ge__(self, *args):
1496  r"""
1497  __ge__(Bond self, Bond o) -> bool
1498  __ge__(Bond self, Particle d) -> bool
1499  """
1500  return _IMP_atom.Bond___ge__(self, *args)
1501 
1502  def __gt__(self, *args):
1503  r"""
1504  __gt__(Bond self, Bond o) -> bool
1505  __gt__(Bond self, Particle d) -> bool
1506  """
1507  return _IMP_atom.Bond___gt__(self, *args)
1508 
1509  def __hash__(self):
1510  r"""__hash__(Bond self) -> std::size_t"""
1511  return _IMP_atom.Bond___hash__(self)
1512 
1513  def __str__(self):
1514  r"""__str__(Bond self) -> std::string"""
1515  return _IMP_atom.Bond___str__(self)
1516 
1517  def __repr__(self):
1518  r"""__repr__(Bond self) -> std::string"""
1519  return _IMP_atom.Bond___repr__(self)
1520 
1521  def _get_as_binary(self):
1522  r"""_get_as_binary(Bond self) -> PyObject *"""
1523  return _IMP_atom.Bond__get_as_binary(self)
1524 
1525  def _set_from_binary(self, p):
1526  r"""_set_from_binary(Bond self, PyObject * p)"""
1527  return _IMP_atom.Bond__set_from_binary(self, p)
1528 
1529  def __getstate__(self):
1530  p = self._get_as_binary()
1531  if len(self.__dict__) > 1:
1532  d = self.__dict__.copy()
1533  del d['this']
1534  p = (d, p)
1535  return p
1536 
1537  def __setstate__(self, p):
1538  if not hasattr(self, 'this'):
1539  self.__init__()
1540  if isinstance(p, tuple):
1541  d, p = p
1542  self.__dict__.update(d)
1543  return self._set_from_binary(p)
1544 
1545  __swig_destroy__ = _IMP_atom.delete_Bond
1546 
1547 # Register Bond in _IMP_atom:
1548 _IMP_atom.Bond_swigregister(Bond)
1549 class Bonded(IMP.Decorator):
1550  r"""Proxy of C++ IMP::atom::Bonded class."""
1551 
1552  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1553 
1554  def __init__(self, *args):
1555  r"""
1556  __init__(Bonded self) -> Bonded
1557  __init__(Bonded self, Model m, ParticleIndex id) -> Bonded
1558  __init__(Bonded self, _ParticleAdaptor d) -> Bonded
1559  """
1560  _IMP_atom.Bonded_swiginit(self, _IMP_atom.new_Bonded(*args))
1561 
1562  def show(self, *args):
1563  r"""show(Bonded self, _ostream out=std::cout)"""
1564  return _IMP_atom.Bonded_show(self, *args)
1565 
1566  @staticmethod
1567  def setup_particle(*args):
1568  r"""
1569  setup_particle(Model m, ParticleIndex pi) -> Bonded
1570  setup_particle(_ParticleAdaptor pa) -> Bonded
1571  """
1572  return _IMP_atom.Bonded_setup_particle(*args)
1573 
1574  @staticmethod
1575  def get_is_setup(*args):
1576  r"""
1577  get_is_setup(_ParticleAdaptor p) -> bool
1578  get_is_setup(Model m, ParticleIndex pi) -> bool
1579  """
1580  return _IMP_atom.Bonded_get_is_setup(*args)
1581 
1582  def get_number_of_bonds(self):
1583  r"""get_number_of_bonds(Bonded self) -> unsigned int"""
1584  return _IMP_atom.Bonded_get_number_of_bonds(self)
1585 
1586  def get_bond_indexes(self):
1587  r"""get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1588  return _IMP_atom.Bonded_get_bond_indexes(self)
1589 
1590  def get_bond(self, i):
1591  r"""get_bond(Bonded self, unsigned int i) -> Bond"""
1592  return _IMP_atom.Bonded_get_bond(self, i)
1593 
1594  def get_bonded(self, i):
1595  r"""get_bonded(Bonded self, unsigned int i) -> Bonded"""
1596  return _IMP_atom.Bonded_get_bonded(self, i)
1597 
1598  def add_attribute(self, *args):
1599  r"""
1600  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1601  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1602  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1603  add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1604  add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1605  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1606  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1607  add_attribute(Bonded self, ObjectKey a0, Object a1)
1608  add_attribute(Bonded self, SparseFloatKey a0, IMP::Float a1)
1609  add_attribute(Bonded self, SparseIntKey a0, IMP::Int a1)
1610  add_attribute(Bonded self, SparseStringKey a0, IMP::String a1)
1611  add_attribute(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1612  """
1613  return _IMP_atom.Bonded_add_attribute(self, *args)
1614 
1615  def get_value(self, *args):
1616  r"""
1617  get_value(Bonded self, FloatKey a0) -> IMP::Float
1618  get_value(Bonded self, IntKey a0) -> IMP::Int
1619  get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1620  get_value(Bonded self, IntsKey a0) -> IMP::Ints
1621  get_value(Bonded self, StringKey a0) -> IMP::String
1622  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1623  get_value(Bonded self, ObjectKey a0) -> Object
1624  get_value(Bonded self, SparseFloatKey a0) -> IMP::Float
1625  get_value(Bonded self, SparseIntKey a0) -> IMP::Int
1626  get_value(Bonded self, SparseStringKey a0) -> IMP::String
1627  get_value(Bonded self, SparseParticleIndexKey a0) -> ParticleIndex
1628  """
1629  return _IMP_atom.Bonded_get_value(self, *args)
1630 
1631  def set_value(self, *args):
1632  r"""
1633  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1634  set_value(Bonded self, IntKey a0, IMP::Int a1)
1635  set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1636  set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1637  set_value(Bonded self, StringKey a0, IMP::String a1)
1638  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1639  set_value(Bonded self, ObjectKey a0, Object a1)
1640  set_value(Bonded self, SparseFloatKey a0, IMP::Float a1)
1641  set_value(Bonded self, SparseIntKey a0, IMP::Int a1)
1642  set_value(Bonded self, SparseStringKey a0, IMP::String a1)
1643  set_value(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1644  """
1645  return _IMP_atom.Bonded_set_value(self, *args)
1646 
1647  def remove_attribute(self, *args):
1648  r"""
1649  remove_attribute(Bonded self, FloatKey a0)
1650  remove_attribute(Bonded self, IntKey a0)
1651  remove_attribute(Bonded self, FloatsKey a0)
1652  remove_attribute(Bonded self, IntsKey a0)
1653  remove_attribute(Bonded self, StringKey a0)
1654  remove_attribute(Bonded self, ParticleIndexKey a0)
1655  remove_attribute(Bonded self, ObjectKey a0)
1656  remove_attribute(Bonded self, SparseFloatKey a0)
1657  remove_attribute(Bonded self, SparseIntKey a0)
1658  remove_attribute(Bonded self, SparseStringKey a0)
1659  remove_attribute(Bonded self, SparseParticleIndexKey a0)
1660  """
1661  return _IMP_atom.Bonded_remove_attribute(self, *args)
1662 
1663  def has_attribute(self, *args):
1664  r"""
1665  has_attribute(Bonded self, FloatKey a0) -> bool
1666  has_attribute(Bonded self, IntKey a0) -> bool
1667  has_attribute(Bonded self, FloatsKey a0) -> bool
1668  has_attribute(Bonded self, IntsKey a0) -> bool
1669  has_attribute(Bonded self, StringKey a0) -> bool
1670  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1671  has_attribute(Bonded self, ObjectKey a0) -> bool
1672  has_attribute(Bonded self, SparseFloatKey a0) -> bool
1673  has_attribute(Bonded self, SparseIntKey a0) -> bool
1674  has_attribute(Bonded self, SparseStringKey a0) -> bool
1675  has_attribute(Bonded self, SparseParticleIndexKey a0) -> bool
1676  """
1677  return _IMP_atom.Bonded_has_attribute(self, *args)
1678 
1679  def get_derivative(self, a0):
1680  r"""get_derivative(Bonded self, FloatKey a0) -> double"""
1681  return _IMP_atom.Bonded_get_derivative(self, a0)
1682 
1683  def get_name(self):
1684  r"""get_name(Bonded self) -> std::string"""
1685  return _IMP_atom.Bonded_get_name(self)
1686 
1687  def clear_caches(self):
1688  r"""clear_caches(Bonded self)"""
1689  return _IMP_atom.Bonded_clear_caches(self)
1690 
1691  def set_name(self, a0):
1692  r"""set_name(Bonded self, std::string a0)"""
1693  return _IMP_atom.Bonded_set_name(self, a0)
1694 
1695  def set_check_level(self, a0):
1696  r"""set_check_level(Bonded self, IMP::CheckLevel a0)"""
1697  return _IMP_atom.Bonded_set_check_level(self, a0)
1698 
1699  def add_to_derivative(self, a0, a1, a2):
1700  r"""add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1701  return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1702 
1703  def set_is_optimized(self, a0, a1):
1704  r"""set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1705  return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1706 
1707  def get_is_optimized(self, a0):
1708  r"""get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1709  return _IMP_atom.Bonded_get_is_optimized(self, a0)
1710 
1711  def get_check_level(self):
1712  r"""get_check_level(Bonded self) -> IMP::CheckLevel"""
1713  return _IMP_atom.Bonded_get_check_level(self)
1714 
1715  def __eq__(self, *args):
1716  r"""
1717  __eq__(Bonded self, Bonded o) -> bool
1718  __eq__(Bonded self, Particle d) -> bool
1719  """
1720  return _IMP_atom.Bonded___eq__(self, *args)
1721 
1722  def __ne__(self, *args):
1723  r"""
1724  __ne__(Bonded self, Bonded o) -> bool
1725  __ne__(Bonded self, Particle d) -> bool
1726  """
1727  return _IMP_atom.Bonded___ne__(self, *args)
1728 
1729  def __le__(self, *args):
1730  r"""
1731  __le__(Bonded self, Bonded o) -> bool
1732  __le__(Bonded self, Particle d) -> bool
1733  """
1734  return _IMP_atom.Bonded___le__(self, *args)
1735 
1736  def __lt__(self, *args):
1737  r"""
1738  __lt__(Bonded self, Bonded o) -> bool
1739  __lt__(Bonded self, Particle d) -> bool
1740  """
1741  return _IMP_atom.Bonded___lt__(self, *args)
1742 
1743  def __ge__(self, *args):
1744  r"""
1745  __ge__(Bonded self, Bonded o) -> bool
1746  __ge__(Bonded self, Particle d) -> bool
1747  """
1748  return _IMP_atom.Bonded___ge__(self, *args)
1749 
1750  def __gt__(self, *args):
1751  r"""
1752  __gt__(Bonded self, Bonded o) -> bool
1753  __gt__(Bonded self, Particle d) -> bool
1754  """
1755  return _IMP_atom.Bonded___gt__(self, *args)
1756 
1757  def __hash__(self):
1758  r"""__hash__(Bonded self) -> std::size_t"""
1759  return _IMP_atom.Bonded___hash__(self)
1760 
1761  def __str__(self):
1762  r"""__str__(Bonded self) -> std::string"""
1763  return _IMP_atom.Bonded___str__(self)
1764 
1765  def __repr__(self):
1766  r"""__repr__(Bonded self) -> std::string"""
1767  return _IMP_atom.Bonded___repr__(self)
1768 
1769  def _get_as_binary(self):
1770  r"""_get_as_binary(Bonded self) -> PyObject *"""
1771  return _IMP_atom.Bonded__get_as_binary(self)
1772 
1773  def _set_from_binary(self, p):
1774  r"""_set_from_binary(Bonded self, PyObject * p)"""
1775  return _IMP_atom.Bonded__set_from_binary(self, p)
1776 
1777  def __getstate__(self):
1778  p = self._get_as_binary()
1779  if len(self.__dict__) > 1:
1780  d = self.__dict__.copy()
1781  del d['this']
1782  p = (d, p)
1783  return p
1784 
1785  def __setstate__(self, p):
1786  if not hasattr(self, 'this'):
1787  self.__init__()
1788  if isinstance(p, tuple):
1789  d, p = p
1790  self.__dict__.update(d)
1791  return self._set_from_binary(p)
1792 
1793  __swig_destroy__ = _IMP_atom.delete_Bonded
1794 
1795 # Register Bonded in _IMP_atom:
1796 _IMP_atom.Bonded_swigregister(Bonded)
1797 
1798 def create_custom_bond(a, b, length, stiffness=-1):
1799  r"""create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond"""
1800  return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1801 
1802 def create_bond(*args):
1803  r"""
1804  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1805  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1806  """
1807  return _IMP_atom.create_bond(*args)
1808 
1809 def destroy_bond(b):
1810  r"""destroy_bond(Bond b)"""
1811  return _IMP_atom.destroy_bond(b)
1812 
1813 def get_bond(a, b):
1814  r"""get_bond(Bonded a, Bonded b) -> Bond"""
1815  return _IMP_atom.get_bond(a, b)
1816 class BondGeometry(IMP.display.SingletonGeometry):
1817  r"""Proxy of C++ IMP::atom::BondGeometry class."""
1818 
1819  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1820 
1821  def __init__(self, *args):
1822  r"""
1823  __init__(BondGeometry self, Particle p) -> BondGeometry
1824  __init__(BondGeometry self, Bond d) -> BondGeometry
1825  """
1826  _IMP_atom.BondGeometry_swiginit(self, _IMP_atom.new_BondGeometry(*args))
1827 
1828  def get_version_info(self):
1829  r"""get_version_info(BondGeometry self) -> VersionInfo"""
1830  return _IMP_atom.BondGeometry_get_version_info(self)
1831  __swig_destroy__ = _IMP_atom.delete_BondGeometry
1832 
1833  def __str__(self):
1834  r"""__str__(BondGeometry self) -> std::string"""
1835  return _IMP_atom.BondGeometry___str__(self)
1836 
1837  def __repr__(self):
1838  r"""__repr__(BondGeometry self) -> std::string"""
1839  return _IMP_atom.BondGeometry___repr__(self)
1840 
1841  @staticmethod
1842  def get_from(o):
1843  return _object_cast_to_BondGeometry(o)
1844 
1845 
1846 # Register BondGeometry in _IMP_atom:
1847 _IMP_atom.BondGeometry_swigregister(BondGeometry)
1848 class BondsGeometry(IMP.display.SingletonsGeometry):
1849  r"""Proxy of C++ IMP::atom::BondsGeometry class."""
1850 
1851  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1852 
1853  def __init__(self, sc):
1854  r"""__init__(BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1855  _IMP_atom.BondsGeometry_swiginit(self, _IMP_atom.new_BondsGeometry(sc))
1856 
1857  def get_version_info(self):
1858  r"""get_version_info(BondsGeometry self) -> VersionInfo"""
1859  return _IMP_atom.BondsGeometry_get_version_info(self)
1860  __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1861 
1862  def __str__(self):
1863  r"""__str__(BondsGeometry self) -> std::string"""
1864  return _IMP_atom.BondsGeometry___str__(self)
1865 
1866  def __repr__(self):
1867  r"""__repr__(BondsGeometry self) -> std::string"""
1868  return _IMP_atom.BondsGeometry___repr__(self)
1869 
1870  @staticmethod
1871  def get_from(o):
1872  return _object_cast_to_BondsGeometry(o)
1873 
1874 
1875 # Register BondsGeometry in _IMP_atom:
1876 _IMP_atom.BondsGeometry_swigregister(BondsGeometry)
1877 class Hierarchy(IMP.core.Hierarchy):
1878  r"""Proxy of C++ IMP::atom::Hierarchy class."""
1879 
1880  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1881 
1882  def __init__(self, *args):
1883  r"""
1884  __init__(Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1885  __init__(Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1886  __init__(Hierarchy self) -> Hierarchy
1887  __init__(Hierarchy self, Hierarchy h) -> Hierarchy
1888  """
1889  _IMP_atom.Hierarchy_swiginit(self, _IMP_atom.new_Hierarchy(*args))
1890 
1891  @staticmethod
1892  def setup_particle(*args):
1893  r"""
1894  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1895  setup_particle(Particle p) -> Hierarchy
1896  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::ParticleIndexesAdaptor()) -> Hierarchy
1897  """
1898  return _IMP_atom.Hierarchy_setup_particle(*args)
1899 
1900  @staticmethod
1901  def get_is_setup(*args):
1902  r"""
1903  get_is_setup(Particle p) -> bool
1904  get_is_setup(Model m, ParticleIndex p) -> bool
1905  """
1906  return _IMP_atom.Hierarchy_get_is_setup(*args)
1907 
1908  def get_is_valid(self, print_info=False):
1909  r"""get_is_valid(Hierarchy self, bool print_info=False) -> bool"""
1910  return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1911 
1912  def add_child(self, o):
1913  r"""add_child(Hierarchy self, Hierarchy o)"""
1914  return _IMP_atom.Hierarchy_add_child(self, o)
1915 
1916  def get_child(self, i):
1917  r"""get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1918  return _IMP_atom.Hierarchy_get_child(self, i)
1919 
1920  def get_children(self):
1921  r"""get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1922  return _IMP_atom.Hierarchy_get_children(self)
1923 
1924  def get_parent(self):
1925  r"""get_parent(Hierarchy self) -> Hierarchy"""
1926  return _IMP_atom.Hierarchy_get_parent(self)
1927 
1928  @staticmethod
1929  def get_traits():
1930  r"""get_traits() -> HierarchyTraits"""
1931  return _IMP_atom.Hierarchy_get_traits()
1932 
1933  def show(self, *args):
1934  r"""
1935  show(Hierarchy self, _ostream out, std::string delimiter)
1936  show(Hierarchy self, _ostream out=std::cout)
1937  """
1938  return _IMP_atom.Hierarchy_show(self, *args)
1939 
1940  def add_attribute(self, *args):
1941  r"""
1942  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1943  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1944  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1945  add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1946  add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1947  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1948  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1949  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1950  add_attribute(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1951  add_attribute(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1952  add_attribute(Hierarchy self, SparseStringKey a0, IMP::String a1)
1953  add_attribute(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1954  """
1955  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1956 
1957  def get_value(self, *args):
1958  r"""
1959  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1960  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1961  get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1962  get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1963  get_value(Hierarchy self, StringKey a0) -> IMP::String
1964  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1965  get_value(Hierarchy self, ObjectKey a0) -> Object
1966  get_value(Hierarchy self, SparseFloatKey a0) -> IMP::Float
1967  get_value(Hierarchy self, SparseIntKey a0) -> IMP::Int
1968  get_value(Hierarchy self, SparseStringKey a0) -> IMP::String
1969  get_value(Hierarchy self, SparseParticleIndexKey a0) -> ParticleIndex
1970  """
1971  return _IMP_atom.Hierarchy_get_value(self, *args)
1972 
1973  def set_value(self, *args):
1974  r"""
1975  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1976  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1977  set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1978  set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1979  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1980  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1981  set_value(Hierarchy self, ObjectKey a0, Object a1)
1982  set_value(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1983  set_value(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1984  set_value(Hierarchy self, SparseStringKey a0, IMP::String a1)
1985  set_value(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1986  """
1987  return _IMP_atom.Hierarchy_set_value(self, *args)
1988 
1989  def remove_attribute(self, *args):
1990  r"""
1991  remove_attribute(Hierarchy self, FloatKey a0)
1992  remove_attribute(Hierarchy self, IntKey a0)
1993  remove_attribute(Hierarchy self, FloatsKey a0)
1994  remove_attribute(Hierarchy self, IntsKey a0)
1995  remove_attribute(Hierarchy self, StringKey a0)
1996  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1997  remove_attribute(Hierarchy self, ObjectKey a0)
1998  remove_attribute(Hierarchy self, SparseFloatKey a0)
1999  remove_attribute(Hierarchy self, SparseIntKey a0)
2000  remove_attribute(Hierarchy self, SparseStringKey a0)
2001  remove_attribute(Hierarchy self, SparseParticleIndexKey a0)
2002  """
2003  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
2004 
2005  def has_attribute(self, *args):
2006  r"""
2007  has_attribute(Hierarchy self, FloatKey a0) -> bool
2008  has_attribute(Hierarchy self, IntKey a0) -> bool
2009  has_attribute(Hierarchy self, FloatsKey a0) -> bool
2010  has_attribute(Hierarchy self, IntsKey a0) -> bool
2011  has_attribute(Hierarchy self, StringKey a0) -> bool
2012  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2013  has_attribute(Hierarchy self, ObjectKey a0) -> bool
2014  has_attribute(Hierarchy self, SparseFloatKey a0) -> bool
2015  has_attribute(Hierarchy self, SparseIntKey a0) -> bool
2016  has_attribute(Hierarchy self, SparseStringKey a0) -> bool
2017  has_attribute(Hierarchy self, SparseParticleIndexKey a0) -> bool
2018  """
2019  return _IMP_atom.Hierarchy_has_attribute(self, *args)
2020 
2021  def get_derivative(self, a0):
2022  r"""get_derivative(Hierarchy self, FloatKey a0) -> double"""
2023  return _IMP_atom.Hierarchy_get_derivative(self, a0)
2024 
2025  def get_name(self):
2026  r"""get_name(Hierarchy self) -> std::string"""
2027  return _IMP_atom.Hierarchy_get_name(self)
2028 
2029  def clear_caches(self):
2030  r"""clear_caches(Hierarchy self)"""
2031  return _IMP_atom.Hierarchy_clear_caches(self)
2032 
2033  def set_name(self, a0):
2034  r"""set_name(Hierarchy self, std::string a0)"""
2035  return _IMP_atom.Hierarchy_set_name(self, a0)
2036 
2037  def set_check_level(self, a0):
2038  r"""set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2039  return _IMP_atom.Hierarchy_set_check_level(self, a0)
2040 
2041  def add_to_derivative(self, a0, a1, a2):
2042  r"""add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2043  return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2044 
2045  def set_is_optimized(self, a0, a1):
2046  r"""set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2047  return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2048 
2049  def get_is_optimized(self, a0):
2050  r"""get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2051  return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2052 
2053  def get_check_level(self):
2054  r"""get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2055  return _IMP_atom.Hierarchy_get_check_level(self)
2056 
2057  def __eq__(self, *args):
2058  r"""
2059  __eq__(Hierarchy self, Hierarchy o) -> bool
2060  __eq__(Hierarchy self, Particle d) -> bool
2061  """
2062  return _IMP_atom.Hierarchy___eq__(self, *args)
2063 
2064  def __ne__(self, *args):
2065  r"""
2066  __ne__(Hierarchy self, Hierarchy o) -> bool
2067  __ne__(Hierarchy self, Particle d) -> bool
2068  """
2069  return _IMP_atom.Hierarchy___ne__(self, *args)
2070 
2071  def __le__(self, *args):
2072  r"""
2073  __le__(Hierarchy self, Hierarchy o) -> bool
2074  __le__(Hierarchy self, Particle d) -> bool
2075  """
2076  return _IMP_atom.Hierarchy___le__(self, *args)
2077 
2078  def __lt__(self, *args):
2079  r"""
2080  __lt__(Hierarchy self, Hierarchy o) -> bool
2081  __lt__(Hierarchy self, Particle d) -> bool
2082  """
2083  return _IMP_atom.Hierarchy___lt__(self, *args)
2084 
2085  def __ge__(self, *args):
2086  r"""
2087  __ge__(Hierarchy self, Hierarchy o) -> bool
2088  __ge__(Hierarchy self, Particle d) -> bool
2089  """
2090  return _IMP_atom.Hierarchy___ge__(self, *args)
2091 
2092  def __gt__(self, *args):
2093  r"""
2094  __gt__(Hierarchy self, Hierarchy o) -> bool
2095  __gt__(Hierarchy self, Particle d) -> bool
2096  """
2097  return _IMP_atom.Hierarchy___gt__(self, *args)
2098 
2099  def __hash__(self):
2100  r"""__hash__(Hierarchy self) -> std::size_t"""
2101  return _IMP_atom.Hierarchy___hash__(self)
2102 
2103  def __str__(self):
2104  r"""__str__(Hierarchy self) -> std::string"""
2105  return _IMP_atom.Hierarchy___str__(self)
2106 
2107  def __repr__(self):
2108  r"""__repr__(Hierarchy self) -> std::string"""
2109  return _IMP_atom.Hierarchy___repr__(self)
2110 
2111  def _get_as_binary(self):
2112  r"""_get_as_binary(Hierarchy self) -> PyObject *"""
2113  return _IMP_atom.Hierarchy__get_as_binary(self)
2114 
2115  def _set_from_binary(self, p):
2116  r"""_set_from_binary(Hierarchy self, PyObject * p)"""
2117  return _IMP_atom.Hierarchy__set_from_binary(self, p)
2118 
2119  def __getstate__(self):
2120  p = self._get_as_binary()
2121  if len(self.__dict__) > 1:
2122  d = self.__dict__.copy()
2123  del d['this']
2124  p = (d, p)
2125  return p
2126 
2127  def __setstate__(self, p):
2128  if not hasattr(self, 'this'):
2129  self.__init__()
2130  if isinstance(p, tuple):
2131  d, p = p
2132  self.__dict__.update(d)
2133  return self._set_from_binary(p)
2134 
2135  __swig_destroy__ = _IMP_atom.delete_Hierarchy
2136 
2137 # Register Hierarchy in _IMP_atom:
2138 _IMP_atom.Hierarchy_swigregister(Hierarchy)
2139 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2140 
2141 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2142 
2143 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2144 
2145 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2146 
2147 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2148 
2149 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2150 
2151 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2152 
2153 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2154 
2155 MASS_TYPE = _IMP_atom.MASS_TYPE
2156 
2157 STATE_TYPE = _IMP_atom.STATE_TYPE
2158 
2159 
2160 def get_by_type(mhd, t):
2161  r"""get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2162  return _IMP_atom.get_by_type(mhd, t)
2163 
2164 def create_fragment(ps):
2165  r"""create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2166  return _IMP_atom.create_fragment(ps)
2167 
2168 def get_internal_bonds(mhd, with_representations=False):
2169  r"""get_internal_bonds(Hierarchy mhd, bool with_representations=False) -> IMP::atom::Bonds"""
2170  return _IMP_atom.get_internal_bonds(mhd, with_representations)
2171 
2172 def get_root(h):
2173  r"""get_root(Hierarchy h) -> Hierarchy"""
2174  return _IMP_atom.get_root(h)
2175 
2176 def show(*args):
2177  r"""show(Hierarchy h, _ostream out=std::cout)"""
2178  return _IMP_atom.show(*args)
2179 
2180 def create_rigid_body(*args):
2181  r"""
2182  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
2183  create_rigid_body(Hierarchy h) -> RigidBody
2184  """
2185  return _IMP_atom.create_rigid_body(*args)
2186 
2187 def create_compatible_rigid_body(h, reference):
2188  r"""create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2189  return _IMP_atom.create_compatible_rigid_body(h, reference)
2190 
2191 def get_is_heterogen(h):
2192  r"""get_is_heterogen(Hierarchy h) -> bool"""
2193  return _IMP_atom.get_is_heterogen(h)
2194 
2195 def create_clone(d):
2196  r"""create_clone(Hierarchy d) -> Hierarchy"""
2197  return _IMP_atom.create_clone(d)
2198 
2199 def create_clone_one(d):
2200  r"""create_clone_one(Hierarchy d) -> Hierarchy"""
2201  return _IMP_atom.create_clone_one(d)
2202 
2203 def destroy(d):
2204  r"""destroy(Hierarchy d)"""
2205  return _IMP_atom.destroy(d)
2206 
2207 def get_bounding_box(h):
2208  r"""get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2209  return _IMP_atom.get_bounding_box(h)
2210 
2211 def get_bounding_sphere(h):
2212  r"""get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2213  return _IMP_atom.get_bounding_sphere(h)
2214 class Angle(IMP.Decorator):
2215  r"""Proxy of C++ IMP::atom::Angle class."""
2216 
2217  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2218 
2219  def __init__(self, *args):
2220  r"""
2221  __init__(Angle self) -> Angle
2222  __init__(Angle self, Model m, ParticleIndex id) -> Angle
2223  __init__(Angle self, _ParticleAdaptor d) -> Angle
2224  """
2225  _IMP_atom.Angle_swiginit(self, _IMP_atom.new_Angle(*args))
2226 
2227  def show(self, *args):
2228  r"""show(Angle self, _ostream out=std::cout)"""
2229  return _IMP_atom.Angle_show(self, *args)
2230 
2231  @staticmethod
2232  def setup_particle(*args):
2233  r"""
2234  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2235  setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c) -> Angle
2236  """
2237  return _IMP_atom.Angle_setup_particle(*args)
2238 
2239  @staticmethod
2240  def get_is_setup(*args):
2241  r"""
2242  get_is_setup(_ParticleAdaptor p) -> bool
2243  get_is_setup(Model m, ParticleIndex pi) -> bool
2244  """
2245  return _IMP_atom.Angle_get_is_setup(*args)
2246 
2247  def get_particle(self, *args):
2248  r"""
2249  get_particle(Angle self) -> Particle
2250  get_particle(Angle self, unsigned int i) -> Particle
2251  """
2252  return _IMP_atom.Angle_get_particle(self, *args)
2253 
2254  def get_ideal(self):
2255  r"""get_ideal(Angle self) -> IMP::Float"""
2256  return _IMP_atom.Angle_get_ideal(self)
2257 
2258  def set_ideal(self, t):
2259  r"""set_ideal(Angle self, IMP::Float t)"""
2260  return _IMP_atom.Angle_set_ideal(self, t)
2261 
2262  def get_stiffness(self):
2263  r"""get_stiffness(Angle self) -> IMP::Float"""
2264  return _IMP_atom.Angle_get_stiffness(self)
2265 
2266  def set_stiffness(self, t):
2267  r"""set_stiffness(Angle self, IMP::Float t)"""
2268  return _IMP_atom.Angle_set_stiffness(self, t)
2269 
2270  @staticmethod
2271  def get_particle_key(i):
2272  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2273  return _IMP_atom.Angle_get_particle_key(i)
2274 
2275  @staticmethod
2276  def get_ideal_key():
2277  r"""get_ideal_key() -> FloatKey"""
2278  return _IMP_atom.Angle_get_ideal_key()
2279 
2280  @staticmethod
2281  def get_stiffness_key():
2282  r"""get_stiffness_key() -> FloatKey"""
2283  return _IMP_atom.Angle_get_stiffness_key()
2284 
2285  def add_attribute(self, *args):
2286  r"""
2287  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2288  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2289  add_attribute(Angle self, IntKey a0, IMP::Int a1)
2290  add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2291  add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2292  add_attribute(Angle self, StringKey a0, IMP::String a1)
2293  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2294  add_attribute(Angle self, ObjectKey a0, Object a1)
2295  add_attribute(Angle self, SparseFloatKey a0, IMP::Float a1)
2296  add_attribute(Angle self, SparseIntKey a0, IMP::Int a1)
2297  add_attribute(Angle self, SparseStringKey a0, IMP::String a1)
2298  add_attribute(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2299  """
2300  return _IMP_atom.Angle_add_attribute(self, *args)
2301 
2302  def get_value(self, *args):
2303  r"""
2304  get_value(Angle self, FloatKey a0) -> IMP::Float
2305  get_value(Angle self, IntKey a0) -> IMP::Int
2306  get_value(Angle self, FloatsKey a0) -> IMP::Floats
2307  get_value(Angle self, IntsKey a0) -> IMP::Ints
2308  get_value(Angle self, StringKey a0) -> IMP::String
2309  get_value(Angle self, ParticleIndexKey a0) -> Particle
2310  get_value(Angle self, ObjectKey a0) -> Object
2311  get_value(Angle self, SparseFloatKey a0) -> IMP::Float
2312  get_value(Angle self, SparseIntKey a0) -> IMP::Int
2313  get_value(Angle self, SparseStringKey a0) -> IMP::String
2314  get_value(Angle self, SparseParticleIndexKey a0) -> ParticleIndex
2315  """
2316  return _IMP_atom.Angle_get_value(self, *args)
2317 
2318  def set_value(self, *args):
2319  r"""
2320  set_value(Angle self, FloatKey a0, IMP::Float a1)
2321  set_value(Angle self, IntKey a0, IMP::Int a1)
2322  set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2323  set_value(Angle self, IntsKey a0, IMP::Ints a1)
2324  set_value(Angle self, StringKey a0, IMP::String a1)
2325  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2326  set_value(Angle self, ObjectKey a0, Object a1)
2327  set_value(Angle self, SparseFloatKey a0, IMP::Float a1)
2328  set_value(Angle self, SparseIntKey a0, IMP::Int a1)
2329  set_value(Angle self, SparseStringKey a0, IMP::String a1)
2330  set_value(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2331  """
2332  return _IMP_atom.Angle_set_value(self, *args)
2333 
2334  def remove_attribute(self, *args):
2335  r"""
2336  remove_attribute(Angle self, FloatKey a0)
2337  remove_attribute(Angle self, IntKey a0)
2338  remove_attribute(Angle self, FloatsKey a0)
2339  remove_attribute(Angle self, IntsKey a0)
2340  remove_attribute(Angle self, StringKey a0)
2341  remove_attribute(Angle self, ParticleIndexKey a0)
2342  remove_attribute(Angle self, ObjectKey a0)
2343  remove_attribute(Angle self, SparseFloatKey a0)
2344  remove_attribute(Angle self, SparseIntKey a0)
2345  remove_attribute(Angle self, SparseStringKey a0)
2346  remove_attribute(Angle self, SparseParticleIndexKey a0)
2347  """
2348  return _IMP_atom.Angle_remove_attribute(self, *args)
2349 
2350  def has_attribute(self, *args):
2351  r"""
2352  has_attribute(Angle self, FloatKey a0) -> bool
2353  has_attribute(Angle self, IntKey a0) -> bool
2354  has_attribute(Angle self, FloatsKey a0) -> bool
2355  has_attribute(Angle self, IntsKey a0) -> bool
2356  has_attribute(Angle self, StringKey a0) -> bool
2357  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2358  has_attribute(Angle self, ObjectKey a0) -> bool
2359  has_attribute(Angle self, SparseFloatKey a0) -> bool
2360  has_attribute(Angle self, SparseIntKey a0) -> bool
2361  has_attribute(Angle self, SparseStringKey a0) -> bool
2362  has_attribute(Angle self, SparseParticleIndexKey a0) -> bool
2363  """
2364  return _IMP_atom.Angle_has_attribute(self, *args)
2365 
2366  def get_derivative(self, a0):
2367  r"""get_derivative(Angle self, FloatKey a0) -> double"""
2368  return _IMP_atom.Angle_get_derivative(self, a0)
2369 
2370  def get_name(self):
2371  r"""get_name(Angle self) -> std::string"""
2372  return _IMP_atom.Angle_get_name(self)
2373 
2374  def clear_caches(self):
2375  r"""clear_caches(Angle self)"""
2376  return _IMP_atom.Angle_clear_caches(self)
2377 
2378  def set_name(self, a0):
2379  r"""set_name(Angle self, std::string a0)"""
2380  return _IMP_atom.Angle_set_name(self, a0)
2381 
2382  def set_check_level(self, a0):
2383  r"""set_check_level(Angle self, IMP::CheckLevel a0)"""
2384  return _IMP_atom.Angle_set_check_level(self, a0)
2385 
2386  def add_to_derivative(self, a0, a1, a2):
2387  r"""add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2388  return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2389 
2390  def set_is_optimized(self, a0, a1):
2391  r"""set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2392  return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2393 
2394  def get_is_optimized(self, a0):
2395  r"""get_is_optimized(Angle self, FloatKey a0) -> bool"""
2396  return _IMP_atom.Angle_get_is_optimized(self, a0)
2397 
2398  def get_check_level(self):
2399  r"""get_check_level(Angle self) -> IMP::CheckLevel"""
2400  return _IMP_atom.Angle_get_check_level(self)
2401 
2402  def __eq__(self, *args):
2403  r"""
2404  __eq__(Angle self, Angle o) -> bool
2405  __eq__(Angle self, Particle d) -> bool
2406  """
2407  return _IMP_atom.Angle___eq__(self, *args)
2408 
2409  def __ne__(self, *args):
2410  r"""
2411  __ne__(Angle self, Angle o) -> bool
2412  __ne__(Angle self, Particle d) -> bool
2413  """
2414  return _IMP_atom.Angle___ne__(self, *args)
2415 
2416  def __le__(self, *args):
2417  r"""
2418  __le__(Angle self, Angle o) -> bool
2419  __le__(Angle self, Particle d) -> bool
2420  """
2421  return _IMP_atom.Angle___le__(self, *args)
2422 
2423  def __lt__(self, *args):
2424  r"""
2425  __lt__(Angle self, Angle o) -> bool
2426  __lt__(Angle self, Particle d) -> bool
2427  """
2428  return _IMP_atom.Angle___lt__(self, *args)
2429 
2430  def __ge__(self, *args):
2431  r"""
2432  __ge__(Angle self, Angle o) -> bool
2433  __ge__(Angle self, Particle d) -> bool
2434  """
2435  return _IMP_atom.Angle___ge__(self, *args)
2436 
2437  def __gt__(self, *args):
2438  r"""
2439  __gt__(Angle self, Angle o) -> bool
2440  __gt__(Angle self, Particle d) -> bool
2441  """
2442  return _IMP_atom.Angle___gt__(self, *args)
2443 
2444  def __hash__(self):
2445  r"""__hash__(Angle self) -> std::size_t"""
2446  return _IMP_atom.Angle___hash__(self)
2447 
2448  def __str__(self):
2449  r"""__str__(Angle self) -> std::string"""
2450  return _IMP_atom.Angle___str__(self)
2451 
2452  def __repr__(self):
2453  r"""__repr__(Angle self) -> std::string"""
2454  return _IMP_atom.Angle___repr__(self)
2455 
2456  def _get_as_binary(self):
2457  r"""_get_as_binary(Angle self) -> PyObject *"""
2458  return _IMP_atom.Angle__get_as_binary(self)
2459 
2460  def _set_from_binary(self, p):
2461  r"""_set_from_binary(Angle self, PyObject * p)"""
2462  return _IMP_atom.Angle__set_from_binary(self, p)
2463 
2464  def __getstate__(self):
2465  p = self._get_as_binary()
2466  if len(self.__dict__) > 1:
2467  d = self.__dict__.copy()
2468  del d['this']
2469  p = (d, p)
2470  return p
2471 
2472  def __setstate__(self, p):
2473  if not hasattr(self, 'this'):
2474  self.__init__()
2475  if isinstance(p, tuple):
2476  d, p = p
2477  self.__dict__.update(d)
2478  return self._set_from_binary(p)
2479 
2480  __swig_destroy__ = _IMP_atom.delete_Angle
2481 
2482 # Register Angle in _IMP_atom:
2483 _IMP_atom.Angle_swigregister(Angle)
2484 class Dihedral(IMP.Decorator):
2485  r"""Proxy of C++ IMP::atom::Dihedral class."""
2486 
2487  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2488 
2489  def __init__(self, *args):
2490  r"""
2491  __init__(Dihedral self) -> Dihedral
2492  __init__(Dihedral self, Model m, ParticleIndex id) -> Dihedral
2493  __init__(Dihedral self, _ParticleAdaptor d) -> Dihedral
2494  """
2495  _IMP_atom.Dihedral_swiginit(self, _IMP_atom.new_Dihedral(*args))
2496 
2497  def show(self, *args):
2498  r"""show(Dihedral self, _ostream out=std::cout)"""
2499  return _IMP_atom.Dihedral_show(self, *args)
2500 
2501  @staticmethod
2502  def setup_particle(*args):
2503  r"""
2504  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2505  setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2506  """
2507  return _IMP_atom.Dihedral_setup_particle(*args)
2508 
2509  @staticmethod
2510  def get_is_setup(*args):
2511  r"""
2512  get_is_setup(_ParticleAdaptor p) -> bool
2513  get_is_setup(Model m, ParticleIndex pi) -> bool
2514  """
2515  return _IMP_atom.Dihedral_get_is_setup(*args)
2516 
2517  def get_particle(self, *args):
2518  r"""
2519  get_particle(Dihedral self) -> Particle
2520  get_particle(Dihedral self, unsigned int i) -> Particle
2521  """
2522  return _IMP_atom.Dihedral_get_particle(self, *args)
2523 
2524  def get_ideal(self):
2525  r"""get_ideal(Dihedral self) -> IMP::Float"""
2526  return _IMP_atom.Dihedral_get_ideal(self)
2527 
2528  def set_ideal(self, t):
2529  r"""set_ideal(Dihedral self, IMP::Float t)"""
2530  return _IMP_atom.Dihedral_set_ideal(self, t)
2531 
2532  def get_multiplicity(self):
2533  r"""get_multiplicity(Dihedral self) -> IMP::Int"""
2534  return _IMP_atom.Dihedral_get_multiplicity(self)
2535 
2536  def set_multiplicity(self, t):
2537  r"""set_multiplicity(Dihedral self, IMP::Int t)"""
2538  return _IMP_atom.Dihedral_set_multiplicity(self, t)
2539 
2540  def get_stiffness(self):
2541  r"""get_stiffness(Dihedral self) -> IMP::Float"""
2542  return _IMP_atom.Dihedral_get_stiffness(self)
2543 
2544  def set_stiffness(self, t):
2545  r"""set_stiffness(Dihedral self, IMP::Float t)"""
2546  return _IMP_atom.Dihedral_set_stiffness(self, t)
2547 
2548  @staticmethod
2549  def get_particle_key(i):
2550  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2551  return _IMP_atom.Dihedral_get_particle_key(i)
2552 
2553  @staticmethod
2554  def get_ideal_key():
2555  r"""get_ideal_key() -> FloatKey"""
2556  return _IMP_atom.Dihedral_get_ideal_key()
2557 
2558  @staticmethod
2559  def get_multiplicity_key():
2560  r"""get_multiplicity_key() -> IntKey"""
2561  return _IMP_atom.Dihedral_get_multiplicity_key()
2562 
2563  @staticmethod
2564  def get_stiffness_key():
2565  r"""get_stiffness_key() -> FloatKey"""
2566  return _IMP_atom.Dihedral_get_stiffness_key()
2567 
2568  def add_attribute(self, *args):
2569  r"""
2570  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2571  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2572  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2573  add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2574  add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2575  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2576  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2577  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2578  add_attribute(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2579  add_attribute(Dihedral self, SparseIntKey a0, IMP::Int a1)
2580  add_attribute(Dihedral self, SparseStringKey a0, IMP::String a1)
2581  add_attribute(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2582  """
2583  return _IMP_atom.Dihedral_add_attribute(self, *args)
2584 
2585  def get_value(self, *args):
2586  r"""
2587  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2588  get_value(Dihedral self, IntKey a0) -> IMP::Int
2589  get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2590  get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2591  get_value(Dihedral self, StringKey a0) -> IMP::String
2592  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2593  get_value(Dihedral self, ObjectKey a0) -> Object
2594  get_value(Dihedral self, SparseFloatKey a0) -> IMP::Float
2595  get_value(Dihedral self, SparseIntKey a0) -> IMP::Int
2596  get_value(Dihedral self, SparseStringKey a0) -> IMP::String
2597  get_value(Dihedral self, SparseParticleIndexKey a0) -> ParticleIndex
2598  """
2599  return _IMP_atom.Dihedral_get_value(self, *args)
2600 
2601  def set_value(self, *args):
2602  r"""
2603  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2604  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2605  set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2606  set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2607  set_value(Dihedral self, StringKey a0, IMP::String a1)
2608  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2609  set_value(Dihedral self, ObjectKey a0, Object a1)
2610  set_value(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2611  set_value(Dihedral self, SparseIntKey a0, IMP::Int a1)
2612  set_value(Dihedral self, SparseStringKey a0, IMP::String a1)
2613  set_value(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2614  """
2615  return _IMP_atom.Dihedral_set_value(self, *args)
2616 
2617  def remove_attribute(self, *args):
2618  r"""
2619  remove_attribute(Dihedral self, FloatKey a0)
2620  remove_attribute(Dihedral self, IntKey a0)
2621  remove_attribute(Dihedral self, FloatsKey a0)
2622  remove_attribute(Dihedral self, IntsKey a0)
2623  remove_attribute(Dihedral self, StringKey a0)
2624  remove_attribute(Dihedral self, ParticleIndexKey a0)
2625  remove_attribute(Dihedral self, ObjectKey a0)
2626  remove_attribute(Dihedral self, SparseFloatKey a0)
2627  remove_attribute(Dihedral self, SparseIntKey a0)
2628  remove_attribute(Dihedral self, SparseStringKey a0)
2629  remove_attribute(Dihedral self, SparseParticleIndexKey a0)
2630  """
2631  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2632 
2633  def has_attribute(self, *args):
2634  r"""
2635  has_attribute(Dihedral self, FloatKey a0) -> bool
2636  has_attribute(Dihedral self, IntKey a0) -> bool
2637  has_attribute(Dihedral self, FloatsKey a0) -> bool
2638  has_attribute(Dihedral self, IntsKey a0) -> bool
2639  has_attribute(Dihedral self, StringKey a0) -> bool
2640  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2641  has_attribute(Dihedral self, ObjectKey a0) -> bool
2642  has_attribute(Dihedral self, SparseFloatKey a0) -> bool
2643  has_attribute(Dihedral self, SparseIntKey a0) -> bool
2644  has_attribute(Dihedral self, SparseStringKey a0) -> bool
2645  has_attribute(Dihedral self, SparseParticleIndexKey a0) -> bool
2646  """
2647  return _IMP_atom.Dihedral_has_attribute(self, *args)
2648 
2649  def get_derivative(self, a0):
2650  r"""get_derivative(Dihedral self, FloatKey a0) -> double"""
2651  return _IMP_atom.Dihedral_get_derivative(self, a0)
2652 
2653  def get_name(self):
2654  r"""get_name(Dihedral self) -> std::string"""
2655  return _IMP_atom.Dihedral_get_name(self)
2656 
2657  def clear_caches(self):
2658  r"""clear_caches(Dihedral self)"""
2659  return _IMP_atom.Dihedral_clear_caches(self)
2660 
2661  def set_name(self, a0):
2662  r"""set_name(Dihedral self, std::string a0)"""
2663  return _IMP_atom.Dihedral_set_name(self, a0)
2664 
2665  def set_check_level(self, a0):
2666  r"""set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2667  return _IMP_atom.Dihedral_set_check_level(self, a0)
2668 
2669  def add_to_derivative(self, a0, a1, a2):
2670  r"""add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2671  return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2672 
2673  def set_is_optimized(self, a0, a1):
2674  r"""set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2675  return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2676 
2677  def get_is_optimized(self, a0):
2678  r"""get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2679  return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2680 
2681  def get_check_level(self):
2682  r"""get_check_level(Dihedral self) -> IMP::CheckLevel"""
2683  return _IMP_atom.Dihedral_get_check_level(self)
2684 
2685  def __eq__(self, *args):
2686  r"""
2687  __eq__(Dihedral self, Dihedral o) -> bool
2688  __eq__(Dihedral self, Particle d) -> bool
2689  """
2690  return _IMP_atom.Dihedral___eq__(self, *args)
2691 
2692  def __ne__(self, *args):
2693  r"""
2694  __ne__(Dihedral self, Dihedral o) -> bool
2695  __ne__(Dihedral self, Particle d) -> bool
2696  """
2697  return _IMP_atom.Dihedral___ne__(self, *args)
2698 
2699  def __le__(self, *args):
2700  r"""
2701  __le__(Dihedral self, Dihedral o) -> bool
2702  __le__(Dihedral self, Particle d) -> bool
2703  """
2704  return _IMP_atom.Dihedral___le__(self, *args)
2705 
2706  def __lt__(self, *args):
2707  r"""
2708  __lt__(Dihedral self, Dihedral o) -> bool
2709  __lt__(Dihedral self, Particle d) -> bool
2710  """
2711  return _IMP_atom.Dihedral___lt__(self, *args)
2712 
2713  def __ge__(self, *args):
2714  r"""
2715  __ge__(Dihedral self, Dihedral o) -> bool
2716  __ge__(Dihedral self, Particle d) -> bool
2717  """
2718  return _IMP_atom.Dihedral___ge__(self, *args)
2719 
2720  def __gt__(self, *args):
2721  r"""
2722  __gt__(Dihedral self, Dihedral o) -> bool
2723  __gt__(Dihedral self, Particle d) -> bool
2724  """
2725  return _IMP_atom.Dihedral___gt__(self, *args)
2726 
2727  def __hash__(self):
2728  r"""__hash__(Dihedral self) -> std::size_t"""
2729  return _IMP_atom.Dihedral___hash__(self)
2730 
2731  def __str__(self):
2732  r"""__str__(Dihedral self) -> std::string"""
2733  return _IMP_atom.Dihedral___str__(self)
2734 
2735  def __repr__(self):
2736  r"""__repr__(Dihedral self) -> std::string"""
2737  return _IMP_atom.Dihedral___repr__(self)
2738 
2739  def _get_as_binary(self):
2740  r"""_get_as_binary(Dihedral self) -> PyObject *"""
2741  return _IMP_atom.Dihedral__get_as_binary(self)
2742 
2743  def _set_from_binary(self, p):
2744  r"""_set_from_binary(Dihedral self, PyObject * p)"""
2745  return _IMP_atom.Dihedral__set_from_binary(self, p)
2746 
2747  def __getstate__(self):
2748  p = self._get_as_binary()
2749  if len(self.__dict__) > 1:
2750  d = self.__dict__.copy()
2751  del d['this']
2752  p = (d, p)
2753  return p
2754 
2755  def __setstate__(self, p):
2756  if not hasattr(self, 'this'):
2757  self.__init__()
2758  if isinstance(p, tuple):
2759  d, p = p
2760  self.__dict__.update(d)
2761  return self._set_from_binary(p)
2762 
2763  __swig_destroy__ = _IMP_atom.delete_Dihedral
2764 
2765 # Register Dihedral in _IMP_atom:
2766 _IMP_atom.Dihedral_swigregister(Dihedral)
2767 class SmoothingFunction(IMP.Object):
2768  r"""Proxy of C++ IMP::atom::SmoothingFunction class."""
2769 
2770  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2771 
2772  def __init__(self, *args, **kwargs):
2773  raise AttributeError("No constructor defined - class is abstract")
2774 
2775  def __call__(self, *args):
2776  r"""
2777  __call__(SmoothingFunction self, double score, double distance) -> double
2778  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2779  """
2780  return _IMP_atom.SmoothingFunction___call__(self, *args)
2781  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2782 
2783  def __str__(self):
2784  r"""__str__(SmoothingFunction self) -> std::string"""
2785  return _IMP_atom.SmoothingFunction___str__(self)
2786 
2787  def __repr__(self):
2788  r"""__repr__(SmoothingFunction self) -> std::string"""
2789  return _IMP_atom.SmoothingFunction___repr__(self)
2790 
2791  @staticmethod
2792  def get_from(o):
2793  return _object_cast_to_SmoothingFunction(o)
2794 
2795 
2796 # Register SmoothingFunction in _IMP_atom:
2797 _IMP_atom.SmoothingFunction_swigregister(SmoothingFunction)
2798 class ForceSwitch(SmoothingFunction):
2799  r"""Proxy of C++ IMP::atom::ForceSwitch class."""
2800 
2801  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2802 
2803  def __init__(self, min_distance, max_distance):
2804  r"""__init__(ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2805  _IMP_atom.ForceSwitch_swiginit(self, _IMP_atom.new_ForceSwitch(min_distance, max_distance))
2806 
2807  def __call__(self, *args):
2808  r"""
2809  __call__(ForceSwitch self, double score, double distance) -> double
2810  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2811  """
2812  return _IMP_atom.ForceSwitch___call__(self, *args)
2813 
2814  def get_version_info(self):
2815  r"""get_version_info(ForceSwitch self) -> VersionInfo"""
2816  return _IMP_atom.ForceSwitch_get_version_info(self)
2817  __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2818 
2819  def __str__(self):
2820  r"""__str__(ForceSwitch self) -> std::string"""
2821  return _IMP_atom.ForceSwitch___str__(self)
2822 
2823  def __repr__(self):
2824  r"""__repr__(ForceSwitch self) -> std::string"""
2825  return _IMP_atom.ForceSwitch___repr__(self)
2826 
2827  @staticmethod
2828  def get_from(o):
2829  return _object_cast_to_ForceSwitch(o)
2830 
2831 
2832 # Register ForceSwitch in _IMP_atom:
2833 _IMP_atom.ForceSwitch_swigregister(ForceSwitch)
2834 class AngleSingletonScore(IMP.SingletonScore):
2835  r"""Proxy of C++ IMP::atom::AngleSingletonScore class."""
2836 
2837  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2838 
2839  def __init__(self, f):
2840  r"""__init__(AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2841  _IMP_atom.AngleSingletonScore_swiginit(self, _IMP_atom.new_AngleSingletonScore(f))
2842 
2843  def do_get_inputs(self, m, pis):
2844  r"""do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2845  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2846 
2847  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
2848  r"""evaluate_indexes(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2849  return _IMP_atom.AngleSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
2850 
2851  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
2852  r"""evaluate_indexes_scores(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2853  return _IMP_atom.AngleSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
2854 
2855  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
2856  r"""evaluate_indexes_delta(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2857  return _IMP_atom.AngleSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
2858 
2859  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
2860  r"""evaluate_if_good_indexes(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2861  return _IMP_atom.AngleSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
2862 
2863  def get_version_info(self):
2864  r"""get_version_info(AngleSingletonScore self) -> VersionInfo"""
2865  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2866  __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2867 
2868  def __str__(self):
2869  r"""__str__(AngleSingletonScore self) -> std::string"""
2870  return _IMP_atom.AngleSingletonScore___str__(self)
2871 
2872  def __repr__(self):
2873  r"""__repr__(AngleSingletonScore self) -> std::string"""
2874  return _IMP_atom.AngleSingletonScore___repr__(self)
2875 
2876  @staticmethod
2877  def get_from(o):
2878  return _object_cast_to_AngleSingletonScore(o)
2879 
2880 
2881 # Register AngleSingletonScore in _IMP_atom:
2882 _IMP_atom.AngleSingletonScore_swigregister(AngleSingletonScore)
2883 class BondEndpointsRefiner(IMP.Refiner):
2884  r"""Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2885 
2886  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2887 
2888  def __init__(self):
2889  r"""__init__(BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2890  _IMP_atom.BondEndpointsRefiner_swiginit(self, _IMP_atom.new_BondEndpointsRefiner())
2891 
2892  def do_get_inputs(self, m, pis):
2893  r"""do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2894  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2895 
2896  def get_version_info(self):
2897  r"""get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2898  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2899  __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2900 
2901  def __str__(self):
2902  r"""__str__(BondEndpointsRefiner self) -> std::string"""
2903  return _IMP_atom.BondEndpointsRefiner___str__(self)
2904 
2905  def __repr__(self):
2906  r"""__repr__(BondEndpointsRefiner self) -> std::string"""
2907  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2908 
2909  @staticmethod
2910  def get_from(o):
2911  return _object_cast_to_BondEndpointsRefiner(o)
2912 
2913 
2914 # Register BondEndpointsRefiner in _IMP_atom:
2915 _IMP_atom.BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2916 class BondPairContainer(IMP.PairContainer):
2917  r"""Proxy of C++ IMP::atom::BondPairContainer class."""
2918 
2919  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2920 
2921  def __init__(self, sc):
2922  r"""__init__(BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2923  _IMP_atom.BondPairContainer_swiginit(self, _IMP_atom.new_BondPairContainer(sc))
2924 
2925  def do_get_inputs(self):
2926  r"""do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2927  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2928 
2929  def do_apply(self, sm):
2930  r"""do_apply(BondPairContainer self, PairModifier sm)"""
2931  return _IMP_atom.BondPairContainer_do_apply(self, sm)
2932 
2933  def do_apply_moved(self, sm, moved_pis, reset_pis):
2934  r"""do_apply_moved(BondPairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
2935  return _IMP_atom.BondPairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
2936 
2937  def get_version_info(self):
2938  r"""get_version_info(BondPairContainer self) -> VersionInfo"""
2939  return _IMP_atom.BondPairContainer_get_version_info(self)
2940  __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2941 
2942  def __str__(self):
2943  r"""__str__(BondPairContainer self) -> std::string"""
2944  return _IMP_atom.BondPairContainer___str__(self)
2945 
2946  def __repr__(self):
2947  r"""__repr__(BondPairContainer self) -> std::string"""
2948  return _IMP_atom.BondPairContainer___repr__(self)
2949 
2950  @staticmethod
2951  def get_from(o):
2952  return _object_cast_to_BondPairContainer(o)
2953 
2954 
2955 # Register BondPairContainer in _IMP_atom:
2956 _IMP_atom.BondPairContainer_swigregister(BondPairContainer)
2957 class BondSingletonScore(IMP.SingletonScore):
2958  r"""Proxy of C++ IMP::atom::BondSingletonScore class."""
2959 
2960  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2961 
2962  def __init__(self, f):
2963  r"""__init__(BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2964  _IMP_atom.BondSingletonScore_swiginit(self, _IMP_atom.new_BondSingletonScore(f))
2965 
2966  def get_unary_function(self):
2967  r"""get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2968  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2969 
2970  def do_get_inputs(self, m, pis):
2971  r"""do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2972  return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2973 
2974  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
2975  r"""evaluate_indexes(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2976  return _IMP_atom.BondSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
2977 
2978  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
2979  r"""evaluate_indexes_scores(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2980  return _IMP_atom.BondSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
2981 
2982  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
2983  r"""evaluate_indexes_delta(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2984  return _IMP_atom.BondSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
2985 
2986  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
2987  r"""evaluate_if_good_indexes(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2988  return _IMP_atom.BondSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
2989 
2990  def get_version_info(self):
2991  r"""get_version_info(BondSingletonScore self) -> VersionInfo"""
2992  return _IMP_atom.BondSingletonScore_get_version_info(self)
2993  __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2994 
2995  def __str__(self):
2996  r"""__str__(BondSingletonScore self) -> std::string"""
2997  return _IMP_atom.BondSingletonScore___str__(self)
2998 
2999  def __repr__(self):
3000  r"""__repr__(BondSingletonScore self) -> std::string"""
3001  return _IMP_atom.BondSingletonScore___repr__(self)
3002 
3003  @staticmethod
3004  def get_from(o):
3005  return _object_cast_to_BondSingletonScore(o)
3006 
3007 
3008 # Register BondSingletonScore in _IMP_atom:
3009 _IMP_atom.BondSingletonScore_swigregister(BondSingletonScore)
3010 class DihedralSingletonScore(IMP.SingletonScore):
3011  r"""Proxy of C++ IMP::atom::DihedralSingletonScore class."""
3012 
3013  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3014 
3015  def __init__(self):
3016  r"""__init__(DihedralSingletonScore self) -> DihedralSingletonScore"""
3017  _IMP_atom.DihedralSingletonScore_swiginit(self, _IMP_atom.new_DihedralSingletonScore())
3018 
3019  def do_get_inputs(self, m, pis):
3020  r"""do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3021  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3022 
3023  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
3024  r"""evaluate_indexes(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3025  return _IMP_atom.DihedralSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
3026 
3027  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
3028  r"""evaluate_indexes_scores(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3029  return _IMP_atom.DihedralSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
3030 
3031  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
3032  r"""evaluate_indexes_delta(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3033  return _IMP_atom.DihedralSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
3034 
3035  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
3036  r"""evaluate_if_good_indexes(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3037  return _IMP_atom.DihedralSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
3038 
3039  def get_version_info(self):
3040  r"""get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3041  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3042  __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
3043 
3044  def __str__(self):
3045  r"""__str__(DihedralSingletonScore self) -> std::string"""
3046  return _IMP_atom.DihedralSingletonScore___str__(self)
3047 
3048  def __repr__(self):
3049  r"""__repr__(DihedralSingletonScore self) -> std::string"""
3050  return _IMP_atom.DihedralSingletonScore___repr__(self)
3051 
3052  @staticmethod
3053  def get_from(o):
3054  return _object_cast_to_DihedralSingletonScore(o)
3055 
3056 
3057  def _get_as_binary(self):
3058  r"""_get_as_binary(DihedralSingletonScore self) -> PyObject *"""
3059  return _IMP_atom.DihedralSingletonScore__get_as_binary(self)
3060 
3061  def _set_from_binary(self, p):
3062  r"""_set_from_binary(DihedralSingletonScore self, PyObject * p)"""
3063  return _IMP_atom.DihedralSingletonScore__set_from_binary(self, p)
3064 
3065  def __getstate__(self):
3066  p = self._get_as_binary()
3067  if len(self.__dict__) > 1:
3068  d = self.__dict__.copy()
3069  del d['this']
3070  p = (d, p)
3071  return p
3072 
3073  def __setstate__(self, p):
3074  if not hasattr(self, 'this'):
3075  self.__init__()
3076  if isinstance(p, tuple):
3077  d, p = p
3078  self.__dict__.update(d)
3079  return self._set_from_binary(p)
3080 
3081 
3082 # Register DihedralSingletonScore in _IMP_atom:
3083 _IMP_atom.DihedralSingletonScore_swigregister(DihedralSingletonScore)
3084 class ImproperSingletonScore(IMP.SingletonScore):
3085  r"""Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3086 
3087  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3088 
3089  def __init__(self, f):
3090  r"""__init__(ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3091  _IMP_atom.ImproperSingletonScore_swiginit(self, _IMP_atom.new_ImproperSingletonScore(f))
3092 
3093  def do_get_inputs(self, m, pis):
3094  r"""do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3095  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3096 
3097  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
3098  r"""evaluate_indexes(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3099  return _IMP_atom.ImproperSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
3100 
3101  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
3102  r"""evaluate_indexes_scores(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3103  return _IMP_atom.ImproperSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
3104 
3105  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
3106  r"""evaluate_indexes_delta(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3107  return _IMP_atom.ImproperSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
3108 
3109  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
3110  r"""evaluate_if_good_indexes(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3111  return _IMP_atom.ImproperSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
3112 
3113  def get_version_info(self):
3114  r"""get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3115  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3116  __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
3117 
3118  def __str__(self):
3119  r"""__str__(ImproperSingletonScore self) -> std::string"""
3120  return _IMP_atom.ImproperSingletonScore___str__(self)
3121 
3122  def __repr__(self):
3123  r"""__repr__(ImproperSingletonScore self) -> std::string"""
3124  return _IMP_atom.ImproperSingletonScore___repr__(self)
3125 
3126  @staticmethod
3127  def get_from(o):
3128  return _object_cast_to_ImproperSingletonScore(o)
3129 
3130 
3131 # Register ImproperSingletonScore in _IMP_atom:
3132 _IMP_atom.ImproperSingletonScore_swigregister(ImproperSingletonScore)
3133 class CenterOfMass(IMP.Decorator):
3134  r"""Proxy of C++ IMP::atom::CenterOfMass class."""
3135 
3136  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3137 
3138  def get_constraint(self):
3139  r"""get_constraint(CenterOfMass self) -> Constraint"""
3140  return _IMP_atom.CenterOfMass_get_constraint(self)
3141 
3142  def get_mass(self):
3143  r"""get_mass(CenterOfMass self) -> IMP::Float"""
3144  return _IMP_atom.CenterOfMass_get_mass(self)
3145 
3146  def get_coordinate(self, i):
3147  r"""get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3148  return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3149 
3150  def get_coordinates(self):
3151  r"""get_coordinates(CenterOfMass self) -> Vector3D"""
3152  return _IMP_atom.CenterOfMass_get_coordinates(self)
3153 
3154  def __init__(self, *args):
3155  r"""
3156  __init__(CenterOfMass self) -> CenterOfMass
3157  __init__(CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3158  __init__(CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3159  """
3160  _IMP_atom.CenterOfMass_swiginit(self, _IMP_atom.new_CenterOfMass(*args))
3161 
3162  def show(self, *args):
3163  r"""show(CenterOfMass self, _ostream out=std::cout)"""
3164  return _IMP_atom.CenterOfMass_show(self, *args)
3165 
3166  @staticmethod
3167  def setup_particle(*args):
3168  r"""
3169  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3170  setup_particle(_ParticleAdaptor pa, _ParticleIndexesAdaptor members) -> CenterOfMass
3171  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3172  setup_particle(_ParticleAdaptor pa, Refiner refiner) -> CenterOfMass
3173  """
3174  return _IMP_atom.CenterOfMass_setup_particle(*args)
3175 
3176  @staticmethod
3177  def teardown_particle(com):
3178  r"""teardown_particle(CenterOfMass com)"""
3179  return _IMP_atom.CenterOfMass_teardown_particle(com)
3180 
3181  @staticmethod
3182  def get_is_setup(*args):
3183  r"""
3184  get_is_setup(_ParticleAdaptor p) -> bool
3185  get_is_setup(Model m, ParticleIndex pi) -> bool
3186  """
3187  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3188 
3189  def add_attribute(self, *args):
3190  r"""
3191  add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3192  add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3193  add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3194  add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3195  add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3196  add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3197  add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3198  add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3199  add_attribute(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3200  add_attribute(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3201  add_attribute(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3202  add_attribute(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3203  """
3204  return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3205 
3206  def get_value(self, *args):
3207  r"""
3208  get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3209  get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3210  get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3211  get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3212  get_value(CenterOfMass self, StringKey a0) -> IMP::String
3213  get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3214  get_value(CenterOfMass self, ObjectKey a0) -> Object
3215  get_value(CenterOfMass self, SparseFloatKey a0) -> IMP::Float
3216  get_value(CenterOfMass self, SparseIntKey a0) -> IMP::Int
3217  get_value(CenterOfMass self, SparseStringKey a0) -> IMP::String
3218  get_value(CenterOfMass self, SparseParticleIndexKey a0) -> ParticleIndex
3219  """
3220  return _IMP_atom.CenterOfMass_get_value(self, *args)
3221 
3222  def set_value(self, *args):
3223  r"""
3224  set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3225  set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3226  set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3227  set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3228  set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3229  set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3230  set_value(CenterOfMass self, ObjectKey a0, Object a1)
3231  set_value(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3232  set_value(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3233  set_value(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3234  set_value(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3235  """
3236  return _IMP_atom.CenterOfMass_set_value(self, *args)
3237 
3238  def remove_attribute(self, *args):
3239  r"""
3240  remove_attribute(CenterOfMass self, FloatKey a0)
3241  remove_attribute(CenterOfMass self, IntKey a0)
3242  remove_attribute(CenterOfMass self, FloatsKey a0)
3243  remove_attribute(CenterOfMass self, IntsKey a0)
3244  remove_attribute(CenterOfMass self, StringKey a0)
3245  remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3246  remove_attribute(CenterOfMass self, ObjectKey a0)
3247  remove_attribute(CenterOfMass self, SparseFloatKey a0)
3248  remove_attribute(CenterOfMass self, SparseIntKey a0)
3249  remove_attribute(CenterOfMass self, SparseStringKey a0)
3250  remove_attribute(CenterOfMass self, SparseParticleIndexKey a0)
3251  """
3252  return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3253 
3254  def has_attribute(self, *args):
3255  r"""
3256  has_attribute(CenterOfMass self, FloatKey a0) -> bool
3257  has_attribute(CenterOfMass self, IntKey a0) -> bool
3258  has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3259  has_attribute(CenterOfMass self, IntsKey a0) -> bool
3260  has_attribute(CenterOfMass self, StringKey a0) -> bool
3261  has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3262  has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3263  has_attribute(CenterOfMass self, SparseFloatKey a0) -> bool
3264  has_attribute(CenterOfMass self, SparseIntKey a0) -> bool
3265  has_attribute(CenterOfMass self, SparseStringKey a0) -> bool
3266  has_attribute(CenterOfMass self, SparseParticleIndexKey a0) -> bool
3267  """
3268  return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3269 
3270  def get_derivative(self, a0):
3271  r"""get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3272  return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3273 
3274  def get_name(self):
3275  r"""get_name(CenterOfMass self) -> std::string"""
3276  return _IMP_atom.CenterOfMass_get_name(self)
3277 
3278  def clear_caches(self):
3279  r"""clear_caches(CenterOfMass self)"""
3280  return _IMP_atom.CenterOfMass_clear_caches(self)
3281 
3282  def set_name(self, a0):
3283  r"""set_name(CenterOfMass self, std::string a0)"""
3284  return _IMP_atom.CenterOfMass_set_name(self, a0)
3285 
3286  def set_check_level(self, a0):
3287  r"""set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3288  return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3289 
3290  def add_to_derivative(self, a0, a1, a2):
3291  r"""add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3292  return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3293 
3294  def set_is_optimized(self, a0, a1):
3295  r"""set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3296  return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3297 
3298  def get_is_optimized(self, a0):
3299  r"""get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3300  return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3301 
3302  def get_check_level(self):
3303  r"""get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3304  return _IMP_atom.CenterOfMass_get_check_level(self)
3305 
3306  def __eq__(self, *args):
3307  r"""
3308  __eq__(CenterOfMass self, CenterOfMass o) -> bool
3309  __eq__(CenterOfMass self, Particle d) -> bool
3310  """
3311  return _IMP_atom.CenterOfMass___eq__(self, *args)
3312 
3313  def __ne__(self, *args):
3314  r"""
3315  __ne__(CenterOfMass self, CenterOfMass o) -> bool
3316  __ne__(CenterOfMass self, Particle d) -> bool
3317  """
3318  return _IMP_atom.CenterOfMass___ne__(self, *args)
3319 
3320  def __le__(self, *args):
3321  r"""
3322  __le__(CenterOfMass self, CenterOfMass o) -> bool
3323  __le__(CenterOfMass self, Particle d) -> bool
3324  """
3325  return _IMP_atom.CenterOfMass___le__(self, *args)
3326 
3327  def __lt__(self, *args):
3328  r"""
3329  __lt__(CenterOfMass self, CenterOfMass o) -> bool
3330  __lt__(CenterOfMass self, Particle d) -> bool
3331  """
3332  return _IMP_atom.CenterOfMass___lt__(self, *args)
3333 
3334  def __ge__(self, *args):
3335  r"""
3336  __ge__(CenterOfMass self, CenterOfMass o) -> bool
3337  __ge__(CenterOfMass self, Particle d) -> bool
3338  """
3339  return _IMP_atom.CenterOfMass___ge__(self, *args)
3340 
3341  def __gt__(self, *args):
3342  r"""
3343  __gt__(CenterOfMass self, CenterOfMass o) -> bool
3344  __gt__(CenterOfMass self, Particle d) -> bool
3345  """
3346  return _IMP_atom.CenterOfMass___gt__(self, *args)
3347 
3348  def __hash__(self):
3349  r"""__hash__(CenterOfMass self) -> std::size_t"""
3350  return _IMP_atom.CenterOfMass___hash__(self)
3351 
3352  def __str__(self):
3353  r"""__str__(CenterOfMass self) -> std::string"""
3354  return _IMP_atom.CenterOfMass___str__(self)
3355 
3356  def __repr__(self):
3357  r"""__repr__(CenterOfMass self) -> std::string"""
3358  return _IMP_atom.CenterOfMass___repr__(self)
3359 
3360  def _get_as_binary(self):
3361  r"""_get_as_binary(CenterOfMass self) -> PyObject *"""
3362  return _IMP_atom.CenterOfMass__get_as_binary(self)
3363 
3364  def _set_from_binary(self, p):
3365  r"""_set_from_binary(CenterOfMass self, PyObject * p)"""
3366  return _IMP_atom.CenterOfMass__set_from_binary(self, p)
3367 
3368  def __getstate__(self):
3369  p = self._get_as_binary()
3370  if len(self.__dict__) > 1:
3371  d = self.__dict__.copy()
3372  del d['this']
3373  p = (d, p)
3374  return p
3375 
3376  def __setstate__(self, p):
3377  if not hasattr(self, 'this'):
3378  self.__init__()
3379  if isinstance(p, tuple):
3380  d, p = p
3381  self.__dict__.update(d)
3382  return self._set_from_binary(p)
3383 
3384  __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3385 
3386 # Register CenterOfMass in _IMP_atom:
3387 _IMP_atom.CenterOfMass_swigregister(CenterOfMass)
3388 class CoverBond(IMP.SingletonModifier):
3389  r"""Proxy of C++ IMP::atom::CoverBond class."""
3390 
3391  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3392 
3393  def __init__(self):
3394  r"""__init__(CoverBond self) -> CoverBond"""
3395  _IMP_atom.CoverBond_swiginit(self, _IMP_atom.new_CoverBond())
3396 
3397  def do_get_inputs(self, m, pis):
3398  r"""do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3399  return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3400 
3401  def do_get_outputs(self, m, pis):
3402  r"""do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3403  return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3404 
3405  def get_version_info(self):
3406  r"""get_version_info(CoverBond self) -> VersionInfo"""
3407  return _IMP_atom.CoverBond_get_version_info(self)
3408  __swig_destroy__ = _IMP_atom.delete_CoverBond
3409 
3410  def __str__(self):
3411  r"""__str__(CoverBond self) -> std::string"""
3412  return _IMP_atom.CoverBond___str__(self)
3413 
3414  def __repr__(self):
3415  r"""__repr__(CoverBond self) -> std::string"""
3416  return _IMP_atom.CoverBond___repr__(self)
3417 
3418  @staticmethod
3419  def get_from(o):
3420  return _object_cast_to_CoverBond(o)
3421 
3422 
3423 # Register CoverBond in _IMP_atom:
3424 _IMP_atom.CoverBond_swigregister(CoverBond)
3425 class Simulator(IMP.Optimizer):
3426  r"""Proxy of C++ IMP::atom::Simulator class."""
3427 
3428  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3429 
3430  def __init__(self, *args):
3431  r"""__init__(Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator"""
3432  if self.__class__ == Simulator:
3433  _self = None
3434  else:
3435  _self = self
3436  _IMP_atom.Simulator_swiginit(self, _IMP_atom.new_Simulator(_self, *args))
3437 
3438  if self.__class__ != Simulator:
3439  _director_objects.register(self)
3440 
3441 
3442 
3443 
3444  def simulate(self, time_in_fs):
3445  r"""simulate(Simulator self, double time_in_fs) -> double"""
3446  return _IMP_atom.Simulator_simulate(self, time_in_fs)
3447 
3448  def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3449  r"""simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3450  return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3451 
3452  def get_temperature(self):
3453  r"""get_temperature(Simulator self) -> double"""
3454  return _IMP_atom.Simulator_get_temperature(self)
3455 
3456  def set_temperature(self, d):
3457  r"""set_temperature(Simulator self, double d)"""
3458  return _IMP_atom.Simulator_set_temperature(self, d)
3459 
3460  def set_maximum_time_step(self, ts):
3461  r"""set_maximum_time_step(Simulator self, double ts)"""
3462  return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3463 
3464  def get_maximum_time_step(self):
3465  r"""get_maximum_time_step(Simulator self) -> double"""
3466  return _IMP_atom.Simulator_get_maximum_time_step(self)
3467 
3468  def get_last_time_step(self):
3469  r"""get_last_time_step(Simulator self) -> double"""
3470  return _IMP_atom.Simulator_get_last_time_step(self)
3471 
3472  def set_time_step(self, ts):
3473  r"""set_time_step(Simulator self, double ts)"""
3474  return _IMP_atom.Simulator_set_time_step(self, ts)
3475 
3476  def get_kt(self):
3477  r"""get_kt(Simulator self) -> double"""
3478  return _IMP_atom.Simulator_get_kt(self)
3479 
3480  def get_current_time(self):
3481  r"""get_current_time(Simulator self) -> double"""
3482  return _IMP_atom.Simulator_get_current_time(self)
3483 
3484  def set_current_time(self, ct):
3485  r"""set_current_time(Simulator self, double ct)"""
3486  return _IMP_atom.Simulator_set_current_time(self, ct)
3487 
3488  def get_simulation_particles(self):
3489  r"""get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3490  return _IMP_atom.Simulator_get_simulation_particles(self)
3491 
3492  def get_simulation_particle_indexes(self):
3493  r"""get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3494  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3495  def __get_particles(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_particles, getfunc=self.get_particle, erasefunc=self.erase_particle, appendfunc=self.add_particle, extendfunc=self.add_particles, clearfunc=self.clear_particles, indexfunc=self._python_index_particle)
3496  def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
3497  def __del_particles(self): IMP._list_util.del_varlist(self.particles)
3498  particles = property(__get_particles, __set_particles, __del_particles, doc="List of ##ucnames")
3499 
3500  def remove_particle(self, d):
3501  r"""remove_particle(Simulator self, Particle d)"""
3502  return _IMP_atom.Simulator_remove_particle(self, d)
3503 
3504  def _python_index_particle(self, d, start, stop):
3505  r"""_python_index_particle(Simulator self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
3506  return _IMP_atom.Simulator__python_index_particle(self, d, start, stop)
3507 
3508  def remove_particles(self, d):
3509  r"""remove_particles(Simulator self, IMP::Particles const & d)"""
3510  return _IMP_atom.Simulator_remove_particles(self, d)
3511 
3512  def set_particles(self, ps):
3513  r"""set_particles(Simulator self, IMP::Particles const & ps)"""
3514  return _IMP_atom.Simulator_set_particles(self, ps)
3515 
3516  def set_particles_order(self, objs):
3517  r"""set_particles_order(Simulator self, IMP::Particles const & objs)"""
3518  return _IMP_atom.Simulator_set_particles_order(self, objs)
3519 
3520  def add_particle(self, obj):
3521  r"""add_particle(Simulator self, Particle obj) -> unsigned int"""
3522  return _IMP_atom.Simulator_add_particle(self, obj)
3523 
3524  def add_particles(self, objs):
3525  r"""add_particles(Simulator self, IMP::Particles const & objs)"""
3526  return _IMP_atom.Simulator_add_particles(self, objs)
3527 
3528  def clear_particles(self):
3529  r"""clear_particles(Simulator self)"""
3530  return _IMP_atom.Simulator_clear_particles(self)
3531 
3532  def get_number_of_particles(self):
3533  r"""get_number_of_particles(Simulator self) -> unsigned int"""
3534  return _IMP_atom.Simulator_get_number_of_particles(self)
3535 
3536  def get_has_particles(self):
3537  r"""get_has_particles(Simulator self) -> bool"""
3538  return _IMP_atom.Simulator_get_has_particles(self)
3539 
3540  def get_particle(self, i):
3541  r"""get_particle(Simulator self, unsigned int i) -> Particle"""
3542  return _IMP_atom.Simulator_get_particle(self, i)
3543 
3544  def get_particles(self):
3545  r"""get_particles(Simulator self) -> IMP::Particles"""
3546  return _IMP_atom.Simulator_get_particles(self)
3547 
3548  def erase_particle(self, i):
3549  r"""erase_particle(Simulator self, unsigned int i)"""
3550  return _IMP_atom.Simulator_erase_particle(self, i)
3551 
3552  def reserve_particles(self, sz):
3553  r"""reserve_particles(Simulator self, unsigned int sz)"""
3554  return _IMP_atom.Simulator_reserve_particles(self, sz)
3555 
3556  def do_optimize(self, max_steps):
3557  r"""do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3558  return _IMP_atom.Simulator_do_optimize(self, max_steps)
3559 
3560  def setup(self, arg0):
3561  r"""setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3562  return _IMP_atom.Simulator_setup(self, arg0)
3563 
3564  def do_step(self, sc, dt):
3565  r"""do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3566  return _IMP_atom.Simulator_do_step(self, sc, dt)
3567 
3568  def get_is_simulation_particle(self, p):
3569  r"""get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3570  return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3571 
3572  def do_simulate(self, time):
3573  r"""do_simulate(Simulator self, double time) -> double"""
3574  return _IMP_atom.Simulator_do_simulate(self, time)
3575 
3576  def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3577  r"""do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3578  return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3579 
3580  def __str__(self):
3581  r"""__str__(Simulator self) -> std::string"""
3582  return _IMP_atom.Simulator___str__(self)
3583 
3584  def __repr__(self):
3585  r"""__repr__(Simulator self) -> std::string"""
3586  return _IMP_atom.Simulator___repr__(self)
3587 
3588  @staticmethod
3589  def get_from(o):
3590  return _object_cast_to_Simulator(o)
3591 
3592 
3593  def get_type_name(self):
3594  return self.__class__.__name__
3595  def do_show(self, out):
3596  pass
3597  def get_version_info(self):
3598  if"IMP::atom" == "IMP":
3599  return VersionInfo(self.__module__,
3600  __import__(self.__module__).get_module_version())
3601  else:
3602  return IMP.VersionInfo(self.__module__,
3603  __import__(self.__module__).get_module_version())
3604  @staticmethod
3605  def get_from(o):
3606  return _object_cast_to_Simulator(o)
3607 
3608  __swig_destroy__ = _IMP_atom.delete_Simulator
3609  def __disown__(self):
3610  self.this.disown()
3611  _IMP_atom.disown_Simulator(self)
3612  return weakref.proxy(self)
3613 
3614  def do_destroy(self):
3615  r"""do_destroy(Simulator self)"""
3616  return _IMP_atom.Simulator_do_destroy(self)
3617 
3618  def handle_set_has_required_score_states(self, arg0):
3619  r"""handle_set_has_required_score_states(Simulator self, bool arg0)"""
3620  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3621 
3622  def do_get_inputs(self):
3623  r"""do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3624  return _IMP_atom.Simulator_do_get_inputs(self)
3625 
3626  def do_get_outputs(self):
3627  r"""do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3628  return _IMP_atom.Simulator_do_get_outputs(self)
3629 
3630  def do_get_interactions(self):
3631  r"""do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3632  return _IMP_atom.Simulator_do_get_interactions(self)
3633 
3634 # Register Simulator in _IMP_atom:
3635 _IMP_atom.Simulator_swigregister(Simulator)
3636 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3637 
3638 class BrownianDynamics(Simulator):
3639  r"""Proxy of C++ IMP::atom::BrownianDynamics class."""
3640 
3641  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3642 
3643  def __init__(self, *args):
3644  r"""__init__(BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics"""
3645  _IMP_atom.BrownianDynamics_swiginit(self, _IMP_atom.new_BrownianDynamics(*args))
3646 
3647  def set_maximum_move(self, ms_in_A):
3648  r"""set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3649  return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3650 
3651  def set_use_stochastic_runge_kutta(self, tf):
3652  r"""set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3653  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3654 
3655  def get_version_info(self):
3656  r"""get_version_info(BrownianDynamics self) -> VersionInfo"""
3657  return _IMP_atom.BrownianDynamics_get_version_info(self)
3658  __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3659 
3660  def __str__(self):
3661  r"""__str__(BrownianDynamics self) -> std::string"""
3662  return _IMP_atom.BrownianDynamics___str__(self)
3663 
3664  def __repr__(self):
3665  r"""__repr__(BrownianDynamics self) -> std::string"""
3666  return _IMP_atom.BrownianDynamics___repr__(self)
3667 
3668  @staticmethod
3669  def get_from(o):
3670  return _object_cast_to_BrownianDynamics(o)
3671 
3672 
3673 # Register BrownianDynamics in _IMP_atom:
3674 _IMP_atom.BrownianDynamics_swigregister(BrownianDynamics)
3675 
3677  r"""get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3678  return _IMP_atom.get_maximum_time_step_estimate(bd)
3679 
3680 def get_harmonic_sigma(D, f):
3681  r"""get_harmonic_sigma(double D, double f) -> double"""
3682  return _IMP_atom.get_harmonic_sigma(D, f)
3683 class BrownianDynamicsTAMD(BrownianDynamics):
3684  r"""Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3685 
3686  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3687 
3688  def __init__(self, *args):
3689  r"""__init__(BrownianDynamicsTAMD self, Model m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0) -> BrownianDynamicsTAMD"""
3690  _IMP_atom.BrownianDynamicsTAMD_swiginit(self, _IMP_atom.new_BrownianDynamicsTAMD(*args))
3691 
3692  def __str__(self):
3693  r"""__str__(BrownianDynamicsTAMD self) -> std::string"""
3694  return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3695 
3696  def __repr__(self):
3697  r"""__repr__(BrownianDynamicsTAMD self) -> std::string"""
3698  return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3699 
3700  @staticmethod
3701  def get_from(o):
3702  return _object_cast_to_BrownianDynamicsTAMD(o)
3703 
3704  __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3705 
3706 # Register BrownianDynamicsTAMD in _IMP_atom:
3707 _IMP_atom.BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3708 class Diffusion(IMP.core.XYZ):
3709  r"""Proxy of C++ IMP::atom::Diffusion class."""
3710 
3711  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3712 
3713  def __init__(self, *args):
3714  r"""
3715  __init__(Diffusion self) -> Diffusion
3716  __init__(Diffusion self, Model m, ParticleIndex id) -> Diffusion
3717  __init__(Diffusion self, _ParticleAdaptor d) -> Diffusion
3718  """
3719  _IMP_atom.Diffusion_swiginit(self, _IMP_atom.new_Diffusion(*args))
3720 
3721  def show(self, *args):
3722  r"""show(Diffusion self, _ostream out=std::cout)"""
3723  return _IMP_atom.Diffusion_show(self, *args)
3724 
3725  @staticmethod
3726  def setup_particle(*args):
3727  r"""
3728  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3729  setup_particle(_ParticleAdaptor pa, IMP::Float D) -> Diffusion
3730  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3731  setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float D) -> Diffusion
3732  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3733  setup_particle(_ParticleAdaptor pa) -> Diffusion
3734  """
3735  return _IMP_atom.Diffusion_setup_particle(*args)
3736 
3737  @staticmethod
3738  def get_is_setup(*args):
3739  r"""
3740  get_is_setup(_ParticleAdaptor p) -> bool
3741  get_is_setup(Model m, ParticleIndex p) -> bool
3742  """
3743  return _IMP_atom.Diffusion_get_is_setup(*args)
3744 
3745  def set_diffusion_coefficient(self, d):
3746  r"""set_diffusion_coefficient(Diffusion self, double d)"""
3747  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3748 
3749  def get_diffusion_coefficient(self):
3750  r"""get_diffusion_coefficient(Diffusion self) -> double"""
3751  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3752 
3753  @staticmethod
3754  def get_diffusion_coefficient_key():
3755  r"""get_diffusion_coefficient_key() -> FloatKey"""
3756  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3757 
3758  def add_attribute(self, *args):
3759  r"""
3760  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3761  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3762  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3763  add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3764  add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3765  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3766  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3767  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3768  add_attribute(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3769  add_attribute(Diffusion self, SparseIntKey a0, IMP::Int a1)
3770  add_attribute(Diffusion self, SparseStringKey a0, IMP::String a1)
3771  add_attribute(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3772  """
3773  return _IMP_atom.Diffusion_add_attribute(self, *args)
3774 
3775  def get_value(self, *args):
3776  r"""
3777  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3778  get_value(Diffusion self, IntKey a0) -> IMP::Int
3779  get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3780  get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3781  get_value(Diffusion self, StringKey a0) -> IMP::String
3782  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3783  get_value(Diffusion self, ObjectKey a0) -> Object
3784  get_value(Diffusion self, SparseFloatKey a0) -> IMP::Float
3785  get_value(Diffusion self, SparseIntKey a0) -> IMP::Int
3786  get_value(Diffusion self, SparseStringKey a0) -> IMP::String
3787  get_value(Diffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3788  """
3789  return _IMP_atom.Diffusion_get_value(self, *args)
3790 
3791  def set_value(self, *args):
3792  r"""
3793  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3794  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3795  set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3796  set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3797  set_value(Diffusion self, StringKey a0, IMP::String a1)
3798  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3799  set_value(Diffusion self, ObjectKey a0, Object a1)
3800  set_value(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3801  set_value(Diffusion self, SparseIntKey a0, IMP::Int a1)
3802  set_value(Diffusion self, SparseStringKey a0, IMP::String a1)
3803  set_value(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3804  """
3805  return _IMP_atom.Diffusion_set_value(self, *args)
3806 
3807  def remove_attribute(self, *args):
3808  r"""
3809  remove_attribute(Diffusion self, FloatKey a0)
3810  remove_attribute(Diffusion self, IntKey a0)
3811  remove_attribute(Diffusion self, FloatsKey a0)
3812  remove_attribute(Diffusion self, IntsKey a0)
3813  remove_attribute(Diffusion self, StringKey a0)
3814  remove_attribute(Diffusion self, ParticleIndexKey a0)
3815  remove_attribute(Diffusion self, ObjectKey a0)
3816  remove_attribute(Diffusion self, SparseFloatKey a0)
3817  remove_attribute(Diffusion self, SparseIntKey a0)
3818  remove_attribute(Diffusion self, SparseStringKey a0)
3819  remove_attribute(Diffusion self, SparseParticleIndexKey a0)
3820  """
3821  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3822 
3823  def has_attribute(self, *args):
3824  r"""
3825  has_attribute(Diffusion self, FloatKey a0) -> bool
3826  has_attribute(Diffusion self, IntKey a0) -> bool
3827  has_attribute(Diffusion self, FloatsKey a0) -> bool
3828  has_attribute(Diffusion self, IntsKey a0) -> bool
3829  has_attribute(Diffusion self, StringKey a0) -> bool
3830  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3831  has_attribute(Diffusion self, ObjectKey a0) -> bool
3832  has_attribute(Diffusion self, SparseFloatKey a0) -> bool
3833  has_attribute(Diffusion self, SparseIntKey a0) -> bool
3834  has_attribute(Diffusion self, SparseStringKey a0) -> bool
3835  has_attribute(Diffusion self, SparseParticleIndexKey a0) -> bool
3836  """
3837  return _IMP_atom.Diffusion_has_attribute(self, *args)
3838 
3839  def get_derivative(self, a0):
3840  r"""get_derivative(Diffusion self, FloatKey a0) -> double"""
3841  return _IMP_atom.Diffusion_get_derivative(self, a0)
3842 
3843  def get_name(self):
3844  r"""get_name(Diffusion self) -> std::string"""
3845  return _IMP_atom.Diffusion_get_name(self)
3846 
3847  def clear_caches(self):
3848  r"""clear_caches(Diffusion self)"""
3849  return _IMP_atom.Diffusion_clear_caches(self)
3850 
3851  def set_name(self, a0):
3852  r"""set_name(Diffusion self, std::string a0)"""
3853  return _IMP_atom.Diffusion_set_name(self, a0)
3854 
3855  def set_check_level(self, a0):
3856  r"""set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3857  return _IMP_atom.Diffusion_set_check_level(self, a0)
3858 
3859  def add_to_derivative(self, a0, a1, a2):
3860  r"""add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3861  return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3862 
3863  def set_is_optimized(self, a0, a1):
3864  r"""set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3865  return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3866 
3867  def get_is_optimized(self, a0):
3868  r"""get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3869  return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3870 
3871  def get_check_level(self):
3872  r"""get_check_level(Diffusion self) -> IMP::CheckLevel"""
3873  return _IMP_atom.Diffusion_get_check_level(self)
3874 
3875  def __eq__(self, *args):
3876  r"""
3877  __eq__(Diffusion self, Diffusion o) -> bool
3878  __eq__(Diffusion self, Particle d) -> bool
3879  """
3880  return _IMP_atom.Diffusion___eq__(self, *args)
3881 
3882  def __ne__(self, *args):
3883  r"""
3884  __ne__(Diffusion self, Diffusion o) -> bool
3885  __ne__(Diffusion self, Particle d) -> bool
3886  """
3887  return _IMP_atom.Diffusion___ne__(self, *args)
3888 
3889  def __le__(self, *args):
3890  r"""
3891  __le__(Diffusion self, Diffusion o) -> bool
3892  __le__(Diffusion self, Particle d) -> bool
3893  """
3894  return _IMP_atom.Diffusion___le__(self, *args)
3895 
3896  def __lt__(self, *args):
3897  r"""
3898  __lt__(Diffusion self, Diffusion o) -> bool
3899  __lt__(Diffusion self, Particle d) -> bool
3900  """
3901  return _IMP_atom.Diffusion___lt__(self, *args)
3902 
3903  def __ge__(self, *args):
3904  r"""
3905  __ge__(Diffusion self, Diffusion o) -> bool
3906  __ge__(Diffusion self, Particle d) -> bool
3907  """
3908  return _IMP_atom.Diffusion___ge__(self, *args)
3909 
3910  def __gt__(self, *args):
3911  r"""
3912  __gt__(Diffusion self, Diffusion o) -> bool
3913  __gt__(Diffusion self, Particle d) -> bool
3914  """
3915  return _IMP_atom.Diffusion___gt__(self, *args)
3916 
3917  def __hash__(self):
3918  r"""__hash__(Diffusion self) -> std::size_t"""
3919  return _IMP_atom.Diffusion___hash__(self)
3920 
3921  def __str__(self):
3922  r"""__str__(Diffusion self) -> std::string"""
3923  return _IMP_atom.Diffusion___str__(self)
3924 
3925  def __repr__(self):
3926  r"""__repr__(Diffusion self) -> std::string"""
3927  return _IMP_atom.Diffusion___repr__(self)
3928 
3929  def _get_as_binary(self):
3930  r"""_get_as_binary(Diffusion self) -> PyObject *"""
3931  return _IMP_atom.Diffusion__get_as_binary(self)
3932 
3933  def _set_from_binary(self, p):
3934  r"""_set_from_binary(Diffusion self, PyObject * p)"""
3935  return _IMP_atom.Diffusion__set_from_binary(self, p)
3936 
3937  def __getstate__(self):
3938  p = self._get_as_binary()
3939  if len(self.__dict__) > 1:
3940  d = self.__dict__.copy()
3941  del d['this']
3942  p = (d, p)
3943  return p
3944 
3945  def __setstate__(self, p):
3946  if not hasattr(self, 'this'):
3947  self.__init__()
3948  if isinstance(p, tuple):
3949  d, p = p
3950  self.__dict__.update(d)
3951  return self._set_from_binary(p)
3952 
3953  __swig_destroy__ = _IMP_atom.delete_Diffusion
3954 
3955 # Register Diffusion in _IMP_atom:
3956 _IMP_atom.Diffusion_swigregister(Diffusion)
3957 
3958 def get_diffusion_coefficient_from_cm2_per_second(din):
3959  r"""get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3960  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3961 class RigidBodyDiffusion(Diffusion):
3962  r"""Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3963 
3964  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3965 
3966  def __init__(self, *args):
3967  r"""
3968  __init__(RigidBodyDiffusion self) -> RigidBodyDiffusion
3969  __init__(RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3970  __init__(RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3971  """
3972  _IMP_atom.RigidBodyDiffusion_swiginit(self, _IMP_atom.new_RigidBodyDiffusion(*args))
3973 
3974  def show(self, *args):
3975  r"""show(RigidBodyDiffusion self, _ostream out=std::cout)"""
3976  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3977 
3978  @staticmethod
3979  def setup_particle(*args):
3980  r"""
3981  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3982  setup_particle(_ParticleAdaptor pa) -> RigidBodyDiffusion
3983  """
3984  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3985 
3987  r"""get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3988  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3989 
3990  def set_rotational_diffusion_coefficient(self, d):
3991  r"""set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3992  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
3993 
3994  @staticmethod
3995  def get_is_setup(*args):
3996  r"""
3997  get_is_setup(_ParticleAdaptor p) -> bool
3998  get_is_setup(Model m, ParticleIndex p) -> bool
3999  """
4000  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4001 
4002  @staticmethod
4003  def get_rotational_diffusion_coefficient_key():
4004  r"""get_rotational_diffusion_coefficient_key() -> FloatKey"""
4005  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4006 
4007  def add_attribute(self, *args):
4008  r"""
4009  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4010  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4011  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4012  add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4013  add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4014  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4015  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4016  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4017  add_attribute(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
4018  add_attribute(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
4019  add_attribute(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
4020  add_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
4021  """
4022  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4023 
4024  def get_value(self, *args):
4025  r"""
4026  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4027  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4028  get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
4029  get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
4030  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4031  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4032  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4033  get_value(RigidBodyDiffusion self, SparseFloatKey a0) -> IMP::Float
4034  get_value(RigidBodyDiffusion self, SparseIntKey a0) -> IMP::Int
4035  get_value(RigidBodyDiffusion self, SparseStringKey a0) -> IMP::String
4036  get_value(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> ParticleIndex
4037  """
4038  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4039 
4040  def set_value(self, *args):
4041  r"""
4042  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4043  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4044  set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4045  set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4046  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4047  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4048  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4049  set_value(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
4050  set_value(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
4051  set_value(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
4052  set_value(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
4053  """
4054  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4055 
4056  def remove_attribute(self, *args):
4057  r"""
4058  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4059  remove_attribute(RigidBodyDiffusion self, IntKey a0)
4060  remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
4061  remove_attribute(RigidBodyDiffusion self, IntsKey a0)
4062  remove_attribute(RigidBodyDiffusion self, StringKey a0)
4063  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4064  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4065  remove_attribute(RigidBodyDiffusion self, SparseFloatKey a0)
4066  remove_attribute(RigidBodyDiffusion self, SparseIntKey a0)
4067  remove_attribute(RigidBodyDiffusion self, SparseStringKey a0)
4068  remove_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0)
4069  """
4070  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4071 
4072  def has_attribute(self, *args):
4073  r"""
4074  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4075  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4076  has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
4077  has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
4078  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4079  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4080  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4081  has_attribute(RigidBodyDiffusion self, SparseFloatKey a0) -> bool
4082  has_attribute(RigidBodyDiffusion self, SparseIntKey a0) -> bool
4083  has_attribute(RigidBodyDiffusion self, SparseStringKey a0) -> bool
4084  has_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> bool
4085  """
4086  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4087 
4088  def get_derivative(self, a0):
4089  r"""get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4090  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4091 
4092  def get_name(self):
4093  r"""get_name(RigidBodyDiffusion self) -> std::string"""
4094  return _IMP_atom.RigidBodyDiffusion_get_name(self)
4095 
4096  def clear_caches(self):
4097  r"""clear_caches(RigidBodyDiffusion self)"""
4098  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4099 
4100  def set_name(self, a0):
4101  r"""set_name(RigidBodyDiffusion self, std::string a0)"""
4102  return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4103 
4104  def set_check_level(self, a0):
4105  r"""set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4106  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4107 
4108  def add_to_derivative(self, a0, a1, a2):
4109  r"""add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4110  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4111 
4112  def set_is_optimized(self, a0, a1):
4113  r"""set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4114  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4115 
4116  def get_is_optimized(self, a0):
4117  r"""get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4118  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4119 
4120  def get_check_level(self):
4121  r"""get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4122  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4123 
4124  def __eq__(self, *args):
4125  r"""
4126  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4127  __eq__(RigidBodyDiffusion self, Particle d) -> bool
4128  """
4129  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4130 
4131  def __ne__(self, *args):
4132  r"""
4133  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4134  __ne__(RigidBodyDiffusion self, Particle d) -> bool
4135  """
4136  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4137 
4138  def __le__(self, *args):
4139  r"""
4140  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4141  __le__(RigidBodyDiffusion self, Particle d) -> bool
4142  """
4143  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4144 
4145  def __lt__(self, *args):
4146  r"""
4147  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4148  __lt__(RigidBodyDiffusion self, Particle d) -> bool
4149  """
4150  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4151 
4152  def __ge__(self, *args):
4153  r"""
4154  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4155  __ge__(RigidBodyDiffusion self, Particle d) -> bool
4156  """
4157  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4158 
4159  def __gt__(self, *args):
4160  r"""
4161  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4162  __gt__(RigidBodyDiffusion self, Particle d) -> bool
4163  """
4164  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4165 
4166  def __hash__(self):
4167  r"""__hash__(RigidBodyDiffusion self) -> std::size_t"""
4168  return _IMP_atom.RigidBodyDiffusion___hash__(self)
4169 
4170  def __str__(self):
4171  r"""__str__(RigidBodyDiffusion self) -> std::string"""
4172  return _IMP_atom.RigidBodyDiffusion___str__(self)
4173 
4174  def __repr__(self):
4175  r"""__repr__(RigidBodyDiffusion self) -> std::string"""
4176  return _IMP_atom.RigidBodyDiffusion___repr__(self)
4177 
4178  def _get_as_binary(self):
4179  r"""_get_as_binary(RigidBodyDiffusion self) -> PyObject *"""
4180  return _IMP_atom.RigidBodyDiffusion__get_as_binary(self)
4181 
4182  def _set_from_binary(self, p):
4183  r"""_set_from_binary(RigidBodyDiffusion self, PyObject * p)"""
4184  return _IMP_atom.RigidBodyDiffusion__set_from_binary(self, p)
4185 
4186  def __getstate__(self):
4187  p = self._get_as_binary()
4188  if len(self.__dict__) > 1:
4189  d = self.__dict__.copy()
4190  del d['this']
4191  p = (d, p)
4192  return p
4193 
4194  def __setstate__(self, p):
4195  if not hasattr(self, 'this'):
4196  self.__init__()
4197  if isinstance(p, tuple):
4198  d, p = p
4199  self.__dict__.update(d)
4200  return self._set_from_binary(p)
4201 
4202  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4203 
4204 # Register RigidBodyDiffusion in _IMP_atom:
4205 _IMP_atom.RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4206 class TAMDParticle(IMP.Decorator):
4207  r"""Proxy of C++ IMP::atom::TAMDParticle class."""
4208 
4209  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4210 
4211  def __init__(self, *args):
4212  r"""
4213  __init__(TAMDParticle self) -> TAMDParticle
4214  __init__(TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4215  __init__(TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4216  """
4217  _IMP_atom.TAMDParticle_swiginit(self, _IMP_atom.new_TAMDParticle(*args))
4218 
4219  def show(self, *args):
4220  r"""show(TAMDParticle self, _ostream out=std::cout)"""
4221  return _IMP_atom.TAMDParticle_show(self, *args)
4222 
4223  @staticmethod
4224  def setup_particle(*args):
4225  r"""
4226  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4227  setup_particle(_ParticleAdaptor pa, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4228  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4229  setup_particle(_ParticleAdaptor pa, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4230  """
4231  return _IMP_atom.TAMDParticle_setup_particle(*args)
4232 
4233  @staticmethod
4234  def get_is_setup(*args):
4235  r"""
4236  get_is_setup(_ParticleAdaptor p) -> bool
4237  get_is_setup(Model m, ParticleIndex p) -> bool
4238  """
4239  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4240 
4241  def get_reference_particle_index(self):
4242  r"""get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4243  return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4244 
4245  def set_temperature_scale_factor(self, tsf):
4246  r"""set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4247  return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4248 
4249  def get_temperature_scale_factor(self):
4250  r"""get_temperature_scale_factor(TAMDParticle self) -> double"""
4251  return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4252 
4253  def set_friction_scale_factor(self, tsf):
4254  r"""set_friction_scale_factor(TAMDParticle self, float tsf)"""
4255  return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4256 
4257  def get_friction_scale_factor(self):
4258  r"""get_friction_scale_factor(TAMDParticle self) -> double"""
4259  return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4260 
4261  def update_coordinates_from_ref(self):
4262  r"""update_coordinates_from_ref(TAMDParticle self)"""
4263  return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4264 
4265  @staticmethod
4266  def get_temperature_scale_factor_key():
4267  r"""get_temperature_scale_factor_key() -> FloatKey"""
4268  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4269 
4270  @staticmethod
4271  def get_friction_scale_factor_key():
4272  r"""get_friction_scale_factor_key() -> FloatKey"""
4273  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4274 
4275  @staticmethod
4276  def get_reference_particle_index_key():
4277  r"""get_reference_particle_index_key() -> ParticleIndexKey"""
4278  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4279 
4280  def add_attribute(self, *args):
4281  r"""
4282  add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4283  add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4284  add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4285  add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4286  add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4287  add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4288  add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4289  add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4290  add_attribute(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4291  add_attribute(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4292  add_attribute(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4293  add_attribute(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4294  """
4295  return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4296 
4297  def get_value(self, *args):
4298  r"""
4299  get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4300  get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4301  get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4302  get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4303  get_value(TAMDParticle self, StringKey a0) -> IMP::String
4304  get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4305  get_value(TAMDParticle self, ObjectKey a0) -> Object
4306  get_value(TAMDParticle self, SparseFloatKey a0) -> IMP::Float
4307  get_value(TAMDParticle self, SparseIntKey a0) -> IMP::Int
4308  get_value(TAMDParticle self, SparseStringKey a0) -> IMP::String
4309  get_value(TAMDParticle self, SparseParticleIndexKey a0) -> ParticleIndex
4310  """
4311  return _IMP_atom.TAMDParticle_get_value(self, *args)
4312 
4313  def set_value(self, *args):
4314  r"""
4315  set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4316  set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4317  set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4318  set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4319  set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4320  set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4321  set_value(TAMDParticle self, ObjectKey a0, Object a1)
4322  set_value(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4323  set_value(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4324  set_value(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4325  set_value(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4326  """
4327  return _IMP_atom.TAMDParticle_set_value(self, *args)
4328 
4329  def remove_attribute(self, *args):
4330  r"""
4331  remove_attribute(TAMDParticle self, FloatKey a0)
4332  remove_attribute(TAMDParticle self, IntKey a0)
4333  remove_attribute(TAMDParticle self, FloatsKey a0)
4334  remove_attribute(TAMDParticle self, IntsKey a0)
4335  remove_attribute(TAMDParticle self, StringKey a0)
4336  remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4337  remove_attribute(TAMDParticle self, ObjectKey a0)
4338  remove_attribute(TAMDParticle self, SparseFloatKey a0)
4339  remove_attribute(TAMDParticle self, SparseIntKey a0)
4340  remove_attribute(TAMDParticle self, SparseStringKey a0)
4341  remove_attribute(TAMDParticle self, SparseParticleIndexKey a0)
4342  """
4343  return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4344 
4345  def has_attribute(self, *args):
4346  r"""
4347  has_attribute(TAMDParticle self, FloatKey a0) -> bool
4348  has_attribute(TAMDParticle self, IntKey a0) -> bool
4349  has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4350  has_attribute(TAMDParticle self, IntsKey a0) -> bool
4351  has_attribute(TAMDParticle self, StringKey a0) -> bool
4352  has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4353  has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4354  has_attribute(TAMDParticle self, SparseFloatKey a0) -> bool
4355  has_attribute(TAMDParticle self, SparseIntKey a0) -> bool
4356  has_attribute(TAMDParticle self, SparseStringKey a0) -> bool
4357  has_attribute(TAMDParticle self, SparseParticleIndexKey a0) -> bool
4358  """
4359  return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4360 
4361  def get_derivative(self, a0):
4362  r"""get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4363  return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4364 
4365  def get_name(self):
4366  r"""get_name(TAMDParticle self) -> std::string"""
4367  return _IMP_atom.TAMDParticle_get_name(self)
4368 
4369  def clear_caches(self):
4370  r"""clear_caches(TAMDParticle self)"""
4371  return _IMP_atom.TAMDParticle_clear_caches(self)
4372 
4373  def set_name(self, a0):
4374  r"""set_name(TAMDParticle self, std::string a0)"""
4375  return _IMP_atom.TAMDParticle_set_name(self, a0)
4376 
4377  def set_check_level(self, a0):
4378  r"""set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4379  return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4380 
4381  def add_to_derivative(self, a0, a1, a2):
4382  r"""add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4383  return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4384 
4385  def set_is_optimized(self, a0, a1):
4386  r"""set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4387  return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4388 
4389  def get_is_optimized(self, a0):
4390  r"""get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4391  return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4392 
4393  def get_check_level(self):
4394  r"""get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4395  return _IMP_atom.TAMDParticle_get_check_level(self)
4396 
4397  def __eq__(self, *args):
4398  r"""
4399  __eq__(TAMDParticle self, TAMDParticle o) -> bool
4400  __eq__(TAMDParticle self, Particle d) -> bool
4401  """
4402  return _IMP_atom.TAMDParticle___eq__(self, *args)
4403 
4404  def __ne__(self, *args):
4405  r"""
4406  __ne__(TAMDParticle self, TAMDParticle o) -> bool
4407  __ne__(TAMDParticle self, Particle d) -> bool
4408  """
4409  return _IMP_atom.TAMDParticle___ne__(self, *args)
4410 
4411  def __le__(self, *args):
4412  r"""
4413  __le__(TAMDParticle self, TAMDParticle o) -> bool
4414  __le__(TAMDParticle self, Particle d) -> bool
4415  """
4416  return _IMP_atom.TAMDParticle___le__(self, *args)
4417 
4418  def __lt__(self, *args):
4419  r"""
4420  __lt__(TAMDParticle self, TAMDParticle o) -> bool
4421  __lt__(TAMDParticle self, Particle d) -> bool
4422  """
4423  return _IMP_atom.TAMDParticle___lt__(self, *args)
4424 
4425  def __ge__(self, *args):
4426  r"""
4427  __ge__(TAMDParticle self, TAMDParticle o) -> bool
4428  __ge__(TAMDParticle self, Particle d) -> bool
4429  """
4430  return _IMP_atom.TAMDParticle___ge__(self, *args)
4431 
4432  def __gt__(self, *args):
4433  r"""
4434  __gt__(TAMDParticle self, TAMDParticle o) -> bool
4435  __gt__(TAMDParticle self, Particle d) -> bool
4436  """
4437  return _IMP_atom.TAMDParticle___gt__(self, *args)
4438 
4439  def __hash__(self):
4440  r"""__hash__(TAMDParticle self) -> std::size_t"""
4441  return _IMP_atom.TAMDParticle___hash__(self)
4442 
4443  def __str__(self):
4444  r"""__str__(TAMDParticle self) -> std::string"""
4445  return _IMP_atom.TAMDParticle___str__(self)
4446 
4447  def __repr__(self):
4448  r"""__repr__(TAMDParticle self) -> std::string"""
4449  return _IMP_atom.TAMDParticle___repr__(self)
4450 
4451  def _get_as_binary(self):
4452  r"""_get_as_binary(TAMDParticle self) -> PyObject *"""
4453  return _IMP_atom.TAMDParticle__get_as_binary(self)
4454 
4455  def _set_from_binary(self, p):
4456  r"""_set_from_binary(TAMDParticle self, PyObject * p)"""
4457  return _IMP_atom.TAMDParticle__set_from_binary(self, p)
4458 
4459  def __getstate__(self):
4460  p = self._get_as_binary()
4461  if len(self.__dict__) > 1:
4462  d = self.__dict__.copy()
4463  del d['this']
4464  p = (d, p)
4465  return p
4466 
4467  def __setstate__(self, p):
4468  if not hasattr(self, 'this'):
4469  self.__init__()
4470  if isinstance(p, tuple):
4471  d, p = p
4472  self.__dict__.update(d)
4473  return self._set_from_binary(p)
4474 
4475  __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4476 
4477 # Register TAMDParticle in _IMP_atom:
4478 _IMP_atom.TAMDParticle_swigregister(TAMDParticle)
4479 class Charged(IMP.core.XYZ):
4480  r"""Proxy of C++ IMP::atom::Charged class."""
4481 
4482  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4483 
4484  def __init__(self, *args):
4485  r"""
4486  __init__(Charged self) -> Charged
4487  __init__(Charged self, Model m, ParticleIndex id) -> Charged
4488  __init__(Charged self, _ParticleAdaptor d) -> Charged
4489  """
4490  _IMP_atom.Charged_swiginit(self, _IMP_atom.new_Charged(*args))
4491 
4492  def show(self, *args):
4493  r"""show(Charged self, _ostream out=std::cout)"""
4494  return _IMP_atom.Charged_show(self, *args)
4495 
4496  @staticmethod
4497  def setup_particle(*args):
4498  r"""
4499  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4500  setup_particle(_ParticleAdaptor pa, IMP::Float charge) -> Charged
4501  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4502  setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float charge) -> Charged
4503  """
4504  return _IMP_atom.Charged_setup_particle(*args)
4505 
4506  def get_charge(self):
4507  r"""get_charge(Charged self) -> IMP::Float"""
4508  return _IMP_atom.Charged_get_charge(self)
4509 
4510  def set_charge(self, t):
4511  r"""set_charge(Charged self, IMP::Float t)"""
4512  return _IMP_atom.Charged_set_charge(self, t)
4513 
4514  @staticmethod
4515  def get_is_setup(*args):
4516  r"""
4517  get_is_setup(_ParticleAdaptor p) -> bool
4518  get_is_setup(Model m, ParticleIndex pi) -> bool
4519  """
4520  return _IMP_atom.Charged_get_is_setup(*args)
4521 
4522  @staticmethod
4523  def get_charge_key():
4524  r"""get_charge_key() -> FloatKey"""
4525  return _IMP_atom.Charged_get_charge_key()
4526 
4527  def add_attribute(self, *args):
4528  r"""
4529  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4530  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4531  add_attribute(Charged self, IntKey a0, IMP::Int a1)
4532  add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
4533  add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
4534  add_attribute(Charged self, StringKey a0, IMP::String a1)
4535  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4536  add_attribute(Charged self, ObjectKey a0, Object a1)
4537  add_attribute(Charged self, SparseFloatKey a0, IMP::Float a1)
4538  add_attribute(Charged self, SparseIntKey a0, IMP::Int a1)
4539  add_attribute(Charged self, SparseStringKey a0, IMP::String a1)
4540  add_attribute(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4541  """
4542  return _IMP_atom.Charged_add_attribute(self, *args)
4543 
4544  def get_value(self, *args):
4545  r"""
4546  get_value(Charged self, FloatKey a0) -> IMP::Float
4547  get_value(Charged self, IntKey a0) -> IMP::Int
4548  get_value(Charged self, FloatsKey a0) -> IMP::Floats
4549  get_value(Charged self, IntsKey a0) -> IMP::Ints
4550  get_value(Charged self, StringKey a0) -> IMP::String
4551  get_value(Charged self, ParticleIndexKey a0) -> Particle
4552  get_value(Charged self, ObjectKey a0) -> Object
4553  get_value(Charged self, SparseFloatKey a0) -> IMP::Float
4554  get_value(Charged self, SparseIntKey a0) -> IMP::Int
4555  get_value(Charged self, SparseStringKey a0) -> IMP::String
4556  get_value(Charged self, SparseParticleIndexKey a0) -> ParticleIndex
4557  """
4558  return _IMP_atom.Charged_get_value(self, *args)
4559 
4560  def set_value(self, *args):
4561  r"""
4562  set_value(Charged self, FloatKey a0, IMP::Float a1)
4563  set_value(Charged self, IntKey a0, IMP::Int a1)
4564  set_value(Charged self, FloatsKey a0, IMP::Floats a1)
4565  set_value(Charged self, IntsKey a0, IMP::Ints a1)
4566  set_value(Charged self, StringKey a0, IMP::String a1)
4567  set_value(Charged self, ParticleIndexKey a0, Particle a1)
4568  set_value(Charged self, ObjectKey a0, Object a1)
4569  set_value(Charged self, SparseFloatKey a0, IMP::Float a1)
4570  set_value(Charged self, SparseIntKey a0, IMP::Int a1)
4571  set_value(Charged self, SparseStringKey a0, IMP::String a1)
4572  set_value(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4573  """
4574  return _IMP_atom.Charged_set_value(self, *args)
4575 
4576  def remove_attribute(self, *args):
4577  r"""
4578  remove_attribute(Charged self, FloatKey a0)
4579  remove_attribute(Charged self, IntKey a0)
4580  remove_attribute(Charged self, FloatsKey a0)
4581  remove_attribute(Charged self, IntsKey a0)
4582  remove_attribute(Charged self, StringKey a0)
4583  remove_attribute(Charged self, ParticleIndexKey a0)
4584  remove_attribute(Charged self, ObjectKey a0)
4585  remove_attribute(Charged self, SparseFloatKey a0)
4586  remove_attribute(Charged self, SparseIntKey a0)
4587  remove_attribute(Charged self, SparseStringKey a0)
4588  remove_attribute(Charged self, SparseParticleIndexKey a0)
4589  """
4590  return _IMP_atom.Charged_remove_attribute(self, *args)
4591 
4592  def has_attribute(self, *args):
4593  r"""
4594  has_attribute(Charged self, FloatKey a0) -> bool
4595  has_attribute(Charged self, IntKey a0) -> bool
4596  has_attribute(Charged self, FloatsKey a0) -> bool
4597  has_attribute(Charged self, IntsKey a0) -> bool
4598  has_attribute(Charged self, StringKey a0) -> bool
4599  has_attribute(Charged self, ParticleIndexKey a0) -> bool
4600  has_attribute(Charged self, ObjectKey a0) -> bool
4601  has_attribute(Charged self, SparseFloatKey a0) -> bool
4602  has_attribute(Charged self, SparseIntKey a0) -> bool
4603  has_attribute(Charged self, SparseStringKey a0) -> bool
4604  has_attribute(Charged self, SparseParticleIndexKey a0) -> bool
4605  """
4606  return _IMP_atom.Charged_has_attribute(self, *args)
4607 
4608  def get_derivative(self, a0):
4609  r"""get_derivative(Charged self, FloatKey a0) -> double"""
4610  return _IMP_atom.Charged_get_derivative(self, a0)
4611 
4612  def get_name(self):
4613  r"""get_name(Charged self) -> std::string"""
4614  return _IMP_atom.Charged_get_name(self)
4615 
4616  def clear_caches(self):
4617  r"""clear_caches(Charged self)"""
4618  return _IMP_atom.Charged_clear_caches(self)
4619 
4620  def set_name(self, a0):
4621  r"""set_name(Charged self, std::string a0)"""
4622  return _IMP_atom.Charged_set_name(self, a0)
4623 
4624  def set_check_level(self, a0):
4625  r"""set_check_level(Charged self, IMP::CheckLevel a0)"""
4626  return _IMP_atom.Charged_set_check_level(self, a0)
4627 
4628  def add_to_derivative(self, a0, a1, a2):
4629  r"""add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4630  return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4631 
4632  def set_is_optimized(self, a0, a1):
4633  r"""set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4634  return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4635 
4636  def get_is_optimized(self, a0):
4637  r"""get_is_optimized(Charged self, FloatKey a0) -> bool"""
4638  return _IMP_atom.Charged_get_is_optimized(self, a0)
4639 
4640  def get_check_level(self):
4641  r"""get_check_level(Charged self) -> IMP::CheckLevel"""
4642  return _IMP_atom.Charged_get_check_level(self)
4643 
4644  def __eq__(self, *args):
4645  r"""
4646  __eq__(Charged self, Charged o) -> bool
4647  __eq__(Charged self, Particle d) -> bool
4648  """
4649  return _IMP_atom.Charged___eq__(self, *args)
4650 
4651  def __ne__(self, *args):
4652  r"""
4653  __ne__(Charged self, Charged o) -> bool
4654  __ne__(Charged self, Particle d) -> bool
4655  """
4656  return _IMP_atom.Charged___ne__(self, *args)
4657 
4658  def __le__(self, *args):
4659  r"""
4660  __le__(Charged self, Charged o) -> bool
4661  __le__(Charged self, Particle d) -> bool
4662  """
4663  return _IMP_atom.Charged___le__(self, *args)
4664 
4665  def __lt__(self, *args):
4666  r"""
4667  __lt__(Charged self, Charged o) -> bool
4668  __lt__(Charged self, Particle d) -> bool
4669  """
4670  return _IMP_atom.Charged___lt__(self, *args)
4671 
4672  def __ge__(self, *args):
4673  r"""
4674  __ge__(Charged self, Charged o) -> bool
4675  __ge__(Charged self, Particle d) -> bool
4676  """
4677  return _IMP_atom.Charged___ge__(self, *args)
4678 
4679  def __gt__(self, *args):
4680  r"""
4681  __gt__(Charged self, Charged o) -> bool
4682  __gt__(Charged self, Particle d) -> bool
4683  """
4684  return _IMP_atom.Charged___gt__(self, *args)
4685 
4686  def __hash__(self):
4687  r"""__hash__(Charged self) -> std::size_t"""
4688  return _IMP_atom.Charged___hash__(self)
4689 
4690  def __str__(self):
4691  r"""__str__(Charged self) -> std::string"""
4692  return _IMP_atom.Charged___str__(self)
4693 
4694  def __repr__(self):
4695  r"""__repr__(Charged self) -> std::string"""
4696  return _IMP_atom.Charged___repr__(self)
4697 
4698  def _get_as_binary(self):
4699  r"""_get_as_binary(Charged self) -> PyObject *"""
4700  return _IMP_atom.Charged__get_as_binary(self)
4701 
4702  def _set_from_binary(self, p):
4703  r"""_set_from_binary(Charged self, PyObject * p)"""
4704  return _IMP_atom.Charged__set_from_binary(self, p)
4705 
4706  def __getstate__(self):
4707  p = self._get_as_binary()
4708  if len(self.__dict__) > 1:
4709  d = self.__dict__.copy()
4710  del d['this']
4711  p = (d, p)
4712  return p
4713 
4714  def __setstate__(self, p):
4715  if not hasattr(self, 'this'):
4716  self.__init__()
4717  if isinstance(p, tuple):
4718  d, p = p
4719  self.__dict__.update(d)
4720  return self._set_from_binary(p)
4721 
4722  __swig_destroy__ = _IMP_atom.delete_Charged
4723 
4724 # Register Charged in _IMP_atom:
4725 _IMP_atom.Charged_swigregister(Charged)
4726 class CoulombPairScore(IMP.PairScore):
4727  r"""Proxy of C++ IMP::atom::CoulombPairScore class."""
4728 
4729  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4730 
4731  def __init__(self, f):
4732  r"""__init__(CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4733  _IMP_atom.CoulombPairScore_swiginit(self, _IMP_atom.new_CoulombPairScore(f))
4734 
4735  def set_relative_dielectric(self, relative_dielectric):
4736  r"""set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4737  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
4738 
4739  def get_relative_dielectric(self):
4740  r"""get_relative_dielectric(CoulombPairScore self) -> double"""
4741  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4742 
4743  def do_get_inputs(self, m, pis):
4744  r"""do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4745  return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
4746 
4747  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
4748  r"""evaluate_indexes(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
4749  return _IMP_atom.CoulombPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
4750 
4751  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
4752  r"""evaluate_indexes_scores(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
4753  return _IMP_atom.CoulombPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
4754 
4755  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
4756  r"""evaluate_indexes_delta(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
4757  return _IMP_atom.CoulombPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
4758 
4759  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
4760  r"""evaluate_if_good_indexes(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
4761  return _IMP_atom.CoulombPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
4762 
4763  def get_version_info(self):
4764  r"""get_version_info(CoulombPairScore self) -> VersionInfo"""
4765  return _IMP_atom.CoulombPairScore_get_version_info(self)
4766  __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4767 
4768  def __str__(self):
4769  r"""__str__(CoulombPairScore self) -> std::string"""
4770  return _IMP_atom.CoulombPairScore___str__(self)
4771 
4772  def __repr__(self):
4773  r"""__repr__(CoulombPairScore self) -> std::string"""
4774  return _IMP_atom.CoulombPairScore___repr__(self)
4775 
4776  @staticmethod
4777  def get_from(o):
4778  return _object_cast_to_CoulombPairScore(o)
4779 
4780 
4781 # Register CoulombPairScore in _IMP_atom:
4782 _IMP_atom.CoulombPairScore_swigregister(CoulombPairScore)
4783 class Domain(Hierarchy):
4784  r"""Proxy of C++ IMP::atom::Domain class."""
4785 
4786  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4787 
4788  def set_index_range(self, ir):
4789  r"""set_index_range(Domain self, IMP::IntRange ir)"""
4790  return _IMP_atom.Domain_set_index_range(self, ir)
4791 
4792  def get_index_range(self):
4793  r"""get_index_range(Domain self) -> IMP::IntRange"""
4794  return _IMP_atom.Domain_get_index_range(self)
4795 
4796  def __init__(self, *args):
4797  r"""
4798  __init__(Domain self) -> Domain
4799  __init__(Domain self, Model m, ParticleIndex id) -> Domain
4800  __init__(Domain self, _ParticleAdaptor d) -> Domain
4801  """
4802  _IMP_atom.Domain_swiginit(self, _IMP_atom.new_Domain(*args))
4803 
4804  @staticmethod
4805  def get_is_setup(*args):
4806  r"""
4807  get_is_setup(Model m, ParticleIndex pi) -> bool
4808  get_is_setup(_ParticleAdaptor p) -> bool
4809  """
4810  return _IMP_atom.Domain_get_is_setup(*args)
4811 
4812  def show(self, *args):
4813  r"""show(Domain self, _ostream out=std::cout)"""
4814  return _IMP_atom.Domain_show(self, *args)
4815 
4816  @staticmethod
4817  def setup_particle(*args):
4818  r"""
4819  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
4820  setup_particle(_ParticleAdaptor pa, Domain other) -> Domain
4821  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
4822  setup_particle(_ParticleAdaptor pa, IMP::IntRange residues) -> Domain
4823  """
4824  return _IMP_atom.Domain_setup_particle(*args)
4825 
4826  def add_attribute(self, *args):
4827  r"""
4828  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4829  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4830  add_attribute(Domain self, IntKey a0, IMP::Int a1)
4831  add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
4832  add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
4833  add_attribute(Domain self, StringKey a0, IMP::String a1)
4834  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4835  add_attribute(Domain self, ObjectKey a0, Object a1)
4836  add_attribute(Domain self, SparseFloatKey a0, IMP::Float a1)
4837  add_attribute(Domain self, SparseIntKey a0, IMP::Int a1)
4838  add_attribute(Domain self, SparseStringKey a0, IMP::String a1)
4839  add_attribute(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4840  """
4841  return _IMP_atom.Domain_add_attribute(self, *args)
4842 
4843  def get_value(self, *args):
4844  r"""
4845  get_value(Domain self, FloatKey a0) -> IMP::Float
4846  get_value(Domain self, IntKey a0) -> IMP::Int
4847  get_value(Domain self, FloatsKey a0) -> IMP::Floats
4848  get_value(Domain self, IntsKey a0) -> IMP::Ints
4849  get_value(Domain self, StringKey a0) -> IMP::String
4850  get_value(Domain self, ParticleIndexKey a0) -> Particle
4851  get_value(Domain self, ObjectKey a0) -> Object
4852  get_value(Domain self, SparseFloatKey a0) -> IMP::Float
4853  get_value(Domain self, SparseIntKey a0) -> IMP::Int
4854  get_value(Domain self, SparseStringKey a0) -> IMP::String
4855  get_value(Domain self, SparseParticleIndexKey a0) -> ParticleIndex
4856  """
4857  return _IMP_atom.Domain_get_value(self, *args)
4858 
4859  def set_value(self, *args):
4860  r"""
4861  set_value(Domain self, FloatKey a0, IMP::Float a1)
4862  set_value(Domain self, IntKey a0, IMP::Int a1)
4863  set_value(Domain self, FloatsKey a0, IMP::Floats a1)
4864  set_value(Domain self, IntsKey a0, IMP::Ints a1)
4865  set_value(Domain self, StringKey a0, IMP::String a1)
4866  set_value(Domain self, ParticleIndexKey a0, Particle a1)
4867  set_value(Domain self, ObjectKey a0, Object a1)
4868  set_value(Domain self, SparseFloatKey a0, IMP::Float a1)
4869  set_value(Domain self, SparseIntKey a0, IMP::Int a1)
4870  set_value(Domain self, SparseStringKey a0, IMP::String a1)
4871  set_value(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4872  """
4873  return _IMP_atom.Domain_set_value(self, *args)
4874 
4875  def remove_attribute(self, *args):
4876  r"""
4877  remove_attribute(Domain self, FloatKey a0)
4878  remove_attribute(Domain self, IntKey a0)
4879  remove_attribute(Domain self, FloatsKey a0)
4880  remove_attribute(Domain self, IntsKey a0)
4881  remove_attribute(Domain self, StringKey a0)
4882  remove_attribute(Domain self, ParticleIndexKey a0)
4883  remove_attribute(Domain self, ObjectKey a0)
4884  remove_attribute(Domain self, SparseFloatKey a0)
4885  remove_attribute(Domain self, SparseIntKey a0)
4886  remove_attribute(Domain self, SparseStringKey a0)
4887  remove_attribute(Domain self, SparseParticleIndexKey a0)
4888  """
4889  return _IMP_atom.Domain_remove_attribute(self, *args)
4890 
4891  def has_attribute(self, *args):
4892  r"""
4893  has_attribute(Domain self, FloatKey a0) -> bool
4894  has_attribute(Domain self, IntKey a0) -> bool
4895  has_attribute(Domain self, FloatsKey a0) -> bool
4896  has_attribute(Domain self, IntsKey a0) -> bool
4897  has_attribute(Domain self, StringKey a0) -> bool
4898  has_attribute(Domain self, ParticleIndexKey a0) -> bool
4899  has_attribute(Domain self, ObjectKey a0) -> bool
4900  has_attribute(Domain self, SparseFloatKey a0) -> bool
4901  has_attribute(Domain self, SparseIntKey a0) -> bool
4902  has_attribute(Domain self, SparseStringKey a0) -> bool
4903  has_attribute(Domain self, SparseParticleIndexKey a0) -> bool
4904  """
4905  return _IMP_atom.Domain_has_attribute(self, *args)
4906 
4907  def get_derivative(self, a0):
4908  r"""get_derivative(Domain self, FloatKey a0) -> double"""
4909  return _IMP_atom.Domain_get_derivative(self, a0)
4910 
4911  def get_name(self):
4912  r"""get_name(Domain self) -> std::string"""
4913  return _IMP_atom.Domain_get_name(self)
4914 
4915  def clear_caches(self):
4916  r"""clear_caches(Domain self)"""
4917  return _IMP_atom.Domain_clear_caches(self)
4918 
4919  def set_name(self, a0):
4920  r"""set_name(Domain self, std::string a0)"""
4921  return _IMP_atom.Domain_set_name(self, a0)
4922 
4923  def set_check_level(self, a0):
4924  r"""set_check_level(Domain self, IMP::CheckLevel a0)"""
4925  return _IMP_atom.Domain_set_check_level(self, a0)
4926 
4927  def add_to_derivative(self, a0, a1, a2):
4928  r"""add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4929  return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
4930 
4931  def set_is_optimized(self, a0, a1):
4932  r"""set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4933  return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
4934 
4935  def get_is_optimized(self, a0):
4936  r"""get_is_optimized(Domain self, FloatKey a0) -> bool"""
4937  return _IMP_atom.Domain_get_is_optimized(self, a0)
4938 
4939  def get_check_level(self):
4940  r"""get_check_level(Domain self) -> IMP::CheckLevel"""
4941  return _IMP_atom.Domain_get_check_level(self)
4942 
4943  def __eq__(self, *args):
4944  r"""
4945  __eq__(Domain self, Domain o) -> bool
4946  __eq__(Domain self, Particle d) -> bool
4947  """
4948  return _IMP_atom.Domain___eq__(self, *args)
4949 
4950  def __ne__(self, *args):
4951  r"""
4952  __ne__(Domain self, Domain o) -> bool
4953  __ne__(Domain self, Particle d) -> bool
4954  """
4955  return _IMP_atom.Domain___ne__(self, *args)
4956 
4957  def __le__(self, *args):
4958  r"""
4959  __le__(Domain self, Domain o) -> bool
4960  __le__(Domain self, Particle d) -> bool
4961  """
4962  return _IMP_atom.Domain___le__(self, *args)
4963 
4964  def __lt__(self, *args):
4965  r"""
4966  __lt__(Domain self, Domain o) -> bool
4967  __lt__(Domain self, Particle d) -> bool
4968  """
4969  return _IMP_atom.Domain___lt__(self, *args)
4970 
4971  def __ge__(self, *args):
4972  r"""
4973  __ge__(Domain self, Domain o) -> bool
4974  __ge__(Domain self, Particle d) -> bool
4975  """
4976  return _IMP_atom.Domain___ge__(self, *args)
4977 
4978  def __gt__(self, *args):
4979  r"""
4980  __gt__(Domain self, Domain o) -> bool
4981  __gt__(Domain self, Particle d) -> bool
4982  """
4983  return _IMP_atom.Domain___gt__(self, *args)
4984 
4985  def __hash__(self):
4986  r"""__hash__(Domain self) -> std::size_t"""
4987  return _IMP_atom.Domain___hash__(self)
4988 
4989  def __str__(self):
4990  r"""__str__(Domain self) -> std::string"""
4991  return _IMP_atom.Domain___str__(self)
4992 
4993  def __repr__(self):
4994  r"""__repr__(Domain self) -> std::string"""
4995  return _IMP_atom.Domain___repr__(self)
4996 
4997  def _get_as_binary(self):
4998  r"""_get_as_binary(Domain self) -> PyObject *"""
4999  return _IMP_atom.Domain__get_as_binary(self)
5000 
5001  def _set_from_binary(self, p):
5002  r"""_set_from_binary(Domain self, PyObject * p)"""
5003  return _IMP_atom.Domain__set_from_binary(self, p)
5004 
5005  def __getstate__(self):
5006  p = self._get_as_binary()
5007  if len(self.__dict__) > 1:
5008  d = self.__dict__.copy()
5009  del d['this']
5010  p = (d, p)
5011  return p
5012 
5013  def __setstate__(self, p):
5014  if not hasattr(self, 'this'):
5015  self.__init__()
5016  if isinstance(p, tuple):
5017  d, p = p
5018  self.__dict__.update(d)
5019  return self._set_from_binary(p)
5020 
5021  __swig_destroy__ = _IMP_atom.delete_Domain
5022 
5023 # Register Domain in _IMP_atom:
5024 _IMP_atom.Domain_swigregister(Domain)
5025 class LennardJones(IMP.core.XYZR):
5026  r"""Proxy of C++ IMP::atom::LennardJones class."""
5027 
5028  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5029 
5030  def __init__(self, *args):
5031  r"""
5032  __init__(LennardJones self) -> LennardJones
5033  __init__(LennardJones self, Model m, ParticleIndex id) -> LennardJones
5034  __init__(LennardJones self, _ParticleAdaptor d) -> LennardJones
5035  """
5036  _IMP_atom.LennardJones_swiginit(self, _IMP_atom.new_LennardJones(*args))
5037 
5038  def show(self, *args):
5039  r"""show(LennardJones self, _ostream out=std::cout)"""
5040  return _IMP_atom.LennardJones_show(self, *args)
5041 
5042  @staticmethod
5043  def setup_particle(*args):
5044  r"""
5045  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5046  setup_particle(_ParticleAdaptor pa) -> LennardJones
5047  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5048  setup_particle(_ParticleAdaptor pa, IMP::Float well_depth) -> LennardJones
5049  """
5050  return _IMP_atom.LennardJones_setup_particle(*args)
5051 
5052  def get_well_depth(self):
5053  r"""get_well_depth(LennardJones self) -> IMP::Float"""
5054  return _IMP_atom.LennardJones_get_well_depth(self)
5055 
5056  def set_well_depth(self, well_depth):
5057  r"""set_well_depth(LennardJones self, IMP::Float well_depth)"""
5058  return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5059 
5060  @staticmethod
5061  def get_is_setup(*args):
5062  r"""
5063  get_is_setup(_ParticleAdaptor p) -> bool
5064  get_is_setup(Model m, ParticleIndex pi) -> bool
5065  """
5066  return _IMP_atom.LennardJones_get_is_setup(*args)
5067 
5068  @staticmethod
5069  def get_well_depth_key():
5070  r"""get_well_depth_key() -> FloatKey"""
5071  return _IMP_atom.LennardJones_get_well_depth_key()
5072 
5073  def add_attribute(self, *args):
5074  r"""
5075  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5076  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5077  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5078  add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
5079  add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
5080  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5081  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5082  add_attribute(LennardJones self, ObjectKey a0, Object a1)
5083  add_attribute(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5084  add_attribute(LennardJones self, SparseIntKey a0, IMP::Int a1)
5085  add_attribute(LennardJones self, SparseStringKey a0, IMP::String a1)
5086  add_attribute(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5087  """
5088  return _IMP_atom.LennardJones_add_attribute(self, *args)
5089 
5090  def get_value(self, *args):
5091  r"""
5092  get_value(LennardJones self, FloatKey a0) -> IMP::Float
5093  get_value(LennardJones self, IntKey a0) -> IMP::Int
5094  get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
5095  get_value(LennardJones self, IntsKey a0) -> IMP::Ints
5096  get_value(LennardJones self, StringKey a0) -> IMP::String
5097  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5098  get_value(LennardJones self, ObjectKey a0) -> Object
5099  get_value(LennardJones self, SparseFloatKey a0) -> IMP::Float
5100  get_value(LennardJones self, SparseIntKey a0) -> IMP::Int
5101  get_value(LennardJones self, SparseStringKey a0) -> IMP::String
5102  get_value(LennardJones self, SparseParticleIndexKey a0) -> ParticleIndex
5103  """
5104  return _IMP_atom.LennardJones_get_value(self, *args)
5105 
5106  def set_value(self, *args):
5107  r"""
5108  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5109  set_value(LennardJones self, IntKey a0, IMP::Int a1)
5110  set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5111  set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5112  set_value(LennardJones self, StringKey a0, IMP::String a1)
5113  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5114  set_value(LennardJones self, ObjectKey a0, Object a1)
5115  set_value(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5116  set_value(LennardJones self, SparseIntKey a0, IMP::Int a1)
5117  set_value(LennardJones self, SparseStringKey a0, IMP::String a1)
5118  set_value(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5119  """
5120  return _IMP_atom.LennardJones_set_value(self, *args)
5121 
5122  def remove_attribute(self, *args):
5123  r"""
5124  remove_attribute(LennardJones self, FloatKey a0)
5125  remove_attribute(LennardJones self, IntKey a0)
5126  remove_attribute(LennardJones self, FloatsKey a0)
5127  remove_attribute(LennardJones self, IntsKey a0)
5128  remove_attribute(LennardJones self, StringKey a0)
5129  remove_attribute(LennardJones self, ParticleIndexKey a0)
5130  remove_attribute(LennardJones self, ObjectKey a0)
5131  remove_attribute(LennardJones self, SparseFloatKey a0)
5132  remove_attribute(LennardJones self, SparseIntKey a0)
5133  remove_attribute(LennardJones self, SparseStringKey a0)
5134  remove_attribute(LennardJones self, SparseParticleIndexKey a0)
5135  """
5136  return _IMP_atom.LennardJones_remove_attribute(self, *args)
5137 
5138  def has_attribute(self, *args):
5139  r"""
5140  has_attribute(LennardJones self, FloatKey a0) -> bool
5141  has_attribute(LennardJones self, IntKey a0) -> bool
5142  has_attribute(LennardJones self, FloatsKey a0) -> bool
5143  has_attribute(LennardJones self, IntsKey a0) -> bool
5144  has_attribute(LennardJones self, StringKey a0) -> bool
5145  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5146  has_attribute(LennardJones self, ObjectKey a0) -> bool
5147  has_attribute(LennardJones self, SparseFloatKey a0) -> bool
5148  has_attribute(LennardJones self, SparseIntKey a0) -> bool
5149  has_attribute(LennardJones self, SparseStringKey a0) -> bool
5150  has_attribute(LennardJones self, SparseParticleIndexKey a0) -> bool
5151  """
5152  return _IMP_atom.LennardJones_has_attribute(self, *args)
5153 
5154  def get_derivative(self, a0):
5155  r"""get_derivative(LennardJones self, FloatKey a0) -> double"""
5156  return _IMP_atom.LennardJones_get_derivative(self, a0)
5157 
5158  def get_name(self):
5159  r"""get_name(LennardJones self) -> std::string"""
5160  return _IMP_atom.LennardJones_get_name(self)
5161 
5162  def clear_caches(self):
5163  r"""clear_caches(LennardJones self)"""
5164  return _IMP_atom.LennardJones_clear_caches(self)
5165 
5166  def set_name(self, a0):
5167  r"""set_name(LennardJones self, std::string a0)"""
5168  return _IMP_atom.LennardJones_set_name(self, a0)
5169 
5170  def set_check_level(self, a0):
5171  r"""set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5172  return _IMP_atom.LennardJones_set_check_level(self, a0)
5173 
5174  def add_to_derivative(self, a0, a1, a2):
5175  r"""add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5176  return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5177 
5178  def set_is_optimized(self, a0, a1):
5179  r"""set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5180  return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5181 
5182  def get_is_optimized(self, a0):
5183  r"""get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5184  return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5185 
5186  def get_check_level(self):
5187  r"""get_check_level(LennardJones self) -> IMP::CheckLevel"""
5188  return _IMP_atom.LennardJones_get_check_level(self)
5189 
5190  def __eq__(self, *args):
5191  r"""
5192  __eq__(LennardJones self, LennardJones o) -> bool
5193  __eq__(LennardJones self, Particle d) -> bool
5194  """
5195  return _IMP_atom.LennardJones___eq__(self, *args)
5196 
5197  def __ne__(self, *args):
5198  r"""
5199  __ne__(LennardJones self, LennardJones o) -> bool
5200  __ne__(LennardJones self, Particle d) -> bool
5201  """
5202  return _IMP_atom.LennardJones___ne__(self, *args)
5203 
5204  def __le__(self, *args):
5205  r"""
5206  __le__(LennardJones self, LennardJones o) -> bool
5207  __le__(LennardJones self, Particle d) -> bool
5208  """
5209  return _IMP_atom.LennardJones___le__(self, *args)
5210 
5211  def __lt__(self, *args):
5212  r"""
5213  __lt__(LennardJones self, LennardJones o) -> bool
5214  __lt__(LennardJones self, Particle d) -> bool
5215  """
5216  return _IMP_atom.LennardJones___lt__(self, *args)
5217 
5218  def __ge__(self, *args):
5219  r"""
5220  __ge__(LennardJones self, LennardJones o) -> bool
5221  __ge__(LennardJones self, Particle d) -> bool
5222  """
5223  return _IMP_atom.LennardJones___ge__(self, *args)
5224 
5225  def __gt__(self, *args):
5226  r"""
5227  __gt__(LennardJones self, LennardJones o) -> bool
5228  __gt__(LennardJones self, Particle d) -> bool
5229  """
5230  return _IMP_atom.LennardJones___gt__(self, *args)
5231 
5232  def __hash__(self):
5233  r"""__hash__(LennardJones self) -> std::size_t"""
5234  return _IMP_atom.LennardJones___hash__(self)
5235 
5236  def __str__(self):
5237  r"""__str__(LennardJones self) -> std::string"""
5238  return _IMP_atom.LennardJones___str__(self)
5239 
5240  def __repr__(self):
5241  r"""__repr__(LennardJones self) -> std::string"""
5242  return _IMP_atom.LennardJones___repr__(self)
5243 
5244  def _get_as_binary(self):
5245  r"""_get_as_binary(LennardJones self) -> PyObject *"""
5246  return _IMP_atom.LennardJones__get_as_binary(self)
5247 
5248  def _set_from_binary(self, p):
5249  r"""_set_from_binary(LennardJones self, PyObject * p)"""
5250  return _IMP_atom.LennardJones__set_from_binary(self, p)
5251 
5252  def __getstate__(self):
5253  p = self._get_as_binary()
5254  if len(self.__dict__) > 1:
5255  d = self.__dict__.copy()
5256  del d['this']
5257  p = (d, p)
5258  return p
5259 
5260  def __setstate__(self, p):
5261  if not hasattr(self, 'this'):
5262  self.__init__()
5263  if isinstance(p, tuple):
5264  d, p = p
5265  self.__dict__.update(d)
5266  return self._set_from_binary(p)
5267 
5268  __swig_destroy__ = _IMP_atom.delete_LennardJones
5269 
5270 # Register LennardJones in _IMP_atom:
5271 _IMP_atom.LennardJones_swigregister(LennardJones)
5272 class LennardJonesPairScore(IMP.PairScore):
5273  r"""Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5274 
5275  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5276 
5277  def __init__(self, f):
5278  r"""__init__(LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5279  _IMP_atom.LennardJonesPairScore_swiginit(self, _IMP_atom.new_LennardJonesPairScore(f))
5280 
5281  def set_repulsive_weight(self, repulsive_weight):
5282  r"""set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5283  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5284 
5285  def get_repulsive_weight(self):
5286  r"""get_repulsive_weight(LennardJonesPairScore self) -> double"""
5287  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5288 
5289  def set_attractive_weight(self, attractive_weight):
5290  r"""set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5291  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5292 
5293  def get_attractive_weight(self):
5294  r"""get_attractive_weight(LennardJonesPairScore self) -> double"""
5295  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5296 
5297  def do_get_inputs(self, m, pis):
5298  r"""do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5299  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5300 
5301  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
5302  r"""evaluate_indexes(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
5303  return _IMP_atom.LennardJonesPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
5304 
5305  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
5306  r"""evaluate_indexes_scores(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
5307  return _IMP_atom.LennardJonesPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
5308 
5309  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
5310  r"""evaluate_indexes_delta(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
5311  return _IMP_atom.LennardJonesPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
5312 
5313  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
5314  r"""evaluate_if_good_indexes(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
5315  return _IMP_atom.LennardJonesPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
5316 
5317  def get_version_info(self):
5318  r"""get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5319  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5320  __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
5321 
5322  def __str__(self):
5323  r"""__str__(LennardJonesPairScore self) -> std::string"""
5324  return _IMP_atom.LennardJonesPairScore___str__(self)
5325 
5326  def __repr__(self):
5327  r"""__repr__(LennardJonesPairScore self) -> std::string"""
5328  return _IMP_atom.LennardJonesPairScore___repr__(self)
5329 
5330  @staticmethod
5331  def get_from(o):
5332  return _object_cast_to_LennardJonesPairScore(o)
5333 
5334 
5335 # Register LennardJonesPairScore in _IMP_atom:
5336 _IMP_atom.LennardJonesPairScore_swigregister(LennardJonesPairScore)
5337 class LennardJonesType(IMP.Object):
5338  r"""Proxy of C++ IMP::atom::LennardJonesType class."""
5339 
5340  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5341 
5342  def __init__(self, *args):
5343  r"""__init__(LennardJonesType self, double well_depth, double radius, std::string name="LennardJonesType%1%") -> LennardJonesType"""
5344  _IMP_atom.LennardJonesType_swiginit(self, _IMP_atom.new_LennardJonesType(*args))
5345 
5346  def get_well_depth(self):
5347  r"""get_well_depth(LennardJonesType self) -> double"""
5348  return _IMP_atom.LennardJonesType_get_well_depth(self)
5349 
5350  def set_well_depth(self, d):
5351  r"""set_well_depth(LennardJonesType self, double d)"""
5352  return _IMP_atom.LennardJonesType_set_well_depth(self, d)
5353 
5354  def get_radius(self):
5355  r"""get_radius(LennardJonesType self) -> double"""
5356  return _IMP_atom.LennardJonesType_get_radius(self)
5357 
5358  def set_radius(self, r):
5359  r"""set_radius(LennardJonesType self, double r)"""
5360  return _IMP_atom.LennardJonesType_set_radius(self, r)
5361 
5362  def get_index(self):
5363  r"""get_index(LennardJonesType self) -> int"""
5364  return _IMP_atom.LennardJonesType_get_index(self)
5365 
5366  def get_version_info(self):
5367  r"""get_version_info(LennardJonesType self) -> VersionInfo"""
5368  return _IMP_atom.LennardJonesType_get_version_info(self)
5369  __swig_destroy__ = _IMP_atom.delete_LennardJonesType
5370 
5371  def __str__(self):
5372  r"""__str__(LennardJonesType self) -> std::string"""
5373  return _IMP_atom.LennardJonesType___str__(self)
5374 
5375  def __repr__(self):
5376  r"""__repr__(LennardJonesType self) -> std::string"""
5377  return _IMP_atom.LennardJonesType___repr__(self)
5378 
5379  @staticmethod
5380  def get_from(o):
5381  return _object_cast_to_LennardJonesType(o)
5382 
5383 
5384 # Register LennardJonesType in _IMP_atom:
5385 _IMP_atom.LennardJonesType_swigregister(LennardJonesType)
5386 class LennardJonesTyped(IMP.core.XYZ):
5387  r"""Proxy of C++ IMP::atom::LennardJonesTyped class."""
5388 
5389  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5390 
5391  def __init__(self, *args):
5392  r"""
5393  __init__(LennardJonesTyped self) -> LennardJonesTyped
5394  __init__(LennardJonesTyped self, Model m, ParticleIndex id) -> LennardJonesTyped
5395  __init__(LennardJonesTyped self, _ParticleAdaptor d) -> LennardJonesTyped
5396  """
5397  _IMP_atom.LennardJonesTyped_swiginit(self, _IMP_atom.new_LennardJonesTyped(*args))
5398 
5399  def show(self, *args):
5400  r"""show(LennardJonesTyped self, _ostream out=std::cout)"""
5401  return _IMP_atom.LennardJonesTyped_show(self, *args)
5402 
5403  @staticmethod
5404  def setup_particle(*args):
5405  r"""
5406  setup_particle(Model m, ParticleIndex pi, LennardJonesType type) -> LennardJonesTyped
5407  setup_particle(_ParticleAdaptor pa, LennardJonesType type) -> LennardJonesTyped
5408  """
5409  return _IMP_atom.LennardJonesTyped_setup_particle(*args)
5410 
5411  @staticmethod
5412  def get_is_setup(*args):
5413  r"""
5414  get_is_setup(_ParticleAdaptor p) -> bool
5415  get_is_setup(Model m, ParticleIndex pi) -> bool
5416  """
5417  return _IMP_atom.LennardJonesTyped_get_is_setup(*args)
5418 
5419  def set_type(self, type):
5420  r"""set_type(LennardJonesTyped self, LennardJonesType type)"""
5421  return _IMP_atom.LennardJonesTyped_set_type(self, type)
5422 
5423  def get_type(self):
5424  r"""get_type(LennardJonesTyped self) -> LennardJonesType"""
5425  return _IMP_atom.LennardJonesTyped_get_type(self)
5426 
5427  def get_index(self):
5428  r"""get_index(LennardJonesTyped self) -> int"""
5429  return _IMP_atom.LennardJonesTyped_get_index(self)
5430 
5431  def get_well_depth(self):
5432  r"""get_well_depth(LennardJonesTyped self) -> double"""
5433  return _IMP_atom.LennardJonesTyped_get_well_depth(self)
5434 
5435  def get_radius(self):
5436  r"""get_radius(LennardJonesTyped self) -> double"""
5437  return _IMP_atom.LennardJonesTyped_get_radius(self)
5438 
5439  @staticmethod
5440  def get_type_key():
5441  r"""get_type_key() -> IntKey"""
5442  return _IMP_atom.LennardJonesTyped_get_type_key()
5443 
5444  def add_attribute(self, *args):
5445  r"""
5446  add_attribute(LennardJonesTyped self, FloatKey k, IMP::Float v, bool opt)
5447  add_attribute(LennardJonesTyped self, FloatKey a0, IMP::Float a1)
5448  add_attribute(LennardJonesTyped self, IntKey a0, IMP::Int a1)
5449  add_attribute(LennardJonesTyped self, FloatsKey a0, IMP::Floats a1)
5450  add_attribute(LennardJonesTyped self, IntsKey a0, IMP::Ints a1)
5451  add_attribute(LennardJonesTyped self, StringKey a0, IMP::String a1)
5452  add_attribute(LennardJonesTyped self, ParticleIndexKey a0, Particle a1)
5453  add_attribute(LennardJonesTyped self, ObjectKey a0, Object a1)
5454  add_attribute(LennardJonesTyped self, SparseFloatKey a0, IMP::Float a1)
5455  add_attribute(LennardJonesTyped self, SparseIntKey a0, IMP::Int a1)
5456  add_attribute(LennardJonesTyped self, SparseStringKey a0, IMP::String a1)
5457  add_attribute(LennardJonesTyped self, SparseParticleIndexKey a0, ParticleIndex a1)
5458  """
5459  return _IMP_atom.LennardJonesTyped_add_attribute(self, *args)
5460 
5461  def get_value(self, *args):
5462  r"""
5463  get_value(LennardJonesTyped self, FloatKey a0) -> IMP::Float
5464  get_value(LennardJonesTyped self, IntKey a0) -> IMP::Int
5465  get_value(LennardJonesTyped self, FloatsKey a0) -> IMP::Floats
5466  get_value(LennardJonesTyped self, IntsKey a0) -> IMP::Ints
5467  get_value(LennardJonesTyped self, StringKey a0) -> IMP::String
5468  get_value(LennardJonesTyped self, ParticleIndexKey a0) -> Particle
5469  get_value(LennardJonesTyped self, ObjectKey a0) -> Object
5470  get_value(LennardJonesTyped self, SparseFloatKey a0) -> IMP::Float
5471  get_value(LennardJonesTyped self, SparseIntKey a0) -> IMP::Int
5472  get_value(LennardJonesTyped self, SparseStringKey a0) -> IMP::String
5473  get_value(LennardJonesTyped self, SparseParticleIndexKey a0) -> ParticleIndex
5474  """
5475  return _IMP_atom.LennardJonesTyped_get_value(self, *args)
5476 
5477  def set_value(self, *args):
5478  r"""
5479  set_value(LennardJonesTyped self, FloatKey a0, IMP::Float a1)
5480  set_value(LennardJonesTyped self, IntKey a0, IMP::Int a1)
5481  set_value(LennardJonesTyped self, FloatsKey a0, IMP::Floats a1)
5482  set_value(LennardJonesTyped self, IntsKey a0, IMP::Ints a1)
5483  set_value(LennardJonesTyped self, StringKey a0, IMP::String a1)
5484  set_value(LennardJonesTyped self, ParticleIndexKey a0, Particle a1)
5485  set_value(LennardJonesTyped self, ObjectKey a0, Object a1)
5486  set_value(LennardJonesTyped self, SparseFloatKey a0, IMP::Float a1)
5487  set_value(LennardJonesTyped self, SparseIntKey a0, IMP::Int a1)
5488  set_value(LennardJonesTyped self, SparseStringKey a0, IMP::String a1)
5489  set_value(LennardJonesTyped self, SparseParticleIndexKey a0, ParticleIndex a1)
5490  """
5491  return _IMP_atom.LennardJonesTyped_set_value(self, *args)
5492 
5493  def remove_attribute(self, *args):
5494  r"""
5495  remove_attribute(LennardJonesTyped self, FloatKey a0)
5496  remove_attribute(LennardJonesTyped self, IntKey a0)
5497  remove_attribute(LennardJonesTyped self, FloatsKey a0)
5498  remove_attribute(LennardJonesTyped self, IntsKey a0)
5499  remove_attribute(LennardJonesTyped self, StringKey a0)
5500  remove_attribute(LennardJonesTyped self, ParticleIndexKey a0)
5501  remove_attribute(LennardJonesTyped self, ObjectKey a0)
5502  remove_attribute(LennardJonesTyped self, SparseFloatKey a0)
5503  remove_attribute(LennardJonesTyped self, SparseIntKey a0)
5504  remove_attribute(LennardJonesTyped self, SparseStringKey a0)
5505  remove_attribute(LennardJonesTyped self, SparseParticleIndexKey a0)
5506  """
5507  return _IMP_atom.LennardJonesTyped_remove_attribute(self, *args)
5508 
5509  def has_attribute(self, *args):
5510  r"""
5511  has_attribute(LennardJonesTyped self, FloatKey a0) -> bool
5512  has_attribute(LennardJonesTyped self, IntKey a0) -> bool
5513  has_attribute(LennardJonesTyped self, FloatsKey a0) -> bool
5514  has_attribute(LennardJonesTyped self, IntsKey a0) -> bool
5515  has_attribute(LennardJonesTyped self, StringKey a0) -> bool
5516  has_attribute(LennardJonesTyped self, ParticleIndexKey a0) -> bool
5517  has_attribute(LennardJonesTyped self, ObjectKey a0) -> bool
5518  has_attribute(LennardJonesTyped self, SparseFloatKey a0) -> bool
5519  has_attribute(LennardJonesTyped self, SparseIntKey a0) -> bool
5520  has_attribute(LennardJonesTyped self, SparseStringKey a0) -> bool
5521  has_attribute(LennardJonesTyped self, SparseParticleIndexKey a0) -> bool
5522  """
5523  return _IMP_atom.LennardJonesTyped_has_attribute(self, *args)
5524 
5525  def get_derivative(self, a0):
5526  r"""get_derivative(LennardJonesTyped self, FloatKey a0) -> double"""
5527  return _IMP_atom.LennardJonesTyped_get_derivative(self, a0)
5528 
5529  def get_name(self):
5530  r"""get_name(LennardJonesTyped self) -> std::string"""
5531  return _IMP_atom.LennardJonesTyped_get_name(self)
5532 
5533  def clear_caches(self):
5534  r"""clear_caches(LennardJonesTyped self)"""
5535  return _IMP_atom.LennardJonesTyped_clear_caches(self)
5536 
5537  def set_name(self, a0):
5538  r"""set_name(LennardJonesTyped self, std::string a0)"""
5539  return _IMP_atom.LennardJonesTyped_set_name(self, a0)
5540 
5541  def set_check_level(self, a0):
5542  r"""set_check_level(LennardJonesTyped self, IMP::CheckLevel a0)"""
5543  return _IMP_atom.LennardJonesTyped_set_check_level(self, a0)
5544 
5545  def add_to_derivative(self, a0, a1, a2):
5546  r"""add_to_derivative(LennardJonesTyped self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5547  return _IMP_atom.LennardJonesTyped_add_to_derivative(self, a0, a1, a2)
5548 
5549  def set_is_optimized(self, a0, a1):
5550  r"""set_is_optimized(LennardJonesTyped self, FloatKey a0, bool a1)"""
5551  return _IMP_atom.LennardJonesTyped_set_is_optimized(self, a0, a1)
5552 
5553  def get_is_optimized(self, a0):
5554  r"""get_is_optimized(LennardJonesTyped self, FloatKey a0) -> bool"""
5555  return _IMP_atom.LennardJonesTyped_get_is_optimized(self, a0)
5556 
5557  def get_check_level(self):
5558  r"""get_check_level(LennardJonesTyped self) -> IMP::CheckLevel"""
5559  return _IMP_atom.LennardJonesTyped_get_check_level(self)
5560 
5561  def __eq__(self, *args):
5562  r"""
5563  __eq__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5564  __eq__(LennardJonesTyped self, Particle d) -> bool
5565  """
5566  return _IMP_atom.LennardJonesTyped___eq__(self, *args)
5567 
5568  def __ne__(self, *args):
5569  r"""
5570  __ne__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5571  __ne__(LennardJonesTyped self, Particle d) -> bool
5572  """
5573  return _IMP_atom.LennardJonesTyped___ne__(self, *args)
5574 
5575  def __le__(self, *args):
5576  r"""
5577  __le__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5578  __le__(LennardJonesTyped self, Particle d) -> bool
5579  """
5580  return _IMP_atom.LennardJonesTyped___le__(self, *args)
5581 
5582  def __lt__(self, *args):
5583  r"""
5584  __lt__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5585  __lt__(LennardJonesTyped self, Particle d) -> bool
5586  """
5587  return _IMP_atom.LennardJonesTyped___lt__(self, *args)
5588 
5589  def __ge__(self, *args):
5590  r"""
5591  __ge__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5592  __ge__(LennardJonesTyped self, Particle d) -> bool
5593  """
5594  return _IMP_atom.LennardJonesTyped___ge__(self, *args)
5595 
5596  def __gt__(self, *args):
5597  r"""
5598  __gt__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5599  __gt__(LennardJonesTyped self, Particle d) -> bool
5600  """
5601  return _IMP_atom.LennardJonesTyped___gt__(self, *args)
5602 
5603  def __hash__(self):
5604  r"""__hash__(LennardJonesTyped self) -> std::size_t"""
5605  return _IMP_atom.LennardJonesTyped___hash__(self)
5606 
5607  def __str__(self):
5608  r"""__str__(LennardJonesTyped self) -> std::string"""
5609  return _IMP_atom.LennardJonesTyped___str__(self)
5610 
5611  def __repr__(self):
5612  r"""__repr__(LennardJonesTyped self) -> std::string"""
5613  return _IMP_atom.LennardJonesTyped___repr__(self)
5614 
5615  def _get_as_binary(self):
5616  r"""_get_as_binary(LennardJonesTyped self) -> PyObject *"""
5617  return _IMP_atom.LennardJonesTyped__get_as_binary(self)
5618 
5619  def _set_from_binary(self, p):
5620  r"""_set_from_binary(LennardJonesTyped self, PyObject * p)"""
5621  return _IMP_atom.LennardJonesTyped__set_from_binary(self, p)
5622 
5623  def __getstate__(self):
5624  p = self._get_as_binary()
5625  if len(self.__dict__) > 1:
5626  d = self.__dict__.copy()
5627  del d['this']
5628  p = (d, p)
5629  return p
5630 
5631  def __setstate__(self, p):
5632  if not hasattr(self, 'this'):
5633  self.__init__()
5634  if isinstance(p, tuple):
5635  d, p = p
5636  self.__dict__.update(d)
5637  return self._set_from_binary(p)
5638 
5639  __swig_destroy__ = _IMP_atom.delete_LennardJonesTyped
5640 
5641 # Register LennardJonesTyped in _IMP_atom:
5642 _IMP_atom.LennardJonesTyped_swigregister(LennardJonesTyped)
5643 class LinearVelocity(IMP.Decorator):
5644  r"""Proxy of C++ IMP::atom::LinearVelocity class."""
5645 
5646  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5647 
5648  def __init__(self, *args):
5649  r"""
5650  __init__(LinearVelocity self) -> LinearVelocity
5651  __init__(LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5652  __init__(LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5653  """
5654  _IMP_atom.LinearVelocity_swiginit(self, _IMP_atom.new_LinearVelocity(*args))
5655 
5656  @staticmethod
5657  def get_is_setup(*args):
5658  r"""
5659  get_is_setup(Model m, ParticleIndex pi) -> bool
5660  get_is_setup(_ParticleAdaptor p) -> bool
5661  """
5662  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5663 
5664  def show(self, *args):
5665  r"""show(LinearVelocity self, _ostream out=std::cout)"""
5666  return _IMP_atom.LinearVelocity_show(self, *args)
5667 
5668  @staticmethod
5669  def setup_particle(*args):
5670  r"""
5671  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5672  setup_particle(_ParticleAdaptor pa) -> LinearVelocity
5673  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5674  setup_particle(_ParticleAdaptor pa, Vector3D v) -> LinearVelocity
5675  """
5676  return _IMP_atom.LinearVelocity_setup_particle(*args)
5677 
5678  def set_velocity(self, v):
5679  r"""set_velocity(LinearVelocity self, Vector3D v)"""
5680  return _IMP_atom.LinearVelocity_set_velocity(self, v)
5681 
5682  def get_velocity(self):
5683  r"""get_velocity(LinearVelocity self) -> Vector3D"""
5684  return _IMP_atom.LinearVelocity_get_velocity(self)
5685 
5686  def add_attribute(self, *args):
5687  r"""
5688  add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5689  add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5690  add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5691  add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5692  add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5693  add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5694  add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5695  add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5696  add_attribute(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5697  add_attribute(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5698  add_attribute(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5699  add_attribute(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5700  """
5701  return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5702 
5703  def get_value(self, *args):
5704  r"""
5705  get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5706  get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5707  get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5708  get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5709  get_value(LinearVelocity self, StringKey a0) -> IMP::String
5710  get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5711  get_value(LinearVelocity self, ObjectKey a0) -> Object
5712  get_value(LinearVelocity self, SparseFloatKey a0) -> IMP::Float
5713  get_value(LinearVelocity self, SparseIntKey a0) -> IMP::Int
5714  get_value(LinearVelocity self, SparseStringKey a0) -> IMP::String
5715  get_value(LinearVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5716  """
5717  return _IMP_atom.LinearVelocity_get_value(self, *args)
5718 
5719  def set_value(self, *args):
5720  r"""
5721  set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5722  set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5723  set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5724  set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5725  set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5726  set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5727  set_value(LinearVelocity self, ObjectKey a0, Object a1)
5728  set_value(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5729  set_value(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5730  set_value(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5731  set_value(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5732  """
5733  return _IMP_atom.LinearVelocity_set_value(self, *args)
5734 
5735  def remove_attribute(self, *args):
5736  r"""
5737  remove_attribute(LinearVelocity self, FloatKey a0)
5738  remove_attribute(LinearVelocity self, IntKey a0)
5739  remove_attribute(LinearVelocity self, FloatsKey a0)
5740  remove_attribute(LinearVelocity self, IntsKey a0)
5741  remove_attribute(LinearVelocity self, StringKey a0)
5742  remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5743  remove_attribute(LinearVelocity self, ObjectKey a0)
5744  remove_attribute(LinearVelocity self, SparseFloatKey a0)
5745  remove_attribute(LinearVelocity self, SparseIntKey a0)
5746  remove_attribute(LinearVelocity self, SparseStringKey a0)
5747  remove_attribute(LinearVelocity self, SparseParticleIndexKey a0)
5748  """
5749  return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5750 
5751  def has_attribute(self, *args):
5752  r"""
5753  has_attribute(LinearVelocity self, FloatKey a0) -> bool
5754  has_attribute(LinearVelocity self, IntKey a0) -> bool
5755  has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5756  has_attribute(LinearVelocity self, IntsKey a0) -> bool
5757  has_attribute(LinearVelocity self, StringKey a0) -> bool
5758  has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5759  has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5760  has_attribute(LinearVelocity self, SparseFloatKey a0) -> bool
5761  has_attribute(LinearVelocity self, SparseIntKey a0) -> bool
5762  has_attribute(LinearVelocity self, SparseStringKey a0) -> bool
5763  has_attribute(LinearVelocity self, SparseParticleIndexKey a0) -> bool
5764  """
5765  return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5766 
5767  def get_derivative(self, a0):
5768  r"""get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5769  return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5770 
5771  def get_name(self):
5772  r"""get_name(LinearVelocity self) -> std::string"""
5773  return _IMP_atom.LinearVelocity_get_name(self)
5774 
5775  def clear_caches(self):
5776  r"""clear_caches(LinearVelocity self)"""
5777  return _IMP_atom.LinearVelocity_clear_caches(self)
5778 
5779  def set_name(self, a0):
5780  r"""set_name(LinearVelocity self, std::string a0)"""
5781  return _IMP_atom.LinearVelocity_set_name(self, a0)
5782 
5783  def set_check_level(self, a0):
5784  r"""set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5785  return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5786 
5787  def add_to_derivative(self, a0, a1, a2):
5788  r"""add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5789  return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5790 
5791  def set_is_optimized(self, a0, a1):
5792  r"""set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5793  return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5794 
5795  def get_is_optimized(self, a0):
5796  r"""get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5797  return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5798 
5799  def get_check_level(self):
5800  r"""get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5801  return _IMP_atom.LinearVelocity_get_check_level(self)
5802 
5803  def __eq__(self, *args):
5804  r"""
5805  __eq__(LinearVelocity self, LinearVelocity o) -> bool
5806  __eq__(LinearVelocity self, Particle d) -> bool
5807  """
5808  return _IMP_atom.LinearVelocity___eq__(self, *args)
5809 
5810  def __ne__(self, *args):
5811  r"""
5812  __ne__(LinearVelocity self, LinearVelocity o) -> bool
5813  __ne__(LinearVelocity self, Particle d) -> bool
5814  """
5815  return _IMP_atom.LinearVelocity___ne__(self, *args)
5816 
5817  def __le__(self, *args):
5818  r"""
5819  __le__(LinearVelocity self, LinearVelocity o) -> bool
5820  __le__(LinearVelocity self, Particle d) -> bool
5821  """
5822  return _IMP_atom.LinearVelocity___le__(self, *args)
5823 
5824  def __lt__(self, *args):
5825  r"""
5826  __lt__(LinearVelocity self, LinearVelocity o) -> bool
5827  __lt__(LinearVelocity self, Particle d) -> bool
5828  """
5829  return _IMP_atom.LinearVelocity___lt__(self, *args)
5830 
5831  def __ge__(self, *args):
5832  r"""
5833  __ge__(LinearVelocity self, LinearVelocity o) -> bool
5834  __ge__(LinearVelocity self, Particle d) -> bool
5835  """
5836  return _IMP_atom.LinearVelocity___ge__(self, *args)
5837 
5838  def __gt__(self, *args):
5839  r"""
5840  __gt__(LinearVelocity self, LinearVelocity o) -> bool
5841  __gt__(LinearVelocity self, Particle d) -> bool
5842  """
5843  return _IMP_atom.LinearVelocity___gt__(self, *args)
5844 
5845  def __hash__(self):
5846  r"""__hash__(LinearVelocity self) -> std::size_t"""
5847  return _IMP_atom.LinearVelocity___hash__(self)
5848 
5849  def __str__(self):
5850  r"""__str__(LinearVelocity self) -> std::string"""
5851  return _IMP_atom.LinearVelocity___str__(self)
5852 
5853  def __repr__(self):
5854  r"""__repr__(LinearVelocity self) -> std::string"""
5855  return _IMP_atom.LinearVelocity___repr__(self)
5856 
5857  def _get_as_binary(self):
5858  r"""_get_as_binary(LinearVelocity self) -> PyObject *"""
5859  return _IMP_atom.LinearVelocity__get_as_binary(self)
5860 
5861  def _set_from_binary(self, p):
5862  r"""_set_from_binary(LinearVelocity self, PyObject * p)"""
5863  return _IMP_atom.LinearVelocity__set_from_binary(self, p)
5864 
5865  def __getstate__(self):
5866  p = self._get_as_binary()
5867  if len(self.__dict__) > 1:
5868  d = self.__dict__.copy()
5869  del d['this']
5870  p = (d, p)
5871  return p
5872 
5873  def __setstate__(self, p):
5874  if not hasattr(self, 'this'):
5875  self.__init__()
5876  if isinstance(p, tuple):
5877  d, p = p
5878  self.__dict__.update(d)
5879  return self._set_from_binary(p)
5880 
5881  __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5882 
5883 # Register LinearVelocity in _IMP_atom:
5884 _IMP_atom.LinearVelocity_swigregister(LinearVelocity)
5885 class AngularVelocity(IMP.Decorator):
5886  r"""Proxy of C++ IMP::atom::AngularVelocity class."""
5887 
5888  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5889 
5890  def __init__(self, *args):
5891  r"""
5892  __init__(AngularVelocity self) -> AngularVelocity
5893  __init__(AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5894  __init__(AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5895  """
5896  _IMP_atom.AngularVelocity_swiginit(self, _IMP_atom.new_AngularVelocity(*args))
5897 
5898  @staticmethod
5899  def get_is_setup(*args):
5900  r"""
5901  get_is_setup(Model m, ParticleIndex pi) -> bool
5902  get_is_setup(_ParticleAdaptor p) -> bool
5903  """
5904  return _IMP_atom.AngularVelocity_get_is_setup(*args)
5905 
5906  def show(self, *args):
5907  r"""show(AngularVelocity self, _ostream out=std::cout)"""
5908  return _IMP_atom.AngularVelocity_show(self, *args)
5909 
5910  @staticmethod
5911  def setup_particle(*args):
5912  r"""
5913  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5914  setup_particle(_ParticleAdaptor pa) -> AngularVelocity
5915  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5916  setup_particle(_ParticleAdaptor pa, Vector4D v) -> AngularVelocity
5917  """
5918  return _IMP_atom.AngularVelocity_setup_particle(*args)
5919 
5920  def set_velocity(self, v):
5921  r"""set_velocity(AngularVelocity self, Vector4D v)"""
5922  return _IMP_atom.AngularVelocity_set_velocity(self, v)
5923 
5924  def get_velocity(self):
5925  r"""get_velocity(AngularVelocity self) -> Vector4D"""
5926  return _IMP_atom.AngularVelocity_get_velocity(self)
5927 
5928  def add_attribute(self, *args):
5929  r"""
5930  add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5931  add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5932  add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5933  add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5934  add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5935  add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5936  add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5937  add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5938  add_attribute(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5939  add_attribute(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5940  add_attribute(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5941  add_attribute(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5942  """
5943  return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5944 
5945  def get_value(self, *args):
5946  r"""
5947  get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5948  get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5949  get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
5950  get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
5951  get_value(AngularVelocity self, StringKey a0) -> IMP::String
5952  get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5953  get_value(AngularVelocity self, ObjectKey a0) -> Object
5954  get_value(AngularVelocity self, SparseFloatKey a0) -> IMP::Float
5955  get_value(AngularVelocity self, SparseIntKey a0) -> IMP::Int
5956  get_value(AngularVelocity self, SparseStringKey a0) -> IMP::String
5957  get_value(AngularVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5958  """
5959  return _IMP_atom.AngularVelocity_get_value(self, *args)
5960 
5961  def set_value(self, *args):
5962  r"""
5963  set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5964  set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5965  set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5966  set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5967  set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5968  set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5969  set_value(AngularVelocity self, ObjectKey a0, Object a1)
5970  set_value(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5971  set_value(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5972  set_value(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5973  set_value(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5974  """
5975  return _IMP_atom.AngularVelocity_set_value(self, *args)
5976 
5977  def remove_attribute(self, *args):
5978  r"""
5979  remove_attribute(AngularVelocity self, FloatKey a0)
5980  remove_attribute(AngularVelocity self, IntKey a0)
5981  remove_attribute(AngularVelocity self, FloatsKey a0)
5982  remove_attribute(AngularVelocity self, IntsKey a0)
5983  remove_attribute(AngularVelocity self, StringKey a0)
5984  remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5985  remove_attribute(AngularVelocity self, ObjectKey a0)
5986  remove_attribute(AngularVelocity self, SparseFloatKey a0)
5987  remove_attribute(AngularVelocity self, SparseIntKey a0)
5988  remove_attribute(AngularVelocity self, SparseStringKey a0)
5989  remove_attribute(AngularVelocity self, SparseParticleIndexKey a0)
5990  """
5991  return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5992 
5993  def has_attribute(self, *args):
5994  r"""
5995  has_attribute(AngularVelocity self, FloatKey a0) -> bool
5996  has_attribute(AngularVelocity self, IntKey a0) -> bool
5997  has_attribute(AngularVelocity self, FloatsKey a0) -> bool
5998  has_attribute(AngularVelocity self, IntsKey a0) -> bool
5999  has_attribute(AngularVelocity self, StringKey a0) -> bool
6000  has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6001  has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6002  has_attribute(AngularVelocity self, SparseFloatKey a0) -> bool
6003  has_attribute(AngularVelocity self, SparseIntKey a0) -> bool
6004  has_attribute(AngularVelocity self, SparseStringKey a0) -> bool
6005  has_attribute(AngularVelocity self, SparseParticleIndexKey a0) -> bool
6006  """
6007  return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6008 
6009  def get_derivative(self, a0):
6010  r"""get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6011  return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6012 
6013  def get_name(self):
6014  r"""get_name(AngularVelocity self) -> std::string"""
6015  return _IMP_atom.AngularVelocity_get_name(self)
6016 
6017  def clear_caches(self):
6018  r"""clear_caches(AngularVelocity self)"""
6019  return _IMP_atom.AngularVelocity_clear_caches(self)
6020 
6021  def set_name(self, a0):
6022  r"""set_name(AngularVelocity self, std::string a0)"""
6023  return _IMP_atom.AngularVelocity_set_name(self, a0)
6024 
6025  def set_check_level(self, a0):
6026  r"""set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6027  return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6028 
6029  def add_to_derivative(self, a0, a1, a2):
6030  r"""add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6031  return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6032 
6033  def set_is_optimized(self, a0, a1):
6034  r"""set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6035  return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6036 
6037  def get_is_optimized(self, a0):
6038  r"""get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6039  return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6040 
6041  def get_check_level(self):
6042  r"""get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6043  return _IMP_atom.AngularVelocity_get_check_level(self)
6044 
6045  def __eq__(self, *args):
6046  r"""
6047  __eq__(AngularVelocity self, AngularVelocity o) -> bool
6048  __eq__(AngularVelocity self, Particle d) -> bool
6049  """
6050  return _IMP_atom.AngularVelocity___eq__(self, *args)
6051 
6052  def __ne__(self, *args):
6053  r"""
6054  __ne__(AngularVelocity self, AngularVelocity o) -> bool
6055  __ne__(AngularVelocity self, Particle d) -> bool
6056  """
6057  return _IMP_atom.AngularVelocity___ne__(self, *args)
6058 
6059  def __le__(self, *args):
6060  r"""
6061  __le__(AngularVelocity self, AngularVelocity o) -> bool
6062  __le__(AngularVelocity self, Particle d) -> bool
6063  """
6064  return _IMP_atom.AngularVelocity___le__(self, *args)
6065 
6066  def __lt__(self, *args):
6067  r"""
6068  __lt__(AngularVelocity self, AngularVelocity o) -> bool
6069  __lt__(AngularVelocity self, Particle d) -> bool
6070  """
6071  return _IMP_atom.AngularVelocity___lt__(self, *args)
6072 
6073  def __ge__(self, *args):
6074  r"""
6075  __ge__(AngularVelocity self, AngularVelocity o) -> bool
6076  __ge__(AngularVelocity self, Particle d) -> bool
6077  """
6078  return _IMP_atom.AngularVelocity___ge__(self, *args)
6079 
6080  def __gt__(self, *args):
6081  r"""
6082  __gt__(AngularVelocity self, AngularVelocity o) -> bool
6083  __gt__(AngularVelocity self, Particle d) -> bool
6084  """
6085  return _IMP_atom.AngularVelocity___gt__(self, *args)
6086 
6087  def __hash__(self):
6088  r"""__hash__(AngularVelocity self) -> std::size_t"""
6089  return _IMP_atom.AngularVelocity___hash__(self)
6090 
6091  def __str__(self):
6092  r"""__str__(AngularVelocity self) -> std::string"""
6093  return _IMP_atom.AngularVelocity___str__(self)
6094 
6095  def __repr__(self):
6096  r"""__repr__(AngularVelocity self) -> std::string"""
6097  return _IMP_atom.AngularVelocity___repr__(self)
6098 
6099  def _get_as_binary(self):
6100  r"""_get_as_binary(AngularVelocity self) -> PyObject *"""
6101  return _IMP_atom.AngularVelocity__get_as_binary(self)
6102 
6103  def _set_from_binary(self, p):
6104  r"""_set_from_binary(AngularVelocity self, PyObject * p)"""
6105  return _IMP_atom.AngularVelocity__set_from_binary(self, p)
6106 
6107  def __getstate__(self):
6108  p = self._get_as_binary()
6109  if len(self.__dict__) > 1:
6110  d = self.__dict__.copy()
6111  del d['this']
6112  p = (d, p)
6113  return p
6114 
6115  def __setstate__(self, p):
6116  if not hasattr(self, 'this'):
6117  self.__init__()
6118  if isinstance(p, tuple):
6119  d, p = p
6120  self.__dict__.update(d)
6121  return self._set_from_binary(p)
6122 
6123  __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6124 
6125 # Register AngularVelocity in _IMP_atom:
6126 _IMP_atom.AngularVelocity_swigregister(AngularVelocity)
6127 class MolecularDynamics(Simulator):
6128  r"""Proxy of C++ IMP::atom::MolecularDynamics class."""
6129 
6130  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6131 
6132  def __init__(self, m):
6133  r"""__init__(MolecularDynamics self, Model m) -> MolecularDynamics"""
6134  _IMP_atom.MolecularDynamics_swiginit(self, _IMP_atom.new_MolecularDynamics(m))
6135 
6136  def get_kinetic_energy(self):
6137  r"""get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6138  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6139 
6140  def get_kinetic_temperature(self, ekinetic):
6141  r"""get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6142  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6143 
6144  def set_velocity_cap(self, velocity_cap):
6145  r"""set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6146  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6147 
6148  def assign_velocities(self, temperature):
6149  r"""assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6150  return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6151 
6152  def setup(self, ps):
6153  r"""setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6154  return _IMP_atom.MolecularDynamics_setup(self, ps)
6155 
6156  def do_step(self, sc, dt):
6157  r"""do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6158  return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6159 
6160  def get_is_simulation_particle(self, p):
6161  r"""get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6162  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6163 
6164  def get_version_info(self):
6165  r"""get_version_info(MolecularDynamics self) -> VersionInfo"""
6166  return _IMP_atom.MolecularDynamics_get_version_info(self)
6167  __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
6168 
6169  def __str__(self):
6170  r"""__str__(MolecularDynamics self) -> std::string"""
6171  return _IMP_atom.MolecularDynamics___str__(self)
6172 
6173  def __repr__(self):
6174  r"""__repr__(MolecularDynamics self) -> std::string"""
6175  return _IMP_atom.MolecularDynamics___repr__(self)
6176 
6177  @staticmethod
6178  def get_from(o):
6179  return _object_cast_to_MolecularDynamics(o)
6180 
6181 
6182 # Register MolecularDynamics in _IMP_atom:
6183 _IMP_atom.MolecularDynamics_swigregister(MolecularDynamics)
6184 class VelocityScalingOptimizerState(IMP.OptimizerState):
6185  r"""Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6186 
6187  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6188 
6189  def __init__(self, m, pis, temperature):
6190  r"""__init__(VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6191  _IMP_atom.VelocityScalingOptimizerState_swiginit(self, _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature))
6192 
6193  def set_particles(self, pis):
6194  r"""set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6195  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6196 
6197  def set_temperature(self, temperature):
6198  r"""set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6199  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6200 
6201  def rescale_velocities(self):
6202  r"""rescale_velocities(VelocityScalingOptimizerState self)"""
6203  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6204 
6205  def get_version_info(self):
6206  r"""get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6207  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6208  __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
6209 
6210  def __str__(self):
6211  r"""__str__(VelocityScalingOptimizerState self) -> std::string"""
6212  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6213 
6214  def __repr__(self):
6215  r"""__repr__(VelocityScalingOptimizerState self) -> std::string"""
6216  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6217 
6218  @staticmethod
6219  def get_from(o):
6220  return _object_cast_to_VelocityScalingOptimizerState(o)
6221 
6222 
6223 # Register VelocityScalingOptimizerState in _IMP_atom:
6224 _IMP_atom.VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6225 class Fragment(Hierarchy):
6226  r"""Proxy of C++ IMP::atom::Fragment class."""
6227 
6228  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6229 
6230  def set_residue_indexes(self, o):
6231  r"""set_residue_indexes(Fragment self, IMP::Ints o)"""
6232  return _IMP_atom.Fragment_set_residue_indexes(self, o)
6233 
6234  def get_residue_indexes(self):
6235  r"""get_residue_indexes(Fragment self) -> IMP::Ints"""
6236  return _IMP_atom.Fragment_get_residue_indexes(self)
6237 
6238  def get_contains_residue(self, rindex):
6239  r"""get_contains_residue(Fragment self, int rindex) -> bool"""
6240  return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6241 
6242  def get_contains_any_sorted_residue(self, rinds):
6243  r"""get_contains_any_sorted_residue(Fragment self, IMP::Ints const & rinds) -> bool"""
6244  return _IMP_atom.Fragment_get_contains_any_sorted_residue(self, rinds)
6245 
6246  def __init__(self, *args):
6247  r"""
6248  __init__(Fragment self) -> Fragment
6249  __init__(Fragment self, Model m, ParticleIndex id) -> Fragment
6250  __init__(Fragment self, _ParticleAdaptor d) -> Fragment
6251  """
6252  _IMP_atom.Fragment_swiginit(self, _IMP_atom.new_Fragment(*args))
6253 
6254  @staticmethod
6255  def get_is_setup(*args):
6256  r"""
6257  get_is_setup(Model m, ParticleIndex pi) -> bool
6258  get_is_setup(_ParticleAdaptor p) -> bool
6259  """
6260  return _IMP_atom.Fragment_get_is_setup(*args)
6261 
6262  def show(self, *args):
6263  r"""show(Fragment self, _ostream out=std::cout)"""
6264  return _IMP_atom.Fragment_show(self, *args)
6265 
6266  @staticmethod
6267  def setup_particle(*args):
6268  r"""
6269  setup_particle(Model m, ParticleIndex pi) -> Fragment
6270  setup_particle(_ParticleAdaptor pa) -> Fragment
6271  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6272  setup_particle(_ParticleAdaptor pa, Fragment other) -> Fragment
6273  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6274  setup_particle(_ParticleAdaptor pa, IMP::Ints residue_indexes) -> Fragment
6275  """
6276  return _IMP_atom.Fragment_setup_particle(*args)
6277 
6278  def add_attribute(self, *args):
6279  r"""
6280  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6281  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6282  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6283  add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
6284  add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
6285  add_attribute(Fragment self, StringKey a0, IMP::String a1)
6286  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6287  add_attribute(Fragment self, ObjectKey a0, Object a1)
6288  add_attribute(Fragment self, SparseFloatKey a0, IMP::Float a1)
6289  add_attribute(Fragment self, SparseIntKey a0, IMP::Int a1)
6290  add_attribute(Fragment self, SparseStringKey a0, IMP::String a1)
6291  add_attribute(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
6292  """
6293  return _IMP_atom.Fragment_add_attribute(self, *args)
6294 
6295  def get_value(self, *args):
6296  r"""
6297  get_value(Fragment self, FloatKey a0) -> IMP::Float
6298  get_value(Fragment self, IntKey a0) -> IMP::Int
6299  get_value(Fragment self, FloatsKey a0) -> IMP::Floats
6300  get_value(Fragment self, IntsKey a0) -> IMP::Ints
6301  get_value(Fragment self, StringKey a0) -> IMP::String
6302  get_value(Fragment self, ParticleIndexKey a0) -> Particle
6303  get_value(Fragment self, ObjectKey a0) -> Object
6304  get_value(Fragment self, SparseFloatKey a0) -> IMP::Float
6305  get_value(Fragment self, SparseIntKey a0) -> IMP::Int
6306  get_value(Fragment self, SparseStringKey a0) -> IMP::String
6307  get_value(Fragment self, SparseParticleIndexKey a0) -> ParticleIndex
6308  """
6309  return _IMP_atom.Fragment_get_value(self, *args)
6310 
6311  def set_value(self, *args):
6312  r"""
6313  set_value(Fragment self, FloatKey a0, IMP::Float a1)
6314  set_value(Fragment self, IntKey a0, IMP::Int a1)
6315  set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
6316  set_value(Fragment self, IntsKey a0, IMP::Ints a1)
6317  set_value(Fragment self, StringKey a0, IMP::String a1)
6318  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6319  set_value(Fragment self, ObjectKey a0, Object a1)
6320  set_value(Fragment self, SparseFloatKey a0, IMP::Float a1)
6321  set_value(Fragment self, SparseIntKey a0, IMP::Int a1)
6322  set_value(Fragment self, SparseStringKey a0, IMP::String a1)
6323  set_value(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
6324  """
6325  return _IMP_atom.Fragment_set_value(self, *args)
6326 
6327  def remove_attribute(self, *args):
6328  r"""
6329  remove_attribute(Fragment self, FloatKey a0)
6330  remove_attribute(Fragment self, IntKey a0)
6331  remove_attribute(Fragment self, FloatsKey a0)
6332  remove_attribute(Fragment self, IntsKey a0)
6333  remove_attribute(Fragment self, StringKey a0)
6334  remove_attribute(Fragment self, ParticleIndexKey a0)
6335  remove_attribute(Fragment self, ObjectKey a0)
6336  remove_attribute(Fragment self, SparseFloatKey a0)
6337  remove_attribute(Fragment self, SparseIntKey a0)
6338  remove_attribute(Fragment self, SparseStringKey a0)
6339  remove_attribute(Fragment self, SparseParticleIndexKey a0)
6340  """
6341  return _IMP_atom.Fragment_remove_attribute(self, *args)
6342 
6343  def has_attribute(self, *args):
6344  r"""
6345  has_attribute(Fragment self, FloatKey a0) -> bool
6346  has_attribute(Fragment self, IntKey a0) -> bool
6347  has_attribute(Fragment self, FloatsKey a0) -> bool
6348  has_attribute(Fragment self, IntsKey a0) -> bool
6349  has_attribute(Fragment self, StringKey a0) -> bool
6350  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6351  has_attribute(Fragment self, ObjectKey a0) -> bool
6352  has_attribute(Fragment self, SparseFloatKey a0) -> bool
6353  has_attribute(Fragment self, SparseIntKey a0) -> bool
6354  has_attribute(Fragment self, SparseStringKey a0) -> bool
6355  has_attribute(Fragment self, SparseParticleIndexKey a0) -> bool
6356  """
6357  return _IMP_atom.Fragment_has_attribute(self, *args)
6358 
6359  def get_derivative(self, a0):
6360  r"""get_derivative(Fragment self, FloatKey a0) -> double"""
6361  return _IMP_atom.Fragment_get_derivative(self, a0)
6362 
6363  def get_name(self):
6364  r"""get_name(Fragment self) -> std::string"""
6365  return _IMP_atom.Fragment_get_name(self)
6366 
6367  def clear_caches(self):
6368  r"""clear_caches(Fragment self)"""
6369  return _IMP_atom.Fragment_clear_caches(self)
6370 
6371  def set_name(self, a0):
6372  r"""set_name(Fragment self, std::string a0)"""
6373  return _IMP_atom.Fragment_set_name(self, a0)
6374 
6375  def set_check_level(self, a0):
6376  r"""set_check_level(Fragment self, IMP::CheckLevel a0)"""
6377  return _IMP_atom.Fragment_set_check_level(self, a0)
6378 
6379  def add_to_derivative(self, a0, a1, a2):
6380  r"""add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6381  return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6382 
6383  def set_is_optimized(self, a0, a1):
6384  r"""set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6385  return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6386 
6387  def get_is_optimized(self, a0):
6388  r"""get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6389  return _IMP_atom.Fragment_get_is_optimized(self, a0)
6390 
6391  def get_check_level(self):
6392  r"""get_check_level(Fragment self) -> IMP::CheckLevel"""
6393  return _IMP_atom.Fragment_get_check_level(self)
6394 
6395  def __eq__(self, *args):
6396  r"""
6397  __eq__(Fragment self, Fragment o) -> bool
6398  __eq__(Fragment self, Particle d) -> bool
6399  """
6400  return _IMP_atom.Fragment___eq__(self, *args)
6401 
6402  def __ne__(self, *args):
6403  r"""
6404  __ne__(Fragment self, Fragment o) -> bool
6405  __ne__(Fragment self, Particle d) -> bool
6406  """
6407  return _IMP_atom.Fragment___ne__(self, *args)
6408 
6409  def __le__(self, *args):
6410  r"""
6411  __le__(Fragment self, Fragment o) -> bool
6412  __le__(Fragment self, Particle d) -> bool
6413  """
6414  return _IMP_atom.Fragment___le__(self, *args)
6415 
6416  def __lt__(self, *args):
6417  r"""
6418  __lt__(Fragment self, Fragment o) -> bool
6419  __lt__(Fragment self, Particle d) -> bool
6420  """
6421  return _IMP_atom.Fragment___lt__(self, *args)
6422 
6423  def __ge__(self, *args):
6424  r"""
6425  __ge__(Fragment self, Fragment o) -> bool
6426  __ge__(Fragment self, Particle d) -> bool
6427  """
6428  return _IMP_atom.Fragment___ge__(self, *args)
6429 
6430  def __gt__(self, *args):
6431  r"""
6432  __gt__(Fragment self, Fragment o) -> bool
6433  __gt__(Fragment self, Particle d) -> bool
6434  """
6435  return _IMP_atom.Fragment___gt__(self, *args)
6436 
6437  def __hash__(self):
6438  r"""__hash__(Fragment self) -> std::size_t"""
6439  return _IMP_atom.Fragment___hash__(self)
6440 
6441  def __str__(self):
6442  r"""__str__(Fragment self) -> std::string"""
6443  return _IMP_atom.Fragment___str__(self)
6444 
6445  def __repr__(self):
6446  r"""__repr__(Fragment self) -> std::string"""
6447  return _IMP_atom.Fragment___repr__(self)
6448 
6449  def _get_as_binary(self):
6450  r"""_get_as_binary(Fragment self) -> PyObject *"""
6451  return _IMP_atom.Fragment__get_as_binary(self)
6452 
6453  def _set_from_binary(self, p):
6454  r"""_set_from_binary(Fragment self, PyObject * p)"""
6455  return _IMP_atom.Fragment__set_from_binary(self, p)
6456 
6457  def __getstate__(self):
6458  p = self._get_as_binary()
6459  if len(self.__dict__) > 1:
6460  d = self.__dict__.copy()
6461  del d['this']
6462  p = (d, p)
6463  return p
6464 
6465  def __setstate__(self, p):
6466  if not hasattr(self, 'this'):
6467  self.__init__()
6468  if isinstance(p, tuple):
6469  d, p = p
6470  self.__dict__.update(d)
6471  return self._set_from_binary(p)
6472 
6473  __swig_destroy__ = _IMP_atom.delete_Fragment
6474 
6475 # Register Fragment in _IMP_atom:
6476 _IMP_atom.Fragment_swigregister(Fragment)
6477 class StereochemistryPairFilter(IMP.PairPredicate):
6478  r"""Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6479 
6480  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6481 
6482  def __init__(self):
6483  r"""__init__(StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6484  _IMP_atom.StereochemistryPairFilter_swiginit(self, _IMP_atom.new_StereochemistryPairFilter())
6485 
6486  def set_bonds(self, bonds):
6487  r"""set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6488  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6489 
6490  def set_angles(self, angles):
6491  r"""set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6492  return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6493 
6494  def set_dihedrals(self, dihedrals):
6495  r"""set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6496  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6497 
6498  def do_get_inputs(self, m, pis):
6499  r"""do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6500  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6501 
6502  def get_value(self, *args):
6503  r"""
6504  get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6505  get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6506  """
6507  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6508 
6509  def get_value_index(self, *args):
6510  r"""
6511  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6512  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6513  """
6514  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6515 
6516  def get_version_info(self):
6517  r"""get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6518  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6519  __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
6520 
6521  def __str__(self):
6522  r"""__str__(StereochemistryPairFilter self) -> std::string"""
6523  return _IMP_atom.StereochemistryPairFilter___str__(self)
6524 
6525  def __repr__(self):
6526  r"""__repr__(StereochemistryPairFilter self) -> std::string"""
6527  return _IMP_atom.StereochemistryPairFilter___repr__(self)
6528 
6529  @staticmethod
6530  def get_from(o):
6531  return _object_cast_to_StereochemistryPairFilter(o)
6532 
6533 
6534 # Register StereochemistryPairFilter in _IMP_atom:
6535 _IMP_atom.StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6536 class SoapPairFilter(IMP.PairPredicate):
6537  r"""Proxy of C++ IMP::atom::SoapPairFilter class."""
6538 
6539  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6540 
6541  def __init__(self, library):
6542  r"""__init__(SoapPairFilter self, std::string library) -> SoapPairFilter"""
6543  _IMP_atom.SoapPairFilter_swiginit(self, _IMP_atom.new_SoapPairFilter(library))
6544 
6545  def do_get_inputs(self, m, pis):
6546  r"""do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6547  return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6548 
6549  def get_value(self, *args):
6550  r"""
6551  get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6552  get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6553  """
6554  return _IMP_atom.SoapPairFilter_get_value(self, *args)
6555 
6556  def get_value_index(self, *args):
6557  r"""
6558  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6559  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6560  """
6561  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6562 
6563  def get_version_info(self):
6564  r"""get_version_info(SoapPairFilter self) -> VersionInfo"""
6565  return _IMP_atom.SoapPairFilter_get_version_info(self)
6566  __swig_destroy__ = _IMP_atom.delete_SoapPairFilter
6567 
6568  def __str__(self):
6569  r"""__str__(SoapPairFilter self) -> std::string"""
6570  return _IMP_atom.SoapPairFilter___str__(self)
6571 
6572  def __repr__(self):
6573  r"""__repr__(SoapPairFilter self) -> std::string"""
6574  return _IMP_atom.SoapPairFilter___repr__(self)
6575 
6576  @staticmethod
6577  def get_from(o):
6578  return _object_cast_to_SoapPairFilter(o)
6579 
6580 
6581 # Register SoapPairFilter in _IMP_atom:
6582 _IMP_atom.SoapPairFilter_swigregister(SoapPairFilter)
6583 class Mass(IMP.Decorator):
6584  r"""Proxy of C++ IMP::atom::Mass class."""
6585 
6586  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6587 
6588  def get_mass(self):
6589  r"""get_mass(Mass self) -> IMP::Float"""
6590  return _IMP_atom.Mass_get_mass(self)
6591 
6592  def set_mass(self, d):
6593  r"""set_mass(Mass self, IMP::Float d)"""
6594  return _IMP_atom.Mass_set_mass(self, d)
6595 
6596  def __init__(self, *args):
6597  r"""
6598  __init__(Mass self) -> Mass
6599  __init__(Mass self, Model m, ParticleIndex id) -> Mass
6600  __init__(Mass self, _ParticleAdaptor d) -> Mass
6601  """
6602  _IMP_atom.Mass_swiginit(self, _IMP_atom.new_Mass(*args))
6603 
6604  @staticmethod
6605  def get_is_setup(*args):
6606  r"""
6607  get_is_setup(Model m, ParticleIndex pi) -> bool
6608  get_is_setup(_ParticleAdaptor p) -> bool
6609  """
6610  return _IMP_atom.Mass_get_is_setup(*args)
6611 
6612  def show(self, *args):
6613  r"""show(Mass self, _ostream out=std::cout)"""
6614  return _IMP_atom.Mass_show(self, *args)
6615 
6616  @staticmethod
6617  def setup_particle(*args):
6618  r"""
6619  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6620  setup_particle(_ParticleAdaptor pa, IMP::Float mass) -> Mass
6621  setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6622  setup_particle(_ParticleAdaptor pa, Mass other) -> Mass
6623  """
6624  return _IMP_atom.Mass_setup_particle(*args)
6625 
6626  @staticmethod
6627  def get_mass_key():
6628  r"""get_mass_key() -> FloatKey"""
6629  return _IMP_atom.Mass_get_mass_key()
6630 
6631  def add_attribute(self, *args):
6632  r"""
6633  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6634  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6635  add_attribute(Mass self, IntKey a0, IMP::Int a1)
6636  add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6637  add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6638  add_attribute(Mass self, StringKey a0, IMP::String a1)
6639  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6640  add_attribute(Mass self, ObjectKey a0, Object a1)
6641  add_attribute(Mass self, SparseFloatKey a0, IMP::Float a1)
6642  add_attribute(Mass self, SparseIntKey a0, IMP::Int a1)
6643  add_attribute(Mass self, SparseStringKey a0, IMP::String a1)
6644  add_attribute(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6645  """
6646  return _IMP_atom.Mass_add_attribute(self, *args)
6647 
6648  def get_value(self, *args):
6649  r"""
6650  get_value(Mass self, FloatKey a0) -> IMP::Float
6651  get_value(Mass self, IntKey a0) -> IMP::Int
6652  get_value(Mass self, FloatsKey a0) -> IMP::Floats
6653  get_value(Mass self, IntsKey a0) -> IMP::Ints
6654  get_value(Mass self, StringKey a0) -> IMP::String
6655  get_value(Mass self, ParticleIndexKey a0) -> Particle
6656  get_value(Mass self, ObjectKey a0) -> Object
6657  get_value(Mass self, SparseFloatKey a0) -> IMP::Float
6658  get_value(Mass self, SparseIntKey a0) -> IMP::Int
6659  get_value(Mass self, SparseStringKey a0) -> IMP::String
6660  get_value(Mass self, SparseParticleIndexKey a0) -> ParticleIndex
6661  """
6662  return _IMP_atom.Mass_get_value(self, *args)
6663 
6664  def set_value(self, *args):
6665  r"""
6666  set_value(Mass self, FloatKey a0, IMP::Float a1)
6667  set_value(Mass self, IntKey a0, IMP::Int a1)
6668  set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6669  set_value(Mass self, IntsKey a0, IMP::Ints a1)
6670  set_value(Mass self, StringKey a0, IMP::String a1)
6671  set_value(Mass self, ParticleIndexKey a0, Particle a1)
6672  set_value(Mass self, ObjectKey a0, Object a1)
6673  set_value(Mass self, SparseFloatKey a0, IMP::Float a1)
6674  set_value(Mass self, SparseIntKey a0, IMP::Int a1)
6675  set_value(Mass self, SparseStringKey a0, IMP::String a1)
6676  set_value(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6677  """
6678  return _IMP_atom.Mass_set_value(self, *args)
6679 
6680  def remove_attribute(self, *args):
6681  r"""
6682  remove_attribute(Mass self, FloatKey a0)
6683  remove_attribute(Mass self, IntKey a0)
6684  remove_attribute(Mass self, FloatsKey a0)
6685  remove_attribute(Mass self, IntsKey a0)
6686  remove_attribute(Mass self, StringKey a0)
6687  remove_attribute(Mass self, ParticleIndexKey a0)
6688  remove_attribute(Mass self, ObjectKey a0)
6689  remove_attribute(Mass self, SparseFloatKey a0)
6690  remove_attribute(Mass self, SparseIntKey a0)
6691  remove_attribute(Mass self, SparseStringKey a0)
6692  remove_attribute(Mass self, SparseParticleIndexKey a0)
6693  """
6694  return _IMP_atom.Mass_remove_attribute(self, *args)
6695 
6696  def has_attribute(self, *args):
6697  r"""
6698  has_attribute(Mass self, FloatKey a0) -> bool
6699  has_attribute(Mass self, IntKey a0) -> bool
6700  has_attribute(Mass self, FloatsKey a0) -> bool
6701  has_attribute(Mass self, IntsKey a0) -> bool
6702  has_attribute(Mass self, StringKey a0) -> bool
6703  has_attribute(Mass self, ParticleIndexKey a0) -> bool
6704  has_attribute(Mass self, ObjectKey a0) -> bool
6705  has_attribute(Mass self, SparseFloatKey a0) -> bool
6706  has_attribute(Mass self, SparseIntKey a0) -> bool
6707  has_attribute(Mass self, SparseStringKey a0) -> bool
6708  has_attribute(Mass self, SparseParticleIndexKey a0) -> bool
6709  """
6710  return _IMP_atom.Mass_has_attribute(self, *args)
6711 
6712  def get_derivative(self, a0):
6713  r"""get_derivative(Mass self, FloatKey a0) -> double"""
6714  return _IMP_atom.Mass_get_derivative(self, a0)
6715 
6716  def get_name(self):
6717  r"""get_name(Mass self) -> std::string"""
6718  return _IMP_atom.Mass_get_name(self)
6719 
6720  def clear_caches(self):
6721  r"""clear_caches(Mass self)"""
6722  return _IMP_atom.Mass_clear_caches(self)
6723 
6724  def set_name(self, a0):
6725  r"""set_name(Mass self, std::string a0)"""
6726  return _IMP_atom.Mass_set_name(self, a0)
6727 
6728  def set_check_level(self, a0):
6729  r"""set_check_level(Mass self, IMP::CheckLevel a0)"""
6730  return _IMP_atom.Mass_set_check_level(self, a0)
6731 
6732  def add_to_derivative(self, a0, a1, a2):
6733  r"""add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6734  return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6735 
6736  def set_is_optimized(self, a0, a1):
6737  r"""set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6738  return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6739 
6740  def get_is_optimized(self, a0):
6741  r"""get_is_optimized(Mass self, FloatKey a0) -> bool"""
6742  return _IMP_atom.Mass_get_is_optimized(self, a0)
6743 
6744  def get_check_level(self):
6745  r"""get_check_level(Mass self) -> IMP::CheckLevel"""
6746  return _IMP_atom.Mass_get_check_level(self)
6747 
6748  def __eq__(self, *args):
6749  r"""
6750  __eq__(Mass self, Mass o) -> bool
6751  __eq__(Mass self, Particle d) -> bool
6752  """
6753  return _IMP_atom.Mass___eq__(self, *args)
6754 
6755  def __ne__(self, *args):
6756  r"""
6757  __ne__(Mass self, Mass o) -> bool
6758  __ne__(Mass self, Particle d) -> bool
6759  """
6760  return _IMP_atom.Mass___ne__(self, *args)
6761 
6762  def __le__(self, *args):
6763  r"""
6764  __le__(Mass self, Mass o) -> bool
6765  __le__(Mass self, Particle d) -> bool
6766  """
6767  return _IMP_atom.Mass___le__(self, *args)
6768 
6769  def __lt__(self, *args):
6770  r"""
6771  __lt__(Mass self, Mass o) -> bool
6772  __lt__(Mass self, Particle d) -> bool
6773  """
6774  return _IMP_atom.Mass___lt__(self, *args)
6775 
6776  def __ge__(self, *args):
6777  r"""
6778  __ge__(Mass self, Mass o) -> bool
6779  __ge__(Mass self, Particle d) -> bool
6780  """
6781  return _IMP_atom.Mass___ge__(self, *args)
6782 
6783  def __gt__(self, *args):
6784  r"""
6785  __gt__(Mass self, Mass o) -> bool
6786  __gt__(Mass self, Particle d) -> bool
6787  """
6788  return _IMP_atom.Mass___gt__(self, *args)
6789 
6790  def __hash__(self):
6791  r"""__hash__(Mass self) -> std::size_t"""
6792  return _IMP_atom.Mass___hash__(self)
6793 
6794  def __str__(self):
6795  r"""__str__(Mass self) -> std::string"""
6796  return _IMP_atom.Mass___str__(self)
6797 
6798  def __repr__(self):
6799  r"""__repr__(Mass self) -> std::string"""
6800  return _IMP_atom.Mass___repr__(self)
6801 
6802  def _get_as_binary(self):
6803  r"""_get_as_binary(Mass self) -> PyObject *"""
6804  return _IMP_atom.Mass__get_as_binary(self)
6805 
6806  def _set_from_binary(self, p):
6807  r"""_set_from_binary(Mass self, PyObject * p)"""
6808  return _IMP_atom.Mass__set_from_binary(self, p)
6809 
6810  def __getstate__(self):
6811  p = self._get_as_binary()
6812  if len(self.__dict__) > 1:
6813  d = self.__dict__.copy()
6814  del d['this']
6815  p = (d, p)
6816  return p
6817 
6818  def __setstate__(self, p):
6819  if not hasattr(self, 'this'):
6820  self.__init__()
6821  if isinstance(p, tuple):
6822  d, p = p
6823  self.__dict__.update(d)
6824  return self._set_from_binary(p)
6825 
6826  __swig_destroy__ = _IMP_atom.delete_Mass
6827 
6828 # Register Mass in _IMP_atom:
6829 _IMP_atom.Mass_swigregister(Mass)
6830 class BondedPairFilter(IMP.PairPredicate):
6831  r"""Proxy of C++ IMP::atom::BondedPairFilter class."""
6832 
6833  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6834 
6835  def __init__(self):
6836  r"""__init__(BondedPairFilter self) -> BondedPairFilter"""
6837  _IMP_atom.BondedPairFilter_swiginit(self, _IMP_atom.new_BondedPairFilter())
6838 
6839  def do_get_inputs(self, m, pis):
6840  r"""do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6841  return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6842 
6843  def get_value(self, *args):
6844  r"""
6845  get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6846  get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6847  """
6848  return _IMP_atom.BondedPairFilter_get_value(self, *args)
6849 
6850  def get_value_index(self, *args):
6851  r"""
6852  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6853  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6854  """
6855  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6856 
6857  def get_version_info(self):
6858  r"""get_version_info(BondedPairFilter self) -> VersionInfo"""
6859  return _IMP_atom.BondedPairFilter_get_version_info(self)
6860  __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
6861 
6862  def __str__(self):
6863  r"""__str__(BondedPairFilter self) -> std::string"""
6864  return _IMP_atom.BondedPairFilter___str__(self)
6865 
6866  def __repr__(self):
6867  r"""__repr__(BondedPairFilter self) -> std::string"""
6868  return _IMP_atom.BondedPairFilter___repr__(self)
6869 
6870  @staticmethod
6871  def get_from(o):
6872  return _object_cast_to_BondedPairFilter(o)
6873 
6874 
6875 # Register BondedPairFilter in _IMP_atom:
6876 _IMP_atom.BondedPairFilter_swigregister(BondedPairFilter)
6877 class Mol2Selector(IMP.Object):
6878  r"""Proxy of C++ IMP::atom::Mol2Selector class."""
6879 
6880  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6881 
6882  def __init__(self, *args, **kwargs):
6883  raise AttributeError("No constructor defined - class is abstract")
6884 
6885  def get_is_selected(self, atom_line):
6886  r"""get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6887  return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6888  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6889 
6890  def __str__(self):
6891  r"""__str__(Mol2Selector self) -> std::string"""
6892  return _IMP_atom.Mol2Selector___str__(self)
6893 
6894  def __repr__(self):
6895  r"""__repr__(Mol2Selector self) -> std::string"""
6896  return _IMP_atom.Mol2Selector___repr__(self)
6897 
6898  @staticmethod
6899  def get_from(o):
6900  return _object_cast_to_Mol2Selector(o)
6901 
6902 
6903 # Register Mol2Selector in _IMP_atom:
6904 _IMP_atom.Mol2Selector_swigregister(Mol2Selector)
6905 class AllMol2Selector(Mol2Selector):
6906  r"""Proxy of C++ IMP::atom::AllMol2Selector class."""
6907 
6908  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6909 
6910  def __str__(self):
6911  r"""__str__(AllMol2Selector self) -> std::string"""
6912  return _IMP_atom.AllMol2Selector___str__(self)
6913 
6914  def __repr__(self):
6915  r"""__repr__(AllMol2Selector self) -> std::string"""
6916  return _IMP_atom.AllMol2Selector___repr__(self)
6917 
6918  @staticmethod
6919  def get_from(o):
6920  return _object_cast_to_AllMol2Selector(o)
6921 
6922 
6923  def __init__(self):
6924  r"""__init__(AllMol2Selector self) -> AllMol2Selector"""
6925  _IMP_atom.AllMol2Selector_swiginit(self, _IMP_atom.new_AllMol2Selector())
6926  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6927 
6928 # Register AllMol2Selector in _IMP_atom:
6929 _IMP_atom.AllMol2Selector_swigregister(AllMol2Selector)
6930 class NonHydrogenMol2Selector(Mol2Selector):
6931  r"""Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6932 
6933  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6934 
6935  def __str__(self):
6936  r"""__str__(NonHydrogenMol2Selector self) -> std::string"""
6937  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6938 
6939  def __repr__(self):
6940  r"""__repr__(NonHydrogenMol2Selector self) -> std::string"""
6941  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6942 
6943  @staticmethod
6944  def get_from(o):
6945  return _object_cast_to_NonHydrogenMol2Selector(o)
6946 
6947 
6948  def __init__(self):
6949  r"""__init__(NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6950  _IMP_atom.NonHydrogenMol2Selector_swiginit(self, _IMP_atom.new_NonHydrogenMol2Selector())
6951  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6952 
6953 # Register NonHydrogenMol2Selector in _IMP_atom:
6954 _IMP_atom.NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
6955 
6956 def read_mol2(mol2_file, model, mol2sel=None):
6957  r"""read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy"""
6958  return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
6959 
6960 def write_mol2(rhd, file_name):
6961  r"""write_mol2(Hierarchy rhd, TextOutput file_name)"""
6962  return _IMP_atom.write_mol2(rhd, file_name)
6963 class SecondaryStructureResidue(IMP.Decorator):
6964  r"""Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
6965 
6966  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6967 
6968  def __init__(self, *args):
6969  r"""
6970  __init__(SecondaryStructureResidue self) -> SecondaryStructureResidue
6971  __init__(SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
6972  __init__(SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
6973  """
6974  _IMP_atom.SecondaryStructureResidue_swiginit(self, _IMP_atom.new_SecondaryStructureResidue(*args))
6975 
6976  def show(self, *args):
6977  r"""show(SecondaryStructureResidue self, _ostream out=std::cout)"""
6978  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
6979 
6980  @staticmethod
6981  def setup_particle(*args):
6982  r"""
6983  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6984  setup_particle(_ParticleAdaptor pa, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6985  setup_particle(Particle res_p) -> SecondaryStructureResidue
6986  """
6987  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
6988 
6989  @staticmethod
6990  def get_is_setup(*args):
6991  r"""
6992  get_is_setup(_ParticleAdaptor p) -> bool
6993  get_is_setup(Model m, ParticleIndex pi) -> bool
6994  """
6995  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
6996 
6997  def get_particle(self):
6998  r"""get_particle(SecondaryStructureResidue self) -> Particle"""
6999  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7000 
7001  def get_all_probabilities(self):
7002  r"""get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7003  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7004 
7005  def get_prob_helix(self):
7006  r"""get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7007  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7008 
7009  def set_prob_helix(self, t):
7010  r"""set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7011  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7012 
7013  def get_prob_strand(self):
7014  r"""get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7015  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7016 
7017  def set_prob_strand(self, t):
7018  r"""set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7019  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7020 
7021  def get_prob_coil(self):
7022  r"""get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7023  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7024 
7025  def set_prob_coil(self, t):
7026  r"""set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7027  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7028 
7029  @staticmethod
7030  def get_prob_helix_key():
7031  r"""get_prob_helix_key() -> FloatKey"""
7032  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7033 
7034  @staticmethod
7035  def get_prob_strand_key():
7036  r"""get_prob_strand_key() -> FloatKey"""
7037  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7038 
7039  @staticmethod
7040  def get_prob_coil_key():
7041  r"""get_prob_coil_key() -> FloatKey"""
7042  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7043 
7044  def add_attribute(self, *args):
7045  r"""
7046  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7047  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7048  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7049  add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7050  add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7051  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7052  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7053  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7054  add_attribute(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
7055  add_attribute(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
7056  add_attribute(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
7057  add_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
7058  """
7059  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7060 
7061  def get_value(self, *args):
7062  r"""
7063  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7064  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7065  get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
7066  get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
7067  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7068  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7069  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7070  get_value(SecondaryStructureResidue self, SparseFloatKey a0) -> IMP::Float
7071  get_value(SecondaryStructureResidue self, SparseIntKey a0) -> IMP::Int
7072  get_value(SecondaryStructureResidue self, SparseStringKey a0) -> IMP::String
7073  get_value(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> ParticleIndex
7074  """
7075  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7076 
7077  def set_value(self, *args):
7078  r"""
7079  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7080  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7081  set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7082  set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7083  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7084  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7085  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7086  set_value(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
7087  set_value(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
7088  set_value(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
7089  set_value(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
7090  """
7091  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7092 
7093  def remove_attribute(self, *args):
7094  r"""
7095  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7096  remove_attribute(SecondaryStructureResidue self, IntKey a0)
7097  remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
7098  remove_attribute(SecondaryStructureResidue self, IntsKey a0)
7099  remove_attribute(SecondaryStructureResidue self, StringKey a0)
7100  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7101  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7102  remove_attribute(SecondaryStructureResidue self, SparseFloatKey a0)
7103  remove_attribute(SecondaryStructureResidue self, SparseIntKey a0)
7104  remove_attribute(SecondaryStructureResidue self, SparseStringKey a0)
7105  remove_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0)
7106  """
7107  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7108 
7109  def has_attribute(self, *args):
7110  r"""
7111  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7112  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7113  has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
7114  has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
7115  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7116  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7117  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7118  has_attribute(SecondaryStructureResidue self, SparseFloatKey a0) -> bool
7119  has_attribute(SecondaryStructureResidue self, SparseIntKey a0) -> bool
7120  has_attribute(SecondaryStructureResidue self, SparseStringKey a0) -> bool
7121  has_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> bool
7122  """
7123  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7124 
7125  def get_derivative(self, a0):
7126  r"""get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7127  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7128 
7129  def get_name(self):
7130  r"""get_name(SecondaryStructureResidue self) -> std::string"""
7131  return _IMP_atom.SecondaryStructureResidue_get_name(self)
7132 
7133  def clear_caches(self):
7134  r"""clear_caches(SecondaryStructureResidue self)"""
7135  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7136 
7137  def set_name(self, a0):
7138  r"""set_name(SecondaryStructureResidue self, std::string a0)"""
7139  return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7140 
7141  def set_check_level(self, a0):
7142  r"""set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7143  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7144 
7145  def add_to_derivative(self, a0, a1, a2):
7146  r"""add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7147  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7148 
7149  def set_is_optimized(self, a0, a1):
7150  r"""set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7151  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7152 
7153  def get_is_optimized(self, a0):
7154  r"""get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7155  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7156 
7157  def get_check_level(self):
7158  r"""get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7159  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7160 
7161  def __eq__(self, *args):
7162  r"""
7163  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7164  __eq__(SecondaryStructureResidue self, Particle d) -> bool
7165  """
7166  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7167 
7168  def __ne__(self, *args):
7169  r"""
7170  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7171  __ne__(SecondaryStructureResidue self, Particle d) -> bool
7172  """
7173  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7174 
7175  def __le__(self, *args):
7176  r"""
7177  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7178  __le__(SecondaryStructureResidue self, Particle d) -> bool
7179  """
7180  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7181 
7182  def __lt__(self, *args):
7183  r"""
7184  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7185  __lt__(SecondaryStructureResidue self, Particle d) -> bool
7186  """
7187  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7188 
7189  def __ge__(self, *args):
7190  r"""
7191  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7192  __ge__(SecondaryStructureResidue self, Particle d) -> bool
7193  """
7194  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7195 
7196  def __gt__(self, *args):
7197  r"""
7198  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7199  __gt__(SecondaryStructureResidue self, Particle d) -> bool
7200  """
7201  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7202 
7203  def __hash__(self):
7204  r"""__hash__(SecondaryStructureResidue self) -> std::size_t"""
7205  return _IMP_atom.SecondaryStructureResidue___hash__(self)
7206 
7207  def __str__(self):
7208  r"""__str__(SecondaryStructureResidue self) -> std::string"""
7209  return _IMP_atom.SecondaryStructureResidue___str__(self)
7210 
7211  def __repr__(self):
7212  r"""__repr__(SecondaryStructureResidue self) -> std::string"""
7213  return _IMP_atom.SecondaryStructureResidue___repr__(self)
7214 
7215  def _get_as_binary(self):
7216  r"""_get_as_binary(SecondaryStructureResidue self) -> PyObject *"""
7217  return _IMP_atom.SecondaryStructureResidue__get_as_binary(self)
7218 
7219  def _set_from_binary(self, p):
7220  r"""_set_from_binary(SecondaryStructureResidue self, PyObject * p)"""
7221  return _IMP_atom.SecondaryStructureResidue__set_from_binary(self, p)
7222 
7223  def __getstate__(self):
7224  p = self._get_as_binary()
7225  if len(self.__dict__) > 1:
7226  d = self.__dict__.copy()
7227  del d['this']
7228  p = (d, p)
7229  return p
7230 
7231  def __setstate__(self, p):
7232  if not hasattr(self, 'this'):
7233  self.__init__()
7234  if isinstance(p, tuple):
7235  d, p = p
7236  self.__dict__.update(d)
7237  return self._set_from_binary(p)
7238 
7239  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7240 
7241 # Register SecondaryStructureResidue in _IMP_atom:
7242 _IMP_atom.SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7243 
7244 def setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res=False):
7245  r"""setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue"""
7246  return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7247 
7248 def setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res=False):
7249  r"""setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues"""
7250  return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7251 
7252 def get_secondary_structure_match_score(ssr1, ssr2):
7253  r"""get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7254  return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7255 
7256 def read_psipred(*args):
7257  r"""
7258  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7259  read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7260  """
7261  return _IMP_atom.read_psipred(*args)
7262 class _ADopeBase(IMP.PairScore):
7263  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Dope > class."""
7264 
7265  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7266  __repr__ = _swig_repr
7267 
7268  def __init__(self, *args):
7269  r"""
7270  __init__(_ADopeBase self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
7271  __init__(_ADopeBase self) -> _ADopeBase
7272  """
7273  _IMP_atom._ADopeBase_swiginit(self, _IMP_atom.new__ADopeBase(*args))
7274 
7275  def do_get_inputs(self, m, pis):
7276  r"""do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7277  return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7278 
7279  def get_score_functor(self):
7280  r"""get_score_functor(_ADopeBase self) -> Dope"""
7281  return _IMP_atom._ADopeBase_get_score_functor(self)
7282 
7283  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7284  r"""evaluate_indexes(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7285  return _IMP_atom._ADopeBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7286 
7287  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7288  r"""evaluate_indexes_scores(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7289  return _IMP_atom._ADopeBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7290 
7291  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7292  r"""evaluate_indexes_delta(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7293  return _IMP_atom._ADopeBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7294 
7295  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7296  r"""evaluate_if_good_indexes(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7297  return _IMP_atom._ADopeBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7298 
7299  def get_version_info(self):
7300  r"""get_version_info(_ADopeBase self) -> VersionInfo"""
7301  return _IMP_atom._ADopeBase_get_version_info(self)
7302  __swig_destroy__ = _IMP_atom.delete__ADopeBase
7303 
7304 # Register _ADopeBase in _IMP_atom:
7305 _IMP_atom._ADopeBase_swigregister(_ADopeBase)
7306 class _BDopeBase(IMP.PairScore):
7307  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > > class."""
7308 
7309  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7310  __repr__ = _swig_repr
7311 
7312  def __init__(self, *args):
7313  r"""
7314  __init__(_BDopeBase self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _BDopeBase
7315  __init__(_BDopeBase self) -> _BDopeBase
7316  """
7317  _IMP_atom._BDopeBase_swiginit(self, _IMP_atom.new__BDopeBase(*args))
7318 
7319  def do_get_inputs(self, m, pis):
7320  r"""do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7321  return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7322 
7323  def get_score_functor(self):
7324  r"""get_score_functor(_BDopeBase self) -> _DopeBase"""
7325  return _IMP_atom._BDopeBase_get_score_functor(self)
7326 
7327  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7328  r"""evaluate_indexes(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7329  return _IMP_atom._BDopeBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7330 
7331  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7332  r"""evaluate_indexes_scores(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7333  return _IMP_atom._BDopeBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7334 
7335  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7336  r"""evaluate_indexes_delta(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7337  return _IMP_atom._BDopeBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7338 
7339  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7340  r"""evaluate_if_good_indexes(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7341  return _IMP_atom._BDopeBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7342 
7343  def get_version_info(self):
7344  r"""get_version_info(_BDopeBase self) -> VersionInfo"""
7345  return _IMP_atom._BDopeBase_get_version_info(self)
7346  __swig_destroy__ = _IMP_atom.delete__BDopeBase
7347 
7348 # Register _BDopeBase in _IMP_atom:
7349 _IMP_atom._BDopeBase_swigregister(_BDopeBase)
7350 class _ALoopStatisticalBase(IMP.PairScore):
7351  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::LoopStatistical > class."""
7352 
7353  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7354  __repr__ = _swig_repr
7355 
7356  def __init__(self, *args):
7357  r"""
7358  __init__(_ALoopStatisticalBase self, LoopStatistical t0, std::string name="FunctorDistancePairScore %1%") -> _ALoopStatisticalBase
7359  __init__(_ALoopStatisticalBase self) -> _ALoopStatisticalBase
7360  """
7361  _IMP_atom._ALoopStatisticalBase_swiginit(self, _IMP_atom.new__ALoopStatisticalBase(*args))
7362 
7363  def do_get_inputs(self, m, pis):
7364  r"""do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7365  return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
7366 
7367  def get_score_functor(self):
7368  r"""get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
7369  return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
7370 
7371  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7372  r"""evaluate_indexes(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7373  return _IMP_atom._ALoopStatisticalBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7374 
7375  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7376  r"""evaluate_indexes_scores(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7377  return _IMP_atom._ALoopStatisticalBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7378 
7379  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7380  r"""evaluate_indexes_delta(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7381  return _IMP_atom._ALoopStatisticalBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7382 
7383  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7384  r"""evaluate_if_good_indexes(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7385  return _IMP_atom._ALoopStatisticalBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7386 
7387  def get_version_info(self):
7388  r"""get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
7389  return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
7390  __swig_destroy__ = _IMP_atom.delete__ALoopStatisticalBase
7391 
7392 # Register _ALoopStatisticalBase in _IMP_atom:
7393 _IMP_atom._ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
7394 class _BLoopStatisticalBase(IMP.PairScore):
7395  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > > class."""
7396 
7397  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7398  __repr__ = _swig_repr
7399 
7400  def __init__(self, *args):
7401  r"""
7402  __init__(_BLoopStatisticalBase self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _BLoopStatisticalBase
7403  __init__(_BLoopStatisticalBase self) -> _BLoopStatisticalBase
7404  """
7405  _IMP_atom._BLoopStatisticalBase_swiginit(self, _IMP_atom.new__BLoopStatisticalBase(*args))
7406 
7407  def do_get_inputs(self, m, pis):
7408  r"""do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7409  return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
7410 
7411  def get_score_functor(self):
7412  r"""get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
7413  return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
7414 
7415  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7416  r"""evaluate_indexes(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7417  return _IMP_atom._BLoopStatisticalBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7418 
7419  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7420  r"""evaluate_indexes_scores(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7421  return _IMP_atom._BLoopStatisticalBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7422 
7423  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7424  r"""evaluate_indexes_delta(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7425  return _IMP_atom._BLoopStatisticalBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7426 
7427  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7428  r"""evaluate_if_good_indexes(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7429  return _IMP_atom._BLoopStatisticalBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7430 
7431  def get_version_info(self):
7432  r"""get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
7433  return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
7434  __swig_destroy__ = _IMP_atom.delete__BLoopStatisticalBase
7435 
7436 # Register _BLoopStatisticalBase in _IMP_atom:
7437 _IMP_atom._BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
7438 class _OrientedSoapBase(IMP.PairScore):
7439  r"""Proxy of C++ IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap > class."""
7440 
7441  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7442  __repr__ = _swig_repr
7443 
7444  def __init__(self, *args):
7445  r"""__init__(_OrientedSoapBase self, IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name="FunctorDistancePairScoreWithCache %1%") -> _OrientedSoapBase"""
7446  _IMP_atom._OrientedSoapBase_swiginit(self, _IMP_atom.new__OrientedSoapBase(*args))
7447 
7448  def do_get_inputs(self, m, pis):
7449  r"""do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7450  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7451 
7452  def get_score_functor(self):
7453  r"""get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7454  return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7455 
7456  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7457  r"""evaluate_indexes(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7458  return _IMP_atom._OrientedSoapBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7459 
7460  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7461  r"""evaluate_indexes_scores(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7462  return _IMP_atom._OrientedSoapBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7463 
7464  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7465  r"""evaluate_indexes_delta(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7466  return _IMP_atom._OrientedSoapBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7467 
7468  def get_version_info(self):
7469  r"""get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7470  return _IMP_atom._OrientedSoapBase_get_version_info(self)
7471  __swig_destroy__ = _IMP_atom.delete__OrientedSoapBase
7472 
7473 # Register _OrientedSoapBase in _IMP_atom:
7474 _IMP_atom._OrientedSoapBase_swigregister(_OrientedSoapBase)
7475 class _SPSFTB(IMP.PairScore):
7476  r"""Proxy of C++ IMP::score_functor::DistancePairScore< score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > > class."""
7477 
7478  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7479  __repr__ = _swig_repr
7480 
7481  def __init__(self, *args):
7482  r"""
7483  __init__(_SPSFTB self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _SPSFTB
7484  __init__(_SPSFTB self) -> _SPSFTB
7485  """
7486  _IMP_atom._SPSFTB_swiginit(self, _IMP_atom.new__SPSFTB(*args))
7487 
7488  def do_get_inputs(self, m, pis):
7489  r"""do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7490  return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7491 
7492  def get_score_functor(self):
7493  r"""get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7494  return _IMP_atom._SPSFTB_get_score_functor(self)
7495 
7496  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7497  r"""evaluate_indexes(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7498  return _IMP_atom._SPSFTB_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7499 
7500  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7501  r"""evaluate_indexes_scores(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7502  return _IMP_atom._SPSFTB_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7503 
7504  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7505  r"""evaluate_indexes_delta(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7506  return _IMP_atom._SPSFTB_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7507 
7508  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7509  r"""evaluate_if_good_indexes(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7510  return _IMP_atom._SPSFTB_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7511 
7512  def get_version_info(self):
7513  r"""get_version_info(_SPSFTB self) -> VersionInfo"""
7514  return _IMP_atom._SPSFTB_get_version_info(self)
7515  __swig_destroy__ = _IMP_atom.delete__SPSFTB
7516 
7517 # Register _SPSFTB in _IMP_atom:
7518 _IMP_atom._SPSFTB_swigregister(_SPSFTB)
7519 class _SPSTF(_SPSFTB):
7520  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType,true,false > class."""
7521 
7522  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7523  __repr__ = _swig_repr
7524 
7525  def __init__(self, *args):
7526  r"""
7527  __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7528  __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7529  """
7530  _IMP_atom._SPSTF_swiginit(self, _IMP_atom.new__SPSTF(*args))
7531  __swig_destroy__ = _IMP_atom.delete__SPSTF
7532 
7533 # Register _SPSTF in _IMP_atom:
7534 _IMP_atom._SPSTF_swigregister(_SPSTF)
7535 class _SPSFT(_BDopeBase):
7536  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::DopeType,false,true > class."""
7537 
7538  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7539  __repr__ = _swig_repr
7540 
7541  def __init__(self, *args):
7542  r"""
7543  __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7544  __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7545  """
7546  _IMP_atom._SPSFT_swiginit(self, _IMP_atom.new__SPSFT(*args))
7547  __swig_destroy__ = _IMP_atom.delete__SPSFT
7548 
7549 # Register _SPSFT in _IMP_atom:
7550 _IMP_atom._SPSFT_swigregister(_SPSFT)
7551 class _SPSFTL(_BLoopStatisticalBase):
7552  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType,false,true > class."""
7553 
7554  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7555  __repr__ = _swig_repr
7556 
7557  def __init__(self, *args):
7558  r"""
7559  __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7560  __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7561  """
7562  _IMP_atom._SPSFTL_swiginit(self, _IMP_atom.new__SPSFTL(*args))
7563  __swig_destroy__ = _IMP_atom.delete__SPSFTL
7564 
7565 # Register _SPSFTL in _IMP_atom:
7566 _IMP_atom._SPSFTL_swigregister(_SPSFTL)
7567 class ProteinLigandAtomPairScore(_SPSTF):
7568  r"""Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7569 
7570  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7571 
7572  def __init__(self, *args):
7573  r"""
7574  __init__(ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
7575  __init__(ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7576  """
7577  _IMP_atom.ProteinLigandAtomPairScore_swiginit(self, _IMP_atom.new_ProteinLigandAtomPairScore(*args))
7578 
7579  def get_maximum_distance(self):
7580  r"""get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7581  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7582 
7583  def __str__(self):
7584  r"""__str__(ProteinLigandAtomPairScore self) -> std::string"""
7585  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7586 
7587  def __repr__(self):
7588  r"""__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7589  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7590 
7591  @staticmethod
7592  def get_from(o):
7593  return _object_cast_to_ProteinLigandAtomPairScore(o)
7594 
7595  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7596 
7597 # Register ProteinLigandAtomPairScore in _IMP_atom:
7598 _IMP_atom.ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7599 class ProteinLigandRestraint(IMP.container.PairsRestraint):
7600  r"""Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7601 
7602  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7603 
7604  def __init__(self, *args):
7605  r"""
7606  __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
7607  __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7608  """
7609  _IMP_atom.ProteinLigandRestraint_swiginit(self, _IMP_atom.new_ProteinLigandRestraint(*args))
7610 
7611  def __str__(self):
7612  r"""__str__(ProteinLigandRestraint self) -> std::string"""
7613  return _IMP_atom.ProteinLigandRestraint___str__(self)
7614 
7615  def __repr__(self):
7616  r"""__repr__(ProteinLigandRestraint self) -> std::string"""
7617  return _IMP_atom.ProteinLigandRestraint___repr__(self)
7618 
7619  @staticmethod
7620  def get_from(o):
7621  return _object_cast_to_ProteinLigandRestraint(o)
7622 
7623  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7624 
7625 # Register ProteinLigandRestraint in _IMP_atom:
7626 _IMP_atom.ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7627 
7629  r"""add_protein_ligand_score_data(Hierarchy h)"""
7630  return _IMP_atom.add_protein_ligand_score_data(h)
7631 class AtomType(IMP._Value):
7632  r"""Proxy of C++ IMP::Key< 8974343 > class."""
7633 
7634  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7635 
7636  def __init__(self, *args):
7637  r"""
7638  __init__(AtomType self) -> AtomType
7639  __init__(AtomType self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7640  __init__(AtomType self, unsigned int i) -> AtomType
7641  """
7642  _IMP_atom.AtomType_swiginit(self, _IMP_atom.new_AtomType(*args))
7643 
7644  @staticmethod
7645  def add_key(sc):
7646  r"""add_key(std::string sc) -> unsigned int"""
7647  return _IMP_atom.AtomType_add_key(sc)
7648 
7649  @staticmethod
7650  def get_key_exists(sc):
7651  r"""get_key_exists(std::string sc) -> bool"""
7652  return _IMP_atom.AtomType_get_key_exists(sc)
7653 
7654  def get_string(self):
7655  r"""get_string(AtomType self) -> std::string const"""
7656  return _IMP_atom.AtomType_get_string(self)
7657 
7658  def __cmp__(self, o):
7659  r"""__cmp__(AtomType self, AtomType o) -> int"""
7660  return _IMP_atom.AtomType___cmp__(self, o)
7661 
7662  def __eq__(self, o):
7663  r"""__eq__(AtomType self, AtomType o) -> bool"""
7664  return _IMP_atom.AtomType___eq__(self, o)
7665 
7666  def __ne__(self, o):
7667  r"""__ne__(AtomType self, AtomType o) -> bool"""
7668  return _IMP_atom.AtomType___ne__(self, o)
7669 
7670  def __lt__(self, o):
7671  r"""__lt__(AtomType self, AtomType o) -> bool"""
7672  return _IMP_atom.AtomType___lt__(self, o)
7673 
7674  def __gt__(self, o):
7675  r"""__gt__(AtomType self, AtomType o) -> bool"""
7676  return _IMP_atom.AtomType___gt__(self, o)
7677 
7678  def __ge__(self, o):
7679  r"""__ge__(AtomType self, AtomType o) -> bool"""
7680  return _IMP_atom.AtomType___ge__(self, o)
7681 
7682  def __le__(self, o):
7683  r"""__le__(AtomType self, AtomType o) -> bool"""
7684  return _IMP_atom.AtomType___le__(self, o)
7685 
7686  def __hash__(self):
7687  r"""__hash__(AtomType self) -> std::size_t"""
7688  return _IMP_atom.AtomType___hash__(self)
7689 
7690  def show(self, *args):
7691  r"""show(AtomType self, _ostream out=std::cout)"""
7692  return _IMP_atom.AtomType_show(self, *args)
7693 
7694  @staticmethod
7695  def add_alias(old_key, new_name):
7696  r"""add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7697  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7698 
7699  @staticmethod
7700  def get_number_of_keys():
7701  r"""get_number_of_keys() -> unsigned int"""
7702  return _IMP_atom.AtomType_get_number_of_keys()
7703 
7704  def get_index(self):
7705  r"""get_index(AtomType self) -> unsigned int"""
7706  return _IMP_atom.AtomType_get_index(self)
7707 
7708  @staticmethod
7709  def show_all(out):
7710  r"""show_all(_ostream out)"""
7711  return _IMP_atom.AtomType_show_all(out)
7712 
7713  @staticmethod
7714  def get_all_strings():
7715  r"""get_all_strings() -> IMP::Vector< std::string >"""
7716  return _IMP_atom.AtomType_get_all_strings()
7717 
7718  @staticmethod
7719  def get_number_unique():
7720  r"""get_number_unique() -> unsigned int"""
7721  return _IMP_atom.AtomType_get_number_unique()
7722 
7723  def __str__(self):
7724  r"""__str__(AtomType self) -> std::string"""
7725  return _IMP_atom.AtomType___str__(self)
7726 
7727  def __repr__(self):
7728  r"""__repr__(AtomType self) -> std::string"""
7729  return _IMP_atom.AtomType___repr__(self)
7730  __swig_destroy__ = _IMP_atom.delete_AtomType
7731 
7732 # Register AtomType in _IMP_atom:
7733 _IMP_atom.AtomType_swigregister(AtomType)
7734 class ResidueType(IMP._Value):
7735  r"""Proxy of C++ IMP::Key< 90784334 > class."""
7736 
7737  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7738 
7739  def __init__(self, *args):
7740  r"""
7741  __init__(ResidueType self) -> ResidueType
7742  __init__(ResidueType self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7743  __init__(ResidueType self, unsigned int i) -> ResidueType
7744  """
7745  _IMP_atom.ResidueType_swiginit(self, _IMP_atom.new_ResidueType(*args))
7746 
7747  @staticmethod
7748  def add_key(sc):
7749  r"""add_key(std::string sc) -> unsigned int"""
7750  return _IMP_atom.ResidueType_add_key(sc)
7751 
7752  @staticmethod
7753  def get_key_exists(sc):
7754  r"""get_key_exists(std::string sc) -> bool"""
7755  return _IMP_atom.ResidueType_get_key_exists(sc)
7756 
7757  def get_string(self):
7758  r"""get_string(ResidueType self) -> std::string const"""
7759  return _IMP_atom.ResidueType_get_string(self)
7760 
7761  def __cmp__(self, o):
7762  r"""__cmp__(ResidueType self, ResidueType o) -> int"""
7763  return _IMP_atom.ResidueType___cmp__(self, o)
7764 
7765  def __eq__(self, o):
7766  r"""__eq__(ResidueType self, ResidueType o) -> bool"""
7767  return _IMP_atom.ResidueType___eq__(self, o)
7768 
7769  def __ne__(self, o):
7770  r"""__ne__(ResidueType self, ResidueType o) -> bool"""
7771  return _IMP_atom.ResidueType___ne__(self, o)
7772 
7773  def __lt__(self, o):
7774  r"""__lt__(ResidueType self, ResidueType o) -> bool"""
7775  return _IMP_atom.ResidueType___lt__(self, o)
7776 
7777  def __gt__(self, o):
7778  r"""__gt__(ResidueType self, ResidueType o) -> bool"""
7779  return _IMP_atom.ResidueType___gt__(self, o)
7780 
7781  def __ge__(self, o):
7782  r"""__ge__(ResidueType self, ResidueType o) -> bool"""
7783  return _IMP_atom.ResidueType___ge__(self, o)
7784 
7785  def __le__(self, o):
7786  r"""__le__(ResidueType self, ResidueType o) -> bool"""
7787  return _IMP_atom.ResidueType___le__(self, o)
7788 
7789  def __hash__(self):
7790  r"""__hash__(ResidueType self) -> std::size_t"""
7791  return _IMP_atom.ResidueType___hash__(self)
7792 
7793  def show(self, *args):
7794  r"""show(ResidueType self, _ostream out=std::cout)"""
7795  return _IMP_atom.ResidueType_show(self, *args)
7796 
7797  @staticmethod
7798  def add_alias(old_key, new_name):
7799  r"""add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7800  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7801 
7802  @staticmethod
7803  def get_number_of_keys():
7804  r"""get_number_of_keys() -> unsigned int"""
7805  return _IMP_atom.ResidueType_get_number_of_keys()
7806 
7807  def get_index(self):
7808  r"""get_index(ResidueType self) -> unsigned int"""
7809  return _IMP_atom.ResidueType_get_index(self)
7810 
7811  @staticmethod
7812  def show_all(out):
7813  r"""show_all(_ostream out)"""
7814  return _IMP_atom.ResidueType_show_all(out)
7815 
7816  @staticmethod
7817  def get_all_strings():
7818  r"""get_all_strings() -> IMP::Vector< std::string >"""
7819  return _IMP_atom.ResidueType_get_all_strings()
7820 
7821  @staticmethod
7822  def get_number_unique():
7823  r"""get_number_unique() -> unsigned int"""
7824  return _IMP_atom.ResidueType_get_number_unique()
7825 
7826  def __str__(self):
7827  r"""__str__(ResidueType self) -> std::string"""
7828  return _IMP_atom.ResidueType___str__(self)
7829 
7830  def __repr__(self):
7831  r"""__repr__(ResidueType self) -> std::string"""
7832  return _IMP_atom.ResidueType___repr__(self)
7833  __swig_destroy__ = _IMP_atom.delete_ResidueType
7834 
7835 # Register ResidueType in _IMP_atom:
7836 _IMP_atom.ResidueType_swigregister(ResidueType)
7837 class ChainType(IMP._Value):
7838  r"""Proxy of C++ IMP::Key< 90784336 > class."""
7839 
7840  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7841 
7842  def __init__(self, *args):
7843  r"""
7844  __init__(ChainType self) -> ChainType
7845  __init__(ChainType self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
7846  __init__(ChainType self, unsigned int i) -> ChainType
7847  """
7848  _IMP_atom.ChainType_swiginit(self, _IMP_atom.new_ChainType(*args))
7849 
7850  @staticmethod
7851  def add_key(sc):
7852  r"""add_key(std::string sc) -> unsigned int"""
7853  return _IMP_atom.ChainType_add_key(sc)
7854 
7855  @staticmethod
7856  def get_key_exists(sc):
7857  r"""get_key_exists(std::string sc) -> bool"""
7858  return _IMP_atom.ChainType_get_key_exists(sc)
7859 
7860  def get_string(self):
7861  r"""get_string(ChainType self) -> std::string const"""
7862  return _IMP_atom.ChainType_get_string(self)
7863 
7864  def __cmp__(self, o):
7865  r"""__cmp__(ChainType self, ChainType o) -> int"""
7866  return _IMP_atom.ChainType___cmp__(self, o)
7867 
7868  def __eq__(self, o):
7869  r"""__eq__(ChainType self, ChainType o) -> bool"""
7870  return _IMP_atom.ChainType___eq__(self, o)
7871 
7872  def __ne__(self, o):
7873  r"""__ne__(ChainType self, ChainType o) -> bool"""
7874  return _IMP_atom.ChainType___ne__(self, o)
7875 
7876  def __lt__(self, o):
7877  r"""__lt__(ChainType self, ChainType o) -> bool"""
7878  return _IMP_atom.ChainType___lt__(self, o)
7879 
7880  def __gt__(self, o):
7881  r"""__gt__(ChainType self, ChainType o) -> bool"""
7882  return _IMP_atom.ChainType___gt__(self, o)
7883 
7884  def __ge__(self, o):
7885  r"""__ge__(ChainType self, ChainType o) -> bool"""
7886  return _IMP_atom.ChainType___ge__(self, o)
7887 
7888  def __le__(self, o):
7889  r"""__le__(ChainType self, ChainType o) -> bool"""
7890  return _IMP_atom.ChainType___le__(self, o)
7891 
7892  def __hash__(self):
7893  r"""__hash__(ChainType self) -> std::size_t"""
7894  return _IMP_atom.ChainType___hash__(self)
7895 
7896  def show(self, *args):
7897  r"""show(ChainType self, _ostream out=std::cout)"""
7898  return _IMP_atom.ChainType_show(self, *args)
7899 
7900  @staticmethod
7901  def add_alias(old_key, new_name):
7902  r"""add_alias(ChainType old_key, std::string new_name) -> ChainType"""
7903  return _IMP_atom.ChainType_add_alias(old_key, new_name)
7904 
7905  @staticmethod
7906  def get_number_of_keys():
7907  r"""get_number_of_keys() -> unsigned int"""
7908  return _IMP_atom.ChainType_get_number_of_keys()
7909 
7910  def get_index(self):
7911  r"""get_index(ChainType self) -> unsigned int"""
7912  return _IMP_atom.ChainType_get_index(self)
7913 
7914  @staticmethod
7915  def show_all(out):
7916  r"""show_all(_ostream out)"""
7917  return _IMP_atom.ChainType_show_all(out)
7918 
7919  @staticmethod
7920  def get_all_strings():
7921  r"""get_all_strings() -> IMP::Vector< std::string >"""
7922  return _IMP_atom.ChainType_get_all_strings()
7923 
7924  @staticmethod
7925  def get_number_unique():
7926  r"""get_number_unique() -> unsigned int"""
7927  return _IMP_atom.ChainType_get_number_unique()
7928 
7929  def __str__(self):
7930  r"""__str__(ChainType self) -> std::string"""
7931  return _IMP_atom.ChainType___str__(self)
7932 
7933  def __repr__(self):
7934  r"""__repr__(ChainType self) -> std::string"""
7935  return _IMP_atom.ChainType___repr__(self)
7936  __swig_destroy__ = _IMP_atom.delete_ChainType
7937 
7938 # Register ChainType in _IMP_atom:
7939 _IMP_atom.ChainType_swigregister(ChainType)
7940 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
7941 
7942 OH = _IMP_atom.OH
7943 
7944 H2O = _IMP_atom.H2O
7945 
7946 H = _IMP_atom.H
7947 
7948 He = _IMP_atom.He
7949 
7950 Li = _IMP_atom.Li
7951 
7952 Be = _IMP_atom.Be
7953 
7954 B = _IMP_atom.B
7955 
7956 C = _IMP_atom.C
7957 
7958 N = _IMP_atom.N
7959 
7960 O = _IMP_atom.O
7961 
7962 F = _IMP_atom.F
7963 
7964 Ne = _IMP_atom.Ne
7965 
7966 Na = _IMP_atom.Na
7967 
7968 Mg = _IMP_atom.Mg
7969 
7970 Al = _IMP_atom.Al
7971 
7972 Si = _IMP_atom.Si
7973 
7974 P = _IMP_atom.P
7975 
7976 S = _IMP_atom.S
7977 
7978 Cl = _IMP_atom.Cl
7979 
7980 Ar = _IMP_atom.Ar
7981 
7982 K = _IMP_atom.K
7983 
7984 Ca = _IMP_atom.Ca
7985 
7986 Sc = _IMP_atom.Sc
7987 
7988 Ti = _IMP_atom.Ti
7989 
7990 V = _IMP_atom.V
7991 
7992 Cr = _IMP_atom.Cr
7993 
7994 Mn = _IMP_atom.Mn
7995 
7996 Fe = _IMP_atom.Fe
7997 
7998 Co = _IMP_atom.Co
7999 
8000 Ni = _IMP_atom.Ni
8001 
8002 Cu = _IMP_atom.Cu
8003 
8004 Zn = _IMP_atom.Zn
8005 
8006 Ga = _IMP_atom.Ga
8007 
8008 Ge = _IMP_atom.Ge
8009 
8010 As = _IMP_atom.As
8011 
8012 Se = _IMP_atom.Se
8013 
8014 Br = _IMP_atom.Br
8015 
8016 Kr = _IMP_atom.Kr
8017 
8018 Rb = _IMP_atom.Rb
8019 
8020 Sr = _IMP_atom.Sr
8021 
8022 Y = _IMP_atom.Y
8023 
8024 Zr = _IMP_atom.Zr
8025 
8026 Nb = _IMP_atom.Nb
8027 
8028 Mo = _IMP_atom.Mo
8029 
8030 Tc = _IMP_atom.Tc
8031 
8032 Ru = _IMP_atom.Ru
8033 
8034 Rh = _IMP_atom.Rh
8035 
8036 Pd = _IMP_atom.Pd
8037 
8038 Ag = _IMP_atom.Ag
8039 
8040 Cd = _IMP_atom.Cd
8041 
8042 In = _IMP_atom.In
8043 
8044 Sn = _IMP_atom.Sn
8045 
8046 Sb = _IMP_atom.Sb
8047 
8048 Te = _IMP_atom.Te
8049 
8050 I = _IMP_atom.I
8051 
8052 Xe = _IMP_atom.Xe
8053 
8054 Cs = _IMP_atom.Cs
8055 
8056 Ba = _IMP_atom.Ba
8057 
8058 La = _IMP_atom.La
8059 
8060 Ce = _IMP_atom.Ce
8061 
8062 Pr = _IMP_atom.Pr
8063 
8064 Nd = _IMP_atom.Nd
8065 
8066 Pm = _IMP_atom.Pm
8067 
8068 Sm = _IMP_atom.Sm
8069 
8070 Eu = _IMP_atom.Eu
8071 
8072 Gd = _IMP_atom.Gd
8073 
8074 Tb = _IMP_atom.Tb
8075 
8076 Dy = _IMP_atom.Dy
8077 
8078 Ho = _IMP_atom.Ho
8079 
8080 Er = _IMP_atom.Er
8081 
8082 Tm = _IMP_atom.Tm
8083 
8084 Yb = _IMP_atom.Yb
8085 
8086 Lu = _IMP_atom.Lu
8087 
8088 Hf = _IMP_atom.Hf
8089 
8090 Ta = _IMP_atom.Ta
8091 
8092 W = _IMP_atom.W
8093 
8094 Re = _IMP_atom.Re
8095 
8096 Os = _IMP_atom.Os
8097 
8098 Ir = _IMP_atom.Ir
8099 
8100 Pt = _IMP_atom.Pt
8101 
8102 Au = _IMP_atom.Au
8103 
8104 Hg = _IMP_atom.Hg
8105 
8106 Tl = _IMP_atom.Tl
8107 
8108 Pb = _IMP_atom.Pb
8109 
8110 Bi = _IMP_atom.Bi
8111 
8112 Po = _IMP_atom.Po
8113 
8114 At = _IMP_atom.At
8115 
8116 Rn = _IMP_atom.Rn
8117 
8118 Fr = _IMP_atom.Fr
8119 
8120 Ra = _IMP_atom.Ra
8121 
8122 Ac = _IMP_atom.Ac
8123 
8124 Th = _IMP_atom.Th
8125 
8126 Pa = _IMP_atom.Pa
8127 
8128 U = _IMP_atom.U
8129 
8130 Np = _IMP_atom.Np
8131 
8132 Pu = _IMP_atom.Pu
8133 
8134 Am = _IMP_atom.Am
8135 
8136 Cm = _IMP_atom.Cm
8137 
8138 Bk = _IMP_atom.Bk
8139 
8140 Cf = _IMP_atom.Cf
8141 
8142 Es = _IMP_atom.Es
8143 
8144 Fm = _IMP_atom.Fm
8145 
8146 Md = _IMP_atom.Md
8147 
8148 No = _IMP_atom.No
8149 
8150 Lr = _IMP_atom.Lr
8151 
8152 Db = _IMP_atom.Db
8153 
8154 Jl = _IMP_atom.Jl
8155 
8156 Rf = _IMP_atom.Rf
8157 
8158 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8159 
8160 
8161 def hash_value(e):
8162  r"""hash_value(IMP::atom::Element e) -> size_t"""
8163  return _IMP_atom.hash_value(e)
8164 class ElementTable(object):
8165  r"""Proxy of C++ IMP::atom::ElementTable class."""
8166 
8167  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8168  __repr__ = _swig_repr
8169 
8170  def __init__(self):
8171  r"""__init__(ElementTable self) -> ElementTable"""
8172  _IMP_atom.ElementTable_swiginit(self, _IMP_atom.new_ElementTable())
8173 
8174  def get_element(self, s):
8175  r"""get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8176  return _IMP_atom.ElementTable_get_element(self, s)
8177 
8178  def get_name(self, e):
8179  r"""get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8180  return _IMP_atom.ElementTable_get_name(self, e)
8181 
8182  def get_mass(self, e):
8183  r"""get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8184  return _IMP_atom.ElementTable_get_mass(self, e)
8185  __swig_destroy__ = _IMP_atom.delete_ElementTable
8186 
8187 # Register ElementTable in _IMP_atom:
8188 _IMP_atom.ElementTable_swigregister(ElementTable)
8189 
8190 def get_element_table():
8191  r"""get_element_table() -> ElementTable"""
8192  return _IMP_atom.get_element_table()
8193 class Atom(Hierarchy):
8194  r"""Proxy of C++ IMP::atom::Atom class."""
8195 
8196  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8197 
8198  def __init__(self, *args):
8199  r"""
8200  __init__(Atom self) -> Atom
8201  __init__(Atom self, Model m, ParticleIndex id) -> Atom
8202  __init__(Atom self, _ParticleAdaptor d) -> Atom
8203  """
8204  _IMP_atom.Atom_swiginit(self, _IMP_atom.new_Atom(*args))
8205 
8206  def show(self, *args):
8207  r"""show(Atom self, _ostream out=std::cout)"""
8208  return _IMP_atom.Atom_show(self, *args)
8209 
8210  @staticmethod
8211  def setup_particle(*args):
8212  r"""
8213  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8214  setup_particle(_ParticleAdaptor pa, Atom other) -> Atom
8215  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8216  setup_particle(_ParticleAdaptor pa, AtomType atom_type) -> Atom
8217  """
8218  return _IMP_atom.Atom_setup_particle(*args)
8219 
8220  @staticmethod
8221  def get_is_setup(*args):
8222  r"""
8223  get_is_setup(_ParticleAdaptor p) -> bool
8224  get_is_setup(Model m, ParticleIndex pi) -> bool
8225  """
8226  return _IMP_atom.Atom_get_is_setup(*args)
8227 
8228  def get_atom_type(self):
8229  r"""get_atom_type(Atom self) -> AtomType"""
8230  return _IMP_atom.Atom_get_atom_type(self)
8231 
8232  def set_atom_type(self, t):
8233  r"""set_atom_type(Atom self, AtomType t)"""
8234  return _IMP_atom.Atom_set_atom_type(self, t)
8235 
8236  def get_element(self):
8237  r"""get_element(Atom self) -> IMP::atom::Element"""
8238  return _IMP_atom.Atom_get_element(self)
8239 
8240  def set_element(self, e):
8241  r"""set_element(Atom self, IMP::atom::Element e)"""
8242  return _IMP_atom.Atom_set_element(self, e)
8243 
8244  def get_occupancy(self):
8245  r"""get_occupancy(Atom self) -> double"""
8246  return _IMP_atom.Atom_get_occupancy(self)
8247 
8248  def set_occupancy(self, occupancy):
8249  r"""set_occupancy(Atom self, double occupancy)"""
8250  return _IMP_atom.Atom_set_occupancy(self, occupancy)
8251 
8252  def get_temperature_factor(self):
8253  r"""get_temperature_factor(Atom self) -> double"""
8254  return _IMP_atom.Atom_get_temperature_factor(self)
8255 
8256  def set_temperature_factor(self, tempFactor):
8257  r"""set_temperature_factor(Atom self, double tempFactor)"""
8258  return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8259 
8260  def get_input_index(self):
8261  r"""get_input_index(Atom self) -> IMP::Int"""
8262  return _IMP_atom.Atom_get_input_index(self)
8263 
8264  def set_input_index(self, t):
8265  r"""set_input_index(Atom self, IMP::Int t)"""
8266  return _IMP_atom.Atom_set_input_index(self, t)
8267 
8268  @staticmethod
8269  def get_atom_type_key():
8270  r"""get_atom_type_key() -> IntKey"""
8271  return _IMP_atom.Atom_get_atom_type_key()
8272 
8273  @staticmethod
8274  def get_element_key():
8275  r"""get_element_key() -> IntKey"""
8276  return _IMP_atom.Atom_get_element_key()
8277 
8278  @staticmethod
8279  def get_input_index_key():
8280  r"""get_input_index_key() -> IntKey"""
8281  return _IMP_atom.Atom_get_input_index_key()
8282 
8283  @staticmethod
8284  def get_occupancy_key():
8285  r"""get_occupancy_key() -> FloatKey"""
8286  return _IMP_atom.Atom_get_occupancy_key()
8287 
8288  @staticmethod
8289  def get_temperature_factor_key():
8290  r"""get_temperature_factor_key() -> FloatKey"""
8291  return _IMP_atom.Atom_get_temperature_factor_key()
8292 
8293  def add_attribute(self, *args):
8294  r"""
8295  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8296  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8297  add_attribute(Atom self, IntKey a0, IMP::Int a1)
8298  add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
8299  add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
8300  add_attribute(Atom self, StringKey a0, IMP::String a1)
8301  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8302  add_attribute(Atom self, ObjectKey a0, Object a1)
8303  add_attribute(Atom self, SparseFloatKey a0, IMP::Float a1)
8304  add_attribute(Atom self, SparseIntKey a0, IMP::Int a1)
8305  add_attribute(Atom self, SparseStringKey a0, IMP::String a1)
8306  add_attribute(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
8307  """
8308  return _IMP_atom.Atom_add_attribute(self, *args)
8309 
8310  def get_value(self, *args):
8311  r"""
8312  get_value(Atom self, FloatKey a0) -> IMP::Float
8313  get_value(Atom self, IntKey a0) -> IMP::Int
8314  get_value(Atom self, FloatsKey a0) -> IMP::Floats
8315  get_value(Atom self, IntsKey a0) -> IMP::Ints
8316  get_value(Atom self, StringKey a0) -> IMP::String
8317  get_value(Atom self, ParticleIndexKey a0) -> Particle
8318  get_value(Atom self, ObjectKey a0) -> Object
8319  get_value(Atom self, SparseFloatKey a0) -> IMP::Float
8320  get_value(Atom self, SparseIntKey a0) -> IMP::Int
8321  get_value(Atom self, SparseStringKey a0) -> IMP::String
8322  get_value(Atom self, SparseParticleIndexKey a0) -> ParticleIndex
8323  """
8324  return _IMP_atom.Atom_get_value(self, *args)
8325 
8326  def set_value(self, *args):
8327  r"""
8328  set_value(Atom self, FloatKey a0, IMP::Float a1)
8329  set_value(Atom self, IntKey a0, IMP::Int a1)
8330  set_value(Atom self, FloatsKey a0, IMP::Floats a1)
8331  set_value(Atom self, IntsKey a0, IMP::Ints a1)
8332  set_value(Atom self, StringKey a0, IMP::String a1)
8333  set_value(Atom self, ParticleIndexKey a0, Particle a1)
8334  set_value(Atom self, ObjectKey a0, Object a1)
8335  set_value(Atom self, SparseFloatKey a0, IMP::Float a1)
8336  set_value(Atom self, SparseIntKey a0, IMP::Int a1)
8337  set_value(Atom self, SparseStringKey a0, IMP::String a1)
8338  set_value(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
8339  """
8340  return _IMP_atom.Atom_set_value(self, *args)
8341 
8342  def remove_attribute(self, *args):
8343  r"""
8344  remove_attribute(Atom self, FloatKey a0)
8345  remove_attribute(Atom self, IntKey a0)
8346  remove_attribute(Atom self, FloatsKey a0)
8347  remove_attribute(Atom self, IntsKey a0)
8348  remove_attribute(Atom self, StringKey a0)
8349  remove_attribute(Atom self, ParticleIndexKey a0)
8350  remove_attribute(Atom self, ObjectKey a0)
8351  remove_attribute(Atom self, SparseFloatKey a0)
8352  remove_attribute(Atom self, SparseIntKey a0)
8353  remove_attribute(Atom self, SparseStringKey a0)
8354  remove_attribute(Atom self, SparseParticleIndexKey a0)
8355  """
8356  return _IMP_atom.Atom_remove_attribute(self, *args)
8357 
8358  def has_attribute(self, *args):
8359  r"""
8360  has_attribute(Atom self, FloatKey a0) -> bool
8361  has_attribute(Atom self, IntKey a0) -> bool
8362  has_attribute(Atom self, FloatsKey a0) -> bool
8363  has_attribute(Atom self, IntsKey a0) -> bool
8364  has_attribute(Atom self, StringKey a0) -> bool
8365  has_attribute(Atom self, ParticleIndexKey a0) -> bool
8366  has_attribute(Atom self, ObjectKey a0) -> bool
8367  has_attribute(Atom self, SparseFloatKey a0) -> bool
8368  has_attribute(Atom self, SparseIntKey a0) -> bool
8369  has_attribute(Atom self, SparseStringKey a0) -> bool
8370  has_attribute(Atom self, SparseParticleIndexKey a0) -> bool
8371  """
8372  return _IMP_atom.Atom_has_attribute(self, *args)
8373 
8374  def get_derivative(self, a0):
8375  r"""get_derivative(Atom self, FloatKey a0) -> double"""
8376  return _IMP_atom.Atom_get_derivative(self, a0)
8377 
8378  def get_name(self):
8379  r"""get_name(Atom self) -> std::string"""
8380  return _IMP_atom.Atom_get_name(self)
8381 
8382  def clear_caches(self):
8383  r"""clear_caches(Atom self)"""
8384  return _IMP_atom.Atom_clear_caches(self)
8385 
8386  def set_name(self, a0):
8387  r"""set_name(Atom self, std::string a0)"""
8388  return _IMP_atom.Atom_set_name(self, a0)
8389 
8390  def set_check_level(self, a0):
8391  r"""set_check_level(Atom self, IMP::CheckLevel a0)"""
8392  return _IMP_atom.Atom_set_check_level(self, a0)
8393 
8394  def add_to_derivative(self, a0, a1, a2):
8395  r"""add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8396  return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8397 
8398  def set_is_optimized(self, a0, a1):
8399  r"""set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8400  return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8401 
8402  def get_is_optimized(self, a0):
8403  r"""get_is_optimized(Atom self, FloatKey a0) -> bool"""
8404  return _IMP_atom.Atom_get_is_optimized(self, a0)
8405 
8406  def get_check_level(self):
8407  r"""get_check_level(Atom self) -> IMP::CheckLevel"""
8408  return _IMP_atom.Atom_get_check_level(self)
8409 
8410  def __eq__(self, *args):
8411  r"""
8412  __eq__(Atom self, Atom o) -> bool
8413  __eq__(Atom self, Particle d) -> bool
8414  """
8415  return _IMP_atom.Atom___eq__(self, *args)
8416 
8417  def __ne__(self, *args):
8418  r"""
8419  __ne__(Atom self, Atom o) -> bool
8420  __ne__(Atom self, Particle d) -> bool
8421  """
8422  return _IMP_atom.Atom___ne__(self, *args)
8423 
8424  def __le__(self, *args):
8425  r"""
8426  __le__(Atom self, Atom o) -> bool
8427  __le__(Atom self, Particle d) -> bool
8428  """
8429  return _IMP_atom.Atom___le__(self, *args)
8430 
8431  def __lt__(self, *args):
8432  r"""
8433  __lt__(Atom self, Atom o) -> bool
8434  __lt__(Atom self, Particle d) -> bool
8435  """
8436  return _IMP_atom.Atom___lt__(self, *args)
8437 
8438  def __ge__(self, *args):
8439  r"""
8440  __ge__(Atom self, Atom o) -> bool
8441  __ge__(Atom self, Particle d) -> bool
8442  """
8443  return _IMP_atom.Atom___ge__(self, *args)
8444 
8445  def __gt__(self, *args):
8446  r"""
8447  __gt__(Atom self, Atom o) -> bool
8448  __gt__(Atom self, Particle d) -> bool
8449  """
8450  return _IMP_atom.Atom___gt__(self, *args)
8451 
8452  def __hash__(self):
8453  r"""__hash__(Atom self) -> std::size_t"""
8454  return _IMP_atom.Atom___hash__(self)
8455 
8456  def __str__(self):
8457  r"""__str__(Atom self) -> std::string"""
8458  return _IMP_atom.Atom___str__(self)
8459 
8460  def __repr__(self):
8461  r"""__repr__(Atom self) -> std::string"""
8462  return _IMP_atom.Atom___repr__(self)
8463 
8464  def _get_as_binary(self):
8465  r"""_get_as_binary(Atom self) -> PyObject *"""
8466  return _IMP_atom.Atom__get_as_binary(self)
8467 
8468  def _set_from_binary(self, p):
8469  r"""_set_from_binary(Atom self, PyObject * p)"""
8470  return _IMP_atom.Atom__set_from_binary(self, p)
8471 
8472  def __getstate__(self):
8473  p = self._get_as_binary()
8474  if len(self.__dict__) > 1:
8475  d = self.__dict__.copy()
8476  del d['this']
8477  p = (d, p)
8478  return p
8479 
8480  def __setstate__(self, p):
8481  if not hasattr(self, 'this'):
8482  self.__init__()
8483  if isinstance(p, tuple):
8484  d, p = p
8485  self.__dict__.update(d)
8486  return self._set_from_binary(p)
8487 
8488  __swig_destroy__ = _IMP_atom.delete_Atom
8489 
8490 # Register Atom in _IMP_atom:
8491 _IMP_atom.Atom_swigregister(Atom)
8492 cvar = _IMP_atom.cvar
8493 AT_UNKNOWN = cvar.AT_UNKNOWN
8494 AT_N = cvar.AT_N
8495 AT_CA = cvar.AT_CA
8496 AT_C = cvar.AT_C
8497 AT_O = cvar.AT_O
8498 AT_H = cvar.AT_H
8499 AT_H1 = cvar.AT_H1
8500 AT_H2 = cvar.AT_H2
8501 AT_H3 = cvar.AT_H3
8502 AT_HA = cvar.AT_HA
8503 AT_HA1 = cvar.AT_HA1
8504 AT_HA2 = cvar.AT_HA2
8505 AT_HA3 = cvar.AT_HA3
8506 AT_CB = cvar.AT_CB
8507 AT_HB = cvar.AT_HB
8508 AT_HB1 = cvar.AT_HB1
8509 AT_HB2 = cvar.AT_HB2
8510 AT_HB3 = cvar.AT_HB3
8511 AT_OXT = cvar.AT_OXT
8512 AT_CH3 = cvar.AT_CH3
8513 AT_CH = cvar.AT_CH
8514 AT_CG = cvar.AT_CG
8515 AT_CG1 = cvar.AT_CG1
8516 AT_CG2 = cvar.AT_CG2
8517 AT_HG = cvar.AT_HG
8518 AT_HG1 = cvar.AT_HG1
8519 AT_HG2 = cvar.AT_HG2
8520 AT_HG3 = cvar.AT_HG3
8521 AT_HG11 = cvar.AT_HG11
8522 AT_HG21 = cvar.AT_HG21
8523 AT_HG31 = cvar.AT_HG31
8524 AT_HG12 = cvar.AT_HG12
8525 AT_HG13 = cvar.AT_HG13
8526 AT_HG22 = cvar.AT_HG22
8527 AT_HG23 = cvar.AT_HG23
8528 AT_HG32 = cvar.AT_HG32
8529 AT_OG = cvar.AT_OG
8530 AT_OG1 = cvar.AT_OG1
8531 AT_SG = cvar.AT_SG
8532 AT_CD = cvar.AT_CD
8533 AT_CD1 = cvar.AT_CD1
8534 AT_CD2 = cvar.AT_CD2
8535 AT_HD = cvar.AT_HD
8536 AT_HD1 = cvar.AT_HD1
8537 AT_HD2 = cvar.AT_HD2
8538 AT_HD3 = cvar.AT_HD3
8539 AT_HD11 = cvar.AT_HD11
8540 AT_HD21 = cvar.AT_HD21
8541 AT_HD31 = cvar.AT_HD31
8542 AT_HD12 = cvar.AT_HD12
8543 AT_HD13 = cvar.AT_HD13
8544 AT_HD22 = cvar.AT_HD22
8545 AT_HD23 = cvar.AT_HD23
8546 AT_HD32 = cvar.AT_HD32
8547 AT_SD = cvar.AT_SD
8548 AT_OD1 = cvar.AT_OD1
8549 AT_OD2 = cvar.AT_OD2
8550 AT_ND1 = cvar.AT_ND1
8551 AT_ND2 = cvar.AT_ND2
8552 AT_CE = cvar.AT_CE
8553 AT_CE1 = cvar.AT_CE1
8554 AT_CE2 = cvar.AT_CE2
8555 AT_CE3 = cvar.AT_CE3
8556 AT_HE = cvar.AT_HE
8557 AT_HE1 = cvar.AT_HE1
8558 AT_HE2 = cvar.AT_HE2
8559 AT_HE3 = cvar.AT_HE3
8560 AT_HE21 = cvar.AT_HE21
8561 AT_HE22 = cvar.AT_HE22
8562 AT_OE1 = cvar.AT_OE1
8563 AT_OE2 = cvar.AT_OE2
8564 AT_NE = cvar.AT_NE
8565 AT_NE1 = cvar.AT_NE1
8566 AT_NE2 = cvar.AT_NE2
8567 AT_CZ = cvar.AT_CZ
8568 AT_CZ2 = cvar.AT_CZ2
8569 AT_CZ3 = cvar.AT_CZ3
8570 AT_NZ = cvar.AT_NZ
8571 AT_HZ = cvar.AT_HZ
8572 AT_HZ1 = cvar.AT_HZ1
8573 AT_HZ2 = cvar.AT_HZ2
8574 AT_HZ3 = cvar.AT_HZ3
8575 AT_CH2 = cvar.AT_CH2
8576 AT_NH1 = cvar.AT_NH1
8577 AT_NH2 = cvar.AT_NH2
8578 AT_OH = cvar.AT_OH
8579 AT_HH = cvar.AT_HH
8580 AT_HH11 = cvar.AT_HH11
8581 AT_HH21 = cvar.AT_HH21
8582 AT_HH2 = cvar.AT_HH2
8583 AT_HH12 = cvar.AT_HH12
8584 AT_HH22 = cvar.AT_HH22
8585 AT_HH13 = cvar.AT_HH13
8586 AT_HH23 = cvar.AT_HH23
8587 AT_HH33 = cvar.AT_HH33
8588 AT_P = cvar.AT_P
8589 AT_OP1 = cvar.AT_OP1
8590 AT_OP2 = cvar.AT_OP2
8591 AT_OP3 = cvar.AT_OP3
8592 AT_O5p = cvar.AT_O5p
8593 AT_C5p = cvar.AT_C5p
8594 AT_H5p = cvar.AT_H5p
8595 AT_H5pp = cvar.AT_H5pp
8596 AT_C4p = cvar.AT_C4p
8597 AT_H4p = cvar.AT_H4p
8598 AT_O4p = cvar.AT_O4p
8599 AT_C1p = cvar.AT_C1p
8600 AT_H1p = cvar.AT_H1p
8601 AT_C3p = cvar.AT_C3p
8602 AT_H3p = cvar.AT_H3p
8603 AT_O3p = cvar.AT_O3p
8604 AT_C2p = cvar.AT_C2p
8605 AT_H2p = cvar.AT_H2p
8606 AT_H2pp = cvar.AT_H2pp
8607 AT_O2p = cvar.AT_O2p
8608 AT_HO2p = cvar.AT_HO2p
8609 AT_N9 = cvar.AT_N9
8610 AT_C8 = cvar.AT_C8
8611 AT_H8 = cvar.AT_H8
8612 AT_N7 = cvar.AT_N7
8613 AT_C5 = cvar.AT_C5
8614 AT_C4 = cvar.AT_C4
8615 AT_N3 = cvar.AT_N3
8616 AT_C2 = cvar.AT_C2
8617 AT_N1 = cvar.AT_N1
8618 AT_C6 = cvar.AT_C6
8619 AT_N6 = cvar.AT_N6
8620 AT_H61 = cvar.AT_H61
8621 AT_H62 = cvar.AT_H62
8622 AT_O6 = cvar.AT_O6
8623 AT_N2 = cvar.AT_N2
8624 AT_NT = cvar.AT_NT
8625 AT_H21 = cvar.AT_H21
8626 AT_H22 = cvar.AT_H22
8627 AT_H6 = cvar.AT_H6
8628 AT_H5 = cvar.AT_H5
8629 AT_O2 = cvar.AT_O2
8630 AT_N4 = cvar.AT_N4
8631 AT_H41 = cvar.AT_H41
8632 AT_H42 = cvar.AT_H42
8633 AT_O4 = cvar.AT_O4
8634 AT_C7 = cvar.AT_C7
8635 AT_H71 = cvar.AT_H71
8636 AT_H72 = cvar.AT_H72
8637 AT_H73 = cvar.AT_H73
8638 AT_O1A = cvar.AT_O1A
8639 AT_O2A = cvar.AT_O2A
8640 AT_O3A = cvar.AT_O3A
8641 AT_O1B = cvar.AT_O1B
8642 AT_O2B = cvar.AT_O2B
8643 AT_O3B = cvar.AT_O3B
8644 AT_CAY = cvar.AT_CAY
8645 AT_CY = cvar.AT_CY
8646 AT_OY = cvar.AT_OY
8647 AT_CAT = cvar.AT_CAT
8648 
8649 
8650 def get_residue(*args):
8651  r"""
8652  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8653  get_residue(Atom d, bool nothrow=False) -> Residue
8654  """
8655  return _IMP_atom.get_residue(*args)
8656 
8657 def get_atom(rd, at):
8658  r"""get_atom(Residue rd, AtomType at) -> Atom"""
8659  return _IMP_atom.get_atom(rd, at)
8660 
8661 def add_atom_type(name, e):
8662  r"""add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8663  return _IMP_atom.add_atom_type(name, e)
8664 
8665 def get_element_for_atom_type(at):
8666  r"""get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8667  return _IMP_atom.get_element_for_atom_type(at)
8668 
8669 def get_atom_type_exists(name):
8670  r"""get_atom_type_exists(std::string name) -> bool"""
8671  return _IMP_atom.get_atom_type_exists(name)
8672 class Residue(Hierarchy):
8673  r"""Proxy of C++ IMP::atom::Residue class."""
8674 
8675  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8676 
8677  def __init__(self, *args):
8678  r"""
8679  __init__(Residue self) -> Residue
8680  __init__(Residue self, Model m, ParticleIndex id) -> Residue
8681  __init__(Residue self, _ParticleAdaptor d) -> Residue
8682  """
8683  _IMP_atom.Residue_swiginit(self, _IMP_atom.new_Residue(*args))
8684 
8685  def show(self, *args):
8686  r"""show(Residue self, _ostream out=std::cout)"""
8687  return _IMP_atom.Residue_show(self, *args)
8688 
8689  @staticmethod
8690  def setup_particle(*args):
8691  r"""
8692  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8693  setup_particle(_ParticleAdaptor pa, ResidueType t, int index, int insertion_code) -> Residue
8694  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8695  setup_particle(_ParticleAdaptor pa, ResidueType t, int index) -> Residue
8696  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8697  setup_particle(_ParticleAdaptor pa, ResidueType t) -> Residue
8698  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8699  setup_particle(_ParticleAdaptor pa, Residue other) -> Residue
8700  """
8701  return _IMP_atom.Residue_setup_particle(*args)
8702 
8703  @staticmethod
8704  def get_is_setup(*args):
8705  r"""
8706  get_is_setup(_ParticleAdaptor p) -> bool
8707  get_is_setup(Model m, ParticleIndex pi) -> bool
8708  """
8709  return _IMP_atom.Residue_get_is_setup(*args)
8710 
8711  def get_residue_type(self):
8712  r"""get_residue_type(Residue self) -> ResidueType"""
8713  return _IMP_atom.Residue_get_residue_type(self)
8714 
8715  def set_residue_type(self, t):
8716  r"""set_residue_type(Residue self, ResidueType t)"""
8717  return _IMP_atom.Residue_set_residue_type(self, t)
8718 
8719  def get_is_protein(self):
8720  r"""get_is_protein(Residue self) -> bool"""
8721  return _IMP_atom.Residue_get_is_protein(self)
8722 
8723  def get_is_dna(self):
8724  r"""get_is_dna(Residue self) -> bool"""
8725  return _IMP_atom.Residue_get_is_dna(self)
8726 
8727  def get_is_rna(self):
8728  r"""get_is_rna(Residue self) -> bool"""
8729  return _IMP_atom.Residue_get_is_rna(self)
8730 
8731  def get_index(self):
8732  r"""get_index(Residue self) -> IMP::Int"""
8733  return _IMP_atom.Residue_get_index(self)
8734 
8735  def set_index(self, t):
8736  r"""set_index(Residue self, IMP::Int t)"""
8737  return _IMP_atom.Residue_set_index(self, t)
8738 
8739  def get_insertion_code(self):
8740  r"""get_insertion_code(Residue self) -> char"""
8741  return _IMP_atom.Residue_get_insertion_code(self)
8742 
8743  def set_insertion_code(self, insertion_code):
8744  r"""set_insertion_code(Residue self, char insertion_code)"""
8745  return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8746 
8747  @staticmethod
8748  def get_index_key():
8749  r"""get_index_key() -> IntKey"""
8750  return _IMP_atom.Residue_get_index_key()
8751 
8752  @staticmethod
8753  def get_residue_type_key():
8754  r"""get_residue_type_key() -> IntKey"""
8755  return _IMP_atom.Residue_get_residue_type_key()
8756 
8757  @staticmethod
8758  def get_insertion_code_key():
8759  r"""get_insertion_code_key() -> IntKey"""
8760  return _IMP_atom.Residue_get_insertion_code_key()
8761 
8762  @staticmethod
8763  def get_type_changed_key():
8764  r"""get_type_changed_key() -> TriggerKey"""
8765  return _IMP_atom.Residue_get_type_changed_key()
8766 
8767  def add_attribute(self, *args):
8768  r"""
8769  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8770  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8771  add_attribute(Residue self, IntKey a0, IMP::Int a1)
8772  add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
8773  add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
8774  add_attribute(Residue self, StringKey a0, IMP::String a1)
8775  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8776  add_attribute(Residue self, ObjectKey a0, Object a1)
8777  add_attribute(Residue self, SparseFloatKey a0, IMP::Float a1)
8778  add_attribute(Residue self, SparseIntKey a0, IMP::Int a1)
8779  add_attribute(Residue self, SparseStringKey a0, IMP::String a1)
8780  add_attribute(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8781  """
8782  return _IMP_atom.Residue_add_attribute(self, *args)
8783 
8784  def get_value(self, *args):
8785  r"""
8786  get_value(Residue self, FloatKey a0) -> IMP::Float
8787  get_value(Residue self, IntKey a0) -> IMP::Int
8788  get_value(Residue self, FloatsKey a0) -> IMP::Floats
8789  get_value(Residue self, IntsKey a0) -> IMP::Ints
8790  get_value(Residue self, StringKey a0) -> IMP::String
8791  get_value(Residue self, ParticleIndexKey a0) -> Particle
8792  get_value(Residue self, ObjectKey a0) -> Object
8793  get_value(Residue self, SparseFloatKey a0) -> IMP::Float
8794  get_value(Residue self, SparseIntKey a0) -> IMP::Int
8795  get_value(Residue self, SparseStringKey a0) -> IMP::String
8796  get_value(Residue self, SparseParticleIndexKey a0) -> ParticleIndex
8797  """
8798  return _IMP_atom.Residue_get_value(self, *args)
8799 
8800  def set_value(self, *args):
8801  r"""
8802  set_value(Residue self, FloatKey a0, IMP::Float a1)
8803  set_value(Residue self, IntKey a0, IMP::Int a1)
8804  set_value(Residue self, FloatsKey a0, IMP::Floats a1)
8805  set_value(Residue self, IntsKey a0, IMP::Ints a1)
8806  set_value(Residue self, StringKey a0, IMP::String a1)
8807  set_value(Residue self, ParticleIndexKey a0, Particle a1)
8808  set_value(Residue self, ObjectKey a0, Object a1)
8809  set_value(Residue self, SparseFloatKey a0, IMP::Float a1)
8810  set_value(Residue self, SparseIntKey a0, IMP::Int a1)
8811  set_value(Residue self, SparseStringKey a0, IMP::String a1)
8812  set_value(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8813  """
8814  return _IMP_atom.Residue_set_value(self, *args)
8815 
8816  def remove_attribute(self, *args):
8817  r"""
8818  remove_attribute(Residue self, FloatKey a0)
8819  remove_attribute(Residue self, IntKey a0)
8820  remove_attribute(Residue self, FloatsKey a0)
8821  remove_attribute(Residue self, IntsKey a0)
8822  remove_attribute(Residue self, StringKey a0)
8823  remove_attribute(Residue self, ParticleIndexKey a0)
8824  remove_attribute(Residue self, ObjectKey a0)
8825  remove_attribute(Residue self, SparseFloatKey a0)
8826  remove_attribute(Residue self, SparseIntKey a0)
8827  remove_attribute(Residue self, SparseStringKey a0)
8828  remove_attribute(Residue self, SparseParticleIndexKey a0)
8829  """
8830  return _IMP_atom.Residue_remove_attribute(self, *args)
8831 
8832  def has_attribute(self, *args):
8833  r"""
8834  has_attribute(Residue self, FloatKey a0) -> bool
8835  has_attribute(Residue self, IntKey a0) -> bool
8836  has_attribute(Residue self, FloatsKey a0) -> bool
8837  has_attribute(Residue self, IntsKey a0) -> bool
8838  has_attribute(Residue self, StringKey a0) -> bool
8839  has_attribute(Residue self, ParticleIndexKey a0) -> bool
8840  has_attribute(Residue self, ObjectKey a0) -> bool
8841  has_attribute(Residue self, SparseFloatKey a0) -> bool
8842  has_attribute(Residue self, SparseIntKey a0) -> bool
8843  has_attribute(Residue self, SparseStringKey a0) -> bool
8844  has_attribute(Residue self, SparseParticleIndexKey a0) -> bool
8845  """
8846  return _IMP_atom.Residue_has_attribute(self, *args)
8847 
8848  def get_derivative(self, a0):
8849  r"""get_derivative(Residue self, FloatKey a0) -> double"""
8850  return _IMP_atom.Residue_get_derivative(self, a0)
8851 
8852  def get_name(self):
8853  r"""get_name(Residue self) -> std::string"""
8854  return _IMP_atom.Residue_get_name(self)
8855 
8856  def clear_caches(self):
8857  r"""clear_caches(Residue self)"""
8858  return _IMP_atom.Residue_clear_caches(self)
8859 
8860  def set_name(self, a0):
8861  r"""set_name(Residue self, std::string a0)"""
8862  return _IMP_atom.Residue_set_name(self, a0)
8863 
8864  def set_check_level(self, a0):
8865  r"""set_check_level(Residue self, IMP::CheckLevel a0)"""
8866  return _IMP_atom.Residue_set_check_level(self, a0)
8867 
8868  def add_to_derivative(self, a0, a1, a2):
8869  r"""add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8870  return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8871 
8872  def set_is_optimized(self, a0, a1):
8873  r"""set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8874  return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8875 
8876  def get_is_optimized(self, a0):
8877  r"""get_is_optimized(Residue self, FloatKey a0) -> bool"""
8878  return _IMP_atom.Residue_get_is_optimized(self, a0)
8879 
8880  def get_check_level(self):
8881  r"""get_check_level(Residue self) -> IMP::CheckLevel"""
8882  return _IMP_atom.Residue_get_check_level(self)
8883 
8884  def __eq__(self, *args):
8885  r"""
8886  __eq__(Residue self, Residue o) -> bool
8887  __eq__(Residue self, Particle d) -> bool
8888  """
8889  return _IMP_atom.Residue___eq__(self, *args)
8890 
8891  def __ne__(self, *args):
8892  r"""
8893  __ne__(Residue self, Residue o) -> bool
8894  __ne__(Residue self, Particle d) -> bool
8895  """
8896  return _IMP_atom.Residue___ne__(self, *args)
8897 
8898  def __le__(self, *args):
8899  r"""
8900  __le__(Residue self, Residue o) -> bool
8901  __le__(Residue self, Particle d) -> bool
8902  """
8903  return _IMP_atom.Residue___le__(self, *args)
8904 
8905  def __lt__(self, *args):
8906  r"""
8907  __lt__(Residue self, Residue o) -> bool
8908  __lt__(Residue self, Particle d) -> bool
8909  """
8910  return _IMP_atom.Residue___lt__(self, *args)
8911 
8912  def __ge__(self, *args):
8913  r"""
8914  __ge__(Residue self, Residue o) -> bool
8915  __ge__(Residue self, Particle d) -> bool
8916  """
8917  return _IMP_atom.Residue___ge__(self, *args)
8918 
8919  def __gt__(self, *args):
8920  r"""
8921  __gt__(Residue self, Residue o) -> bool
8922  __gt__(Residue self, Particle d) -> bool
8923  """
8924  return _IMP_atom.Residue___gt__(self, *args)
8925 
8926  def __hash__(self):
8927  r"""__hash__(Residue self) -> std::size_t"""
8928  return _IMP_atom.Residue___hash__(self)
8929 
8930  def __str__(self):
8931  r"""__str__(Residue self) -> std::string"""
8932  return _IMP_atom.Residue___str__(self)
8933 
8934  def __repr__(self):
8935  r"""__repr__(Residue self) -> std::string"""
8936  return _IMP_atom.Residue___repr__(self)
8937 
8938  def _get_as_binary(self):
8939  r"""_get_as_binary(Residue self) -> PyObject *"""
8940  return _IMP_atom.Residue__get_as_binary(self)
8941 
8942  def _set_from_binary(self, p):
8943  r"""_set_from_binary(Residue self, PyObject * p)"""
8944  return _IMP_atom.Residue__set_from_binary(self, p)
8945 
8946  def __getstate__(self):
8947  p = self._get_as_binary()
8948  if len(self.__dict__) > 1:
8949  d = self.__dict__.copy()
8950  del d['this']
8951  p = (d, p)
8952  return p
8953 
8954  def __setstate__(self, p):
8955  if not hasattr(self, 'this'):
8956  self.__init__()
8957  if isinstance(p, tuple):
8958  d, p = p
8959  self.__dict__.update(d)
8960  return self._set_from_binary(p)
8961 
8962  __swig_destroy__ = _IMP_atom.delete_Residue
8963 
8964 # Register Residue in _IMP_atom:
8965 _IMP_atom.Residue_swigregister(Residue)
8966 UNK = cvar.UNK
8967 GLY = cvar.GLY
8968 ALA = cvar.ALA
8969 VAL = cvar.VAL
8970 LEU = cvar.LEU
8971 ILE = cvar.ILE
8972 SER = cvar.SER
8973 THR = cvar.THR
8974 CYS = cvar.CYS
8975 MET = cvar.MET
8976 PRO = cvar.PRO
8977 ASP = cvar.ASP
8978 ASN = cvar.ASN
8979 GLU = cvar.GLU
8980 GLN = cvar.GLN
8981 LYS = cvar.LYS
8982 ARG = cvar.ARG
8983 HIS = cvar.HIS
8984 PHE = cvar.PHE
8985 TYR = cvar.TYR
8986 TRP = cvar.TRP
8987 ACE = cvar.ACE
8988 NH2 = cvar.NH2
8989 MSE = cvar.MSE
8990 ADE = cvar.ADE
8991 URA = cvar.URA
8992 CYT = cvar.CYT
8993 GUA = cvar.GUA
8994 THY = cvar.THY
8995 DADE = cvar.DADE
8996 DURA = cvar.DURA
8997 DCYT = cvar.DCYT
8998 DGUA = cvar.DGUA
8999 DTHY = cvar.DTHY
9000 HOH = cvar.HOH
9001 HEME = cvar.HEME
9002 POP = cvar.POP
9003 
9004 
9005 def get_next_residue(rd):
9006  r"""get_next_residue(Residue rd) -> Hierarchy"""
9007  return _IMP_atom.get_next_residue(rd)
9008 
9009 def get_previous_residue(rd):
9010  r"""get_previous_residue(Residue rd) -> Hierarchy"""
9011  return _IMP_atom.get_previous_residue(rd)
9012 
9013 def get_one_letter_code(c):
9014  r"""get_one_letter_code(ResidueType c) -> char"""
9015  return _IMP_atom.get_one_letter_code(c)
9016 BALLS = _IMP_atom.BALLS
9017 
9018 DENSITIES = _IMP_atom.DENSITIES
9019 
9020 class Representation(Hierarchy):
9021  r"""Proxy of C++ IMP::atom::Representation class."""
9022 
9023  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9024 
9025  @staticmethod
9026  def setup_particle(*args):
9027  r"""
9028  setup_particle(Model m, ParticleIndex pi) -> Representation
9029  setup_particle(_ParticleAdaptor pa) -> Representation
9030  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9031  setup_particle(_ParticleAdaptor pa, double resolution) -> Representation
9032  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9033  setup_particle(_ParticleAdaptor pa, Representation other) -> Representation
9034  """
9035  return _IMP_atom.Representation_setup_particle(*args)
9036 
9037  def __init__(self, *args):
9038  r"""
9039  __init__(Representation self) -> Representation
9040  __init__(Representation self, Model m, ParticleIndex id) -> Representation
9041  __init__(Representation self, _ParticleAdaptor d) -> Representation
9042  """
9043  _IMP_atom.Representation_swiginit(self, _IMP_atom.new_Representation(*args))
9044 
9045  def show(self, *args):
9046  r"""show(Representation self, _ostream out=std::cout)"""
9047  return _IMP_atom.Representation_show(self, *args)
9048 
9049  @staticmethod
9050  def get_is_setup(*args):
9051  r"""
9052  get_is_setup(_ParticleAdaptor p) -> bool
9053  get_is_setup(Model m, ParticleIndex pi) -> bool
9054  """
9055  return _IMP_atom.Representation_get_is_setup(*args)
9056 
9057  def get_representation(self, *args):
9058  r"""get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy"""
9059  return _IMP_atom.Representation_get_representation(self, *args)
9060 
9061  def get_representations(self, *args):
9062  r"""get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies"""
9063  return _IMP_atom.Representation_get_representations(self, *args)
9064 
9065  def add_representation(self, *args):
9066  r"""add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)"""
9067  return _IMP_atom.Representation_add_representation(self, *args)
9068 
9069  def get_resolutions(self, *args):
9070  r"""get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats"""
9071  return _IMP_atom.Representation_get_resolutions(self, *args)
9072 
9073  def remove_representation(self, rep):
9074  r"""remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
9075  return _IMP_atom.Representation_remove_representation(self, rep)
9076 
9077  def update_parents(self):
9078  r"""update_parents(Representation self)"""
9079  return _IMP_atom.Representation_update_parents(self)
9080 
9081  def add_attribute(self, *args):
9082  r"""
9083  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9084  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9085  add_attribute(Representation self, IntKey a0, IMP::Int a1)
9086  add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
9087  add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
9088  add_attribute(Representation self, StringKey a0, IMP::String a1)
9089  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9090  add_attribute(Representation self, ObjectKey a0, Object a1)
9091  add_attribute(Representation self, SparseFloatKey a0, IMP::Float a1)
9092  add_attribute(Representation self, SparseIntKey a0, IMP::Int a1)
9093  add_attribute(Representation self, SparseStringKey a0, IMP::String a1)
9094  add_attribute(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
9095  """
9096  return _IMP_atom.Representation_add_attribute(self, *args)
9097 
9098  def get_value(self, *args):
9099  r"""
9100  get_value(Representation self, FloatKey a0) -> IMP::Float
9101  get_value(Representation self, IntKey a0) -> IMP::Int
9102  get_value(Representation self, FloatsKey a0) -> IMP::Floats
9103  get_value(Representation self, IntsKey a0) -> IMP::Ints
9104  get_value(Representation self, StringKey a0) -> IMP::String
9105  get_value(Representation self, ParticleIndexKey a0) -> Particle
9106  get_value(Representation self, ObjectKey a0) -> Object
9107  get_value(Representation self, SparseFloatKey a0) -> IMP::Float
9108  get_value(Representation self, SparseIntKey a0) -> IMP::Int
9109  get_value(Representation self, SparseStringKey a0) -> IMP::String
9110  get_value(Representation self, SparseParticleIndexKey a0) -> ParticleIndex
9111  """
9112  return _IMP_atom.Representation_get_value(self, *args)
9113 
9114  def set_value(self, *args):
9115  r"""
9116  set_value(Representation self, FloatKey a0, IMP::Float a1)
9117  set_value(Representation self, IntKey a0, IMP::Int a1)
9118  set_value(Representation self, FloatsKey a0, IMP::Floats a1)
9119  set_value(Representation self, IntsKey a0, IMP::Ints a1)
9120  set_value(Representation self, StringKey a0, IMP::String a1)
9121  set_value(Representation self, ParticleIndexKey a0, Particle a1)
9122  set_value(Representation self, ObjectKey a0, Object a1)
9123  set_value(Representation self, SparseFloatKey a0, IMP::Float a1)
9124  set_value(Representation self, SparseIntKey a0, IMP::Int a1)
9125  set_value(Representation self, SparseStringKey a0, IMP::String a1)
9126  set_value(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
9127  """
9128  return _IMP_atom.Representation_set_value(self, *args)
9129 
9130  def remove_attribute(self, *args):
9131  r"""
9132  remove_attribute(Representation self, FloatKey a0)
9133  remove_attribute(Representation self, IntKey a0)
9134  remove_attribute(Representation self, FloatsKey a0)
9135  remove_attribute(Representation self, IntsKey a0)
9136  remove_attribute(Representation self, StringKey a0)
9137  remove_attribute(Representation self, ParticleIndexKey a0)
9138  remove_attribute(Representation self, ObjectKey a0)
9139  remove_attribute(Representation self, SparseFloatKey a0)
9140  remove_attribute(Representation self, SparseIntKey a0)
9141  remove_attribute(Representation self, SparseStringKey a0)
9142  remove_attribute(Representation self, SparseParticleIndexKey a0)
9143  """
9144  return _IMP_atom.Representation_remove_attribute(self, *args)
9145 
9146  def has_attribute(self, *args):
9147  r"""
9148  has_attribute(Representation self, FloatKey a0) -> bool
9149  has_attribute(Representation self, IntKey a0) -> bool
9150  has_attribute(Representation self, FloatsKey a0) -> bool
9151  has_attribute(Representation self, IntsKey a0) -> bool
9152  has_attribute(Representation self, StringKey a0) -> bool
9153  has_attribute(Representation self, ParticleIndexKey a0) -> bool
9154  has_attribute(Representation self, ObjectKey a0) -> bool
9155  has_attribute(Representation self, SparseFloatKey a0) -> bool
9156  has_attribute(Representation self, SparseIntKey a0) -> bool
9157  has_attribute(Representation self, SparseStringKey a0) -> bool
9158  has_attribute(Representation self, SparseParticleIndexKey a0) -> bool
9159  """
9160  return _IMP_atom.Representation_has_attribute(self, *args)
9161 
9162  def get_derivative(self, a0):
9163  r"""get_derivative(Representation self, FloatKey a0) -> double"""
9164  return _IMP_atom.Representation_get_derivative(self, a0)
9165 
9166  def get_name(self):
9167  r"""get_name(Representation self) -> std::string"""
9168  return _IMP_atom.Representation_get_name(self)
9169 
9170  def clear_caches(self):
9171  r"""clear_caches(Representation self)"""
9172  return _IMP_atom.Representation_clear_caches(self)
9173 
9174  def set_name(self, a0):
9175  r"""set_name(Representation self, std::string a0)"""
9176  return _IMP_atom.Representation_set_name(self, a0)
9177 
9178  def set_check_level(self, a0):
9179  r"""set_check_level(Representation self, IMP::CheckLevel a0)"""
9180  return _IMP_atom.Representation_set_check_level(self, a0)
9181 
9182  def add_to_derivative(self, a0, a1, a2):
9183  r"""add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9184  return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9185 
9186  def set_is_optimized(self, a0, a1):
9187  r"""set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9188  return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9189 
9190  def get_is_optimized(self, a0):
9191  r"""get_is_optimized(Representation self, FloatKey a0) -> bool"""
9192  return _IMP_atom.Representation_get_is_optimized(self, a0)
9193 
9194  def get_check_level(self):
9195  r"""get_check_level(Representation self) -> IMP::CheckLevel"""
9196  return _IMP_atom.Representation_get_check_level(self)
9197 
9198  def __eq__(self, *args):
9199  r"""
9200  __eq__(Representation self, Representation o) -> bool
9201  __eq__(Representation self, Particle d) -> bool
9202  """
9203  return _IMP_atom.Representation___eq__(self, *args)
9204 
9205  def __ne__(self, *args):
9206  r"""
9207  __ne__(Representation self, Representation o) -> bool
9208  __ne__(Representation self, Particle d) -> bool
9209  """
9210  return _IMP_atom.Representation___ne__(self, *args)
9211 
9212  def __le__(self, *args):
9213  r"""
9214  __le__(Representation self, Representation o) -> bool
9215  __le__(Representation self, Particle d) -> bool
9216  """
9217  return _IMP_atom.Representation___le__(self, *args)
9218 
9219  def __lt__(self, *args):
9220  r"""
9221  __lt__(Representation self, Representation o) -> bool
9222  __lt__(Representation self, Particle d) -> bool
9223  """
9224  return _IMP_atom.Representation___lt__(self, *args)
9225 
9226  def __ge__(self, *args):
9227  r"""
9228  __ge__(Representation self, Representation o) -> bool
9229  __ge__(Representation self, Particle d) -> bool
9230  """
9231  return _IMP_atom.Representation___ge__(self, *args)
9232 
9233  def __gt__(self, *args):
9234  r"""
9235  __gt__(Representation self, Representation o) -> bool
9236  __gt__(Representation self, Particle d) -> bool
9237  """
9238  return _IMP_atom.Representation___gt__(self, *args)
9239 
9240  def __hash__(self):
9241  r"""__hash__(Representation self) -> std::size_t"""
9242  return _IMP_atom.Representation___hash__(self)
9243 
9244  def __str__(self):
9245  r"""__str__(Representation self) -> std::string"""
9246  return _IMP_atom.Representation___str__(self)
9247 
9248  def __repr__(self):
9249  r"""__repr__(Representation self) -> std::string"""
9250  return _IMP_atom.Representation___repr__(self)
9251 
9252  def _get_as_binary(self):
9253  r"""_get_as_binary(Representation self) -> PyObject *"""
9254  return _IMP_atom.Representation__get_as_binary(self)
9255 
9256  def _set_from_binary(self, p):
9257  r"""_set_from_binary(Representation self, PyObject * p)"""
9258  return _IMP_atom.Representation__set_from_binary(self, p)
9259 
9260  def __getstate__(self):
9261  p = self._get_as_binary()
9262  if len(self.__dict__) > 1:
9263  d = self.__dict__.copy()
9264  del d['this']
9265  p = (d, p)
9266  return p
9267 
9268  def __setstate__(self, p):
9269  if not hasattr(self, 'this'):
9270  self.__init__()
9271  if isinstance(p, tuple):
9272  d, p = p
9273  self.__dict__.update(d)
9274  return self._set_from_binary(p)
9275 
9276  __swig_destroy__ = _IMP_atom.delete_Representation
9277 
9278 # Register Representation in _IMP_atom:
9279 _IMP_atom.Representation_swigregister(Representation)
9280 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9281 
9282 
9283 def get_resolution(*args):
9284  r"""
9285  get_resolution(Model m, ParticleIndex pi) -> double
9286  get_resolution(Hierarchy h) -> double
9287  """
9288  return _IMP_atom.get_resolution(*args)
9289 
9290 def get_representation(h, nothrow=False):
9291  r"""get_representation(Hierarchy h, bool nothrow=False) -> Representation"""
9292  return _IMP_atom.get_representation(h, nothrow)
9293 
9294 def show_with_representations(*args):
9295  r"""show_with_representations(Hierarchy h, _ostream out=std::cout)"""
9296  return _IMP_atom.show_with_representations(*args)
9297 class State(Hierarchy):
9298  r"""Proxy of C++ IMP::atom::State class."""
9299 
9300  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9301 
9302  @staticmethod
9303  def setup_particle(*args):
9304  r"""
9305  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9306  setup_particle(_ParticleAdaptor pa, unsigned int index) -> State
9307  setup_particle(Model m, ParticleIndex pi, State other) -> State
9308  setup_particle(_ParticleAdaptor pa, State other) -> State
9309  """
9310  return _IMP_atom.State_setup_particle(*args)
9311 
9312  def __init__(self, *args):
9313  r"""
9314  __init__(State self) -> State
9315  __init__(State self, Model m, ParticleIndex id) -> State
9316  __init__(State self, _ParticleAdaptor d) -> State
9317  """
9318  _IMP_atom.State_swiginit(self, _IMP_atom.new_State(*args))
9319 
9320  def show(self, *args):
9321  r"""show(State self, _ostream out=std::cout)"""
9322  return _IMP_atom.State_show(self, *args)
9323 
9324  @staticmethod
9325  def get_is_setup(*args):
9326  r"""
9327  get_is_setup(_ParticleAdaptor p) -> bool
9328  get_is_setup(Model m, ParticleIndex pi) -> bool
9329  """
9330  return _IMP_atom.State_get_is_setup(*args)
9331 
9332  def get_state_index(self):
9333  r"""get_state_index(State self) -> unsigned int"""
9334  return _IMP_atom.State_get_state_index(self)
9335 
9336  def add_attribute(self, *args):
9337  r"""
9338  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9339  add_attribute(State self, FloatKey a0, IMP::Float a1)
9340  add_attribute(State self, IntKey a0, IMP::Int a1)
9341  add_attribute(State self, FloatsKey a0, IMP::Floats a1)
9342  add_attribute(State self, IntsKey a0, IMP::Ints a1)
9343  add_attribute(State self, StringKey a0, IMP::String a1)
9344  add_attribute(State self, ParticleIndexKey a0, Particle a1)
9345  add_attribute(State self, ObjectKey a0, Object a1)
9346  add_attribute(State self, SparseFloatKey a0, IMP::Float a1)
9347  add_attribute(State self, SparseIntKey a0, IMP::Int a1)
9348  add_attribute(State self, SparseStringKey a0, IMP::String a1)
9349  add_attribute(State self, SparseParticleIndexKey a0, ParticleIndex a1)
9350  """
9351  return _IMP_atom.State_add_attribute(self, *args)
9352 
9353  def get_value(self, *args):
9354  r"""
9355  get_value(State self, FloatKey a0) -> IMP::Float
9356  get_value(State self, IntKey a0) -> IMP::Int
9357  get_value(State self, FloatsKey a0) -> IMP::Floats
9358  get_value(State self, IntsKey a0) -> IMP::Ints
9359  get_value(State self, StringKey a0) -> IMP::String
9360  get_value(State self, ParticleIndexKey a0) -> Particle
9361  get_value(State self, ObjectKey a0) -> Object
9362  get_value(State self, SparseFloatKey a0) -> IMP::Float
9363  get_value(State self, SparseIntKey a0) -> IMP::Int
9364  get_value(State self, SparseStringKey a0) -> IMP::String
9365  get_value(State self, SparseParticleIndexKey a0) -> ParticleIndex
9366  """
9367  return _IMP_atom.State_get_value(self, *args)
9368 
9369  def set_value(self, *args):
9370  r"""
9371  set_value(State self, FloatKey a0, IMP::Float a1)
9372  set_value(State self, IntKey a0, IMP::Int a1)
9373  set_value(State self, FloatsKey a0, IMP::Floats a1)
9374  set_value(State self, IntsKey a0, IMP::Ints a1)
9375  set_value(State self, StringKey a0, IMP::String a1)
9376  set_value(State self, ParticleIndexKey a0, Particle a1)
9377  set_value(State self, ObjectKey a0, Object a1)
9378  set_value(State self, SparseFloatKey a0, IMP::Float a1)
9379  set_value(State self, SparseIntKey a0, IMP::Int a1)
9380  set_value(State self, SparseStringKey a0, IMP::String a1)
9381  set_value(State self, SparseParticleIndexKey a0, ParticleIndex a1)
9382  """
9383  return _IMP_atom.State_set_value(self, *args)
9384 
9385  def remove_attribute(self, *args):
9386  r"""
9387  remove_attribute(State self, FloatKey a0)
9388  remove_attribute(State self, IntKey a0)
9389  remove_attribute(State self, FloatsKey a0)
9390  remove_attribute(State self, IntsKey a0)
9391  remove_attribute(State self, StringKey a0)
9392  remove_attribute(State self, ParticleIndexKey a0)
9393  remove_attribute(State self, ObjectKey a0)
9394  remove_attribute(State self, SparseFloatKey a0)
9395  remove_attribute(State self, SparseIntKey a0)
9396  remove_attribute(State self, SparseStringKey a0)
9397  remove_attribute(State self, SparseParticleIndexKey a0)
9398  """
9399  return _IMP_atom.State_remove_attribute(self, *args)
9400 
9401  def has_attribute(self, *args):
9402  r"""
9403  has_attribute(State self, FloatKey a0) -> bool
9404  has_attribute(State self, IntKey a0) -> bool
9405  has_attribute(State self, FloatsKey a0) -> bool
9406  has_attribute(State self, IntsKey a0) -> bool
9407  has_attribute(State self, StringKey a0) -> bool
9408  has_attribute(State self, ParticleIndexKey a0) -> bool
9409  has_attribute(State self, ObjectKey a0) -> bool
9410  has_attribute(State self, SparseFloatKey a0) -> bool
9411  has_attribute(State self, SparseIntKey a0) -> bool
9412  has_attribute(State self, SparseStringKey a0) -> bool
9413  has_attribute(State self, SparseParticleIndexKey a0) -> bool
9414  """
9415  return _IMP_atom.State_has_attribute(self, *args)
9416 
9417  def get_derivative(self, a0):
9418  r"""get_derivative(State self, FloatKey a0) -> double"""
9419  return _IMP_atom.State_get_derivative(self, a0)
9420 
9421  def get_name(self):
9422  r"""get_name(State self) -> std::string"""
9423  return _IMP_atom.State_get_name(self)
9424 
9425  def clear_caches(self):
9426  r"""clear_caches(State self)"""
9427  return _IMP_atom.State_clear_caches(self)
9428 
9429  def set_name(self, a0):
9430  r"""set_name(State self, std::string a0)"""
9431  return _IMP_atom.State_set_name(self, a0)
9432 
9433  def set_check_level(self, a0):
9434  r"""set_check_level(State self, IMP::CheckLevel a0)"""
9435  return _IMP_atom.State_set_check_level(self, a0)
9436 
9437  def add_to_derivative(self, a0, a1, a2):
9438  r"""add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9439  return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9440 
9441  def set_is_optimized(self, a0, a1):
9442  r"""set_is_optimized(State self, FloatKey a0, bool a1)"""
9443  return _IMP_atom.State_set_is_optimized(self, a0, a1)
9444 
9445  def get_is_optimized(self, a0):
9446  r"""get_is_optimized(State self, FloatKey a0) -> bool"""
9447  return _IMP_atom.State_get_is_optimized(self, a0)
9448 
9449  def get_check_level(self):
9450  r"""get_check_level(State self) -> IMP::CheckLevel"""
9451  return _IMP_atom.State_get_check_level(self)
9452 
9453  def __eq__(self, *args):
9454  r"""
9455  __eq__(State self, State o) -> bool
9456  __eq__(State self, Particle d) -> bool
9457  """
9458  return _IMP_atom.State___eq__(self, *args)
9459 
9460  def __ne__(self, *args):
9461  r"""
9462  __ne__(State self, State o) -> bool
9463  __ne__(State self, Particle d) -> bool
9464  """
9465  return _IMP_atom.State___ne__(self, *args)
9466 
9467  def __le__(self, *args):
9468  r"""
9469  __le__(State self, State o) -> bool
9470  __le__(State self, Particle d) -> bool
9471  """
9472  return _IMP_atom.State___le__(self, *args)
9473 
9474  def __lt__(self, *args):
9475  r"""
9476  __lt__(State self, State o) -> bool
9477  __lt__(State self, Particle d) -> bool
9478  """
9479  return _IMP_atom.State___lt__(self, *args)
9480 
9481  def __ge__(self, *args):
9482  r"""
9483  __ge__(State self, State o) -> bool
9484  __ge__(State self, Particle d) -> bool
9485  """
9486  return _IMP_atom.State___ge__(self, *args)
9487 
9488  def __gt__(self, *args):
9489  r"""
9490  __gt__(State self, State o) -> bool
9491  __gt__(State self, Particle d) -> bool
9492  """
9493  return _IMP_atom.State___gt__(self, *args)
9494 
9495  def __hash__(self):
9496  r"""__hash__(State self) -> std::size_t"""
9497  return _IMP_atom.State___hash__(self)
9498 
9499  def __str__(self):
9500  r"""__str__(State self) -> std::string"""
9501  return _IMP_atom.State___str__(self)
9502 
9503  def __repr__(self):
9504  r"""__repr__(State self) -> std::string"""
9505  return _IMP_atom.State___repr__(self)
9506 
9507  def _get_as_binary(self):
9508  r"""_get_as_binary(State self) -> PyObject *"""
9509  return _IMP_atom.State__get_as_binary(self)
9510 
9511  def _set_from_binary(self, p):
9512  r"""_set_from_binary(State self, PyObject * p)"""
9513  return _IMP_atom.State__set_from_binary(self, p)
9514 
9515  def __getstate__(self):
9516  p = self._get_as_binary()
9517  if len(self.__dict__) > 1:
9518  d = self.__dict__.copy()
9519  del d['this']
9520  p = (d, p)
9521  return p
9522 
9523  def __setstate__(self, p):
9524  if not hasattr(self, 'this'):
9525  self.__init__()
9526  if isinstance(p, tuple):
9527  d, p = p
9528  self.__dict__.update(d)
9529  return self._set_from_binary(p)
9530 
9531  __swig_destroy__ = _IMP_atom.delete_State
9532 
9533 # Register State in _IMP_atom:
9534 _IMP_atom.State_swigregister(State)
9535 
9536 def get_state_index(h):
9537  r"""get_state_index(Hierarchy h) -> int"""
9538  return _IMP_atom.get_state_index(h)
9539 
9540 def get_phi_dihedral_atoms(rd):
9541  r"""get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9542  return _IMP_atom.get_phi_dihedral_atoms(rd)
9543 
9544 def get_psi_dihedral_atoms(rd):
9545  r"""get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9546  return _IMP_atom.get_psi_dihedral_atoms(rd)
9547 
9548 def get_omega_dihedral_atoms(rd):
9549  r"""get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9550  return _IMP_atom.get_omega_dihedral_atoms(rd)
9551 
9553  r"""get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
9554  return _IMP_atom.get_chi_dihedral_atom_types(rt)
9555 
9556 def get_chi_dihedral_atoms(rd):
9557  r"""get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
9558  return _IMP_atom.get_chi_dihedral_atoms(rd)
9559 
9561  r"""get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
9562  return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
9563 class Molecule(Hierarchy):
9564  r"""Proxy of C++ IMP::atom::Molecule class."""
9565 
9566  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9567 
9568  def __init__(self, *args):
9569  r"""
9570  __init__(Molecule self) -> Molecule
9571  __init__(Molecule self, Model m, ParticleIndex id) -> Molecule
9572  __init__(Molecule self, _ParticleAdaptor d) -> Molecule
9573  """
9574  _IMP_atom.Molecule_swiginit(self, _IMP_atom.new_Molecule(*args))
9575 
9576  def show(self, *args):
9577  r"""show(Molecule self, _ostream out=std::cout)"""
9578  return _IMP_atom.Molecule_show(self, *args)
9579 
9580  @staticmethod
9581  def setup_particle(*args):
9582  r"""
9583  setup_particle(Model m, ParticleIndex pi) -> Molecule
9584  setup_particle(_ParticleAdaptor pa) -> Molecule
9585  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9586  setup_particle(_ParticleAdaptor pa, Molecule other) -> Molecule
9587  """
9588  return _IMP_atom.Molecule_setup_particle(*args)
9589 
9590  @staticmethod
9591  def get_is_setup(*args):
9592  r"""
9593  get_is_setup(_ParticleAdaptor p) -> bool
9594  get_is_setup(Model m, ParticleIndex pi) -> bool
9595  """
9596  return _IMP_atom.Molecule_get_is_setup(*args)
9597 
9598  def add_attribute(self, *args):
9599  r"""
9600  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9601  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9602  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9603  add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
9604  add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
9605  add_attribute(Molecule self, StringKey a0, IMP::String a1)
9606  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9607  add_attribute(Molecule self, ObjectKey a0, Object a1)
9608  add_attribute(Molecule self, SparseFloatKey a0, IMP::Float a1)
9609  add_attribute(Molecule self, SparseIntKey a0, IMP::Int a1)
9610  add_attribute(Molecule self, SparseStringKey a0, IMP::String a1)
9611  add_attribute(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9612  """
9613  return _IMP_atom.Molecule_add_attribute(self, *args)
9614 
9615  def get_value(self, *args):
9616  r"""
9617  get_value(Molecule self, FloatKey a0) -> IMP::Float
9618  get_value(Molecule self, IntKey a0) -> IMP::Int
9619  get_value(Molecule self, FloatsKey a0) -> IMP::Floats
9620  get_value(Molecule self, IntsKey a0) -> IMP::Ints
9621  get_value(Molecule self, StringKey a0) -> IMP::String
9622  get_value(Molecule self, ParticleIndexKey a0) -> Particle
9623  get_value(Molecule self, ObjectKey a0) -> Object
9624  get_value(Molecule self, SparseFloatKey a0) -> IMP::Float
9625  get_value(Molecule self, SparseIntKey a0) -> IMP::Int
9626  get_value(Molecule self, SparseStringKey a0) -> IMP::String
9627  get_value(Molecule self, SparseParticleIndexKey a0) -> ParticleIndex
9628  """
9629  return _IMP_atom.Molecule_get_value(self, *args)
9630 
9631  def set_value(self, *args):
9632  r"""
9633  set_value(Molecule self, FloatKey a0, IMP::Float a1)
9634  set_value(Molecule self, IntKey a0, IMP::Int a1)
9635  set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
9636  set_value(Molecule self, IntsKey a0, IMP::Ints a1)
9637  set_value(Molecule self, StringKey a0, IMP::String a1)
9638  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9639  set_value(Molecule self, ObjectKey a0, Object a1)
9640  set_value(Molecule self, SparseFloatKey a0, IMP::Float a1)
9641  set_value(Molecule self, SparseIntKey a0, IMP::Int a1)
9642  set_value(Molecule self, SparseStringKey a0, IMP::String a1)
9643  set_value(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9644  """
9645  return _IMP_atom.Molecule_set_value(self, *args)
9646 
9647  def remove_attribute(self, *args):
9648  r"""
9649  remove_attribute(Molecule self, FloatKey a0)
9650  remove_attribute(Molecule self, IntKey a0)
9651  remove_attribute(Molecule self, FloatsKey a0)
9652  remove_attribute(Molecule self, IntsKey a0)
9653  remove_attribute(Molecule self, StringKey a0)
9654  remove_attribute(Molecule self, ParticleIndexKey a0)
9655  remove_attribute(Molecule self, ObjectKey a0)
9656  remove_attribute(Molecule self, SparseFloatKey a0)
9657  remove_attribute(Molecule self, SparseIntKey a0)
9658  remove_attribute(Molecule self, SparseStringKey a0)
9659  remove_attribute(Molecule self, SparseParticleIndexKey a0)
9660  """
9661  return _IMP_atom.Molecule_remove_attribute(self, *args)
9662 
9663  def has_attribute(self, *args):
9664  r"""
9665  has_attribute(Molecule self, FloatKey a0) -> bool
9666  has_attribute(Molecule self, IntKey a0) -> bool
9667  has_attribute(Molecule self, FloatsKey a0) -> bool
9668  has_attribute(Molecule self, IntsKey a0) -> bool
9669  has_attribute(Molecule self, StringKey a0) -> bool
9670  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9671  has_attribute(Molecule self, ObjectKey a0) -> bool
9672  has_attribute(Molecule self, SparseFloatKey a0) -> bool
9673  has_attribute(Molecule self, SparseIntKey a0) -> bool
9674  has_attribute(Molecule self, SparseStringKey a0) -> bool
9675  has_attribute(Molecule self, SparseParticleIndexKey a0) -> bool
9676  """
9677  return _IMP_atom.Molecule_has_attribute(self, *args)
9678 
9679  def get_derivative(self, a0):
9680  r"""get_derivative(Molecule self, FloatKey a0) -> double"""
9681  return _IMP_atom.Molecule_get_derivative(self, a0)
9682 
9683  def get_name(self):
9684  r"""get_name(Molecule self) -> std::string"""
9685  return _IMP_atom.Molecule_get_name(self)
9686 
9687  def clear_caches(self):
9688  r"""clear_caches(Molecule self)"""
9689  return _IMP_atom.Molecule_clear_caches(self)
9690 
9691  def set_name(self, a0):
9692  r"""set_name(Molecule self, std::string a0)"""
9693  return _IMP_atom.Molecule_set_name(self, a0)
9694 
9695  def set_check_level(self, a0):
9696  r"""set_check_level(Molecule self, IMP::CheckLevel a0)"""
9697  return _IMP_atom.Molecule_set_check_level(self, a0)
9698 
9699  def add_to_derivative(self, a0, a1, a2):
9700  r"""add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9701  return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9702 
9703  def set_is_optimized(self, a0, a1):
9704  r"""set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9705  return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9706 
9707  def get_is_optimized(self, a0):
9708  r"""get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9709  return _IMP_atom.Molecule_get_is_optimized(self, a0)
9710 
9711  def get_check_level(self):
9712  r"""get_check_level(Molecule self) -> IMP::CheckLevel"""
9713  return _IMP_atom.Molecule_get_check_level(self)
9714 
9715  def __eq__(self, *args):
9716  r"""
9717  __eq__(Molecule self, Molecule o) -> bool
9718  __eq__(Molecule self, Particle d) -> bool
9719  """
9720  return _IMP_atom.Molecule___eq__(self, *args)
9721 
9722  def __ne__(self, *args):
9723  r"""
9724  __ne__(Molecule self, Molecule o) -> bool
9725  __ne__(Molecule self, Particle d) -> bool
9726  """
9727  return _IMP_atom.Molecule___ne__(self, *args)
9728 
9729  def __le__(self, *args):
9730  r"""
9731  __le__(Molecule self, Molecule o) -> bool
9732  __le__(Molecule self, Particle d) -> bool
9733  """
9734  return _IMP_atom.Molecule___le__(self, *args)
9735 
9736  def __lt__(self, *args):
9737  r"""
9738  __lt__(Molecule self, Molecule o) -> bool
9739  __lt__(Molecule self, Particle d) -> bool
9740  """
9741  return _IMP_atom.Molecule___lt__(self, *args)
9742 
9743  def __ge__(self, *args):
9744  r"""
9745  __ge__(Molecule self, Molecule o) -> bool
9746  __ge__(Molecule self, Particle d) -> bool
9747  """
9748  return _IMP_atom.Molecule___ge__(self, *args)
9749 
9750  def __gt__(self, *args):
9751  r"""
9752  __gt__(Molecule self, Molecule o) -> bool
9753  __gt__(Molecule self, Particle d) -> bool
9754  """
9755  return _IMP_atom.Molecule___gt__(self, *args)
9756 
9757  def __hash__(self):
9758  r"""__hash__(Molecule self) -> std::size_t"""
9759  return _IMP_atom.Molecule___hash__(self)
9760 
9761  def __str__(self):
9762  r"""__str__(Molecule self) -> std::string"""
9763  return _IMP_atom.Molecule___str__(self)
9764 
9765  def __repr__(self):
9766  r"""__repr__(Molecule self) -> std::string"""
9767  return _IMP_atom.Molecule___repr__(self)
9768 
9769  def _get_as_binary(self):
9770  r"""_get_as_binary(Molecule self) -> PyObject *"""
9771  return _IMP_atom.Molecule__get_as_binary(self)
9772 
9773  def _set_from_binary(self, p):
9774  r"""_set_from_binary(Molecule self, PyObject * p)"""
9775  return _IMP_atom.Molecule__set_from_binary(self, p)
9776 
9777  def __getstate__(self):
9778  p = self._get_as_binary()
9779  if len(self.__dict__) > 1:
9780  d = self.__dict__.copy()
9781  del d['this']
9782  p = (d, p)
9783  return p
9784 
9785  def __setstate__(self, p):
9786  if not hasattr(self, 'this'):
9787  self.__init__()
9788  if isinstance(p, tuple):
9789  d, p = p
9790  self.__dict__.update(d)
9791  return self._set_from_binary(p)
9792 
9793  __swig_destroy__ = _IMP_atom.delete_Molecule
9794 
9795 # Register Molecule in _IMP_atom:
9796 _IMP_atom.Molecule_swigregister(Molecule)
9797 
9798 def get_molecule_name(h):
9799  r"""get_molecule_name(Hierarchy h) -> std::string"""
9800  return _IMP_atom.get_molecule_name(h)
9801 class Copy(Molecule):
9802  r"""Proxy of C++ IMP::atom::Copy class."""
9803 
9804  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9805 
9806  @staticmethod
9807  def get_copy_index_key():
9808  r"""get_copy_index_key() -> IntKey"""
9809  return _IMP_atom.Copy_get_copy_index_key()
9810 
9811  def __init__(self, *args):
9812  r"""
9813  __init__(Copy self) -> Copy
9814  __init__(Copy self, Model m, ParticleIndex id) -> Copy
9815  __init__(Copy self, _ParticleAdaptor d) -> Copy
9816  """
9817  _IMP_atom.Copy_swiginit(self, _IMP_atom.new_Copy(*args))
9818 
9819  def show(self, *args):
9820  r"""show(Copy self, _ostream out=std::cout)"""
9821  return _IMP_atom.Copy_show(self, *args)
9822 
9823  @staticmethod
9824  def setup_particle(*args):
9825  r"""
9826  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9827  setup_particle(_ParticleAdaptor pa, IMP::Int number) -> Copy
9828  """
9829  return _IMP_atom.Copy_setup_particle(*args)
9830 
9831  @staticmethod
9832  def get_is_setup(*args):
9833  r"""
9834  get_is_setup(_ParticleAdaptor p) -> bool
9835  get_is_setup(Model m, ParticleIndex pi) -> bool
9836  """
9837  return _IMP_atom.Copy_get_is_setup(*args)
9838 
9839  def get_copy_index(self):
9840  r"""get_copy_index(Copy self) -> int"""
9841  return _IMP_atom.Copy_get_copy_index(self)
9842 
9843  def add_attribute(self, *args):
9844  r"""
9845  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9846  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9847  add_attribute(Copy self, IntKey a0, IMP::Int a1)
9848  add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
9849  add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
9850  add_attribute(Copy self, StringKey a0, IMP::String a1)
9851  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9852  add_attribute(Copy self, ObjectKey a0, Object a1)
9853  add_attribute(Copy self, SparseFloatKey a0, IMP::Float a1)
9854  add_attribute(Copy self, SparseIntKey a0, IMP::Int a1)
9855  add_attribute(Copy self, SparseStringKey a0, IMP::String a1)
9856  add_attribute(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9857  """
9858  return _IMP_atom.Copy_add_attribute(self, *args)
9859 
9860  def get_value(self, *args):
9861  r"""
9862  get_value(Copy self, FloatKey a0) -> IMP::Float
9863  get_value(Copy self, IntKey a0) -> IMP::Int
9864  get_value(Copy self, FloatsKey a0) -> IMP::Floats
9865  get_value(Copy self, IntsKey a0) -> IMP::Ints
9866  get_value(Copy self, StringKey a0) -> IMP::String
9867  get_value(Copy self, ParticleIndexKey a0) -> Particle
9868  get_value(Copy self, ObjectKey a0) -> Object
9869  get_value(Copy self, SparseFloatKey a0) -> IMP::Float
9870  get_value(Copy self, SparseIntKey a0) -> IMP::Int
9871  get_value(Copy self, SparseStringKey a0) -> IMP::String
9872  get_value(Copy self, SparseParticleIndexKey a0) -> ParticleIndex
9873  """
9874  return _IMP_atom.Copy_get_value(self, *args)
9875 
9876  def set_value(self, *args):
9877  r"""
9878  set_value(Copy self, FloatKey a0, IMP::Float a1)
9879  set_value(Copy self, IntKey a0, IMP::Int a1)
9880  set_value(Copy self, FloatsKey a0, IMP::Floats a1)
9881  set_value(Copy self, IntsKey a0, IMP::Ints a1)
9882  set_value(Copy self, StringKey a0, IMP::String a1)
9883  set_value(Copy self, ParticleIndexKey a0, Particle a1)
9884  set_value(Copy self, ObjectKey a0, Object a1)
9885  set_value(Copy self, SparseFloatKey a0, IMP::Float a1)
9886  set_value(Copy self, SparseIntKey a0, IMP::Int a1)
9887  set_value(Copy self, SparseStringKey a0, IMP::String a1)
9888  set_value(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9889  """
9890  return _IMP_atom.Copy_set_value(self, *args)
9891 
9892  def remove_attribute(self, *args):
9893  r"""
9894  remove_attribute(Copy self, FloatKey a0)
9895  remove_attribute(Copy self, IntKey a0)
9896  remove_attribute(Copy self, FloatsKey a0)
9897  remove_attribute(Copy self, IntsKey a0)
9898  remove_attribute(Copy self, StringKey a0)
9899  remove_attribute(Copy self, ParticleIndexKey a0)
9900  remove_attribute(Copy self, ObjectKey a0)
9901  remove_attribute(Copy self, SparseFloatKey a0)
9902  remove_attribute(Copy self, SparseIntKey a0)
9903  remove_attribute(Copy self, SparseStringKey a0)
9904  remove_attribute(Copy self, SparseParticleIndexKey a0)
9905  """
9906  return _IMP_atom.Copy_remove_attribute(self, *args)
9907 
9908  def has_attribute(self, *args):
9909  r"""
9910  has_attribute(Copy self, FloatKey a0) -> bool
9911  has_attribute(Copy self, IntKey a0) -> bool
9912  has_attribute(Copy self, FloatsKey a0) -> bool
9913  has_attribute(Copy self, IntsKey a0) -> bool
9914  has_attribute(Copy self, StringKey a0) -> bool
9915  has_attribute(Copy self, ParticleIndexKey a0) -> bool
9916  has_attribute(Copy self, ObjectKey a0) -> bool
9917  has_attribute(Copy self, SparseFloatKey a0) -> bool
9918  has_attribute(Copy self, SparseIntKey a0) -> bool
9919  has_attribute(Copy self, SparseStringKey a0) -> bool
9920  has_attribute(Copy self, SparseParticleIndexKey a0) -> bool
9921  """
9922  return _IMP_atom.Copy_has_attribute(self, *args)
9923 
9924  def get_derivative(self, a0):
9925  r"""get_derivative(Copy self, FloatKey a0) -> double"""
9926  return _IMP_atom.Copy_get_derivative(self, a0)
9927 
9928  def get_name(self):
9929  r"""get_name(Copy self) -> std::string"""
9930  return _IMP_atom.Copy_get_name(self)
9931 
9932  def clear_caches(self):
9933  r"""clear_caches(Copy self)"""
9934  return _IMP_atom.Copy_clear_caches(self)
9935 
9936  def set_name(self, a0):
9937  r"""set_name(Copy self, std::string a0)"""
9938  return _IMP_atom.Copy_set_name(self, a0)
9939 
9940  def set_check_level(self, a0):
9941  r"""set_check_level(Copy self, IMP::CheckLevel a0)"""
9942  return _IMP_atom.Copy_set_check_level(self, a0)
9943 
9944  def add_to_derivative(self, a0, a1, a2):
9945  r"""add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9946  return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9947 
9948  def set_is_optimized(self, a0, a1):
9949  r"""set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9950  return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9951 
9952  def get_is_optimized(self, a0):
9953  r"""get_is_optimized(Copy self, FloatKey a0) -> bool"""
9954  return _IMP_atom.Copy_get_is_optimized(self, a0)
9955 
9956  def get_check_level(self):
9957  r"""get_check_level(Copy self) -> IMP::CheckLevel"""
9958  return _IMP_atom.Copy_get_check_level(self)
9959 
9960  def __eq__(self, *args):
9961  r"""
9962  __eq__(Copy self, Copy o) -> bool
9963  __eq__(Copy self, Particle d) -> bool
9964  """
9965  return _IMP_atom.Copy___eq__(self, *args)
9966 
9967  def __ne__(self, *args):
9968  r"""
9969  __ne__(Copy self, Copy o) -> bool
9970  __ne__(Copy self, Particle d) -> bool
9971  """
9972  return _IMP_atom.Copy___ne__(self, *args)
9973 
9974  def __le__(self, *args):
9975  r"""
9976  __le__(Copy self, Copy o) -> bool
9977  __le__(Copy self, Particle d) -> bool
9978  """
9979  return _IMP_atom.Copy___le__(self, *args)
9980 
9981  def __lt__(self, *args):
9982  r"""
9983  __lt__(Copy self, Copy o) -> bool
9984  __lt__(Copy self, Particle d) -> bool
9985  """
9986  return _IMP_atom.Copy___lt__(self, *args)
9987 
9988  def __ge__(self, *args):
9989  r"""
9990  __ge__(Copy self, Copy o) -> bool
9991  __ge__(Copy self, Particle d) -> bool
9992  """
9993  return _IMP_atom.Copy___ge__(self, *args)
9994 
9995  def __gt__(self, *args):
9996  r"""
9997  __gt__(Copy self, Copy o) -> bool
9998  __gt__(Copy self, Particle d) -> bool
9999  """
10000  return _IMP_atom.Copy___gt__(self, *args)
10001 
10002  def __hash__(self):
10003  r"""__hash__(Copy self) -> std::size_t"""
10004  return _IMP_atom.Copy___hash__(self)
10005 
10006  def __str__(self):
10007  r"""__str__(Copy self) -> std::string"""
10008  return _IMP_atom.Copy___str__(self)
10009 
10010  def __repr__(self):
10011  r"""__repr__(Copy self) -> std::string"""
10012  return _IMP_atom.Copy___repr__(self)
10013 
10014  def _get_as_binary(self):
10015  r"""_get_as_binary(Copy self) -> PyObject *"""
10016  return _IMP_atom.Copy__get_as_binary(self)
10017 
10018  def _set_from_binary(self, p):
10019  r"""_set_from_binary(Copy self, PyObject * p)"""
10020  return _IMP_atom.Copy__set_from_binary(self, p)
10021 
10022  def __getstate__(self):
10023  p = self._get_as_binary()
10024  if len(self.__dict__) > 1:
10025  d = self.__dict__.copy()
10026  del d['this']
10027  p = (d, p)
10028  return p
10029 
10030  def __setstate__(self, p):
10031  if not hasattr(self, 'this'):
10032  self.__init__()
10033  if isinstance(p, tuple):
10034  d, p = p
10035  self.__dict__.update(d)
10036  return self._set_from_binary(p)
10037 
10038  __swig_destroy__ = _IMP_atom.delete_Copy
10039 
10040 # Register Copy in _IMP_atom:
10041 _IMP_atom.Copy_swigregister(Copy)
10042 
10043 def get_copy_index(h):
10044  r"""get_copy_index(Hierarchy h) -> int"""
10045  return _IMP_atom.get_copy_index(h)
10046 class Chain(Hierarchy):
10047  r"""Proxy of C++ IMP::atom::Chain class."""
10048 
10049  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10050 
10051  def __init__(self, *args):
10052  r"""
10053  __init__(Chain self) -> Chain
10054  __init__(Chain self, Model m, ParticleIndex id) -> Chain
10055  __init__(Chain self, _ParticleAdaptor d) -> Chain
10056  """
10057  _IMP_atom.Chain_swiginit(self, _IMP_atom.new_Chain(*args))
10058 
10059  def show(self, *args):
10060  r"""show(Chain self, _ostream out=std::cout)"""
10061  return _IMP_atom.Chain_show(self, *args)
10062 
10063  @staticmethod
10064  def setup_particle(*args):
10065  r"""
10066  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
10067  setup_particle(_ParticleAdaptor pa, std::string id) -> Chain
10068  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
10069  setup_particle(_ParticleAdaptor pa, char id) -> Chain
10070  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
10071  setup_particle(_ParticleAdaptor pa, Chain other) -> Chain
10072  """
10073  return _IMP_atom.Chain_setup_particle(*args)
10074 
10075  @staticmethod
10076  def get_is_setup(*args):
10077  r"""
10078  get_is_setup(_ParticleAdaptor p) -> bool
10079  get_is_setup(Model m, ParticleIndex pi) -> bool
10080  """
10081  return _IMP_atom.Chain_get_is_setup(*args)
10082 
10083  def get_id(self):
10084  r"""get_id(Chain self) -> std::string"""
10085  return _IMP_atom.Chain_get_id(self)
10086 
10087  def set_id(self, c):
10088  r"""set_id(Chain self, std::string c)"""
10089  return _IMP_atom.Chain_set_id(self, c)
10090 
10091  def get_label_asym_id(self):
10092  r"""get_label_asym_id(Chain self) -> std::string"""
10093  return _IMP_atom.Chain_get_label_asym_id(self)
10094 
10095  def set_label_asym_id(self, c):
10096  r"""set_label_asym_id(Chain self, std::string c)"""
10097  return _IMP_atom.Chain_set_label_asym_id(self, c)
10098 
10099  def get_sequence(self):
10100  r"""get_sequence(Chain self) -> std::string"""
10101  return _IMP_atom.Chain_get_sequence(self)
10102 
10103  def set_sequence(self, sequence):
10104  r"""set_sequence(Chain self, std::string sequence)"""
10105  return _IMP_atom.Chain_set_sequence(self, sequence)
10106 
10107  def get_sequence_offset(self):
10108  r"""get_sequence_offset(Chain self) -> int"""
10109  return _IMP_atom.Chain_get_sequence_offset(self)
10110 
10111  def set_sequence_offset(self, offset):
10112  r"""set_sequence_offset(Chain self, int offset)"""
10113  return _IMP_atom.Chain_set_sequence_offset(self, offset)
10114 
10115  def get_uniprot_accession(self):
10116  r"""get_uniprot_accession(Chain self) -> std::string"""
10117  return _IMP_atom.Chain_get_uniprot_accession(self)
10118 
10119  def set_uniprot_accession(self, accession):
10120  r"""set_uniprot_accession(Chain self, std::string accession)"""
10121  return _IMP_atom.Chain_set_uniprot_accession(self, accession)
10122 
10123  def get_chain_type(self):
10124  r"""get_chain_type(Chain self) -> ChainType"""
10125  return _IMP_atom.Chain_get_chain_type(self)
10126 
10127  def set_chain_type(self, t):
10128  r"""set_chain_type(Chain self, ChainType t)"""
10129  return _IMP_atom.Chain_set_chain_type(self, t)
10130 
10131  @staticmethod
10132  def get_id_key():
10133  r"""get_id_key() -> SparseStringKey"""
10134  return _IMP_atom.Chain_get_id_key()
10135 
10136  @staticmethod
10137  def get_label_asym_id_key():
10138  r"""get_label_asym_id_key() -> SparseStringKey"""
10139  return _IMP_atom.Chain_get_label_asym_id_key()
10140 
10141  @staticmethod
10142  def get_sequence_key():
10143  r"""get_sequence_key() -> SparseStringKey"""
10144  return _IMP_atom.Chain_get_sequence_key()
10145 
10146  @staticmethod
10147  def get_sequence_offset_key():
10148  r"""get_sequence_offset_key() -> SparseIntKey"""
10149  return _IMP_atom.Chain_get_sequence_offset_key()
10150 
10151  @staticmethod
10152  def get_uniprot_accession_key():
10153  r"""get_uniprot_accession_key() -> SparseStringKey"""
10154  return _IMP_atom.Chain_get_uniprot_accession_key()
10155 
10156  @staticmethod
10157  def get_chain_type_key():
10158  r"""get_chain_type_key() -> SparseIntKey"""
10159  return _IMP_atom.Chain_get_chain_type_key()
10160 
10161  def add_attribute(self, *args):
10162  r"""
10163  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
10164  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
10165  add_attribute(Chain self, IntKey a0, IMP::Int a1)
10166  add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
10167  add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
10168  add_attribute(Chain self, StringKey a0, IMP::String a1)
10169  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
10170  add_attribute(Chain self, ObjectKey a0, Object a1)
10171  add_attribute(Chain self, SparseFloatKey a0, IMP::Float a1)
10172  add_attribute(Chain self, SparseIntKey a0, IMP::Int a1)
10173  add_attribute(Chain self, SparseStringKey a0, IMP::String a1)
10174  add_attribute(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
10175  """
10176  return _IMP_atom.Chain_add_attribute(self, *args)
10177 
10178  def get_value(self, *args):
10179  r"""
10180  get_value(Chain self, FloatKey a0) -> IMP::Float
10181  get_value(Chain self, IntKey a0) -> IMP::Int
10182  get_value(Chain self, FloatsKey a0) -> IMP::Floats
10183  get_value(Chain self, IntsKey a0) -> IMP::Ints
10184  get_value(Chain self, StringKey a0) -> IMP::String
10185  get_value(Chain self, ParticleIndexKey a0) -> Particle
10186  get_value(Chain self, ObjectKey a0) -> Object
10187  get_value(Chain self, SparseFloatKey a0) -> IMP::Float
10188  get_value(Chain self, SparseIntKey a0) -> IMP::Int
10189  get_value(Chain self, SparseStringKey a0) -> IMP::String
10190  get_value(Chain self, SparseParticleIndexKey a0) -> ParticleIndex
10191  """
10192  return _IMP_atom.Chain_get_value(self, *args)
10193 
10194  def set_value(self, *args):
10195  r"""
10196  set_value(Chain self, FloatKey a0, IMP::Float a1)
10197  set_value(Chain self, IntKey a0, IMP::Int a1)
10198  set_value(Chain self, FloatsKey a0, IMP::Floats a1)
10199  set_value(Chain self, IntsKey a0, IMP::Ints a1)
10200  set_value(Chain self, StringKey a0, IMP::String a1)
10201  set_value(Chain self, ParticleIndexKey a0, Particle a1)
10202  set_value(Chain self, ObjectKey a0, Object a1)
10203  set_value(Chain self, SparseFloatKey a0, IMP::Float a1)
10204  set_value(Chain self, SparseIntKey a0, IMP::Int a1)
10205  set_value(Chain self, SparseStringKey a0, IMP::String a1)
10206  set_value(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
10207  """
10208  return _IMP_atom.Chain_set_value(self, *args)
10209 
10210  def remove_attribute(self, *args):
10211  r"""
10212  remove_attribute(Chain self, FloatKey a0)
10213  remove_attribute(Chain self, IntKey a0)
10214  remove_attribute(Chain self, FloatsKey a0)
10215  remove_attribute(Chain self, IntsKey a0)
10216  remove_attribute(Chain self, StringKey a0)
10217  remove_attribute(Chain self, ParticleIndexKey a0)
10218  remove_attribute(Chain self, ObjectKey a0)
10219  remove_attribute(Chain self, SparseFloatKey a0)
10220  remove_attribute(Chain self, SparseIntKey a0)
10221  remove_attribute(Chain self, SparseStringKey a0)
10222  remove_attribute(Chain self, SparseParticleIndexKey a0)
10223  """
10224  return _IMP_atom.Chain_remove_attribute(self, *args)
10225 
10226  def has_attribute(self, *args):
10227  r"""
10228  has_attribute(Chain self, FloatKey a0) -> bool
10229  has_attribute(Chain self, IntKey a0) -> bool
10230  has_attribute(Chain self, FloatsKey a0) -> bool
10231  has_attribute(Chain self, IntsKey a0) -> bool
10232  has_attribute(Chain self, StringKey a0) -> bool
10233  has_attribute(Chain self, ParticleIndexKey a0) -> bool
10234  has_attribute(Chain self, ObjectKey a0) -> bool
10235  has_attribute(Chain self, SparseFloatKey a0) -> bool
10236  has_attribute(Chain self, SparseIntKey a0) -> bool
10237  has_attribute(Chain self, SparseStringKey a0) -> bool
10238  has_attribute(Chain self, SparseParticleIndexKey a0) -> bool
10239  """
10240  return _IMP_atom.Chain_has_attribute(self, *args)
10241 
10242  def get_derivative(self, a0):
10243  r"""get_derivative(Chain self, FloatKey a0) -> double"""
10244  return _IMP_atom.Chain_get_derivative(self, a0)
10245 
10246  def get_name(self):
10247  r"""get_name(Chain self) -> std::string"""
10248  return _IMP_atom.Chain_get_name(self)
10249 
10250  def clear_caches(self):
10251  r"""clear_caches(Chain self)"""
10252  return _IMP_atom.Chain_clear_caches(self)
10253 
10254  def set_name(self, a0):
10255  r"""set_name(Chain self, std::string a0)"""
10256  return _IMP_atom.Chain_set_name(self, a0)
10257 
10258  def set_check_level(self, a0):
10259  r"""set_check_level(Chain self, IMP::CheckLevel a0)"""
10260  return _IMP_atom.Chain_set_check_level(self, a0)
10261 
10262  def add_to_derivative(self, a0, a1, a2):
10263  r"""add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10264  return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
10265 
10266  def set_is_optimized(self, a0, a1):
10267  r"""set_is_optimized(Chain self, FloatKey a0, bool a1)"""
10268  return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
10269 
10270  def get_is_optimized(self, a0):
10271  r"""get_is_optimized(Chain self, FloatKey a0) -> bool"""
10272  return _IMP_atom.Chain_get_is_optimized(self, a0)
10273 
10274  def get_check_level(self):
10275  r"""get_check_level(Chain self) -> IMP::CheckLevel"""
10276  return _IMP_atom.Chain_get_check_level(self)
10277 
10278  def __eq__(self, *args):
10279  r"""
10280  __eq__(Chain self, Chain o) -> bool
10281  __eq__(Chain self, Particle d) -> bool
10282  """
10283  return _IMP_atom.Chain___eq__(self, *args)
10284 
10285  def __ne__(self, *args):
10286  r"""
10287  __ne__(Chain self, Chain o) -> bool
10288  __ne__(Chain self, Particle d) -> bool
10289  """
10290  return _IMP_atom.Chain___ne__(self, *args)
10291 
10292  def __le__(self, *args):
10293  r"""
10294  __le__(Chain self, Chain o) -> bool
10295  __le__(Chain self, Particle d) -> bool
10296  """
10297  return _IMP_atom.Chain___le__(self, *args)
10298 
10299  def __lt__(self, *args):
10300  r"""
10301  __lt__(Chain self, Chain o) -> bool
10302  __lt__(Chain self, Particle d) -> bool
10303  """
10304  return _IMP_atom.Chain___lt__(self, *args)
10305 
10306  def __ge__(self, *args):
10307  r"""
10308  __ge__(Chain self, Chain o) -> bool
10309  __ge__(Chain self, Particle d) -> bool
10310  """
10311  return _IMP_atom.Chain___ge__(self, *args)
10312 
10313  def __gt__(self, *args):
10314  r"""
10315  __gt__(Chain self, Chain o) -> bool
10316  __gt__(Chain self, Particle d) -> bool
10317  """
10318  return _IMP_atom.Chain___gt__(self, *args)
10319 
10320  def __hash__(self):
10321  r"""__hash__(Chain self) -> std::size_t"""
10322  return _IMP_atom.Chain___hash__(self)
10323 
10324  def __str__(self):
10325  r"""__str__(Chain self) -> std::string"""
10326  return _IMP_atom.Chain___str__(self)
10327 
10328  def __repr__(self):
10329  r"""__repr__(Chain self) -> std::string"""
10330  return _IMP_atom.Chain___repr__(self)
10331 
10332  def _get_as_binary(self):
10333  r"""_get_as_binary(Chain self) -> PyObject *"""
10334  return _IMP_atom.Chain__get_as_binary(self)
10335 
10336  def _set_from_binary(self, p):
10337  r"""_set_from_binary(Chain self, PyObject * p)"""
10338  return _IMP_atom.Chain__set_from_binary(self, p)
10339 
10340  def __getstate__(self):
10341  p = self._get_as_binary()
10342  if len(self.__dict__) > 1:
10343  d = self.__dict__.copy()
10344  del d['this']
10345  p = (d, p)
10346  return p
10347 
10348  def __setstate__(self, p):
10349  if not hasattr(self, 'this'):
10350  self.__init__()
10351  if isinstance(p, tuple):
10352  d, p = p
10353  self.__dict__.update(d)
10354  return self._set_from_binary(p)
10355 
10356  __swig_destroy__ = _IMP_atom.delete_Chain
10357 
10358 # Register Chain in _IMP_atom:
10359 _IMP_atom.Chain_swigregister(Chain)
10360 UnknownChainType = cvar.UnknownChainType
10361 DPolypeptide = cvar.DPolypeptide
10362 LPolypeptide = cvar.LPolypeptide
10363 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
10364 Polyribonucleotide = cvar.Polyribonucleotide
10365 DPolysaccharide = cvar.DPolysaccharide
10366 LPolysaccharide = cvar.LPolysaccharide
10367 Protein = cvar.Protein
10368 DNA = cvar.DNA
10369 RNA = cvar.RNA
10370 
10371 
10372 def get_chain(h):
10373  r"""get_chain(Hierarchy h) -> Chain"""
10374  return _IMP_atom.get_chain(h)
10375 
10376 def get_chain_id(h):
10377  r"""get_chain_id(Hierarchy h) -> std::string"""
10378  return _IMP_atom.get_chain_id(h)
10379 class Selection(IMP._ParticleIndexesAdaptor):
10380  r"""Proxy of C++ IMP::atom::Selection class."""
10381 
10382  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10383  NONE = _IMP_atom.Selection_NONE
10384 
10385  C = _IMP_atom.Selection_C
10386 
10387  N = _IMP_atom.Selection_N
10388 
10389 
10390  def __init__(self, *args):
10391  r"""
10392  __init__(Selection self) -> Selection
10393  __init__(Selection self, Hierarchy h) -> Selection
10394  __init__(Selection self, Particle h) -> Selection
10395  __init__(Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10396  __init__(Selection self, IMP::ParticlesTemp const & h) -> Selection
10397  """
10398  _IMP_atom.Selection_swiginit(self, _IMP_atom.new_Selection(*args))
10399 
10400  def create_clone(self):
10401  r"""create_clone(Selection self) -> Selection"""
10402  return _IMP_atom.Selection_create_clone(self)
10403 
10404  def get_hierarchies(self):
10405  r"""get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10406  return _IMP_atom.Selection_get_hierarchies(self)
10407 
10408  def set_molecules(self, mols):
10409  r"""set_molecules(Selection self, IMP::Strings mols)"""
10410  return _IMP_atom.Selection_set_molecules(self, mols)
10411 
10412  def set_resolution(self, r):
10413  r"""set_resolution(Selection self, double r)"""
10414  return _IMP_atom.Selection_set_resolution(self, r)
10415 
10416  def set_representation_type(self, t):
10417  r"""set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10418  return _IMP_atom.Selection_set_representation_type(self, t)
10419 
10420  def set_state_index(self, state):
10421  r"""set_state_index(Selection self, int state)"""
10422  return _IMP_atom.Selection_set_state_index(self, state)
10423 
10424  def set_state_indexes(self, states):
10425  r"""set_state_indexes(Selection self, IMP::Ints states)"""
10426  return _IMP_atom.Selection_set_state_indexes(self, states)
10427 
10428  def set_terminus(self, t):
10429  r"""set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10430  return _IMP_atom.Selection_set_terminus(self, t)
10431 
10432  def set_element(self, e):
10433  r"""set_element(Selection self, IMP::atom::Element e)"""
10434  return _IMP_atom.Selection_set_element(self, e)
10435 
10436  def set_chain_ids(self, chains):
10437  r"""set_chain_ids(Selection self, IMP::Strings chains)"""
10438  return _IMP_atom.Selection_set_chain_ids(self, chains)
10439 
10440  def set_chains(self, chains):
10441  r"""set_chains(Selection self, IMP::Strings chains)"""
10442  return _IMP_atom.Selection_set_chains(self, chains)
10443 
10444  def set_residue_indexes(self, indexes):
10445  r"""set_residue_indexes(Selection self, IMP::Ints indexes)"""
10446  return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10447 
10448  def set_atom_types(self, types):
10449  r"""set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10450  return _IMP_atom.Selection_set_atom_types(self, types)
10451 
10452  def set_residue_types(self, types):
10453  r"""set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10454  return _IMP_atom.Selection_set_residue_types(self, types)
10455 
10456  def set_domains(self, names):
10457  r"""set_domains(Selection self, IMP::Strings names)"""
10458  return _IMP_atom.Selection_set_domains(self, names)
10459 
10460  def set_molecule(self, mol):
10461  r"""set_molecule(Selection self, std::string mol)"""
10462  return _IMP_atom.Selection_set_molecule(self, mol)
10463 
10464  def set_chain_id(self, c):
10465  r"""set_chain_id(Selection self, std::string c)"""
10466  return _IMP_atom.Selection_set_chain_id(self, c)
10467 
10468  def set_chain(self, c):
10469  r"""set_chain(Selection self, std::string c)"""
10470  return _IMP_atom.Selection_set_chain(self, c)
10471 
10472  def set_residue_index(self, i):
10473  r"""set_residue_index(Selection self, int i)"""
10474  return _IMP_atom.Selection_set_residue_index(self, i)
10475 
10476  def set_atom_type(self, types):
10477  r"""set_atom_type(Selection self, AtomType types)"""
10478  return _IMP_atom.Selection_set_atom_type(self, types)
10479 
10480  def set_residue_type(self, type):
10481  r"""set_residue_type(Selection self, ResidueType type)"""
10482  return _IMP_atom.Selection_set_residue_type(self, type)
10483 
10484  def set_domain(self, name):
10485  r"""set_domain(Selection self, std::string name)"""
10486  return _IMP_atom.Selection_set_domain(self, name)
10487 
10488  def set_copy_index(self, copy):
10489  r"""set_copy_index(Selection self, unsigned int copy)"""
10490  return _IMP_atom.Selection_set_copy_index(self, copy)
10491 
10492  def set_copy_indexes(self, copies):
10493  r"""set_copy_indexes(Selection self, IMP::Ints copies)"""
10494  return _IMP_atom.Selection_set_copy_indexes(self, copies)
10495 
10496  def set_particle_type(self, t):
10497  r"""set_particle_type(Selection self, ParticleType t)"""
10498  return _IMP_atom.Selection_set_particle_type(self, t)
10499 
10500  def set_particle_types(self, t):
10501  r"""set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10502  return _IMP_atom.Selection_set_particle_types(self, t)
10503 
10504  def set_hierarchy_types(self, types):
10505  r"""set_hierarchy_types(Selection self, IMP::Ints types)"""
10506  return _IMP_atom.Selection_set_hierarchy_types(self, types)
10507 
10508  def set_intersection(self, s):
10509  r"""set_intersection(Selection self, Selection s)"""
10510  return _IMP_atom.Selection_set_intersection(self, s)
10511 
10512  def set_union(self, s):
10513  r"""set_union(Selection self, Selection s)"""
10514  return _IMP_atom.Selection_set_union(self, s)
10515 
10516  def set_symmetric_difference(self, s):
10517  r"""set_symmetric_difference(Selection self, Selection s)"""
10518  return _IMP_atom.Selection_set_symmetric_difference(self, s)
10519 
10520  def set_difference(self, s):
10521  r"""set_difference(Selection self, Selection s)"""
10522  return _IMP_atom.Selection_set_difference(self, s)
10523 
10524  def get_selected_particles(self, with_representation=True):
10525  r"""get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp"""
10526  return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10527 
10528  def get_selected_particle_indexes(self, with_representation=True):
10529  r"""get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes"""
10530  return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10531 
10532  def show(self, *args):
10533  r"""show(Selection self, _ostream out=std::cout)"""
10534  return _IMP_atom.Selection_show(self, *args)
10535 
10536  def __str__(self):
10537  r"""__str__(Selection self) -> std::string"""
10538  return _IMP_atom.Selection___str__(self)
10539 
10540  def __repr__(self):
10541  r"""__repr__(Selection self) -> std::string"""
10542  return _IMP_atom.Selection___repr__(self)
10543 
10544  def __init__(self, hierarchy=None,
10545  hierarchies=None, **params):
10546  if hierarchy and hierarchies:
10547  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
10548  if hierarchy:
10549  this = _IMP_atom.new_Selection(hierarchy)
10550  try: self.this.append(this)
10551  except: self.this = this
10552  elif hierarchies:
10553  this = _IMP_atom.new_Selection(hierarchies)
10554  try: self.this.append(this)
10555  except: self.this = this
10556  else:
10557  raise ValueError("Either hierarchy or hierarchies must be provided.")
10558  for k in params.keys():
10559  eval("self.set_%s(params[k])"%k)
10560 
10561  def union(self, s):
10562  news = self.create_clone()
10563  news.union_update(s)
10564  return news
10565  def intersection(self, s):
10566  news = self.create_clone()
10567  news.intersection_update(s)
10568  return news
10569  def symmetric_difference(self, s):
10570  news = self.create_clone()
10571  news.symmetric_difference_update(s)
10572  return news
10573  def difference(self, s):
10574  news = self.create_clone()
10575  news.difference_update(s)
10576  return news
10577  def union_update(self, s):
10578  self.set_union(s)
10579  return self
10580  def intersection_update(self, s):
10581  self.set_intersection(s)
10582  return self
10583  def symmetric_difference_update(self, s):
10584  self.set_symmetric_difference(s)
10585  return self
10586  def difference_update(self, s):
10587  self.set_difference(s)
10588  return self
10589  __or__ = union
10590  __and__ = intersection
10591  __xor__ = symmetric_difference
10592  __sub__ = difference
10593  __ior__ = union_update
10594  __iand__ = intersection_update
10595  __ixor__ = symmetric_difference_update
10596  __isub__ = difference_update
10597 
10598  __swig_destroy__ = _IMP_atom.delete_Selection
10599 
10600 # Register Selection in _IMP_atom:
10601 _IMP_atom.Selection_swigregister(Selection)
10602 
10603 def create_distance_restraint(*args):
10604  r"""create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint"""
10605  return _IMP_atom.create_distance_restraint(*args)
10606 
10608  r"""
10609  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
10610  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10611  """
10612  return _IMP_atom.create_connectivity_restraint(*args)
10613 
10615  r"""
10616  create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
10617  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10618  """
10619  return _IMP_atom.create_internal_connectivity_restraint(*args)
10620 
10621 def create_cover(*args):
10622  r"""create_cover(Selection s, std::string name=std::string()) -> XYZR"""
10623  return _IMP_atom.create_cover(*args)
10624 
10625 def get_mass(*args):
10626  r"""
10627  get_mass(ResidueType c) -> double
10628  get_mass(Selection s) -> double
10629  """
10630  return _IMP_atom.get_mass(*args)
10631 
10632 def get_volume(s):
10633  r"""get_volume(Selection s) -> double"""
10634  return _IMP_atom.get_volume(s)
10635 
10636 def get_surface_area(s):
10637  r"""get_surface_area(Selection s) -> double"""
10638  return _IMP_atom.get_surface_area(s)
10639 
10640 def get_leaves(*args):
10641  r"""
10642  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10643  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10644  get_leaves(Selection h) -> IMP::atom::Hierarchies
10645  """
10646  return _IMP_atom.get_leaves(*args)
10647 class SelectionGeometry(IMP.display.Geometry):
10648  r"""Proxy of C++ IMP::atom::SelectionGeometry class."""
10649 
10650  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10651 
10652  def __init__(self, *args):
10653  r"""__init__(SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry"""
10654  _IMP_atom.SelectionGeometry_swiginit(self, _IMP_atom.new_SelectionGeometry(*args))
10655 
10656  def get_version_info(self):
10657  r"""get_version_info(SelectionGeometry self) -> VersionInfo"""
10658  return _IMP_atom.SelectionGeometry_get_version_info(self)
10659  __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
10660 
10661  def __str__(self):
10662  r"""__str__(SelectionGeometry self) -> std::string"""
10663  return _IMP_atom.SelectionGeometry___str__(self)
10664 
10665  def __repr__(self):
10666  r"""__repr__(SelectionGeometry self) -> std::string"""
10667  return _IMP_atom.SelectionGeometry___repr__(self)
10668 
10669  @staticmethod
10670  def get_from(o):
10671  return _object_cast_to_SelectionGeometry(o)
10672 
10673 
10674 # Register SelectionGeometry in _IMP_atom:
10675 _IMP_atom.SelectionGeometry_swigregister(SelectionGeometry)
10676 
10677 def get_rmsd(*args):
10678  r"""
10679  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10680  get_rmsd(Selection s0, Selection s1) -> double
10681  """
10682  return _IMP_atom.get_rmsd(*args)
10683 
10684 def get_rmsd_transforming_first(*args):
10685  r"""
10686  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10687  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10688  """
10689  return _IMP_atom.get_rmsd_transforming_first(*args)
10690 
10691 def get_placement_score(source, target):
10692  r"""get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10693  return _IMP_atom.get_placement_score(source, target)
10694 
10695 def get_component_placement_score(ref1, ref2, mdl1, mdl2):
10696  r"""get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> IMP::FloatPair"""
10697  return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10698 
10699 def get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2):
10700  r"""get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> double"""
10701  return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10702 
10703 def get_radius_of_gyration(*args):
10704  r"""
10705  get_radius_of_gyration(Selection s) -> double
10706  get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10707  """
10708  return _IMP_atom.get_radius_of_gyration(*args)
10709 class ForceFieldParameters(IMP.Object):
10710  r"""Proxy of C++ IMP::atom::ForceFieldParameters class."""
10711 
10712  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10713 
10714  def __init__(self):
10715  r"""__init__(ForceFieldParameters self) -> ForceFieldParameters"""
10716  _IMP_atom.ForceFieldParameters_swiginit(self, _IMP_atom.new_ForceFieldParameters())
10717 
10718  def get_radius(self, atom):
10719  r"""get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10720  return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10721 
10722  def get_epsilon(self, atom):
10723  r"""get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10724  return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10725 
10726  def add_radii(self, *args):
10727  r"""add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=IMP::FloatKey("radius"))"""
10728  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10729 
10730  def add_well_depths(self, mhd):
10731  r"""add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10732  return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10733 
10734  def add_lennard_jones_types(self, mhd):
10735  r"""add_lennard_jones_types(ForceFieldParameters self, Hierarchy mhd)"""
10736  return _IMP_atom.ForceFieldParameters_add_lennard_jones_types(self, mhd)
10737 
10738  def add_bonds(self, mhd):
10739  r"""add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10740  return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10741  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10742 
10743  def __str__(self):
10744  r"""__str__(ForceFieldParameters self) -> std::string"""
10745  return _IMP_atom.ForceFieldParameters___str__(self)
10746 
10747  def __repr__(self):
10748  r"""__repr__(ForceFieldParameters self) -> std::string"""
10749  return _IMP_atom.ForceFieldParameters___repr__(self)
10750 
10751  @staticmethod
10752  def get_from(o):
10753  return _object_cast_to_ForceFieldParameters(o)
10754 
10755 
10756 # Register ForceFieldParameters in _IMP_atom:
10757 _IMP_atom.ForceFieldParameters_swigregister(ForceFieldParameters)
10758 class CHARMMAtomTopology(object):
10759  r"""Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10760 
10761  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10762 
10763  def __init__(self, *args):
10764  r"""
10765  __init__(CHARMMAtomTopology self) -> CHARMMAtomTopology
10766  __init__(CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10767  __init__(CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10768  """
10769  _IMP_atom.CHARMMAtomTopology_swiginit(self, _IMP_atom.new_CHARMMAtomTopology(*args))
10770 
10771  def get_name(self):
10772  r"""get_name(CHARMMAtomTopology self) -> std::string"""
10773  return _IMP_atom.CHARMMAtomTopology_get_name(self)
10774 
10775  def get_charmm_type(self):
10776  r"""get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10777  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10778 
10779  def get_charge(self):
10780  r"""get_charge(CHARMMAtomTopology self) -> double"""
10781  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10782 
10783  def set_charmm_type(self, charmm_type):
10784  r"""set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10785  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10786 
10787  def set_charge(self, charge):
10788  r"""set_charge(CHARMMAtomTopology self, double charge)"""
10789  return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10790 
10791  def show(self, *args):
10792  r"""show(CHARMMAtomTopology self, _ostream out=std::cout)"""
10793  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10794 
10795  def __str__(self):
10796  r"""__str__(CHARMMAtomTopology self) -> std::string"""
10797  return _IMP_atom.CHARMMAtomTopology___str__(self)
10798 
10799  def __repr__(self):
10800  r"""__repr__(CHARMMAtomTopology self) -> std::string"""
10801  return _IMP_atom.CHARMMAtomTopology___repr__(self)
10802 
10803  def _get_as_binary(self):
10804  r"""_get_as_binary(CHARMMAtomTopology self) -> PyObject *"""
10805  return _IMP_atom.CHARMMAtomTopology__get_as_binary(self)
10806 
10807  def _set_from_binary(self, p):
10808  r"""_set_from_binary(CHARMMAtomTopology self, PyObject * p)"""
10809  return _IMP_atom.CHARMMAtomTopology__set_from_binary(self, p)
10810 
10811  def __getstate__(self):
10812  p = self._get_as_binary()
10813  if len(self.__dict__) > 1:
10814  d = self.__dict__.copy()
10815  del d['this']
10816  p = (d, p)
10817  return p
10818 
10819  def __setstate__(self, p):
10820  if not hasattr(self, 'this'):
10821  self.__init__()
10822  if isinstance(p, tuple):
10823  d, p = p
10824  self.__dict__.update(d)
10825  return self._set_from_binary(p)
10826 
10827  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10828 
10829 # Register CHARMMAtomTopology in _IMP_atom:
10830 _IMP_atom.CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10831 class CHARMMBondEndpoint(object):
10832  r"""Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10833 
10834  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10835 
10836  def __init__(self, atom_name, residue=None):
10837  r"""__init__(CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint"""
10838  _IMP_atom.CHARMMBondEndpoint_swiginit(self, _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue))
10839 
10840  def get_atom_name(self):
10841  r"""get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10842  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10843 
10844  def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10845  r"""get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue, std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom"""
10846  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10847 
10848  def show(self, *args):
10849  r"""show(CHARMMBondEndpoint self, _ostream out=std::cout)"""
10850  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10851 
10852  def __str__(self):
10853  r"""__str__(CHARMMBondEndpoint self) -> std::string"""
10854  return _IMP_atom.CHARMMBondEndpoint___str__(self)
10855 
10856  def __repr__(self):
10857  r"""__repr__(CHARMMBondEndpoint self) -> std::string"""
10858  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10859  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10860 
10861 # Register CHARMMBondEndpoint in _IMP_atom:
10862 _IMP_atom.CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10863 class CHARMMDihedral(object):
10864  r"""Proxy of C++ IMP::atom::CHARMMConnection< 4 > class."""
10865 
10866  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10867  __repr__ = _swig_repr
10868 
10869  def __init__(self, atoms):
10870  r"""__init__(CHARMMDihedral self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10871  _IMP_atom.CHARMMDihedral_swiginit(self, _IMP_atom.new_CHARMMDihedral(atoms))
10872 
10873  def get_endpoint(self, i):
10874  r"""get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10875  return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10876 
10877  def get_contains_atom(self, name):
10878  r"""get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10879  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10880 
10881  def show(self, *args):
10882  r"""show(CHARMMDihedral self, _ostream out=std::cout)"""
10883  return _IMP_atom.CHARMMDihedral_show(self, *args)
10884  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10885 
10886 # Register CHARMMDihedral in _IMP_atom:
10887 _IMP_atom.CHARMMDihedral_swigregister(CHARMMDihedral)
10888 class CHARMMInternalCoordinate(CHARMMDihedral):
10889  r"""Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10890 
10891  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10892 
10893  def __init__(self, *args):
10894  r"""
10895  __init__(CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10896  __init__(CHARMMInternalCoordinate self, IMP::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10897  """
10898  _IMP_atom.CHARMMInternalCoordinate_swiginit(self, _IMP_atom.new_CHARMMInternalCoordinate(*args))
10899 
10900  def get_first_distance(self):
10901  r"""get_first_distance(CHARMMInternalCoordinate self) -> float"""
10902  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10903 
10904  def get_second_distance(self):
10905  r"""get_second_distance(CHARMMInternalCoordinate self) -> float"""
10906  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10907 
10908  def get_first_angle(self):
10909  r"""get_first_angle(CHARMMInternalCoordinate self) -> float"""
10910  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10911 
10912  def get_second_angle(self):
10913  r"""get_second_angle(CHARMMInternalCoordinate self) -> float"""
10914  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10915 
10916  def get_dihedral(self):
10917  r"""get_dihedral(CHARMMInternalCoordinate self) -> float"""
10918  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10919 
10920  def get_improper(self):
10921  r"""get_improper(CHARMMInternalCoordinate self) -> bool"""
10922  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10923 
10924  def show(self, *args):
10925  r"""show(CHARMMInternalCoordinate self, _ostream out=std::cout)"""
10926  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10927 
10928  def __str__(self):
10929  r"""__str__(CHARMMInternalCoordinate self) -> std::string"""
10930  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10931 
10932  def __repr__(self):
10933  r"""__repr__(CHARMMInternalCoordinate self) -> std::string"""
10934  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10935  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10936 
10937 # Register CHARMMInternalCoordinate in _IMP_atom:
10938 _IMP_atom.CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10939 class CHARMMResidueTopologyBase(IMP.Object):
10940  r"""Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10941 
10942  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10943 
10944  def __init__(self, *args, **kwargs):
10945  raise AttributeError("No constructor defined")
10946 
10947  def get_type(self):
10948  r"""get_type(CHARMMResidueTopologyBase self) -> std::string"""
10949  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10950 
10951  def get_number_of_atoms(self):
10952  r"""get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10953  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10954 
10955  def add_atom(self, atom):
10956  r"""add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10957  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10958 
10959  def get_atom(self, *args):
10960  r"""
10961  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10962  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10963  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10964  """
10965  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10966 
10967  def get_number_of_bonds(self):
10968  r"""get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10969  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10970 
10971  def add_bond(self, bond):
10972  r"""add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
10973  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10974 
10975  def get_number_of_angles(self):
10976  r"""get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10977  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10978 
10979  def add_angle(self, bond):
10980  r"""add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
10981  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10982 
10983  def get_number_of_dihedrals(self):
10984  r"""get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10985  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10986 
10987  def add_dihedral(self, bond):
10988  r"""add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10989  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10990 
10991  def get_number_of_impropers(self):
10992  r"""get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10993  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10994 
10995  def add_improper(self, bond):
10996  r"""add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10997  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10998 
10999  def get_number_of_internal_coordinates(self):
11000  r"""get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11001  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11002 
11003  def add_internal_coordinate(self, ic):
11004  r"""add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11005  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11006 
11007  def get_internal_coordinate(self, index):
11008  r"""get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11009  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11010 
11011  def get_bond(self, index):
11012  r"""get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
11013  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11014 
11015  def get_angle(self, index):
11016  r"""get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
11017  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11018 
11019  def get_dihedral(self, index):
11020  r"""get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11021  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11022 
11023  def get_improper(self, index):
11024  r"""get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11025  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11026 
11027  def get_version_info(self):
11028  r"""get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11029  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11030  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
11031 
11032  def __str__(self):
11033  r"""__str__(CHARMMResidueTopologyBase self) -> std::string"""
11034  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11035 
11036  def __repr__(self):
11037  r"""__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11038  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11039 
11040  @staticmethod
11041  def get_from(o):
11042  return _object_cast_to_CHARMMResidueTopologyBase(o)
11043 
11044 
11045 # Register CHARMMResidueTopologyBase in _IMP_atom:
11046 _IMP_atom.CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11047 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11048  r"""Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
11049 
11050  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11051 
11052  def __init__(self, *args):
11053  r"""
11054  __init__(CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11055  __init__(CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11056  """
11057  _IMP_atom.CHARMMIdealResidueTopology_swiginit(self, _IMP_atom.new_CHARMMIdealResidueTopology(*args))
11058 
11059  def remove_atom(self, name):
11060  r"""remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11061  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11062 
11063  def set_default_first_patch(self, patch):
11064  r"""set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11065  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11066 
11067  def set_default_last_patch(self, patch):
11068  r"""set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11069  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11070 
11071  def get_default_first_patch(self):
11072  r"""get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11073  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11074 
11075  def get_default_last_patch(self):
11076  r"""get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11077  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11078  __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
11079 
11080  def __str__(self):
11081  r"""__str__(CHARMMIdealResidueTopology self) -> std::string"""
11082  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11083 
11084  def __repr__(self):
11085  r"""__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11086  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11087 
11088  @staticmethod
11089  def get_from(o):
11090  return _object_cast_to_CHARMMIdealResidueTopology(o)
11091 
11092 
11093 # Register CHARMMIdealResidueTopology in _IMP_atom:
11094 _IMP_atom.CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11095 class CHARMMPatch(CHARMMResidueTopologyBase):
11096  r"""Proxy of C++ IMP::atom::CHARMMPatch class."""
11097 
11098  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11099 
11100  def __init__(self, type):
11101  r"""__init__(CHARMMPatch self, std::string type) -> CHARMMPatch"""
11102  _IMP_atom.CHARMMPatch_swiginit(self, _IMP_atom.new_CHARMMPatch(type))
11103 
11104  def add_removed_atom(self, name):
11105  r"""add_removed_atom(CHARMMPatch self, std::string name)"""
11106  return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11107 
11108  def get_number_of_removed_atoms(self):
11109  r"""get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11110  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11111 
11112  def get_removed_atom(self, i):
11113  r"""get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11114  return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11115 
11116  def apply(self, *args):
11117  r"""
11118  apply(CHARMMPatch self, CHARMMResidueTopology res)
11119  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11120  """
11121  return _IMP_atom.CHARMMPatch_apply(self, *args)
11122  __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
11123 
11124  def __str__(self):
11125  r"""__str__(CHARMMPatch self) -> std::string"""
11126  return _IMP_atom.CHARMMPatch___str__(self)
11127 
11128  def __repr__(self):
11129  r"""__repr__(CHARMMPatch self) -> std::string"""
11130  return _IMP_atom.CHARMMPatch___repr__(self)
11131 
11132  @staticmethod
11133  def get_from(o):
11134  return _object_cast_to_CHARMMPatch(o)
11135 
11136 
11137 # Register CHARMMPatch in _IMP_atom:
11138 _IMP_atom.CHARMMPatch_swigregister(CHARMMPatch)
11139 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11140  r"""Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
11141 
11142  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11143 
11144  def __init__(self, *args):
11145  r"""
11146  __init__(CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11147  __init__(CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11148  """
11149  _IMP_atom.CHARMMResidueTopology_swiginit(self, _IMP_atom.new_CHARMMResidueTopology(*args))
11150 
11151  def get_patched(self):
11152  r"""get_patched(CHARMMResidueTopology self) -> bool"""
11153  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11154 
11155  def set_patched(self, patched):
11156  r"""set_patched(CHARMMResidueTopology self, bool patched)"""
11157  return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11158  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
11159 
11160  def __str__(self):
11161  r"""__str__(CHARMMResidueTopology self) -> std::string"""
11162  return _IMP_atom.CHARMMResidueTopology___str__(self)
11163 
11164  def __repr__(self):
11165  r"""__repr__(CHARMMResidueTopology self) -> std::string"""
11166  return _IMP_atom.CHARMMResidueTopology___repr__(self)
11167 
11168  @staticmethod
11169  def get_from(o):
11170  return _object_cast_to_CHARMMResidueTopology(o)
11171 
11172 
11173 # Register CHARMMResidueTopology in _IMP_atom:
11174 _IMP_atom.CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11175 class CHARMMAtom(Atom):
11176  r"""Proxy of C++ IMP::atom::CHARMMAtom class."""
11177 
11178  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11179 
11180  def __init__(self, *args):
11181  r"""
11182  __init__(CHARMMAtom self) -> CHARMMAtom
11183  __init__(CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11184  __init__(CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11185  """
11186  _IMP_atom.CHARMMAtom_swiginit(self, _IMP_atom.new_CHARMMAtom(*args))
11187 
11188  def show(self, *args):
11189  r"""show(CHARMMAtom self, _ostream out=std::cout)"""
11190  return _IMP_atom.CHARMMAtom_show(self, *args)
11191 
11192  @staticmethod
11193  def setup_particle(*args):
11194  r"""
11195  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11196  setup_particle(_ParticleAdaptor pa, IMP::String charmm_type) -> CHARMMAtom
11197  """
11198  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11199 
11200  def get_charmm_type(self):
11201  r"""get_charmm_type(CHARMMAtom self) -> IMP::String"""
11202  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11203 
11204  def set_charmm_type(self, t):
11205  r"""set_charmm_type(CHARMMAtom self, IMP::String t)"""
11206  return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11207 
11208  @staticmethod
11209  def get_is_setup(*args):
11210  r"""
11211  get_is_setup(_ParticleAdaptor p) -> bool
11212  get_is_setup(Model m, ParticleIndex pi) -> bool
11213  """
11214  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11215 
11216  @staticmethod
11217  def get_charmm_type_key():
11218  r"""get_charmm_type_key() -> StringKey"""
11219  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11220 
11221  def add_attribute(self, *args):
11222  r"""
11223  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11224  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11225  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11226  add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11227  add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11228  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11229  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11230  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11231  add_attribute(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
11232  add_attribute(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
11233  add_attribute(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
11234  add_attribute(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
11235  """
11236  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11237 
11238  def get_value(self, *args):
11239  r"""
11240  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11241  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11242  get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
11243  get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
11244  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11245  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11246  get_value(CHARMMAtom self, ObjectKey a0) -> Object
11247  get_value(CHARMMAtom self, SparseFloatKey a0) -> IMP::Float
11248  get_value(CHARMMAtom self, SparseIntKey a0) -> IMP::Int
11249  get_value(CHARMMAtom self, SparseStringKey a0) -> IMP::String
11250  get_value(CHARMMAtom self, SparseParticleIndexKey a0) -> ParticleIndex
11251  """
11252  return _IMP_atom.CHARMMAtom_get_value(self, *args)
11253 
11254  def set_value(self, *args):
11255  r"""
11256  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11257  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11258  set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11259  set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11260  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11261  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11262  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11263  set_value(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
11264  set_value(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
11265  set_value(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
11266  set_value(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
11267  """
11268  return _IMP_atom.CHARMMAtom_set_value(self, *args)
11269 
11270  def remove_attribute(self, *args):
11271  r"""
11272  remove_attribute(CHARMMAtom self, FloatKey a0)
11273  remove_attribute(CHARMMAtom self, IntKey a0)
11274  remove_attribute(CHARMMAtom self, FloatsKey a0)
11275  remove_attribute(CHARMMAtom self, IntsKey a0)
11276  remove_attribute(CHARMMAtom self, StringKey a0)
11277  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11278  remove_attribute(CHARMMAtom self, ObjectKey a0)
11279  remove_attribute(CHARMMAtom self, SparseFloatKey a0)
11280  remove_attribute(CHARMMAtom self, SparseIntKey a0)
11281  remove_attribute(CHARMMAtom self, SparseStringKey a0)
11282  remove_attribute(CHARMMAtom self, SparseParticleIndexKey a0)
11283  """
11284  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11285 
11286  def has_attribute(self, *args):
11287  r"""
11288  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11289  has_attribute(CHARMMAtom self, IntKey a0) -> bool
11290  has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
11291  has_attribute(CHARMMAtom self, IntsKey a0) -> bool
11292  has_attribute(CHARMMAtom self, StringKey a0) -> bool
11293  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11294  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11295  has_attribute(CHARMMAtom self, SparseFloatKey a0) -> bool
11296  has_attribute(CHARMMAtom self, SparseIntKey a0) -> bool
11297  has_attribute(CHARMMAtom self, SparseStringKey a0) -> bool
11298  has_attribute(CHARMMAtom self, SparseParticleIndexKey a0) -> bool
11299  """
11300  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11301 
11302  def get_derivative(self, a0):
11303  r"""get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11304  return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11305 
11306  def get_name(self):
11307  r"""get_name(CHARMMAtom self) -> std::string"""
11308  return _IMP_atom.CHARMMAtom_get_name(self)
11309 
11310  def clear_caches(self):
11311  r"""clear_caches(CHARMMAtom self)"""
11312  return _IMP_atom.CHARMMAtom_clear_caches(self)
11313 
11314  def set_name(self, a0):
11315  r"""set_name(CHARMMAtom self, std::string a0)"""
11316  return _IMP_atom.CHARMMAtom_set_name(self, a0)
11317 
11318  def set_check_level(self, a0):
11319  r"""set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11320  return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11321 
11322  def add_to_derivative(self, a0, a1, a2):
11323  r"""add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11324  return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11325 
11326  def set_is_optimized(self, a0, a1):
11327  r"""set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11328  return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11329 
11330  def get_is_optimized(self, a0):
11331  r"""get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11332  return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11333 
11334  def get_check_level(self):
11335  r"""get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11336  return _IMP_atom.CHARMMAtom_get_check_level(self)
11337 
11338  def __eq__(self, *args):
11339  r"""
11340  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11341  __eq__(CHARMMAtom self, Particle d) -> bool
11342  """
11343  return _IMP_atom.CHARMMAtom___eq__(self, *args)
11344 
11345  def __ne__(self, *args):
11346  r"""
11347  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11348  __ne__(CHARMMAtom self, Particle d) -> bool
11349  """
11350  return _IMP_atom.CHARMMAtom___ne__(self, *args)
11351 
11352  def __le__(self, *args):
11353  r"""
11354  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11355  __le__(CHARMMAtom self, Particle d) -> bool
11356  """
11357  return _IMP_atom.CHARMMAtom___le__(self, *args)
11358 
11359  def __lt__(self, *args):
11360  r"""
11361  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11362  __lt__(CHARMMAtom self, Particle d) -> bool
11363  """
11364  return _IMP_atom.CHARMMAtom___lt__(self, *args)
11365 
11366  def __ge__(self, *args):
11367  r"""
11368  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11369  __ge__(CHARMMAtom self, Particle d) -> bool
11370  """
11371  return _IMP_atom.CHARMMAtom___ge__(self, *args)
11372 
11373  def __gt__(self, *args):
11374  r"""
11375  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11376  __gt__(CHARMMAtom self, Particle d) -> bool
11377  """
11378  return _IMP_atom.CHARMMAtom___gt__(self, *args)
11379 
11380  def __hash__(self):
11381  r"""__hash__(CHARMMAtom self) -> std::size_t"""
11382  return _IMP_atom.CHARMMAtom___hash__(self)
11383 
11384  def __str__(self):
11385  r"""__str__(CHARMMAtom self) -> std::string"""
11386  return _IMP_atom.CHARMMAtom___str__(self)
11387 
11388  def __repr__(self):
11389  r"""__repr__(CHARMMAtom self) -> std::string"""
11390  return _IMP_atom.CHARMMAtom___repr__(self)
11391 
11392  def _get_as_binary(self):
11393  r"""_get_as_binary(CHARMMAtom self) -> PyObject *"""
11394  return _IMP_atom.CHARMMAtom__get_as_binary(self)
11395 
11396  def _set_from_binary(self, p):
11397  r"""_set_from_binary(CHARMMAtom self, PyObject * p)"""
11398  return _IMP_atom.CHARMMAtom__set_from_binary(self, p)
11399 
11400  def __getstate__(self):
11401  p = self._get_as_binary()
11402  if len(self.__dict__) > 1:
11403  d = self.__dict__.copy()
11404  del d['this']
11405  p = (d, p)
11406  return p
11407 
11408  def __setstate__(self, p):
11409  if not hasattr(self, 'this'):
11410  self.__init__()
11411  if isinstance(p, tuple):
11412  d, p = p
11413  self.__dict__.update(d)
11414  return self._set_from_binary(p)
11415 
11416  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11417 
11418 # Register CHARMMAtom in _IMP_atom:
11419 _IMP_atom.CHARMMAtom_swigregister(CHARMMAtom)
11420 
11421 def get_charmm_untyped_atoms(hierarchy):
11422  r"""get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11423  return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11424 
11425 def remove_charmm_untyped_atoms(hierarchy):
11426  r"""remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11427  return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11428 class CHARMMBondParameters(object):
11429  r"""Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11430 
11431  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11432  force_constant = property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set, doc=r"""force_constant : double""")
11433  ideal = property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set, doc=r"""ideal : double""")
11434 
11435  def __init__(self):
11436  r"""__init__(CHARMMBondParameters self) -> CHARMMBondParameters"""
11437  _IMP_atom.CHARMMBondParameters_swiginit(self, _IMP_atom.new_CHARMMBondParameters())
11438 
11439  def show(self, *args):
11440  r"""show(CHARMMBondParameters self, _ostream out=std::cout)"""
11441  return _IMP_atom.CHARMMBondParameters_show(self, *args)
11442 
11443  def __str__(self):
11444  r"""__str__(CHARMMBondParameters self) -> std::string"""
11445  return _IMP_atom.CHARMMBondParameters___str__(self)
11446 
11447  def __repr__(self):
11448  r"""__repr__(CHARMMBondParameters self) -> std::string"""
11449  return _IMP_atom.CHARMMBondParameters___repr__(self)
11450 
11451  def _get_as_binary(self):
11452  r"""_get_as_binary(CHARMMBondParameters self) -> PyObject *"""
11453  return _IMP_atom.CHARMMBondParameters__get_as_binary(self)
11454 
11455  def _set_from_binary(self, p):
11456  r"""_set_from_binary(CHARMMBondParameters self, PyObject * p)"""
11457  return _IMP_atom.CHARMMBondParameters__set_from_binary(self, p)
11458 
11459  def __getstate__(self):
11460  p = self._get_as_binary()
11461  if len(self.__dict__) > 1:
11462  d = self.__dict__.copy()
11463  del d['this']
11464  p = (d, p)
11465  return p
11466 
11467  def __setstate__(self, p):
11468  if not hasattr(self, 'this'):
11469  self.__init__()
11470  if isinstance(p, tuple):
11471  d, p = p
11472  self.__dict__.update(d)
11473  return self._set_from_binary(p)
11474 
11475  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11476 
11477 # Register CHARMMBondParameters in _IMP_atom:
11478 _IMP_atom.CHARMMBondParameters_swigregister(CHARMMBondParameters)
11479 class CHARMMDihedralParameters(object):
11480  r"""Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11481 
11482  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11483  force_constant = property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set, doc=r"""force_constant : double""")
11484  multiplicity = property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set, doc=r"""multiplicity : int""")
11485  ideal = property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set, doc=r"""ideal : double""")
11486 
11487  def __init__(self):
11488  r"""__init__(CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11489  _IMP_atom.CHARMMDihedralParameters_swiginit(self, _IMP_atom.new_CHARMMDihedralParameters())
11490 
11491  def show(self, *args):
11492  r"""show(CHARMMDihedralParameters self, _ostream out=std::cout)"""
11493  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11494 
11495  def __str__(self):
11496  r"""__str__(CHARMMDihedralParameters self) -> std::string"""
11497  return _IMP_atom.CHARMMDihedralParameters___str__(self)
11498 
11499  def __repr__(self):
11500  r"""__repr__(CHARMMDihedralParameters self) -> std::string"""
11501  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11502 
11503  def _get_as_binary(self):
11504  r"""_get_as_binary(CHARMMDihedralParameters self) -> PyObject *"""
11505  return _IMP_atom.CHARMMDihedralParameters__get_as_binary(self)
11506 
11507  def _set_from_binary(self, p):
11508  r"""_set_from_binary(CHARMMDihedralParameters self, PyObject * p)"""
11509  return _IMP_atom.CHARMMDihedralParameters__set_from_binary(self, p)
11510 
11511  def __getstate__(self):
11512  p = self._get_as_binary()
11513  if len(self.__dict__) > 1:
11514  d = self.__dict__.copy()
11515  del d['this']
11516  p = (d, p)
11517  return p
11518 
11519  def __setstate__(self, p):
11520  if not hasattr(self, 'this'):
11521  self.__init__()
11522  if isinstance(p, tuple):
11523  d, p = p
11524  self.__dict__.update(d)
11525  return self._set_from_binary(p)
11526 
11527  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11528 
11529 # Register CHARMMDihedralParameters in _IMP_atom:
11530 _IMP_atom.CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11531 class CHARMMParameters(ForceFieldParameters):
11532  r"""Proxy of C++ IMP::atom::CHARMMParameters class."""
11533 
11534  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11535 
11536  def __init__(self, *args):
11537  r"""__init__(CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters"""
11538  _IMP_atom.CHARMMParameters_swiginit(self, _IMP_atom.new_CHARMMParameters(*args))
11539 
11540  def add_residue_topology(self, res):
11541  r"""add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11542  return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11543 
11544  def get_residue_topology(self, type):
11545  r"""get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11546  return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11547 
11548  def add_patch(self, patch):
11549  r"""add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11550  return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11551 
11552  def get_patch(self, name):
11553  r"""get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11554  return _IMP_atom.CHARMMParameters_get_patch(self, name)
11555 
11556  def create_topology(self, hierarchy):
11557  r"""create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11558  return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11559 
11560  def get_bond_parameters(self, type1, type2):
11561  r"""get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11562  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11563 
11564  def get_angle_parameters(self, type1, type2, type3):
11565  r"""get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11566  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11567 
11568  def get_dihedral_parameters(self, type1, type2, type3, type4):
11569  r"""get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11570  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11571 
11572  def get_improper_parameters(self, type1, type2, type3, type4):
11573  r"""get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11574  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11575 
11576  def create_angles(self, bonds):
11577  r"""create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11578  return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11579 
11580  def create_dihedrals(self, bonds):
11581  r"""create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11582  return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11583 
11584  def get_version_info(self):
11585  r"""get_version_info(CHARMMParameters self) -> VersionInfo"""
11586  return _IMP_atom.CHARMMParameters_get_version_info(self)
11587  __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
11588 
11589  def __str__(self):
11590  r"""__str__(CHARMMParameters self) -> std::string"""
11591  return _IMP_atom.CHARMMParameters___str__(self)
11592 
11593  def __repr__(self):
11594  r"""__repr__(CHARMMParameters self) -> std::string"""
11595  return _IMP_atom.CHARMMParameters___repr__(self)
11596 
11597  @staticmethod
11598  def get_from(o):
11599  return _object_cast_to_CHARMMParameters(o)
11600 
11601 
11602 # Register CHARMMParameters in _IMP_atom:
11603 _IMP_atom.CHARMMParameters_swigregister(CHARMMParameters)
11604 
11606  r"""get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11607  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11608 
11610  r"""get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11611  return _IMP_atom.get_all_atom_CHARMM_parameters()
11612 class CHARMMSegmentTopology(IMP.Object):
11613  r"""Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11614 
11615  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11616  def __get_residues(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_residues, getfunc=self.get_residue, erasefunc=self.erase_residue, appendfunc=self.add_residue, extendfunc=self.add_residues, clearfunc=self.clear_residues, indexfunc=self._python_index_residue)
11617  def __set_residues(self, obj): IMP._list_util.set_varlist(self.residues, obj)
11618  def __del_residues(self): IMP._list_util.del_varlist(self.residues)
11619  residues = property(__get_residues, __set_residues, __del_residues, doc="List of ##ucnames")
11620 
11621  def remove_residue(self, d):
11622  r"""remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11623  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11624 
11625  def _python_index_residue(self, d, start, stop):
11626  r"""_python_index_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11627  return _IMP_atom.CHARMMSegmentTopology__python_index_residue(self, d, start, stop)
11628 
11629  def remove_residues(self, d):
11630  r"""remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11631  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11632 
11633  def set_residues(self, ps):
11634  r"""set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11635  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11636 
11637  def set_residues_order(self, objs):
11638  r"""set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11639  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11640 
11641  def add_residue(self, obj):
11642  r"""add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11643  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11644 
11645  def add_residues(self, objs):
11646  r"""add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11647  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11648 
11649  def clear_residues(self):
11650  r"""clear_residues(CHARMMSegmentTopology self)"""
11651  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11652 
11653  def get_number_of_residues(self):
11654  r"""get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11655  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11656 
11657  def get_has_residues(self):
11658  r"""get_has_residues(CHARMMSegmentTopology self) -> bool"""
11659  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11660 
11661  def get_residue(self, i):
11662  r"""get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11663  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11664 
11665  def get_residues(self):
11666  r"""get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11667  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11668 
11669  def erase_residue(self, i):
11670  r"""erase_residue(CHARMMSegmentTopology self, unsigned int i)"""
11671  return _IMP_atom.CHARMMSegmentTopology_erase_residue(self, i)
11672 
11673  def reserve_residues(self, sz):
11674  r"""reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11675  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11676 
11677  def get_version_info(self):
11678  r"""get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11679  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11680  __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
11681 
11682  def __init__(self, *args):
11683  r"""__init__(CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology"""
11684  _IMP_atom.CHARMMSegmentTopology_swiginit(self, _IMP_atom.new_CHARMMSegmentTopology(*args))
11685 
11686  def apply_default_patches(self, ff):
11687  r"""apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11688  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11689 
11690  def __str__(self):
11691  r"""__str__(CHARMMSegmentTopology self) -> std::string"""
11692  return _IMP_atom.CHARMMSegmentTopology___str__(self)
11693 
11694  def __repr__(self):
11695  r"""__repr__(CHARMMSegmentTopology self) -> std::string"""
11696  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11697 
11698  @staticmethod
11699  def get_from(o):
11700  return _object_cast_to_CHARMMSegmentTopology(o)
11701 
11702 
11703 # Register CHARMMSegmentTopology in _IMP_atom:
11704 _IMP_atom.CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11705 class CHARMMTopology(IMP.Object):
11706  r"""Proxy of C++ IMP::atom::CHARMMTopology class."""
11707 
11708  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11709 
11710  def __init__(self, *args):
11711  r"""__init__(CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology"""
11712  _IMP_atom.CHARMMTopology_swiginit(self, _IMP_atom.new_CHARMMTopology(*args))
11713 
11714  def get_parameters(self):
11715  r"""get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11716  return _IMP_atom.CHARMMTopology_get_parameters(self)
11717 
11718  def add_sequence(self, sequence):
11719  r"""add_sequence(CHARMMTopology self, std::string sequence)"""
11720  return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11721 
11722  def apply_default_patches(self):
11723  r"""apply_default_patches(CHARMMTopology self)"""
11724  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11725 
11726  def create_hierarchy(self, model):
11727  r"""create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11728  return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11729 
11730  def add_atom_types(self, hierarchy):
11731  r"""add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11732  return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11733 
11734  def add_coordinates(self, hierarchy):
11735  r"""add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11736  return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11737 
11738  def add_missing_atoms(self, hierarchy):
11739  r"""add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11740  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11741 
11742  def setup_hierarchy(self, hierarchy):
11743  r"""setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11744  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11745 
11746  def add_charges(self, hierarchy):
11747  r"""add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11748  return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11749 
11750  def add_bonds(self, hierarchy):
11751  r"""add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11752  return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11753 
11754  def add_dihedrals(self, hierarchy):
11755  r"""add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11756  return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11757 
11758  def add_impropers(self, hierarchy):
11759  r"""add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11760  return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11761  def __get_segments(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_segments, getfunc=self.get_segment, erasefunc=self.erase_segment, appendfunc=self.add_segment, extendfunc=self.add_segments, clearfunc=self.clear_segments, indexfunc=self._python_index_segment)
11762  def __set_segments(self, obj): IMP._list_util.set_varlist(self.segments, obj)
11763  def __del_segments(self): IMP._list_util.del_varlist(self.segments)
11764  segments = property(__get_segments, __set_segments, __del_segments, doc="List of ##ucnames")
11765 
11766  def remove_segment(self, d):
11767  r"""remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11768  return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11769 
11770  def _python_index_segment(self, d, start, stop):
11771  r"""_python_index_segment(CHARMMTopology self, CHARMMSegmentTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11772  return _IMP_atom.CHARMMTopology__python_index_segment(self, d, start, stop)
11773 
11774  def remove_segments(self, d):
11775  r"""remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11776  return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11777 
11778  def set_segments(self, ps):
11779  r"""set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11780  return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11781 
11782  def set_segments_order(self, objs):
11783  r"""set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11784  return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11785 
11786  def add_segment(self, obj):
11787  r"""add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11788  return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11789 
11790  def add_segments(self, objs):
11791  r"""add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11792  return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11793 
11794  def clear_segments(self):
11795  r"""clear_segments(CHARMMTopology self)"""
11796  return _IMP_atom.CHARMMTopology_clear_segments(self)
11797 
11798  def get_number_of_segments(self):
11799  r"""get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11800  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11801 
11802  def get_has_segments(self):
11803  r"""get_has_segments(CHARMMTopology self) -> bool"""
11804  return _IMP_atom.CHARMMTopology_get_has_segments(self)
11805 
11806  def get_segment(self, i):
11807  r"""get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11808  return _IMP_atom.CHARMMTopology_get_segment(self, i)
11809 
11810  def get_segments(self):
11811  r"""get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11812  return _IMP_atom.CHARMMTopology_get_segments(self)
11813 
11814  def erase_segment(self, i):
11815  r"""erase_segment(CHARMMTopology self, unsigned int i)"""
11816  return _IMP_atom.CHARMMTopology_erase_segment(self, i)
11817 
11818  def reserve_segments(self, sz):
11819  r"""reserve_segments(CHARMMTopology self, unsigned int sz)"""
11820  return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11821 
11822  def get_version_info(self):
11823  r"""get_version_info(CHARMMTopology self) -> VersionInfo"""
11824  return _IMP_atom.CHARMMTopology_get_version_info(self)
11825  __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
11826 
11827  def __str__(self):
11828  r"""__str__(CHARMMTopology self) -> std::string"""
11829  return _IMP_atom.CHARMMTopology___str__(self)
11830 
11831  def __repr__(self):
11832  r"""__repr__(CHARMMTopology self) -> std::string"""
11833  return _IMP_atom.CHARMMTopology___repr__(self)
11834 
11835  @staticmethod
11836  def get_from(o):
11837  return _object_cast_to_CHARMMTopology(o)
11838 
11839 
11840 # Register CHARMMTopology in _IMP_atom:
11841 _IMP_atom.CHARMMTopology_swigregister(CHARMMTopology)
11842 class CHARMMStereochemistryRestraint(IMP.Restraint):
11843  r"""Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11844 
11845  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11846 
11847  def __init__(self, *args):
11848  r"""
11849  __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11850  __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11851  """
11852  _IMP_atom.CHARMMStereochemistryRestraint_swiginit(self, _IMP_atom.new_CHARMMStereochemistryRestraint(*args))
11853 
11854  def get_pair_filter(self):
11855  r"""get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11856  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11857 
11858  def get_full_pair_filter(self):
11859  r"""get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11860  return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11861 
11862  def do_get_inputs(self):
11863  r"""do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11864  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11865 
11866  def get_version_info(self):
11867  r"""get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11868  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11869  __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
11870 
11871  def __str__(self):
11872  r"""__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11873  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11874 
11875  def __repr__(self):
11876  r"""__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11877  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11878 
11879  @staticmethod
11880  def get_from(o):
11881  return _object_cast_to_CHARMMStereochemistryRestraint(o)
11882 
11883 
11884 # Register CHARMMStereochemistryRestraint in _IMP_atom:
11885 _IMP_atom.CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11886 
11887 def add_bonds(*args):
11888  r"""add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())"""
11889  return _IMP_atom.add_bonds(*args)
11890 
11891 def add_radii(*args):
11892  r"""add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(), FloatKey radius_key=IMP::FloatKey("radius"))"""
11893  return _IMP_atom.add_radii(*args)
11894 ALBER = _IMP_atom.ALBER
11895 
11896 HARPAZ = _IMP_atom.HARPAZ
11897 
11898 ANDERSSON = _IMP_atom.ANDERSSON
11899 
11900 TSAI = _IMP_atom.TSAI
11901 
11902 QUILLIN = _IMP_atom.QUILLIN
11903 
11904 SQUIRE = _IMP_atom.SQUIRE
11905 
11906 
11907 def get_protein_density_from_reference(densityReference):
11908  r"""get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11909  return _IMP_atom.get_protein_density_from_reference(densityReference)
11910 
11911 def get_volume_from_mass(*args):
11912  r"""get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11913  return _IMP_atom.get_volume_from_mass(*args)
11914 
11915 def get_mass_from_volume(*args):
11916  r"""get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11917  return _IMP_atom.get_mass_from_volume(*args)
11918 
11920  r"""get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11921  return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11922 
11924  r"""get_volume_from_residue_type(ResidueType rt) -> double"""
11925  return _IMP_atom.get_volume_from_residue_type(rt)
11926 
11927 def get_molarity(n, volume):
11928  r"""get_molarity(double n, double volume) -> double"""
11929  return _IMP_atom.get_molarity(n, volume)
11930 
11931 def get_kd(na, nb, nab, volume):
11932  r"""get_kd(double na, double nb, double nab, double volume) -> double"""
11933  return _IMP_atom.get_kd(na, nb, nab, volume)
11934 
11935 def get_einstein_diffusion_coefficient(r, temp=-1):
11936  r"""get_einstein_diffusion_coefficient(double r, double temp=-1) -> double"""
11937  return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
11938 
11940  r"""get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double"""
11941  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
11942 
11943 def get_diffusion_length(*args):
11944  r"""
11945  get_diffusion_length(double D, double t) -> double
11946  get_diffusion_length(double D, double force, double t, double temp=-1) -> double
11947  """
11948  return _IMP_atom.get_diffusion_length(*args)
11949 
11950 def get_diffusion_angle(D, dtfs):
11951  r"""get_diffusion_angle(double D, double dtfs) -> double"""
11952  return _IMP_atom.get_diffusion_angle(D, dtfs)
11953 
11954 def get_diffusion_coefficient(*args):
11955  r"""
11956  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
11957  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
11958  """
11959  return _IMP_atom.get_diffusion_coefficient(*args)
11960 
11961 def get_rotational_diffusion_coefficient(orientations, dt):
11962  r"""get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
11963  return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
11964 
11965 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11966  r"""get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11967  return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11968 
11969 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
11970  r"""get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11971  return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11972 
11973 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
11974  r"""get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11975  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11976 class EzRestraint(IMP.Restraint):
11977  r"""Proxy of C++ IMP::atom::EzRestraint class."""
11978 
11979  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11980 
11981  def __init__(self, m, ps):
11982  r"""__init__(EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11983  _IMP_atom.EzRestraint_swiginit(self, _IMP_atom.new_EzRestraint(m, ps))
11984 
11985  def get_version_info(self):
11986  r"""get_version_info(EzRestraint self) -> VersionInfo"""
11987  return _IMP_atom.EzRestraint_get_version_info(self)
11988  __swig_destroy__ = _IMP_atom.delete_EzRestraint
11989 
11990  def __str__(self):
11991  r"""__str__(EzRestraint self) -> std::string"""
11992  return _IMP_atom.EzRestraint___str__(self)
11993 
11994  def __repr__(self):
11995  r"""__repr__(EzRestraint self) -> std::string"""
11996  return _IMP_atom.EzRestraint___repr__(self)
11997 
11998  @staticmethod
11999  def get_from(o):
12000  return _object_cast_to_EzRestraint(o)
12001 
12002 
12003 # Register EzRestraint in _IMP_atom:
12004 _IMP_atom.EzRestraint_swigregister(EzRestraint)
12005 
12006 def create_protein(*args):
12007  r"""
12008  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1, bool ismol=True) -> Hierarchy
12009  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12010  """
12011  return _IMP_atom.create_protein(*args)
12012 
12014  r"""
12015  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12016  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12017  """
12018  return _IMP_atom.create_simplified_along_backbone(*args)
12019 
12020 def create_simplified_from_volume(h, resolution):
12021  r"""create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12022  return _IMP_atom.create_simplified_from_volume(h, resolution)
12023 
12024 def create_simplified_assembly_from_volume(h, resolution):
12025  r"""create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12026  return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12027 
12028 def get_residue_indexes(h):
12029  r"""get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12030  return _IMP_atom.get_residue_indexes(h)
12031 
12032 def get_residue_type(*args):
12033  r"""
12034  get_residue_type(char c) -> ResidueType
12035  get_residue_type(Hierarchy h) -> ResidueType
12036  """
12037  return _IMP_atom.get_residue_type(*args)
12038 
12039 def get_atom_type(h):
12040  r"""get_atom_type(Hierarchy h) -> AtomType"""
12041  return _IMP_atom.get_atom_type(h)
12042 
12043 def get_domain_name(h):
12044  r"""get_domain_name(Hierarchy h) -> std::string"""
12045  return _IMP_atom.get_domain_name(h)
12046 
12048  r"""
12049  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12050  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12051  """
12052  return _IMP_atom.create_excluded_volume_restraint(*args)
12053 
12054 def setup_as_approximation(*args):
12055  r"""
12056  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12057  setup_as_approximation(Hierarchy h, double resolution=-1)
12058  """
12059  return _IMP_atom.setup_as_approximation(*args)
12060 class _HierarchyTreeVertexIndex(object):
12061  r"""Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
12062 
12063  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12064  __repr__ = _swig_repr
12065 
12066  def __init__(self):
12067  r"""__init__(_HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12068  _IMP_atom._HierarchyTreeVertexIndex_swiginit(self, _IMP_atom.new__HierarchyTreeVertexIndex())
12069  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12070 
12071 # Register _HierarchyTreeVertexIndex in _IMP_atom:
12072 _IMP_atom._HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12073 
12074 def show_as_graphviz(name, out):
12075  r"""show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12076  return _IMP_atom.show_as_graphviz(name, out)
12077 
12078 def get_vertex_index(g):
12079  r"""get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12080  return _IMP_atom.get_vertex_index(g)
12081 
12082 def get_hierarchy_tree(h):
12083  r"""get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12084  return _IMP_atom.get_hierarchy_tree(h)
12085 class HierarchyGeometry(IMP.display.SingletonGeometry):
12086  r"""Proxy of C++ IMP::atom::HierarchyGeometry class."""
12087 
12088  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12089 
12090  def __init__(self, d, resolution=0):
12091  r"""__init__(HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry"""
12092  _IMP_atom.HierarchyGeometry_swiginit(self, _IMP_atom.new_HierarchyGeometry(d, resolution))
12093 
12094  def get_version_info(self):
12095  r"""get_version_info(HierarchyGeometry self) -> VersionInfo"""
12096  return _IMP_atom.HierarchyGeometry_get_version_info(self)
12097  __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
12098 
12099  def __str__(self):
12100  r"""__str__(HierarchyGeometry self) -> std::string"""
12101  return _IMP_atom.HierarchyGeometry___str__(self)
12102 
12103  def __repr__(self):
12104  r"""__repr__(HierarchyGeometry self) -> std::string"""
12105  return _IMP_atom.HierarchyGeometry___repr__(self)
12106 
12107  @staticmethod
12108  def get_from(o):
12109  return _object_cast_to_HierarchyGeometry(o)
12110 
12111 
12112 # Register HierarchyGeometry in _IMP_atom:
12113 _IMP_atom.HierarchyGeometry_swigregister(HierarchyGeometry)
12114 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
12115  r"""Proxy of C++ IMP::atom::HierarchiesGeometry class."""
12116 
12117  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12118 
12119  def __init__(self, sc, resolution=-1):
12120  r"""__init__(HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry"""
12121  _IMP_atom.HierarchiesGeometry_swiginit(self, _IMP_atom.new_HierarchiesGeometry(sc, resolution))
12122 
12123  def get_version_info(self):
12124  r"""get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12125  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12126  __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
12127 
12128  def __str__(self):
12129  r"""__str__(HierarchiesGeometry self) -> std::string"""
12130  return _IMP_atom.HierarchiesGeometry___str__(self)
12131 
12132  def __repr__(self):
12133  r"""__repr__(HierarchiesGeometry self) -> std::string"""
12134  return _IMP_atom.HierarchiesGeometry___repr__(self)
12135 
12136  @staticmethod
12137  def get_from(o):
12138  return _object_cast_to_HierarchiesGeometry(o)
12139 
12140 
12141 # Register HierarchiesGeometry in _IMP_atom:
12142 _IMP_atom.HierarchiesGeometry_swigregister(HierarchiesGeometry)
12143 
12144 def transform(*args):
12145  r"""
12146  transform(Hierarchy h, Transformation3D tr)
12147  transform(Hierarchy h, Transformation3D tr)
12148  """
12149  return _IMP_atom.transform(*args)
12150 class DopePairScore(_ADopeBase):
12151  r"""Proxy of C++ IMP::atom::DopePairScore class."""
12152 
12153  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12154 
12155  def __init__(self, *args):
12156  r"""
12157  __init__(DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
12158  __init__(DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12159  """
12160  _IMP_atom.DopePairScore_swiginit(self, _IMP_atom.new_DopePairScore(*args))
12161 
12162  def __str__(self):
12163  r"""__str__(DopePairScore self) -> std::string"""
12164  return _IMP_atom.DopePairScore___str__(self)
12165 
12166  def __repr__(self):
12167  r"""__repr__(DopePairScore self) -> std::string"""
12168  return _IMP_atom.DopePairScore___repr__(self)
12169 
12170  @staticmethod
12171  def get_from(o):
12172  return _object_cast_to_DopePairScore(o)
12173 
12174  __swig_destroy__ = _IMP_atom.delete_DopePairScore
12175 
12176 # Register DopePairScore in _IMP_atom:
12177 _IMP_atom.DopePairScore_swigregister(DopePairScore)
12178 
12179 def add_dope_score_data(h):
12180  r"""add_dope_score_data(Hierarchy h)"""
12181  return _IMP_atom.add_dope_score_data(h)
12182 class LoopStatisticalPairScore(_ALoopStatisticalBase):
12183  r"""Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
12184 
12185  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12186 
12187  def __init__(self, *args):
12188  r"""
12189  __init__(LoopStatisticalPairScore self, double threshold=std::numeric_limits< double >::max()) -> LoopStatisticalPairScore
12190  __init__(LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
12191  """
12192  _IMP_atom.LoopStatisticalPairScore_swiginit(self, _IMP_atom.new_LoopStatisticalPairScore(*args))
12193 
12194  def __str__(self):
12195  r"""__str__(LoopStatisticalPairScore self) -> std::string"""
12196  return _IMP_atom.LoopStatisticalPairScore___str__(self)
12197 
12198  def __repr__(self):
12199  r"""__repr__(LoopStatisticalPairScore self) -> std::string"""
12200  return _IMP_atom.LoopStatisticalPairScore___repr__(self)
12201 
12202  @staticmethod
12203  def get_from(o):
12204  return _object_cast_to_LoopStatisticalPairScore(o)
12205 
12206  __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
12207 
12208 # Register LoopStatisticalPairScore in _IMP_atom:
12209 _IMP_atom.LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
12210 
12212  r"""add_loop_statistical_score_data(Hierarchy h)"""
12213  return _IMP_atom.add_loop_statistical_score_data(h)
12214 class OrientedSoapPairScore(_OrientedSoapBase):
12215  r"""Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
12216 
12217  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12218 
12219  def __init__(self, library):
12220  r"""__init__(OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12221  _IMP_atom.OrientedSoapPairScore_swiginit(self, _IMP_atom.new_OrientedSoapPairScore(library))
12222 
12223  def get_pair_filter(self):
12224  r"""get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12225  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12226 
12227  def __str__(self):
12228  r"""__str__(OrientedSoapPairScore self) -> std::string"""
12229  return _IMP_atom.OrientedSoapPairScore___str__(self)
12230 
12231  def __repr__(self):
12232  r"""__repr__(OrientedSoapPairScore self) -> std::string"""
12233  return _IMP_atom.OrientedSoapPairScore___repr__(self)
12234 
12235  @staticmethod
12236  def get_from(o):
12237  return _object_cast_to_OrientedSoapPairScore(o)
12238 
12239  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12240 
12241 # Register OrientedSoapPairScore in _IMP_atom:
12242 _IMP_atom.OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12243 class SameResiduePairFilter(IMP.PairPredicate):
12244  r"""Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12245 
12246  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12247 
12248  def __init__(self):
12249  r"""__init__(SameResiduePairFilter self) -> SameResiduePairFilter"""
12250  _IMP_atom.SameResiduePairFilter_swiginit(self, _IMP_atom.new_SameResiduePairFilter())
12251 
12252  def do_get_inputs(self, m, pis):
12253  r"""do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12254  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12255 
12256  def get_value(self, *args):
12257  r"""
12258  get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12259  get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12260  """
12261  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12262 
12263  def get_value_index(self, *args):
12264  r"""
12265  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12266  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12267  """
12268  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12269 
12270  def get_version_info(self):
12271  r"""get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12272  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12273  __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
12274 
12275  def __str__(self):
12276  r"""__str__(SameResiduePairFilter self) -> std::string"""
12277  return _IMP_atom.SameResiduePairFilter___str__(self)
12278 
12279  def __repr__(self):
12280  r"""__repr__(SameResiduePairFilter self) -> std::string"""
12281  return _IMP_atom.SameResiduePairFilter___repr__(self)
12282 
12283  @staticmethod
12284  def get_from(o):
12285  return _object_cast_to_SameResiduePairFilter(o)
12286 
12287 
12288 # Register SameResiduePairFilter in _IMP_atom:
12289 _IMP_atom.SameResiduePairFilter_swigregister(SameResiduePairFilter)
12290 class RemoveRigidMotionOptimizerState(IMP.OptimizerState):
12291  r"""Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12292 
12293  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12294 
12295  def __init__(self, m, pis):
12296  r"""__init__(RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12297  _IMP_atom.RemoveRigidMotionOptimizerState_swiginit(self, _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis))
12298 
12299  def set_particles(self, pis):
12300  r"""set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12301  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12302 
12303  def remove_rigid_motion(self):
12304  r"""remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12305  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12306 
12307  def get_version_info(self):
12308  r"""get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12309  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12310  __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
12311 
12312  def __str__(self):
12313  r"""__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12314  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12315 
12316  def __repr__(self):
12317  r"""__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12318  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12319 
12320  @staticmethod
12321  def get_from(o):
12322  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12323 
12324 
12325 # Register RemoveRigidMotionOptimizerState in _IMP_atom:
12326 _IMP_atom.RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12327 class BerendsenThermostatOptimizerState(IMP.OptimizerState):
12328  r"""Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12329 
12330  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12331 
12332  def __init__(self, pis, temperature, tau):
12333  r"""__init__(BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12334  _IMP_atom.BerendsenThermostatOptimizerState_swiginit(self, _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau))
12335 
12336  def set_particles(self, pis):
12337  r"""set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12338  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12339 
12340  def get_temperature(self):
12341  r"""get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12342  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12343 
12344  def get_tau(self):
12345  r"""get_tau(BerendsenThermostatOptimizerState self) -> double"""
12346  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12347 
12348  def set_temperature(self, temperature):
12349  r"""set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12350  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12351 
12352  def set_tau(self, tau):
12353  r"""set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12354  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12355 
12356  def rescale_velocities(self):
12357  r"""rescale_velocities(BerendsenThermostatOptimizerState self)"""
12358  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12359 
12360  def get_version_info(self):
12361  r"""get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12362  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12363  __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
12364 
12365  def __str__(self):
12366  r"""__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12367  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12368 
12369  def __repr__(self):
12370  r"""__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12371  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12372 
12373  @staticmethod
12374  def get_from(o):
12375  return _object_cast_to_BerendsenThermostatOptimizerState(o)
12376 
12377 
12378 # Register BerendsenThermostatOptimizerState in _IMP_atom:
12379 _IMP_atom.BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12380 class LangevinThermostatOptimizerState(IMP.OptimizerState):
12381  r"""Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12382 
12383  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12384 
12385  def __init__(self, m, pis, temperature, gamma):
12386  r"""__init__(LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12387  _IMP_atom.LangevinThermostatOptimizerState_swiginit(self, _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma))
12388 
12389  def set_particles(self, pis):
12390  r"""set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12391  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12392 
12393  def get_temperature(self):
12394  r"""get_temperature(LangevinThermostatOptimizerState self) -> double"""
12395  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12396 
12397  def get_gamma(self):
12398  r"""get_gamma(LangevinThermostatOptimizerState self) -> double"""
12399  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12400 
12401  def set_temperature(self, temperature):
12402  r"""set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12403  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12404 
12405  def set_gamma(self, gamma):
12406  r"""set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12407  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12408 
12409  def rescale_velocities(self):
12410  r"""rescale_velocities(LangevinThermostatOptimizerState self)"""
12411  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12412 
12413  def get_version_info(self):
12414  r"""get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12415  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12416  __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
12417 
12418  def __str__(self):
12419  r"""__str__(LangevinThermostatOptimizerState self) -> std::string"""
12420  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12421 
12422  def __repr__(self):
12423  r"""__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12424  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12425 
12426  @staticmethod
12427  def get_from(o):
12428  return _object_cast_to_LangevinThermostatOptimizerState(o)
12429 
12430 
12431 # Register LangevinThermostatOptimizerState in _IMP_atom:
12432 _IMP_atom.LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12433 class PDBRecord(IMP._Value):
12434  r"""Proxy of C++ IMP::atom::PDBRecord class."""
12435 
12436  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12437 
12438  def __init__(self):
12439  r"""__init__(PDBRecord self) -> PDBRecord"""
12440  _IMP_atom.PDBRecord_swiginit(self, _IMP_atom.new_PDBRecord())
12441 
12442  def get_alt_loc_indicator(self):
12443  r"""get_alt_loc_indicator(PDBRecord self) -> std::string"""
12444  return _IMP_atom.PDBRecord_get_alt_loc_indicator(self)
12445 
12446  def get_is_atom(self):
12447  r"""get_is_atom(PDBRecord self) -> bool"""
12448  return _IMP_atom.PDBRecord_get_is_atom(self)
12449 
12450  def get_trimmed_atom_name(self):
12451  r"""get_trimmed_atom_name(PDBRecord self) -> std::string"""
12452  return _IMP_atom.PDBRecord_get_trimmed_atom_name(self)
12453 
12454  def get_padded_atom_name(self):
12455  r"""get_padded_atom_name(PDBRecord self) -> std::string"""
12456  return _IMP_atom.PDBRecord_get_padded_atom_name(self)
12457 
12458  def get_residue_name(self):
12459  r"""get_residue_name(PDBRecord self) -> std::string"""
12460  return _IMP_atom.PDBRecord_get_residue_name(self)
12461 
12462  def get_chain_id(self):
12463  r"""get_chain_id(PDBRecord self) -> std::string"""
12464  return _IMP_atom.PDBRecord_get_chain_id(self)
12465 
12466  def get_element(self):
12467  r"""get_element(PDBRecord self) -> std::string"""
12468  return _IMP_atom.PDBRecord_get_element(self)
12469 
12470  def show(self, *args):
12471  r"""show(PDBRecord self, _ostream out=std::cout)"""
12472  return _IMP_atom.PDBRecord_show(self, *args)
12473 
12474  def __str__(self):
12475  r"""__str__(PDBRecord self) -> std::string"""
12476  return _IMP_atom.PDBRecord___str__(self)
12477 
12478  def __repr__(self):
12479  r"""__repr__(PDBRecord self) -> std::string"""
12480  return _IMP_atom.PDBRecord___repr__(self)
12481  __swig_destroy__ = _IMP_atom.delete_PDBRecord
12482 
12483 # Register PDBRecord in _IMP_atom:
12484 _IMP_atom.PDBRecord_swigregister(PDBRecord)
12485 class PDBSelector(IMP.Object):
12486  r"""Proxy of C++ IMP::atom::PDBSelector class."""
12487 
12488  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12489 
12490  def __init__(self, name):
12491  r"""__init__(PDBSelector self, std::string name) -> PDBSelector"""
12492  if self.__class__ == PDBSelector:
12493  _self = None
12494  else:
12495  _self = self
12496  _IMP_atom.PDBSelector_swiginit(self, _IMP_atom.new_PDBSelector(_self, name))
12497 
12498  if self.__class__ != PDBSelector:
12499  _director_objects.register(self)
12500 
12501 
12502 
12503 
12504  def get_is_selected(self, record):
12505  r"""get_is_selected(PDBSelector self, PDBRecord record) -> bool"""
12506  return _IMP_atom.PDBSelector_get_is_selected(self, record)
12507  __swig_destroy__ = _IMP_atom.delete_PDBSelector
12508 
12509  def __str__(self):
12510  r"""__str__(PDBSelector self) -> std::string"""
12511  return _IMP_atom.PDBSelector___str__(self)
12512 
12513  def __repr__(self):
12514  r"""__repr__(PDBSelector self) -> std::string"""
12515  return _IMP_atom.PDBSelector___repr__(self)
12516 
12517  @staticmethod
12518  def get_from(o):
12519  return _object_cast_to_PDBSelector(o)
12520 
12521 
12522  def get_type_name(self):
12523  return self.__class__.__name__
12524  def do_show(self, out):
12525  pass
12526  def get_version_info(self):
12527  if"IMP::atom" == "IMP":
12528  return VersionInfo(self.__module__,
12529  __import__(self.__module__).get_module_version())
12530  else:
12531  return IMP.VersionInfo(self.__module__,
12532  __import__(self.__module__).get_module_version())
12533  @staticmethod
12534  def get_from(o):
12535  return _object_cast_to_PDBSelector(o)
12536 
12537 
12538  def __and__(self, s):
12539  return AndPDBSelector(self, s)
12540  def __or__(self, s):
12541  return OrPDBSelector(self, s)
12542  def __xor__(self, s):
12543  return XorPDBSelector(self, s)
12544  def __invert__(self):
12545  return NotPDBSelector(self)
12546  def __sub__(self, s):
12547  return AndPDBSelector(self, NotPDBSelector(s))
12548 
12549  def __disown__(self):
12550  self.this.disown()
12551  _IMP_atom.disown_PDBSelector(self)
12552  return weakref.proxy(self)
12553 
12554  def do_destroy(self):
12555  r"""do_destroy(PDBSelector self)"""
12556  return _IMP_atom.PDBSelector_do_destroy(self)
12557 
12558 # Register PDBSelector in _IMP_atom:
12559 _IMP_atom.PDBSelector_swigregister(PDBSelector)
12560 class NonAlternativePDBSelector(PDBSelector):
12561  r"""Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12562 
12563  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12564 
12565  def __init__(self, *args):
12566  r"""__init__(NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector"""
12567  _IMP_atom.NonAlternativePDBSelector_swiginit(self, _IMP_atom.new_NonAlternativePDBSelector(*args))
12568 
12569  def get_version_info(self):
12570  r"""get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12571  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12572  __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
12573 
12574  def __str__(self):
12575  r"""__str__(NonAlternativePDBSelector self) -> std::string"""
12576  return _IMP_atom.NonAlternativePDBSelector___str__(self)
12577 
12578  def __repr__(self):
12579  r"""__repr__(NonAlternativePDBSelector self) -> std::string"""
12580  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12581 
12582  @staticmethod
12583  def get_from(o):
12584  return _object_cast_to_NonAlternativePDBSelector(o)
12585 
12586 
12587 # Register NonAlternativePDBSelector in _IMP_atom:
12588 _IMP_atom.NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12589 class ATOMPDBSelector(NonAlternativePDBSelector):
12590  r"""Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12591 
12592  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12593 
12594  def __init__(self, *args):
12595  r"""__init__(ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector"""
12596  _IMP_atom.ATOMPDBSelector_swiginit(self, _IMP_atom.new_ATOMPDBSelector(*args))
12597  __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
12598 
12599  def __str__(self):
12600  r"""__str__(ATOMPDBSelector self) -> std::string"""
12601  return _IMP_atom.ATOMPDBSelector___str__(self)
12602 
12603  def __repr__(self):
12604  r"""__repr__(ATOMPDBSelector self) -> std::string"""
12605  return _IMP_atom.ATOMPDBSelector___repr__(self)
12606 
12607  @staticmethod
12608  def get_from(o):
12609  return _object_cast_to_ATOMPDBSelector(o)
12610 
12611 
12612 # Register ATOMPDBSelector in _IMP_atom:
12613 _IMP_atom.ATOMPDBSelector_swigregister(ATOMPDBSelector)
12614 class CAlphaPDBSelector(NonAlternativePDBSelector):
12615  r"""Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12616 
12617  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12618 
12619  def __init__(self, *args):
12620  r"""__init__(CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector"""
12621  _IMP_atom.CAlphaPDBSelector_swiginit(self, _IMP_atom.new_CAlphaPDBSelector(*args))
12622  __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
12623 
12624  def __str__(self):
12625  r"""__str__(CAlphaPDBSelector self) -> std::string"""
12626  return _IMP_atom.CAlphaPDBSelector___str__(self)
12627 
12628  def __repr__(self):
12629  r"""__repr__(CAlphaPDBSelector self) -> std::string"""
12630  return _IMP_atom.CAlphaPDBSelector___repr__(self)
12631 
12632  @staticmethod
12633  def get_from(o):
12634  return _object_cast_to_CAlphaPDBSelector(o)
12635 
12636 
12637 # Register CAlphaPDBSelector in _IMP_atom:
12638 _IMP_atom.CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12639 class CBetaPDBSelector(NonAlternativePDBSelector):
12640  r"""Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12641 
12642  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12643 
12644  def __init__(self, *args):
12645  r"""__init__(CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector"""
12646  _IMP_atom.CBetaPDBSelector_swiginit(self, _IMP_atom.new_CBetaPDBSelector(*args))
12647  __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
12648 
12649  def __str__(self):
12650  r"""__str__(CBetaPDBSelector self) -> std::string"""
12651  return _IMP_atom.CBetaPDBSelector___str__(self)
12652 
12653  def __repr__(self):
12654  r"""__repr__(CBetaPDBSelector self) -> std::string"""
12655  return _IMP_atom.CBetaPDBSelector___repr__(self)
12656 
12657  @staticmethod
12658  def get_from(o):
12659  return _object_cast_to_CBetaPDBSelector(o)
12660 
12661 
12662 # Register CBetaPDBSelector in _IMP_atom:
12663 _IMP_atom.CBetaPDBSelector_swigregister(CBetaPDBSelector)
12664 class AtomTypePDBSelector(PDBSelector):
12665  r"""Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12666 
12667  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12668 
12669  def __init__(self, *args):
12670  r"""__init__(AtomTypePDBSelector self, IMP::Strings atom_types, std::string name="AtomTypePDBSelector%1%") -> AtomTypePDBSelector"""
12671  _IMP_atom.AtomTypePDBSelector_swiginit(self, _IMP_atom.new_AtomTypePDBSelector(*args))
12672 
12673  def get_version_info(self):
12674  r"""get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12675  return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12676  __swig_destroy__ = _IMP_atom.delete_AtomTypePDBSelector
12677 
12678  def __str__(self):
12679  r"""__str__(AtomTypePDBSelector self) -> std::string"""
12680  return _IMP_atom.AtomTypePDBSelector___str__(self)
12681 
12682  def __repr__(self):
12683  r"""__repr__(AtomTypePDBSelector self) -> std::string"""
12684  return _IMP_atom.AtomTypePDBSelector___repr__(self)
12685 
12686  @staticmethod
12687  def get_from(o):
12688  return _object_cast_to_AtomTypePDBSelector(o)
12689 
12690 
12691 # Register AtomTypePDBSelector in _IMP_atom:
12692 _IMP_atom.AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12693 class ResidueTypePDBSelector(PDBSelector):
12694  r"""Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12695 
12696  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12697 
12698  def __init__(self, *args):
12699  r"""__init__(ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name="ResidueTypePDBSelector%1%") -> ResidueTypePDBSelector"""
12700  _IMP_atom.ResidueTypePDBSelector_swiginit(self, _IMP_atom.new_ResidueTypePDBSelector(*args))
12701 
12702  def get_version_info(self):
12703  r"""get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12704  return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12705  __swig_destroy__ = _IMP_atom.delete_ResidueTypePDBSelector
12706 
12707  def __str__(self):
12708  r"""__str__(ResidueTypePDBSelector self) -> std::string"""
12709  return _IMP_atom.ResidueTypePDBSelector___str__(self)
12710 
12711  def __repr__(self):
12712  r"""__repr__(ResidueTypePDBSelector self) -> std::string"""
12713  return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12714 
12715  @staticmethod
12716  def get_from(o):
12717  return _object_cast_to_ResidueTypePDBSelector(o)
12718 
12719 
12720 # Register ResidueTypePDBSelector in _IMP_atom:
12721 _IMP_atom.ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12722 class CPDBSelector(NonAlternativePDBSelector):
12723  r"""Proxy of C++ IMP::atom::CPDBSelector class."""
12724 
12725  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12726 
12727  def __init__(self, *args):
12728  r"""__init__(CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector"""
12729  _IMP_atom.CPDBSelector_swiginit(self, _IMP_atom.new_CPDBSelector(*args))
12730  __swig_destroy__ = _IMP_atom.delete_CPDBSelector
12731 
12732  def __str__(self):
12733  r"""__str__(CPDBSelector self) -> std::string"""
12734  return _IMP_atom.CPDBSelector___str__(self)
12735 
12736  def __repr__(self):
12737  r"""__repr__(CPDBSelector self) -> std::string"""
12738  return _IMP_atom.CPDBSelector___repr__(self)
12739 
12740  @staticmethod
12741  def get_from(o):
12742  return _object_cast_to_CPDBSelector(o)
12743 
12744 
12745 # Register CPDBSelector in _IMP_atom:
12746 _IMP_atom.CPDBSelector_swigregister(CPDBSelector)
12747 class NPDBSelector(NonAlternativePDBSelector):
12748  r"""Proxy of C++ IMP::atom::NPDBSelector class."""
12749 
12750  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12751 
12752  def __init__(self, *args):
12753  r"""__init__(NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector"""
12754  _IMP_atom.NPDBSelector_swiginit(self, _IMP_atom.new_NPDBSelector(*args))
12755  __swig_destroy__ = _IMP_atom.delete_NPDBSelector
12756 
12757  def __str__(self):
12758  r"""__str__(NPDBSelector self) -> std::string"""
12759  return _IMP_atom.NPDBSelector___str__(self)
12760 
12761  def __repr__(self):
12762  r"""__repr__(NPDBSelector self) -> std::string"""
12763  return _IMP_atom.NPDBSelector___repr__(self)
12764 
12765  @staticmethod
12766  def get_from(o):
12767  return _object_cast_to_NPDBSelector(o)
12768 
12769 
12770 # Register NPDBSelector in _IMP_atom:
12771 _IMP_atom.NPDBSelector_swigregister(NPDBSelector)
12772 class AllPDBSelector(PDBSelector):
12773  r"""Proxy of C++ IMP::atom::AllPDBSelector class."""
12774 
12775  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12776 
12777  def __init__(self, *args):
12778  r"""__init__(AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector"""
12779  _IMP_atom.AllPDBSelector_swiginit(self, _IMP_atom.new_AllPDBSelector(*args))
12780 
12781  def get_version_info(self):
12782  r"""get_version_info(AllPDBSelector self) -> VersionInfo"""
12783  return _IMP_atom.AllPDBSelector_get_version_info(self)
12784  __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
12785 
12786  def __str__(self):
12787  r"""__str__(AllPDBSelector self) -> std::string"""
12788  return _IMP_atom.AllPDBSelector___str__(self)
12789 
12790  def __repr__(self):
12791  r"""__repr__(AllPDBSelector self) -> std::string"""
12792  return _IMP_atom.AllPDBSelector___repr__(self)
12793 
12794  @staticmethod
12795  def get_from(o):
12796  return _object_cast_to_AllPDBSelector(o)
12797 
12798 
12799 # Register AllPDBSelector in _IMP_atom:
12800 _IMP_atom.AllPDBSelector_swigregister(AllPDBSelector)
12801 class ChainPDBSelector(NonAlternativePDBSelector):
12802  r"""Proxy of C++ IMP::atom::ChainPDBSelector class."""
12803 
12804  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12805  __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
12806 
12807  def __init__(self, *args):
12808  r"""__init__(ChainPDBSelector self, IMP::Strings chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector"""
12809  _IMP_atom.ChainPDBSelector_swiginit(self, _IMP_atom.new_ChainPDBSelector(*args))
12810 
12811  def __str__(self):
12812  r"""__str__(ChainPDBSelector self) -> std::string"""
12813  return _IMP_atom.ChainPDBSelector___str__(self)
12814 
12815  def __repr__(self):
12816  r"""__repr__(ChainPDBSelector self) -> std::string"""
12817  return _IMP_atom.ChainPDBSelector___repr__(self)
12818 
12819  @staticmethod
12820  def get_from(o):
12821  return _object_cast_to_ChainPDBSelector(o)
12822 
12823 
12824 # Register ChainPDBSelector in _IMP_atom:
12825 _IMP_atom.ChainPDBSelector_swigregister(ChainPDBSelector)
12826 class WaterPDBSelector(NonAlternativePDBSelector):
12827  r"""Proxy of C++ IMP::atom::WaterPDBSelector class."""
12828 
12829  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12830 
12831  def __init__(self, *args):
12832  r"""__init__(WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector"""
12833  _IMP_atom.WaterPDBSelector_swiginit(self, _IMP_atom.new_WaterPDBSelector(*args))
12834  __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
12835 
12836  def __str__(self):
12837  r"""__str__(WaterPDBSelector self) -> std::string"""
12838  return _IMP_atom.WaterPDBSelector___str__(self)
12839 
12840  def __repr__(self):
12841  r"""__repr__(WaterPDBSelector self) -> std::string"""
12842  return _IMP_atom.WaterPDBSelector___repr__(self)
12843 
12844  @staticmethod
12845  def get_from(o):
12846  return _object_cast_to_WaterPDBSelector(o)
12847 
12848 
12849 # Register WaterPDBSelector in _IMP_atom:
12850 _IMP_atom.WaterPDBSelector_swigregister(WaterPDBSelector)
12851 class HydrogenPDBSelector(NonAlternativePDBSelector):
12852  r"""Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12853 
12854  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12855 
12856  def __init__(self, *args):
12857  r"""__init__(HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector"""
12858  _IMP_atom.HydrogenPDBSelector_swiginit(self, _IMP_atom.new_HydrogenPDBSelector(*args))
12859  __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
12860 
12861  def __str__(self):
12862  r"""__str__(HydrogenPDBSelector self) -> std::string"""
12863  return _IMP_atom.HydrogenPDBSelector___str__(self)
12864 
12865  def __repr__(self):
12866  r"""__repr__(HydrogenPDBSelector self) -> std::string"""
12867  return _IMP_atom.HydrogenPDBSelector___repr__(self)
12868 
12869  @staticmethod
12870  def get_from(o):
12871  return _object_cast_to_HydrogenPDBSelector(o)
12872 
12873 
12874 # Register HydrogenPDBSelector in _IMP_atom:
12875 _IMP_atom.HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12876 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12877  r"""Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12878 
12879  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12880  __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
12881 
12882  def __init__(self, *args):
12883  r"""
12884  __init__(NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12885  __init__(NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12886  """
12887  _IMP_atom.NonWaterNonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args))
12888 
12889  def __str__(self):
12890  r"""__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12891  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12892 
12893  def __repr__(self):
12894  r"""__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12895  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12896 
12897  @staticmethod
12898  def get_from(o):
12899  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12900 
12901 
12902 # Register NonWaterNonHydrogenPDBSelector in _IMP_atom:
12903 _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12904 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12905  r"""Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12906 
12907  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12908  __swig_destroy__ = _IMP_atom.delete_NonHydrogenPDBSelector
12909 
12910  def __init__(self, *args):
12911  r"""
12912  __init__(NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12913  __init__(NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12914  """
12915  _IMP_atom.NonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonHydrogenPDBSelector(*args))
12916 
12917  def __str__(self):
12918  r"""__str__(NonHydrogenPDBSelector self) -> std::string"""
12919  return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12920 
12921  def __repr__(self):
12922  r"""__repr__(NonHydrogenPDBSelector self) -> std::string"""
12923  return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12924 
12925  @staticmethod
12926  def get_from(o):
12927  return _object_cast_to_NonHydrogenPDBSelector(o)
12928 
12929 
12930 # Register NonHydrogenPDBSelector in _IMP_atom:
12931 _IMP_atom.NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12932 class NonWaterPDBSelector(NonAlternativePDBSelector):
12933  r"""Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12934 
12935  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12936  __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
12937 
12938  def __init__(self, *args):
12939  r"""
12940  __init__(NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12941  __init__(NonWaterPDBSelector self) -> NonWaterPDBSelector
12942  """
12943  _IMP_atom.NonWaterPDBSelector_swiginit(self, _IMP_atom.new_NonWaterPDBSelector(*args))
12944 
12945  def __str__(self):
12946  r"""__str__(NonWaterPDBSelector self) -> std::string"""
12947  return _IMP_atom.NonWaterPDBSelector___str__(self)
12948 
12949  def __repr__(self):
12950  r"""__repr__(NonWaterPDBSelector self) -> std::string"""
12951  return _IMP_atom.NonWaterPDBSelector___repr__(self)
12952 
12953  @staticmethod
12954  def get_from(o):
12955  return _object_cast_to_NonWaterPDBSelector(o)
12956 
12957 
12958 # Register NonWaterPDBSelector in _IMP_atom:
12959 _IMP_atom.NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12960 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12961  r"""Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12962 
12963  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12964 
12965  def __init__(self, *args):
12966  r"""__init__(BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector"""
12967  _IMP_atom.BackbonePDBSelector_swiginit(self, _IMP_atom.new_BackbonePDBSelector(*args))
12968  __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
12969 
12970  def __str__(self):
12971  r"""__str__(BackbonePDBSelector self) -> std::string"""
12972  return _IMP_atom.BackbonePDBSelector___str__(self)
12973 
12974  def __repr__(self):
12975  r"""__repr__(BackbonePDBSelector self) -> std::string"""
12976  return _IMP_atom.BackbonePDBSelector___repr__(self)
12977 
12978  @staticmethod
12979  def get_from(o):
12980  return _object_cast_to_BackbonePDBSelector(o)
12981 
12982 
12983 # Register BackbonePDBSelector in _IMP_atom:
12984 _IMP_atom.BackbonePDBSelector_swigregister(BackbonePDBSelector)
12985 class PPDBSelector(NonAlternativePDBSelector):
12986  r"""Proxy of C++ IMP::atom::PPDBSelector class."""
12987 
12988  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12989 
12990  def __init__(self, *args):
12991  r"""__init__(PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector"""
12992  _IMP_atom.PPDBSelector_swiginit(self, _IMP_atom.new_PPDBSelector(*args))
12993  __swig_destroy__ = _IMP_atom.delete_PPDBSelector
12994 
12995  def __str__(self):
12996  r"""__str__(PPDBSelector self) -> std::string"""
12997  return _IMP_atom.PPDBSelector___str__(self)
12998 
12999  def __repr__(self):
13000  r"""__repr__(PPDBSelector self) -> std::string"""
13001  return _IMP_atom.PPDBSelector___repr__(self)
13002 
13003  @staticmethod
13004  def get_from(o):
13005  return _object_cast_to_PPDBSelector(o)
13006 
13007 
13008 # Register PPDBSelector in _IMP_atom:
13009 _IMP_atom.PPDBSelector_swigregister(PPDBSelector)
13010 class AndPDBSelector(PDBSelector):
13011  r"""Proxy of C++ IMP::atom::AndPDBSelector class."""
13012 
13013  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13014 
13015  def get_version_info(self):
13016  r"""get_version_info(AndPDBSelector self) -> VersionInfo"""
13017  return _IMP_atom.AndPDBSelector_get_version_info(self)
13018  __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
13019 
13020  def __init__(self, a, b):
13021  r"""__init__(AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13022  _IMP_atom.AndPDBSelector_swiginit(self, _IMP_atom.new_AndPDBSelector(a, b))
13023 
13024  def __str__(self):
13025  r"""__str__(AndPDBSelector self) -> std::string"""
13026  return _IMP_atom.AndPDBSelector___str__(self)
13027 
13028  def __repr__(self):
13029  r"""__repr__(AndPDBSelector self) -> std::string"""
13030  return _IMP_atom.AndPDBSelector___repr__(self)
13031 
13032  @staticmethod
13033  def get_from(o):
13034  return _object_cast_to_AndPDBSelector(o)
13035 
13036 
13037 # Register AndPDBSelector in _IMP_atom:
13038 _IMP_atom.AndPDBSelector_swigregister(AndPDBSelector)
13039 class OrPDBSelector(PDBSelector):
13040  r"""Proxy of C++ IMP::atom::OrPDBSelector class."""
13041 
13042  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13043 
13044  def get_version_info(self):
13045  r"""get_version_info(OrPDBSelector self) -> VersionInfo"""
13046  return _IMP_atom.OrPDBSelector_get_version_info(self)
13047  __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
13048 
13049  def __init__(self, a, b):
13050  r"""__init__(OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13051  _IMP_atom.OrPDBSelector_swiginit(self, _IMP_atom.new_OrPDBSelector(a, b))
13052 
13053  def __str__(self):
13054  r"""__str__(OrPDBSelector self) -> std::string"""
13055  return _IMP_atom.OrPDBSelector___str__(self)
13056 
13057  def __repr__(self):
13058  r"""__repr__(OrPDBSelector self) -> std::string"""
13059  return _IMP_atom.OrPDBSelector___repr__(self)
13060 
13061  @staticmethod
13062  def get_from(o):
13063  return _object_cast_to_OrPDBSelector(o)
13064 
13065 
13066 # Register OrPDBSelector in _IMP_atom:
13067 _IMP_atom.OrPDBSelector_swigregister(OrPDBSelector)
13068 class XorPDBSelector(PDBSelector):
13069  r"""Proxy of C++ IMP::atom::XorPDBSelector class."""
13070 
13071  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13072 
13073  def get_version_info(self):
13074  r"""get_version_info(XorPDBSelector self) -> VersionInfo"""
13075  return _IMP_atom.XorPDBSelector_get_version_info(self)
13076  __swig_destroy__ = _IMP_atom.delete_XorPDBSelector
13077 
13078  def __init__(self, a, b):
13079  r"""__init__(XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13080  _IMP_atom.XorPDBSelector_swiginit(self, _IMP_atom.new_XorPDBSelector(a, b))
13081 
13082  def __str__(self):
13083  r"""__str__(XorPDBSelector self) -> std::string"""
13084  return _IMP_atom.XorPDBSelector___str__(self)
13085 
13086  def __repr__(self):
13087  r"""__repr__(XorPDBSelector self) -> std::string"""
13088  return _IMP_atom.XorPDBSelector___repr__(self)
13089 
13090  @staticmethod
13091  def get_from(o):
13092  return _object_cast_to_XorPDBSelector(o)
13093 
13094 
13095 # Register XorPDBSelector in _IMP_atom:
13096 _IMP_atom.XorPDBSelector_swigregister(XorPDBSelector)
13097 class NotPDBSelector(PDBSelector):
13098  r"""Proxy of C++ IMP::atom::NotPDBSelector class."""
13099 
13100  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13101 
13102  def get_version_info(self):
13103  r"""get_version_info(NotPDBSelector self) -> VersionInfo"""
13104  return _IMP_atom.NotPDBSelector_get_version_info(self)
13105  __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
13106 
13107  def __init__(self, a):
13108  r"""__init__(NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13109  _IMP_atom.NotPDBSelector_swiginit(self, _IMP_atom.new_NotPDBSelector(a))
13110 
13111  def __str__(self):
13112  r"""__str__(NotPDBSelector self) -> std::string"""
13113  return _IMP_atom.NotPDBSelector___str__(self)
13114 
13115  def __repr__(self):
13116  r"""__repr__(NotPDBSelector self) -> std::string"""
13117  return _IMP_atom.NotPDBSelector___repr__(self)
13118 
13119  @staticmethod
13120  def get_from(o):
13121  return _object_cast_to_NotPDBSelector(o)
13122 
13123 
13124 # Register NotPDBSelector in _IMP_atom:
13125 _IMP_atom.NotPDBSelector_swigregister(NotPDBSelector)
13126 
13127 def get_default_pdb_selector():
13128  r"""get_default_pdb_selector() -> PDBSelector"""
13129  return _IMP_atom.get_default_pdb_selector()
13130 
13131 def read_pdb(*args):
13132  r"""
13133  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool no_radii=False) -> Hierarchy
13134  read_pdb(TextInput input, int model, Hierarchy h)
13135  """
13136  return _IMP_atom.read_pdb(*args)
13137 
13138 def read_multimodel_pdb(*args):
13139  r"""read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13140  return _IMP_atom.read_multimodel_pdb(*args)
13141 
13142 def write_pdb(mhd, out, model=1):
13143  r"""write_pdb(Selection mhd, TextOutput out, unsigned int model=1)"""
13144  return _IMP_atom.write_pdb(mhd, out, model)
13145 
13146 def write_pdb_of_c_alphas(mhd, out, model=1):
13147  r"""write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)"""
13148  return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13149 
13150 def write_multimodel_pdb(mhd, out):
13151  r"""write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13152  return _IMP_atom.write_multimodel_pdb(mhd, out)
13153 
13154 def get_pdb_string(*args):
13155  r"""get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ', int res_index=1, char res_icode=' ', double occupancy=1.00, double tempFactor=0.00, IMP::atom::Element e=C) -> std::string"""
13156  return _IMP_atom.get_pdb_string(*args)
13157 
13158 def get_pdb_conect_record_string(arg1, arg2):
13159  r"""get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13160  return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13161 class WritePDBOptimizerState(IMP.OptimizerState):
13162  r"""Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13163 
13164  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13165 
13166  def __init__(self, *args):
13167  r"""
13168  __init__(WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13169  __init__(WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13170  __init__(WritePDBOptimizerState self) -> WritePDBOptimizerState
13171  """
13172  _IMP_atom.WritePDBOptimizerState_swiginit(self, _IMP_atom.new_WritePDBOptimizerState(*args))
13173 
13174  def get_version_info(self):
13175  r"""get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13176  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13177  __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
13178 
13179  def __str__(self):
13180  r"""__str__(WritePDBOptimizerState self) -> std::string"""
13181  return _IMP_atom.WritePDBOptimizerState___str__(self)
13182 
13183  def __repr__(self):
13184  r"""__repr__(WritePDBOptimizerState self) -> std::string"""
13185  return _IMP_atom.WritePDBOptimizerState___repr__(self)
13186 
13187  @staticmethod
13188  def get_from(o):
13189  return _object_cast_to_WritePDBOptimizerState(o)
13190 
13191 
13192  def _get_as_binary(self):
13193  r"""_get_as_binary(WritePDBOptimizerState self) -> PyObject *"""
13194  return _IMP_atom.WritePDBOptimizerState__get_as_binary(self)
13195 
13196  def _set_from_binary(self, p):
13197  r"""_set_from_binary(WritePDBOptimizerState self, PyObject * p)"""
13198  return _IMP_atom.WritePDBOptimizerState__set_from_binary(self, p)
13199 
13200  def __getstate__(self):
13201  p = self._get_as_binary()
13202  if len(self.__dict__) > 1:
13203  d = self.__dict__.copy()
13204  del d['this']
13205  p = (d, p)
13206  return p
13207 
13208  def __setstate__(self, p):
13209  if not hasattr(self, 'this'):
13210  self.__init__()
13211  if isinstance(p, tuple):
13212  d, p = p
13213  self.__dict__.update(d)
13214  return self._set_from_binary(p)
13215 
13216 
13217 # Register WritePDBOptimizerState in _IMP_atom:
13218 _IMP_atom.WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13219 
13220 def read_multimodel_mmcif(*args):
13221  r"""read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13222  return _IMP_atom.read_multimodel_mmcif(*args)
13223 
13224 def read_mmcif(*args):
13225  r"""read_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13226  return _IMP_atom.read_mmcif(*args)
13227 
13228 def read_multimodel_bcif(*args):
13229  r"""read_multimodel_bcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13230  return _IMP_atom.read_multimodel_bcif(*args)
13231 
13232 def read_bcif(*args):
13233  r"""read_bcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13234  return _IMP_atom.read_bcif(*args)
13235 
13236 def read_pdb_any(*args):
13237  r"""read_pdb_any(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13238  return _IMP_atom.read_pdb_any(*args)
13239 
13240 def read_multimodel_pdb_any(*args):
13241  r"""read_multimodel_pdb_any(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13242  return _IMP_atom.read_multimodel_pdb_any(*args)
13243 
13244 def read_pdb_or_mmcif(*args):
13245  r"""read_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13246  return _IMP_atom.read_pdb_or_mmcif(*args)
13247 
13248 def read_multimodel_pdb_or_mmcif(*args):
13249  r"""read_multimodel_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13250  return _IMP_atom.read_multimodel_pdb_or_mmcif(*args)
13251 
13252 def get_kt(T):
13253  r"""get_kt(double T) -> double"""
13254  return _IMP_atom.get_kt(T)
13255 class CAAngleRestraint(IMP.Restraint):
13256  r"""Proxy of C++ IMP::atom::CAAngleRestraint class."""
13257 
13258  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13259 
13260  def __init__(self, m, p1, p2, p3, phi0, score):
13261  r"""__init__(CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13262  _IMP_atom.CAAngleRestraint_swiginit(self, _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score))
13263 
13264  def do_get_inputs(self):
13265  r"""do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13266  return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13267 
13268  def get_version_info(self):
13269  r"""get_version_info(CAAngleRestraint self) -> VersionInfo"""
13270  return _IMP_atom.CAAngleRestraint_get_version_info(self)
13271  __swig_destroy__ = _IMP_atom.delete_CAAngleRestraint
13272 
13273  def __str__(self):
13274  r"""__str__(CAAngleRestraint self) -> std::string"""
13275  return _IMP_atom.CAAngleRestraint___str__(self)
13276 
13277  def __repr__(self):
13278  r"""__repr__(CAAngleRestraint self) -> std::string"""
13279  return _IMP_atom.CAAngleRestraint___repr__(self)
13280 
13281  @staticmethod
13282  def get_from(o):
13283  return _object_cast_to_CAAngleRestraint(o)
13284 
13285 
13286 # Register CAAngleRestraint in _IMP_atom:
13287 _IMP_atom.CAAngleRestraint_swigregister(CAAngleRestraint)
13288 class CADihedralRestraint(IMP.Restraint):
13289  r"""Proxy of C++ IMP::atom::CADihedralRestraint class."""
13290 
13291  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13292 
13293  def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13294  r"""__init__(CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
13295  _IMP_atom.CADihedralRestraint_swiginit(self, _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score))
13296 
13297  def do_get_inputs(self):
13298  r"""do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13299  return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13300 
13301  def get_version_info(self):
13302  r"""get_version_info(CADihedralRestraint self) -> VersionInfo"""
13303  return _IMP_atom.CADihedralRestraint_get_version_info(self)
13304  __swig_destroy__ = _IMP_atom.delete_CADihedralRestraint
13305 
13306  def __str__(self):
13307  r"""__str__(CADihedralRestraint self) -> std::string"""
13308  return _IMP_atom.CADihedralRestraint___str__(self)
13309 
13310  def __repr__(self):
13311  r"""__repr__(CADihedralRestraint self) -> std::string"""
13312  return _IMP_atom.CADihedralRestraint___repr__(self)
13313 
13314  @staticmethod
13315  def get_from(o):
13316  return _object_cast_to_CADihedralRestraint(o)
13317 
13318 
13319 # Register CADihedralRestraint in _IMP_atom:
13320 _IMP_atom.CADihedralRestraint_swigregister(CADihedralRestraint)
13321 class StructureSource(IMP.Decorator):
13322  r"""Proxy of C++ IMP::atom::StructureSource class."""
13323 
13324  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13325 
13326  def get_source_id(self):
13327  r"""get_source_id(StructureSource self) -> std::string"""
13328  return _IMP_atom.StructureSource_get_source_id(self)
13329 
13330  def get_source_chain_id(self):
13331  r"""get_source_chain_id(StructureSource self) -> std::string"""
13332  return _IMP_atom.StructureSource_get_source_chain_id(self)
13333 
13334  def set_source_id(self, source_id):
13335  r"""set_source_id(StructureSource self, std::string source_id)"""
13336  return _IMP_atom.StructureSource_set_source_id(self, source_id)
13337 
13338  def set_source_chain_id(self, source_chain_id):
13339  r"""set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13340  return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13341 
13342  def __init__(self, *args):
13343  r"""
13344  __init__(StructureSource self) -> StructureSource
13345  __init__(StructureSource self, Model m, ParticleIndex id) -> StructureSource
13346  __init__(StructureSource self, _ParticleAdaptor d) -> StructureSource
13347  """
13348  _IMP_atom.StructureSource_swiginit(self, _IMP_atom.new_StructureSource(*args))
13349 
13350  @staticmethod
13351  def get_is_setup(*args):
13352  r"""
13353  get_is_setup(Model m, ParticleIndex pi) -> bool
13354  get_is_setup(_ParticleAdaptor p) -> bool
13355  """
13356  return _IMP_atom.StructureSource_get_is_setup(*args)
13357 
13358  def show(self, *args):
13359  r"""show(StructureSource self, _ostream out=std::cout)"""
13360  return _IMP_atom.StructureSource_show(self, *args)
13361 
13362  @staticmethod
13363  def setup_particle(*args):
13364  r"""
13365  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13366  setup_particle(_ParticleAdaptor pa, std::string source_id, std::string source_chain_id) -> StructureSource
13367  """
13368  return _IMP_atom.StructureSource_setup_particle(*args)
13369 
13370  def add_attribute(self, *args):
13371  r"""
13372  add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13373  add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13374  add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13375  add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
13376  add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
13377  add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13378  add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13379  add_attribute(StructureSource self, ObjectKey a0, Object a1)
13380  add_attribute(StructureSource self, SparseFloatKey a0, IMP::Float a1)
13381  add_attribute(StructureSource self, SparseIntKey a0, IMP::Int a1)
13382  add_attribute(StructureSource self, SparseStringKey a0, IMP::String a1)
13383  add_attribute(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
13384  """
13385  return _IMP_atom.StructureSource_add_attribute(self, *args)
13386 
13387  def get_value(self, *args):
13388  r"""
13389  get_value(StructureSource self, FloatKey a0) -> IMP::Float
13390  get_value(StructureSource self, IntKey a0) -> IMP::Int
13391  get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
13392  get_value(StructureSource self, IntsKey a0) -> IMP::Ints
13393  get_value(StructureSource self, StringKey a0) -> IMP::String
13394  get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13395  get_value(StructureSource self, ObjectKey a0) -> Object
13396  get_value(StructureSource self, SparseFloatKey a0) -> IMP::Float
13397  get_value(StructureSource self, SparseIntKey a0) -> IMP::Int
13398  get_value(StructureSource self, SparseStringKey a0) -> IMP::String
13399  get_value(StructureSource self, SparseParticleIndexKey a0) -> ParticleIndex
13400  """
13401  return _IMP_atom.StructureSource_get_value(self, *args)
13402 
13403  def set_value(self, *args):
13404  r"""
13405  set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13406  set_value(StructureSource self, IntKey a0, IMP::Int a1)
13407  set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
13408  set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
13409  set_value(StructureSource self, StringKey a0, IMP::String a1)
13410  set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13411  set_value(StructureSource self, ObjectKey a0, Object a1)
13412  set_value(StructureSource self, SparseFloatKey a0, IMP::Float a1)
13413  set_value(StructureSource self, SparseIntKey a0, IMP::Int a1)
13414  set_value(StructureSource self, SparseStringKey a0, IMP::String a1)
13415  set_value(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
13416  """
13417  return _IMP_atom.StructureSource_set_value(self, *args)
13418 
13419  def remove_attribute(self, *args):
13420  r"""
13421  remove_attribute(StructureSource self, FloatKey a0)
13422  remove_attribute(StructureSource self, IntKey a0)
13423  remove_attribute(StructureSource self, FloatsKey a0)
13424  remove_attribute(StructureSource self, IntsKey a0)
13425  remove_attribute(StructureSource self, StringKey a0)
13426  remove_attribute(StructureSource self, ParticleIndexKey a0)
13427  remove_attribute(StructureSource self, ObjectKey a0)
13428  remove_attribute(StructureSource self, SparseFloatKey a0)
13429  remove_attribute(StructureSource self, SparseIntKey a0)
13430  remove_attribute(StructureSource self, SparseStringKey a0)
13431  remove_attribute(StructureSource self, SparseParticleIndexKey a0)
13432  """
13433  return _IMP_atom.StructureSource_remove_attribute(self, *args)
13434 
13435  def has_attribute(self, *args):
13436  r"""
13437  has_attribute(StructureSource self, FloatKey a0) -> bool
13438  has_attribute(StructureSource self, IntKey a0) -> bool
13439  has_attribute(StructureSource self, FloatsKey a0) -> bool
13440  has_attribute(StructureSource self, IntsKey a0) -> bool
13441  has_attribute(StructureSource self, StringKey a0) -> bool
13442  has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13443  has_attribute(StructureSource self, ObjectKey a0) -> bool
13444  has_attribute(StructureSource self, SparseFloatKey a0) -> bool
13445  has_attribute(StructureSource self, SparseIntKey a0) -> bool
13446  has_attribute(StructureSource self, SparseStringKey a0) -> bool
13447  has_attribute(StructureSource self, SparseParticleIndexKey a0) -> bool
13448  """
13449  return _IMP_atom.StructureSource_has_attribute(self, *args)
13450 
13451  def get_derivative(self, a0):
13452  r"""get_derivative(StructureSource self, FloatKey a0) -> double"""
13453  return _IMP_atom.StructureSource_get_derivative(self, a0)
13454 
13455  def get_name(self):
13456  r"""get_name(StructureSource self) -> std::string"""
13457  return _IMP_atom.StructureSource_get_name(self)
13458 
13459  def clear_caches(self):
13460  r"""clear_caches(StructureSource self)"""
13461  return _IMP_atom.StructureSource_clear_caches(self)
13462 
13463  def set_name(self, a0):
13464  r"""set_name(StructureSource self, std::string a0)"""
13465  return _IMP_atom.StructureSource_set_name(self, a0)
13466 
13467  def set_check_level(self, a0):
13468  r"""set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13469  return _IMP_atom.StructureSource_set_check_level(self, a0)
13470 
13471  def add_to_derivative(self, a0, a1, a2):
13472  r"""add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13473  return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13474 
13475  def set_is_optimized(self, a0, a1):
13476  r"""set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13477  return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13478 
13479  def get_is_optimized(self, a0):
13480  r"""get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13481  return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13482 
13483  def get_check_level(self):
13484  r"""get_check_level(StructureSource self) -> IMP::CheckLevel"""
13485  return _IMP_atom.StructureSource_get_check_level(self)
13486 
13487  def __eq__(self, *args):
13488  r"""
13489  __eq__(StructureSource self, StructureSource o) -> bool
13490  __eq__(StructureSource self, Particle d) -> bool
13491  """
13492  return _IMP_atom.StructureSource___eq__(self, *args)
13493 
13494  def __ne__(self, *args):
13495  r"""
13496  __ne__(StructureSource self, StructureSource o) -> bool
13497  __ne__(StructureSource self, Particle d) -> bool
13498  """
13499  return _IMP_atom.StructureSource___ne__(self, *args)
13500 
13501  def __le__(self, *args):
13502  r"""
13503  __le__(StructureSource self, StructureSource o) -> bool
13504  __le__(StructureSource self, Particle d) -> bool
13505  """
13506  return _IMP_atom.StructureSource___le__(self, *args)
13507 
13508  def __lt__(self, *args):
13509  r"""
13510  __lt__(StructureSource self, StructureSource o) -> bool
13511  __lt__(StructureSource self, Particle d) -> bool
13512  """
13513  return _IMP_atom.StructureSource___lt__(self, *args)
13514 
13515  def __ge__(self, *args):
13516  r"""
13517  __ge__(StructureSource self, StructureSource o) -> bool
13518  __ge__(StructureSource self, Particle d) -> bool
13519  """
13520  return _IMP_atom.StructureSource___ge__(self, *args)
13521 
13522  def __gt__(self, *args):
13523  r"""
13524  __gt__(StructureSource self, StructureSource o) -> bool
13525  __gt__(StructureSource self, Particle d) -> bool
13526  """
13527  return _IMP_atom.StructureSource___gt__(self, *args)
13528 
13529  def __hash__(self):
13530  r"""__hash__(StructureSource self) -> std::size_t"""
13531  return _IMP_atom.StructureSource___hash__(self)
13532 
13533  def __str__(self):
13534  r"""__str__(StructureSource self) -> std::string"""
13535  return _IMP_atom.StructureSource___str__(self)
13536 
13537  def __repr__(self):
13538  r"""__repr__(StructureSource self) -> std::string"""
13539  return _IMP_atom.StructureSource___repr__(self)
13540 
13541  def _get_as_binary(self):
13542  r"""_get_as_binary(StructureSource self) -> PyObject *"""
13543  return _IMP_atom.StructureSource__get_as_binary(self)
13544 
13545  def _set_from_binary(self, p):
13546  r"""_set_from_binary(StructureSource self, PyObject * p)"""
13547  return _IMP_atom.StructureSource__set_from_binary(self, p)
13548 
13549  def __getstate__(self):
13550  p = self._get_as_binary()
13551  if len(self.__dict__) > 1:
13552  d = self.__dict__.copy()
13553  del d['this']
13554  p = (d, p)
13555  return p
13556 
13557  def __setstate__(self, p):
13558  if not hasattr(self, 'this'):
13559  self.__init__()
13560  if isinstance(p, tuple):
13561  d, p = p
13562  self.__dict__.update(d)
13563  return self._set_from_binary(p)
13564 
13565  __swig_destroy__ = _IMP_atom.delete_StructureSource
13566 
13567 # Register StructureSource in _IMP_atom:
13568 _IMP_atom.StructureSource_swigregister(StructureSource)
13569 
13570 def __lshift__(*args):
13571  r"""
13572  __lshift__(_ostream out, Bonded n) -> _ostream
13573  __lshift__(_ostream out, Bond n) -> _ostream
13574  __lshift__(_ostream out, Hierarchy n) -> _ostream
13575  __lshift__(_ostream out, Angle n) -> _ostream
13576  __lshift__(_ostream out, Dihedral n) -> _ostream
13577  __lshift__(_ostream out, CenterOfMass n) -> _ostream
13578  __lshift__(_ostream out, Diffusion n) -> _ostream
13579  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13580  __lshift__(_ostream out, TAMDParticle n) -> _ostream
13581  __lshift__(_ostream out, Charged n) -> _ostream
13582  __lshift__(_ostream out, Domain n) -> _ostream
13583  __lshift__(_ostream out, LennardJones n) -> _ostream
13584  __lshift__(_ostream out, LennardJonesTyped n) -> _ostream
13585  __lshift__(_ostream out, Fragment n) -> _ostream
13586  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13587  __lshift__(_ostream out, Atom n) -> _ostream
13588  __lshift__(_ostream out, Residue n) -> _ostream
13589  __lshift__(_ostream out, Representation n) -> _ostream
13590  __lshift__(_ostream out, State n) -> _ostream
13591  __lshift__(_ostream out, Molecule n) -> _ostream
13592  __lshift__(_ostream out, Copy n) -> _ostream
13593  __lshift__(_ostream out, Chain n) -> _ostream
13594  __lshift__(_ostream out, StructureSource n) -> _ostream
13595  """
13596  return _IMP_atom.__lshift__(*args)
13597 class HelixRestraint(IMP.Restraint):
13598  r"""Proxy of C++ IMP::atom::HelixRestraint class."""
13599 
13600  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13601 
13602  def __init__(self, rs, ideal=True):
13603  r"""__init__(HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint"""
13604  _IMP_atom.HelixRestraint_swiginit(self, _IMP_atom.new_HelixRestraint(rs, ideal))
13605 
13606  def get_number_of_bonds(self):
13607  r"""get_number_of_bonds(HelixRestraint self) -> int"""
13608  return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13609 
13610  def get_number_of_dihedrals(self):
13611  r"""get_number_of_dihedrals(HelixRestraint self) -> int"""
13612  return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13613 
13614  def do_get_inputs(self):
13615  r"""do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13616  return _IMP_atom.HelixRestraint_do_get_inputs(self)
13617 
13618  def get_version_info(self):
13619  r"""get_version_info(HelixRestraint self) -> VersionInfo"""
13620  return _IMP_atom.HelixRestraint_get_version_info(self)
13621  __swig_destroy__ = _IMP_atom.delete_HelixRestraint
13622 
13623  def __str__(self):
13624  r"""__str__(HelixRestraint self) -> std::string"""
13625  return _IMP_atom.HelixRestraint___str__(self)
13626 
13627  def __repr__(self):
13628  r"""__repr__(HelixRestraint self) -> std::string"""
13629  return _IMP_atom.HelixRestraint___repr__(self)
13630 
13631  @staticmethod
13632  def get_from(o):
13633  return _object_cast_to_HelixRestraint(o)
13634 
13635 
13636 # Register HelixRestraint in _IMP_atom:
13637 _IMP_atom.HelixRestraint_swigregister(HelixRestraint)
13638 
13640  r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
13641  return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
13642 
13643 def show_molecular_hierarchy(*args):
13644  r"""show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream"""
13645  return _IMP_atom.show_molecular_hierarchy(*args)
13646 class CHARMMBond(object):
13647  r"""Proxy of C++ IMP::atom::CHARMMConnection< 2 > class."""
13648 
13649  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13650  __repr__ = _swig_repr
13651 
13652  def __init__(self, atoms):
13653  r"""__init__(CHARMMBond self, IMP::Strings const & atoms) -> CHARMMBond"""
13654  _IMP_atom.CHARMMBond_swiginit(self, _IMP_atom.new_CHARMMBond(atoms))
13655 
13656  def get_endpoint(self, i):
13657  r"""get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13658  return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13659 
13660  def get_contains_atom(self, name):
13661  r"""get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13662  return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13663 
13664  def show(self, *args):
13665  r"""show(CHARMMBond self, _ostream out=std::cout)"""
13666  return _IMP_atom.CHARMMBond_show(self, *args)
13667  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13668 
13669 # Register CHARMMBond in _IMP_atom:
13670 _IMP_atom.CHARMMBond_swigregister(CHARMMBond)
13671 class CHARMMAngle(object):
13672  r"""Proxy of C++ IMP::atom::CHARMMConnection< 3 > class."""
13673 
13674  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13675  __repr__ = _swig_repr
13676 
13677  def __init__(self, atoms):
13678  r"""__init__(CHARMMAngle self, IMP::Strings const & atoms) -> CHARMMAngle"""
13679  _IMP_atom.CHARMMAngle_swiginit(self, _IMP_atom.new_CHARMMAngle(atoms))
13680 
13681  def get_endpoint(self, i):
13682  r"""get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13683  return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13684 
13685  def get_contains_atom(self, name):
13686  r"""get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13687  return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13688 
13689  def show(self, *args):
13690  r"""show(CHARMMAngle self, _ostream out=std::cout)"""
13691  return _IMP_atom.CHARMMAngle_show(self, *args)
13692  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13693 
13694 # Register CHARMMAngle in _IMP_atom:
13695 _IMP_atom.CHARMMAngle_swigregister(CHARMMAngle)
13696 
13697 def _get_native_overlap_cpp(m1, m2, threshold):
13698  r"""_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2, double threshold) -> double"""
13699  return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13700 
13701 def _get_drmsd_cpp(m0, m1):
13702  r"""_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1) -> double"""
13703  return _IMP_atom._get_drmsd_cpp(m0, m1)
13704 
13705 def _get_drmsd_Q_cpp(m0, m1, threshold):
13706  r"""_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, double threshold) -> double"""
13707  return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13708 
13709 def _get_drms_cpp(m1, m2):
13710  r"""_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2) -> double"""
13711  return _IMP_atom._get_drms_cpp(m1, m2)
13712 
13713 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13714  r"""_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2, IMP::IntRanges const & ranges) -> double"""
13715  return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13716 
13717 def get_native_overlap(a, b, d):
13718  va= [IMP.algebra.get_vector(x) for x in a]
13719  vb= [IMP.algebra.get_vector(x) for x in b]
13720  return _get_native_overlap_cpp(va, vb, d)
13721 
13722 def get_drmsd(a, b):
13723  va= [IMP.algebra.get_vector(x) for x in a]
13724  vb= [IMP.algebra.get_vector(x) for x in b]
13725  return _get_drmsd_cpp(va, vb)
13726 
13727 def get_drms(a, b):
13728  va= [IMP.algebra.get_vector(x) for x in a]
13729  vb= [IMP.algebra.get_vector(x) for x in b]
13730  return _get_drms_cpp(va, vb)
13731 
13732 def get_drmsd_Q(a, b, t):
13733  va= [IMP.algebra.get_vector(x) for x in a]
13734  vb= [IMP.algebra.get_vector(x) for x in b]
13735  return _get_drmsd_Q_cpp(va, vb, t)
13736 
13737 def get_rigid_bodies_drms(a, b, ranges):
13738  va= [IMP.algebra.get_vector(x) for x in a]
13739  vb= [IMP.algebra.get_vector(x) for x in b]
13740 #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
13741  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13742 
13743 
13744 class _LennardJonesTypedPairScore(IMP.PairScore):
13745  r"""Proxy of C++ IMP::atom::LennardJonesTypedPairScore< IMP::atom::SmoothingFunction > class."""
13746 
13747  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13748  __repr__ = _swig_repr
13749 
13750  def __init__(self, f):
13751  r"""__init__(_LennardJonesTypedPairScore self, SmoothingFunction f) -> _LennardJonesTypedPairScore"""
13752  _IMP_atom._LennardJonesTypedPairScore_swiginit(self, _IMP_atom.new__LennardJonesTypedPairScore(f))
13753 
13754  def set_repulsive_weight(self, repulsive_weight):
13755  r"""set_repulsive_weight(_LennardJonesTypedPairScore self, double repulsive_weight)"""
13756  return _IMP_atom._LennardJonesTypedPairScore_set_repulsive_weight(self, repulsive_weight)
13757 
13758  def get_repulsive_weight(self):
13759  r"""get_repulsive_weight(_LennardJonesTypedPairScore self) -> double"""
13760  return _IMP_atom._LennardJonesTypedPairScore_get_repulsive_weight(self)
13761 
13762  def set_attractive_weight(self, attractive_weight):
13763  r"""set_attractive_weight(_LennardJonesTypedPairScore self, double attractive_weight)"""
13764  return _IMP_atom._LennardJonesTypedPairScore_set_attractive_weight(self, attractive_weight)
13765 
13766  def get_attractive_weight(self):
13767  r"""get_attractive_weight(_LennardJonesTypedPairScore self) -> double"""
13768  return _IMP_atom._LennardJonesTypedPairScore_get_attractive_weight(self)
13769 
13770  def do_get_inputs(self, m, pis):
13771  r"""do_get_inputs(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
13772  return _IMP_atom._LennardJonesTypedPairScore_do_get_inputs(self, m, pis)
13773 
13774  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
13775  r"""evaluate_indexes(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13776  return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
13777 
13778  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
13779  r"""evaluate_indexes_scores(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13780  return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
13781 
13782  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
13783  r"""evaluate_indexes_delta(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13784  return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
13785 
13786  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
13787  r"""evaluate_if_good_indexes(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13788  return _IMP_atom._LennardJonesTypedPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
13789 
13790  def get_version_info(self):
13791  r"""get_version_info(_LennardJonesTypedPairScore self) -> VersionInfo"""
13792  return _IMP_atom._LennardJonesTypedPairScore_get_version_info(self)
13793  __swig_destroy__ = _IMP_atom.delete__LennardJonesTypedPairScore
13794 
13795  @staticmethod
13796  def get_from(o):
13797  return _object_cast_to__LennardJonesTypedPairScore(o)
13798 
13799 
13800 # Register _LennardJonesTypedPairScore in _IMP_atom:
13801 _IMP_atom._LennardJonesTypedPairScore_swigregister(_LennardJonesTypedPairScore)
13802 class _SwitchedLennardJonesTypedPairScore(IMP.PairScore):
13803  r"""Proxy of C++ IMP::atom::LennardJonesTypedPairScore< IMP::atom::ForceSwitch > class."""
13804 
13805  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13806  __repr__ = _swig_repr
13807 
13808  def __init__(self, f):
13809  r"""__init__(_SwitchedLennardJonesTypedPairScore self, ForceSwitch f) -> _SwitchedLennardJonesTypedPairScore"""
13810  _IMP_atom._SwitchedLennardJonesTypedPairScore_swiginit(self, _IMP_atom.new__SwitchedLennardJonesTypedPairScore(f))
13811 
13812  def set_repulsive_weight(self, repulsive_weight):
13813  r"""set_repulsive_weight(_SwitchedLennardJonesTypedPairScore self, double repulsive_weight)"""
13814  return _IMP_atom._SwitchedLennardJonesTypedPairScore_set_repulsive_weight(self, repulsive_weight)
13815 
13816  def get_repulsive_weight(self):
13817  r"""get_repulsive_weight(_SwitchedLennardJonesTypedPairScore self) -> double"""
13818  return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_repulsive_weight(self)
13819 
13820  def set_attractive_weight(self, attractive_weight):
13821  r"""set_attractive_weight(_SwitchedLennardJonesTypedPairScore self, double attractive_weight)"""
13822  return _IMP_atom._SwitchedLennardJonesTypedPairScore_set_attractive_weight(self, attractive_weight)
13823 
13824  def get_attractive_weight(self):
13825  r"""get_attractive_weight(_SwitchedLennardJonesTypedPairScore self) -> double"""
13826  return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_attractive_weight(self)
13827 
13828  def do_get_inputs(self, m, pis):
13829  r"""do_get_inputs(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
13830  return _IMP_atom._SwitchedLennardJonesTypedPairScore_do_get_inputs(self, m, pis)
13831 
13832  def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
13833  r"""evaluate_indexes(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13834  return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
13835 
13836  def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
13837  r"""evaluate_indexes_scores(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13838  return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
13839 
13840  def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
13841  r"""evaluate_indexes_delta(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13842  return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
13843 
13844  def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
13845  r"""evaluate_if_good_indexes(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13846  return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
13847 
13848  def get_version_info(self):
13849  r"""get_version_info(_SwitchedLennardJonesTypedPairScore self) -> VersionInfo"""
13850  return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_version_info(self)
13851  __swig_destroy__ = _IMP_atom.delete__SwitchedLennardJonesTypedPairScore
13852 
13853  @staticmethod
13854  def get_from(o):
13855  return _object_cast_to__SwitchedLennardJonesTypedPairScore(o)
13856 
13857 
13858 # Register _SwitchedLennardJonesTypedPairScore in _IMP_atom:
13859 _IMP_atom._SwitchedLennardJonesTypedPairScore_swigregister(_SwitchedLennardJonesTypedPairScore)
13860 
13861 class LennardJonesTypedPairScore(_SwitchedLennardJonesTypedPairScore.__bases__[0]):
13862  def __init__(self, f):
13863  if isinstance(f, ForceSwitch):
13864  p = _SwitchedLennardJonesTypedPairScore(f)
13865  else:
13866  p = _LennardJonesTypedPairScore(f)
13867  self.__dict__['_proxied'] = p
13868  def __getattr__(self, key):
13869  return getattr(self._proxied, key)
13870  def __setattr__(self, key, val):
13871  return setattr(self._proxied, key, val)
13872 
13873  @staticmethod
13874  def get_from(o):
13875  try:
13876  p = _SwitchedLennardJonesTypedPairScore.get_from(o)
13877  except ValueError:
13878  p = _LennardJonesTypedPairScore.get_from(o)
13879  obj = object.__new__(LennardJonesTypedPairScore)
13880  obj.__dict__['_proxied'] = p
13881  return obj
13882 
13883 
13884 def get_module_version():
13885  r"""get_module_version() -> std::string const"""
13886  return _IMP_atom.get_module_version()
13887 
13888 def get_example_path(fname):
13889  r"""get_example_path(std::string fname) -> std::string"""
13890  return _IMP_atom.get_example_path(fname)
13891 
13892 def get_data_path(fname):
13893  r"""get_data_path(std::string fname) -> std::string"""
13894  return _IMP_atom.get_data_path(fname)
13895 
13896 from . import _version_check
13897 _version_check.check_version(get_module_version())
13898 __version__ = get_module_version()
13899 
13900 
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:44
A shared container for Pairs.
Definition: PairContainer.h:39
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
double get_einstein_rotational_diffusion_coefficient(double r, double temp=-1)
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the mmCIF file.
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
setup
Definition: setup.py:1
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchies read_multimodel_pdb_any(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB-like file.
Definition: mmcif.h:86
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
Hierarchies read_multimodel_bcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the BinaryCIF file.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square)
Convert spring constant from kcal/mol/A^2 to femtonewton/A.
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Definition: atom/distance.h:49
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
Definition: BoundingBoxD.h:281
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Add vdW radius from given force field.
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
ParticleIndexQuads get_chi_dihedral_particle_indexes(Residue rd)
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Composable functors to implement scores via compile-time composition.
double get_angle(const Line3D &a, const Line3D &b)
Get angle in radians between two lines around their closest points.
Hierarchy read_bcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the BinaryCIF file.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
double get_kd(double na, double nb, double nab, double volume)
Definition: estimates.h:101
double get_diffusion_angle(double D, double dtfs)
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
Hierarchy read_pdb_any(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB-like file.
Definition: mmcif.h:61
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
Definition: BoundingBoxD.h:170
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Definition: Object.h:111
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &orientations, double dt)
Base class for all optimizers.
Definition: Optimizer.h:48
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
Definition: estimates.h:92
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
Definition: VersionInfo.h:29
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Definition: Vector3D.h:77
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void add_loop_statistical_score_data(atom::Hierarchy h)
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:119
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom)
Convert force from kcal/mol/A to femtonewtons.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:31
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
Definition: Refiner.h:34
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
Definition: atom/distance.h:85
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
Add bonds using definitions from given force field parameters.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
double get_diffusion_length(double D, double t)
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27