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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.2.1
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 2007-2024 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_atom
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_ATOM_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
79  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
83  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
87  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
95  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
99  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
103  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
107  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
111  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
115  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
119  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
123  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
127  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
131  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
135  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
140  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_ATOM_SwigPyIterator in _IMP_atom:
147 _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_atom.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_atom.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_atom.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_atom.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_atom.IMP_MEMORY
167 
168 IMP_NONE = _IMP_atom.IMP_NONE
169 
170 IMP_USAGE = _IMP_atom.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_atom.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_atom.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_atom.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_atom._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_atom:
237 _IMP_atom._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
310 
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
312 
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
314 
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
318 
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
320 
321 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
322 
323 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
324 
325 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
326 
327 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
328 
329 import IMP.core
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
333 
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
335 
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
337 
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
345 
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 
348 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
349 
350 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
351 
352 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
353 
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
355 
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
359 
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
361 
362 import IMP.container
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
364 
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
366 
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
368 
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
370 
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
372 
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
374 
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
376 
377 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
378 
379 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
380 
381 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
382 
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
384 
385 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
386 
387 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
388 
389 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
390 
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
392 
393 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
394 
396  r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex > class."""
397 
398  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
399  __repr__ = _swig_repr
400 
401  def __init__(self):
402  r"""__init__(HierarchyTree self) -> HierarchyTree"""
403  _IMP_atom.HierarchyTree_swiginit(self, _IMP_atom.new_HierarchyTree())
404 
405  def get_graph(self):
406  r"""get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
407  return _IMP_atom.HierarchyTree_get_graph(self)
408 
409  def get_vertices(self):
410  r"""get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
411  return _IMP_atom.HierarchyTree_get_vertices(self)
412 
413  def get_vertex_name(self, i):
414  r"""get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
415  return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
416 
417  def get_in_neighbors(self, v):
418  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"""
419  return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
420 
421  def get_out_neighbors(self, v):
422  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"""
423  return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
424 
425  def show_graphviz(self, *args):
426  r"""show_graphviz(HierarchyTree self, _ostream out=std::cout)"""
427  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
428 
429  def get_graphviz_string(self):
430  r"""get_graphviz_string(HierarchyTree self) -> std::string"""
431  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
432 
433  def add_edge(self, v0, v1):
434  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)"""
435  return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
436 
437  def add_vertex(self, l):
438  r"""add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
439  return _IMP_atom.HierarchyTree_add_vertex(self, l)
440 
441  def remove_vertex(self, l):
442  r"""remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
443  return _IMP_atom.HierarchyTree_remove_vertex(self, l)
444  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
445 
446 # Register HierarchyTree in _IMP_atom:
447 _IMP_atom.HierarchyTree_swigregister(HierarchyTree)
448 
449 _value_types.append("HierarchyTree")
450 
451 
452 PDBRecords=list
453 _plural_types.append("PDBRecords")
454 _value_types.append("PDBRecord")
455 
456 
457 _object_types.append("PDBSelector")
458 
459 
460 def _object_cast_to_PDBSelector(o):
461  r"""_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
462  return _IMP_atom._object_cast_to_PDBSelector(o)
463 
464 def Angles(l=[]):
465  return [Angle(x) for x in l]
466 _plural_types.append("Angles")
467 
468 
469 _value_types.append("Angle")
470 
471 
472 def Atoms(l=[]):
473  return [Atom(x) for x in l]
474 _plural_types.append("Atoms")
475 
476 
477 _value_types.append("Atom")
478 
479 
480 def Bonds(l=[]):
481  return [Bond(x) for x in l]
482 _plural_types.append("Bonds")
483 
484 
485 _value_types.append("Bond")
486 
487 
488 def Bondeds(l=[]):
489  return [Bonded(x) for x in l]
490 _plural_types.append("Bondeds")
491 
492 
493 _value_types.append("Bonded")
494 
495 
496 def CHARMMAtomList(l=[]):
497  return [CHARMMAtom(x) for x in l]
498 _plural_types.append("CHARMMAtomList")
499 
500 
501 _value_types.append("CHARMMAtom")
502 
503 
504 def Chains(l=[]):
505  return [Chain(x) for x in l]
506 _plural_types.append("Chains")
507 
508 
509 _value_types.append("Chain")
510 
511 
512 def CenterOfMasses(l=[]):
513  return [CenterOfMass(x) for x in l]
514 _plural_types.append("CenterOfMasses")
515 
516 
517 _value_types.append("CenterOfMass")
518 
519 
520 def Chargeds(l=[]):
521  return [Charged(x) for x in l]
522 _plural_types.append("Chargeds")
523 
524 
525 _value_types.append("Charged")
526 
527 
528 def Diffusions(l=[]):
529  return [Diffusion(x) for x in l]
530 _plural_types.append("Diffusions")
531 
532 
533 _value_types.append("Diffusion")
534 
535 
536 def RigidBodyDiffusions(l=[]):
537  return [RigidBodyDiffusion(x) for x in l]
538 _plural_types.append("RigidBodyDiffusions")
539 
540 
541 _value_types.append("RigidBodyDiffusion")
542 
543 
544 def TAMDParticles(l=[]):
545  return [TAMDParticle(x) for x in l]
546 _plural_types.append("TAMDParticles")
547 
548 
549 _value_types.append("TAMDParticle")
550 
551 
552 def TAMDCentroids(l=[]):
553  return [TAMDCentroid(x) for x in l]
554 _plural_types.append("TAMDCentroids")
555 
556 
557 _value_types.append("TAMDCentroid")
558 
559 
560 def Dihedrals(l=[]):
561  return [Dihedral(x) for x in l]
562 _plural_types.append("Dihedrals")
563 
564 
565 _value_types.append("Dihedral")
566 
567 
568 def Domains(l=[]):
569  return [Domain(x) for x in l]
570 _plural_types.append("Domains")
571 
572 
573 _value_types.append("Domain")
574 
575 
576 def Fragments(l=[]):
577  return [Fragment(x) for x in l]
578 _plural_types.append("Fragments")
579 
580 
581 _value_types.append("Fragment")
582 
583 
584 def Hierarchies(l=[]):
585  return [Hierarchy(x) for x in l]
586 _plural_types.append("Hierarchies")
587 
588 
589 _value_types.append("Hierarchy")
590 
591 
592 def LennardJonesList(l=[]):
593  return [LennardJones(x) for x in l]
594 _plural_types.append("LennardJonesList")
595 
596 
597 _value_types.append("LennardJones")
598 
599 
600 def Masses(l=[]):
601  return [Mass(x) for x in l]
602 _plural_types.append("Masses")
603 
604 
605 _value_types.append("Mass")
606 
607 
608 def LinearVelocities(l=[]):
609  return [LinearVelocity(x) for x in l]
610 _plural_types.append("LinearVelocities")
611 
612 
613 _value_types.append("LinearVelocity")
614 
615 
616 def AngularVelocities(l=[]):
617  return [AngularVelocity(x) for x in l]
618 _plural_types.append("AngularVelocities")
619 
620 
621 _value_types.append("AngularVelocity")
622 
623 
624 def Molecules(l=[]):
625  return [Molecule(x) for x in l]
626 _plural_types.append("Molecules")
627 
628 
629 _value_types.append("Molecule")
630 
631 
632 def Residues(l=[]):
633  return [Residue(x) for x in l]
634 _plural_types.append("Residues")
635 
636 
637 _value_types.append("Residue")
638 
639 
640 def Representations(l=[]):
641  return [Representation(x) for x in l]
642 _plural_types.append("Representations")
643 
644 
645 _value_types.append("Representation")
646 
647 
648 def States(l=[]):
649  return [State(x) for x in l]
650 _plural_types.append("States")
651 
652 
653 _value_types.append("State")
654 
655 
656 def Copies(l=[]):
657  return [Copy(x) for x in l]
658 _plural_types.append("Copies")
659 
660 
661 _value_types.append("Copy")
662 
663 
664 def SecondaryStructureResidues(l=[]):
665  return [SecondaryStructureResidue(x) for x in l]
666 _plural_types.append("SecondaryStructureResidues")
667 
668 
669 _value_types.append("SecondaryStructureResidue")
670 
671 
672 def StructureSources(l=[]):
673  return [StructureSource(x) for x in l]
674 _plural_types.append("StructureSources")
675 
676 
677 _value_types.append("StructureSource")
678 
679 
680 _object_types.append("Simulator")
681 
682 
683 def _object_cast_to_Simulator(o):
684  r"""_object_cast_to_Simulator(Object o) -> Simulator"""
685  return _IMP_atom._object_cast_to_Simulator(o)
686 
687 _object_types.append("ATOMPDBSelector")
688 
689 
690 def _object_cast_to_ATOMPDBSelector(o):
691  r"""_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
692  return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
693 
694 _object_types.append("AllMol2Selector")
695 
696 
697 def _object_cast_to_AllMol2Selector(o):
698  r"""_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
699  return _IMP_atom._object_cast_to_AllMol2Selector(o)
700 
701 _object_types.append("AllPDBSelector")
702 
703 
704 def _object_cast_to_AllPDBSelector(o):
705  r"""_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
706  return _IMP_atom._object_cast_to_AllPDBSelector(o)
707 
708 _object_types.append("AndPDBSelector")
709 
710 
711 def _object_cast_to_AndPDBSelector(o):
712  r"""_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
713  return _IMP_atom._object_cast_to_AndPDBSelector(o)
714 
715 _object_types.append("XorPDBSelector")
716 
717 
718 def _object_cast_to_XorPDBSelector(o):
719  r"""_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
720  return _IMP_atom._object_cast_to_XorPDBSelector(o)
721 
722 _object_types.append("ResidueTypePDBSelector")
723 
724 
725 def _object_cast_to_ResidueTypePDBSelector(o):
726  r"""_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
727  return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
728 
729 _object_types.append("AtomTypePDBSelector")
730 
731 
732 def _object_cast_to_AtomTypePDBSelector(o):
733  r"""_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
734  return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
735 
736 _object_types.append("AngleSingletonScore")
737 
738 
739 def _object_cast_to_AngleSingletonScore(o):
740  r"""_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
741  return _IMP_atom._object_cast_to_AngleSingletonScore(o)
742 
743 _object_types.append("BondEndpointsRefiner")
744 
745 
746 def _object_cast_to_BondEndpointsRefiner(o):
747  r"""_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
748  return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
749 
750 _object_types.append("BondPairContainer")
751 
752 
753 def _object_cast_to_BondPairContainer(o):
754  r"""_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
755  return _IMP_atom._object_cast_to_BondPairContainer(o)
756 
757 _object_types.append("BondSingletonScore")
758 
759 
760 def _object_cast_to_BondSingletonScore(o):
761  r"""_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
762  return _IMP_atom._object_cast_to_BondSingletonScore(o)
763 
764 _object_types.append("BondedPairFilter")
765 
766 
767 def _object_cast_to_BondedPairFilter(o):
768  r"""_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
769  return _IMP_atom._object_cast_to_BondedPairFilter(o)
770 
771 _object_types.append("BrownianDynamics")
772 
773 
774 def _object_cast_to_BrownianDynamics(o):
775  r"""_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
776  return _IMP_atom._object_cast_to_BrownianDynamics(o)
777 
778 _object_types.append("BrownianDynamicsTAMD")
779 
780 
781 def _object_cast_to_BrownianDynamicsTAMD(o):
782  r"""_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
783  return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
784 
785 _object_types.append("CAlphaPDBSelector")
786 
787 
788 def _object_cast_to_CAlphaPDBSelector(o):
789  r"""_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
790  return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
791 
792 _object_types.append("CBetaPDBSelector")
793 
794 
795 def _object_cast_to_CBetaPDBSelector(o):
796  r"""_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
797  return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
798 
799 _object_types.append("BackbonePDBSelector")
800 
801 
802 def _object_cast_to_BackbonePDBSelector(o):
803  r"""_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
804  return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
805 
806 _object_types.append("CHARMMParameters")
807 
808 
809 def _object_cast_to_CHARMMParameters(o):
810  r"""_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
811  return _IMP_atom._object_cast_to_CHARMMParameters(o)
812 
813 _object_types.append("CHARMMResidueTopology")
814 
815 
816 def _object_cast_to_CHARMMResidueTopology(o):
817  r"""_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
818  return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
819 
820 _object_types.append("CHARMMSegmentTopology")
821 
822 
823 def _object_cast_to_CHARMMSegmentTopology(o):
824  r"""_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
825  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
826 
827 _object_types.append("CHARMMStereochemistryRestraint")
828 
829 
830 def _object_cast_to_CHARMMStereochemistryRestraint(o):
831  r"""_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
832  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
833 
834 _object_types.append("CHARMMTopology")
835 
836 
837 def _object_cast_to_CHARMMTopology(o):
838  r"""_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
839  return _IMP_atom._object_cast_to_CHARMMTopology(o)
840 
841 _object_types.append("CPDBSelector")
842 
843 
844 def _object_cast_to_CPDBSelector(o):
845  r"""_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
846  return _IMP_atom._object_cast_to_CPDBSelector(o)
847 
848 _object_types.append("ChainPDBSelector")
849 
850 
851 def _object_cast_to_ChainPDBSelector(o):
852  r"""_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
853  return _IMP_atom._object_cast_to_ChainPDBSelector(o)
854 
855 _object_types.append("CoulombPairScore")
856 
857 
858 def _object_cast_to_CoulombPairScore(o):
859  r"""_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
860  return _IMP_atom._object_cast_to_CoulombPairScore(o)
861 
862 _object_types.append("CoverBond")
863 
864 
865 def _object_cast_to_CoverBond(o):
866  r"""_object_cast_to_CoverBond(Object o) -> CoverBond"""
867  return _IMP_atom._object_cast_to_CoverBond(o)
868 
869 _object_types.append("DihedralSingletonScore")
870 
871 
872 def _object_cast_to_DihedralSingletonScore(o):
873  r"""_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
874  return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
875 
876 _object_types.append("DopePairScore")
877 
878 
879 def _object_cast_to_DopePairScore(o):
880  r"""_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
881  return _IMP_atom._object_cast_to_DopePairScore(o)
882 
883 _object_types.append("LoopStatisticalPairScore")
884 
885 
886 def _object_cast_to_LoopStatisticalPairScore(o):
887  r"""_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
888  return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
889 
890 _object_types.append("OrientedSoapPairScore")
891 
892 
893 def _object_cast_to_OrientedSoapPairScore(o):
894  r"""_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
895  return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
896 
897 _object_types.append("EzRestraint")
898 
899 
900 def _object_cast_to_EzRestraint(o):
901  r"""_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
902  return _IMP_atom._object_cast_to_EzRestraint(o)
903 
904 _object_types.append("ForceFieldParameters")
905 
906 
907 def _object_cast_to_ForceFieldParameters(o):
908  r"""_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
909  return _IMP_atom._object_cast_to_ForceFieldParameters(o)
910 
911 _object_types.append("ForceSwitch")
912 
913 
914 def _object_cast_to_ForceSwitch(o):
915  r"""_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
916  return _IMP_atom._object_cast_to_ForceSwitch(o)
917 
918 _object_types.append("HydrogenPDBSelector")
919 
920 
921 def _object_cast_to_HydrogenPDBSelector(o):
922  r"""_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
923  return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
924 
925 _object_types.append("ImproperSingletonScore")
926 
927 
928 def _object_cast_to_ImproperSingletonScore(o):
929  r"""_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
930  return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
931 
932 _object_types.append("LennardJonesPairScore")
933 
934 
935 def _object_cast_to_LennardJonesPairScore(o):
936  r"""_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
937  return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
938 
939 _object_types.append("Mol2Selector")
940 
941 
942 def _object_cast_to_Mol2Selector(o):
943  r"""_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
944  return _IMP_atom._object_cast_to_Mol2Selector(o)
945 
946 _object_types.append("MolecularDynamics")
947 
948 
949 def _object_cast_to_MolecularDynamics(o):
950  r"""_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
951  return _IMP_atom._object_cast_to_MolecularDynamics(o)
952 
953 _object_types.append("NPDBSelector")
954 
955 
956 def _object_cast_to_NPDBSelector(o):
957  r"""_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
958  return _IMP_atom._object_cast_to_NPDBSelector(o)
959 
960 _object_types.append("NonAlternativePDBSelector")
961 
962 
963 def _object_cast_to_NonAlternativePDBSelector(o):
964  r"""_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
965  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
966 
967 _object_types.append("NonHydrogenMol2Selector")
968 
969 
970 def _object_cast_to_NonHydrogenMol2Selector(o):
971  r"""_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
972  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
973 
974 _object_types.append("NonHydrogenPDBSelector")
975 
976 
977 def _object_cast_to_NonHydrogenPDBSelector(o):
978  r"""_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
979  return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
980 
981 _object_types.append("NonWaterNonHydrogenPDBSelector")
982 
983 
984 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
985  r"""_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
986  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
987 
988 _object_types.append("NonWaterPDBSelector")
989 
990 
991 def _object_cast_to_NonWaterPDBSelector(o):
992  r"""_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
993  return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
994 
995 _object_types.append("NotPDBSelector")
996 
997 
998 def _object_cast_to_NotPDBSelector(o):
999  r"""_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1000  return _IMP_atom._object_cast_to_NotPDBSelector(o)
1001 
1002 _object_types.append("OrPDBSelector")
1003 
1004 
1005 def _object_cast_to_OrPDBSelector(o):
1006  r"""_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1007  return _IMP_atom._object_cast_to_OrPDBSelector(o)
1008 
1009 _object_types.append("PPDBSelector")
1010 
1011 
1012 def _object_cast_to_PPDBSelector(o):
1013  r"""_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1014  return _IMP_atom._object_cast_to_PPDBSelector(o)
1015 
1016 _object_types.append("ProteinLigandAtomPairScore")
1017 
1018 
1019 def _object_cast_to_ProteinLigandAtomPairScore(o):
1020  r"""_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1021  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1022 
1023 _object_types.append("ProteinLigandRestraint")
1024 
1025 
1026 def _object_cast_to_ProteinLigandRestraint(o):
1027  r"""_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1028  return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1029 
1030 _object_types.append("SameResiduePairFilter")
1031 
1032 
1033 def _object_cast_to_SameResiduePairFilter(o):
1034  r"""_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1035  return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1036 
1037 _object_types.append("SoapPairFilter")
1038 
1039 
1040 def _object_cast_to_SoapPairFilter(o):
1041  r"""_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1042  return _IMP_atom._object_cast_to_SoapPairFilter(o)
1043 
1044 _object_types.append("SmoothingFunction")
1045 
1046 
1047 def _object_cast_to_SmoothingFunction(o):
1048  r"""_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1049  return _IMP_atom._object_cast_to_SmoothingFunction(o)
1050 
1051 _object_types.append("StereochemistryPairFilter")
1052 
1053 
1054 def _object_cast_to_StereochemistryPairFilter(o):
1055  r"""_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1056  return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1057 
1058 _object_types.append("VelocityScalingOptimizerState")
1059 
1060 
1061 def _object_cast_to_VelocityScalingOptimizerState(o):
1062  r"""_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1063  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1064 
1065 _object_types.append("WaterPDBSelector")
1066 
1067 
1068 def _object_cast_to_WaterPDBSelector(o):
1069  r"""_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1070  return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1071 
1072 _object_types.append("WritePDBOptimizerState")
1073 
1074 
1075 def _object_cast_to_WritePDBOptimizerState(o):
1076  r"""_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1077  return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1078 
1079 AtomTypes=list
1080 _plural_types.append("AtomTypes")
1081 _value_types.append("AtomType")
1082 
1083 
1084 CHARMMAtomTopologies=list
1085 _plural_types.append("CHARMMAtomTopologies")
1086 _value_types.append("CHARMMAtomTopology")
1087 
1088 
1089 CHARMMBondEndpoints=list
1090 _plural_types.append("CHARMMBondEndpoints")
1091 _value_types.append("CHARMMBondEndpoint")
1092 
1093 
1094 CHARMMBondParametersList=list
1095 _plural_types.append("CHARMMBondParametersList")
1096 _value_types.append("CHARMMBondParameters")
1097 
1098 
1099 CHARMMDihedralParametersList=list
1100 _plural_types.append("CHARMMDihedralParametersList")
1101 _value_types.append("CHARMMDihedralParameters")
1102 
1103 
1104 _object_types.append("CHARMMIdealResidueTopology")
1105 
1106 
1107 def _object_cast_to_CHARMMIdealResidueTopology(o):
1108  r"""_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1109  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1110 
1111 CHARMMInternalCoordinates=list
1112 _plural_types.append("CHARMMInternalCoordinates")
1113 _value_types.append("CHARMMInternalCoordinate")
1114 
1115 
1116 _object_types.append("CHARMMPatch")
1117 
1118 
1119 def _object_cast_to_CHARMMPatch(o):
1120  r"""_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1121  return _IMP_atom._object_cast_to_CHARMMPatch(o)
1122 
1123 _object_types.append("CHARMMResidueTopologyBase")
1124 
1125 
1126 def _object_cast_to_CHARMMResidueTopologyBase(o):
1127  r"""_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1128  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1129 
1130 ResidueTypes=list
1131 _plural_types.append("ResidueTypes")
1132 _value_types.append("ResidueType")
1133 
1134 
1135 ChainTypes=list
1136 _plural_types.append("ChainTypes")
1137 _value_types.append("ChainType")
1138 
1139 
1140 Selections=list
1141 _plural_types.append("Selections")
1142 _value_types.append("Selection")
1143 
1144 
1145 _object_types.append("RemoveRigidMotionOptimizerState")
1146 
1147 
1148 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1149  r"""_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1150  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1151 
1152 _object_types.append("BerendsenThermostatOptimizerState")
1153 
1154 
1155 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1156  r"""_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1157  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1158 
1159 _object_types.append("LangevinThermostatOptimizerState")
1160 
1161 
1162 def _object_cast_to_LangevinThermostatOptimizerState(o):
1163  r"""_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1164  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1165 
1166 _object_types.append("SelectionGeometry")
1167 
1168 
1169 def _object_cast_to_SelectionGeometry(o):
1170  r"""_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1171  return _IMP_atom._object_cast_to_SelectionGeometry(o)
1172 
1173 _object_types.append("HierarchyGeometry")
1174 
1175 
1176 def _object_cast_to_HierarchyGeometry(o):
1177  r"""_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1178  return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1179 
1180 _object_types.append("HierarchiesGeometry")
1181 
1182 
1183 def _object_cast_to_HierarchiesGeometry(o):
1184  r"""_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1185  return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1186 
1187 _object_types.append("BondGeometry")
1188 
1189 
1190 def _object_cast_to_BondGeometry(o):
1191  r"""_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1192  return _IMP_atom._object_cast_to_BondGeometry(o)
1193 
1194 _object_types.append("BondsGeometry")
1195 
1196 
1197 def _object_cast_to_BondsGeometry(o):
1198  r"""_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1199  return _IMP_atom._object_cast_to_BondsGeometry(o)
1200 
1201 _object_types.append("CAAngleRestraint")
1202 
1203 
1204 def _object_cast_to_CAAngleRestraint(o):
1205  r"""_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1206  return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1207 
1208 _object_types.append("CADihedralRestraint")
1209 
1210 
1211 def _object_cast_to_CADihedralRestraint(o):
1212  r"""_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1213  return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1214 
1215 _object_types.append("HelixRestraint")
1216 
1217 
1218 def _object_cast_to_HelixRestraint(o):
1219  r"""_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1220  return _IMP_atom._object_cast_to_HelixRestraint(o)
1221 
1222 CHARMMDihedrals=list
1223 _plural_types.append("CHARMMDihedrals")
1224 _value_types.append("CHARMMDihedral")
1225 
1226 
1227 CHARMMBonds=list
1228 _plural_types.append("CHARMMBonds")
1229 _value_types.append("CHARMMBond")
1230 
1231 
1232 CHARMMAngles=list
1233 _plural_types.append("CHARMMAngles")
1234 _value_types.append("CHARMMAngle")
1235 
1236 class Bond(IMP.Decorator):
1237  r"""Proxy of C++ IMP::atom::Bond class."""
1238 
1239  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1240 
1241  def __init__(self, *args):
1242  r"""
1243  __init__(Bond self) -> Bond
1244  __init__(Bond self, Model m, ParticleIndex id) -> Bond
1245  __init__(Bond self, _ParticleAdaptor d) -> Bond
1246  """
1247  _IMP_atom.Bond_swiginit(self, _IMP_atom.new_Bond(*args))
1248 
1249  def show(self, *args):
1250  r"""show(Bond self, _ostream out=std::cout)"""
1251  return _IMP_atom.Bond_show(self, *args)
1252 
1253  @staticmethod
1254  def get_is_setup(*args):
1255  r"""
1256  get_is_setup(_ParticleAdaptor p) -> bool
1257  get_is_setup(Model m, ParticleIndex pi) -> bool
1258  """
1259  return _IMP_atom.Bond_get_is_setup(*args)
1260  UNKNOWN = _IMP_atom.Bond_UNKNOWN
1261 
1262  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1263 
1264  SINGLE = _IMP_atom.Bond_SINGLE
1265 
1266  DOUBLE = _IMP_atom.Bond_DOUBLE
1267 
1268  TRIPLE = _IMP_atom.Bond_TRIPLE
1269 
1270  HYDROGEN = _IMP_atom.Bond_HYDROGEN
1271 
1272  SALT = _IMP_atom.Bond_SALT
1273 
1274  PEPTIDE = _IMP_atom.Bond_PEPTIDE
1275 
1276  AMIDE = _IMP_atom.Bond_AMIDE
1277 
1278  AROMATIC = _IMP_atom.Bond_AROMATIC
1279 
1280 
1281  def get_bonded(self, i):
1282  r"""get_bonded(Bond self, unsigned int i) -> Bonded"""
1283  return _IMP_atom.Bond_get_bonded(self, i)
1284 
1285  def get_type(self):
1286  r"""get_type(Bond self) -> IMP::Int"""
1287  return _IMP_atom.Bond_get_type(self)
1288 
1289  def set_type(self, t):
1290  r"""set_type(Bond self, IMP::Int t)"""
1291  return _IMP_atom.Bond_set_type(self, t)
1292 
1293  def get_order(self):
1294  r"""get_order(Bond self) -> IMP::Int"""
1295  return _IMP_atom.Bond_get_order(self)
1296 
1297  def set_order(self, t):
1298  r"""set_order(Bond self, IMP::Int t)"""
1299  return _IMP_atom.Bond_set_order(self, t)
1300 
1301  def get_length(self):
1302  r"""get_length(Bond self) -> IMP::Float"""
1303  return _IMP_atom.Bond_get_length(self)
1304 
1305  def set_length(self, t):
1306  r"""set_length(Bond self, IMP::Float t)"""
1307  return _IMP_atom.Bond_set_length(self, t)
1308 
1309  def get_stiffness(self):
1310  r"""get_stiffness(Bond self) -> IMP::Float"""
1311  return _IMP_atom.Bond_get_stiffness(self)
1312 
1313  def set_stiffness(self, t):
1314  r"""set_stiffness(Bond self, IMP::Float t)"""
1315  return _IMP_atom.Bond_set_stiffness(self, t)
1316 
1317  @staticmethod
1318  def get_length_key():
1319  r"""get_length_key() -> FloatKey"""
1320  return _IMP_atom.Bond_get_length_key()
1321 
1322  def add_attribute(self, *args):
1323  r"""
1324  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1325  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1326  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1327  add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1328  add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1329  add_attribute(Bond self, StringKey a0, IMP::String a1)
1330  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1331  add_attribute(Bond self, ObjectKey a0, Object a1)
1332  add_attribute(Bond self, SparseFloatKey a0, IMP::Float a1)
1333  add_attribute(Bond self, SparseIntKey a0, IMP::Int a1)
1334  add_attribute(Bond self, SparseStringKey a0, IMP::String a1)
1335  add_attribute(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1336  """
1337  return _IMP_atom.Bond_add_attribute(self, *args)
1338 
1339  def get_value(self, *args):
1340  r"""
1341  get_value(Bond self, FloatKey a0) -> IMP::Float
1342  get_value(Bond self, IntKey a0) -> IMP::Int
1343  get_value(Bond self, FloatsKey a0) -> IMP::Floats
1344  get_value(Bond self, IntsKey a0) -> IMP::Ints
1345  get_value(Bond self, StringKey a0) -> IMP::String
1346  get_value(Bond self, ParticleIndexKey a0) -> Particle
1347  get_value(Bond self, ObjectKey a0) -> Object
1348  get_value(Bond self, SparseFloatKey a0) -> IMP::Float
1349  get_value(Bond self, SparseIntKey a0) -> IMP::Int
1350  get_value(Bond self, SparseStringKey a0) -> IMP::String
1351  get_value(Bond self, SparseParticleIndexKey a0) -> ParticleIndex
1352  """
1353  return _IMP_atom.Bond_get_value(self, *args)
1354 
1355  def set_value(self, *args):
1356  r"""
1357  set_value(Bond self, FloatKey a0, IMP::Float a1)
1358  set_value(Bond self, IntKey a0, IMP::Int a1)
1359  set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1360  set_value(Bond self, IntsKey a0, IMP::Ints a1)
1361  set_value(Bond self, StringKey a0, IMP::String a1)
1362  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1363  set_value(Bond self, ObjectKey a0, Object a1)
1364  set_value(Bond self, SparseFloatKey a0, IMP::Float a1)
1365  set_value(Bond self, SparseIntKey a0, IMP::Int a1)
1366  set_value(Bond self, SparseStringKey a0, IMP::String a1)
1367  set_value(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1368  """
1369  return _IMP_atom.Bond_set_value(self, *args)
1370 
1371  def remove_attribute(self, *args):
1372  r"""
1373  remove_attribute(Bond self, FloatKey a0)
1374  remove_attribute(Bond self, IntKey a0)
1375  remove_attribute(Bond self, FloatsKey a0)
1376  remove_attribute(Bond self, IntsKey a0)
1377  remove_attribute(Bond self, StringKey a0)
1378  remove_attribute(Bond self, ParticleIndexKey a0)
1379  remove_attribute(Bond self, ObjectKey a0)
1380  remove_attribute(Bond self, SparseFloatKey a0)
1381  remove_attribute(Bond self, SparseIntKey a0)
1382  remove_attribute(Bond self, SparseStringKey a0)
1383  remove_attribute(Bond self, SparseParticleIndexKey a0)
1384  """
1385  return _IMP_atom.Bond_remove_attribute(self, *args)
1386 
1387  def has_attribute(self, *args):
1388  r"""
1389  has_attribute(Bond self, FloatKey a0) -> bool
1390  has_attribute(Bond self, IntKey a0) -> bool
1391  has_attribute(Bond self, FloatsKey a0) -> bool
1392  has_attribute(Bond self, IntsKey a0) -> bool
1393  has_attribute(Bond self, StringKey a0) -> bool
1394  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1395  has_attribute(Bond self, ObjectKey a0) -> bool
1396  has_attribute(Bond self, SparseFloatKey a0) -> bool
1397  has_attribute(Bond self, SparseIntKey a0) -> bool
1398  has_attribute(Bond self, SparseStringKey a0) -> bool
1399  has_attribute(Bond self, SparseParticleIndexKey a0) -> bool
1400  """
1401  return _IMP_atom.Bond_has_attribute(self, *args)
1402 
1403  def get_derivative(self, a0):
1404  r"""get_derivative(Bond self, FloatKey a0) -> double"""
1405  return _IMP_atom.Bond_get_derivative(self, a0)
1406 
1407  def get_name(self):
1408  r"""get_name(Bond self) -> std::string"""
1409  return _IMP_atom.Bond_get_name(self)
1410 
1411  def clear_caches(self):
1412  r"""clear_caches(Bond self)"""
1413  return _IMP_atom.Bond_clear_caches(self)
1414 
1415  def set_name(self, a0):
1416  r"""set_name(Bond self, std::string a0)"""
1417  return _IMP_atom.Bond_set_name(self, a0)
1418 
1419  def set_check_level(self, a0):
1420  r"""set_check_level(Bond self, IMP::CheckLevel a0)"""
1421  return _IMP_atom.Bond_set_check_level(self, a0)
1422 
1423  def add_to_derivative(self, a0, a1, a2):
1424  r"""add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1425  return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1426 
1427  def set_is_optimized(self, a0, a1):
1428  r"""set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1429  return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1430 
1431  def get_is_optimized(self, a0):
1432  r"""get_is_optimized(Bond self, FloatKey a0) -> bool"""
1433  return _IMP_atom.Bond_get_is_optimized(self, a0)
1434 
1435  def get_check_level(self):
1436  r"""get_check_level(Bond self) -> IMP::CheckLevel"""
1437  return _IMP_atom.Bond_get_check_level(self)
1438 
1439  def __eq__(self, *args):
1440  r"""
1441  __eq__(Bond self, Bond o) -> bool
1442  __eq__(Bond self, Particle d) -> bool
1443  """
1444  return _IMP_atom.Bond___eq__(self, *args)
1445 
1446  def __ne__(self, *args):
1447  r"""
1448  __ne__(Bond self, Bond o) -> bool
1449  __ne__(Bond self, Particle d) -> bool
1450  """
1451  return _IMP_atom.Bond___ne__(self, *args)
1452 
1453  def __le__(self, *args):
1454  r"""
1455  __le__(Bond self, Bond o) -> bool
1456  __le__(Bond self, Particle d) -> bool
1457  """
1458  return _IMP_atom.Bond___le__(self, *args)
1459 
1460  def __lt__(self, *args):
1461  r"""
1462  __lt__(Bond self, Bond o) -> bool
1463  __lt__(Bond self, Particle d) -> bool
1464  """
1465  return _IMP_atom.Bond___lt__(self, *args)
1466 
1467  def __ge__(self, *args):
1468  r"""
1469  __ge__(Bond self, Bond o) -> bool
1470  __ge__(Bond self, Particle d) -> bool
1471  """
1472  return _IMP_atom.Bond___ge__(self, *args)
1473 
1474  def __gt__(self, *args):
1475  r"""
1476  __gt__(Bond self, Bond o) -> bool
1477  __gt__(Bond self, Particle d) -> bool
1478  """
1479  return _IMP_atom.Bond___gt__(self, *args)
1480 
1481  def __hash__(self):
1482  r"""__hash__(Bond self) -> std::size_t"""
1483  return _IMP_atom.Bond___hash__(self)
1484 
1485  def __str__(self):
1486  r"""__str__(Bond self) -> std::string"""
1487  return _IMP_atom.Bond___str__(self)
1488 
1489  def __repr__(self):
1490  r"""__repr__(Bond self) -> std::string"""
1491  return _IMP_atom.Bond___repr__(self)
1492 
1493  def _get_as_binary(self):
1494  r"""_get_as_binary(Bond self) -> PyObject *"""
1495  return _IMP_atom.Bond__get_as_binary(self)
1496 
1497  def _set_from_binary(self, p):
1498  r"""_set_from_binary(Bond self, PyObject * p)"""
1499  return _IMP_atom.Bond__set_from_binary(self, p)
1500 
1501  def __getstate__(self):
1502  p = self._get_as_binary()
1503  if len(self.__dict__) > 1:
1504  d = self.__dict__.copy()
1505  del d['this']
1506  p = (d, p)
1507  return p
1508 
1509  def __setstate__(self, p):
1510  if not hasattr(self, 'this'):
1511  self.__init__()
1512  if isinstance(p, tuple):
1513  d, p = p
1514  self.__dict__.update(d)
1515  return self._set_from_binary(p)
1516 
1517  __swig_destroy__ = _IMP_atom.delete_Bond
1518 
1519 # Register Bond in _IMP_atom:
1520 _IMP_atom.Bond_swigregister(Bond)
1521 class Bonded(IMP.Decorator):
1522  r"""Proxy of C++ IMP::atom::Bonded class."""
1523 
1524  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1525 
1526  def __init__(self, *args):
1527  r"""
1528  __init__(Bonded self) -> Bonded
1529  __init__(Bonded self, Model m, ParticleIndex id) -> Bonded
1530  __init__(Bonded self, _ParticleAdaptor d) -> Bonded
1531  """
1532  _IMP_atom.Bonded_swiginit(self, _IMP_atom.new_Bonded(*args))
1533 
1534  def show(self, *args):
1535  r"""show(Bonded self, _ostream out=std::cout)"""
1536  return _IMP_atom.Bonded_show(self, *args)
1537 
1538  @staticmethod
1539  def setup_particle(*args):
1540  r"""
1541  setup_particle(Model m, ParticleIndex pi) -> Bonded
1542  setup_particle(_ParticleAdaptor pa) -> Bonded
1543  """
1544  return _IMP_atom.Bonded_setup_particle(*args)
1545 
1546  @staticmethod
1547  def get_is_setup(*args):
1548  r"""
1549  get_is_setup(_ParticleAdaptor p) -> bool
1550  get_is_setup(Model m, ParticleIndex pi) -> bool
1551  """
1552  return _IMP_atom.Bonded_get_is_setup(*args)
1553 
1554  def get_number_of_bonds(self):
1555  r"""get_number_of_bonds(Bonded self) -> unsigned int"""
1556  return _IMP_atom.Bonded_get_number_of_bonds(self)
1557 
1558  def get_bond_indexes(self):
1559  r"""get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1560  return _IMP_atom.Bonded_get_bond_indexes(self)
1561 
1562  def get_bond(self, i):
1563  r"""get_bond(Bonded self, unsigned int i) -> Bond"""
1564  return _IMP_atom.Bonded_get_bond(self, i)
1565 
1566  def get_bonded(self, i):
1567  r"""get_bonded(Bonded self, unsigned int i) -> Bonded"""
1568  return _IMP_atom.Bonded_get_bonded(self, i)
1569 
1570  def add_attribute(self, *args):
1571  r"""
1572  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1573  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1574  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1575  add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1576  add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1577  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1578  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1579  add_attribute(Bonded self, ObjectKey a0, Object a1)
1580  add_attribute(Bonded self, SparseFloatKey a0, IMP::Float a1)
1581  add_attribute(Bonded self, SparseIntKey a0, IMP::Int a1)
1582  add_attribute(Bonded self, SparseStringKey a0, IMP::String a1)
1583  add_attribute(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1584  """
1585  return _IMP_atom.Bonded_add_attribute(self, *args)
1586 
1587  def get_value(self, *args):
1588  r"""
1589  get_value(Bonded self, FloatKey a0) -> IMP::Float
1590  get_value(Bonded self, IntKey a0) -> IMP::Int
1591  get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1592  get_value(Bonded self, IntsKey a0) -> IMP::Ints
1593  get_value(Bonded self, StringKey a0) -> IMP::String
1594  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1595  get_value(Bonded self, ObjectKey a0) -> Object
1596  get_value(Bonded self, SparseFloatKey a0) -> IMP::Float
1597  get_value(Bonded self, SparseIntKey a0) -> IMP::Int
1598  get_value(Bonded self, SparseStringKey a0) -> IMP::String
1599  get_value(Bonded self, SparseParticleIndexKey a0) -> ParticleIndex
1600  """
1601  return _IMP_atom.Bonded_get_value(self, *args)
1602 
1603  def set_value(self, *args):
1604  r"""
1605  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1606  set_value(Bonded self, IntKey a0, IMP::Int a1)
1607  set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1608  set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1609  set_value(Bonded self, StringKey a0, IMP::String a1)
1610  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1611  set_value(Bonded self, ObjectKey a0, Object a1)
1612  set_value(Bonded self, SparseFloatKey a0, IMP::Float a1)
1613  set_value(Bonded self, SparseIntKey a0, IMP::Int a1)
1614  set_value(Bonded self, SparseStringKey a0, IMP::String a1)
1615  set_value(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1616  """
1617  return _IMP_atom.Bonded_set_value(self, *args)
1618 
1619  def remove_attribute(self, *args):
1620  r"""
1621  remove_attribute(Bonded self, FloatKey a0)
1622  remove_attribute(Bonded self, IntKey a0)
1623  remove_attribute(Bonded self, FloatsKey a0)
1624  remove_attribute(Bonded self, IntsKey a0)
1625  remove_attribute(Bonded self, StringKey a0)
1626  remove_attribute(Bonded self, ParticleIndexKey a0)
1627  remove_attribute(Bonded self, ObjectKey a0)
1628  remove_attribute(Bonded self, SparseFloatKey a0)
1629  remove_attribute(Bonded self, SparseIntKey a0)
1630  remove_attribute(Bonded self, SparseStringKey a0)
1631  remove_attribute(Bonded self, SparseParticleIndexKey a0)
1632  """
1633  return _IMP_atom.Bonded_remove_attribute(self, *args)
1634 
1635  def has_attribute(self, *args):
1636  r"""
1637  has_attribute(Bonded self, FloatKey a0) -> bool
1638  has_attribute(Bonded self, IntKey a0) -> bool
1639  has_attribute(Bonded self, FloatsKey a0) -> bool
1640  has_attribute(Bonded self, IntsKey a0) -> bool
1641  has_attribute(Bonded self, StringKey a0) -> bool
1642  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1643  has_attribute(Bonded self, ObjectKey a0) -> bool
1644  has_attribute(Bonded self, SparseFloatKey a0) -> bool
1645  has_attribute(Bonded self, SparseIntKey a0) -> bool
1646  has_attribute(Bonded self, SparseStringKey a0) -> bool
1647  has_attribute(Bonded self, SparseParticleIndexKey a0) -> bool
1648  """
1649  return _IMP_atom.Bonded_has_attribute(self, *args)
1650 
1651  def get_derivative(self, a0):
1652  r"""get_derivative(Bonded self, FloatKey a0) -> double"""
1653  return _IMP_atom.Bonded_get_derivative(self, a0)
1654 
1655  def get_name(self):
1656  r"""get_name(Bonded self) -> std::string"""
1657  return _IMP_atom.Bonded_get_name(self)
1658 
1659  def clear_caches(self):
1660  r"""clear_caches(Bonded self)"""
1661  return _IMP_atom.Bonded_clear_caches(self)
1662 
1663  def set_name(self, a0):
1664  r"""set_name(Bonded self, std::string a0)"""
1665  return _IMP_atom.Bonded_set_name(self, a0)
1666 
1667  def set_check_level(self, a0):
1668  r"""set_check_level(Bonded self, IMP::CheckLevel a0)"""
1669  return _IMP_atom.Bonded_set_check_level(self, a0)
1670 
1671  def add_to_derivative(self, a0, a1, a2):
1672  r"""add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1673  return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1674 
1675  def set_is_optimized(self, a0, a1):
1676  r"""set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1677  return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1678 
1679  def get_is_optimized(self, a0):
1680  r"""get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1681  return _IMP_atom.Bonded_get_is_optimized(self, a0)
1682 
1683  def get_check_level(self):
1684  r"""get_check_level(Bonded self) -> IMP::CheckLevel"""
1685  return _IMP_atom.Bonded_get_check_level(self)
1686 
1687  def __eq__(self, *args):
1688  r"""
1689  __eq__(Bonded self, Bonded o) -> bool
1690  __eq__(Bonded self, Particle d) -> bool
1691  """
1692  return _IMP_atom.Bonded___eq__(self, *args)
1693 
1694  def __ne__(self, *args):
1695  r"""
1696  __ne__(Bonded self, Bonded o) -> bool
1697  __ne__(Bonded self, Particle d) -> bool
1698  """
1699  return _IMP_atom.Bonded___ne__(self, *args)
1700 
1701  def __le__(self, *args):
1702  r"""
1703  __le__(Bonded self, Bonded o) -> bool
1704  __le__(Bonded self, Particle d) -> bool
1705  """
1706  return _IMP_atom.Bonded___le__(self, *args)
1707 
1708  def __lt__(self, *args):
1709  r"""
1710  __lt__(Bonded self, Bonded o) -> bool
1711  __lt__(Bonded self, Particle d) -> bool
1712  """
1713  return _IMP_atom.Bonded___lt__(self, *args)
1714 
1715  def __ge__(self, *args):
1716  r"""
1717  __ge__(Bonded self, Bonded o) -> bool
1718  __ge__(Bonded self, Particle d) -> bool
1719  """
1720  return _IMP_atom.Bonded___ge__(self, *args)
1721 
1722  def __gt__(self, *args):
1723  r"""
1724  __gt__(Bonded self, Bonded o) -> bool
1725  __gt__(Bonded self, Particle d) -> bool
1726  """
1727  return _IMP_atom.Bonded___gt__(self, *args)
1728 
1729  def __hash__(self):
1730  r"""__hash__(Bonded self) -> std::size_t"""
1731  return _IMP_atom.Bonded___hash__(self)
1732 
1733  def __str__(self):
1734  r"""__str__(Bonded self) -> std::string"""
1735  return _IMP_atom.Bonded___str__(self)
1736 
1737  def __repr__(self):
1738  r"""__repr__(Bonded self) -> std::string"""
1739  return _IMP_atom.Bonded___repr__(self)
1740 
1741  def _get_as_binary(self):
1742  r"""_get_as_binary(Bonded self) -> PyObject *"""
1743  return _IMP_atom.Bonded__get_as_binary(self)
1744 
1745  def _set_from_binary(self, p):
1746  r"""_set_from_binary(Bonded self, PyObject * p)"""
1747  return _IMP_atom.Bonded__set_from_binary(self, p)
1748 
1749  def __getstate__(self):
1750  p = self._get_as_binary()
1751  if len(self.__dict__) > 1:
1752  d = self.__dict__.copy()
1753  del d['this']
1754  p = (d, p)
1755  return p
1756 
1757  def __setstate__(self, p):
1758  if not hasattr(self, 'this'):
1759  self.__init__()
1760  if isinstance(p, tuple):
1761  d, p = p
1762  self.__dict__.update(d)
1763  return self._set_from_binary(p)
1764 
1765  __swig_destroy__ = _IMP_atom.delete_Bonded
1766 
1767 # Register Bonded in _IMP_atom:
1768 _IMP_atom.Bonded_swigregister(Bonded)
1769 
1770 def create_custom_bond(a, b, length, stiffness=-1):
1771  r"""create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond"""
1772  return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1773 
1774 def create_bond(*args):
1775  r"""
1776  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1777  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1778  """
1779  return _IMP_atom.create_bond(*args)
1780 
1781 def destroy_bond(b):
1782  r"""destroy_bond(Bond b)"""
1783  return _IMP_atom.destroy_bond(b)
1784 
1785 def get_bond(a, b):
1786  r"""get_bond(Bonded a, Bonded b) -> Bond"""
1787  return _IMP_atom.get_bond(a, b)
1788 class BondGeometry(IMP.display.SingletonGeometry):
1789  r"""Proxy of C++ IMP::atom::BondGeometry class."""
1790 
1791  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1792 
1793  def __init__(self, *args):
1794  r"""
1795  __init__(BondGeometry self, Particle p) -> BondGeometry
1796  __init__(BondGeometry self, Bond d) -> BondGeometry
1797  """
1798  _IMP_atom.BondGeometry_swiginit(self, _IMP_atom.new_BondGeometry(*args))
1799 
1800  def get_version_info(self):
1801  r"""get_version_info(BondGeometry self) -> VersionInfo"""
1802  return _IMP_atom.BondGeometry_get_version_info(self)
1803  __swig_destroy__ = _IMP_atom.delete_BondGeometry
1804 
1805  def __str__(self):
1806  r"""__str__(BondGeometry self) -> std::string"""
1807  return _IMP_atom.BondGeometry___str__(self)
1808 
1809  def __repr__(self):
1810  r"""__repr__(BondGeometry self) -> std::string"""
1811  return _IMP_atom.BondGeometry___repr__(self)
1812 
1813  @staticmethod
1814  def get_from(o):
1815  return _object_cast_to_BondGeometry(o)
1816 
1817 
1818 # Register BondGeometry in _IMP_atom:
1819 _IMP_atom.BondGeometry_swigregister(BondGeometry)
1820 class BondsGeometry(IMP.display.SingletonsGeometry):
1821  r"""Proxy of C++ IMP::atom::BondsGeometry class."""
1822 
1823  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1824 
1825  def __init__(self, sc):
1826  r"""__init__(BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1827  _IMP_atom.BondsGeometry_swiginit(self, _IMP_atom.new_BondsGeometry(sc))
1828 
1829  def get_version_info(self):
1830  r"""get_version_info(BondsGeometry self) -> VersionInfo"""
1831  return _IMP_atom.BondsGeometry_get_version_info(self)
1832  __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1833 
1834  def __str__(self):
1835  r"""__str__(BondsGeometry self) -> std::string"""
1836  return _IMP_atom.BondsGeometry___str__(self)
1837 
1838  def __repr__(self):
1839  r"""__repr__(BondsGeometry self) -> std::string"""
1840  return _IMP_atom.BondsGeometry___repr__(self)
1841 
1842  @staticmethod
1843  def get_from(o):
1844  return _object_cast_to_BondsGeometry(o)
1845 
1846 
1847 # Register BondsGeometry in _IMP_atom:
1848 _IMP_atom.BondsGeometry_swigregister(BondsGeometry)
1849 class Hierarchy(IMP.core.Hierarchy):
1850  r"""Proxy of C++ IMP::atom::Hierarchy class."""
1851 
1852  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1853 
1854  def __init__(self, *args):
1855  r"""
1856  __init__(Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1857  __init__(Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1858  __init__(Hierarchy self) -> Hierarchy
1859  __init__(Hierarchy self, Hierarchy h) -> Hierarchy
1860  """
1861  _IMP_atom.Hierarchy_swiginit(self, _IMP_atom.new_Hierarchy(*args))
1862 
1863  @staticmethod
1864  def setup_particle(*args):
1865  r"""
1866  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1867  setup_particle(Particle p) -> Hierarchy
1868  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::ParticleIndexesAdaptor()) -> Hierarchy
1869  """
1870  return _IMP_atom.Hierarchy_setup_particle(*args)
1871 
1872  @staticmethod
1873  def get_is_setup(*args):
1874  r"""
1875  get_is_setup(Particle p) -> bool
1876  get_is_setup(Model m, ParticleIndex p) -> bool
1877  """
1878  return _IMP_atom.Hierarchy_get_is_setup(*args)
1879 
1880  def get_is_valid(self, print_info=False):
1881  r"""get_is_valid(Hierarchy self, bool print_info=False) -> bool"""
1882  return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1883 
1884  def add_child(self, o):
1885  r"""add_child(Hierarchy self, Hierarchy o)"""
1886  return _IMP_atom.Hierarchy_add_child(self, o)
1887 
1888  def get_child(self, i):
1889  r"""get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1890  return _IMP_atom.Hierarchy_get_child(self, i)
1891 
1892  def get_children(self):
1893  r"""get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1894  return _IMP_atom.Hierarchy_get_children(self)
1895 
1896  def get_parent(self):
1897  r"""get_parent(Hierarchy self) -> Hierarchy"""
1898  return _IMP_atom.Hierarchy_get_parent(self)
1899 
1900  @staticmethod
1901  def get_traits():
1902  r"""get_traits() -> HierarchyTraits"""
1903  return _IMP_atom.Hierarchy_get_traits()
1904 
1905  def show(self, *args):
1906  r"""
1907  show(Hierarchy self, _ostream out, std::string delimiter)
1908  show(Hierarchy self, _ostream out=std::cout)
1909  """
1910  return _IMP_atom.Hierarchy_show(self, *args)
1911 
1912  def add_attribute(self, *args):
1913  r"""
1914  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1915  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1916  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1917  add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1918  add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1919  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1920  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1921  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1922  add_attribute(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1923  add_attribute(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1924  add_attribute(Hierarchy self, SparseStringKey a0, IMP::String a1)
1925  add_attribute(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1926  """
1927  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1928 
1929  def get_value(self, *args):
1930  r"""
1931  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1932  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1933  get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1934  get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1935  get_value(Hierarchy self, StringKey a0) -> IMP::String
1936  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1937  get_value(Hierarchy self, ObjectKey a0) -> Object
1938  get_value(Hierarchy self, SparseFloatKey a0) -> IMP::Float
1939  get_value(Hierarchy self, SparseIntKey a0) -> IMP::Int
1940  get_value(Hierarchy self, SparseStringKey a0) -> IMP::String
1941  get_value(Hierarchy self, SparseParticleIndexKey a0) -> ParticleIndex
1942  """
1943  return _IMP_atom.Hierarchy_get_value(self, *args)
1944 
1945  def set_value(self, *args):
1946  r"""
1947  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1948  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1949  set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1950  set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1951  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1952  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1953  set_value(Hierarchy self, ObjectKey a0, Object a1)
1954  set_value(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1955  set_value(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1956  set_value(Hierarchy self, SparseStringKey a0, IMP::String a1)
1957  set_value(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1958  """
1959  return _IMP_atom.Hierarchy_set_value(self, *args)
1960 
1961  def remove_attribute(self, *args):
1962  r"""
1963  remove_attribute(Hierarchy self, FloatKey a0)
1964  remove_attribute(Hierarchy self, IntKey a0)
1965  remove_attribute(Hierarchy self, FloatsKey a0)
1966  remove_attribute(Hierarchy self, IntsKey a0)
1967  remove_attribute(Hierarchy self, StringKey a0)
1968  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1969  remove_attribute(Hierarchy self, ObjectKey a0)
1970  remove_attribute(Hierarchy self, SparseFloatKey a0)
1971  remove_attribute(Hierarchy self, SparseIntKey a0)
1972  remove_attribute(Hierarchy self, SparseStringKey a0)
1973  remove_attribute(Hierarchy self, SparseParticleIndexKey a0)
1974  """
1975  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1976 
1977  def has_attribute(self, *args):
1978  r"""
1979  has_attribute(Hierarchy self, FloatKey a0) -> bool
1980  has_attribute(Hierarchy self, IntKey a0) -> bool
1981  has_attribute(Hierarchy self, FloatsKey a0) -> bool
1982  has_attribute(Hierarchy self, IntsKey a0) -> bool
1983  has_attribute(Hierarchy self, StringKey a0) -> bool
1984  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1985  has_attribute(Hierarchy self, ObjectKey a0) -> bool
1986  has_attribute(Hierarchy self, SparseFloatKey a0) -> bool
1987  has_attribute(Hierarchy self, SparseIntKey a0) -> bool
1988  has_attribute(Hierarchy self, SparseStringKey a0) -> bool
1989  has_attribute(Hierarchy self, SparseParticleIndexKey a0) -> bool
1990  """
1991  return _IMP_atom.Hierarchy_has_attribute(self, *args)
1992 
1993  def get_derivative(self, a0):
1994  r"""get_derivative(Hierarchy self, FloatKey a0) -> double"""
1995  return _IMP_atom.Hierarchy_get_derivative(self, a0)
1996 
1997  def get_name(self):
1998  r"""get_name(Hierarchy self) -> std::string"""
1999  return _IMP_atom.Hierarchy_get_name(self)
2000 
2001  def clear_caches(self):
2002  r"""clear_caches(Hierarchy self)"""
2003  return _IMP_atom.Hierarchy_clear_caches(self)
2004 
2005  def set_name(self, a0):
2006  r"""set_name(Hierarchy self, std::string a0)"""
2007  return _IMP_atom.Hierarchy_set_name(self, a0)
2008 
2009  def set_check_level(self, a0):
2010  r"""set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2011  return _IMP_atom.Hierarchy_set_check_level(self, a0)
2012 
2013  def add_to_derivative(self, a0, a1, a2):
2014  r"""add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2015  return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2016 
2017  def set_is_optimized(self, a0, a1):
2018  r"""set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2019  return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2020 
2021  def get_is_optimized(self, a0):
2022  r"""get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2023  return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2024 
2025  def get_check_level(self):
2026  r"""get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2027  return _IMP_atom.Hierarchy_get_check_level(self)
2028 
2029  def __eq__(self, *args):
2030  r"""
2031  __eq__(Hierarchy self, Hierarchy o) -> bool
2032  __eq__(Hierarchy self, Particle d) -> bool
2033  """
2034  return _IMP_atom.Hierarchy___eq__(self, *args)
2035 
2036  def __ne__(self, *args):
2037  r"""
2038  __ne__(Hierarchy self, Hierarchy o) -> bool
2039  __ne__(Hierarchy self, Particle d) -> bool
2040  """
2041  return _IMP_atom.Hierarchy___ne__(self, *args)
2042 
2043  def __le__(self, *args):
2044  r"""
2045  __le__(Hierarchy self, Hierarchy o) -> bool
2046  __le__(Hierarchy self, Particle d) -> bool
2047  """
2048  return _IMP_atom.Hierarchy___le__(self, *args)
2049 
2050  def __lt__(self, *args):
2051  r"""
2052  __lt__(Hierarchy self, Hierarchy o) -> bool
2053  __lt__(Hierarchy self, Particle d) -> bool
2054  """
2055  return _IMP_atom.Hierarchy___lt__(self, *args)
2056 
2057  def __ge__(self, *args):
2058  r"""
2059  __ge__(Hierarchy self, Hierarchy o) -> bool
2060  __ge__(Hierarchy self, Particle d) -> bool
2061  """
2062  return _IMP_atom.Hierarchy___ge__(self, *args)
2063 
2064  def __gt__(self, *args):
2065  r"""
2066  __gt__(Hierarchy self, Hierarchy o) -> bool
2067  __gt__(Hierarchy self, Particle d) -> bool
2068  """
2069  return _IMP_atom.Hierarchy___gt__(self, *args)
2070 
2071  def __hash__(self):
2072  r"""__hash__(Hierarchy self) -> std::size_t"""
2073  return _IMP_atom.Hierarchy___hash__(self)
2074 
2075  def __str__(self):
2076  r"""__str__(Hierarchy self) -> std::string"""
2077  return _IMP_atom.Hierarchy___str__(self)
2078 
2079  def __repr__(self):
2080  r"""__repr__(Hierarchy self) -> std::string"""
2081  return _IMP_atom.Hierarchy___repr__(self)
2082 
2083  def _get_as_binary(self):
2084  r"""_get_as_binary(Hierarchy self) -> PyObject *"""
2085  return _IMP_atom.Hierarchy__get_as_binary(self)
2086 
2087  def _set_from_binary(self, p):
2088  r"""_set_from_binary(Hierarchy self, PyObject * p)"""
2089  return _IMP_atom.Hierarchy__set_from_binary(self, p)
2090 
2091  def __getstate__(self):
2092  p = self._get_as_binary()
2093  if len(self.__dict__) > 1:
2094  d = self.__dict__.copy()
2095  del d['this']
2096  p = (d, p)
2097  return p
2098 
2099  def __setstate__(self, p):
2100  if not hasattr(self, 'this'):
2101  self.__init__()
2102  if isinstance(p, tuple):
2103  d, p = p
2104  self.__dict__.update(d)
2105  return self._set_from_binary(p)
2106 
2107  __swig_destroy__ = _IMP_atom.delete_Hierarchy
2108 
2109 # Register Hierarchy in _IMP_atom:
2110 _IMP_atom.Hierarchy_swigregister(Hierarchy)
2111 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2112 
2113 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2114 
2115 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2116 
2117 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2118 
2119 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2120 
2121 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2122 
2123 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2124 
2125 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2126 
2127 MASS_TYPE = _IMP_atom.MASS_TYPE
2128 
2129 STATE_TYPE = _IMP_atom.STATE_TYPE
2130 
2131 
2132 def get_by_type(mhd, t):
2133  r"""get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2134  return _IMP_atom.get_by_type(mhd, t)
2135 
2136 def create_fragment(ps):
2137  r"""create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2138  return _IMP_atom.create_fragment(ps)
2139 
2140 def get_internal_bonds(mhd):
2141  r"""get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2142  return _IMP_atom.get_internal_bonds(mhd)
2143 
2144 def get_root(h):
2145  r"""get_root(Hierarchy h) -> Hierarchy"""
2146  return _IMP_atom.get_root(h)
2147 
2148 def show(*args):
2149  r"""show(Hierarchy h, _ostream out=std::cout)"""
2150  return _IMP_atom.show(*args)
2151 
2152 def create_rigid_body(*args):
2153  r"""
2154  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
2155  create_rigid_body(Hierarchy h) -> RigidBody
2156  """
2157  return _IMP_atom.create_rigid_body(*args)
2158 
2159 def create_compatible_rigid_body(h, reference):
2160  r"""create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2161  return _IMP_atom.create_compatible_rigid_body(h, reference)
2162 
2163 def get_is_heterogen(h):
2164  r"""get_is_heterogen(Hierarchy h) -> bool"""
2165  return _IMP_atom.get_is_heterogen(h)
2166 
2167 def create_clone(d):
2168  r"""create_clone(Hierarchy d) -> Hierarchy"""
2169  return _IMP_atom.create_clone(d)
2170 
2171 def create_clone_one(d):
2172  r"""create_clone_one(Hierarchy d) -> Hierarchy"""
2173  return _IMP_atom.create_clone_one(d)
2174 
2175 def destroy(d):
2176  r"""destroy(Hierarchy d)"""
2177  return _IMP_atom.destroy(d)
2178 
2179 def get_bounding_box(h):
2180  r"""get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2181  return _IMP_atom.get_bounding_box(h)
2182 
2183 def get_bounding_sphere(h):
2184  r"""get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2185  return _IMP_atom.get_bounding_sphere(h)
2186 class Angle(IMP.Decorator):
2187  r"""Proxy of C++ IMP::atom::Angle class."""
2188 
2189  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2190 
2191  def __init__(self, *args):
2192  r"""
2193  __init__(Angle self) -> Angle
2194  __init__(Angle self, Model m, ParticleIndex id) -> Angle
2195  __init__(Angle self, _ParticleAdaptor d) -> Angle
2196  """
2197  _IMP_atom.Angle_swiginit(self, _IMP_atom.new_Angle(*args))
2198 
2199  def show(self, *args):
2200  r"""show(Angle self, _ostream out=std::cout)"""
2201  return _IMP_atom.Angle_show(self, *args)
2202 
2203  @staticmethod
2204  def setup_particle(*args):
2205  r"""
2206  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2207  setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c) -> Angle
2208  """
2209  return _IMP_atom.Angle_setup_particle(*args)
2210 
2211  @staticmethod
2212  def get_is_setup(*args):
2213  r"""
2214  get_is_setup(_ParticleAdaptor p) -> bool
2215  get_is_setup(Model m, ParticleIndex pi) -> bool
2216  """
2217  return _IMP_atom.Angle_get_is_setup(*args)
2218 
2219  def get_particle(self, *args):
2220  r"""
2221  get_particle(Angle self) -> Particle
2222  get_particle(Angle self, unsigned int i) -> Particle
2223  """
2224  return _IMP_atom.Angle_get_particle(self, *args)
2225 
2226  def get_ideal(self):
2227  r"""get_ideal(Angle self) -> IMP::Float"""
2228  return _IMP_atom.Angle_get_ideal(self)
2229 
2230  def set_ideal(self, t):
2231  r"""set_ideal(Angle self, IMP::Float t)"""
2232  return _IMP_atom.Angle_set_ideal(self, t)
2233 
2234  def get_stiffness(self):
2235  r"""get_stiffness(Angle self) -> IMP::Float"""
2236  return _IMP_atom.Angle_get_stiffness(self)
2237 
2238  def set_stiffness(self, t):
2239  r"""set_stiffness(Angle self, IMP::Float t)"""
2240  return _IMP_atom.Angle_set_stiffness(self, t)
2241 
2242  @staticmethod
2243  def get_particle_key(i):
2244  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2245  return _IMP_atom.Angle_get_particle_key(i)
2246 
2247  @staticmethod
2248  def get_ideal_key():
2249  r"""get_ideal_key() -> FloatKey"""
2250  return _IMP_atom.Angle_get_ideal_key()
2251 
2252  @staticmethod
2253  def get_stiffness_key():
2254  r"""get_stiffness_key() -> FloatKey"""
2255  return _IMP_atom.Angle_get_stiffness_key()
2256 
2257  def add_attribute(self, *args):
2258  r"""
2259  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2260  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2261  add_attribute(Angle self, IntKey a0, IMP::Int a1)
2262  add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2263  add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2264  add_attribute(Angle self, StringKey a0, IMP::String a1)
2265  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2266  add_attribute(Angle self, ObjectKey a0, Object a1)
2267  add_attribute(Angle self, SparseFloatKey a0, IMP::Float a1)
2268  add_attribute(Angle self, SparseIntKey a0, IMP::Int a1)
2269  add_attribute(Angle self, SparseStringKey a0, IMP::String a1)
2270  add_attribute(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2271  """
2272  return _IMP_atom.Angle_add_attribute(self, *args)
2273 
2274  def get_value(self, *args):
2275  r"""
2276  get_value(Angle self, FloatKey a0) -> IMP::Float
2277  get_value(Angle self, IntKey a0) -> IMP::Int
2278  get_value(Angle self, FloatsKey a0) -> IMP::Floats
2279  get_value(Angle self, IntsKey a0) -> IMP::Ints
2280  get_value(Angle self, StringKey a0) -> IMP::String
2281  get_value(Angle self, ParticleIndexKey a0) -> Particle
2282  get_value(Angle self, ObjectKey a0) -> Object
2283  get_value(Angle self, SparseFloatKey a0) -> IMP::Float
2284  get_value(Angle self, SparseIntKey a0) -> IMP::Int
2285  get_value(Angle self, SparseStringKey a0) -> IMP::String
2286  get_value(Angle self, SparseParticleIndexKey a0) -> ParticleIndex
2287  """
2288  return _IMP_atom.Angle_get_value(self, *args)
2289 
2290  def set_value(self, *args):
2291  r"""
2292  set_value(Angle self, FloatKey a0, IMP::Float a1)
2293  set_value(Angle self, IntKey a0, IMP::Int a1)
2294  set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2295  set_value(Angle self, IntsKey a0, IMP::Ints a1)
2296  set_value(Angle self, StringKey a0, IMP::String a1)
2297  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2298  set_value(Angle self, ObjectKey a0, Object a1)
2299  set_value(Angle self, SparseFloatKey a0, IMP::Float a1)
2300  set_value(Angle self, SparseIntKey a0, IMP::Int a1)
2301  set_value(Angle self, SparseStringKey a0, IMP::String a1)
2302  set_value(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2303  """
2304  return _IMP_atom.Angle_set_value(self, *args)
2305 
2306  def remove_attribute(self, *args):
2307  r"""
2308  remove_attribute(Angle self, FloatKey a0)
2309  remove_attribute(Angle self, IntKey a0)
2310  remove_attribute(Angle self, FloatsKey a0)
2311  remove_attribute(Angle self, IntsKey a0)
2312  remove_attribute(Angle self, StringKey a0)
2313  remove_attribute(Angle self, ParticleIndexKey a0)
2314  remove_attribute(Angle self, ObjectKey a0)
2315  remove_attribute(Angle self, SparseFloatKey a0)
2316  remove_attribute(Angle self, SparseIntKey a0)
2317  remove_attribute(Angle self, SparseStringKey a0)
2318  remove_attribute(Angle self, SparseParticleIndexKey a0)
2319  """
2320  return _IMP_atom.Angle_remove_attribute(self, *args)
2321 
2322  def has_attribute(self, *args):
2323  r"""
2324  has_attribute(Angle self, FloatKey a0) -> bool
2325  has_attribute(Angle self, IntKey a0) -> bool
2326  has_attribute(Angle self, FloatsKey a0) -> bool
2327  has_attribute(Angle self, IntsKey a0) -> bool
2328  has_attribute(Angle self, StringKey a0) -> bool
2329  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2330  has_attribute(Angle self, ObjectKey a0) -> bool
2331  has_attribute(Angle self, SparseFloatKey a0) -> bool
2332  has_attribute(Angle self, SparseIntKey a0) -> bool
2333  has_attribute(Angle self, SparseStringKey a0) -> bool
2334  has_attribute(Angle self, SparseParticleIndexKey a0) -> bool
2335  """
2336  return _IMP_atom.Angle_has_attribute(self, *args)
2337 
2338  def get_derivative(self, a0):
2339  r"""get_derivative(Angle self, FloatKey a0) -> double"""
2340  return _IMP_atom.Angle_get_derivative(self, a0)
2341 
2342  def get_name(self):
2343  r"""get_name(Angle self) -> std::string"""
2344  return _IMP_atom.Angle_get_name(self)
2345 
2346  def clear_caches(self):
2347  r"""clear_caches(Angle self)"""
2348  return _IMP_atom.Angle_clear_caches(self)
2349 
2350  def set_name(self, a0):
2351  r"""set_name(Angle self, std::string a0)"""
2352  return _IMP_atom.Angle_set_name(self, a0)
2353 
2354  def set_check_level(self, a0):
2355  r"""set_check_level(Angle self, IMP::CheckLevel a0)"""
2356  return _IMP_atom.Angle_set_check_level(self, a0)
2357 
2358  def add_to_derivative(self, a0, a1, a2):
2359  r"""add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2360  return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2361 
2362  def set_is_optimized(self, a0, a1):
2363  r"""set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2364  return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2365 
2366  def get_is_optimized(self, a0):
2367  r"""get_is_optimized(Angle self, FloatKey a0) -> bool"""
2368  return _IMP_atom.Angle_get_is_optimized(self, a0)
2369 
2370  def get_check_level(self):
2371  r"""get_check_level(Angle self) -> IMP::CheckLevel"""
2372  return _IMP_atom.Angle_get_check_level(self)
2373 
2374  def __eq__(self, *args):
2375  r"""
2376  __eq__(Angle self, Angle o) -> bool
2377  __eq__(Angle self, Particle d) -> bool
2378  """
2379  return _IMP_atom.Angle___eq__(self, *args)
2380 
2381  def __ne__(self, *args):
2382  r"""
2383  __ne__(Angle self, Angle o) -> bool
2384  __ne__(Angle self, Particle d) -> bool
2385  """
2386  return _IMP_atom.Angle___ne__(self, *args)
2387 
2388  def __le__(self, *args):
2389  r"""
2390  __le__(Angle self, Angle o) -> bool
2391  __le__(Angle self, Particle d) -> bool
2392  """
2393  return _IMP_atom.Angle___le__(self, *args)
2394 
2395  def __lt__(self, *args):
2396  r"""
2397  __lt__(Angle self, Angle o) -> bool
2398  __lt__(Angle self, Particle d) -> bool
2399  """
2400  return _IMP_atom.Angle___lt__(self, *args)
2401 
2402  def __ge__(self, *args):
2403  r"""
2404  __ge__(Angle self, Angle o) -> bool
2405  __ge__(Angle self, Particle d) -> bool
2406  """
2407  return _IMP_atom.Angle___ge__(self, *args)
2408 
2409  def __gt__(self, *args):
2410  r"""
2411  __gt__(Angle self, Angle o) -> bool
2412  __gt__(Angle self, Particle d) -> bool
2413  """
2414  return _IMP_atom.Angle___gt__(self, *args)
2415 
2416  def __hash__(self):
2417  r"""__hash__(Angle self) -> std::size_t"""
2418  return _IMP_atom.Angle___hash__(self)
2419 
2420  def __str__(self):
2421  r"""__str__(Angle self) -> std::string"""
2422  return _IMP_atom.Angle___str__(self)
2423 
2424  def __repr__(self):
2425  r"""__repr__(Angle self) -> std::string"""
2426  return _IMP_atom.Angle___repr__(self)
2427 
2428  def _get_as_binary(self):
2429  r"""_get_as_binary(Angle self) -> PyObject *"""
2430  return _IMP_atom.Angle__get_as_binary(self)
2431 
2432  def _set_from_binary(self, p):
2433  r"""_set_from_binary(Angle self, PyObject * p)"""
2434  return _IMP_atom.Angle__set_from_binary(self, p)
2435 
2436  def __getstate__(self):
2437  p = self._get_as_binary()
2438  if len(self.__dict__) > 1:
2439  d = self.__dict__.copy()
2440  del d['this']
2441  p = (d, p)
2442  return p
2443 
2444  def __setstate__(self, p):
2445  if not hasattr(self, 'this'):
2446  self.__init__()
2447  if isinstance(p, tuple):
2448  d, p = p
2449  self.__dict__.update(d)
2450  return self._set_from_binary(p)
2451 
2452  __swig_destroy__ = _IMP_atom.delete_Angle
2453 
2454 # Register Angle in _IMP_atom:
2455 _IMP_atom.Angle_swigregister(Angle)
2456 class Dihedral(IMP.Decorator):
2457  r"""Proxy of C++ IMP::atom::Dihedral class."""
2458 
2459  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2460 
2461  def __init__(self, *args):
2462  r"""
2463  __init__(Dihedral self) -> Dihedral
2464  __init__(Dihedral self, Model m, ParticleIndex id) -> Dihedral
2465  __init__(Dihedral self, _ParticleAdaptor d) -> Dihedral
2466  """
2467  _IMP_atom.Dihedral_swiginit(self, _IMP_atom.new_Dihedral(*args))
2468 
2469  def show(self, *args):
2470  r"""show(Dihedral self, _ostream out=std::cout)"""
2471  return _IMP_atom.Dihedral_show(self, *args)
2472 
2473  @staticmethod
2474  def setup_particle(*args):
2475  r"""
2476  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2477  setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2478  """
2479  return _IMP_atom.Dihedral_setup_particle(*args)
2480 
2481  @staticmethod
2482  def get_is_setup(*args):
2483  r"""
2484  get_is_setup(_ParticleAdaptor p) -> bool
2485  get_is_setup(Model m, ParticleIndex pi) -> bool
2486  """
2487  return _IMP_atom.Dihedral_get_is_setup(*args)
2488 
2489  def get_particle(self, *args):
2490  r"""
2491  get_particle(Dihedral self) -> Particle
2492  get_particle(Dihedral self, unsigned int i) -> Particle
2493  """
2494  return _IMP_atom.Dihedral_get_particle(self, *args)
2495 
2496  def get_ideal(self):
2497  r"""get_ideal(Dihedral self) -> IMP::Float"""
2498  return _IMP_atom.Dihedral_get_ideal(self)
2499 
2500  def set_ideal(self, t):
2501  r"""set_ideal(Dihedral self, IMP::Float t)"""
2502  return _IMP_atom.Dihedral_set_ideal(self, t)
2503 
2504  def get_multiplicity(self):
2505  r"""get_multiplicity(Dihedral self) -> IMP::Int"""
2506  return _IMP_atom.Dihedral_get_multiplicity(self)
2507 
2508  def set_multiplicity(self, t):
2509  r"""set_multiplicity(Dihedral self, IMP::Int t)"""
2510  return _IMP_atom.Dihedral_set_multiplicity(self, t)
2511 
2512  def get_stiffness(self):
2513  r"""get_stiffness(Dihedral self) -> IMP::Float"""
2514  return _IMP_atom.Dihedral_get_stiffness(self)
2515 
2516  def set_stiffness(self, t):
2517  r"""set_stiffness(Dihedral self, IMP::Float t)"""
2518  return _IMP_atom.Dihedral_set_stiffness(self, t)
2519 
2520  @staticmethod
2521  def get_particle_key(i):
2522  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2523  return _IMP_atom.Dihedral_get_particle_key(i)
2524 
2525  @staticmethod
2526  def get_ideal_key():
2527  r"""get_ideal_key() -> FloatKey"""
2528  return _IMP_atom.Dihedral_get_ideal_key()
2529 
2530  @staticmethod
2531  def get_multiplicity_key():
2532  r"""get_multiplicity_key() -> IntKey"""
2533  return _IMP_atom.Dihedral_get_multiplicity_key()
2534 
2535  @staticmethod
2536  def get_stiffness_key():
2537  r"""get_stiffness_key() -> FloatKey"""
2538  return _IMP_atom.Dihedral_get_stiffness_key()
2539 
2540  def add_attribute(self, *args):
2541  r"""
2542  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2543  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2544  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2545  add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2546  add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2547  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2548  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2549  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2550  add_attribute(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2551  add_attribute(Dihedral self, SparseIntKey a0, IMP::Int a1)
2552  add_attribute(Dihedral self, SparseStringKey a0, IMP::String a1)
2553  add_attribute(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2554  """
2555  return _IMP_atom.Dihedral_add_attribute(self, *args)
2556 
2557  def get_value(self, *args):
2558  r"""
2559  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2560  get_value(Dihedral self, IntKey a0) -> IMP::Int
2561  get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2562  get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2563  get_value(Dihedral self, StringKey a0) -> IMP::String
2564  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2565  get_value(Dihedral self, ObjectKey a0) -> Object
2566  get_value(Dihedral self, SparseFloatKey a0) -> IMP::Float
2567  get_value(Dihedral self, SparseIntKey a0) -> IMP::Int
2568  get_value(Dihedral self, SparseStringKey a0) -> IMP::String
2569  get_value(Dihedral self, SparseParticleIndexKey a0) -> ParticleIndex
2570  """
2571  return _IMP_atom.Dihedral_get_value(self, *args)
2572 
2573  def set_value(self, *args):
2574  r"""
2575  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2576  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2577  set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2578  set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2579  set_value(Dihedral self, StringKey a0, IMP::String a1)
2580  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2581  set_value(Dihedral self, ObjectKey a0, Object a1)
2582  set_value(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2583  set_value(Dihedral self, SparseIntKey a0, IMP::Int a1)
2584  set_value(Dihedral self, SparseStringKey a0, IMP::String a1)
2585  set_value(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2586  """
2587  return _IMP_atom.Dihedral_set_value(self, *args)
2588 
2589  def remove_attribute(self, *args):
2590  r"""
2591  remove_attribute(Dihedral self, FloatKey a0)
2592  remove_attribute(Dihedral self, IntKey a0)
2593  remove_attribute(Dihedral self, FloatsKey a0)
2594  remove_attribute(Dihedral self, IntsKey a0)
2595  remove_attribute(Dihedral self, StringKey a0)
2596  remove_attribute(Dihedral self, ParticleIndexKey a0)
2597  remove_attribute(Dihedral self, ObjectKey a0)
2598  remove_attribute(Dihedral self, SparseFloatKey a0)
2599  remove_attribute(Dihedral self, SparseIntKey a0)
2600  remove_attribute(Dihedral self, SparseStringKey a0)
2601  remove_attribute(Dihedral self, SparseParticleIndexKey a0)
2602  """
2603  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2604 
2605  def has_attribute(self, *args):
2606  r"""
2607  has_attribute(Dihedral self, FloatKey a0) -> bool
2608  has_attribute(Dihedral self, IntKey a0) -> bool
2609  has_attribute(Dihedral self, FloatsKey a0) -> bool
2610  has_attribute(Dihedral self, IntsKey a0) -> bool
2611  has_attribute(Dihedral self, StringKey a0) -> bool
2612  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2613  has_attribute(Dihedral self, ObjectKey a0) -> bool
2614  has_attribute(Dihedral self, SparseFloatKey a0) -> bool
2615  has_attribute(Dihedral self, SparseIntKey a0) -> bool
2616  has_attribute(Dihedral self, SparseStringKey a0) -> bool
2617  has_attribute(Dihedral self, SparseParticleIndexKey a0) -> bool
2618  """
2619  return _IMP_atom.Dihedral_has_attribute(self, *args)
2620 
2621  def get_derivative(self, a0):
2622  r"""get_derivative(Dihedral self, FloatKey a0) -> double"""
2623  return _IMP_atom.Dihedral_get_derivative(self, a0)
2624 
2625  def get_name(self):
2626  r"""get_name(Dihedral self) -> std::string"""
2627  return _IMP_atom.Dihedral_get_name(self)
2628 
2629  def clear_caches(self):
2630  r"""clear_caches(Dihedral self)"""
2631  return _IMP_atom.Dihedral_clear_caches(self)
2632 
2633  def set_name(self, a0):
2634  r"""set_name(Dihedral self, std::string a0)"""
2635  return _IMP_atom.Dihedral_set_name(self, a0)
2636 
2637  def set_check_level(self, a0):
2638  r"""set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2639  return _IMP_atom.Dihedral_set_check_level(self, a0)
2640 
2641  def add_to_derivative(self, a0, a1, a2):
2642  r"""add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2643  return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2644 
2645  def set_is_optimized(self, a0, a1):
2646  r"""set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2647  return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2648 
2649  def get_is_optimized(self, a0):
2650  r"""get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2651  return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2652 
2653  def get_check_level(self):
2654  r"""get_check_level(Dihedral self) -> IMP::CheckLevel"""
2655  return _IMP_atom.Dihedral_get_check_level(self)
2656 
2657  def __eq__(self, *args):
2658  r"""
2659  __eq__(Dihedral self, Dihedral o) -> bool
2660  __eq__(Dihedral self, Particle d) -> bool
2661  """
2662  return _IMP_atom.Dihedral___eq__(self, *args)
2663 
2664  def __ne__(self, *args):
2665  r"""
2666  __ne__(Dihedral self, Dihedral o) -> bool
2667  __ne__(Dihedral self, Particle d) -> bool
2668  """
2669  return _IMP_atom.Dihedral___ne__(self, *args)
2670 
2671  def __le__(self, *args):
2672  r"""
2673  __le__(Dihedral self, Dihedral o) -> bool
2674  __le__(Dihedral self, Particle d) -> bool
2675  """
2676  return _IMP_atom.Dihedral___le__(self, *args)
2677 
2678  def __lt__(self, *args):
2679  r"""
2680  __lt__(Dihedral self, Dihedral o) -> bool
2681  __lt__(Dihedral self, Particle d) -> bool
2682  """
2683  return _IMP_atom.Dihedral___lt__(self, *args)
2684 
2685  def __ge__(self, *args):
2686  r"""
2687  __ge__(Dihedral self, Dihedral o) -> bool
2688  __ge__(Dihedral self, Particle d) -> bool
2689  """
2690  return _IMP_atom.Dihedral___ge__(self, *args)
2691 
2692  def __gt__(self, *args):
2693  r"""
2694  __gt__(Dihedral self, Dihedral o) -> bool
2695  __gt__(Dihedral self, Particle d) -> bool
2696  """
2697  return _IMP_atom.Dihedral___gt__(self, *args)
2698 
2699  def __hash__(self):
2700  r"""__hash__(Dihedral self) -> std::size_t"""
2701  return _IMP_atom.Dihedral___hash__(self)
2702 
2703  def __str__(self):
2704  r"""__str__(Dihedral self) -> std::string"""
2705  return _IMP_atom.Dihedral___str__(self)
2706 
2707  def __repr__(self):
2708  r"""__repr__(Dihedral self) -> std::string"""
2709  return _IMP_atom.Dihedral___repr__(self)
2710 
2711  def _get_as_binary(self):
2712  r"""_get_as_binary(Dihedral self) -> PyObject *"""
2713  return _IMP_atom.Dihedral__get_as_binary(self)
2714 
2715  def _set_from_binary(self, p):
2716  r"""_set_from_binary(Dihedral self, PyObject * p)"""
2717  return _IMP_atom.Dihedral__set_from_binary(self, p)
2718 
2719  def __getstate__(self):
2720  p = self._get_as_binary()
2721  if len(self.__dict__) > 1:
2722  d = self.__dict__.copy()
2723  del d['this']
2724  p = (d, p)
2725  return p
2726 
2727  def __setstate__(self, p):
2728  if not hasattr(self, 'this'):
2729  self.__init__()
2730  if isinstance(p, tuple):
2731  d, p = p
2732  self.__dict__.update(d)
2733  return self._set_from_binary(p)
2734 
2735  __swig_destroy__ = _IMP_atom.delete_Dihedral
2736 
2737 # Register Dihedral in _IMP_atom:
2738 _IMP_atom.Dihedral_swigregister(Dihedral)
2739 class SmoothingFunction(IMP.Object):
2740  r"""Proxy of C++ IMP::atom::SmoothingFunction class."""
2741 
2742  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2743 
2744  def __init__(self, *args, **kwargs):
2745  raise AttributeError("No constructor defined - class is abstract")
2746 
2747  def __call__(self, *args):
2748  r"""
2749  __call__(SmoothingFunction self, double score, double distance) -> double
2750  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2751  """
2752  return _IMP_atom.SmoothingFunction___call__(self, *args)
2753  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2754 
2755  def __str__(self):
2756  r"""__str__(SmoothingFunction self) -> std::string"""
2757  return _IMP_atom.SmoothingFunction___str__(self)
2758 
2759  def __repr__(self):
2760  r"""__repr__(SmoothingFunction self) -> std::string"""
2761  return _IMP_atom.SmoothingFunction___repr__(self)
2762 
2763  @staticmethod
2764  def get_from(o):
2765  return _object_cast_to_SmoothingFunction(o)
2766 
2767 
2768 # Register SmoothingFunction in _IMP_atom:
2769 _IMP_atom.SmoothingFunction_swigregister(SmoothingFunction)
2770 class ForceSwitch(SmoothingFunction):
2771  r"""Proxy of C++ IMP::atom::ForceSwitch class."""
2772 
2773  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2774 
2775  def __init__(self, min_distance, max_distance):
2776  r"""__init__(ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2777  _IMP_atom.ForceSwitch_swiginit(self, _IMP_atom.new_ForceSwitch(min_distance, max_distance))
2778 
2779  def __call__(self, *args):
2780  r"""
2781  __call__(ForceSwitch self, double score, double distance) -> double
2782  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2783  """
2784  return _IMP_atom.ForceSwitch___call__(self, *args)
2785 
2786  def get_version_info(self):
2787  r"""get_version_info(ForceSwitch self) -> VersionInfo"""
2788  return _IMP_atom.ForceSwitch_get_version_info(self)
2789  __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2790 
2791  def __str__(self):
2792  r"""__str__(ForceSwitch self) -> std::string"""
2793  return _IMP_atom.ForceSwitch___str__(self)
2794 
2795  def __repr__(self):
2796  r"""__repr__(ForceSwitch self) -> std::string"""
2797  return _IMP_atom.ForceSwitch___repr__(self)
2798 
2799  @staticmethod
2800  def get_from(o):
2801  return _object_cast_to_ForceSwitch(o)
2802 
2803 
2804 # Register ForceSwitch in _IMP_atom:
2805 _IMP_atom.ForceSwitch_swigregister(ForceSwitch)
2806 class AngleSingletonScore(IMP.SingletonScore):
2807  r"""Proxy of C++ IMP::atom::AngleSingletonScore class."""
2808 
2809  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2810 
2811  def __init__(self, f):
2812  r"""__init__(AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2813  _IMP_atom.AngleSingletonScore_swiginit(self, _IMP_atom.new_AngleSingletonScore(f))
2814 
2815  def do_get_inputs(self, m, pis):
2816  r"""do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2817  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2818 
2819  def get_version_info(self):
2820  r"""get_version_info(AngleSingletonScore self) -> VersionInfo"""
2821  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2822  __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2823 
2824  def __str__(self):
2825  r"""__str__(AngleSingletonScore self) -> std::string"""
2826  return _IMP_atom.AngleSingletonScore___str__(self)
2827 
2828  def __repr__(self):
2829  r"""__repr__(AngleSingletonScore self) -> std::string"""
2830  return _IMP_atom.AngleSingletonScore___repr__(self)
2831 
2832  @staticmethod
2833  def get_from(o):
2834  return _object_cast_to_AngleSingletonScore(o)
2835 
2836 
2837 # Register AngleSingletonScore in _IMP_atom:
2838 _IMP_atom.AngleSingletonScore_swigregister(AngleSingletonScore)
2839 class BondEndpointsRefiner(IMP.Refiner):
2840  r"""Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2841 
2842  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2843 
2844  def __init__(self):
2845  r"""__init__(BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2846  _IMP_atom.BondEndpointsRefiner_swiginit(self, _IMP_atom.new_BondEndpointsRefiner())
2847 
2848  def do_get_inputs(self, m, pis):
2849  r"""do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2850  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2851 
2852  def get_version_info(self):
2853  r"""get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2854  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2855  __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2856 
2857  def __str__(self):
2858  r"""__str__(BondEndpointsRefiner self) -> std::string"""
2859  return _IMP_atom.BondEndpointsRefiner___str__(self)
2860 
2861  def __repr__(self):
2862  r"""__repr__(BondEndpointsRefiner self) -> std::string"""
2863  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2864 
2865  @staticmethod
2866  def get_from(o):
2867  return _object_cast_to_BondEndpointsRefiner(o)
2868 
2869 
2870 # Register BondEndpointsRefiner in _IMP_atom:
2871 _IMP_atom.BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2872 class BondPairContainer(IMP.PairContainer):
2873  r"""Proxy of C++ IMP::atom::BondPairContainer class."""
2874 
2875  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2876 
2877  def __init__(self, sc):
2878  r"""__init__(BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2879  _IMP_atom.BondPairContainer_swiginit(self, _IMP_atom.new_BondPairContainer(sc))
2880 
2881  def do_get_inputs(self):
2882  r"""do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2883  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2884 
2885  def do_apply(self, sm):
2886  r"""do_apply(BondPairContainer self, PairModifier sm)"""
2887  return _IMP_atom.BondPairContainer_do_apply(self, sm)
2888 
2889  def do_apply_moved(self, sm, moved_pis, reset_pis):
2890  r"""do_apply_moved(BondPairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
2891  return _IMP_atom.BondPairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
2892 
2893  def get_version_info(self):
2894  r"""get_version_info(BondPairContainer self) -> VersionInfo"""
2895  return _IMP_atom.BondPairContainer_get_version_info(self)
2896  __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2897 
2898  def __str__(self):
2899  r"""__str__(BondPairContainer self) -> std::string"""
2900  return _IMP_atom.BondPairContainer___str__(self)
2901 
2902  def __repr__(self):
2903  r"""__repr__(BondPairContainer self) -> std::string"""
2904  return _IMP_atom.BondPairContainer___repr__(self)
2905 
2906  @staticmethod
2907  def get_from(o):
2908  return _object_cast_to_BondPairContainer(o)
2909 
2910 
2911 # Register BondPairContainer in _IMP_atom:
2912 _IMP_atom.BondPairContainer_swigregister(BondPairContainer)
2913 class BondSingletonScore(IMP.SingletonScore):
2914  r"""Proxy of C++ IMP::atom::BondSingletonScore class."""
2915 
2916  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2917 
2918  def __init__(self, f):
2919  r"""__init__(BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2920  _IMP_atom.BondSingletonScore_swiginit(self, _IMP_atom.new_BondSingletonScore(f))
2921 
2922  def get_unary_function(self):
2923  r"""get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2924  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2925 
2926  def do_get_inputs(self, m, pis):
2927  r"""do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2928  return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2929 
2930  def get_version_info(self):
2931  r"""get_version_info(BondSingletonScore self) -> VersionInfo"""
2932  return _IMP_atom.BondSingletonScore_get_version_info(self)
2933  __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2934 
2935  def __str__(self):
2936  r"""__str__(BondSingletonScore self) -> std::string"""
2937  return _IMP_atom.BondSingletonScore___str__(self)
2938 
2939  def __repr__(self):
2940  r"""__repr__(BondSingletonScore self) -> std::string"""
2941  return _IMP_atom.BondSingletonScore___repr__(self)
2942 
2943  @staticmethod
2944  def get_from(o):
2945  return _object_cast_to_BondSingletonScore(o)
2946 
2947 
2948 # Register BondSingletonScore in _IMP_atom:
2949 _IMP_atom.BondSingletonScore_swigregister(BondSingletonScore)
2950 class DihedralSingletonScore(IMP.SingletonScore):
2951  r"""Proxy of C++ IMP::atom::DihedralSingletonScore class."""
2952 
2953  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2954 
2955  def __init__(self):
2956  r"""__init__(DihedralSingletonScore self) -> DihedralSingletonScore"""
2957  _IMP_atom.DihedralSingletonScore_swiginit(self, _IMP_atom.new_DihedralSingletonScore())
2958 
2959  def do_get_inputs(self, m, pis):
2960  r"""do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2961  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
2962 
2963  def get_version_info(self):
2964  r"""get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2965  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2966  __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
2967 
2968  def __str__(self):
2969  r"""__str__(DihedralSingletonScore self) -> std::string"""
2970  return _IMP_atom.DihedralSingletonScore___str__(self)
2971 
2972  def __repr__(self):
2973  r"""__repr__(DihedralSingletonScore self) -> std::string"""
2974  return _IMP_atom.DihedralSingletonScore___repr__(self)
2975 
2976  @staticmethod
2977  def get_from(o):
2978  return _object_cast_to_DihedralSingletonScore(o)
2979 
2980 
2981  def _get_as_binary(self):
2982  r"""_get_as_binary(DihedralSingletonScore self) -> PyObject *"""
2983  return _IMP_atom.DihedralSingletonScore__get_as_binary(self)
2984 
2985  def _set_from_binary(self, p):
2986  r"""_set_from_binary(DihedralSingletonScore self, PyObject * p)"""
2987  return _IMP_atom.DihedralSingletonScore__set_from_binary(self, p)
2988 
2989  def __getstate__(self):
2990  p = self._get_as_binary()
2991  if len(self.__dict__) > 1:
2992  d = self.__dict__.copy()
2993  del d['this']
2994  p = (d, p)
2995  return p
2996 
2997  def __setstate__(self, p):
2998  if not hasattr(self, 'this'):
2999  self.__init__()
3000  if isinstance(p, tuple):
3001  d, p = p
3002  self.__dict__.update(d)
3003  return self._set_from_binary(p)
3004 
3005 
3006 # Register DihedralSingletonScore in _IMP_atom:
3007 _IMP_atom.DihedralSingletonScore_swigregister(DihedralSingletonScore)
3008 class ImproperSingletonScore(IMP.SingletonScore):
3009  r"""Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3010 
3011  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3012 
3013  def __init__(self, f):
3014  r"""__init__(ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3015  _IMP_atom.ImproperSingletonScore_swiginit(self, _IMP_atom.new_ImproperSingletonScore(f))
3016 
3017  def do_get_inputs(self, m, pis):
3018  r"""do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3019  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3020 
3021  def get_version_info(self):
3022  r"""get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3023  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3024  __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
3025 
3026  def __str__(self):
3027  r"""__str__(ImproperSingletonScore self) -> std::string"""
3028  return _IMP_atom.ImproperSingletonScore___str__(self)
3029 
3030  def __repr__(self):
3031  r"""__repr__(ImproperSingletonScore self) -> std::string"""
3032  return _IMP_atom.ImproperSingletonScore___repr__(self)
3033 
3034  @staticmethod
3035  def get_from(o):
3036  return _object_cast_to_ImproperSingletonScore(o)
3037 
3038 
3039 # Register ImproperSingletonScore in _IMP_atom:
3040 _IMP_atom.ImproperSingletonScore_swigregister(ImproperSingletonScore)
3041 class CenterOfMass(IMP.Decorator):
3042  r"""Proxy of C++ IMP::atom::CenterOfMass class."""
3043 
3044  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3045 
3046  def get_constraint(self):
3047  r"""get_constraint(CenterOfMass self) -> Constraint"""
3048  return _IMP_atom.CenterOfMass_get_constraint(self)
3049 
3050  def get_mass(self):
3051  r"""get_mass(CenterOfMass self) -> IMP::Float"""
3052  return _IMP_atom.CenterOfMass_get_mass(self)
3053 
3054  def get_coordinate(self, i):
3055  r"""get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3056  return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3057 
3058  def get_coordinates(self):
3059  r"""get_coordinates(CenterOfMass self) -> Vector3D"""
3060  return _IMP_atom.CenterOfMass_get_coordinates(self)
3061 
3062  def __init__(self, *args):
3063  r"""
3064  __init__(CenterOfMass self) -> CenterOfMass
3065  __init__(CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3066  __init__(CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3067  """
3068  _IMP_atom.CenterOfMass_swiginit(self, _IMP_atom.new_CenterOfMass(*args))
3069 
3070  def show(self, *args):
3071  r"""show(CenterOfMass self, _ostream out=std::cout)"""
3072  return _IMP_atom.CenterOfMass_show(self, *args)
3073 
3074  @staticmethod
3075  def setup_particle(*args):
3076  r"""
3077  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3078  setup_particle(_ParticleAdaptor pa, _ParticleIndexesAdaptor members) -> CenterOfMass
3079  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3080  setup_particle(_ParticleAdaptor pa, Refiner refiner) -> CenterOfMass
3081  """
3082  return _IMP_atom.CenterOfMass_setup_particle(*args)
3083 
3084  @staticmethod
3085  def teardown_particle(com):
3086  r"""teardown_particle(CenterOfMass com)"""
3087  return _IMP_atom.CenterOfMass_teardown_particle(com)
3088 
3089  @staticmethod
3090  def get_is_setup(*args):
3091  r"""
3092  get_is_setup(_ParticleAdaptor p) -> bool
3093  get_is_setup(Model m, ParticleIndex pi) -> bool
3094  """
3095  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3096 
3097  def add_attribute(self, *args):
3098  r"""
3099  add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3100  add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3101  add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3102  add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3103  add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3104  add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3105  add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3106  add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3107  add_attribute(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3108  add_attribute(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3109  add_attribute(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3110  add_attribute(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3111  """
3112  return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3113 
3114  def get_value(self, *args):
3115  r"""
3116  get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3117  get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3118  get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3119  get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3120  get_value(CenterOfMass self, StringKey a0) -> IMP::String
3121  get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3122  get_value(CenterOfMass self, ObjectKey a0) -> Object
3123  get_value(CenterOfMass self, SparseFloatKey a0) -> IMP::Float
3124  get_value(CenterOfMass self, SparseIntKey a0) -> IMP::Int
3125  get_value(CenterOfMass self, SparseStringKey a0) -> IMP::String
3126  get_value(CenterOfMass self, SparseParticleIndexKey a0) -> ParticleIndex
3127  """
3128  return _IMP_atom.CenterOfMass_get_value(self, *args)
3129 
3130  def set_value(self, *args):
3131  r"""
3132  set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3133  set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3134  set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3135  set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3136  set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3137  set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3138  set_value(CenterOfMass self, ObjectKey a0, Object a1)
3139  set_value(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3140  set_value(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3141  set_value(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3142  set_value(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3143  """
3144  return _IMP_atom.CenterOfMass_set_value(self, *args)
3145 
3146  def remove_attribute(self, *args):
3147  r"""
3148  remove_attribute(CenterOfMass self, FloatKey a0)
3149  remove_attribute(CenterOfMass self, IntKey a0)
3150  remove_attribute(CenterOfMass self, FloatsKey a0)
3151  remove_attribute(CenterOfMass self, IntsKey a0)
3152  remove_attribute(CenterOfMass self, StringKey a0)
3153  remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3154  remove_attribute(CenterOfMass self, ObjectKey a0)
3155  remove_attribute(CenterOfMass self, SparseFloatKey a0)
3156  remove_attribute(CenterOfMass self, SparseIntKey a0)
3157  remove_attribute(CenterOfMass self, SparseStringKey a0)
3158  remove_attribute(CenterOfMass self, SparseParticleIndexKey a0)
3159  """
3160  return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3161 
3162  def has_attribute(self, *args):
3163  r"""
3164  has_attribute(CenterOfMass self, FloatKey a0) -> bool
3165  has_attribute(CenterOfMass self, IntKey a0) -> bool
3166  has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3167  has_attribute(CenterOfMass self, IntsKey a0) -> bool
3168  has_attribute(CenterOfMass self, StringKey a0) -> bool
3169  has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3170  has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3171  has_attribute(CenterOfMass self, SparseFloatKey a0) -> bool
3172  has_attribute(CenterOfMass self, SparseIntKey a0) -> bool
3173  has_attribute(CenterOfMass self, SparseStringKey a0) -> bool
3174  has_attribute(CenterOfMass self, SparseParticleIndexKey a0) -> bool
3175  """
3176  return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3177 
3178  def get_derivative(self, a0):
3179  r"""get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3180  return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3181 
3182  def get_name(self):
3183  r"""get_name(CenterOfMass self) -> std::string"""
3184  return _IMP_atom.CenterOfMass_get_name(self)
3185 
3186  def clear_caches(self):
3187  r"""clear_caches(CenterOfMass self)"""
3188  return _IMP_atom.CenterOfMass_clear_caches(self)
3189 
3190  def set_name(self, a0):
3191  r"""set_name(CenterOfMass self, std::string a0)"""
3192  return _IMP_atom.CenterOfMass_set_name(self, a0)
3193 
3194  def set_check_level(self, a0):
3195  r"""set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3196  return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3197 
3198  def add_to_derivative(self, a0, a1, a2):
3199  r"""add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3200  return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3201 
3202  def set_is_optimized(self, a0, a1):
3203  r"""set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3204  return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3205 
3206  def get_is_optimized(self, a0):
3207  r"""get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3208  return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3209 
3210  def get_check_level(self):
3211  r"""get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3212  return _IMP_atom.CenterOfMass_get_check_level(self)
3213 
3214  def __eq__(self, *args):
3215  r"""
3216  __eq__(CenterOfMass self, CenterOfMass o) -> bool
3217  __eq__(CenterOfMass self, Particle d) -> bool
3218  """
3219  return _IMP_atom.CenterOfMass___eq__(self, *args)
3220 
3221  def __ne__(self, *args):
3222  r"""
3223  __ne__(CenterOfMass self, CenterOfMass o) -> bool
3224  __ne__(CenterOfMass self, Particle d) -> bool
3225  """
3226  return _IMP_atom.CenterOfMass___ne__(self, *args)
3227 
3228  def __le__(self, *args):
3229  r"""
3230  __le__(CenterOfMass self, CenterOfMass o) -> bool
3231  __le__(CenterOfMass self, Particle d) -> bool
3232  """
3233  return _IMP_atom.CenterOfMass___le__(self, *args)
3234 
3235  def __lt__(self, *args):
3236  r"""
3237  __lt__(CenterOfMass self, CenterOfMass o) -> bool
3238  __lt__(CenterOfMass self, Particle d) -> bool
3239  """
3240  return _IMP_atom.CenterOfMass___lt__(self, *args)
3241 
3242  def __ge__(self, *args):
3243  r"""
3244  __ge__(CenterOfMass self, CenterOfMass o) -> bool
3245  __ge__(CenterOfMass self, Particle d) -> bool
3246  """
3247  return _IMP_atom.CenterOfMass___ge__(self, *args)
3248 
3249  def __gt__(self, *args):
3250  r"""
3251  __gt__(CenterOfMass self, CenterOfMass o) -> bool
3252  __gt__(CenterOfMass self, Particle d) -> bool
3253  """
3254  return _IMP_atom.CenterOfMass___gt__(self, *args)
3255 
3256  def __hash__(self):
3257  r"""__hash__(CenterOfMass self) -> std::size_t"""
3258  return _IMP_atom.CenterOfMass___hash__(self)
3259 
3260  def __str__(self):
3261  r"""__str__(CenterOfMass self) -> std::string"""
3262  return _IMP_atom.CenterOfMass___str__(self)
3263 
3264  def __repr__(self):
3265  r"""__repr__(CenterOfMass self) -> std::string"""
3266  return _IMP_atom.CenterOfMass___repr__(self)
3267 
3268  def _get_as_binary(self):
3269  r"""_get_as_binary(CenterOfMass self) -> PyObject *"""
3270  return _IMP_atom.CenterOfMass__get_as_binary(self)
3271 
3272  def _set_from_binary(self, p):
3273  r"""_set_from_binary(CenterOfMass self, PyObject * p)"""
3274  return _IMP_atom.CenterOfMass__set_from_binary(self, p)
3275 
3276  def __getstate__(self):
3277  p = self._get_as_binary()
3278  if len(self.__dict__) > 1:
3279  d = self.__dict__.copy()
3280  del d['this']
3281  p = (d, p)
3282  return p
3283 
3284  def __setstate__(self, p):
3285  if not hasattr(self, 'this'):
3286  self.__init__()
3287  if isinstance(p, tuple):
3288  d, p = p
3289  self.__dict__.update(d)
3290  return self._set_from_binary(p)
3291 
3292  __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3293 
3294 # Register CenterOfMass in _IMP_atom:
3295 _IMP_atom.CenterOfMass_swigregister(CenterOfMass)
3296 class CoverBond(IMP.SingletonModifier):
3297  r"""Proxy of C++ IMP::atom::CoverBond class."""
3298 
3299  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3300 
3301  def __init__(self):
3302  r"""__init__(CoverBond self) -> CoverBond"""
3303  _IMP_atom.CoverBond_swiginit(self, _IMP_atom.new_CoverBond())
3304 
3305  def do_get_inputs(self, m, pis):
3306  r"""do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3307  return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3308 
3309  def do_get_outputs(self, m, pis):
3310  r"""do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3311  return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3312 
3313  def get_version_info(self):
3314  r"""get_version_info(CoverBond self) -> VersionInfo"""
3315  return _IMP_atom.CoverBond_get_version_info(self)
3316  __swig_destroy__ = _IMP_atom.delete_CoverBond
3317 
3318  def __str__(self):
3319  r"""__str__(CoverBond self) -> std::string"""
3320  return _IMP_atom.CoverBond___str__(self)
3321 
3322  def __repr__(self):
3323  r"""__repr__(CoverBond self) -> std::string"""
3324  return _IMP_atom.CoverBond___repr__(self)
3325 
3326  @staticmethod
3327  def get_from(o):
3328  return _object_cast_to_CoverBond(o)
3329 
3330 
3331 # Register CoverBond in _IMP_atom:
3332 _IMP_atom.CoverBond_swigregister(CoverBond)
3333 class Simulator(IMP.Optimizer):
3334  r"""Proxy of C++ IMP::atom::Simulator class."""
3335 
3336  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3337 
3338  def __init__(self, *args):
3339  r"""__init__(Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator"""
3340  if self.__class__ == Simulator:
3341  _self = None
3342  else:
3343  _self = self
3344  _IMP_atom.Simulator_swiginit(self, _IMP_atom.new_Simulator(_self, *args))
3345 
3346  if self.__class__ != Simulator:
3347  _director_objects.register(self)
3348 
3349 
3350 
3351 
3352  def simulate(self, time_in_fs):
3353  r"""simulate(Simulator self, double time_in_fs) -> double"""
3354  return _IMP_atom.Simulator_simulate(self, time_in_fs)
3355 
3356  def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3357  r"""simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3358  return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3359 
3360  def get_temperature(self):
3361  r"""get_temperature(Simulator self) -> double"""
3362  return _IMP_atom.Simulator_get_temperature(self)
3363 
3364  def set_temperature(self, d):
3365  r"""set_temperature(Simulator self, double d)"""
3366  return _IMP_atom.Simulator_set_temperature(self, d)
3367 
3368  def set_maximum_time_step(self, ts):
3369  r"""set_maximum_time_step(Simulator self, double ts)"""
3370  return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3371 
3372  def get_maximum_time_step(self):
3373  r"""get_maximum_time_step(Simulator self) -> double"""
3374  return _IMP_atom.Simulator_get_maximum_time_step(self)
3375 
3376  def get_last_time_step(self):
3377  r"""get_last_time_step(Simulator self) -> double"""
3378  return _IMP_atom.Simulator_get_last_time_step(self)
3379 
3380  def set_time_step(self, ts):
3381  r"""set_time_step(Simulator self, double ts)"""
3382  return _IMP_atom.Simulator_set_time_step(self, ts)
3383 
3384  def get_kt(self):
3385  r"""get_kt(Simulator self) -> double"""
3386  return _IMP_atom.Simulator_get_kt(self)
3387 
3388  def get_current_time(self):
3389  r"""get_current_time(Simulator self) -> double"""
3390  return _IMP_atom.Simulator_get_current_time(self)
3391 
3392  def set_current_time(self, ct):
3393  r"""set_current_time(Simulator self, double ct)"""
3394  return _IMP_atom.Simulator_set_current_time(self, ct)
3395 
3396  def get_simulation_particles(self):
3397  r"""get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3398  return _IMP_atom.Simulator_get_simulation_particles(self)
3399 
3400  def get_simulation_particle_indexes(self):
3401  r"""get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3402  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3403  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)
3404  def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
3405  def __del_particles(self): IMP._list_util.del_varlist(self.particles)
3406  particles = property(__get_particles, __set_particles, __del_particles, doc="List of ##ucnames")
3407 
3408  def remove_particle(self, d):
3409  r"""remove_particle(Simulator self, Particle d)"""
3410  return _IMP_atom.Simulator_remove_particle(self, d)
3411 
3412  def _python_index_particle(self, d, start, stop):
3413  r"""_python_index_particle(Simulator self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
3414  return _IMP_atom.Simulator__python_index_particle(self, d, start, stop)
3415 
3416  def remove_particles(self, d):
3417  r"""remove_particles(Simulator self, IMP::Particles const & d)"""
3418  return _IMP_atom.Simulator_remove_particles(self, d)
3419 
3420  def set_particles(self, ps):
3421  r"""set_particles(Simulator self, IMP::Particles const & ps)"""
3422  return _IMP_atom.Simulator_set_particles(self, ps)
3423 
3424  def set_particles_order(self, objs):
3425  r"""set_particles_order(Simulator self, IMP::Particles const & objs)"""
3426  return _IMP_atom.Simulator_set_particles_order(self, objs)
3427 
3428  def add_particle(self, obj):
3429  r"""add_particle(Simulator self, Particle obj) -> unsigned int"""
3430  return _IMP_atom.Simulator_add_particle(self, obj)
3431 
3432  def add_particles(self, objs):
3433  r"""add_particles(Simulator self, IMP::Particles const & objs)"""
3434  return _IMP_atom.Simulator_add_particles(self, objs)
3435 
3436  def clear_particles(self):
3437  r"""clear_particles(Simulator self)"""
3438  return _IMP_atom.Simulator_clear_particles(self)
3439 
3440  def get_number_of_particles(self):
3441  r"""get_number_of_particles(Simulator self) -> unsigned int"""
3442  return _IMP_atom.Simulator_get_number_of_particles(self)
3443 
3444  def get_has_particles(self):
3445  r"""get_has_particles(Simulator self) -> bool"""
3446  return _IMP_atom.Simulator_get_has_particles(self)
3447 
3448  def get_particle(self, i):
3449  r"""get_particle(Simulator self, unsigned int i) -> Particle"""
3450  return _IMP_atom.Simulator_get_particle(self, i)
3451 
3452  def get_particles(self):
3453  r"""get_particles(Simulator self) -> IMP::Particles"""
3454  return _IMP_atom.Simulator_get_particles(self)
3455 
3456  def erase_particle(self, i):
3457  r"""erase_particle(Simulator self, unsigned int i)"""
3458  return _IMP_atom.Simulator_erase_particle(self, i)
3459 
3460  def reserve_particles(self, sz):
3461  r"""reserve_particles(Simulator self, unsigned int sz)"""
3462  return _IMP_atom.Simulator_reserve_particles(self, sz)
3463 
3464  def do_optimize(self, max_steps):
3465  r"""do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3466  return _IMP_atom.Simulator_do_optimize(self, max_steps)
3467 
3468  def setup(self, arg0):
3469  r"""setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3470  return _IMP_atom.Simulator_setup(self, arg0)
3471 
3472  def do_step(self, sc, dt):
3473  r"""do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3474  return _IMP_atom.Simulator_do_step(self, sc, dt)
3475 
3476  def get_is_simulation_particle(self, p):
3477  r"""get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3478  return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3479 
3480  def do_simulate(self, time):
3481  r"""do_simulate(Simulator self, double time) -> double"""
3482  return _IMP_atom.Simulator_do_simulate(self, time)
3483 
3484  def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3485  r"""do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3486  return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3487 
3488  def __str__(self):
3489  r"""__str__(Simulator self) -> std::string"""
3490  return _IMP_atom.Simulator___str__(self)
3491 
3492  def __repr__(self):
3493  r"""__repr__(Simulator self) -> std::string"""
3494  return _IMP_atom.Simulator___repr__(self)
3495 
3496  @staticmethod
3497  def get_from(o):
3498  return _object_cast_to_Simulator(o)
3499 
3500 
3501  def get_type_name(self):
3502  return self.__class__.__name__
3503  def do_show(self, out):
3504  pass
3505  def get_version_info(self):
3506  if"IMP::atom" == "IMP":
3507  return VersionInfo(self.__module__,
3508  __import__(self.__module__).get_module_version())
3509  else:
3510  return IMP.VersionInfo(self.__module__,
3511  __import__(self.__module__).get_module_version())
3512  @staticmethod
3513  def get_from(o):
3514  return _object_cast_to_Simulator(o)
3515 
3516  __swig_destroy__ = _IMP_atom.delete_Simulator
3517  def __disown__(self):
3518  self.this.disown()
3519  _IMP_atom.disown_Simulator(self)
3520  return weakref.proxy(self)
3521 
3522  def do_destroy(self):
3523  r"""do_destroy(Simulator self)"""
3524  return _IMP_atom.Simulator_do_destroy(self)
3525 
3526  def handle_set_has_required_score_states(self, arg0):
3527  r"""handle_set_has_required_score_states(Simulator self, bool arg0)"""
3528  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3529 
3530  def do_get_inputs(self):
3531  r"""do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3532  return _IMP_atom.Simulator_do_get_inputs(self)
3533 
3534  def do_get_outputs(self):
3535  r"""do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3536  return _IMP_atom.Simulator_do_get_outputs(self)
3537 
3538  def do_get_interactions(self):
3539  r"""do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3540  return _IMP_atom.Simulator_do_get_interactions(self)
3541 
3542 # Register Simulator in _IMP_atom:
3543 _IMP_atom.Simulator_swigregister(Simulator)
3544 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3545 
3546 class BrownianDynamics(Simulator):
3547  r"""Proxy of C++ IMP::atom::BrownianDynamics class."""
3548 
3549  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3550 
3551  def __init__(self, *args):
3552  r"""__init__(BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics"""
3553  _IMP_atom.BrownianDynamics_swiginit(self, _IMP_atom.new_BrownianDynamics(*args))
3554 
3555  def set_maximum_move(self, ms_in_A):
3556  r"""set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3557  return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3558 
3559  def set_use_stochastic_runge_kutta(self, tf):
3560  r"""set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3561  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3562 
3563  def get_version_info(self):
3564  r"""get_version_info(BrownianDynamics self) -> VersionInfo"""
3565  return _IMP_atom.BrownianDynamics_get_version_info(self)
3566  __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3567 
3568  def __str__(self):
3569  r"""__str__(BrownianDynamics self) -> std::string"""
3570  return _IMP_atom.BrownianDynamics___str__(self)
3571 
3572  def __repr__(self):
3573  r"""__repr__(BrownianDynamics self) -> std::string"""
3574  return _IMP_atom.BrownianDynamics___repr__(self)
3575 
3576  @staticmethod
3577  def get_from(o):
3578  return _object_cast_to_BrownianDynamics(o)
3579 
3580 
3581 # Register BrownianDynamics in _IMP_atom:
3582 _IMP_atom.BrownianDynamics_swigregister(BrownianDynamics)
3583 
3585  r"""get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3586  return _IMP_atom.get_maximum_time_step_estimate(bd)
3587 
3588 def get_harmonic_sigma(D, f):
3589  r"""get_harmonic_sigma(double D, double f) -> double"""
3590  return _IMP_atom.get_harmonic_sigma(D, f)
3591 class BrownianDynamicsTAMD(BrownianDynamics):
3592  r"""Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3593 
3594  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3595 
3596  def __init__(self, *args):
3597  r"""__init__(BrownianDynamicsTAMD self, Model m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0) -> BrownianDynamicsTAMD"""
3598  _IMP_atom.BrownianDynamicsTAMD_swiginit(self, _IMP_atom.new_BrownianDynamicsTAMD(*args))
3599 
3600  def __str__(self):
3601  r"""__str__(BrownianDynamicsTAMD self) -> std::string"""
3602  return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3603 
3604  def __repr__(self):
3605  r"""__repr__(BrownianDynamicsTAMD self) -> std::string"""
3606  return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3607 
3608  @staticmethod
3609  def get_from(o):
3610  return _object_cast_to_BrownianDynamicsTAMD(o)
3611 
3612  __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3613 
3614 # Register BrownianDynamicsTAMD in _IMP_atom:
3615 _IMP_atom.BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3616 class Diffusion(IMP.core.XYZ):
3617  r"""Proxy of C++ IMP::atom::Diffusion class."""
3618 
3619  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3620 
3621  def __init__(self, *args):
3622  r"""
3623  __init__(Diffusion self) -> Diffusion
3624  __init__(Diffusion self, Model m, ParticleIndex id) -> Diffusion
3625  __init__(Diffusion self, _ParticleAdaptor d) -> Diffusion
3626  """
3627  _IMP_atom.Diffusion_swiginit(self, _IMP_atom.new_Diffusion(*args))
3628 
3629  def show(self, *args):
3630  r"""show(Diffusion self, _ostream out=std::cout)"""
3631  return _IMP_atom.Diffusion_show(self, *args)
3632 
3633  @staticmethod
3634  def setup_particle(*args):
3635  r"""
3636  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3637  setup_particle(_ParticleAdaptor pa, IMP::Float D) -> Diffusion
3638  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3639  setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float D) -> Diffusion
3640  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3641  setup_particle(_ParticleAdaptor pa) -> Diffusion
3642  """
3643  return _IMP_atom.Diffusion_setup_particle(*args)
3644 
3645  @staticmethod
3646  def get_is_setup(*args):
3647  r"""
3648  get_is_setup(_ParticleAdaptor p) -> bool
3649  get_is_setup(Model m, ParticleIndex p) -> bool
3650  """
3651  return _IMP_atom.Diffusion_get_is_setup(*args)
3652 
3653  def set_diffusion_coefficient(self, d):
3654  r"""set_diffusion_coefficient(Diffusion self, double d)"""
3655  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3656 
3657  def get_diffusion_coefficient(self):
3658  r"""get_diffusion_coefficient(Diffusion self) -> double"""
3659  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3660 
3661  @staticmethod
3662  def get_diffusion_coefficient_key():
3663  r"""get_diffusion_coefficient_key() -> FloatKey"""
3664  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3665 
3666  def add_attribute(self, *args):
3667  r"""
3668  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3669  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3670  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3671  add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3672  add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3673  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3674  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3675  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3676  add_attribute(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3677  add_attribute(Diffusion self, SparseIntKey a0, IMP::Int a1)
3678  add_attribute(Diffusion self, SparseStringKey a0, IMP::String a1)
3679  add_attribute(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3680  """
3681  return _IMP_atom.Diffusion_add_attribute(self, *args)
3682 
3683  def get_value(self, *args):
3684  r"""
3685  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3686  get_value(Diffusion self, IntKey a0) -> IMP::Int
3687  get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3688  get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3689  get_value(Diffusion self, StringKey a0) -> IMP::String
3690  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3691  get_value(Diffusion self, ObjectKey a0) -> Object
3692  get_value(Diffusion self, SparseFloatKey a0) -> IMP::Float
3693  get_value(Diffusion self, SparseIntKey a0) -> IMP::Int
3694  get_value(Diffusion self, SparseStringKey a0) -> IMP::String
3695  get_value(Diffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3696  """
3697  return _IMP_atom.Diffusion_get_value(self, *args)
3698 
3699  def set_value(self, *args):
3700  r"""
3701  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3702  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3703  set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3704  set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3705  set_value(Diffusion self, StringKey a0, IMP::String a1)
3706  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3707  set_value(Diffusion self, ObjectKey a0, Object a1)
3708  set_value(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3709  set_value(Diffusion self, SparseIntKey a0, IMP::Int a1)
3710  set_value(Diffusion self, SparseStringKey a0, IMP::String a1)
3711  set_value(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3712  """
3713  return _IMP_atom.Diffusion_set_value(self, *args)
3714 
3715  def remove_attribute(self, *args):
3716  r"""
3717  remove_attribute(Diffusion self, FloatKey a0)
3718  remove_attribute(Diffusion self, IntKey a0)
3719  remove_attribute(Diffusion self, FloatsKey a0)
3720  remove_attribute(Diffusion self, IntsKey a0)
3721  remove_attribute(Diffusion self, StringKey a0)
3722  remove_attribute(Diffusion self, ParticleIndexKey a0)
3723  remove_attribute(Diffusion self, ObjectKey a0)
3724  remove_attribute(Diffusion self, SparseFloatKey a0)
3725  remove_attribute(Diffusion self, SparseIntKey a0)
3726  remove_attribute(Diffusion self, SparseStringKey a0)
3727  remove_attribute(Diffusion self, SparseParticleIndexKey a0)
3728  """
3729  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3730 
3731  def has_attribute(self, *args):
3732  r"""
3733  has_attribute(Diffusion self, FloatKey a0) -> bool
3734  has_attribute(Diffusion self, IntKey a0) -> bool
3735  has_attribute(Diffusion self, FloatsKey a0) -> bool
3736  has_attribute(Diffusion self, IntsKey a0) -> bool
3737  has_attribute(Diffusion self, StringKey a0) -> bool
3738  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3739  has_attribute(Diffusion self, ObjectKey a0) -> bool
3740  has_attribute(Diffusion self, SparseFloatKey a0) -> bool
3741  has_attribute(Diffusion self, SparseIntKey a0) -> bool
3742  has_attribute(Diffusion self, SparseStringKey a0) -> bool
3743  has_attribute(Diffusion self, SparseParticleIndexKey a0) -> bool
3744  """
3745  return _IMP_atom.Diffusion_has_attribute(self, *args)
3746 
3747  def get_derivative(self, a0):
3748  r"""get_derivative(Diffusion self, FloatKey a0) -> double"""
3749  return _IMP_atom.Diffusion_get_derivative(self, a0)
3750 
3751  def get_name(self):
3752  r"""get_name(Diffusion self) -> std::string"""
3753  return _IMP_atom.Diffusion_get_name(self)
3754 
3755  def clear_caches(self):
3756  r"""clear_caches(Diffusion self)"""
3757  return _IMP_atom.Diffusion_clear_caches(self)
3758 
3759  def set_name(self, a0):
3760  r"""set_name(Diffusion self, std::string a0)"""
3761  return _IMP_atom.Diffusion_set_name(self, a0)
3762 
3763  def set_check_level(self, a0):
3764  r"""set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3765  return _IMP_atom.Diffusion_set_check_level(self, a0)
3766 
3767  def add_to_derivative(self, a0, a1, a2):
3768  r"""add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3769  return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3770 
3771  def set_is_optimized(self, a0, a1):
3772  r"""set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3773  return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3774 
3775  def get_is_optimized(self, a0):
3776  r"""get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3777  return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3778 
3779  def get_check_level(self):
3780  r"""get_check_level(Diffusion self) -> IMP::CheckLevel"""
3781  return _IMP_atom.Diffusion_get_check_level(self)
3782 
3783  def __eq__(self, *args):
3784  r"""
3785  __eq__(Diffusion self, Diffusion o) -> bool
3786  __eq__(Diffusion self, Particle d) -> bool
3787  """
3788  return _IMP_atom.Diffusion___eq__(self, *args)
3789 
3790  def __ne__(self, *args):
3791  r"""
3792  __ne__(Diffusion self, Diffusion o) -> bool
3793  __ne__(Diffusion self, Particle d) -> bool
3794  """
3795  return _IMP_atom.Diffusion___ne__(self, *args)
3796 
3797  def __le__(self, *args):
3798  r"""
3799  __le__(Diffusion self, Diffusion o) -> bool
3800  __le__(Diffusion self, Particle d) -> bool
3801  """
3802  return _IMP_atom.Diffusion___le__(self, *args)
3803 
3804  def __lt__(self, *args):
3805  r"""
3806  __lt__(Diffusion self, Diffusion o) -> bool
3807  __lt__(Diffusion self, Particle d) -> bool
3808  """
3809  return _IMP_atom.Diffusion___lt__(self, *args)
3810 
3811  def __ge__(self, *args):
3812  r"""
3813  __ge__(Diffusion self, Diffusion o) -> bool
3814  __ge__(Diffusion self, Particle d) -> bool
3815  """
3816  return _IMP_atom.Diffusion___ge__(self, *args)
3817 
3818  def __gt__(self, *args):
3819  r"""
3820  __gt__(Diffusion self, Diffusion o) -> bool
3821  __gt__(Diffusion self, Particle d) -> bool
3822  """
3823  return _IMP_atom.Diffusion___gt__(self, *args)
3824 
3825  def __hash__(self):
3826  r"""__hash__(Diffusion self) -> std::size_t"""
3827  return _IMP_atom.Diffusion___hash__(self)
3828 
3829  def __str__(self):
3830  r"""__str__(Diffusion self) -> std::string"""
3831  return _IMP_atom.Diffusion___str__(self)
3832 
3833  def __repr__(self):
3834  r"""__repr__(Diffusion self) -> std::string"""
3835  return _IMP_atom.Diffusion___repr__(self)
3836 
3837  def _get_as_binary(self):
3838  r"""_get_as_binary(Diffusion self) -> PyObject *"""
3839  return _IMP_atom.Diffusion__get_as_binary(self)
3840 
3841  def _set_from_binary(self, p):
3842  r"""_set_from_binary(Diffusion self, PyObject * p)"""
3843  return _IMP_atom.Diffusion__set_from_binary(self, p)
3844 
3845  def __getstate__(self):
3846  p = self._get_as_binary()
3847  if len(self.__dict__) > 1:
3848  d = self.__dict__.copy()
3849  del d['this']
3850  p = (d, p)
3851  return p
3852 
3853  def __setstate__(self, p):
3854  if not hasattr(self, 'this'):
3855  self.__init__()
3856  if isinstance(p, tuple):
3857  d, p = p
3858  self.__dict__.update(d)
3859  return self._set_from_binary(p)
3860 
3861  __swig_destroy__ = _IMP_atom.delete_Diffusion
3862 
3863 # Register Diffusion in _IMP_atom:
3864 _IMP_atom.Diffusion_swigregister(Diffusion)
3865 
3866 def get_diffusion_coefficient_from_cm2_per_second(din):
3867  r"""get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3868  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3869 class RigidBodyDiffusion(Diffusion):
3870  r"""Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3871 
3872  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3873 
3874  def __init__(self, *args):
3875  r"""
3876  __init__(RigidBodyDiffusion self) -> RigidBodyDiffusion
3877  __init__(RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3878  __init__(RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3879  """
3880  _IMP_atom.RigidBodyDiffusion_swiginit(self, _IMP_atom.new_RigidBodyDiffusion(*args))
3881 
3882  def show(self, *args):
3883  r"""show(RigidBodyDiffusion self, _ostream out=std::cout)"""
3884  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3885 
3886  @staticmethod
3887  def setup_particle(*args):
3888  r"""
3889  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3890  setup_particle(_ParticleAdaptor pa) -> RigidBodyDiffusion
3891  """
3892  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3893 
3895  r"""get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3896  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3897 
3898  def set_rotational_diffusion_coefficient(self, d):
3899  r"""set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3900  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
3901 
3902  @staticmethod
3903  def get_is_setup(*args):
3904  r"""
3905  get_is_setup(_ParticleAdaptor p) -> bool
3906  get_is_setup(Model m, ParticleIndex p) -> bool
3907  """
3908  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3909 
3910  @staticmethod
3911  def get_rotational_diffusion_coefficient_key():
3912  r"""get_rotational_diffusion_coefficient_key() -> FloatKey"""
3913  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3914 
3915  def add_attribute(self, *args):
3916  r"""
3917  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3918  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3919  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3920  add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3921  add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3922  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3923  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3924  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3925  add_attribute(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
3926  add_attribute(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
3927  add_attribute(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
3928  add_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3929  """
3930  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3931 
3932  def get_value(self, *args):
3933  r"""
3934  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3935  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3936  get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
3937  get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
3938  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3939  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3940  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
3941  get_value(RigidBodyDiffusion self, SparseFloatKey a0) -> IMP::Float
3942  get_value(RigidBodyDiffusion self, SparseIntKey a0) -> IMP::Int
3943  get_value(RigidBodyDiffusion self, SparseStringKey a0) -> IMP::String
3944  get_value(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3945  """
3946  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3947 
3948  def set_value(self, *args):
3949  r"""
3950  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3951  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3952  set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3953  set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3954  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3955  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3956  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3957  set_value(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
3958  set_value(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
3959  set_value(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
3960  set_value(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3961  """
3962  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3963 
3964  def remove_attribute(self, *args):
3965  r"""
3966  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3967  remove_attribute(RigidBodyDiffusion self, IntKey a0)
3968  remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
3969  remove_attribute(RigidBodyDiffusion self, IntsKey a0)
3970  remove_attribute(RigidBodyDiffusion self, StringKey a0)
3971  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3972  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3973  remove_attribute(RigidBodyDiffusion self, SparseFloatKey a0)
3974  remove_attribute(RigidBodyDiffusion self, SparseIntKey a0)
3975  remove_attribute(RigidBodyDiffusion self, SparseStringKey a0)
3976  remove_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0)
3977  """
3978  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3979 
3980  def has_attribute(self, *args):
3981  r"""
3982  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3983  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3984  has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
3985  has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
3986  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3987  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3988  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3989  has_attribute(RigidBodyDiffusion self, SparseFloatKey a0) -> bool
3990  has_attribute(RigidBodyDiffusion self, SparseIntKey a0) -> bool
3991  has_attribute(RigidBodyDiffusion self, SparseStringKey a0) -> bool
3992  has_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> bool
3993  """
3994  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3995 
3996  def get_derivative(self, a0):
3997  r"""get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3998  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
3999 
4000  def get_name(self):
4001  r"""get_name(RigidBodyDiffusion self) -> std::string"""
4002  return _IMP_atom.RigidBodyDiffusion_get_name(self)
4003 
4004  def clear_caches(self):
4005  r"""clear_caches(RigidBodyDiffusion self)"""
4006  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4007 
4008  def set_name(self, a0):
4009  r"""set_name(RigidBodyDiffusion self, std::string a0)"""
4010  return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4011 
4012  def set_check_level(self, a0):
4013  r"""set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4014  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4015 
4016  def add_to_derivative(self, a0, a1, a2):
4017  r"""add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4018  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4019 
4020  def set_is_optimized(self, a0, a1):
4021  r"""set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4022  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4023 
4024  def get_is_optimized(self, a0):
4025  r"""get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4026  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4027 
4028  def get_check_level(self):
4029  r"""get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4030  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4031 
4032  def __eq__(self, *args):
4033  r"""
4034  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4035  __eq__(RigidBodyDiffusion self, Particle d) -> bool
4036  """
4037  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4038 
4039  def __ne__(self, *args):
4040  r"""
4041  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4042  __ne__(RigidBodyDiffusion self, Particle d) -> bool
4043  """
4044  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4045 
4046  def __le__(self, *args):
4047  r"""
4048  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4049  __le__(RigidBodyDiffusion self, Particle d) -> bool
4050  """
4051  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4052 
4053  def __lt__(self, *args):
4054  r"""
4055  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4056  __lt__(RigidBodyDiffusion self, Particle d) -> bool
4057  """
4058  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4059 
4060  def __ge__(self, *args):
4061  r"""
4062  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4063  __ge__(RigidBodyDiffusion self, Particle d) -> bool
4064  """
4065  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4066 
4067  def __gt__(self, *args):
4068  r"""
4069  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4070  __gt__(RigidBodyDiffusion self, Particle d) -> bool
4071  """
4072  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4073 
4074  def __hash__(self):
4075  r"""__hash__(RigidBodyDiffusion self) -> std::size_t"""
4076  return _IMP_atom.RigidBodyDiffusion___hash__(self)
4077 
4078  def __str__(self):
4079  r"""__str__(RigidBodyDiffusion self) -> std::string"""
4080  return _IMP_atom.RigidBodyDiffusion___str__(self)
4081 
4082  def __repr__(self):
4083  r"""__repr__(RigidBodyDiffusion self) -> std::string"""
4084  return _IMP_atom.RigidBodyDiffusion___repr__(self)
4085 
4086  def _get_as_binary(self):
4087  r"""_get_as_binary(RigidBodyDiffusion self) -> PyObject *"""
4088  return _IMP_atom.RigidBodyDiffusion__get_as_binary(self)
4089 
4090  def _set_from_binary(self, p):
4091  r"""_set_from_binary(RigidBodyDiffusion self, PyObject * p)"""
4092  return _IMP_atom.RigidBodyDiffusion__set_from_binary(self, p)
4093 
4094  def __getstate__(self):
4095  p = self._get_as_binary()
4096  if len(self.__dict__) > 1:
4097  d = self.__dict__.copy()
4098  del d['this']
4099  p = (d, p)
4100  return p
4101 
4102  def __setstate__(self, p):
4103  if not hasattr(self, 'this'):
4104  self.__init__()
4105  if isinstance(p, tuple):
4106  d, p = p
4107  self.__dict__.update(d)
4108  return self._set_from_binary(p)
4109 
4110  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4111 
4112 # Register RigidBodyDiffusion in _IMP_atom:
4113 _IMP_atom.RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4114 class TAMDParticle(IMP.Decorator):
4115  r"""Proxy of C++ IMP::atom::TAMDParticle class."""
4116 
4117  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4118 
4119  def __init__(self, *args):
4120  r"""
4121  __init__(TAMDParticle self) -> TAMDParticle
4122  __init__(TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4123  __init__(TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4124  """
4125  _IMP_atom.TAMDParticle_swiginit(self, _IMP_atom.new_TAMDParticle(*args))
4126 
4127  def show(self, *args):
4128  r"""show(TAMDParticle self, _ostream out=std::cout)"""
4129  return _IMP_atom.TAMDParticle_show(self, *args)
4130 
4131  @staticmethod
4132  def setup_particle(*args):
4133  r"""
4134  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4135  setup_particle(_ParticleAdaptor pa, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4136  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4137  setup_particle(_ParticleAdaptor pa, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4138  """
4139  return _IMP_atom.TAMDParticle_setup_particle(*args)
4140 
4141  @staticmethod
4142  def get_is_setup(*args):
4143  r"""
4144  get_is_setup(_ParticleAdaptor p) -> bool
4145  get_is_setup(Model m, ParticleIndex p) -> bool
4146  """
4147  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4148 
4149  def get_reference_particle_index(self):
4150  r"""get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4151  return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4152 
4153  def set_temperature_scale_factor(self, tsf):
4154  r"""set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4155  return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4156 
4157  def get_temperature_scale_factor(self):
4158  r"""get_temperature_scale_factor(TAMDParticle self) -> double"""
4159  return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4160 
4161  def set_friction_scale_factor(self, tsf):
4162  r"""set_friction_scale_factor(TAMDParticle self, float tsf)"""
4163  return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4164 
4165  def get_friction_scale_factor(self):
4166  r"""get_friction_scale_factor(TAMDParticle self) -> double"""
4167  return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4168 
4169  def update_coordinates_from_ref(self):
4170  r"""update_coordinates_from_ref(TAMDParticle self)"""
4171  return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4172 
4173  @staticmethod
4174  def get_temperature_scale_factor_key():
4175  r"""get_temperature_scale_factor_key() -> FloatKey"""
4176  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4177 
4178  @staticmethod
4179  def get_friction_scale_factor_key():
4180  r"""get_friction_scale_factor_key() -> FloatKey"""
4181  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4182 
4183  @staticmethod
4184  def get_reference_particle_index_key():
4185  r"""get_reference_particle_index_key() -> ParticleIndexKey"""
4186  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4187 
4188  def add_attribute(self, *args):
4189  r"""
4190  add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4191  add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4192  add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4193  add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4194  add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4195  add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4196  add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4197  add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4198  add_attribute(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4199  add_attribute(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4200  add_attribute(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4201  add_attribute(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4202  """
4203  return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4204 
4205  def get_value(self, *args):
4206  r"""
4207  get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4208  get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4209  get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4210  get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4211  get_value(TAMDParticle self, StringKey a0) -> IMP::String
4212  get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4213  get_value(TAMDParticle self, ObjectKey a0) -> Object
4214  get_value(TAMDParticle self, SparseFloatKey a0) -> IMP::Float
4215  get_value(TAMDParticle self, SparseIntKey a0) -> IMP::Int
4216  get_value(TAMDParticle self, SparseStringKey a0) -> IMP::String
4217  get_value(TAMDParticle self, SparseParticleIndexKey a0) -> ParticleIndex
4218  """
4219  return _IMP_atom.TAMDParticle_get_value(self, *args)
4220 
4221  def set_value(self, *args):
4222  r"""
4223  set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4224  set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4225  set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4226  set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4227  set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4228  set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4229  set_value(TAMDParticle self, ObjectKey a0, Object a1)
4230  set_value(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4231  set_value(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4232  set_value(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4233  set_value(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4234  """
4235  return _IMP_atom.TAMDParticle_set_value(self, *args)
4236 
4237  def remove_attribute(self, *args):
4238  r"""
4239  remove_attribute(TAMDParticle self, FloatKey a0)
4240  remove_attribute(TAMDParticle self, IntKey a0)
4241  remove_attribute(TAMDParticle self, FloatsKey a0)
4242  remove_attribute(TAMDParticle self, IntsKey a0)
4243  remove_attribute(TAMDParticle self, StringKey a0)
4244  remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4245  remove_attribute(TAMDParticle self, ObjectKey a0)
4246  remove_attribute(TAMDParticle self, SparseFloatKey a0)
4247  remove_attribute(TAMDParticle self, SparseIntKey a0)
4248  remove_attribute(TAMDParticle self, SparseStringKey a0)
4249  remove_attribute(TAMDParticle self, SparseParticleIndexKey a0)
4250  """
4251  return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4252 
4253  def has_attribute(self, *args):
4254  r"""
4255  has_attribute(TAMDParticle self, FloatKey a0) -> bool
4256  has_attribute(TAMDParticle self, IntKey a0) -> bool
4257  has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4258  has_attribute(TAMDParticle self, IntsKey a0) -> bool
4259  has_attribute(TAMDParticle self, StringKey a0) -> bool
4260  has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4261  has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4262  has_attribute(TAMDParticle self, SparseFloatKey a0) -> bool
4263  has_attribute(TAMDParticle self, SparseIntKey a0) -> bool
4264  has_attribute(TAMDParticle self, SparseStringKey a0) -> bool
4265  has_attribute(TAMDParticle self, SparseParticleIndexKey a0) -> bool
4266  """
4267  return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4268 
4269  def get_derivative(self, a0):
4270  r"""get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4271  return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4272 
4273  def get_name(self):
4274  r"""get_name(TAMDParticle self) -> std::string"""
4275  return _IMP_atom.TAMDParticle_get_name(self)
4276 
4277  def clear_caches(self):
4278  r"""clear_caches(TAMDParticle self)"""
4279  return _IMP_atom.TAMDParticle_clear_caches(self)
4280 
4281  def set_name(self, a0):
4282  r"""set_name(TAMDParticle self, std::string a0)"""
4283  return _IMP_atom.TAMDParticle_set_name(self, a0)
4284 
4285  def set_check_level(self, a0):
4286  r"""set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4287  return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4288 
4289  def add_to_derivative(self, a0, a1, a2):
4290  r"""add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4291  return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4292 
4293  def set_is_optimized(self, a0, a1):
4294  r"""set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4295  return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4296 
4297  def get_is_optimized(self, a0):
4298  r"""get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4299  return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4300 
4301  def get_check_level(self):
4302  r"""get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4303  return _IMP_atom.TAMDParticle_get_check_level(self)
4304 
4305  def __eq__(self, *args):
4306  r"""
4307  __eq__(TAMDParticle self, TAMDParticle o) -> bool
4308  __eq__(TAMDParticle self, Particle d) -> bool
4309  """
4310  return _IMP_atom.TAMDParticle___eq__(self, *args)
4311 
4312  def __ne__(self, *args):
4313  r"""
4314  __ne__(TAMDParticle self, TAMDParticle o) -> bool
4315  __ne__(TAMDParticle self, Particle d) -> bool
4316  """
4317  return _IMP_atom.TAMDParticle___ne__(self, *args)
4318 
4319  def __le__(self, *args):
4320  r"""
4321  __le__(TAMDParticle self, TAMDParticle o) -> bool
4322  __le__(TAMDParticle self, Particle d) -> bool
4323  """
4324  return _IMP_atom.TAMDParticle___le__(self, *args)
4325 
4326  def __lt__(self, *args):
4327  r"""
4328  __lt__(TAMDParticle self, TAMDParticle o) -> bool
4329  __lt__(TAMDParticle self, Particle d) -> bool
4330  """
4331  return _IMP_atom.TAMDParticle___lt__(self, *args)
4332 
4333  def __ge__(self, *args):
4334  r"""
4335  __ge__(TAMDParticle self, TAMDParticle o) -> bool
4336  __ge__(TAMDParticle self, Particle d) -> bool
4337  """
4338  return _IMP_atom.TAMDParticle___ge__(self, *args)
4339 
4340  def __gt__(self, *args):
4341  r"""
4342  __gt__(TAMDParticle self, TAMDParticle o) -> bool
4343  __gt__(TAMDParticle self, Particle d) -> bool
4344  """
4345  return _IMP_atom.TAMDParticle___gt__(self, *args)
4346 
4347  def __hash__(self):
4348  r"""__hash__(TAMDParticle self) -> std::size_t"""
4349  return _IMP_atom.TAMDParticle___hash__(self)
4350 
4351  def __str__(self):
4352  r"""__str__(TAMDParticle self) -> std::string"""
4353  return _IMP_atom.TAMDParticle___str__(self)
4354 
4355  def __repr__(self):
4356  r"""__repr__(TAMDParticle self) -> std::string"""
4357  return _IMP_atom.TAMDParticle___repr__(self)
4358 
4359  def _get_as_binary(self):
4360  r"""_get_as_binary(TAMDParticle self) -> PyObject *"""
4361  return _IMP_atom.TAMDParticle__get_as_binary(self)
4362 
4363  def _set_from_binary(self, p):
4364  r"""_set_from_binary(TAMDParticle self, PyObject * p)"""
4365  return _IMP_atom.TAMDParticle__set_from_binary(self, p)
4366 
4367  def __getstate__(self):
4368  p = self._get_as_binary()
4369  if len(self.__dict__) > 1:
4370  d = self.__dict__.copy()
4371  del d['this']
4372  p = (d, p)
4373  return p
4374 
4375  def __setstate__(self, p):
4376  if not hasattr(self, 'this'):
4377  self.__init__()
4378  if isinstance(p, tuple):
4379  d, p = p
4380  self.__dict__.update(d)
4381  return self._set_from_binary(p)
4382 
4383  __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4384 
4385 # Register TAMDParticle in _IMP_atom:
4386 _IMP_atom.TAMDParticle_swigregister(TAMDParticle)
4387 class Charged(IMP.core.XYZ):
4388  r"""Proxy of C++ IMP::atom::Charged class."""
4389 
4390  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4391 
4392  def __init__(self, *args):
4393  r"""
4394  __init__(Charged self) -> Charged
4395  __init__(Charged self, Model m, ParticleIndex id) -> Charged
4396  __init__(Charged self, _ParticleAdaptor d) -> Charged
4397  """
4398  _IMP_atom.Charged_swiginit(self, _IMP_atom.new_Charged(*args))
4399 
4400  def show(self, *args):
4401  r"""show(Charged self, _ostream out=std::cout)"""
4402  return _IMP_atom.Charged_show(self, *args)
4403 
4404  @staticmethod
4405  def setup_particle(*args):
4406  r"""
4407  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4408  setup_particle(_ParticleAdaptor pa, IMP::Float charge) -> Charged
4409  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4410  setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float charge) -> Charged
4411  """
4412  return _IMP_atom.Charged_setup_particle(*args)
4413 
4414  def get_charge(self):
4415  r"""get_charge(Charged self) -> IMP::Float"""
4416  return _IMP_atom.Charged_get_charge(self)
4417 
4418  def set_charge(self, t):
4419  r"""set_charge(Charged self, IMP::Float t)"""
4420  return _IMP_atom.Charged_set_charge(self, t)
4421 
4422  @staticmethod
4423  def get_is_setup(*args):
4424  r"""
4425  get_is_setup(_ParticleAdaptor p) -> bool
4426  get_is_setup(Model m, ParticleIndex pi) -> bool
4427  """
4428  return _IMP_atom.Charged_get_is_setup(*args)
4429 
4430  @staticmethod
4431  def get_charge_key():
4432  r"""get_charge_key() -> FloatKey"""
4433  return _IMP_atom.Charged_get_charge_key()
4434 
4435  def add_attribute(self, *args):
4436  r"""
4437  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4438  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4439  add_attribute(Charged self, IntKey a0, IMP::Int a1)
4440  add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
4441  add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
4442  add_attribute(Charged self, StringKey a0, IMP::String a1)
4443  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4444  add_attribute(Charged self, ObjectKey a0, Object a1)
4445  add_attribute(Charged self, SparseFloatKey a0, IMP::Float a1)
4446  add_attribute(Charged self, SparseIntKey a0, IMP::Int a1)
4447  add_attribute(Charged self, SparseStringKey a0, IMP::String a1)
4448  add_attribute(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4449  """
4450  return _IMP_atom.Charged_add_attribute(self, *args)
4451 
4452  def get_value(self, *args):
4453  r"""
4454  get_value(Charged self, FloatKey a0) -> IMP::Float
4455  get_value(Charged self, IntKey a0) -> IMP::Int
4456  get_value(Charged self, FloatsKey a0) -> IMP::Floats
4457  get_value(Charged self, IntsKey a0) -> IMP::Ints
4458  get_value(Charged self, StringKey a0) -> IMP::String
4459  get_value(Charged self, ParticleIndexKey a0) -> Particle
4460  get_value(Charged self, ObjectKey a0) -> Object
4461  get_value(Charged self, SparseFloatKey a0) -> IMP::Float
4462  get_value(Charged self, SparseIntKey a0) -> IMP::Int
4463  get_value(Charged self, SparseStringKey a0) -> IMP::String
4464  get_value(Charged self, SparseParticleIndexKey a0) -> ParticleIndex
4465  """
4466  return _IMP_atom.Charged_get_value(self, *args)
4467 
4468  def set_value(self, *args):
4469  r"""
4470  set_value(Charged self, FloatKey a0, IMP::Float a1)
4471  set_value(Charged self, IntKey a0, IMP::Int a1)
4472  set_value(Charged self, FloatsKey a0, IMP::Floats a1)
4473  set_value(Charged self, IntsKey a0, IMP::Ints a1)
4474  set_value(Charged self, StringKey a0, IMP::String a1)
4475  set_value(Charged self, ParticleIndexKey a0, Particle a1)
4476  set_value(Charged self, ObjectKey a0, Object a1)
4477  set_value(Charged self, SparseFloatKey a0, IMP::Float a1)
4478  set_value(Charged self, SparseIntKey a0, IMP::Int a1)
4479  set_value(Charged self, SparseStringKey a0, IMP::String a1)
4480  set_value(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4481  """
4482  return _IMP_atom.Charged_set_value(self, *args)
4483 
4484  def remove_attribute(self, *args):
4485  r"""
4486  remove_attribute(Charged self, FloatKey a0)
4487  remove_attribute(Charged self, IntKey a0)
4488  remove_attribute(Charged self, FloatsKey a0)
4489  remove_attribute(Charged self, IntsKey a0)
4490  remove_attribute(Charged self, StringKey a0)
4491  remove_attribute(Charged self, ParticleIndexKey a0)
4492  remove_attribute(Charged self, ObjectKey a0)
4493  remove_attribute(Charged self, SparseFloatKey a0)
4494  remove_attribute(Charged self, SparseIntKey a0)
4495  remove_attribute(Charged self, SparseStringKey a0)
4496  remove_attribute(Charged self, SparseParticleIndexKey a0)
4497  """
4498  return _IMP_atom.Charged_remove_attribute(self, *args)
4499 
4500  def has_attribute(self, *args):
4501  r"""
4502  has_attribute(Charged self, FloatKey a0) -> bool
4503  has_attribute(Charged self, IntKey a0) -> bool
4504  has_attribute(Charged self, FloatsKey a0) -> bool
4505  has_attribute(Charged self, IntsKey a0) -> bool
4506  has_attribute(Charged self, StringKey a0) -> bool
4507  has_attribute(Charged self, ParticleIndexKey a0) -> bool
4508  has_attribute(Charged self, ObjectKey a0) -> bool
4509  has_attribute(Charged self, SparseFloatKey a0) -> bool
4510  has_attribute(Charged self, SparseIntKey a0) -> bool
4511  has_attribute(Charged self, SparseStringKey a0) -> bool
4512  has_attribute(Charged self, SparseParticleIndexKey a0) -> bool
4513  """
4514  return _IMP_atom.Charged_has_attribute(self, *args)
4515 
4516  def get_derivative(self, a0):
4517  r"""get_derivative(Charged self, FloatKey a0) -> double"""
4518  return _IMP_atom.Charged_get_derivative(self, a0)
4519 
4520  def get_name(self):
4521  r"""get_name(Charged self) -> std::string"""
4522  return _IMP_atom.Charged_get_name(self)
4523 
4524  def clear_caches(self):
4525  r"""clear_caches(Charged self)"""
4526  return _IMP_atom.Charged_clear_caches(self)
4527 
4528  def set_name(self, a0):
4529  r"""set_name(Charged self, std::string a0)"""
4530  return _IMP_atom.Charged_set_name(self, a0)
4531 
4532  def set_check_level(self, a0):
4533  r"""set_check_level(Charged self, IMP::CheckLevel a0)"""
4534  return _IMP_atom.Charged_set_check_level(self, a0)
4535 
4536  def add_to_derivative(self, a0, a1, a2):
4537  r"""add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4538  return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4539 
4540  def set_is_optimized(self, a0, a1):
4541  r"""set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4542  return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4543 
4544  def get_is_optimized(self, a0):
4545  r"""get_is_optimized(Charged self, FloatKey a0) -> bool"""
4546  return _IMP_atom.Charged_get_is_optimized(self, a0)
4547 
4548  def get_check_level(self):
4549  r"""get_check_level(Charged self) -> IMP::CheckLevel"""
4550  return _IMP_atom.Charged_get_check_level(self)
4551 
4552  def __eq__(self, *args):
4553  r"""
4554  __eq__(Charged self, Charged o) -> bool
4555  __eq__(Charged self, Particle d) -> bool
4556  """
4557  return _IMP_atom.Charged___eq__(self, *args)
4558 
4559  def __ne__(self, *args):
4560  r"""
4561  __ne__(Charged self, Charged o) -> bool
4562  __ne__(Charged self, Particle d) -> bool
4563  """
4564  return _IMP_atom.Charged___ne__(self, *args)
4565 
4566  def __le__(self, *args):
4567  r"""
4568  __le__(Charged self, Charged o) -> bool
4569  __le__(Charged self, Particle d) -> bool
4570  """
4571  return _IMP_atom.Charged___le__(self, *args)
4572 
4573  def __lt__(self, *args):
4574  r"""
4575  __lt__(Charged self, Charged o) -> bool
4576  __lt__(Charged self, Particle d) -> bool
4577  """
4578  return _IMP_atom.Charged___lt__(self, *args)
4579 
4580  def __ge__(self, *args):
4581  r"""
4582  __ge__(Charged self, Charged o) -> bool
4583  __ge__(Charged self, Particle d) -> bool
4584  """
4585  return _IMP_atom.Charged___ge__(self, *args)
4586 
4587  def __gt__(self, *args):
4588  r"""
4589  __gt__(Charged self, Charged o) -> bool
4590  __gt__(Charged self, Particle d) -> bool
4591  """
4592  return _IMP_atom.Charged___gt__(self, *args)
4593 
4594  def __hash__(self):
4595  r"""__hash__(Charged self) -> std::size_t"""
4596  return _IMP_atom.Charged___hash__(self)
4597 
4598  def __str__(self):
4599  r"""__str__(Charged self) -> std::string"""
4600  return _IMP_atom.Charged___str__(self)
4601 
4602  def __repr__(self):
4603  r"""__repr__(Charged self) -> std::string"""
4604  return _IMP_atom.Charged___repr__(self)
4605 
4606  def _get_as_binary(self):
4607  r"""_get_as_binary(Charged self) -> PyObject *"""
4608  return _IMP_atom.Charged__get_as_binary(self)
4609 
4610  def _set_from_binary(self, p):
4611  r"""_set_from_binary(Charged self, PyObject * p)"""
4612  return _IMP_atom.Charged__set_from_binary(self, p)
4613 
4614  def __getstate__(self):
4615  p = self._get_as_binary()
4616  if len(self.__dict__) > 1:
4617  d = self.__dict__.copy()
4618  del d['this']
4619  p = (d, p)
4620  return p
4621 
4622  def __setstate__(self, p):
4623  if not hasattr(self, 'this'):
4624  self.__init__()
4625  if isinstance(p, tuple):
4626  d, p = p
4627  self.__dict__.update(d)
4628  return self._set_from_binary(p)
4629 
4630  __swig_destroy__ = _IMP_atom.delete_Charged
4631 
4632 # Register Charged in _IMP_atom:
4633 _IMP_atom.Charged_swigregister(Charged)
4634 class CoulombPairScore(IMP.PairScore):
4635  r"""Proxy of C++ IMP::atom::CoulombPairScore class."""
4636 
4637  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4638 
4639  def __init__(self, f):
4640  r"""__init__(CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4641  _IMP_atom.CoulombPairScore_swiginit(self, _IMP_atom.new_CoulombPairScore(f))
4642 
4643  def set_relative_dielectric(self, relative_dielectric):
4644  r"""set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4645  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
4646 
4647  def get_relative_dielectric(self):
4648  r"""get_relative_dielectric(CoulombPairScore self) -> double"""
4649  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4650 
4651  def do_get_inputs(self, m, pis):
4652  r"""do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4653  return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
4654 
4655  def get_version_info(self):
4656  r"""get_version_info(CoulombPairScore self) -> VersionInfo"""
4657  return _IMP_atom.CoulombPairScore_get_version_info(self)
4658  __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4659 
4660  def __str__(self):
4661  r"""__str__(CoulombPairScore self) -> std::string"""
4662  return _IMP_atom.CoulombPairScore___str__(self)
4663 
4664  def __repr__(self):
4665  r"""__repr__(CoulombPairScore self) -> std::string"""
4666  return _IMP_atom.CoulombPairScore___repr__(self)
4667 
4668  @staticmethod
4669  def get_from(o):
4670  return _object_cast_to_CoulombPairScore(o)
4671 
4672 
4673 # Register CoulombPairScore in _IMP_atom:
4674 _IMP_atom.CoulombPairScore_swigregister(CoulombPairScore)
4675 class Domain(Hierarchy):
4676  r"""Proxy of C++ IMP::atom::Domain class."""
4677 
4678  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4679 
4680  def set_index_range(self, ir):
4681  r"""set_index_range(Domain self, IMP::IntRange ir)"""
4682  return _IMP_atom.Domain_set_index_range(self, ir)
4683 
4684  def get_index_range(self):
4685  r"""get_index_range(Domain self) -> IMP::IntRange"""
4686  return _IMP_atom.Domain_get_index_range(self)
4687 
4688  def __init__(self, *args):
4689  r"""
4690  __init__(Domain self) -> Domain
4691  __init__(Domain self, Model m, ParticleIndex id) -> Domain
4692  __init__(Domain self, _ParticleAdaptor d) -> Domain
4693  """
4694  _IMP_atom.Domain_swiginit(self, _IMP_atom.new_Domain(*args))
4695 
4696  @staticmethod
4697  def get_is_setup(*args):
4698  r"""
4699  get_is_setup(Model m, ParticleIndex pi) -> bool
4700  get_is_setup(_ParticleAdaptor p) -> bool
4701  """
4702  return _IMP_atom.Domain_get_is_setup(*args)
4703 
4704  def show(self, *args):
4705  r"""show(Domain self, _ostream out=std::cout)"""
4706  return _IMP_atom.Domain_show(self, *args)
4707 
4708  @staticmethod
4709  def setup_particle(*args):
4710  r"""
4711  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
4712  setup_particle(_ParticleAdaptor pa, Domain other) -> Domain
4713  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
4714  setup_particle(_ParticleAdaptor pa, IMP::IntRange residues) -> Domain
4715  """
4716  return _IMP_atom.Domain_setup_particle(*args)
4717 
4718  def add_attribute(self, *args):
4719  r"""
4720  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4721  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4722  add_attribute(Domain self, IntKey a0, IMP::Int a1)
4723  add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
4724  add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
4725  add_attribute(Domain self, StringKey a0, IMP::String a1)
4726  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4727  add_attribute(Domain self, ObjectKey a0, Object a1)
4728  add_attribute(Domain self, SparseFloatKey a0, IMP::Float a1)
4729  add_attribute(Domain self, SparseIntKey a0, IMP::Int a1)
4730  add_attribute(Domain self, SparseStringKey a0, IMP::String a1)
4731  add_attribute(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4732  """
4733  return _IMP_atom.Domain_add_attribute(self, *args)
4734 
4735  def get_value(self, *args):
4736  r"""
4737  get_value(Domain self, FloatKey a0) -> IMP::Float
4738  get_value(Domain self, IntKey a0) -> IMP::Int
4739  get_value(Domain self, FloatsKey a0) -> IMP::Floats
4740  get_value(Domain self, IntsKey a0) -> IMP::Ints
4741  get_value(Domain self, StringKey a0) -> IMP::String
4742  get_value(Domain self, ParticleIndexKey a0) -> Particle
4743  get_value(Domain self, ObjectKey a0) -> Object
4744  get_value(Domain self, SparseFloatKey a0) -> IMP::Float
4745  get_value(Domain self, SparseIntKey a0) -> IMP::Int
4746  get_value(Domain self, SparseStringKey a0) -> IMP::String
4747  get_value(Domain self, SparseParticleIndexKey a0) -> ParticleIndex
4748  """
4749  return _IMP_atom.Domain_get_value(self, *args)
4750 
4751  def set_value(self, *args):
4752  r"""
4753  set_value(Domain self, FloatKey a0, IMP::Float a1)
4754  set_value(Domain self, IntKey a0, IMP::Int a1)
4755  set_value(Domain self, FloatsKey a0, IMP::Floats a1)
4756  set_value(Domain self, IntsKey a0, IMP::Ints a1)
4757  set_value(Domain self, StringKey a0, IMP::String a1)
4758  set_value(Domain self, ParticleIndexKey a0, Particle a1)
4759  set_value(Domain self, ObjectKey a0, Object a1)
4760  set_value(Domain self, SparseFloatKey a0, IMP::Float a1)
4761  set_value(Domain self, SparseIntKey a0, IMP::Int a1)
4762  set_value(Domain self, SparseStringKey a0, IMP::String a1)
4763  set_value(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4764  """
4765  return _IMP_atom.Domain_set_value(self, *args)
4766 
4767  def remove_attribute(self, *args):
4768  r"""
4769  remove_attribute(Domain self, FloatKey a0)
4770  remove_attribute(Domain self, IntKey a0)
4771  remove_attribute(Domain self, FloatsKey a0)
4772  remove_attribute(Domain self, IntsKey a0)
4773  remove_attribute(Domain self, StringKey a0)
4774  remove_attribute(Domain self, ParticleIndexKey a0)
4775  remove_attribute(Domain self, ObjectKey a0)
4776  remove_attribute(Domain self, SparseFloatKey a0)
4777  remove_attribute(Domain self, SparseIntKey a0)
4778  remove_attribute(Domain self, SparseStringKey a0)
4779  remove_attribute(Domain self, SparseParticleIndexKey a0)
4780  """
4781  return _IMP_atom.Domain_remove_attribute(self, *args)
4782 
4783  def has_attribute(self, *args):
4784  r"""
4785  has_attribute(Domain self, FloatKey a0) -> bool
4786  has_attribute(Domain self, IntKey a0) -> bool
4787  has_attribute(Domain self, FloatsKey a0) -> bool
4788  has_attribute(Domain self, IntsKey a0) -> bool
4789  has_attribute(Domain self, StringKey a0) -> bool
4790  has_attribute(Domain self, ParticleIndexKey a0) -> bool
4791  has_attribute(Domain self, ObjectKey a0) -> bool
4792  has_attribute(Domain self, SparseFloatKey a0) -> bool
4793  has_attribute(Domain self, SparseIntKey a0) -> bool
4794  has_attribute(Domain self, SparseStringKey a0) -> bool
4795  has_attribute(Domain self, SparseParticleIndexKey a0) -> bool
4796  """
4797  return _IMP_atom.Domain_has_attribute(self, *args)
4798 
4799  def get_derivative(self, a0):
4800  r"""get_derivative(Domain self, FloatKey a0) -> double"""
4801  return _IMP_atom.Domain_get_derivative(self, a0)
4802 
4803  def get_name(self):
4804  r"""get_name(Domain self) -> std::string"""
4805  return _IMP_atom.Domain_get_name(self)
4806 
4807  def clear_caches(self):
4808  r"""clear_caches(Domain self)"""
4809  return _IMP_atom.Domain_clear_caches(self)
4810 
4811  def set_name(self, a0):
4812  r"""set_name(Domain self, std::string a0)"""
4813  return _IMP_atom.Domain_set_name(self, a0)
4814 
4815  def set_check_level(self, a0):
4816  r"""set_check_level(Domain self, IMP::CheckLevel a0)"""
4817  return _IMP_atom.Domain_set_check_level(self, a0)
4818 
4819  def add_to_derivative(self, a0, a1, a2):
4820  r"""add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4821  return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
4822 
4823  def set_is_optimized(self, a0, a1):
4824  r"""set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4825  return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
4826 
4827  def get_is_optimized(self, a0):
4828  r"""get_is_optimized(Domain self, FloatKey a0) -> bool"""
4829  return _IMP_atom.Domain_get_is_optimized(self, a0)
4830 
4831  def get_check_level(self):
4832  r"""get_check_level(Domain self) -> IMP::CheckLevel"""
4833  return _IMP_atom.Domain_get_check_level(self)
4834 
4835  def __eq__(self, *args):
4836  r"""
4837  __eq__(Domain self, Domain o) -> bool
4838  __eq__(Domain self, Particle d) -> bool
4839  """
4840  return _IMP_atom.Domain___eq__(self, *args)
4841 
4842  def __ne__(self, *args):
4843  r"""
4844  __ne__(Domain self, Domain o) -> bool
4845  __ne__(Domain self, Particle d) -> bool
4846  """
4847  return _IMP_atom.Domain___ne__(self, *args)
4848 
4849  def __le__(self, *args):
4850  r"""
4851  __le__(Domain self, Domain o) -> bool
4852  __le__(Domain self, Particle d) -> bool
4853  """
4854  return _IMP_atom.Domain___le__(self, *args)
4855 
4856  def __lt__(self, *args):
4857  r"""
4858  __lt__(Domain self, Domain o) -> bool
4859  __lt__(Domain self, Particle d) -> bool
4860  """
4861  return _IMP_atom.Domain___lt__(self, *args)
4862 
4863  def __ge__(self, *args):
4864  r"""
4865  __ge__(Domain self, Domain o) -> bool
4866  __ge__(Domain self, Particle d) -> bool
4867  """
4868  return _IMP_atom.Domain___ge__(self, *args)
4869 
4870  def __gt__(self, *args):
4871  r"""
4872  __gt__(Domain self, Domain o) -> bool
4873  __gt__(Domain self, Particle d) -> bool
4874  """
4875  return _IMP_atom.Domain___gt__(self, *args)
4876 
4877  def __hash__(self):
4878  r"""__hash__(Domain self) -> std::size_t"""
4879  return _IMP_atom.Domain___hash__(self)
4880 
4881  def __str__(self):
4882  r"""__str__(Domain self) -> std::string"""
4883  return _IMP_atom.Domain___str__(self)
4884 
4885  def __repr__(self):
4886  r"""__repr__(Domain self) -> std::string"""
4887  return _IMP_atom.Domain___repr__(self)
4888 
4889  def _get_as_binary(self):
4890  r"""_get_as_binary(Domain self) -> PyObject *"""
4891  return _IMP_atom.Domain__get_as_binary(self)
4892 
4893  def _set_from_binary(self, p):
4894  r"""_set_from_binary(Domain self, PyObject * p)"""
4895  return _IMP_atom.Domain__set_from_binary(self, p)
4896 
4897  def __getstate__(self):
4898  p = self._get_as_binary()
4899  if len(self.__dict__) > 1:
4900  d = self.__dict__.copy()
4901  del d['this']
4902  p = (d, p)
4903  return p
4904 
4905  def __setstate__(self, p):
4906  if not hasattr(self, 'this'):
4907  self.__init__()
4908  if isinstance(p, tuple):
4909  d, p = p
4910  self.__dict__.update(d)
4911  return self._set_from_binary(p)
4912 
4913  __swig_destroy__ = _IMP_atom.delete_Domain
4914 
4915 # Register Domain in _IMP_atom:
4916 _IMP_atom.Domain_swigregister(Domain)
4917 class LennardJones(IMP.core.XYZR):
4918  r"""Proxy of C++ IMP::atom::LennardJones class."""
4919 
4920  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4921 
4922  def __init__(self, *args):
4923  r"""
4924  __init__(LennardJones self) -> LennardJones
4925  __init__(LennardJones self, Model m, ParticleIndex id) -> LennardJones
4926  __init__(LennardJones self, _ParticleAdaptor d) -> LennardJones
4927  """
4928  _IMP_atom.LennardJones_swiginit(self, _IMP_atom.new_LennardJones(*args))
4929 
4930  def show(self, *args):
4931  r"""show(LennardJones self, _ostream out=std::cout)"""
4932  return _IMP_atom.LennardJones_show(self, *args)
4933 
4934  @staticmethod
4935  def setup_particle(*args):
4936  r"""
4937  setup_particle(Model m, ParticleIndex pi) -> LennardJones
4938  setup_particle(_ParticleAdaptor pa) -> LennardJones
4939  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4940  setup_particle(_ParticleAdaptor pa, IMP::Float well_depth) -> LennardJones
4941  """
4942  return _IMP_atom.LennardJones_setup_particle(*args)
4943 
4944  def get_well_depth(self):
4945  r"""get_well_depth(LennardJones self) -> IMP::Float"""
4946  return _IMP_atom.LennardJones_get_well_depth(self)
4947 
4948  def set_well_depth(self, well_depth):
4949  r"""set_well_depth(LennardJones self, IMP::Float well_depth)"""
4950  return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
4951 
4952  @staticmethod
4953  def get_is_setup(*args):
4954  r"""
4955  get_is_setup(_ParticleAdaptor p) -> bool
4956  get_is_setup(Model m, ParticleIndex pi) -> bool
4957  """
4958  return _IMP_atom.LennardJones_get_is_setup(*args)
4959 
4960  @staticmethod
4961  def get_well_depth_key():
4962  r"""get_well_depth_key() -> FloatKey"""
4963  return _IMP_atom.LennardJones_get_well_depth_key()
4964 
4965  def add_attribute(self, *args):
4966  r"""
4967  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
4968  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
4969  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
4970  add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
4971  add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
4972  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
4973  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
4974  add_attribute(LennardJones self, ObjectKey a0, Object a1)
4975  add_attribute(LennardJones self, SparseFloatKey a0, IMP::Float a1)
4976  add_attribute(LennardJones self, SparseIntKey a0, IMP::Int a1)
4977  add_attribute(LennardJones self, SparseStringKey a0, IMP::String a1)
4978  add_attribute(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
4979  """
4980  return _IMP_atom.LennardJones_add_attribute(self, *args)
4981 
4982  def get_value(self, *args):
4983  r"""
4984  get_value(LennardJones self, FloatKey a0) -> IMP::Float
4985  get_value(LennardJones self, IntKey a0) -> IMP::Int
4986  get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
4987  get_value(LennardJones self, IntsKey a0) -> IMP::Ints
4988  get_value(LennardJones self, StringKey a0) -> IMP::String
4989  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
4990  get_value(LennardJones self, ObjectKey a0) -> Object
4991  get_value(LennardJones self, SparseFloatKey a0) -> IMP::Float
4992  get_value(LennardJones self, SparseIntKey a0) -> IMP::Int
4993  get_value(LennardJones self, SparseStringKey a0) -> IMP::String
4994  get_value(LennardJones self, SparseParticleIndexKey a0) -> ParticleIndex
4995  """
4996  return _IMP_atom.LennardJones_get_value(self, *args)
4997 
4998  def set_value(self, *args):
4999  r"""
5000  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5001  set_value(LennardJones self, IntKey a0, IMP::Int a1)
5002  set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5003  set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5004  set_value(LennardJones self, StringKey a0, IMP::String a1)
5005  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5006  set_value(LennardJones self, ObjectKey a0, Object a1)
5007  set_value(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5008  set_value(LennardJones self, SparseIntKey a0, IMP::Int a1)
5009  set_value(LennardJones self, SparseStringKey a0, IMP::String a1)
5010  set_value(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5011  """
5012  return _IMP_atom.LennardJones_set_value(self, *args)
5013 
5014  def remove_attribute(self, *args):
5015  r"""
5016  remove_attribute(LennardJones self, FloatKey a0)
5017  remove_attribute(LennardJones self, IntKey a0)
5018  remove_attribute(LennardJones self, FloatsKey a0)
5019  remove_attribute(LennardJones self, IntsKey a0)
5020  remove_attribute(LennardJones self, StringKey a0)
5021  remove_attribute(LennardJones self, ParticleIndexKey a0)
5022  remove_attribute(LennardJones self, ObjectKey a0)
5023  remove_attribute(LennardJones self, SparseFloatKey a0)
5024  remove_attribute(LennardJones self, SparseIntKey a0)
5025  remove_attribute(LennardJones self, SparseStringKey a0)
5026  remove_attribute(LennardJones self, SparseParticleIndexKey a0)
5027  """
5028  return _IMP_atom.LennardJones_remove_attribute(self, *args)
5029 
5030  def has_attribute(self, *args):
5031  r"""
5032  has_attribute(LennardJones self, FloatKey a0) -> bool
5033  has_attribute(LennardJones self, IntKey a0) -> bool
5034  has_attribute(LennardJones self, FloatsKey a0) -> bool
5035  has_attribute(LennardJones self, IntsKey a0) -> bool
5036  has_attribute(LennardJones self, StringKey a0) -> bool
5037  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5038  has_attribute(LennardJones self, ObjectKey a0) -> bool
5039  has_attribute(LennardJones self, SparseFloatKey a0) -> bool
5040  has_attribute(LennardJones self, SparseIntKey a0) -> bool
5041  has_attribute(LennardJones self, SparseStringKey a0) -> bool
5042  has_attribute(LennardJones self, SparseParticleIndexKey a0) -> bool
5043  """
5044  return _IMP_atom.LennardJones_has_attribute(self, *args)
5045 
5046  def get_derivative(self, a0):
5047  r"""get_derivative(LennardJones self, FloatKey a0) -> double"""
5048  return _IMP_atom.LennardJones_get_derivative(self, a0)
5049 
5050  def get_name(self):
5051  r"""get_name(LennardJones self) -> std::string"""
5052  return _IMP_atom.LennardJones_get_name(self)
5053 
5054  def clear_caches(self):
5055  r"""clear_caches(LennardJones self)"""
5056  return _IMP_atom.LennardJones_clear_caches(self)
5057 
5058  def set_name(self, a0):
5059  r"""set_name(LennardJones self, std::string a0)"""
5060  return _IMP_atom.LennardJones_set_name(self, a0)
5061 
5062  def set_check_level(self, a0):
5063  r"""set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5064  return _IMP_atom.LennardJones_set_check_level(self, a0)
5065 
5066  def add_to_derivative(self, a0, a1, a2):
5067  r"""add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5068  return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5069 
5070  def set_is_optimized(self, a0, a1):
5071  r"""set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5072  return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5073 
5074  def get_is_optimized(self, a0):
5075  r"""get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5076  return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5077 
5078  def get_check_level(self):
5079  r"""get_check_level(LennardJones self) -> IMP::CheckLevel"""
5080  return _IMP_atom.LennardJones_get_check_level(self)
5081 
5082  def __eq__(self, *args):
5083  r"""
5084  __eq__(LennardJones self, LennardJones o) -> bool
5085  __eq__(LennardJones self, Particle d) -> bool
5086  """
5087  return _IMP_atom.LennardJones___eq__(self, *args)
5088 
5089  def __ne__(self, *args):
5090  r"""
5091  __ne__(LennardJones self, LennardJones o) -> bool
5092  __ne__(LennardJones self, Particle d) -> bool
5093  """
5094  return _IMP_atom.LennardJones___ne__(self, *args)
5095 
5096  def __le__(self, *args):
5097  r"""
5098  __le__(LennardJones self, LennardJones o) -> bool
5099  __le__(LennardJones self, Particle d) -> bool
5100  """
5101  return _IMP_atom.LennardJones___le__(self, *args)
5102 
5103  def __lt__(self, *args):
5104  r"""
5105  __lt__(LennardJones self, LennardJones o) -> bool
5106  __lt__(LennardJones self, Particle d) -> bool
5107  """
5108  return _IMP_atom.LennardJones___lt__(self, *args)
5109 
5110  def __ge__(self, *args):
5111  r"""
5112  __ge__(LennardJones self, LennardJones o) -> bool
5113  __ge__(LennardJones self, Particle d) -> bool
5114  """
5115  return _IMP_atom.LennardJones___ge__(self, *args)
5116 
5117  def __gt__(self, *args):
5118  r"""
5119  __gt__(LennardJones self, LennardJones o) -> bool
5120  __gt__(LennardJones self, Particle d) -> bool
5121  """
5122  return _IMP_atom.LennardJones___gt__(self, *args)
5123 
5124  def __hash__(self):
5125  r"""__hash__(LennardJones self) -> std::size_t"""
5126  return _IMP_atom.LennardJones___hash__(self)
5127 
5128  def __str__(self):
5129  r"""__str__(LennardJones self) -> std::string"""
5130  return _IMP_atom.LennardJones___str__(self)
5131 
5132  def __repr__(self):
5133  r"""__repr__(LennardJones self) -> std::string"""
5134  return _IMP_atom.LennardJones___repr__(self)
5135 
5136  def _get_as_binary(self):
5137  r"""_get_as_binary(LennardJones self) -> PyObject *"""
5138  return _IMP_atom.LennardJones__get_as_binary(self)
5139 
5140  def _set_from_binary(self, p):
5141  r"""_set_from_binary(LennardJones self, PyObject * p)"""
5142  return _IMP_atom.LennardJones__set_from_binary(self, p)
5143 
5144  def __getstate__(self):
5145  p = self._get_as_binary()
5146  if len(self.__dict__) > 1:
5147  d = self.__dict__.copy()
5148  del d['this']
5149  p = (d, p)
5150  return p
5151 
5152  def __setstate__(self, p):
5153  if not hasattr(self, 'this'):
5154  self.__init__()
5155  if isinstance(p, tuple):
5156  d, p = p
5157  self.__dict__.update(d)
5158  return self._set_from_binary(p)
5159 
5160  __swig_destroy__ = _IMP_atom.delete_LennardJones
5161 
5162 # Register LennardJones in _IMP_atom:
5163 _IMP_atom.LennardJones_swigregister(LennardJones)
5164 class LennardJonesPairScore(IMP.PairScore):
5165  r"""Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5166 
5167  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5168 
5169  def __init__(self, f):
5170  r"""__init__(LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5171  _IMP_atom.LennardJonesPairScore_swiginit(self, _IMP_atom.new_LennardJonesPairScore(f))
5172 
5173  def set_repulsive_weight(self, repulsive_weight):
5174  r"""set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5175  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5176 
5177  def get_repulsive_weight(self):
5178  r"""get_repulsive_weight(LennardJonesPairScore self) -> double"""
5179  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5180 
5181  def set_attractive_weight(self, attractive_weight):
5182  r"""set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5183  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5184 
5185  def get_attractive_weight(self):
5186  r"""get_attractive_weight(LennardJonesPairScore self) -> double"""
5187  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5188 
5189  def do_get_inputs(self, m, pis):
5190  r"""do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5191  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5192 
5193  def get_version_info(self):
5194  r"""get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5195  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5196  __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
5197 
5198  def __str__(self):
5199  r"""__str__(LennardJonesPairScore self) -> std::string"""
5200  return _IMP_atom.LennardJonesPairScore___str__(self)
5201 
5202  def __repr__(self):
5203  r"""__repr__(LennardJonesPairScore self) -> std::string"""
5204  return _IMP_atom.LennardJonesPairScore___repr__(self)
5205 
5206  @staticmethod
5207  def get_from(o):
5208  return _object_cast_to_LennardJonesPairScore(o)
5209 
5210 
5211 # Register LennardJonesPairScore in _IMP_atom:
5212 _IMP_atom.LennardJonesPairScore_swigregister(LennardJonesPairScore)
5213 class LinearVelocity(IMP.Decorator):
5214  r"""Proxy of C++ IMP::atom::LinearVelocity class."""
5215 
5216  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5217 
5218  def __init__(self, *args):
5219  r"""
5220  __init__(LinearVelocity self) -> LinearVelocity
5221  __init__(LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5222  __init__(LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5223  """
5224  _IMP_atom.LinearVelocity_swiginit(self, _IMP_atom.new_LinearVelocity(*args))
5225 
5226  @staticmethod
5227  def get_is_setup(*args):
5228  r"""
5229  get_is_setup(Model m, ParticleIndex pi) -> bool
5230  get_is_setup(_ParticleAdaptor p) -> bool
5231  """
5232  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5233 
5234  def show(self, *args):
5235  r"""show(LinearVelocity self, _ostream out=std::cout)"""
5236  return _IMP_atom.LinearVelocity_show(self, *args)
5237 
5238  @staticmethod
5239  def setup_particle(*args):
5240  r"""
5241  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5242  setup_particle(_ParticleAdaptor pa) -> LinearVelocity
5243  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5244  setup_particle(_ParticleAdaptor pa, Vector3D v) -> LinearVelocity
5245  """
5246  return _IMP_atom.LinearVelocity_setup_particle(*args)
5247 
5248  def set_velocity(self, v):
5249  r"""set_velocity(LinearVelocity self, Vector3D v)"""
5250  return _IMP_atom.LinearVelocity_set_velocity(self, v)
5251 
5252  def get_velocity(self):
5253  r"""get_velocity(LinearVelocity self) -> Vector3D"""
5254  return _IMP_atom.LinearVelocity_get_velocity(self)
5255 
5256  def add_attribute(self, *args):
5257  r"""
5258  add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5259  add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5260  add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5261  add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5262  add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5263  add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5264  add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5265  add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5266  add_attribute(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5267  add_attribute(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5268  add_attribute(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5269  add_attribute(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5270  """
5271  return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5272 
5273  def get_value(self, *args):
5274  r"""
5275  get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5276  get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5277  get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5278  get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5279  get_value(LinearVelocity self, StringKey a0) -> IMP::String
5280  get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5281  get_value(LinearVelocity self, ObjectKey a0) -> Object
5282  get_value(LinearVelocity self, SparseFloatKey a0) -> IMP::Float
5283  get_value(LinearVelocity self, SparseIntKey a0) -> IMP::Int
5284  get_value(LinearVelocity self, SparseStringKey a0) -> IMP::String
5285  get_value(LinearVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5286  """
5287  return _IMP_atom.LinearVelocity_get_value(self, *args)
5288 
5289  def set_value(self, *args):
5290  r"""
5291  set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5292  set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5293  set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5294  set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5295  set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5296  set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5297  set_value(LinearVelocity self, ObjectKey a0, Object a1)
5298  set_value(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5299  set_value(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5300  set_value(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5301  set_value(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5302  """
5303  return _IMP_atom.LinearVelocity_set_value(self, *args)
5304 
5305  def remove_attribute(self, *args):
5306  r"""
5307  remove_attribute(LinearVelocity self, FloatKey a0)
5308  remove_attribute(LinearVelocity self, IntKey a0)
5309  remove_attribute(LinearVelocity self, FloatsKey a0)
5310  remove_attribute(LinearVelocity self, IntsKey a0)
5311  remove_attribute(LinearVelocity self, StringKey a0)
5312  remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5313  remove_attribute(LinearVelocity self, ObjectKey a0)
5314  remove_attribute(LinearVelocity self, SparseFloatKey a0)
5315  remove_attribute(LinearVelocity self, SparseIntKey a0)
5316  remove_attribute(LinearVelocity self, SparseStringKey a0)
5317  remove_attribute(LinearVelocity self, SparseParticleIndexKey a0)
5318  """
5319  return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5320 
5321  def has_attribute(self, *args):
5322  r"""
5323  has_attribute(LinearVelocity self, FloatKey a0) -> bool
5324  has_attribute(LinearVelocity self, IntKey a0) -> bool
5325  has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5326  has_attribute(LinearVelocity self, IntsKey a0) -> bool
5327  has_attribute(LinearVelocity self, StringKey a0) -> bool
5328  has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5329  has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5330  has_attribute(LinearVelocity self, SparseFloatKey a0) -> bool
5331  has_attribute(LinearVelocity self, SparseIntKey a0) -> bool
5332  has_attribute(LinearVelocity self, SparseStringKey a0) -> bool
5333  has_attribute(LinearVelocity self, SparseParticleIndexKey a0) -> bool
5334  """
5335  return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5336 
5337  def get_derivative(self, a0):
5338  r"""get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5339  return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5340 
5341  def get_name(self):
5342  r"""get_name(LinearVelocity self) -> std::string"""
5343  return _IMP_atom.LinearVelocity_get_name(self)
5344 
5345  def clear_caches(self):
5346  r"""clear_caches(LinearVelocity self)"""
5347  return _IMP_atom.LinearVelocity_clear_caches(self)
5348 
5349  def set_name(self, a0):
5350  r"""set_name(LinearVelocity self, std::string a0)"""
5351  return _IMP_atom.LinearVelocity_set_name(self, a0)
5352 
5353  def set_check_level(self, a0):
5354  r"""set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5355  return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5356 
5357  def add_to_derivative(self, a0, a1, a2):
5358  r"""add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5359  return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5360 
5361  def set_is_optimized(self, a0, a1):
5362  r"""set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5363  return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5364 
5365  def get_is_optimized(self, a0):
5366  r"""get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5367  return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5368 
5369  def get_check_level(self):
5370  r"""get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5371  return _IMP_atom.LinearVelocity_get_check_level(self)
5372 
5373  def __eq__(self, *args):
5374  r"""
5375  __eq__(LinearVelocity self, LinearVelocity o) -> bool
5376  __eq__(LinearVelocity self, Particle d) -> bool
5377  """
5378  return _IMP_atom.LinearVelocity___eq__(self, *args)
5379 
5380  def __ne__(self, *args):
5381  r"""
5382  __ne__(LinearVelocity self, LinearVelocity o) -> bool
5383  __ne__(LinearVelocity self, Particle d) -> bool
5384  """
5385  return _IMP_atom.LinearVelocity___ne__(self, *args)
5386 
5387  def __le__(self, *args):
5388  r"""
5389  __le__(LinearVelocity self, LinearVelocity o) -> bool
5390  __le__(LinearVelocity self, Particle d) -> bool
5391  """
5392  return _IMP_atom.LinearVelocity___le__(self, *args)
5393 
5394  def __lt__(self, *args):
5395  r"""
5396  __lt__(LinearVelocity self, LinearVelocity o) -> bool
5397  __lt__(LinearVelocity self, Particle d) -> bool
5398  """
5399  return _IMP_atom.LinearVelocity___lt__(self, *args)
5400 
5401  def __ge__(self, *args):
5402  r"""
5403  __ge__(LinearVelocity self, LinearVelocity o) -> bool
5404  __ge__(LinearVelocity self, Particle d) -> bool
5405  """
5406  return _IMP_atom.LinearVelocity___ge__(self, *args)
5407 
5408  def __gt__(self, *args):
5409  r"""
5410  __gt__(LinearVelocity self, LinearVelocity o) -> bool
5411  __gt__(LinearVelocity self, Particle d) -> bool
5412  """
5413  return _IMP_atom.LinearVelocity___gt__(self, *args)
5414 
5415  def __hash__(self):
5416  r"""__hash__(LinearVelocity self) -> std::size_t"""
5417  return _IMP_atom.LinearVelocity___hash__(self)
5418 
5419  def __str__(self):
5420  r"""__str__(LinearVelocity self) -> std::string"""
5421  return _IMP_atom.LinearVelocity___str__(self)
5422 
5423  def __repr__(self):
5424  r"""__repr__(LinearVelocity self) -> std::string"""
5425  return _IMP_atom.LinearVelocity___repr__(self)
5426 
5427  def _get_as_binary(self):
5428  r"""_get_as_binary(LinearVelocity self) -> PyObject *"""
5429  return _IMP_atom.LinearVelocity__get_as_binary(self)
5430 
5431  def _set_from_binary(self, p):
5432  r"""_set_from_binary(LinearVelocity self, PyObject * p)"""
5433  return _IMP_atom.LinearVelocity__set_from_binary(self, p)
5434 
5435  def __getstate__(self):
5436  p = self._get_as_binary()
5437  if len(self.__dict__) > 1:
5438  d = self.__dict__.copy()
5439  del d['this']
5440  p = (d, p)
5441  return p
5442 
5443  def __setstate__(self, p):
5444  if not hasattr(self, 'this'):
5445  self.__init__()
5446  if isinstance(p, tuple):
5447  d, p = p
5448  self.__dict__.update(d)
5449  return self._set_from_binary(p)
5450 
5451  __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5452 
5453 # Register LinearVelocity in _IMP_atom:
5454 _IMP_atom.LinearVelocity_swigregister(LinearVelocity)
5455 class AngularVelocity(IMP.Decorator):
5456  r"""Proxy of C++ IMP::atom::AngularVelocity class."""
5457 
5458  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5459 
5460  def __init__(self, *args):
5461  r"""
5462  __init__(AngularVelocity self) -> AngularVelocity
5463  __init__(AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5464  __init__(AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5465  """
5466  _IMP_atom.AngularVelocity_swiginit(self, _IMP_atom.new_AngularVelocity(*args))
5467 
5468  @staticmethod
5469  def get_is_setup(*args):
5470  r"""
5471  get_is_setup(Model m, ParticleIndex pi) -> bool
5472  get_is_setup(_ParticleAdaptor p) -> bool
5473  """
5474  return _IMP_atom.AngularVelocity_get_is_setup(*args)
5475 
5476  def show(self, *args):
5477  r"""show(AngularVelocity self, _ostream out=std::cout)"""
5478  return _IMP_atom.AngularVelocity_show(self, *args)
5479 
5480  @staticmethod
5481  def setup_particle(*args):
5482  r"""
5483  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5484  setup_particle(_ParticleAdaptor pa) -> AngularVelocity
5485  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5486  setup_particle(_ParticleAdaptor pa, Vector4D v) -> AngularVelocity
5487  """
5488  return _IMP_atom.AngularVelocity_setup_particle(*args)
5489 
5490  def set_velocity(self, v):
5491  r"""set_velocity(AngularVelocity self, Vector4D v)"""
5492  return _IMP_atom.AngularVelocity_set_velocity(self, v)
5493 
5494  def get_velocity(self):
5495  r"""get_velocity(AngularVelocity self) -> Vector4D"""
5496  return _IMP_atom.AngularVelocity_get_velocity(self)
5497 
5498  def add_attribute(self, *args):
5499  r"""
5500  add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5501  add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5502  add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5503  add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5504  add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5505  add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5506  add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5507  add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5508  add_attribute(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5509  add_attribute(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5510  add_attribute(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5511  add_attribute(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5512  """
5513  return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5514 
5515  def get_value(self, *args):
5516  r"""
5517  get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5518  get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5519  get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
5520  get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
5521  get_value(AngularVelocity self, StringKey a0) -> IMP::String
5522  get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5523  get_value(AngularVelocity self, ObjectKey a0) -> Object
5524  get_value(AngularVelocity self, SparseFloatKey a0) -> IMP::Float
5525  get_value(AngularVelocity self, SparseIntKey a0) -> IMP::Int
5526  get_value(AngularVelocity self, SparseStringKey a0) -> IMP::String
5527  get_value(AngularVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5528  """
5529  return _IMP_atom.AngularVelocity_get_value(self, *args)
5530 
5531  def set_value(self, *args):
5532  r"""
5533  set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5534  set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5535  set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5536  set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5537  set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5538  set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5539  set_value(AngularVelocity self, ObjectKey a0, Object a1)
5540  set_value(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5541  set_value(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5542  set_value(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5543  set_value(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5544  """
5545  return _IMP_atom.AngularVelocity_set_value(self, *args)
5546 
5547  def remove_attribute(self, *args):
5548  r"""
5549  remove_attribute(AngularVelocity self, FloatKey a0)
5550  remove_attribute(AngularVelocity self, IntKey a0)
5551  remove_attribute(AngularVelocity self, FloatsKey a0)
5552  remove_attribute(AngularVelocity self, IntsKey a0)
5553  remove_attribute(AngularVelocity self, StringKey a0)
5554  remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5555  remove_attribute(AngularVelocity self, ObjectKey a0)
5556  remove_attribute(AngularVelocity self, SparseFloatKey a0)
5557  remove_attribute(AngularVelocity self, SparseIntKey a0)
5558  remove_attribute(AngularVelocity self, SparseStringKey a0)
5559  remove_attribute(AngularVelocity self, SparseParticleIndexKey a0)
5560  """
5561  return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5562 
5563  def has_attribute(self, *args):
5564  r"""
5565  has_attribute(AngularVelocity self, FloatKey a0) -> bool
5566  has_attribute(AngularVelocity self, IntKey a0) -> bool
5567  has_attribute(AngularVelocity self, FloatsKey a0) -> bool
5568  has_attribute(AngularVelocity self, IntsKey a0) -> bool
5569  has_attribute(AngularVelocity self, StringKey a0) -> bool
5570  has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
5571  has_attribute(AngularVelocity self, ObjectKey a0) -> bool
5572  has_attribute(AngularVelocity self, SparseFloatKey a0) -> bool
5573  has_attribute(AngularVelocity self, SparseIntKey a0) -> bool
5574  has_attribute(AngularVelocity self, SparseStringKey a0) -> bool
5575  has_attribute(AngularVelocity self, SparseParticleIndexKey a0) -> bool
5576  """
5577  return _IMP_atom.AngularVelocity_has_attribute(self, *args)
5578 
5579  def get_derivative(self, a0):
5580  r"""get_derivative(AngularVelocity self, FloatKey a0) -> double"""
5581  return _IMP_atom.AngularVelocity_get_derivative(self, a0)
5582 
5583  def get_name(self):
5584  r"""get_name(AngularVelocity self) -> std::string"""
5585  return _IMP_atom.AngularVelocity_get_name(self)
5586 
5587  def clear_caches(self):
5588  r"""clear_caches(AngularVelocity self)"""
5589  return _IMP_atom.AngularVelocity_clear_caches(self)
5590 
5591  def set_name(self, a0):
5592  r"""set_name(AngularVelocity self, std::string a0)"""
5593  return _IMP_atom.AngularVelocity_set_name(self, a0)
5594 
5595  def set_check_level(self, a0):
5596  r"""set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
5597  return _IMP_atom.AngularVelocity_set_check_level(self, a0)
5598 
5599  def add_to_derivative(self, a0, a1, a2):
5600  r"""add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5601  return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
5602 
5603  def set_is_optimized(self, a0, a1):
5604  r"""set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
5605  return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
5606 
5607  def get_is_optimized(self, a0):
5608  r"""get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
5609  return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
5610 
5611  def get_check_level(self):
5612  r"""get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
5613  return _IMP_atom.AngularVelocity_get_check_level(self)
5614 
5615  def __eq__(self, *args):
5616  r"""
5617  __eq__(AngularVelocity self, AngularVelocity o) -> bool
5618  __eq__(AngularVelocity self, Particle d) -> bool
5619  """
5620  return _IMP_atom.AngularVelocity___eq__(self, *args)
5621 
5622  def __ne__(self, *args):
5623  r"""
5624  __ne__(AngularVelocity self, AngularVelocity o) -> bool
5625  __ne__(AngularVelocity self, Particle d) -> bool
5626  """
5627  return _IMP_atom.AngularVelocity___ne__(self, *args)
5628 
5629  def __le__(self, *args):
5630  r"""
5631  __le__(AngularVelocity self, AngularVelocity o) -> bool
5632  __le__(AngularVelocity self, Particle d) -> bool
5633  """
5634  return _IMP_atom.AngularVelocity___le__(self, *args)
5635 
5636  def __lt__(self, *args):
5637  r"""
5638  __lt__(AngularVelocity self, AngularVelocity o) -> bool
5639  __lt__(AngularVelocity self, Particle d) -> bool
5640  """
5641  return _IMP_atom.AngularVelocity___lt__(self, *args)
5642 
5643  def __ge__(self, *args):
5644  r"""
5645  __ge__(AngularVelocity self, AngularVelocity o) -> bool
5646  __ge__(AngularVelocity self, Particle d) -> bool
5647  """
5648  return _IMP_atom.AngularVelocity___ge__(self, *args)
5649 
5650  def __gt__(self, *args):
5651  r"""
5652  __gt__(AngularVelocity self, AngularVelocity o) -> bool
5653  __gt__(AngularVelocity self, Particle d) -> bool
5654  """
5655  return _IMP_atom.AngularVelocity___gt__(self, *args)
5656 
5657  def __hash__(self):
5658  r"""__hash__(AngularVelocity self) -> std::size_t"""
5659  return _IMP_atom.AngularVelocity___hash__(self)
5660 
5661  def __str__(self):
5662  r"""__str__(AngularVelocity self) -> std::string"""
5663  return _IMP_atom.AngularVelocity___str__(self)
5664 
5665  def __repr__(self):
5666  r"""__repr__(AngularVelocity self) -> std::string"""
5667  return _IMP_atom.AngularVelocity___repr__(self)
5668 
5669  def _get_as_binary(self):
5670  r"""_get_as_binary(AngularVelocity self) -> PyObject *"""
5671  return _IMP_atom.AngularVelocity__get_as_binary(self)
5672 
5673  def _set_from_binary(self, p):
5674  r"""_set_from_binary(AngularVelocity self, PyObject * p)"""
5675  return _IMP_atom.AngularVelocity__set_from_binary(self, p)
5676 
5677  def __getstate__(self):
5678  p = self._get_as_binary()
5679  if len(self.__dict__) > 1:
5680  d = self.__dict__.copy()
5681  del d['this']
5682  p = (d, p)
5683  return p
5684 
5685  def __setstate__(self, p):
5686  if not hasattr(self, 'this'):
5687  self.__init__()
5688  if isinstance(p, tuple):
5689  d, p = p
5690  self.__dict__.update(d)
5691  return self._set_from_binary(p)
5692 
5693  __swig_destroy__ = _IMP_atom.delete_AngularVelocity
5694 
5695 # Register AngularVelocity in _IMP_atom:
5696 _IMP_atom.AngularVelocity_swigregister(AngularVelocity)
5697 class MolecularDynamics(Simulator):
5698  r"""Proxy of C++ IMP::atom::MolecularDynamics class."""
5699 
5700  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5701 
5702  def __init__(self, m):
5703  r"""__init__(MolecularDynamics self, Model m) -> MolecularDynamics"""
5704  _IMP_atom.MolecularDynamics_swiginit(self, _IMP_atom.new_MolecularDynamics(m))
5705 
5706  def get_kinetic_energy(self):
5707  r"""get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
5708  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
5709 
5710  def get_kinetic_temperature(self, ekinetic):
5711  r"""get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
5712  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
5713 
5714  def set_velocity_cap(self, velocity_cap):
5715  r"""set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
5716  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
5717 
5718  def assign_velocities(self, temperature):
5719  r"""assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
5720  return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
5721 
5722  def setup(self, ps):
5723  r"""setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
5724  return _IMP_atom.MolecularDynamics_setup(self, ps)
5725 
5726  def do_step(self, sc, dt):
5727  r"""do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
5728  return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
5729 
5730  def get_is_simulation_particle(self, p):
5731  r"""get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
5732  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
5733 
5734  def get_version_info(self):
5735  r"""get_version_info(MolecularDynamics self) -> VersionInfo"""
5736  return _IMP_atom.MolecularDynamics_get_version_info(self)
5737  __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
5738 
5739  def __str__(self):
5740  r"""__str__(MolecularDynamics self) -> std::string"""
5741  return _IMP_atom.MolecularDynamics___str__(self)
5742 
5743  def __repr__(self):
5744  r"""__repr__(MolecularDynamics self) -> std::string"""
5745  return _IMP_atom.MolecularDynamics___repr__(self)
5746 
5747  @staticmethod
5748  def get_from(o):
5749  return _object_cast_to_MolecularDynamics(o)
5750 
5751 
5752 # Register MolecularDynamics in _IMP_atom:
5753 _IMP_atom.MolecularDynamics_swigregister(MolecularDynamics)
5754 class VelocityScalingOptimizerState(IMP.OptimizerState):
5755  r"""Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
5756 
5757  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5758 
5759  def __init__(self, m, pis, temperature):
5760  r"""__init__(VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
5761  _IMP_atom.VelocityScalingOptimizerState_swiginit(self, _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature))
5762 
5763  def set_particles(self, pis):
5764  r"""set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
5765  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
5766 
5767  def set_temperature(self, temperature):
5768  r"""set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
5769  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
5770 
5771  def rescale_velocities(self):
5772  r"""rescale_velocities(VelocityScalingOptimizerState self)"""
5773  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
5774 
5775  def get_version_info(self):
5776  r"""get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
5777  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
5778  __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
5779 
5780  def __str__(self):
5781  r"""__str__(VelocityScalingOptimizerState self) -> std::string"""
5782  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
5783 
5784  def __repr__(self):
5785  r"""__repr__(VelocityScalingOptimizerState self) -> std::string"""
5786  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
5787 
5788  @staticmethod
5789  def get_from(o):
5790  return _object_cast_to_VelocityScalingOptimizerState(o)
5791 
5792 
5793 # Register VelocityScalingOptimizerState in _IMP_atom:
5794 _IMP_atom.VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
5795 class Fragment(Hierarchy):
5796  r"""Proxy of C++ IMP::atom::Fragment class."""
5797 
5798  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
5799 
5800  def set_residue_indexes(self, o):
5801  r"""set_residue_indexes(Fragment self, IMP::Ints o)"""
5802  return _IMP_atom.Fragment_set_residue_indexes(self, o)
5803 
5804  def get_residue_indexes(self):
5805  r"""get_residue_indexes(Fragment self) -> IMP::Ints"""
5806  return _IMP_atom.Fragment_get_residue_indexes(self)
5807 
5808  def get_contains_residue(self, rindex):
5809  r"""get_contains_residue(Fragment self, int rindex) -> bool"""
5810  return _IMP_atom.Fragment_get_contains_residue(self, rindex)
5811 
5812  def get_contains_any_sorted_residue(self, rinds):
5813  r"""get_contains_any_sorted_residue(Fragment self, IMP::Ints const & rinds) -> bool"""
5814  return _IMP_atom.Fragment_get_contains_any_sorted_residue(self, rinds)
5815 
5816  def __init__(self, *args):
5817  r"""
5818  __init__(Fragment self) -> Fragment
5819  __init__(Fragment self, Model m, ParticleIndex id) -> Fragment
5820  __init__(Fragment self, _ParticleAdaptor d) -> Fragment
5821  """
5822  _IMP_atom.Fragment_swiginit(self, _IMP_atom.new_Fragment(*args))
5823 
5824  @staticmethod
5825  def get_is_setup(*args):
5826  r"""
5827  get_is_setup(Model m, ParticleIndex pi) -> bool
5828  get_is_setup(_ParticleAdaptor p) -> bool
5829  """
5830  return _IMP_atom.Fragment_get_is_setup(*args)
5831 
5832  def show(self, *args):
5833  r"""show(Fragment self, _ostream out=std::cout)"""
5834  return _IMP_atom.Fragment_show(self, *args)
5835 
5836  @staticmethod
5837  def setup_particle(*args):
5838  r"""
5839  setup_particle(Model m, ParticleIndex pi) -> Fragment
5840  setup_particle(_ParticleAdaptor pa) -> Fragment
5841  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
5842  setup_particle(_ParticleAdaptor pa, Fragment other) -> Fragment
5843  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
5844  setup_particle(_ParticleAdaptor pa, IMP::Ints residue_indexes) -> Fragment
5845  """
5846  return _IMP_atom.Fragment_setup_particle(*args)
5847 
5848  def add_attribute(self, *args):
5849  r"""
5850  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
5851  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
5852  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
5853  add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
5854  add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
5855  add_attribute(Fragment self, StringKey a0, IMP::String a1)
5856  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
5857  add_attribute(Fragment self, ObjectKey a0, Object a1)
5858  add_attribute(Fragment self, SparseFloatKey a0, IMP::Float a1)
5859  add_attribute(Fragment self, SparseIntKey a0, IMP::Int a1)
5860  add_attribute(Fragment self, SparseStringKey a0, IMP::String a1)
5861  add_attribute(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
5862  """
5863  return _IMP_atom.Fragment_add_attribute(self, *args)
5864 
5865  def get_value(self, *args):
5866  r"""
5867  get_value(Fragment self, FloatKey a0) -> IMP::Float
5868  get_value(Fragment self, IntKey a0) -> IMP::Int
5869  get_value(Fragment self, FloatsKey a0) -> IMP::Floats
5870  get_value(Fragment self, IntsKey a0) -> IMP::Ints
5871  get_value(Fragment self, StringKey a0) -> IMP::String
5872  get_value(Fragment self, ParticleIndexKey a0) -> Particle
5873  get_value(Fragment self, ObjectKey a0) -> Object
5874  get_value(Fragment self, SparseFloatKey a0) -> IMP::Float
5875  get_value(Fragment self, SparseIntKey a0) -> IMP::Int
5876  get_value(Fragment self, SparseStringKey a0) -> IMP::String
5877  get_value(Fragment self, SparseParticleIndexKey a0) -> ParticleIndex
5878  """
5879  return _IMP_atom.Fragment_get_value(self, *args)
5880 
5881  def set_value(self, *args):
5882  r"""
5883  set_value(Fragment self, FloatKey a0, IMP::Float a1)
5884  set_value(Fragment self, IntKey a0, IMP::Int a1)
5885  set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
5886  set_value(Fragment self, IntsKey a0, IMP::Ints a1)
5887  set_value(Fragment self, StringKey a0, IMP::String a1)
5888  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
5889  set_value(Fragment self, ObjectKey a0, Object a1)
5890  set_value(Fragment self, SparseFloatKey a0, IMP::Float a1)
5891  set_value(Fragment self, SparseIntKey a0, IMP::Int a1)
5892  set_value(Fragment self, SparseStringKey a0, IMP::String a1)
5893  set_value(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
5894  """
5895  return _IMP_atom.Fragment_set_value(self, *args)
5896 
5897  def remove_attribute(self, *args):
5898  r"""
5899  remove_attribute(Fragment self, FloatKey a0)
5900  remove_attribute(Fragment self, IntKey a0)
5901  remove_attribute(Fragment self, FloatsKey a0)
5902  remove_attribute(Fragment self, IntsKey a0)
5903  remove_attribute(Fragment self, StringKey a0)
5904  remove_attribute(Fragment self, ParticleIndexKey a0)
5905  remove_attribute(Fragment self, ObjectKey a0)
5906  remove_attribute(Fragment self, SparseFloatKey a0)
5907  remove_attribute(Fragment self, SparseIntKey a0)
5908  remove_attribute(Fragment self, SparseStringKey a0)
5909  remove_attribute(Fragment self, SparseParticleIndexKey a0)
5910  """
5911  return _IMP_atom.Fragment_remove_attribute(self, *args)
5912 
5913  def has_attribute(self, *args):
5914  r"""
5915  has_attribute(Fragment self, FloatKey a0) -> bool
5916  has_attribute(Fragment self, IntKey a0) -> bool
5917  has_attribute(Fragment self, FloatsKey a0) -> bool
5918  has_attribute(Fragment self, IntsKey a0) -> bool
5919  has_attribute(Fragment self, StringKey a0) -> bool
5920  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
5921  has_attribute(Fragment self, ObjectKey a0) -> bool
5922  has_attribute(Fragment self, SparseFloatKey a0) -> bool
5923  has_attribute(Fragment self, SparseIntKey a0) -> bool
5924  has_attribute(Fragment self, SparseStringKey a0) -> bool
5925  has_attribute(Fragment self, SparseParticleIndexKey a0) -> bool
5926  """
5927  return _IMP_atom.Fragment_has_attribute(self, *args)
5928 
5929  def get_derivative(self, a0):
5930  r"""get_derivative(Fragment self, FloatKey a0) -> double"""
5931  return _IMP_atom.Fragment_get_derivative(self, a0)
5932 
5933  def get_name(self):
5934  r"""get_name(Fragment self) -> std::string"""
5935  return _IMP_atom.Fragment_get_name(self)
5936 
5937  def clear_caches(self):
5938  r"""clear_caches(Fragment self)"""
5939  return _IMP_atom.Fragment_clear_caches(self)
5940 
5941  def set_name(self, a0):
5942  r"""set_name(Fragment self, std::string a0)"""
5943  return _IMP_atom.Fragment_set_name(self, a0)
5944 
5945  def set_check_level(self, a0):
5946  r"""set_check_level(Fragment self, IMP::CheckLevel a0)"""
5947  return _IMP_atom.Fragment_set_check_level(self, a0)
5948 
5949  def add_to_derivative(self, a0, a1, a2):
5950  r"""add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5951  return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
5952 
5953  def set_is_optimized(self, a0, a1):
5954  r"""set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
5955  return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
5956 
5957  def get_is_optimized(self, a0):
5958  r"""get_is_optimized(Fragment self, FloatKey a0) -> bool"""
5959  return _IMP_atom.Fragment_get_is_optimized(self, a0)
5960 
5961  def get_check_level(self):
5962  r"""get_check_level(Fragment self) -> IMP::CheckLevel"""
5963  return _IMP_atom.Fragment_get_check_level(self)
5964 
5965  def __eq__(self, *args):
5966  r"""
5967  __eq__(Fragment self, Fragment o) -> bool
5968  __eq__(Fragment self, Particle d) -> bool
5969  """
5970  return _IMP_atom.Fragment___eq__(self, *args)
5971 
5972  def __ne__(self, *args):
5973  r"""
5974  __ne__(Fragment self, Fragment o) -> bool
5975  __ne__(Fragment self, Particle d) -> bool
5976  """
5977  return _IMP_atom.Fragment___ne__(self, *args)
5978 
5979  def __le__(self, *args):
5980  r"""
5981  __le__(Fragment self, Fragment o) -> bool
5982  __le__(Fragment self, Particle d) -> bool
5983  """
5984  return _IMP_atom.Fragment___le__(self, *args)
5985 
5986  def __lt__(self, *args):
5987  r"""
5988  __lt__(Fragment self, Fragment o) -> bool
5989  __lt__(Fragment self, Particle d) -> bool
5990  """
5991  return _IMP_atom.Fragment___lt__(self, *args)
5992 
5993  def __ge__(self, *args):
5994  r"""
5995  __ge__(Fragment self, Fragment o) -> bool
5996  __ge__(Fragment self, Particle d) -> bool
5997  """
5998  return _IMP_atom.Fragment___ge__(self, *args)
5999 
6000  def __gt__(self, *args):
6001  r"""
6002  __gt__(Fragment self, Fragment o) -> bool
6003  __gt__(Fragment self, Particle d) -> bool
6004  """
6005  return _IMP_atom.Fragment___gt__(self, *args)
6006 
6007  def __hash__(self):
6008  r"""__hash__(Fragment self) -> std::size_t"""
6009  return _IMP_atom.Fragment___hash__(self)
6010 
6011  def __str__(self):
6012  r"""__str__(Fragment self) -> std::string"""
6013  return _IMP_atom.Fragment___str__(self)
6014 
6015  def __repr__(self):
6016  r"""__repr__(Fragment self) -> std::string"""
6017  return _IMP_atom.Fragment___repr__(self)
6018 
6019  def _get_as_binary(self):
6020  r"""_get_as_binary(Fragment self) -> PyObject *"""
6021  return _IMP_atom.Fragment__get_as_binary(self)
6022 
6023  def _set_from_binary(self, p):
6024  r"""_set_from_binary(Fragment self, PyObject * p)"""
6025  return _IMP_atom.Fragment__set_from_binary(self, p)
6026 
6027  def __getstate__(self):
6028  p = self._get_as_binary()
6029  if len(self.__dict__) > 1:
6030  d = self.__dict__.copy()
6031  del d['this']
6032  p = (d, p)
6033  return p
6034 
6035  def __setstate__(self, p):
6036  if not hasattr(self, 'this'):
6037  self.__init__()
6038  if isinstance(p, tuple):
6039  d, p = p
6040  self.__dict__.update(d)
6041  return self._set_from_binary(p)
6042 
6043  __swig_destroy__ = _IMP_atom.delete_Fragment
6044 
6045 # Register Fragment in _IMP_atom:
6046 _IMP_atom.Fragment_swigregister(Fragment)
6047 class StereochemistryPairFilter(IMP.PairPredicate):
6048  r"""Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6049 
6050  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6051 
6052  def __init__(self):
6053  r"""__init__(StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6054  _IMP_atom.StereochemistryPairFilter_swiginit(self, _IMP_atom.new_StereochemistryPairFilter())
6055 
6056  def set_bonds(self, bonds):
6057  r"""set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6058  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6059 
6060  def set_angles(self, angles):
6061  r"""set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6062  return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6063 
6064  def set_dihedrals(self, dihedrals):
6065  r"""set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6066  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6067 
6068  def do_get_inputs(self, m, pis):
6069  r"""do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6070  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6071 
6072  def get_value(self, *args):
6073  r"""
6074  get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6075  get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6076  """
6077  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6078 
6079  def get_value_index(self, *args):
6080  r"""
6081  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6082  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6083  """
6084  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6085 
6086  def get_version_info(self):
6087  r"""get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6088  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6089  __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
6090 
6091  def __str__(self):
6092  r"""__str__(StereochemistryPairFilter self) -> std::string"""
6093  return _IMP_atom.StereochemistryPairFilter___str__(self)
6094 
6095  def __repr__(self):
6096  r"""__repr__(StereochemistryPairFilter self) -> std::string"""
6097  return _IMP_atom.StereochemistryPairFilter___repr__(self)
6098 
6099  @staticmethod
6100  def get_from(o):
6101  return _object_cast_to_StereochemistryPairFilter(o)
6102 
6103 
6104 # Register StereochemistryPairFilter in _IMP_atom:
6105 _IMP_atom.StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6106 class SoapPairFilter(IMP.PairPredicate):
6107  r"""Proxy of C++ IMP::atom::SoapPairFilter class."""
6108 
6109  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6110 
6111  def __init__(self, library):
6112  r"""__init__(SoapPairFilter self, std::string library) -> SoapPairFilter"""
6113  _IMP_atom.SoapPairFilter_swiginit(self, _IMP_atom.new_SoapPairFilter(library))
6114 
6115  def do_get_inputs(self, m, pis):
6116  r"""do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6117  return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6118 
6119  def get_value(self, *args):
6120  r"""
6121  get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6122  get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6123  """
6124  return _IMP_atom.SoapPairFilter_get_value(self, *args)
6125 
6126  def get_value_index(self, *args):
6127  r"""
6128  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6129  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6130  """
6131  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6132 
6133  def get_version_info(self):
6134  r"""get_version_info(SoapPairFilter self) -> VersionInfo"""
6135  return _IMP_atom.SoapPairFilter_get_version_info(self)
6136  __swig_destroy__ = _IMP_atom.delete_SoapPairFilter
6137 
6138  def __str__(self):
6139  r"""__str__(SoapPairFilter self) -> std::string"""
6140  return _IMP_atom.SoapPairFilter___str__(self)
6141 
6142  def __repr__(self):
6143  r"""__repr__(SoapPairFilter self) -> std::string"""
6144  return _IMP_atom.SoapPairFilter___repr__(self)
6145 
6146  @staticmethod
6147  def get_from(o):
6148  return _object_cast_to_SoapPairFilter(o)
6149 
6150 
6151 # Register SoapPairFilter in _IMP_atom:
6152 _IMP_atom.SoapPairFilter_swigregister(SoapPairFilter)
6153 class Mass(IMP.Decorator):
6154  r"""Proxy of C++ IMP::atom::Mass class."""
6155 
6156  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6157 
6158  def get_mass(self):
6159  r"""get_mass(Mass self) -> IMP::Float"""
6160  return _IMP_atom.Mass_get_mass(self)
6161 
6162  def set_mass(self, d):
6163  r"""set_mass(Mass self, IMP::Float d)"""
6164  return _IMP_atom.Mass_set_mass(self, d)
6165 
6166  def __init__(self, *args):
6167  r"""
6168  __init__(Mass self) -> Mass
6169  __init__(Mass self, Model m, ParticleIndex id) -> Mass
6170  __init__(Mass self, _ParticleAdaptor d) -> Mass
6171  """
6172  _IMP_atom.Mass_swiginit(self, _IMP_atom.new_Mass(*args))
6173 
6174  @staticmethod
6175  def get_is_setup(*args):
6176  r"""
6177  get_is_setup(Model m, ParticleIndex pi) -> bool
6178  get_is_setup(_ParticleAdaptor p) -> bool
6179  """
6180  return _IMP_atom.Mass_get_is_setup(*args)
6181 
6182  def show(self, *args):
6183  r"""show(Mass self, _ostream out=std::cout)"""
6184  return _IMP_atom.Mass_show(self, *args)
6185 
6186  @staticmethod
6187  def setup_particle(*args):
6188  r"""
6189  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6190  setup_particle(_ParticleAdaptor pa, IMP::Float mass) -> Mass
6191  setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6192  setup_particle(_ParticleAdaptor pa, Mass other) -> Mass
6193  """
6194  return _IMP_atom.Mass_setup_particle(*args)
6195 
6196  @staticmethod
6197  def get_mass_key():
6198  r"""get_mass_key() -> FloatKey"""
6199  return _IMP_atom.Mass_get_mass_key()
6200 
6201  def add_attribute(self, *args):
6202  r"""
6203  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6204  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6205  add_attribute(Mass self, IntKey a0, IMP::Int a1)
6206  add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6207  add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6208  add_attribute(Mass self, StringKey a0, IMP::String a1)
6209  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6210  add_attribute(Mass self, ObjectKey a0, Object a1)
6211  add_attribute(Mass self, SparseFloatKey a0, IMP::Float a1)
6212  add_attribute(Mass self, SparseIntKey a0, IMP::Int a1)
6213  add_attribute(Mass self, SparseStringKey a0, IMP::String a1)
6214  add_attribute(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6215  """
6216  return _IMP_atom.Mass_add_attribute(self, *args)
6217 
6218  def get_value(self, *args):
6219  r"""
6220  get_value(Mass self, FloatKey a0) -> IMP::Float
6221  get_value(Mass self, IntKey a0) -> IMP::Int
6222  get_value(Mass self, FloatsKey a0) -> IMP::Floats
6223  get_value(Mass self, IntsKey a0) -> IMP::Ints
6224  get_value(Mass self, StringKey a0) -> IMP::String
6225  get_value(Mass self, ParticleIndexKey a0) -> Particle
6226  get_value(Mass self, ObjectKey a0) -> Object
6227  get_value(Mass self, SparseFloatKey a0) -> IMP::Float
6228  get_value(Mass self, SparseIntKey a0) -> IMP::Int
6229  get_value(Mass self, SparseStringKey a0) -> IMP::String
6230  get_value(Mass self, SparseParticleIndexKey a0) -> ParticleIndex
6231  """
6232  return _IMP_atom.Mass_get_value(self, *args)
6233 
6234  def set_value(self, *args):
6235  r"""
6236  set_value(Mass self, FloatKey a0, IMP::Float a1)
6237  set_value(Mass self, IntKey a0, IMP::Int a1)
6238  set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6239  set_value(Mass self, IntsKey a0, IMP::Ints a1)
6240  set_value(Mass self, StringKey a0, IMP::String a1)
6241  set_value(Mass self, ParticleIndexKey a0, Particle a1)
6242  set_value(Mass self, ObjectKey a0, Object a1)
6243  set_value(Mass self, SparseFloatKey a0, IMP::Float a1)
6244  set_value(Mass self, SparseIntKey a0, IMP::Int a1)
6245  set_value(Mass self, SparseStringKey a0, IMP::String a1)
6246  set_value(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6247  """
6248  return _IMP_atom.Mass_set_value(self, *args)
6249 
6250  def remove_attribute(self, *args):
6251  r"""
6252  remove_attribute(Mass self, FloatKey a0)
6253  remove_attribute(Mass self, IntKey a0)
6254  remove_attribute(Mass self, FloatsKey a0)
6255  remove_attribute(Mass self, IntsKey a0)
6256  remove_attribute(Mass self, StringKey a0)
6257  remove_attribute(Mass self, ParticleIndexKey a0)
6258  remove_attribute(Mass self, ObjectKey a0)
6259  remove_attribute(Mass self, SparseFloatKey a0)
6260  remove_attribute(Mass self, SparseIntKey a0)
6261  remove_attribute(Mass self, SparseStringKey a0)
6262  remove_attribute(Mass self, SparseParticleIndexKey a0)
6263  """
6264  return _IMP_atom.Mass_remove_attribute(self, *args)
6265 
6266  def has_attribute(self, *args):
6267  r"""
6268  has_attribute(Mass self, FloatKey a0) -> bool
6269  has_attribute(Mass self, IntKey a0) -> bool
6270  has_attribute(Mass self, FloatsKey a0) -> bool
6271  has_attribute(Mass self, IntsKey a0) -> bool
6272  has_attribute(Mass self, StringKey a0) -> bool
6273  has_attribute(Mass self, ParticleIndexKey a0) -> bool
6274  has_attribute(Mass self, ObjectKey a0) -> bool
6275  has_attribute(Mass self, SparseFloatKey a0) -> bool
6276  has_attribute(Mass self, SparseIntKey a0) -> bool
6277  has_attribute(Mass self, SparseStringKey a0) -> bool
6278  has_attribute(Mass self, SparseParticleIndexKey a0) -> bool
6279  """
6280  return _IMP_atom.Mass_has_attribute(self, *args)
6281 
6282  def get_derivative(self, a0):
6283  r"""get_derivative(Mass self, FloatKey a0) -> double"""
6284  return _IMP_atom.Mass_get_derivative(self, a0)
6285 
6286  def get_name(self):
6287  r"""get_name(Mass self) -> std::string"""
6288  return _IMP_atom.Mass_get_name(self)
6289 
6290  def clear_caches(self):
6291  r"""clear_caches(Mass self)"""
6292  return _IMP_atom.Mass_clear_caches(self)
6293 
6294  def set_name(self, a0):
6295  r"""set_name(Mass self, std::string a0)"""
6296  return _IMP_atom.Mass_set_name(self, a0)
6297 
6298  def set_check_level(self, a0):
6299  r"""set_check_level(Mass self, IMP::CheckLevel a0)"""
6300  return _IMP_atom.Mass_set_check_level(self, a0)
6301 
6302  def add_to_derivative(self, a0, a1, a2):
6303  r"""add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6304  return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6305 
6306  def set_is_optimized(self, a0, a1):
6307  r"""set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6308  return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6309 
6310  def get_is_optimized(self, a0):
6311  r"""get_is_optimized(Mass self, FloatKey a0) -> bool"""
6312  return _IMP_atom.Mass_get_is_optimized(self, a0)
6313 
6314  def get_check_level(self):
6315  r"""get_check_level(Mass self) -> IMP::CheckLevel"""
6316  return _IMP_atom.Mass_get_check_level(self)
6317 
6318  def __eq__(self, *args):
6319  r"""
6320  __eq__(Mass self, Mass o) -> bool
6321  __eq__(Mass self, Particle d) -> bool
6322  """
6323  return _IMP_atom.Mass___eq__(self, *args)
6324 
6325  def __ne__(self, *args):
6326  r"""
6327  __ne__(Mass self, Mass o) -> bool
6328  __ne__(Mass self, Particle d) -> bool
6329  """
6330  return _IMP_atom.Mass___ne__(self, *args)
6331 
6332  def __le__(self, *args):
6333  r"""
6334  __le__(Mass self, Mass o) -> bool
6335  __le__(Mass self, Particle d) -> bool
6336  """
6337  return _IMP_atom.Mass___le__(self, *args)
6338 
6339  def __lt__(self, *args):
6340  r"""
6341  __lt__(Mass self, Mass o) -> bool
6342  __lt__(Mass self, Particle d) -> bool
6343  """
6344  return _IMP_atom.Mass___lt__(self, *args)
6345 
6346  def __ge__(self, *args):
6347  r"""
6348  __ge__(Mass self, Mass o) -> bool
6349  __ge__(Mass self, Particle d) -> bool
6350  """
6351  return _IMP_atom.Mass___ge__(self, *args)
6352 
6353  def __gt__(self, *args):
6354  r"""
6355  __gt__(Mass self, Mass o) -> bool
6356  __gt__(Mass self, Particle d) -> bool
6357  """
6358  return _IMP_atom.Mass___gt__(self, *args)
6359 
6360  def __hash__(self):
6361  r"""__hash__(Mass self) -> std::size_t"""
6362  return _IMP_atom.Mass___hash__(self)
6363 
6364  def __str__(self):
6365  r"""__str__(Mass self) -> std::string"""
6366  return _IMP_atom.Mass___str__(self)
6367 
6368  def __repr__(self):
6369  r"""__repr__(Mass self) -> std::string"""
6370  return _IMP_atom.Mass___repr__(self)
6371 
6372  def _get_as_binary(self):
6373  r"""_get_as_binary(Mass self) -> PyObject *"""
6374  return _IMP_atom.Mass__get_as_binary(self)
6375 
6376  def _set_from_binary(self, p):
6377  r"""_set_from_binary(Mass self, PyObject * p)"""
6378  return _IMP_atom.Mass__set_from_binary(self, p)
6379 
6380  def __getstate__(self):
6381  p = self._get_as_binary()
6382  if len(self.__dict__) > 1:
6383  d = self.__dict__.copy()
6384  del d['this']
6385  p = (d, p)
6386  return p
6387 
6388  def __setstate__(self, p):
6389  if not hasattr(self, 'this'):
6390  self.__init__()
6391  if isinstance(p, tuple):
6392  d, p = p
6393  self.__dict__.update(d)
6394  return self._set_from_binary(p)
6395 
6396  __swig_destroy__ = _IMP_atom.delete_Mass
6397 
6398 # Register Mass in _IMP_atom:
6399 _IMP_atom.Mass_swigregister(Mass)
6400 class BondedPairFilter(IMP.PairPredicate):
6401  r"""Proxy of C++ IMP::atom::BondedPairFilter class."""
6402 
6403  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6404 
6405  def __init__(self):
6406  r"""__init__(BondedPairFilter self) -> BondedPairFilter"""
6407  _IMP_atom.BondedPairFilter_swiginit(self, _IMP_atom.new_BondedPairFilter())
6408 
6409  def do_get_inputs(self, m, pis):
6410  r"""do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6411  return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6412 
6413  def get_value(self, *args):
6414  r"""
6415  get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6416  get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6417  """
6418  return _IMP_atom.BondedPairFilter_get_value(self, *args)
6419 
6420  def get_value_index(self, *args):
6421  r"""
6422  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6423  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6424  """
6425  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6426 
6427  def get_version_info(self):
6428  r"""get_version_info(BondedPairFilter self) -> VersionInfo"""
6429  return _IMP_atom.BondedPairFilter_get_version_info(self)
6430  __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
6431 
6432  def __str__(self):
6433  r"""__str__(BondedPairFilter self) -> std::string"""
6434  return _IMP_atom.BondedPairFilter___str__(self)
6435 
6436  def __repr__(self):
6437  r"""__repr__(BondedPairFilter self) -> std::string"""
6438  return _IMP_atom.BondedPairFilter___repr__(self)
6439 
6440  @staticmethod
6441  def get_from(o):
6442  return _object_cast_to_BondedPairFilter(o)
6443 
6444 
6445 # Register BondedPairFilter in _IMP_atom:
6446 _IMP_atom.BondedPairFilter_swigregister(BondedPairFilter)
6447 class Mol2Selector(IMP.Object):
6448  r"""Proxy of C++ IMP::atom::Mol2Selector class."""
6449 
6450  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6451 
6452  def __init__(self, *args, **kwargs):
6453  raise AttributeError("No constructor defined - class is abstract")
6454 
6455  def get_is_selected(self, atom_line):
6456  r"""get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6457  return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6458  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6459 
6460  def __str__(self):
6461  r"""__str__(Mol2Selector self) -> std::string"""
6462  return _IMP_atom.Mol2Selector___str__(self)
6463 
6464  def __repr__(self):
6465  r"""__repr__(Mol2Selector self) -> std::string"""
6466  return _IMP_atom.Mol2Selector___repr__(self)
6467 
6468  @staticmethod
6469  def get_from(o):
6470  return _object_cast_to_Mol2Selector(o)
6471 
6472 
6473 # Register Mol2Selector in _IMP_atom:
6474 _IMP_atom.Mol2Selector_swigregister(Mol2Selector)
6475 class AllMol2Selector(Mol2Selector):
6476  r"""Proxy of C++ IMP::atom::AllMol2Selector class."""
6477 
6478  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6479 
6480  def __str__(self):
6481  r"""__str__(AllMol2Selector self) -> std::string"""
6482  return _IMP_atom.AllMol2Selector___str__(self)
6483 
6484  def __repr__(self):
6485  r"""__repr__(AllMol2Selector self) -> std::string"""
6486  return _IMP_atom.AllMol2Selector___repr__(self)
6487 
6488  @staticmethod
6489  def get_from(o):
6490  return _object_cast_to_AllMol2Selector(o)
6491 
6492 
6493  def __init__(self):
6494  r"""__init__(AllMol2Selector self) -> AllMol2Selector"""
6495  _IMP_atom.AllMol2Selector_swiginit(self, _IMP_atom.new_AllMol2Selector())
6496  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6497 
6498 # Register AllMol2Selector in _IMP_atom:
6499 _IMP_atom.AllMol2Selector_swigregister(AllMol2Selector)
6500 class NonHydrogenMol2Selector(Mol2Selector):
6501  r"""Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6502 
6503  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6504 
6505  def __str__(self):
6506  r"""__str__(NonHydrogenMol2Selector self) -> std::string"""
6507  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6508 
6509  def __repr__(self):
6510  r"""__repr__(NonHydrogenMol2Selector self) -> std::string"""
6511  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6512 
6513  @staticmethod
6514  def get_from(o):
6515  return _object_cast_to_NonHydrogenMol2Selector(o)
6516 
6517 
6518  def __init__(self):
6519  r"""__init__(NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6520  _IMP_atom.NonHydrogenMol2Selector_swiginit(self, _IMP_atom.new_NonHydrogenMol2Selector())
6521  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6522 
6523 # Register NonHydrogenMol2Selector in _IMP_atom:
6524 _IMP_atom.NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
6525 
6526 def read_mol2(mol2_file, model, mol2sel=None):
6527  r"""read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy"""
6528  return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
6529 
6530 def write_mol2(rhd, file_name):
6531  r"""write_mol2(Hierarchy rhd, TextOutput file_name)"""
6532  return _IMP_atom.write_mol2(rhd, file_name)
6533 class SecondaryStructureResidue(IMP.Decorator):
6534  r"""Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
6535 
6536  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6537 
6538  def __init__(self, *args):
6539  r"""
6540  __init__(SecondaryStructureResidue self) -> SecondaryStructureResidue
6541  __init__(SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
6542  __init__(SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
6543  """
6544  _IMP_atom.SecondaryStructureResidue_swiginit(self, _IMP_atom.new_SecondaryStructureResidue(*args))
6545 
6546  def show(self, *args):
6547  r"""show(SecondaryStructureResidue self, _ostream out=std::cout)"""
6548  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
6549 
6550  @staticmethod
6551  def setup_particle(*args):
6552  r"""
6553  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6554  setup_particle(_ParticleAdaptor pa, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6555  setup_particle(Particle res_p) -> SecondaryStructureResidue
6556  """
6557  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
6558 
6559  @staticmethod
6560  def get_is_setup(*args):
6561  r"""
6562  get_is_setup(_ParticleAdaptor p) -> bool
6563  get_is_setup(Model m, ParticleIndex pi) -> bool
6564  """
6565  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
6566 
6567  def get_particle(self):
6568  r"""get_particle(SecondaryStructureResidue self) -> Particle"""
6569  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
6570 
6571  def get_all_probabilities(self):
6572  r"""get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
6573  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
6574 
6575  def get_prob_helix(self):
6576  r"""get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
6577  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
6578 
6579  def set_prob_helix(self, t):
6580  r"""set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
6581  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
6582 
6583  def get_prob_strand(self):
6584  r"""get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
6585  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
6586 
6587  def set_prob_strand(self, t):
6588  r"""set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
6589  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
6590 
6591  def get_prob_coil(self):
6592  r"""get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
6593  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
6594 
6595  def set_prob_coil(self, t):
6596  r"""set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
6597  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
6598 
6599  @staticmethod
6600  def get_prob_helix_key():
6601  r"""get_prob_helix_key() -> FloatKey"""
6602  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
6603 
6604  @staticmethod
6605  def get_prob_strand_key():
6606  r"""get_prob_strand_key() -> FloatKey"""
6607  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
6608 
6609  @staticmethod
6610  def get_prob_coil_key():
6611  r"""get_prob_coil_key() -> FloatKey"""
6612  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
6613 
6614  def add_attribute(self, *args):
6615  r"""
6616  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
6617  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6618  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6619  add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6620  add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6621  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6622  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6623  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6624  add_attribute(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
6625  add_attribute(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
6626  add_attribute(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
6627  add_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
6628  """
6629  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
6630 
6631  def get_value(self, *args):
6632  r"""
6633  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
6634  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
6635  get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
6636  get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
6637  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
6638  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
6639  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
6640  get_value(SecondaryStructureResidue self, SparseFloatKey a0) -> IMP::Float
6641  get_value(SecondaryStructureResidue self, SparseIntKey a0) -> IMP::Int
6642  get_value(SecondaryStructureResidue self, SparseStringKey a0) -> IMP::String
6643  get_value(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> ParticleIndex
6644  """
6645  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
6646 
6647  def set_value(self, *args):
6648  r"""
6649  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6650  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6651  set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6652  set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6653  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6654  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6655  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6656  set_value(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
6657  set_value(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
6658  set_value(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
6659  set_value(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
6660  """
6661  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
6662 
6663  def remove_attribute(self, *args):
6664  r"""
6665  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
6666  remove_attribute(SecondaryStructureResidue self, IntKey a0)
6667  remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
6668  remove_attribute(SecondaryStructureResidue self, IntsKey a0)
6669  remove_attribute(SecondaryStructureResidue self, StringKey a0)
6670  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
6671  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
6672  remove_attribute(SecondaryStructureResidue self, SparseFloatKey a0)
6673  remove_attribute(SecondaryStructureResidue self, SparseIntKey a0)
6674  remove_attribute(SecondaryStructureResidue self, SparseStringKey a0)
6675  remove_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0)
6676  """
6677  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
6678 
6679  def has_attribute(self, *args):
6680  r"""
6681  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
6682  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
6683  has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
6684  has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
6685  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
6686  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
6687  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
6688  has_attribute(SecondaryStructureResidue self, SparseFloatKey a0) -> bool
6689  has_attribute(SecondaryStructureResidue self, SparseIntKey a0) -> bool
6690  has_attribute(SecondaryStructureResidue self, SparseStringKey a0) -> bool
6691  has_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> bool
6692  """
6693  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
6694 
6695  def get_derivative(self, a0):
6696  r"""get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
6697  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
6698 
6699  def get_name(self):
6700  r"""get_name(SecondaryStructureResidue self) -> std::string"""
6701  return _IMP_atom.SecondaryStructureResidue_get_name(self)
6702 
6703  def clear_caches(self):
6704  r"""clear_caches(SecondaryStructureResidue self)"""
6705  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
6706 
6707  def set_name(self, a0):
6708  r"""set_name(SecondaryStructureResidue self, std::string a0)"""
6709  return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
6710 
6711  def set_check_level(self, a0):
6712  r"""set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
6713  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
6714 
6715  def add_to_derivative(self, a0, a1, a2):
6716  r"""add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6717  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
6718 
6719  def set_is_optimized(self, a0, a1):
6720  r"""set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
6721  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
6722 
6723  def get_is_optimized(self, a0):
6724  r"""get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
6725  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
6726 
6727  def get_check_level(self):
6728  r"""get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
6729  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
6730 
6731  def __eq__(self, *args):
6732  r"""
6733  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6734  __eq__(SecondaryStructureResidue self, Particle d) -> bool
6735  """
6736  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
6737 
6738  def __ne__(self, *args):
6739  r"""
6740  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6741  __ne__(SecondaryStructureResidue self, Particle d) -> bool
6742  """
6743  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
6744 
6745  def __le__(self, *args):
6746  r"""
6747  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6748  __le__(SecondaryStructureResidue self, Particle d) -> bool
6749  """
6750  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
6751 
6752  def __lt__(self, *args):
6753  r"""
6754  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6755  __lt__(SecondaryStructureResidue self, Particle d) -> bool
6756  """
6757  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
6758 
6759  def __ge__(self, *args):
6760  r"""
6761  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6762  __ge__(SecondaryStructureResidue self, Particle d) -> bool
6763  """
6764  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
6765 
6766  def __gt__(self, *args):
6767  r"""
6768  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6769  __gt__(SecondaryStructureResidue self, Particle d) -> bool
6770  """
6771  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
6772 
6773  def __hash__(self):
6774  r"""__hash__(SecondaryStructureResidue self) -> std::size_t"""
6775  return _IMP_atom.SecondaryStructureResidue___hash__(self)
6776 
6777  def __str__(self):
6778  r"""__str__(SecondaryStructureResidue self) -> std::string"""
6779  return _IMP_atom.SecondaryStructureResidue___str__(self)
6780 
6781  def __repr__(self):
6782  r"""__repr__(SecondaryStructureResidue self) -> std::string"""
6783  return _IMP_atom.SecondaryStructureResidue___repr__(self)
6784 
6785  def _get_as_binary(self):
6786  r"""_get_as_binary(SecondaryStructureResidue self) -> PyObject *"""
6787  return _IMP_atom.SecondaryStructureResidue__get_as_binary(self)
6788 
6789  def _set_from_binary(self, p):
6790  r"""_set_from_binary(SecondaryStructureResidue self, PyObject * p)"""
6791  return _IMP_atom.SecondaryStructureResidue__set_from_binary(self, p)
6792 
6793  def __getstate__(self):
6794  p = self._get_as_binary()
6795  if len(self.__dict__) > 1:
6796  d = self.__dict__.copy()
6797  del d['this']
6798  p = (d, p)
6799  return p
6800 
6801  def __setstate__(self, p):
6802  if not hasattr(self, 'this'):
6803  self.__init__()
6804  if isinstance(p, tuple):
6805  d, p = p
6806  self.__dict__.update(d)
6807  return self._set_from_binary(p)
6808 
6809  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
6810 
6811 # Register SecondaryStructureResidue in _IMP_atom:
6812 _IMP_atom.SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
6813 
6814 def setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res=False):
6815  r"""setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue"""
6816  return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
6817 
6818 def setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res=False):
6819  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"""
6820  return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
6821 
6822 def get_secondary_structure_match_score(ssr1, ssr2):
6823  r"""get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
6824  return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
6825 
6826 def read_psipred(*args):
6827  r"""
6828  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
6829  read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
6830  """
6831  return _IMP_atom.read_psipred(*args)
6832 class _ADopeBase(IMP.PairScore):
6833  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Dope > class."""
6834 
6835  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6836  __repr__ = _swig_repr
6837 
6838  def __init__(self, *args):
6839  r"""
6840  __init__(_ADopeBase self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
6841  __init__(_ADopeBase self) -> _ADopeBase
6842  """
6843  _IMP_atom._ADopeBase_swiginit(self, _IMP_atom.new__ADopeBase(*args))
6844 
6845  def do_get_inputs(self, m, pis):
6846  r"""do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6847  return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
6848 
6849  def get_score_functor(self):
6850  r"""get_score_functor(_ADopeBase self) -> Dope"""
6851  return _IMP_atom._ADopeBase_get_score_functor(self)
6852 
6853  def get_version_info(self):
6854  r"""get_version_info(_ADopeBase self) -> VersionInfo"""
6855  return _IMP_atom._ADopeBase_get_version_info(self)
6856  __swig_destroy__ = _IMP_atom.delete__ADopeBase
6857 
6858 # Register _ADopeBase in _IMP_atom:
6859 _IMP_atom._ADopeBase_swigregister(_ADopeBase)
6860 class _BDopeBase(IMP.PairScore):
6861  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > > class."""
6862 
6863  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6864  __repr__ = _swig_repr
6865 
6866  def __init__(self, *args):
6867  r"""
6868  __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
6869  __init__(_BDopeBase self) -> _BDopeBase
6870  """
6871  _IMP_atom._BDopeBase_swiginit(self, _IMP_atom.new__BDopeBase(*args))
6872 
6873  def do_get_inputs(self, m, pis):
6874  r"""do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6875  return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
6876 
6877  def get_score_functor(self):
6878  r"""get_score_functor(_BDopeBase self) -> _DopeBase"""
6879  return _IMP_atom._BDopeBase_get_score_functor(self)
6880 
6881  def get_version_info(self):
6882  r"""get_version_info(_BDopeBase self) -> VersionInfo"""
6883  return _IMP_atom._BDopeBase_get_version_info(self)
6884  __swig_destroy__ = _IMP_atom.delete__BDopeBase
6885 
6886 # Register _BDopeBase in _IMP_atom:
6887 _IMP_atom._BDopeBase_swigregister(_BDopeBase)
6888 class _ALoopStatisticalBase(IMP.PairScore):
6889  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::LoopStatistical > class."""
6890 
6891  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6892  __repr__ = _swig_repr
6893 
6894  def __init__(self, *args):
6895  r"""
6896  __init__(_ALoopStatisticalBase self, LoopStatistical t0, std::string name="FunctorDistancePairScore %1%") -> _ALoopStatisticalBase
6897  __init__(_ALoopStatisticalBase self) -> _ALoopStatisticalBase
6898  """
6899  _IMP_atom._ALoopStatisticalBase_swiginit(self, _IMP_atom.new__ALoopStatisticalBase(*args))
6900 
6901  def do_get_inputs(self, m, pis):
6902  r"""do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6903  return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
6904 
6905  def get_score_functor(self):
6906  r"""get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
6907  return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
6908 
6909  def get_version_info(self):
6910  r"""get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
6911  return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
6912  __swig_destroy__ = _IMP_atom.delete__ALoopStatisticalBase
6913 
6914 # Register _ALoopStatisticalBase in _IMP_atom:
6915 _IMP_atom._ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
6916 class _BLoopStatisticalBase(IMP.PairScore):
6917  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > > class."""
6918 
6919  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6920  __repr__ = _swig_repr
6921 
6922  def __init__(self, *args):
6923  r"""
6924  __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
6925  __init__(_BLoopStatisticalBase self) -> _BLoopStatisticalBase
6926  """
6927  _IMP_atom._BLoopStatisticalBase_swiginit(self, _IMP_atom.new__BLoopStatisticalBase(*args))
6928 
6929  def do_get_inputs(self, m, pis):
6930  r"""do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6931  return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
6932 
6933  def get_score_functor(self):
6934  r"""get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
6935  return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
6936 
6937  def get_version_info(self):
6938  r"""get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
6939  return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
6940  __swig_destroy__ = _IMP_atom.delete__BLoopStatisticalBase
6941 
6942 # Register _BLoopStatisticalBase in _IMP_atom:
6943 _IMP_atom._BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
6944 class _OrientedSoapBase(IMP.PairScore):
6945  r"""Proxy of C++ IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap > class."""
6946 
6947  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6948  __repr__ = _swig_repr
6949 
6950  def __init__(self, *args):
6951  r"""__init__(_OrientedSoapBase self, IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name="FunctorDistancePairScoreWithCache %1%") -> _OrientedSoapBase"""
6952  _IMP_atom._OrientedSoapBase_swiginit(self, _IMP_atom.new__OrientedSoapBase(*args))
6953 
6954  def do_get_inputs(self, m, pis):
6955  r"""do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6956  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
6957 
6958  def get_score_functor(self):
6959  r"""get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
6960  return _IMP_atom._OrientedSoapBase_get_score_functor(self)
6961 
6962  def get_version_info(self):
6963  r"""get_version_info(_OrientedSoapBase self) -> VersionInfo"""
6964  return _IMP_atom._OrientedSoapBase_get_version_info(self)
6965  __swig_destroy__ = _IMP_atom.delete__OrientedSoapBase
6966 
6967 # Register _OrientedSoapBase in _IMP_atom:
6968 _IMP_atom._OrientedSoapBase_swigregister(_OrientedSoapBase)
6969 class _SPSFTB(IMP.PairScore):
6970  r"""Proxy of C++ IMP::score_functor::DistancePairScore< score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > > class."""
6971 
6972  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
6973  __repr__ = _swig_repr
6974 
6975  def __init__(self, *args):
6976  r"""
6977  __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
6978  __init__(_SPSFTB self) -> _SPSFTB
6979  """
6980  _IMP_atom._SPSFTB_swiginit(self, _IMP_atom.new__SPSFTB(*args))
6981 
6982  def do_get_inputs(self, m, pis):
6983  r"""do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6984  return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
6985 
6986  def get_score_functor(self):
6987  r"""get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
6988  return _IMP_atom._SPSFTB_get_score_functor(self)
6989 
6990  def get_version_info(self):
6991  r"""get_version_info(_SPSFTB self) -> VersionInfo"""
6992  return _IMP_atom._SPSFTB_get_version_info(self)
6993  __swig_destroy__ = _IMP_atom.delete__SPSFTB
6994 
6995 # Register _SPSFTB in _IMP_atom:
6996 _IMP_atom._SPSFTB_swigregister(_SPSFTB)
6997 class _SPSTF(_SPSFTB):
6998  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType,true,false > class."""
6999 
7000  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7001  __repr__ = _swig_repr
7002 
7003  def __init__(self, *args):
7004  r"""
7005  __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7006  __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7007  """
7008  _IMP_atom._SPSTF_swiginit(self, _IMP_atom.new__SPSTF(*args))
7009  __swig_destroy__ = _IMP_atom.delete__SPSTF
7010 
7011 # Register _SPSTF in _IMP_atom:
7012 _IMP_atom._SPSTF_swigregister(_SPSTF)
7013 class _SPSFT(_BDopeBase):
7014  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::DopeType,false,true > class."""
7015 
7016  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7017  __repr__ = _swig_repr
7018 
7019  def __init__(self, *args):
7020  r"""
7021  __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7022  __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7023  """
7024  _IMP_atom._SPSFT_swiginit(self, _IMP_atom.new__SPSFT(*args))
7025  __swig_destroy__ = _IMP_atom.delete__SPSFT
7026 
7027 # Register _SPSFT in _IMP_atom:
7028 _IMP_atom._SPSFT_swigregister(_SPSFT)
7029 class _SPSFTL(_BLoopStatisticalBase):
7030  r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType,false,true > class."""
7031 
7032  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7033  __repr__ = _swig_repr
7034 
7035  def __init__(self, *args):
7036  r"""
7037  __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7038  __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7039  """
7040  _IMP_atom._SPSFTL_swiginit(self, _IMP_atom.new__SPSFTL(*args))
7041  __swig_destroy__ = _IMP_atom.delete__SPSFTL
7042 
7043 # Register _SPSFTL in _IMP_atom:
7044 _IMP_atom._SPSFTL_swigregister(_SPSFTL)
7045 class ProteinLigandAtomPairScore(_SPSTF):
7046  r"""Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7047 
7048  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7049 
7050  def __init__(self, *args):
7051  r"""
7052  __init__(ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
7053  __init__(ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7054  """
7055  _IMP_atom.ProteinLigandAtomPairScore_swiginit(self, _IMP_atom.new_ProteinLigandAtomPairScore(*args))
7056 
7057  def get_maximum_distance(self):
7058  r"""get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7059  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7060 
7061  def __str__(self):
7062  r"""__str__(ProteinLigandAtomPairScore self) -> std::string"""
7063  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7064 
7065  def __repr__(self):
7066  r"""__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7067  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7068 
7069  @staticmethod
7070  def get_from(o):
7071  return _object_cast_to_ProteinLigandAtomPairScore(o)
7072 
7073  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7074 
7075 # Register ProteinLigandAtomPairScore in _IMP_atom:
7076 _IMP_atom.ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7077 class ProteinLigandRestraint(IMP.container.PairsRestraint):
7078  r"""Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7079 
7080  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7081 
7082  def __init__(self, *args):
7083  r"""
7084  __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
7085  __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7086  """
7087  _IMP_atom.ProteinLigandRestraint_swiginit(self, _IMP_atom.new_ProteinLigandRestraint(*args))
7088 
7089  def __str__(self):
7090  r"""__str__(ProteinLigandRestraint self) -> std::string"""
7091  return _IMP_atom.ProteinLigandRestraint___str__(self)
7092 
7093  def __repr__(self):
7094  r"""__repr__(ProteinLigandRestraint self) -> std::string"""
7095  return _IMP_atom.ProteinLigandRestraint___repr__(self)
7096 
7097  @staticmethod
7098  def get_from(o):
7099  return _object_cast_to_ProteinLigandRestraint(o)
7100 
7101  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7102 
7103 # Register ProteinLigandRestraint in _IMP_atom:
7104 _IMP_atom.ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7105 
7107  r"""add_protein_ligand_score_data(Hierarchy h)"""
7108  return _IMP_atom.add_protein_ligand_score_data(h)
7109 class AtomType(IMP._Value):
7110  r"""Proxy of C++ IMP::Key< 8974343 > class."""
7111 
7112  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7113 
7114  def __init__(self, *args):
7115  r"""
7116  __init__(AtomType self) -> AtomType
7117  __init__(AtomType self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7118  __init__(AtomType self, unsigned int i) -> AtomType
7119  """
7120  _IMP_atom.AtomType_swiginit(self, _IMP_atom.new_AtomType(*args))
7121 
7122  @staticmethod
7123  def add_key(sc):
7124  r"""add_key(std::string sc) -> unsigned int"""
7125  return _IMP_atom.AtomType_add_key(sc)
7126 
7127  @staticmethod
7128  def get_key_exists(sc):
7129  r"""get_key_exists(std::string sc) -> bool"""
7130  return _IMP_atom.AtomType_get_key_exists(sc)
7131 
7132  def get_string(self):
7133  r"""get_string(AtomType self) -> std::string const"""
7134  return _IMP_atom.AtomType_get_string(self)
7135 
7136  def __cmp__(self, o):
7137  r"""__cmp__(AtomType self, AtomType o) -> int"""
7138  return _IMP_atom.AtomType___cmp__(self, o)
7139 
7140  def __eq__(self, o):
7141  r"""__eq__(AtomType self, AtomType o) -> bool"""
7142  return _IMP_atom.AtomType___eq__(self, o)
7143 
7144  def __ne__(self, o):
7145  r"""__ne__(AtomType self, AtomType o) -> bool"""
7146  return _IMP_atom.AtomType___ne__(self, o)
7147 
7148  def __lt__(self, o):
7149  r"""__lt__(AtomType self, AtomType o) -> bool"""
7150  return _IMP_atom.AtomType___lt__(self, o)
7151 
7152  def __gt__(self, o):
7153  r"""__gt__(AtomType self, AtomType o) -> bool"""
7154  return _IMP_atom.AtomType___gt__(self, o)
7155 
7156  def __ge__(self, o):
7157  r"""__ge__(AtomType self, AtomType o) -> bool"""
7158  return _IMP_atom.AtomType___ge__(self, o)
7159 
7160  def __le__(self, o):
7161  r"""__le__(AtomType self, AtomType o) -> bool"""
7162  return _IMP_atom.AtomType___le__(self, o)
7163 
7164  def __hash__(self):
7165  r"""__hash__(AtomType self) -> std::size_t"""
7166  return _IMP_atom.AtomType___hash__(self)
7167 
7168  def show(self, *args):
7169  r"""show(AtomType self, _ostream out=std::cout)"""
7170  return _IMP_atom.AtomType_show(self, *args)
7171 
7172  @staticmethod
7173  def add_alias(old_key, new_name):
7174  r"""add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7175  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7176 
7177  @staticmethod
7178  def get_number_of_keys():
7179  r"""get_number_of_keys() -> unsigned int"""
7180  return _IMP_atom.AtomType_get_number_of_keys()
7181 
7182  def get_index(self):
7183  r"""get_index(AtomType self) -> unsigned int"""
7184  return _IMP_atom.AtomType_get_index(self)
7185 
7186  @staticmethod
7187  def show_all(out):
7188  r"""show_all(_ostream out)"""
7189  return _IMP_atom.AtomType_show_all(out)
7190 
7191  @staticmethod
7192  def get_all_strings():
7193  r"""get_all_strings() -> IMP::Vector< std::string >"""
7194  return _IMP_atom.AtomType_get_all_strings()
7195 
7196  @staticmethod
7197  def get_number_unique():
7198  r"""get_number_unique() -> unsigned int"""
7199  return _IMP_atom.AtomType_get_number_unique()
7200 
7201  def __str__(self):
7202  r"""__str__(AtomType self) -> std::string"""
7203  return _IMP_atom.AtomType___str__(self)
7204 
7205  def __repr__(self):
7206  r"""__repr__(AtomType self) -> std::string"""
7207  return _IMP_atom.AtomType___repr__(self)
7208  __swig_destroy__ = _IMP_atom.delete_AtomType
7209 
7210 # Register AtomType in _IMP_atom:
7211 _IMP_atom.AtomType_swigregister(AtomType)
7212 class ResidueType(IMP._Value):
7213  r"""Proxy of C++ IMP::Key< 90784334 > class."""
7214 
7215  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7216 
7217  def __init__(self, *args):
7218  r"""
7219  __init__(ResidueType self) -> ResidueType
7220  __init__(ResidueType self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7221  __init__(ResidueType self, unsigned int i) -> ResidueType
7222  """
7223  _IMP_atom.ResidueType_swiginit(self, _IMP_atom.new_ResidueType(*args))
7224 
7225  @staticmethod
7226  def add_key(sc):
7227  r"""add_key(std::string sc) -> unsigned int"""
7228  return _IMP_atom.ResidueType_add_key(sc)
7229 
7230  @staticmethod
7231  def get_key_exists(sc):
7232  r"""get_key_exists(std::string sc) -> bool"""
7233  return _IMP_atom.ResidueType_get_key_exists(sc)
7234 
7235  def get_string(self):
7236  r"""get_string(ResidueType self) -> std::string const"""
7237  return _IMP_atom.ResidueType_get_string(self)
7238 
7239  def __cmp__(self, o):
7240  r"""__cmp__(ResidueType self, ResidueType o) -> int"""
7241  return _IMP_atom.ResidueType___cmp__(self, o)
7242 
7243  def __eq__(self, o):
7244  r"""__eq__(ResidueType self, ResidueType o) -> bool"""
7245  return _IMP_atom.ResidueType___eq__(self, o)
7246 
7247  def __ne__(self, o):
7248  r"""__ne__(ResidueType self, ResidueType o) -> bool"""
7249  return _IMP_atom.ResidueType___ne__(self, o)
7250 
7251  def __lt__(self, o):
7252  r"""__lt__(ResidueType self, ResidueType o) -> bool"""
7253  return _IMP_atom.ResidueType___lt__(self, o)
7254 
7255  def __gt__(self, o):
7256  r"""__gt__(ResidueType self, ResidueType o) -> bool"""
7257  return _IMP_atom.ResidueType___gt__(self, o)
7258 
7259  def __ge__(self, o):
7260  r"""__ge__(ResidueType self, ResidueType o) -> bool"""
7261  return _IMP_atom.ResidueType___ge__(self, o)
7262 
7263  def __le__(self, o):
7264  r"""__le__(ResidueType self, ResidueType o) -> bool"""
7265  return _IMP_atom.ResidueType___le__(self, o)
7266 
7267  def __hash__(self):
7268  r"""__hash__(ResidueType self) -> std::size_t"""
7269  return _IMP_atom.ResidueType___hash__(self)
7270 
7271  def show(self, *args):
7272  r"""show(ResidueType self, _ostream out=std::cout)"""
7273  return _IMP_atom.ResidueType_show(self, *args)
7274 
7275  @staticmethod
7276  def add_alias(old_key, new_name):
7277  r"""add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7278  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7279 
7280  @staticmethod
7281  def get_number_of_keys():
7282  r"""get_number_of_keys() -> unsigned int"""
7283  return _IMP_atom.ResidueType_get_number_of_keys()
7284 
7285  def get_index(self):
7286  r"""get_index(ResidueType self) -> unsigned int"""
7287  return _IMP_atom.ResidueType_get_index(self)
7288 
7289  @staticmethod
7290  def show_all(out):
7291  r"""show_all(_ostream out)"""
7292  return _IMP_atom.ResidueType_show_all(out)
7293 
7294  @staticmethod
7295  def get_all_strings():
7296  r"""get_all_strings() -> IMP::Vector< std::string >"""
7297  return _IMP_atom.ResidueType_get_all_strings()
7298 
7299  @staticmethod
7300  def get_number_unique():
7301  r"""get_number_unique() -> unsigned int"""
7302  return _IMP_atom.ResidueType_get_number_unique()
7303 
7304  def __str__(self):
7305  r"""__str__(ResidueType self) -> std::string"""
7306  return _IMP_atom.ResidueType___str__(self)
7307 
7308  def __repr__(self):
7309  r"""__repr__(ResidueType self) -> std::string"""
7310  return _IMP_atom.ResidueType___repr__(self)
7311  __swig_destroy__ = _IMP_atom.delete_ResidueType
7312 
7313 # Register ResidueType in _IMP_atom:
7314 _IMP_atom.ResidueType_swigregister(ResidueType)
7315 class ChainType(IMP._Value):
7316  r"""Proxy of C++ IMP::Key< 90784336 > class."""
7317 
7318  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7319 
7320  def __init__(self, *args):
7321  r"""
7322  __init__(ChainType self) -> ChainType
7323  __init__(ChainType self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
7324  __init__(ChainType self, unsigned int i) -> ChainType
7325  """
7326  _IMP_atom.ChainType_swiginit(self, _IMP_atom.new_ChainType(*args))
7327 
7328  @staticmethod
7329  def add_key(sc):
7330  r"""add_key(std::string sc) -> unsigned int"""
7331  return _IMP_atom.ChainType_add_key(sc)
7332 
7333  @staticmethod
7334  def get_key_exists(sc):
7335  r"""get_key_exists(std::string sc) -> bool"""
7336  return _IMP_atom.ChainType_get_key_exists(sc)
7337 
7338  def get_string(self):
7339  r"""get_string(ChainType self) -> std::string const"""
7340  return _IMP_atom.ChainType_get_string(self)
7341 
7342  def __cmp__(self, o):
7343  r"""__cmp__(ChainType self, ChainType o) -> int"""
7344  return _IMP_atom.ChainType___cmp__(self, o)
7345 
7346  def __eq__(self, o):
7347  r"""__eq__(ChainType self, ChainType o) -> bool"""
7348  return _IMP_atom.ChainType___eq__(self, o)
7349 
7350  def __ne__(self, o):
7351  r"""__ne__(ChainType self, ChainType o) -> bool"""
7352  return _IMP_atom.ChainType___ne__(self, o)
7353 
7354  def __lt__(self, o):
7355  r"""__lt__(ChainType self, ChainType o) -> bool"""
7356  return _IMP_atom.ChainType___lt__(self, o)
7357 
7358  def __gt__(self, o):
7359  r"""__gt__(ChainType self, ChainType o) -> bool"""
7360  return _IMP_atom.ChainType___gt__(self, o)
7361 
7362  def __ge__(self, o):
7363  r"""__ge__(ChainType self, ChainType o) -> bool"""
7364  return _IMP_atom.ChainType___ge__(self, o)
7365 
7366  def __le__(self, o):
7367  r"""__le__(ChainType self, ChainType o) -> bool"""
7368  return _IMP_atom.ChainType___le__(self, o)
7369 
7370  def __hash__(self):
7371  r"""__hash__(ChainType self) -> std::size_t"""
7372  return _IMP_atom.ChainType___hash__(self)
7373 
7374  def show(self, *args):
7375  r"""show(ChainType self, _ostream out=std::cout)"""
7376  return _IMP_atom.ChainType_show(self, *args)
7377 
7378  @staticmethod
7379  def add_alias(old_key, new_name):
7380  r"""add_alias(ChainType old_key, std::string new_name) -> ChainType"""
7381  return _IMP_atom.ChainType_add_alias(old_key, new_name)
7382 
7383  @staticmethod
7384  def get_number_of_keys():
7385  r"""get_number_of_keys() -> unsigned int"""
7386  return _IMP_atom.ChainType_get_number_of_keys()
7387 
7388  def get_index(self):
7389  r"""get_index(ChainType self) -> unsigned int"""
7390  return _IMP_atom.ChainType_get_index(self)
7391 
7392  @staticmethod
7393  def show_all(out):
7394  r"""show_all(_ostream out)"""
7395  return _IMP_atom.ChainType_show_all(out)
7396 
7397  @staticmethod
7398  def get_all_strings():
7399  r"""get_all_strings() -> IMP::Vector< std::string >"""
7400  return _IMP_atom.ChainType_get_all_strings()
7401 
7402  @staticmethod
7403  def get_number_unique():
7404  r"""get_number_unique() -> unsigned int"""
7405  return _IMP_atom.ChainType_get_number_unique()
7406 
7407  def __str__(self):
7408  r"""__str__(ChainType self) -> std::string"""
7409  return _IMP_atom.ChainType___str__(self)
7410 
7411  def __repr__(self):
7412  r"""__repr__(ChainType self) -> std::string"""
7413  return _IMP_atom.ChainType___repr__(self)
7414  __swig_destroy__ = _IMP_atom.delete_ChainType
7415 
7416 # Register ChainType in _IMP_atom:
7417 _IMP_atom.ChainType_swigregister(ChainType)
7418 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
7419 
7420 OH = _IMP_atom.OH
7421 
7422 H2O = _IMP_atom.H2O
7423 
7424 H = _IMP_atom.H
7425 
7426 He = _IMP_atom.He
7427 
7428 Li = _IMP_atom.Li
7429 
7430 Be = _IMP_atom.Be
7431 
7432 B = _IMP_atom.B
7433 
7434 C = _IMP_atom.C
7435 
7436 N = _IMP_atom.N
7437 
7438 O = _IMP_atom.O
7439 
7440 F = _IMP_atom.F
7441 
7442 Ne = _IMP_atom.Ne
7443 
7444 Na = _IMP_atom.Na
7445 
7446 Mg = _IMP_atom.Mg
7447 
7448 Al = _IMP_atom.Al
7449 
7450 Si = _IMP_atom.Si
7451 
7452 P = _IMP_atom.P
7453 
7454 S = _IMP_atom.S
7455 
7456 Cl = _IMP_atom.Cl
7457 
7458 Ar = _IMP_atom.Ar
7459 
7460 K = _IMP_atom.K
7461 
7462 Ca = _IMP_atom.Ca
7463 
7464 Sc = _IMP_atom.Sc
7465 
7466 Ti = _IMP_atom.Ti
7467 
7468 V = _IMP_atom.V
7469 
7470 Cr = _IMP_atom.Cr
7471 
7472 Mn = _IMP_atom.Mn
7473 
7474 Fe = _IMP_atom.Fe
7475 
7476 Co = _IMP_atom.Co
7477 
7478 Ni = _IMP_atom.Ni
7479 
7480 Cu = _IMP_atom.Cu
7481 
7482 Zn = _IMP_atom.Zn
7483 
7484 Ga = _IMP_atom.Ga
7485 
7486 Ge = _IMP_atom.Ge
7487 
7488 As = _IMP_atom.As
7489 
7490 Se = _IMP_atom.Se
7491 
7492 Br = _IMP_atom.Br
7493 
7494 Kr = _IMP_atom.Kr
7495 
7496 Rb = _IMP_atom.Rb
7497 
7498 Sr = _IMP_atom.Sr
7499 
7500 Y = _IMP_atom.Y
7501 
7502 Zr = _IMP_atom.Zr
7503 
7504 Nb = _IMP_atom.Nb
7505 
7506 Mo = _IMP_atom.Mo
7507 
7508 Tc = _IMP_atom.Tc
7509 
7510 Ru = _IMP_atom.Ru
7511 
7512 Rh = _IMP_atom.Rh
7513 
7514 Pd = _IMP_atom.Pd
7515 
7516 Ag = _IMP_atom.Ag
7517 
7518 Cd = _IMP_atom.Cd
7519 
7520 In = _IMP_atom.In
7521 
7522 Sn = _IMP_atom.Sn
7523 
7524 Sb = _IMP_atom.Sb
7525 
7526 Te = _IMP_atom.Te
7527 
7528 I = _IMP_atom.I
7529 
7530 Xe = _IMP_atom.Xe
7531 
7532 Cs = _IMP_atom.Cs
7533 
7534 Ba = _IMP_atom.Ba
7535 
7536 La = _IMP_atom.La
7537 
7538 Ce = _IMP_atom.Ce
7539 
7540 Pr = _IMP_atom.Pr
7541 
7542 Nd = _IMP_atom.Nd
7543 
7544 Pm = _IMP_atom.Pm
7545 
7546 Sm = _IMP_atom.Sm
7547 
7548 Eu = _IMP_atom.Eu
7549 
7550 Gd = _IMP_atom.Gd
7551 
7552 Tb = _IMP_atom.Tb
7553 
7554 Dy = _IMP_atom.Dy
7555 
7556 Ho = _IMP_atom.Ho
7557 
7558 Er = _IMP_atom.Er
7559 
7560 Tm = _IMP_atom.Tm
7561 
7562 Yb = _IMP_atom.Yb
7563 
7564 Lu = _IMP_atom.Lu
7565 
7566 Hf = _IMP_atom.Hf
7567 
7568 Ta = _IMP_atom.Ta
7569 
7570 W = _IMP_atom.W
7571 
7572 Re = _IMP_atom.Re
7573 
7574 Os = _IMP_atom.Os
7575 
7576 Ir = _IMP_atom.Ir
7577 
7578 Pt = _IMP_atom.Pt
7579 
7580 Au = _IMP_atom.Au
7581 
7582 Hg = _IMP_atom.Hg
7583 
7584 Tl = _IMP_atom.Tl
7585 
7586 Pb = _IMP_atom.Pb
7587 
7588 Bi = _IMP_atom.Bi
7589 
7590 Po = _IMP_atom.Po
7591 
7592 At = _IMP_atom.At
7593 
7594 Rn = _IMP_atom.Rn
7595 
7596 Fr = _IMP_atom.Fr
7597 
7598 Ra = _IMP_atom.Ra
7599 
7600 Ac = _IMP_atom.Ac
7601 
7602 Th = _IMP_atom.Th
7603 
7604 Pa = _IMP_atom.Pa
7605 
7606 U = _IMP_atom.U
7607 
7608 Np = _IMP_atom.Np
7609 
7610 Pu = _IMP_atom.Pu
7611 
7612 Am = _IMP_atom.Am
7613 
7614 Cm = _IMP_atom.Cm
7615 
7616 Bk = _IMP_atom.Bk
7617 
7618 Cf = _IMP_atom.Cf
7619 
7620 Es = _IMP_atom.Es
7621 
7622 Fm = _IMP_atom.Fm
7623 
7624 Md = _IMP_atom.Md
7625 
7626 No = _IMP_atom.No
7627 
7628 Lr = _IMP_atom.Lr
7629 
7630 Db = _IMP_atom.Db
7631 
7632 Jl = _IMP_atom.Jl
7633 
7634 Rf = _IMP_atom.Rf
7635 
7636 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
7637 
7638 
7639 def hash_value(e):
7640  r"""hash_value(IMP::atom::Element e) -> size_t"""
7641  return _IMP_atom.hash_value(e)
7642 class ElementTable(object):
7643  r"""Proxy of C++ IMP::atom::ElementTable class."""
7644 
7645  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7646  __repr__ = _swig_repr
7647 
7648  def __init__(self):
7649  r"""__init__(ElementTable self) -> ElementTable"""
7650  _IMP_atom.ElementTable_swiginit(self, _IMP_atom.new_ElementTable())
7651 
7652  def get_element(self, s):
7653  r"""get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
7654  return _IMP_atom.ElementTable_get_element(self, s)
7655 
7656  def get_name(self, e):
7657  r"""get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
7658  return _IMP_atom.ElementTable_get_name(self, e)
7659 
7660  def get_mass(self, e):
7661  r"""get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
7662  return _IMP_atom.ElementTable_get_mass(self, e)
7663  __swig_destroy__ = _IMP_atom.delete_ElementTable
7664 
7665 # Register ElementTable in _IMP_atom:
7666 _IMP_atom.ElementTable_swigregister(ElementTable)
7667 
7668 def get_element_table():
7669  r"""get_element_table() -> ElementTable"""
7670  return _IMP_atom.get_element_table()
7671 class Atom(Hierarchy):
7672  r"""Proxy of C++ IMP::atom::Atom class."""
7673 
7674  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
7675 
7676  def __init__(self, *args):
7677  r"""
7678  __init__(Atom self) -> Atom
7679  __init__(Atom self, Model m, ParticleIndex id) -> Atom
7680  __init__(Atom self, _ParticleAdaptor d) -> Atom
7681  """
7682  _IMP_atom.Atom_swiginit(self, _IMP_atom.new_Atom(*args))
7683 
7684  def show(self, *args):
7685  r"""show(Atom self, _ostream out=std::cout)"""
7686  return _IMP_atom.Atom_show(self, *args)
7687 
7688  @staticmethod
7689  def setup_particle(*args):
7690  r"""
7691  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
7692  setup_particle(_ParticleAdaptor pa, Atom other) -> Atom
7693  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
7694  setup_particle(_ParticleAdaptor pa, AtomType atom_type) -> Atom
7695  """
7696  return _IMP_atom.Atom_setup_particle(*args)
7697 
7698  @staticmethod
7699  def get_is_setup(*args):
7700  r"""
7701  get_is_setup(_ParticleAdaptor p) -> bool
7702  get_is_setup(Model m, ParticleIndex pi) -> bool
7703  """
7704  return _IMP_atom.Atom_get_is_setup(*args)
7705 
7706  def get_atom_type(self):
7707  r"""get_atom_type(Atom self) -> AtomType"""
7708  return _IMP_atom.Atom_get_atom_type(self)
7709 
7710  def set_atom_type(self, t):
7711  r"""set_atom_type(Atom self, AtomType t)"""
7712  return _IMP_atom.Atom_set_atom_type(self, t)
7713 
7714  def get_element(self):
7715  r"""get_element(Atom self) -> IMP::atom::Element"""
7716  return _IMP_atom.Atom_get_element(self)
7717 
7718  def set_element(self, e):
7719  r"""set_element(Atom self, IMP::atom::Element e)"""
7720  return _IMP_atom.Atom_set_element(self, e)
7721 
7722  def get_occupancy(self):
7723  r"""get_occupancy(Atom self) -> double"""
7724  return _IMP_atom.Atom_get_occupancy(self)
7725 
7726  def set_occupancy(self, occupancy):
7727  r"""set_occupancy(Atom self, double occupancy)"""
7728  return _IMP_atom.Atom_set_occupancy(self, occupancy)
7729 
7730  def get_temperature_factor(self):
7731  r"""get_temperature_factor(Atom self) -> double"""
7732  return _IMP_atom.Atom_get_temperature_factor(self)
7733 
7734  def set_temperature_factor(self, tempFactor):
7735  r"""set_temperature_factor(Atom self, double tempFactor)"""
7736  return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
7737 
7738  def get_input_index(self):
7739  r"""get_input_index(Atom self) -> IMP::Int"""
7740  return _IMP_atom.Atom_get_input_index(self)
7741 
7742  def set_input_index(self, t):
7743  r"""set_input_index(Atom self, IMP::Int t)"""
7744  return _IMP_atom.Atom_set_input_index(self, t)
7745 
7746  @staticmethod
7747  def get_atom_type_key():
7748  r"""get_atom_type_key() -> IntKey"""
7749  return _IMP_atom.Atom_get_atom_type_key()
7750 
7751  @staticmethod
7752  def get_element_key():
7753  r"""get_element_key() -> IntKey"""
7754  return _IMP_atom.Atom_get_element_key()
7755 
7756  @staticmethod
7757  def get_input_index_key():
7758  r"""get_input_index_key() -> IntKey"""
7759  return _IMP_atom.Atom_get_input_index_key()
7760 
7761  @staticmethod
7762  def get_occupancy_key():
7763  r"""get_occupancy_key() -> FloatKey"""
7764  return _IMP_atom.Atom_get_occupancy_key()
7765 
7766  @staticmethod
7767  def get_temperature_factor_key():
7768  r"""get_temperature_factor_key() -> FloatKey"""
7769  return _IMP_atom.Atom_get_temperature_factor_key()
7770 
7771  def add_attribute(self, *args):
7772  r"""
7773  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
7774  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
7775  add_attribute(Atom self, IntKey a0, IMP::Int a1)
7776  add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
7777  add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
7778  add_attribute(Atom self, StringKey a0, IMP::String a1)
7779  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
7780  add_attribute(Atom self, ObjectKey a0, Object a1)
7781  add_attribute(Atom self, SparseFloatKey a0, IMP::Float a1)
7782  add_attribute(Atom self, SparseIntKey a0, IMP::Int a1)
7783  add_attribute(Atom self, SparseStringKey a0, IMP::String a1)
7784  add_attribute(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
7785  """
7786  return _IMP_atom.Atom_add_attribute(self, *args)
7787 
7788  def get_value(self, *args):
7789  r"""
7790  get_value(Atom self, FloatKey a0) -> IMP::Float
7791  get_value(Atom self, IntKey a0) -> IMP::Int
7792  get_value(Atom self, FloatsKey a0) -> IMP::Floats
7793  get_value(Atom self, IntsKey a0) -> IMP::Ints
7794  get_value(Atom self, StringKey a0) -> IMP::String
7795  get_value(Atom self, ParticleIndexKey a0) -> Particle
7796  get_value(Atom self, ObjectKey a0) -> Object
7797  get_value(Atom self, SparseFloatKey a0) -> IMP::Float
7798  get_value(Atom self, SparseIntKey a0) -> IMP::Int
7799  get_value(Atom self, SparseStringKey a0) -> IMP::String
7800  get_value(Atom self, SparseParticleIndexKey a0) -> ParticleIndex
7801  """
7802  return _IMP_atom.Atom_get_value(self, *args)
7803 
7804  def set_value(self, *args):
7805  r"""
7806  set_value(Atom self, FloatKey a0, IMP::Float a1)
7807  set_value(Atom self, IntKey a0, IMP::Int a1)
7808  set_value(Atom self, FloatsKey a0, IMP::Floats a1)
7809  set_value(Atom self, IntsKey a0, IMP::Ints a1)
7810  set_value(Atom self, StringKey a0, IMP::String a1)
7811  set_value(Atom self, ParticleIndexKey a0, Particle a1)
7812  set_value(Atom self, ObjectKey a0, Object a1)
7813  set_value(Atom self, SparseFloatKey a0, IMP::Float a1)
7814  set_value(Atom self, SparseIntKey a0, IMP::Int a1)
7815  set_value(Atom self, SparseStringKey a0, IMP::String a1)
7816  set_value(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
7817  """
7818  return _IMP_atom.Atom_set_value(self, *args)
7819 
7820  def remove_attribute(self, *args):
7821  r"""
7822  remove_attribute(Atom self, FloatKey a0)
7823  remove_attribute(Atom self, IntKey a0)
7824  remove_attribute(Atom self, FloatsKey a0)
7825  remove_attribute(Atom self, IntsKey a0)
7826  remove_attribute(Atom self, StringKey a0)
7827  remove_attribute(Atom self, ParticleIndexKey a0)
7828  remove_attribute(Atom self, ObjectKey a0)
7829  remove_attribute(Atom self, SparseFloatKey a0)
7830  remove_attribute(Atom self, SparseIntKey a0)
7831  remove_attribute(Atom self, SparseStringKey a0)
7832  remove_attribute(Atom self, SparseParticleIndexKey a0)
7833  """
7834  return _IMP_atom.Atom_remove_attribute(self, *args)
7835 
7836  def has_attribute(self, *args):
7837  r"""
7838  has_attribute(Atom self, FloatKey a0) -> bool
7839  has_attribute(Atom self, IntKey a0) -> bool
7840  has_attribute(Atom self, FloatsKey a0) -> bool
7841  has_attribute(Atom self, IntsKey a0) -> bool
7842  has_attribute(Atom self, StringKey a0) -> bool
7843  has_attribute(Atom self, ParticleIndexKey a0) -> bool
7844  has_attribute(Atom self, ObjectKey a0) -> bool
7845  has_attribute(Atom self, SparseFloatKey a0) -> bool
7846  has_attribute(Atom self, SparseIntKey a0) -> bool
7847  has_attribute(Atom self, SparseStringKey a0) -> bool
7848  has_attribute(Atom self, SparseParticleIndexKey a0) -> bool
7849  """
7850  return _IMP_atom.Atom_has_attribute(self, *args)
7851 
7852  def get_derivative(self, a0):
7853  r"""get_derivative(Atom self, FloatKey a0) -> double"""
7854  return _IMP_atom.Atom_get_derivative(self, a0)
7855 
7856  def get_name(self):
7857  r"""get_name(Atom self) -> std::string"""
7858  return _IMP_atom.Atom_get_name(self)
7859 
7860  def clear_caches(self):
7861  r"""clear_caches(Atom self)"""
7862  return _IMP_atom.Atom_clear_caches(self)
7863 
7864  def set_name(self, a0):
7865  r"""set_name(Atom self, std::string a0)"""
7866  return _IMP_atom.Atom_set_name(self, a0)
7867 
7868  def set_check_level(self, a0):
7869  r"""set_check_level(Atom self, IMP::CheckLevel a0)"""
7870  return _IMP_atom.Atom_set_check_level(self, a0)
7871 
7872  def add_to_derivative(self, a0, a1, a2):
7873  r"""add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7874  return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
7875 
7876  def set_is_optimized(self, a0, a1):
7877  r"""set_is_optimized(Atom self, FloatKey a0, bool a1)"""
7878  return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
7879 
7880  def get_is_optimized(self, a0):
7881  r"""get_is_optimized(Atom self, FloatKey a0) -> bool"""
7882  return _IMP_atom.Atom_get_is_optimized(self, a0)
7883 
7884  def get_check_level(self):
7885  r"""get_check_level(Atom self) -> IMP::CheckLevel"""
7886  return _IMP_atom.Atom_get_check_level(self)
7887 
7888  def __eq__(self, *args):
7889  r"""
7890  __eq__(Atom self, Atom o) -> bool
7891  __eq__(Atom self, Particle d) -> bool
7892  """
7893  return _IMP_atom.Atom___eq__(self, *args)
7894 
7895  def __ne__(self, *args):
7896  r"""
7897  __ne__(Atom self, Atom o) -> bool
7898  __ne__(Atom self, Particle d) -> bool
7899  """
7900  return _IMP_atom.Atom___ne__(self, *args)
7901 
7902  def __le__(self, *args):
7903  r"""
7904  __le__(Atom self, Atom o) -> bool
7905  __le__(Atom self, Particle d) -> bool
7906  """
7907  return _IMP_atom.Atom___le__(self, *args)
7908 
7909  def __lt__(self, *args):
7910  r"""
7911  __lt__(Atom self, Atom o) -> bool
7912  __lt__(Atom self, Particle d) -> bool
7913  """
7914  return _IMP_atom.Atom___lt__(self, *args)
7915 
7916  def __ge__(self, *args):
7917  r"""
7918  __ge__(Atom self, Atom o) -> bool
7919  __ge__(Atom self, Particle d) -> bool
7920  """
7921  return _IMP_atom.Atom___ge__(self, *args)
7922 
7923  def __gt__(self, *args):
7924  r"""
7925  __gt__(Atom self, Atom o) -> bool
7926  __gt__(Atom self, Particle d) -> bool
7927  """
7928  return _IMP_atom.Atom___gt__(self, *args)
7929 
7930  def __hash__(self):
7931  r"""__hash__(Atom self) -> std::size_t"""
7932  return _IMP_atom.Atom___hash__(self)
7933 
7934  def __str__(self):
7935  r"""__str__(Atom self) -> std::string"""
7936  return _IMP_atom.Atom___str__(self)
7937 
7938  def __repr__(self):
7939  r"""__repr__(Atom self) -> std::string"""
7940  return _IMP_atom.Atom___repr__(self)
7941 
7942  def _get_as_binary(self):
7943  r"""_get_as_binary(Atom self) -> PyObject *"""
7944  return _IMP_atom.Atom__get_as_binary(self)
7945 
7946  def _set_from_binary(self, p):
7947  r"""_set_from_binary(Atom self, PyObject * p)"""
7948  return _IMP_atom.Atom__set_from_binary(self, p)
7949 
7950  def __getstate__(self):
7951  p = self._get_as_binary()
7952  if len(self.__dict__) > 1:
7953  d = self.__dict__.copy()
7954  del d['this']
7955  p = (d, p)
7956  return p
7957 
7958  def __setstate__(self, p):
7959  if not hasattr(self, 'this'):
7960  self.__init__()
7961  if isinstance(p, tuple):
7962  d, p = p
7963  self.__dict__.update(d)
7964  return self._set_from_binary(p)
7965 
7966  __swig_destroy__ = _IMP_atom.delete_Atom
7967 
7968 # Register Atom in _IMP_atom:
7969 _IMP_atom.Atom_swigregister(Atom)
7970 cvar = _IMP_atom.cvar
7971 AT_UNKNOWN = cvar.AT_UNKNOWN
7972 AT_N = cvar.AT_N
7973 AT_CA = cvar.AT_CA
7974 AT_C = cvar.AT_C
7975 AT_O = cvar.AT_O
7976 AT_H = cvar.AT_H
7977 AT_H1 = cvar.AT_H1
7978 AT_H2 = cvar.AT_H2
7979 AT_H3 = cvar.AT_H3
7980 AT_HA = cvar.AT_HA
7981 AT_HA1 = cvar.AT_HA1
7982 AT_HA2 = cvar.AT_HA2
7983 AT_HA3 = cvar.AT_HA3
7984 AT_CB = cvar.AT_CB
7985 AT_HB = cvar.AT_HB
7986 AT_HB1 = cvar.AT_HB1
7987 AT_HB2 = cvar.AT_HB2
7988 AT_HB3 = cvar.AT_HB3
7989 AT_OXT = cvar.AT_OXT
7990 AT_CH3 = cvar.AT_CH3
7991 AT_CH = cvar.AT_CH
7992 AT_CG = cvar.AT_CG
7993 AT_CG1 = cvar.AT_CG1
7994 AT_CG2 = cvar.AT_CG2
7995 AT_HG = cvar.AT_HG
7996 AT_HG1 = cvar.AT_HG1
7997 AT_HG2 = cvar.AT_HG2
7998 AT_HG3 = cvar.AT_HG3
7999 AT_HG11 = cvar.AT_HG11
8000 AT_HG21 = cvar.AT_HG21
8001 AT_HG31 = cvar.AT_HG31
8002 AT_HG12 = cvar.AT_HG12
8003 AT_HG13 = cvar.AT_HG13
8004 AT_HG22 = cvar.AT_HG22
8005 AT_HG23 = cvar.AT_HG23
8006 AT_HG32 = cvar.AT_HG32
8007 AT_OG = cvar.AT_OG
8008 AT_OG1 = cvar.AT_OG1
8009 AT_SG = cvar.AT_SG
8010 AT_CD = cvar.AT_CD
8011 AT_CD1 = cvar.AT_CD1
8012 AT_CD2 = cvar.AT_CD2
8013 AT_HD = cvar.AT_HD
8014 AT_HD1 = cvar.AT_HD1
8015 AT_HD2 = cvar.AT_HD2
8016 AT_HD3 = cvar.AT_HD3
8017 AT_HD11 = cvar.AT_HD11
8018 AT_HD21 = cvar.AT_HD21
8019 AT_HD31 = cvar.AT_HD31
8020 AT_HD12 = cvar.AT_HD12
8021 AT_HD13 = cvar.AT_HD13
8022 AT_HD22 = cvar.AT_HD22
8023 AT_HD23 = cvar.AT_HD23
8024 AT_HD32 = cvar.AT_HD32
8025 AT_SD = cvar.AT_SD
8026 AT_OD1 = cvar.AT_OD1
8027 AT_OD2 = cvar.AT_OD2
8028 AT_ND1 = cvar.AT_ND1
8029 AT_ND2 = cvar.AT_ND2
8030 AT_CE = cvar.AT_CE
8031 AT_CE1 = cvar.AT_CE1
8032 AT_CE2 = cvar.AT_CE2
8033 AT_CE3 = cvar.AT_CE3
8034 AT_HE = cvar.AT_HE
8035 AT_HE1 = cvar.AT_HE1
8036 AT_HE2 = cvar.AT_HE2
8037 AT_HE3 = cvar.AT_HE3
8038 AT_HE21 = cvar.AT_HE21
8039 AT_HE22 = cvar.AT_HE22
8040 AT_OE1 = cvar.AT_OE1
8041 AT_OE2 = cvar.AT_OE2
8042 AT_NE = cvar.AT_NE
8043 AT_NE1 = cvar.AT_NE1
8044 AT_NE2 = cvar.AT_NE2
8045 AT_CZ = cvar.AT_CZ
8046 AT_CZ2 = cvar.AT_CZ2
8047 AT_CZ3 = cvar.AT_CZ3
8048 AT_NZ = cvar.AT_NZ
8049 AT_HZ = cvar.AT_HZ
8050 AT_HZ1 = cvar.AT_HZ1
8051 AT_HZ2 = cvar.AT_HZ2
8052 AT_HZ3 = cvar.AT_HZ3
8053 AT_CH2 = cvar.AT_CH2
8054 AT_NH1 = cvar.AT_NH1
8055 AT_NH2 = cvar.AT_NH2
8056 AT_OH = cvar.AT_OH
8057 AT_HH = cvar.AT_HH
8058 AT_HH11 = cvar.AT_HH11
8059 AT_HH21 = cvar.AT_HH21
8060 AT_HH2 = cvar.AT_HH2
8061 AT_HH12 = cvar.AT_HH12
8062 AT_HH22 = cvar.AT_HH22
8063 AT_HH13 = cvar.AT_HH13
8064 AT_HH23 = cvar.AT_HH23
8065 AT_HH33 = cvar.AT_HH33
8066 AT_P = cvar.AT_P
8067 AT_OP1 = cvar.AT_OP1
8068 AT_OP2 = cvar.AT_OP2
8069 AT_OP3 = cvar.AT_OP3
8070 AT_O5p = cvar.AT_O5p
8071 AT_C5p = cvar.AT_C5p
8072 AT_H5p = cvar.AT_H5p
8073 AT_H5pp = cvar.AT_H5pp
8074 AT_C4p = cvar.AT_C4p
8075 AT_H4p = cvar.AT_H4p
8076 AT_O4p = cvar.AT_O4p
8077 AT_C1p = cvar.AT_C1p
8078 AT_H1p = cvar.AT_H1p
8079 AT_C3p = cvar.AT_C3p
8080 AT_H3p = cvar.AT_H3p
8081 AT_O3p = cvar.AT_O3p
8082 AT_C2p = cvar.AT_C2p
8083 AT_H2p = cvar.AT_H2p
8084 AT_H2pp = cvar.AT_H2pp
8085 AT_O2p = cvar.AT_O2p
8086 AT_HO2p = cvar.AT_HO2p
8087 AT_N9 = cvar.AT_N9
8088 AT_C8 = cvar.AT_C8
8089 AT_H8 = cvar.AT_H8
8090 AT_N7 = cvar.AT_N7
8091 AT_C5 = cvar.AT_C5
8092 AT_C4 = cvar.AT_C4
8093 AT_N3 = cvar.AT_N3
8094 AT_C2 = cvar.AT_C2
8095 AT_N1 = cvar.AT_N1
8096 AT_C6 = cvar.AT_C6
8097 AT_N6 = cvar.AT_N6
8098 AT_H61 = cvar.AT_H61
8099 AT_H62 = cvar.AT_H62
8100 AT_O6 = cvar.AT_O6
8101 AT_N2 = cvar.AT_N2
8102 AT_NT = cvar.AT_NT
8103 AT_H21 = cvar.AT_H21
8104 AT_H22 = cvar.AT_H22
8105 AT_H6 = cvar.AT_H6
8106 AT_H5 = cvar.AT_H5
8107 AT_O2 = cvar.AT_O2
8108 AT_N4 = cvar.AT_N4
8109 AT_H41 = cvar.AT_H41
8110 AT_H42 = cvar.AT_H42
8111 AT_O4 = cvar.AT_O4
8112 AT_C7 = cvar.AT_C7
8113 AT_H71 = cvar.AT_H71
8114 AT_H72 = cvar.AT_H72
8115 AT_H73 = cvar.AT_H73
8116 AT_O1A = cvar.AT_O1A
8117 AT_O2A = cvar.AT_O2A
8118 AT_O3A = cvar.AT_O3A
8119 AT_O1B = cvar.AT_O1B
8120 AT_O2B = cvar.AT_O2B
8121 AT_O3B = cvar.AT_O3B
8122 AT_CAY = cvar.AT_CAY
8123 AT_CY = cvar.AT_CY
8124 AT_OY = cvar.AT_OY
8125 AT_CAT = cvar.AT_CAT
8126 
8127 
8128 def get_residue(*args):
8129  r"""
8130  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8131  get_residue(Atom d, bool nothrow=False) -> Residue
8132  """
8133  return _IMP_atom.get_residue(*args)
8134 
8135 def get_atom(rd, at):
8136  r"""get_atom(Residue rd, AtomType at) -> Atom"""
8137  return _IMP_atom.get_atom(rd, at)
8138 
8139 def add_atom_type(name, e):
8140  r"""add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8141  return _IMP_atom.add_atom_type(name, e)
8142 
8143 def get_element_for_atom_type(at):
8144  r"""get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8145  return _IMP_atom.get_element_for_atom_type(at)
8146 
8147 def get_atom_type_exists(name):
8148  r"""get_atom_type_exists(std::string name) -> bool"""
8149  return _IMP_atom.get_atom_type_exists(name)
8150 class Residue(Hierarchy):
8151  r"""Proxy of C++ IMP::atom::Residue class."""
8152 
8153  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8154 
8155  def __init__(self, *args):
8156  r"""
8157  __init__(Residue self) -> Residue
8158  __init__(Residue self, Model m, ParticleIndex id) -> Residue
8159  __init__(Residue self, _ParticleAdaptor d) -> Residue
8160  """
8161  _IMP_atom.Residue_swiginit(self, _IMP_atom.new_Residue(*args))
8162 
8163  def show(self, *args):
8164  r"""show(Residue self, _ostream out=std::cout)"""
8165  return _IMP_atom.Residue_show(self, *args)
8166 
8167  @staticmethod
8168  def setup_particle(*args):
8169  r"""
8170  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8171  setup_particle(_ParticleAdaptor pa, ResidueType t, int index, int insertion_code) -> Residue
8172  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8173  setup_particle(_ParticleAdaptor pa, ResidueType t, int index) -> Residue
8174  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8175  setup_particle(_ParticleAdaptor pa, ResidueType t) -> Residue
8176  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8177  setup_particle(_ParticleAdaptor pa, Residue other) -> Residue
8178  """
8179  return _IMP_atom.Residue_setup_particle(*args)
8180 
8181  @staticmethod
8182  def get_is_setup(*args):
8183  r"""
8184  get_is_setup(_ParticleAdaptor p) -> bool
8185  get_is_setup(Model m, ParticleIndex pi) -> bool
8186  """
8187  return _IMP_atom.Residue_get_is_setup(*args)
8188 
8189  def get_residue_type(self):
8190  r"""get_residue_type(Residue self) -> ResidueType"""
8191  return _IMP_atom.Residue_get_residue_type(self)
8192 
8193  def set_residue_type(self, t):
8194  r"""set_residue_type(Residue self, ResidueType t)"""
8195  return _IMP_atom.Residue_set_residue_type(self, t)
8196 
8197  def get_is_protein(self):
8198  r"""get_is_protein(Residue self) -> bool"""
8199  return _IMP_atom.Residue_get_is_protein(self)
8200 
8201  def get_is_dna(self):
8202  r"""get_is_dna(Residue self) -> bool"""
8203  return _IMP_atom.Residue_get_is_dna(self)
8204 
8205  def get_is_rna(self):
8206  r"""get_is_rna(Residue self) -> bool"""
8207  return _IMP_atom.Residue_get_is_rna(self)
8208 
8209  def get_index(self):
8210  r"""get_index(Residue self) -> IMP::Int"""
8211  return _IMP_atom.Residue_get_index(self)
8212 
8213  def set_index(self, t):
8214  r"""set_index(Residue self, IMP::Int t)"""
8215  return _IMP_atom.Residue_set_index(self, t)
8216 
8217  def get_insertion_code(self):
8218  r"""get_insertion_code(Residue self) -> char"""
8219  return _IMP_atom.Residue_get_insertion_code(self)
8220 
8221  def set_insertion_code(self, insertion_code):
8222  r"""set_insertion_code(Residue self, char insertion_code)"""
8223  return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8224 
8225  @staticmethod
8226  def get_index_key():
8227  r"""get_index_key() -> IntKey"""
8228  return _IMP_atom.Residue_get_index_key()
8229 
8230  @staticmethod
8231  def get_residue_type_key():
8232  r"""get_residue_type_key() -> IntKey"""
8233  return _IMP_atom.Residue_get_residue_type_key()
8234 
8235  @staticmethod
8236  def get_insertion_code_key():
8237  r"""get_insertion_code_key() -> IntKey"""
8238  return _IMP_atom.Residue_get_insertion_code_key()
8239 
8240  @staticmethod
8241  def get_type_changed_key():
8242  r"""get_type_changed_key() -> TriggerKey"""
8243  return _IMP_atom.Residue_get_type_changed_key()
8244 
8245  def add_attribute(self, *args):
8246  r"""
8247  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8248  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8249  add_attribute(Residue self, IntKey a0, IMP::Int a1)
8250  add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
8251  add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
8252  add_attribute(Residue self, StringKey a0, IMP::String a1)
8253  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8254  add_attribute(Residue self, ObjectKey a0, Object a1)
8255  add_attribute(Residue self, SparseFloatKey a0, IMP::Float a1)
8256  add_attribute(Residue self, SparseIntKey a0, IMP::Int a1)
8257  add_attribute(Residue self, SparseStringKey a0, IMP::String a1)
8258  add_attribute(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8259  """
8260  return _IMP_atom.Residue_add_attribute(self, *args)
8261 
8262  def get_value(self, *args):
8263  r"""
8264  get_value(Residue self, FloatKey a0) -> IMP::Float
8265  get_value(Residue self, IntKey a0) -> IMP::Int
8266  get_value(Residue self, FloatsKey a0) -> IMP::Floats
8267  get_value(Residue self, IntsKey a0) -> IMP::Ints
8268  get_value(Residue self, StringKey a0) -> IMP::String
8269  get_value(Residue self, ParticleIndexKey a0) -> Particle
8270  get_value(Residue self, ObjectKey a0) -> Object
8271  get_value(Residue self, SparseFloatKey a0) -> IMP::Float
8272  get_value(Residue self, SparseIntKey a0) -> IMP::Int
8273  get_value(Residue self, SparseStringKey a0) -> IMP::String
8274  get_value(Residue self, SparseParticleIndexKey a0) -> ParticleIndex
8275  """
8276  return _IMP_atom.Residue_get_value(self, *args)
8277 
8278  def set_value(self, *args):
8279  r"""
8280  set_value(Residue self, FloatKey a0, IMP::Float a1)
8281  set_value(Residue self, IntKey a0, IMP::Int a1)
8282  set_value(Residue self, FloatsKey a0, IMP::Floats a1)
8283  set_value(Residue self, IntsKey a0, IMP::Ints a1)
8284  set_value(Residue self, StringKey a0, IMP::String a1)
8285  set_value(Residue self, ParticleIndexKey a0, Particle a1)
8286  set_value(Residue self, ObjectKey a0, Object a1)
8287  set_value(Residue self, SparseFloatKey a0, IMP::Float a1)
8288  set_value(Residue self, SparseIntKey a0, IMP::Int a1)
8289  set_value(Residue self, SparseStringKey a0, IMP::String a1)
8290  set_value(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8291  """
8292  return _IMP_atom.Residue_set_value(self, *args)
8293 
8294  def remove_attribute(self, *args):
8295  r"""
8296  remove_attribute(Residue self, FloatKey a0)
8297  remove_attribute(Residue self, IntKey a0)
8298  remove_attribute(Residue self, FloatsKey a0)
8299  remove_attribute(Residue self, IntsKey a0)
8300  remove_attribute(Residue self, StringKey a0)
8301  remove_attribute(Residue self, ParticleIndexKey a0)
8302  remove_attribute(Residue self, ObjectKey a0)
8303  remove_attribute(Residue self, SparseFloatKey a0)
8304  remove_attribute(Residue self, SparseIntKey a0)
8305  remove_attribute(Residue self, SparseStringKey a0)
8306  remove_attribute(Residue self, SparseParticleIndexKey a0)
8307  """
8308  return _IMP_atom.Residue_remove_attribute(self, *args)
8309 
8310  def has_attribute(self, *args):
8311  r"""
8312  has_attribute(Residue self, FloatKey a0) -> bool
8313  has_attribute(Residue self, IntKey a0) -> bool
8314  has_attribute(Residue self, FloatsKey a0) -> bool
8315  has_attribute(Residue self, IntsKey a0) -> bool
8316  has_attribute(Residue self, StringKey a0) -> bool
8317  has_attribute(Residue self, ParticleIndexKey a0) -> bool
8318  has_attribute(Residue self, ObjectKey a0) -> bool
8319  has_attribute(Residue self, SparseFloatKey a0) -> bool
8320  has_attribute(Residue self, SparseIntKey a0) -> bool
8321  has_attribute(Residue self, SparseStringKey a0) -> bool
8322  has_attribute(Residue self, SparseParticleIndexKey a0) -> bool
8323  """
8324  return _IMP_atom.Residue_has_attribute(self, *args)
8325 
8326  def get_derivative(self, a0):
8327  r"""get_derivative(Residue self, FloatKey a0) -> double"""
8328  return _IMP_atom.Residue_get_derivative(self, a0)
8329 
8330  def get_name(self):
8331  r"""get_name(Residue self) -> std::string"""
8332  return _IMP_atom.Residue_get_name(self)
8333 
8334  def clear_caches(self):
8335  r"""clear_caches(Residue self)"""
8336  return _IMP_atom.Residue_clear_caches(self)
8337 
8338  def set_name(self, a0):
8339  r"""set_name(Residue self, std::string a0)"""
8340  return _IMP_atom.Residue_set_name(self, a0)
8341 
8342  def set_check_level(self, a0):
8343  r"""set_check_level(Residue self, IMP::CheckLevel a0)"""
8344  return _IMP_atom.Residue_set_check_level(self, a0)
8345 
8346  def add_to_derivative(self, a0, a1, a2):
8347  r"""add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8348  return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8349 
8350  def set_is_optimized(self, a0, a1):
8351  r"""set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8352  return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8353 
8354  def get_is_optimized(self, a0):
8355  r"""get_is_optimized(Residue self, FloatKey a0) -> bool"""
8356  return _IMP_atom.Residue_get_is_optimized(self, a0)
8357 
8358  def get_check_level(self):
8359  r"""get_check_level(Residue self) -> IMP::CheckLevel"""
8360  return _IMP_atom.Residue_get_check_level(self)
8361 
8362  def __eq__(self, *args):
8363  r"""
8364  __eq__(Residue self, Residue o) -> bool
8365  __eq__(Residue self, Particle d) -> bool
8366  """
8367  return _IMP_atom.Residue___eq__(self, *args)
8368 
8369  def __ne__(self, *args):
8370  r"""
8371  __ne__(Residue self, Residue o) -> bool
8372  __ne__(Residue self, Particle d) -> bool
8373  """
8374  return _IMP_atom.Residue___ne__(self, *args)
8375 
8376  def __le__(self, *args):
8377  r"""
8378  __le__(Residue self, Residue o) -> bool
8379  __le__(Residue self, Particle d) -> bool
8380  """
8381  return _IMP_atom.Residue___le__(self, *args)
8382 
8383  def __lt__(self, *args):
8384  r"""
8385  __lt__(Residue self, Residue o) -> bool
8386  __lt__(Residue self, Particle d) -> bool
8387  """
8388  return _IMP_atom.Residue___lt__(self, *args)
8389 
8390  def __ge__(self, *args):
8391  r"""
8392  __ge__(Residue self, Residue o) -> bool
8393  __ge__(Residue self, Particle d) -> bool
8394  """
8395  return _IMP_atom.Residue___ge__(self, *args)
8396 
8397  def __gt__(self, *args):
8398  r"""
8399  __gt__(Residue self, Residue o) -> bool
8400  __gt__(Residue self, Particle d) -> bool
8401  """
8402  return _IMP_atom.Residue___gt__(self, *args)
8403 
8404  def __hash__(self):
8405  r"""__hash__(Residue self) -> std::size_t"""
8406  return _IMP_atom.Residue___hash__(self)
8407 
8408  def __str__(self):
8409  r"""__str__(Residue self) -> std::string"""
8410  return _IMP_atom.Residue___str__(self)
8411 
8412  def __repr__(self):
8413  r"""__repr__(Residue self) -> std::string"""
8414  return _IMP_atom.Residue___repr__(self)
8415 
8416  def _get_as_binary(self):
8417  r"""_get_as_binary(Residue self) -> PyObject *"""
8418  return _IMP_atom.Residue__get_as_binary(self)
8419 
8420  def _set_from_binary(self, p):
8421  r"""_set_from_binary(Residue self, PyObject * p)"""
8422  return _IMP_atom.Residue__set_from_binary(self, p)
8423 
8424  def __getstate__(self):
8425  p = self._get_as_binary()
8426  if len(self.__dict__) > 1:
8427  d = self.__dict__.copy()
8428  del d['this']
8429  p = (d, p)
8430  return p
8431 
8432  def __setstate__(self, p):
8433  if not hasattr(self, 'this'):
8434  self.__init__()
8435  if isinstance(p, tuple):
8436  d, p = p
8437  self.__dict__.update(d)
8438  return self._set_from_binary(p)
8439 
8440  __swig_destroy__ = _IMP_atom.delete_Residue
8441 
8442 # Register Residue in _IMP_atom:
8443 _IMP_atom.Residue_swigregister(Residue)
8444 UNK = cvar.UNK
8445 GLY = cvar.GLY
8446 ALA = cvar.ALA
8447 VAL = cvar.VAL
8448 LEU = cvar.LEU
8449 ILE = cvar.ILE
8450 SER = cvar.SER
8451 THR = cvar.THR
8452 CYS = cvar.CYS
8453 MET = cvar.MET
8454 PRO = cvar.PRO
8455 ASP = cvar.ASP
8456 ASN = cvar.ASN
8457 GLU = cvar.GLU
8458 GLN = cvar.GLN
8459 LYS = cvar.LYS
8460 ARG = cvar.ARG
8461 HIS = cvar.HIS
8462 PHE = cvar.PHE
8463 TYR = cvar.TYR
8464 TRP = cvar.TRP
8465 ACE = cvar.ACE
8466 NH2 = cvar.NH2
8467 MSE = cvar.MSE
8468 ADE = cvar.ADE
8469 URA = cvar.URA
8470 CYT = cvar.CYT
8471 GUA = cvar.GUA
8472 THY = cvar.THY
8473 DADE = cvar.DADE
8474 DURA = cvar.DURA
8475 DCYT = cvar.DCYT
8476 DGUA = cvar.DGUA
8477 DTHY = cvar.DTHY
8478 HOH = cvar.HOH
8479 HEME = cvar.HEME
8480 POP = cvar.POP
8481 
8482 
8483 def get_next_residue(rd):
8484  r"""get_next_residue(Residue rd) -> Hierarchy"""
8485  return _IMP_atom.get_next_residue(rd)
8486 
8487 def get_previous_residue(rd):
8488  r"""get_previous_residue(Residue rd) -> Hierarchy"""
8489  return _IMP_atom.get_previous_residue(rd)
8490 
8491 def get_one_letter_code(c):
8492  r"""get_one_letter_code(ResidueType c) -> char"""
8493  return _IMP_atom.get_one_letter_code(c)
8494 BALLS = _IMP_atom.BALLS
8495 
8496 DENSITIES = _IMP_atom.DENSITIES
8497 
8498 class Representation(Hierarchy):
8499  r"""Proxy of C++ IMP::atom::Representation class."""
8500 
8501  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8502 
8503  @staticmethod
8504  def setup_particle(*args):
8505  r"""
8506  setup_particle(Model m, ParticleIndex pi) -> Representation
8507  setup_particle(_ParticleAdaptor pa) -> Representation
8508  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
8509  setup_particle(_ParticleAdaptor pa, double resolution) -> Representation
8510  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
8511  setup_particle(_ParticleAdaptor pa, Representation other) -> Representation
8512  """
8513  return _IMP_atom.Representation_setup_particle(*args)
8514 
8515  def __init__(self, *args):
8516  r"""
8517  __init__(Representation self) -> Representation
8518  __init__(Representation self, Model m, ParticleIndex id) -> Representation
8519  __init__(Representation self, _ParticleAdaptor d) -> Representation
8520  """
8521  _IMP_atom.Representation_swiginit(self, _IMP_atom.new_Representation(*args))
8522 
8523  def show(self, *args):
8524  r"""show(Representation self, _ostream out=std::cout)"""
8525  return _IMP_atom.Representation_show(self, *args)
8526 
8527  @staticmethod
8528  def get_is_setup(*args):
8529  r"""
8530  get_is_setup(_ParticleAdaptor p) -> bool
8531  get_is_setup(Model m, ParticleIndex pi) -> bool
8532  """
8533  return _IMP_atom.Representation_get_is_setup(*args)
8534 
8535  def get_representation(self, *args):
8536  r"""get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy"""
8537  return _IMP_atom.Representation_get_representation(self, *args)
8538 
8539  def get_representations(self, *args):
8540  r"""get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies"""
8541  return _IMP_atom.Representation_get_representations(self, *args)
8542 
8543  def add_representation(self, *args):
8544  r"""add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)"""
8545  return _IMP_atom.Representation_add_representation(self, *args)
8546 
8547  def get_resolutions(self, *args):
8548  r"""get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats"""
8549  return _IMP_atom.Representation_get_resolutions(self, *args)
8550 
8551  def remove_representation(self, rep):
8552  r"""remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
8553  return _IMP_atom.Representation_remove_representation(self, rep)
8554 
8555  def update_parents(self):
8556  r"""update_parents(Representation self)"""
8557  return _IMP_atom.Representation_update_parents(self)
8558 
8559  def add_attribute(self, *args):
8560  r"""
8561  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
8562  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
8563  add_attribute(Representation self, IntKey a0, IMP::Int a1)
8564  add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
8565  add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
8566  add_attribute(Representation self, StringKey a0, IMP::String a1)
8567  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
8568  add_attribute(Representation self, ObjectKey a0, Object a1)
8569  add_attribute(Representation self, SparseFloatKey a0, IMP::Float a1)
8570  add_attribute(Representation self, SparseIntKey a0, IMP::Int a1)
8571  add_attribute(Representation self, SparseStringKey a0, IMP::String a1)
8572  add_attribute(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
8573  """
8574  return _IMP_atom.Representation_add_attribute(self, *args)
8575 
8576  def get_value(self, *args):
8577  r"""
8578  get_value(Representation self, FloatKey a0) -> IMP::Float
8579  get_value(Representation self, IntKey a0) -> IMP::Int
8580  get_value(Representation self, FloatsKey a0) -> IMP::Floats
8581  get_value(Representation self, IntsKey a0) -> IMP::Ints
8582  get_value(Representation self, StringKey a0) -> IMP::String
8583  get_value(Representation self, ParticleIndexKey a0) -> Particle
8584  get_value(Representation self, ObjectKey a0) -> Object
8585  get_value(Representation self, SparseFloatKey a0) -> IMP::Float
8586  get_value(Representation self, SparseIntKey a0) -> IMP::Int
8587  get_value(Representation self, SparseStringKey a0) -> IMP::String
8588  get_value(Representation self, SparseParticleIndexKey a0) -> ParticleIndex
8589  """
8590  return _IMP_atom.Representation_get_value(self, *args)
8591 
8592  def set_value(self, *args):
8593  r"""
8594  set_value(Representation self, FloatKey a0, IMP::Float a1)
8595  set_value(Representation self, IntKey a0, IMP::Int a1)
8596  set_value(Representation self, FloatsKey a0, IMP::Floats a1)
8597  set_value(Representation self, IntsKey a0, IMP::Ints a1)
8598  set_value(Representation self, StringKey a0, IMP::String a1)
8599  set_value(Representation self, ParticleIndexKey a0, Particle a1)
8600  set_value(Representation self, ObjectKey a0, Object a1)
8601  set_value(Representation self, SparseFloatKey a0, IMP::Float a1)
8602  set_value(Representation self, SparseIntKey a0, IMP::Int a1)
8603  set_value(Representation self, SparseStringKey a0, IMP::String a1)
8604  set_value(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
8605  """
8606  return _IMP_atom.Representation_set_value(self, *args)
8607 
8608  def remove_attribute(self, *args):
8609  r"""
8610  remove_attribute(Representation self, FloatKey a0)
8611  remove_attribute(Representation self, IntKey a0)
8612  remove_attribute(Representation self, FloatsKey a0)
8613  remove_attribute(Representation self, IntsKey a0)
8614  remove_attribute(Representation self, StringKey a0)
8615  remove_attribute(Representation self, ParticleIndexKey a0)
8616  remove_attribute(Representation self, ObjectKey a0)
8617  remove_attribute(Representation self, SparseFloatKey a0)
8618  remove_attribute(Representation self, SparseIntKey a0)
8619  remove_attribute(Representation self, SparseStringKey a0)
8620  remove_attribute(Representation self, SparseParticleIndexKey a0)
8621  """
8622  return _IMP_atom.Representation_remove_attribute(self, *args)
8623 
8624  def has_attribute(self, *args):
8625  r"""
8626  has_attribute(Representation self, FloatKey a0) -> bool
8627  has_attribute(Representation self, IntKey a0) -> bool
8628  has_attribute(Representation self, FloatsKey a0) -> bool
8629  has_attribute(Representation self, IntsKey a0) -> bool
8630  has_attribute(Representation self, StringKey a0) -> bool
8631  has_attribute(Representation self, ParticleIndexKey a0) -> bool
8632  has_attribute(Representation self, ObjectKey a0) -> bool
8633  has_attribute(Representation self, SparseFloatKey a0) -> bool
8634  has_attribute(Representation self, SparseIntKey a0) -> bool
8635  has_attribute(Representation self, SparseStringKey a0) -> bool
8636  has_attribute(Representation self, SparseParticleIndexKey a0) -> bool
8637  """
8638  return _IMP_atom.Representation_has_attribute(self, *args)
8639 
8640  def get_derivative(self, a0):
8641  r"""get_derivative(Representation self, FloatKey a0) -> double"""
8642  return _IMP_atom.Representation_get_derivative(self, a0)
8643 
8644  def get_name(self):
8645  r"""get_name(Representation self) -> std::string"""
8646  return _IMP_atom.Representation_get_name(self)
8647 
8648  def clear_caches(self):
8649  r"""clear_caches(Representation self)"""
8650  return _IMP_atom.Representation_clear_caches(self)
8651 
8652  def set_name(self, a0):
8653  r"""set_name(Representation self, std::string a0)"""
8654  return _IMP_atom.Representation_set_name(self, a0)
8655 
8656  def set_check_level(self, a0):
8657  r"""set_check_level(Representation self, IMP::CheckLevel a0)"""
8658  return _IMP_atom.Representation_set_check_level(self, a0)
8659 
8660  def add_to_derivative(self, a0, a1, a2):
8661  r"""add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8662  return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
8663 
8664  def set_is_optimized(self, a0, a1):
8665  r"""set_is_optimized(Representation self, FloatKey a0, bool a1)"""
8666  return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
8667 
8668  def get_is_optimized(self, a0):
8669  r"""get_is_optimized(Representation self, FloatKey a0) -> bool"""
8670  return _IMP_atom.Representation_get_is_optimized(self, a0)
8671 
8672  def get_check_level(self):
8673  r"""get_check_level(Representation self) -> IMP::CheckLevel"""
8674  return _IMP_atom.Representation_get_check_level(self)
8675 
8676  def __eq__(self, *args):
8677  r"""
8678  __eq__(Representation self, Representation o) -> bool
8679  __eq__(Representation self, Particle d) -> bool
8680  """
8681  return _IMP_atom.Representation___eq__(self, *args)
8682 
8683  def __ne__(self, *args):
8684  r"""
8685  __ne__(Representation self, Representation o) -> bool
8686  __ne__(Representation self, Particle d) -> bool
8687  """
8688  return _IMP_atom.Representation___ne__(self, *args)
8689 
8690  def __le__(self, *args):
8691  r"""
8692  __le__(Representation self, Representation o) -> bool
8693  __le__(Representation self, Particle d) -> bool
8694  """
8695  return _IMP_atom.Representation___le__(self, *args)
8696 
8697  def __lt__(self, *args):
8698  r"""
8699  __lt__(Representation self, Representation o) -> bool
8700  __lt__(Representation self, Particle d) -> bool
8701  """
8702  return _IMP_atom.Representation___lt__(self, *args)
8703 
8704  def __ge__(self, *args):
8705  r"""
8706  __ge__(Representation self, Representation o) -> bool
8707  __ge__(Representation self, Particle d) -> bool
8708  """
8709  return _IMP_atom.Representation___ge__(self, *args)
8710 
8711  def __gt__(self, *args):
8712  r"""
8713  __gt__(Representation self, Representation o) -> bool
8714  __gt__(Representation self, Particle d) -> bool
8715  """
8716  return _IMP_atom.Representation___gt__(self, *args)
8717 
8718  def __hash__(self):
8719  r"""__hash__(Representation self) -> std::size_t"""
8720  return _IMP_atom.Representation___hash__(self)
8721 
8722  def __str__(self):
8723  r"""__str__(Representation self) -> std::string"""
8724  return _IMP_atom.Representation___str__(self)
8725 
8726  def __repr__(self):
8727  r"""__repr__(Representation self) -> std::string"""
8728  return _IMP_atom.Representation___repr__(self)
8729 
8730  def _get_as_binary(self):
8731  r"""_get_as_binary(Representation self) -> PyObject *"""
8732  return _IMP_atom.Representation__get_as_binary(self)
8733 
8734  def _set_from_binary(self, p):
8735  r"""_set_from_binary(Representation self, PyObject * p)"""
8736  return _IMP_atom.Representation__set_from_binary(self, p)
8737 
8738  def __getstate__(self):
8739  p = self._get_as_binary()
8740  if len(self.__dict__) > 1:
8741  d = self.__dict__.copy()
8742  del d['this']
8743  p = (d, p)
8744  return p
8745 
8746  def __setstate__(self, p):
8747  if not hasattr(self, 'this'):
8748  self.__init__()
8749  if isinstance(p, tuple):
8750  d, p = p
8751  self.__dict__.update(d)
8752  return self._set_from_binary(p)
8753 
8754  __swig_destroy__ = _IMP_atom.delete_Representation
8755 
8756 # Register Representation in _IMP_atom:
8757 _IMP_atom.Representation_swigregister(Representation)
8758 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
8759 
8760 
8761 def get_resolution(*args):
8762  r"""
8763  get_resolution(Model m, ParticleIndex pi) -> double
8764  get_resolution(Hierarchy h) -> double
8765  """
8766  return _IMP_atom.get_resolution(*args)
8767 
8768 def get_representation(h, nothrow=False):
8769  r"""get_representation(Hierarchy h, bool nothrow=False) -> Representation"""
8770  return _IMP_atom.get_representation(h, nothrow)
8771 
8772 def show_with_representations(*args):
8773  r"""show_with_representations(Hierarchy h, _ostream out=std::cout)"""
8774  return _IMP_atom.show_with_representations(*args)
8775 class State(Hierarchy):
8776  r"""Proxy of C++ IMP::atom::State class."""
8777 
8778  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
8779 
8780  @staticmethod
8781  def setup_particle(*args):
8782  r"""
8783  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
8784  setup_particle(_ParticleAdaptor pa, unsigned int index) -> State
8785  setup_particle(Model m, ParticleIndex pi, State other) -> State
8786  setup_particle(_ParticleAdaptor pa, State other) -> State
8787  """
8788  return _IMP_atom.State_setup_particle(*args)
8789 
8790  def __init__(self, *args):
8791  r"""
8792  __init__(State self) -> State
8793  __init__(State self, Model m, ParticleIndex id) -> State
8794  __init__(State self, _ParticleAdaptor d) -> State
8795  """
8796  _IMP_atom.State_swiginit(self, _IMP_atom.new_State(*args))
8797 
8798  def show(self, *args):
8799  r"""show(State self, _ostream out=std::cout)"""
8800  return _IMP_atom.State_show(self, *args)
8801 
8802  @staticmethod
8803  def get_is_setup(*args):
8804  r"""
8805  get_is_setup(_ParticleAdaptor p) -> bool
8806  get_is_setup(Model m, ParticleIndex pi) -> bool
8807  """
8808  return _IMP_atom.State_get_is_setup(*args)
8809 
8810  def get_state_index(self):
8811  r"""get_state_index(State self) -> unsigned int"""
8812  return _IMP_atom.State_get_state_index(self)
8813 
8814  def add_attribute(self, *args):
8815  r"""
8816  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
8817  add_attribute(State self, FloatKey a0, IMP::Float a1)
8818  add_attribute(State self, IntKey a0, IMP::Int a1)
8819  add_attribute(State self, FloatsKey a0, IMP::Floats a1)
8820  add_attribute(State self, IntsKey a0, IMP::Ints a1)
8821  add_attribute(State self, StringKey a0, IMP::String a1)
8822  add_attribute(State self, ParticleIndexKey a0, Particle a1)
8823  add_attribute(State self, ObjectKey a0, Object a1)
8824  add_attribute(State self, SparseFloatKey a0, IMP::Float a1)
8825  add_attribute(State self, SparseIntKey a0, IMP::Int a1)
8826  add_attribute(State self, SparseStringKey a0, IMP::String a1)
8827  add_attribute(State self, SparseParticleIndexKey a0, ParticleIndex a1)
8828  """
8829  return _IMP_atom.State_add_attribute(self, *args)
8830 
8831  def get_value(self, *args):
8832  r"""
8833  get_value(State self, FloatKey a0) -> IMP::Float
8834  get_value(State self, IntKey a0) -> IMP::Int
8835  get_value(State self, FloatsKey a0) -> IMP::Floats
8836  get_value(State self, IntsKey a0) -> IMP::Ints
8837  get_value(State self, StringKey a0) -> IMP::String
8838  get_value(State self, ParticleIndexKey a0) -> Particle
8839  get_value(State self, ObjectKey a0) -> Object
8840  get_value(State self, SparseFloatKey a0) -> IMP::Float
8841  get_value(State self, SparseIntKey a0) -> IMP::Int
8842  get_value(State self, SparseStringKey a0) -> IMP::String
8843  get_value(State self, SparseParticleIndexKey a0) -> ParticleIndex
8844  """
8845  return _IMP_atom.State_get_value(self, *args)
8846 
8847  def set_value(self, *args):
8848  r"""
8849  set_value(State self, FloatKey a0, IMP::Float a1)
8850  set_value(State self, IntKey a0, IMP::Int a1)
8851  set_value(State self, FloatsKey a0, IMP::Floats a1)
8852  set_value(State self, IntsKey a0, IMP::Ints a1)
8853  set_value(State self, StringKey a0, IMP::String a1)
8854  set_value(State self, ParticleIndexKey a0, Particle a1)
8855  set_value(State self, ObjectKey a0, Object a1)
8856  set_value(State self, SparseFloatKey a0, IMP::Float a1)
8857  set_value(State self, SparseIntKey a0, IMP::Int a1)
8858  set_value(State self, SparseStringKey a0, IMP::String a1)
8859  set_value(State self, SparseParticleIndexKey a0, ParticleIndex a1)
8860  """
8861  return _IMP_atom.State_set_value(self, *args)
8862 
8863  def remove_attribute(self, *args):
8864  r"""
8865  remove_attribute(State self, FloatKey a0)
8866  remove_attribute(State self, IntKey a0)
8867  remove_attribute(State self, FloatsKey a0)
8868  remove_attribute(State self, IntsKey a0)
8869  remove_attribute(State self, StringKey a0)
8870  remove_attribute(State self, ParticleIndexKey a0)
8871  remove_attribute(State self, ObjectKey a0)
8872  remove_attribute(State self, SparseFloatKey a0)
8873  remove_attribute(State self, SparseIntKey a0)
8874  remove_attribute(State self, SparseStringKey a0)
8875  remove_attribute(State self, SparseParticleIndexKey a0)
8876  """
8877  return _IMP_atom.State_remove_attribute(self, *args)
8878 
8879  def has_attribute(self, *args):
8880  r"""
8881  has_attribute(State self, FloatKey a0) -> bool
8882  has_attribute(State self, IntKey a0) -> bool
8883  has_attribute(State self, FloatsKey a0) -> bool
8884  has_attribute(State self, IntsKey a0) -> bool
8885  has_attribute(State self, StringKey a0) -> bool
8886  has_attribute(State self, ParticleIndexKey a0) -> bool
8887  has_attribute(State self, ObjectKey a0) -> bool
8888  has_attribute(State self, SparseFloatKey a0) -> bool
8889  has_attribute(State self, SparseIntKey a0) -> bool
8890  has_attribute(State self, SparseStringKey a0) -> bool
8891  has_attribute(State self, SparseParticleIndexKey a0) -> bool
8892  """
8893  return _IMP_atom.State_has_attribute(self, *args)
8894 
8895  def get_derivative(self, a0):
8896  r"""get_derivative(State self, FloatKey a0) -> double"""
8897  return _IMP_atom.State_get_derivative(self, a0)
8898 
8899  def get_name(self):
8900  r"""get_name(State self) -> std::string"""
8901  return _IMP_atom.State_get_name(self)
8902 
8903  def clear_caches(self):
8904  r"""clear_caches(State self)"""
8905  return _IMP_atom.State_clear_caches(self)
8906 
8907  def set_name(self, a0):
8908  r"""set_name(State self, std::string a0)"""
8909  return _IMP_atom.State_set_name(self, a0)
8910 
8911  def set_check_level(self, a0):
8912  r"""set_check_level(State self, IMP::CheckLevel a0)"""
8913  return _IMP_atom.State_set_check_level(self, a0)
8914 
8915  def add_to_derivative(self, a0, a1, a2):
8916  r"""add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8917  return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
8918 
8919  def set_is_optimized(self, a0, a1):
8920  r"""set_is_optimized(State self, FloatKey a0, bool a1)"""
8921  return _IMP_atom.State_set_is_optimized(self, a0, a1)
8922 
8923  def get_is_optimized(self, a0):
8924  r"""get_is_optimized(State self, FloatKey a0) -> bool"""
8925  return _IMP_atom.State_get_is_optimized(self, a0)
8926 
8927  def get_check_level(self):
8928  r"""get_check_level(State self) -> IMP::CheckLevel"""
8929  return _IMP_atom.State_get_check_level(self)
8930 
8931  def __eq__(self, *args):
8932  r"""
8933  __eq__(State self, State o) -> bool
8934  __eq__(State self, Particle d) -> bool
8935  """
8936  return _IMP_atom.State___eq__(self, *args)
8937 
8938  def __ne__(self, *args):
8939  r"""
8940  __ne__(State self, State o) -> bool
8941  __ne__(State self, Particle d) -> bool
8942  """
8943  return _IMP_atom.State___ne__(self, *args)
8944 
8945  def __le__(self, *args):
8946  r"""
8947  __le__(State self, State o) -> bool
8948  __le__(State self, Particle d) -> bool
8949  """
8950  return _IMP_atom.State___le__(self, *args)
8951 
8952  def __lt__(self, *args):
8953  r"""
8954  __lt__(State self, State o) -> bool
8955  __lt__(State self, Particle d) -> bool
8956  """
8957  return _IMP_atom.State___lt__(self, *args)
8958 
8959  def __ge__(self, *args):
8960  r"""
8961  __ge__(State self, State o) -> bool
8962  __ge__(State self, Particle d) -> bool
8963  """
8964  return _IMP_atom.State___ge__(self, *args)
8965 
8966  def __gt__(self, *args):
8967  r"""
8968  __gt__(State self, State o) -> bool
8969  __gt__(State self, Particle d) -> bool
8970  """
8971  return _IMP_atom.State___gt__(self, *args)
8972 
8973  def __hash__(self):
8974  r"""__hash__(State self) -> std::size_t"""
8975  return _IMP_atom.State___hash__(self)
8976 
8977  def __str__(self):
8978  r"""__str__(State self) -> std::string"""
8979  return _IMP_atom.State___str__(self)
8980 
8981  def __repr__(self):
8982  r"""__repr__(State self) -> std::string"""
8983  return _IMP_atom.State___repr__(self)
8984 
8985  def _get_as_binary(self):
8986  r"""_get_as_binary(State self) -> PyObject *"""
8987  return _IMP_atom.State__get_as_binary(self)
8988 
8989  def _set_from_binary(self, p):
8990  r"""_set_from_binary(State self, PyObject * p)"""
8991  return _IMP_atom.State__set_from_binary(self, p)
8992 
8993  def __getstate__(self):
8994  p = self._get_as_binary()
8995  if len(self.__dict__) > 1:
8996  d = self.__dict__.copy()
8997  del d['this']
8998  p = (d, p)
8999  return p
9000 
9001  def __setstate__(self, p):
9002  if not hasattr(self, 'this'):
9003  self.__init__()
9004  if isinstance(p, tuple):
9005  d, p = p
9006  self.__dict__.update(d)
9007  return self._set_from_binary(p)
9008 
9009  __swig_destroy__ = _IMP_atom.delete_State
9010 
9011 # Register State in _IMP_atom:
9012 _IMP_atom.State_swigregister(State)
9013 
9014 def get_state_index(h):
9015  r"""get_state_index(Hierarchy h) -> int"""
9016  return _IMP_atom.get_state_index(h)
9017 
9018 def get_phi_dihedral_atoms(rd):
9019  r"""get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9020  return _IMP_atom.get_phi_dihedral_atoms(rd)
9021 
9022 def get_psi_dihedral_atoms(rd):
9023  r"""get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9024  return _IMP_atom.get_psi_dihedral_atoms(rd)
9025 
9026 def get_omega_dihedral_atoms(rd):
9027  r"""get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9028  return _IMP_atom.get_omega_dihedral_atoms(rd)
9029 
9031  r"""get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
9032  return _IMP_atom.get_chi_dihedral_atom_types(rt)
9033 
9034 def get_chi_dihedral_atoms(rd):
9035  r"""get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
9036  return _IMP_atom.get_chi_dihedral_atoms(rd)
9037 
9039  r"""get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
9040  return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
9041 class Molecule(Hierarchy):
9042  r"""Proxy of C++ IMP::atom::Molecule class."""
9043 
9044  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9045 
9046  def __init__(self, *args):
9047  r"""
9048  __init__(Molecule self) -> Molecule
9049  __init__(Molecule self, Model m, ParticleIndex id) -> Molecule
9050  __init__(Molecule self, _ParticleAdaptor d) -> Molecule
9051  """
9052  _IMP_atom.Molecule_swiginit(self, _IMP_atom.new_Molecule(*args))
9053 
9054  def show(self, *args):
9055  r"""show(Molecule self, _ostream out=std::cout)"""
9056  return _IMP_atom.Molecule_show(self, *args)
9057 
9058  @staticmethod
9059  def setup_particle(*args):
9060  r"""
9061  setup_particle(Model m, ParticleIndex pi) -> Molecule
9062  setup_particle(_ParticleAdaptor pa) -> Molecule
9063  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9064  setup_particle(_ParticleAdaptor pa, Molecule other) -> Molecule
9065  """
9066  return _IMP_atom.Molecule_setup_particle(*args)
9067 
9068  @staticmethod
9069  def get_is_setup(*args):
9070  r"""
9071  get_is_setup(_ParticleAdaptor p) -> bool
9072  get_is_setup(Model m, ParticleIndex pi) -> bool
9073  """
9074  return _IMP_atom.Molecule_get_is_setup(*args)
9075 
9076  def add_attribute(self, *args):
9077  r"""
9078  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9079  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9080  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9081  add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
9082  add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
9083  add_attribute(Molecule self, StringKey a0, IMP::String a1)
9084  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9085  add_attribute(Molecule self, ObjectKey a0, Object a1)
9086  add_attribute(Molecule self, SparseFloatKey a0, IMP::Float a1)
9087  add_attribute(Molecule self, SparseIntKey a0, IMP::Int a1)
9088  add_attribute(Molecule self, SparseStringKey a0, IMP::String a1)
9089  add_attribute(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9090  """
9091  return _IMP_atom.Molecule_add_attribute(self, *args)
9092 
9093  def get_value(self, *args):
9094  r"""
9095  get_value(Molecule self, FloatKey a0) -> IMP::Float
9096  get_value(Molecule self, IntKey a0) -> IMP::Int
9097  get_value(Molecule self, FloatsKey a0) -> IMP::Floats
9098  get_value(Molecule self, IntsKey a0) -> IMP::Ints
9099  get_value(Molecule self, StringKey a0) -> IMP::String
9100  get_value(Molecule self, ParticleIndexKey a0) -> Particle
9101  get_value(Molecule self, ObjectKey a0) -> Object
9102  get_value(Molecule self, SparseFloatKey a0) -> IMP::Float
9103  get_value(Molecule self, SparseIntKey a0) -> IMP::Int
9104  get_value(Molecule self, SparseStringKey a0) -> IMP::String
9105  get_value(Molecule self, SparseParticleIndexKey a0) -> ParticleIndex
9106  """
9107  return _IMP_atom.Molecule_get_value(self, *args)
9108 
9109  def set_value(self, *args):
9110  r"""
9111  set_value(Molecule self, FloatKey a0, IMP::Float a1)
9112  set_value(Molecule self, IntKey a0, IMP::Int a1)
9113  set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
9114  set_value(Molecule self, IntsKey a0, IMP::Ints a1)
9115  set_value(Molecule self, StringKey a0, IMP::String a1)
9116  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9117  set_value(Molecule self, ObjectKey a0, Object a1)
9118  set_value(Molecule self, SparseFloatKey a0, IMP::Float a1)
9119  set_value(Molecule self, SparseIntKey a0, IMP::Int a1)
9120  set_value(Molecule self, SparseStringKey a0, IMP::String a1)
9121  set_value(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9122  """
9123  return _IMP_atom.Molecule_set_value(self, *args)
9124 
9125  def remove_attribute(self, *args):
9126  r"""
9127  remove_attribute(Molecule self, FloatKey a0)
9128  remove_attribute(Molecule self, IntKey a0)
9129  remove_attribute(Molecule self, FloatsKey a0)
9130  remove_attribute(Molecule self, IntsKey a0)
9131  remove_attribute(Molecule self, StringKey a0)
9132  remove_attribute(Molecule self, ParticleIndexKey a0)
9133  remove_attribute(Molecule self, ObjectKey a0)
9134  remove_attribute(Molecule self, SparseFloatKey a0)
9135  remove_attribute(Molecule self, SparseIntKey a0)
9136  remove_attribute(Molecule self, SparseStringKey a0)
9137  remove_attribute(Molecule self, SparseParticleIndexKey a0)
9138  """
9139  return _IMP_atom.Molecule_remove_attribute(self, *args)
9140 
9141  def has_attribute(self, *args):
9142  r"""
9143  has_attribute(Molecule self, FloatKey a0) -> bool
9144  has_attribute(Molecule self, IntKey a0) -> bool
9145  has_attribute(Molecule self, FloatsKey a0) -> bool
9146  has_attribute(Molecule self, IntsKey a0) -> bool
9147  has_attribute(Molecule self, StringKey a0) -> bool
9148  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9149  has_attribute(Molecule self, ObjectKey a0) -> bool
9150  has_attribute(Molecule self, SparseFloatKey a0) -> bool
9151  has_attribute(Molecule self, SparseIntKey a0) -> bool
9152  has_attribute(Molecule self, SparseStringKey a0) -> bool
9153  has_attribute(Molecule self, SparseParticleIndexKey a0) -> bool
9154  """
9155  return _IMP_atom.Molecule_has_attribute(self, *args)
9156 
9157  def get_derivative(self, a0):
9158  r"""get_derivative(Molecule self, FloatKey a0) -> double"""
9159  return _IMP_atom.Molecule_get_derivative(self, a0)
9160 
9161  def get_name(self):
9162  r"""get_name(Molecule self) -> std::string"""
9163  return _IMP_atom.Molecule_get_name(self)
9164 
9165  def clear_caches(self):
9166  r"""clear_caches(Molecule self)"""
9167  return _IMP_atom.Molecule_clear_caches(self)
9168 
9169  def set_name(self, a0):
9170  r"""set_name(Molecule self, std::string a0)"""
9171  return _IMP_atom.Molecule_set_name(self, a0)
9172 
9173  def set_check_level(self, a0):
9174  r"""set_check_level(Molecule self, IMP::CheckLevel a0)"""
9175  return _IMP_atom.Molecule_set_check_level(self, a0)
9176 
9177  def add_to_derivative(self, a0, a1, a2):
9178  r"""add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9179  return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9180 
9181  def set_is_optimized(self, a0, a1):
9182  r"""set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9183  return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9184 
9185  def get_is_optimized(self, a0):
9186  r"""get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9187  return _IMP_atom.Molecule_get_is_optimized(self, a0)
9188 
9189  def get_check_level(self):
9190  r"""get_check_level(Molecule self) -> IMP::CheckLevel"""
9191  return _IMP_atom.Molecule_get_check_level(self)
9192 
9193  def __eq__(self, *args):
9194  r"""
9195  __eq__(Molecule self, Molecule o) -> bool
9196  __eq__(Molecule self, Particle d) -> bool
9197  """
9198  return _IMP_atom.Molecule___eq__(self, *args)
9199 
9200  def __ne__(self, *args):
9201  r"""
9202  __ne__(Molecule self, Molecule o) -> bool
9203  __ne__(Molecule self, Particle d) -> bool
9204  """
9205  return _IMP_atom.Molecule___ne__(self, *args)
9206 
9207  def __le__(self, *args):
9208  r"""
9209  __le__(Molecule self, Molecule o) -> bool
9210  __le__(Molecule self, Particle d) -> bool
9211  """
9212  return _IMP_atom.Molecule___le__(self, *args)
9213 
9214  def __lt__(self, *args):
9215  r"""
9216  __lt__(Molecule self, Molecule o) -> bool
9217  __lt__(Molecule self, Particle d) -> bool
9218  """
9219  return _IMP_atom.Molecule___lt__(self, *args)
9220 
9221  def __ge__(self, *args):
9222  r"""
9223  __ge__(Molecule self, Molecule o) -> bool
9224  __ge__(Molecule self, Particle d) -> bool
9225  """
9226  return _IMP_atom.Molecule___ge__(self, *args)
9227 
9228  def __gt__(self, *args):
9229  r"""
9230  __gt__(Molecule self, Molecule o) -> bool
9231  __gt__(Molecule self, Particle d) -> bool
9232  """
9233  return _IMP_atom.Molecule___gt__(self, *args)
9234 
9235  def __hash__(self):
9236  r"""__hash__(Molecule self) -> std::size_t"""
9237  return _IMP_atom.Molecule___hash__(self)
9238 
9239  def __str__(self):
9240  r"""__str__(Molecule self) -> std::string"""
9241  return _IMP_atom.Molecule___str__(self)
9242 
9243  def __repr__(self):
9244  r"""__repr__(Molecule self) -> std::string"""
9245  return _IMP_atom.Molecule___repr__(self)
9246 
9247  def _get_as_binary(self):
9248  r"""_get_as_binary(Molecule self) -> PyObject *"""
9249  return _IMP_atom.Molecule__get_as_binary(self)
9250 
9251  def _set_from_binary(self, p):
9252  r"""_set_from_binary(Molecule self, PyObject * p)"""
9253  return _IMP_atom.Molecule__set_from_binary(self, p)
9254 
9255  def __getstate__(self):
9256  p = self._get_as_binary()
9257  if len(self.__dict__) > 1:
9258  d = self.__dict__.copy()
9259  del d['this']
9260  p = (d, p)
9261  return p
9262 
9263  def __setstate__(self, p):
9264  if not hasattr(self, 'this'):
9265  self.__init__()
9266  if isinstance(p, tuple):
9267  d, p = p
9268  self.__dict__.update(d)
9269  return self._set_from_binary(p)
9270 
9271  __swig_destroy__ = _IMP_atom.delete_Molecule
9272 
9273 # Register Molecule in _IMP_atom:
9274 _IMP_atom.Molecule_swigregister(Molecule)
9275 
9276 def get_molecule_name(h):
9277  r"""get_molecule_name(Hierarchy h) -> std::string"""
9278  return _IMP_atom.get_molecule_name(h)
9279 class Copy(Molecule):
9280  r"""Proxy of C++ IMP::atom::Copy class."""
9281 
9282  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9283 
9284  @staticmethod
9285  def get_copy_index_key():
9286  r"""get_copy_index_key() -> IntKey"""
9287  return _IMP_atom.Copy_get_copy_index_key()
9288 
9289  def __init__(self, *args):
9290  r"""
9291  __init__(Copy self) -> Copy
9292  __init__(Copy self, Model m, ParticleIndex id) -> Copy
9293  __init__(Copy self, _ParticleAdaptor d) -> Copy
9294  """
9295  _IMP_atom.Copy_swiginit(self, _IMP_atom.new_Copy(*args))
9296 
9297  def show(self, *args):
9298  r"""show(Copy self, _ostream out=std::cout)"""
9299  return _IMP_atom.Copy_show(self, *args)
9300 
9301  @staticmethod
9302  def setup_particle(*args):
9303  r"""
9304  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9305  setup_particle(_ParticleAdaptor pa, IMP::Int number) -> Copy
9306  """
9307  return _IMP_atom.Copy_setup_particle(*args)
9308 
9309  @staticmethod
9310  def get_is_setup(*args):
9311  r"""
9312  get_is_setup(_ParticleAdaptor p) -> bool
9313  get_is_setup(Model m, ParticleIndex pi) -> bool
9314  """
9315  return _IMP_atom.Copy_get_is_setup(*args)
9316 
9317  def get_copy_index(self):
9318  r"""get_copy_index(Copy self) -> int"""
9319  return _IMP_atom.Copy_get_copy_index(self)
9320 
9321  def add_attribute(self, *args):
9322  r"""
9323  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9324  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9325  add_attribute(Copy self, IntKey a0, IMP::Int a1)
9326  add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
9327  add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
9328  add_attribute(Copy self, StringKey a0, IMP::String a1)
9329  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9330  add_attribute(Copy self, ObjectKey a0, Object a1)
9331  add_attribute(Copy self, SparseFloatKey a0, IMP::Float a1)
9332  add_attribute(Copy self, SparseIntKey a0, IMP::Int a1)
9333  add_attribute(Copy self, SparseStringKey a0, IMP::String a1)
9334  add_attribute(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9335  """
9336  return _IMP_atom.Copy_add_attribute(self, *args)
9337 
9338  def get_value(self, *args):
9339  r"""
9340  get_value(Copy self, FloatKey a0) -> IMP::Float
9341  get_value(Copy self, IntKey a0) -> IMP::Int
9342  get_value(Copy self, FloatsKey a0) -> IMP::Floats
9343  get_value(Copy self, IntsKey a0) -> IMP::Ints
9344  get_value(Copy self, StringKey a0) -> IMP::String
9345  get_value(Copy self, ParticleIndexKey a0) -> Particle
9346  get_value(Copy self, ObjectKey a0) -> Object
9347  get_value(Copy self, SparseFloatKey a0) -> IMP::Float
9348  get_value(Copy self, SparseIntKey a0) -> IMP::Int
9349  get_value(Copy self, SparseStringKey a0) -> IMP::String
9350  get_value(Copy self, SparseParticleIndexKey a0) -> ParticleIndex
9351  """
9352  return _IMP_atom.Copy_get_value(self, *args)
9353 
9354  def set_value(self, *args):
9355  r"""
9356  set_value(Copy self, FloatKey a0, IMP::Float a1)
9357  set_value(Copy self, IntKey a0, IMP::Int a1)
9358  set_value(Copy self, FloatsKey a0, IMP::Floats a1)
9359  set_value(Copy self, IntsKey a0, IMP::Ints a1)
9360  set_value(Copy self, StringKey a0, IMP::String a1)
9361  set_value(Copy self, ParticleIndexKey a0, Particle a1)
9362  set_value(Copy self, ObjectKey a0, Object a1)
9363  set_value(Copy self, SparseFloatKey a0, IMP::Float a1)
9364  set_value(Copy self, SparseIntKey a0, IMP::Int a1)
9365  set_value(Copy self, SparseStringKey a0, IMP::String a1)
9366  set_value(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9367  """
9368  return _IMP_atom.Copy_set_value(self, *args)
9369 
9370  def remove_attribute(self, *args):
9371  r"""
9372  remove_attribute(Copy self, FloatKey a0)
9373  remove_attribute(Copy self, IntKey a0)
9374  remove_attribute(Copy self, FloatsKey a0)
9375  remove_attribute(Copy self, IntsKey a0)
9376  remove_attribute(Copy self, StringKey a0)
9377  remove_attribute(Copy self, ParticleIndexKey a0)
9378  remove_attribute(Copy self, ObjectKey a0)
9379  remove_attribute(Copy self, SparseFloatKey a0)
9380  remove_attribute(Copy self, SparseIntKey a0)
9381  remove_attribute(Copy self, SparseStringKey a0)
9382  remove_attribute(Copy self, SparseParticleIndexKey a0)
9383  """
9384  return _IMP_atom.Copy_remove_attribute(self, *args)
9385 
9386  def has_attribute(self, *args):
9387  r"""
9388  has_attribute(Copy self, FloatKey a0) -> bool
9389  has_attribute(Copy self, IntKey a0) -> bool
9390  has_attribute(Copy self, FloatsKey a0) -> bool
9391  has_attribute(Copy self, IntsKey a0) -> bool
9392  has_attribute(Copy self, StringKey a0) -> bool
9393  has_attribute(Copy self, ParticleIndexKey a0) -> bool
9394  has_attribute(Copy self, ObjectKey a0) -> bool
9395  has_attribute(Copy self, SparseFloatKey a0) -> bool
9396  has_attribute(Copy self, SparseIntKey a0) -> bool
9397  has_attribute(Copy self, SparseStringKey a0) -> bool
9398  has_attribute(Copy self, SparseParticleIndexKey a0) -> bool
9399  """
9400  return _IMP_atom.Copy_has_attribute(self, *args)
9401 
9402  def get_derivative(self, a0):
9403  r"""get_derivative(Copy self, FloatKey a0) -> double"""
9404  return _IMP_atom.Copy_get_derivative(self, a0)
9405 
9406  def get_name(self):
9407  r"""get_name(Copy self) -> std::string"""
9408  return _IMP_atom.Copy_get_name(self)
9409 
9410  def clear_caches(self):
9411  r"""clear_caches(Copy self)"""
9412  return _IMP_atom.Copy_clear_caches(self)
9413 
9414  def set_name(self, a0):
9415  r"""set_name(Copy self, std::string a0)"""
9416  return _IMP_atom.Copy_set_name(self, a0)
9417 
9418  def set_check_level(self, a0):
9419  r"""set_check_level(Copy self, IMP::CheckLevel a0)"""
9420  return _IMP_atom.Copy_set_check_level(self, a0)
9421 
9422  def add_to_derivative(self, a0, a1, a2):
9423  r"""add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9424  return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9425 
9426  def set_is_optimized(self, a0, a1):
9427  r"""set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9428  return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9429 
9430  def get_is_optimized(self, a0):
9431  r"""get_is_optimized(Copy self, FloatKey a0) -> bool"""
9432  return _IMP_atom.Copy_get_is_optimized(self, a0)
9433 
9434  def get_check_level(self):
9435  r"""get_check_level(Copy self) -> IMP::CheckLevel"""
9436  return _IMP_atom.Copy_get_check_level(self)
9437 
9438  def __eq__(self, *args):
9439  r"""
9440  __eq__(Copy self, Copy o) -> bool
9441  __eq__(Copy self, Particle d) -> bool
9442  """
9443  return _IMP_atom.Copy___eq__(self, *args)
9444 
9445  def __ne__(self, *args):
9446  r"""
9447  __ne__(Copy self, Copy o) -> bool
9448  __ne__(Copy self, Particle d) -> bool
9449  """
9450  return _IMP_atom.Copy___ne__(self, *args)
9451 
9452  def __le__(self, *args):
9453  r"""
9454  __le__(Copy self, Copy o) -> bool
9455  __le__(Copy self, Particle d) -> bool
9456  """
9457  return _IMP_atom.Copy___le__(self, *args)
9458 
9459  def __lt__(self, *args):
9460  r"""
9461  __lt__(Copy self, Copy o) -> bool
9462  __lt__(Copy self, Particle d) -> bool
9463  """
9464  return _IMP_atom.Copy___lt__(self, *args)
9465 
9466  def __ge__(self, *args):
9467  r"""
9468  __ge__(Copy self, Copy o) -> bool
9469  __ge__(Copy self, Particle d) -> bool
9470  """
9471  return _IMP_atom.Copy___ge__(self, *args)
9472 
9473  def __gt__(self, *args):
9474  r"""
9475  __gt__(Copy self, Copy o) -> bool
9476  __gt__(Copy self, Particle d) -> bool
9477  """
9478  return _IMP_atom.Copy___gt__(self, *args)
9479 
9480  def __hash__(self):
9481  r"""__hash__(Copy self) -> std::size_t"""
9482  return _IMP_atom.Copy___hash__(self)
9483 
9484  def __str__(self):
9485  r"""__str__(Copy self) -> std::string"""
9486  return _IMP_atom.Copy___str__(self)
9487 
9488  def __repr__(self):
9489  r"""__repr__(Copy self) -> std::string"""
9490  return _IMP_atom.Copy___repr__(self)
9491 
9492  def _get_as_binary(self):
9493  r"""_get_as_binary(Copy self) -> PyObject *"""
9494  return _IMP_atom.Copy__get_as_binary(self)
9495 
9496  def _set_from_binary(self, p):
9497  r"""_set_from_binary(Copy self, PyObject * p)"""
9498  return _IMP_atom.Copy__set_from_binary(self, p)
9499 
9500  def __getstate__(self):
9501  p = self._get_as_binary()
9502  if len(self.__dict__) > 1:
9503  d = self.__dict__.copy()
9504  del d['this']
9505  p = (d, p)
9506  return p
9507 
9508  def __setstate__(self, p):
9509  if not hasattr(self, 'this'):
9510  self.__init__()
9511  if isinstance(p, tuple):
9512  d, p = p
9513  self.__dict__.update(d)
9514  return self._set_from_binary(p)
9515 
9516  __swig_destroy__ = _IMP_atom.delete_Copy
9517 
9518 # Register Copy in _IMP_atom:
9519 _IMP_atom.Copy_swigregister(Copy)
9520 
9521 def get_copy_index(h):
9522  r"""get_copy_index(Hierarchy h) -> int"""
9523  return _IMP_atom.get_copy_index(h)
9524 class Chain(Hierarchy):
9525  r"""Proxy of C++ IMP::atom::Chain class."""
9526 
9527  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9528 
9529  def __init__(self, *args):
9530  r"""
9531  __init__(Chain self) -> Chain
9532  __init__(Chain self, Model m, ParticleIndex id) -> Chain
9533  __init__(Chain self, _ParticleAdaptor d) -> Chain
9534  """
9535  _IMP_atom.Chain_swiginit(self, _IMP_atom.new_Chain(*args))
9536 
9537  def show(self, *args):
9538  r"""show(Chain self, _ostream out=std::cout)"""
9539  return _IMP_atom.Chain_show(self, *args)
9540 
9541  @staticmethod
9542  def setup_particle(*args):
9543  r"""
9544  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
9545  setup_particle(_ParticleAdaptor pa, std::string id) -> Chain
9546  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
9547  setup_particle(_ParticleAdaptor pa, char id) -> Chain
9548  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
9549  setup_particle(_ParticleAdaptor pa, Chain other) -> Chain
9550  """
9551  return _IMP_atom.Chain_setup_particle(*args)
9552 
9553  @staticmethod
9554  def get_is_setup(*args):
9555  r"""
9556  get_is_setup(_ParticleAdaptor p) -> bool
9557  get_is_setup(Model m, ParticleIndex pi) -> bool
9558  """
9559  return _IMP_atom.Chain_get_is_setup(*args)
9560 
9561  def get_id(self):
9562  r"""get_id(Chain self) -> std::string"""
9563  return _IMP_atom.Chain_get_id(self)
9564 
9565  def set_id(self, c):
9566  r"""set_id(Chain self, std::string c)"""
9567  return _IMP_atom.Chain_set_id(self, c)
9568 
9569  def get_sequence(self):
9570  r"""get_sequence(Chain self) -> std::string"""
9571  return _IMP_atom.Chain_get_sequence(self)
9572 
9573  def set_sequence(self, sequence):
9574  r"""set_sequence(Chain self, std::string sequence)"""
9575  return _IMP_atom.Chain_set_sequence(self, sequence)
9576 
9577  def get_sequence_offset(self):
9578  r"""get_sequence_offset(Chain self) -> int"""
9579  return _IMP_atom.Chain_get_sequence_offset(self)
9580 
9581  def set_sequence_offset(self, offset):
9582  r"""set_sequence_offset(Chain self, int offset)"""
9583  return _IMP_atom.Chain_set_sequence_offset(self, offset)
9584 
9585  def get_uniprot_accession(self):
9586  r"""get_uniprot_accession(Chain self) -> std::string"""
9587  return _IMP_atom.Chain_get_uniprot_accession(self)
9588 
9589  def set_uniprot_accession(self, accession):
9590  r"""set_uniprot_accession(Chain self, std::string accession)"""
9591  return _IMP_atom.Chain_set_uniprot_accession(self, accession)
9592 
9593  def get_chain_type(self):
9594  r"""get_chain_type(Chain self) -> ChainType"""
9595  return _IMP_atom.Chain_get_chain_type(self)
9596 
9597  def set_chain_type(self, t):
9598  r"""set_chain_type(Chain self, ChainType t)"""
9599  return _IMP_atom.Chain_set_chain_type(self, t)
9600 
9601  @staticmethod
9602  def get_id_key():
9603  r"""get_id_key() -> SparseStringKey"""
9604  return _IMP_atom.Chain_get_id_key()
9605 
9606  @staticmethod
9607  def get_sequence_key():
9608  r"""get_sequence_key() -> SparseStringKey"""
9609  return _IMP_atom.Chain_get_sequence_key()
9610 
9611  @staticmethod
9612  def get_sequence_offset_key():
9613  r"""get_sequence_offset_key() -> SparseIntKey"""
9614  return _IMP_atom.Chain_get_sequence_offset_key()
9615 
9616  @staticmethod
9617  def get_uniprot_accession_key():
9618  r"""get_uniprot_accession_key() -> SparseStringKey"""
9619  return _IMP_atom.Chain_get_uniprot_accession_key()
9620 
9621  @staticmethod
9622  def get_chain_type_key():
9623  r"""get_chain_type_key() -> SparseIntKey"""
9624  return _IMP_atom.Chain_get_chain_type_key()
9625 
9626  def add_attribute(self, *args):
9627  r"""
9628  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
9629  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
9630  add_attribute(Chain self, IntKey a0, IMP::Int a1)
9631  add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
9632  add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
9633  add_attribute(Chain self, StringKey a0, IMP::String a1)
9634  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
9635  add_attribute(Chain self, ObjectKey a0, Object a1)
9636  add_attribute(Chain self, SparseFloatKey a0, IMP::Float a1)
9637  add_attribute(Chain self, SparseIntKey a0, IMP::Int a1)
9638  add_attribute(Chain self, SparseStringKey a0, IMP::String a1)
9639  add_attribute(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
9640  """
9641  return _IMP_atom.Chain_add_attribute(self, *args)
9642 
9643  def get_value(self, *args):
9644  r"""
9645  get_value(Chain self, FloatKey a0) -> IMP::Float
9646  get_value(Chain self, IntKey a0) -> IMP::Int
9647  get_value(Chain self, FloatsKey a0) -> IMP::Floats
9648  get_value(Chain self, IntsKey a0) -> IMP::Ints
9649  get_value(Chain self, StringKey a0) -> IMP::String
9650  get_value(Chain self, ParticleIndexKey a0) -> Particle
9651  get_value(Chain self, ObjectKey a0) -> Object
9652  get_value(Chain self, SparseFloatKey a0) -> IMP::Float
9653  get_value(Chain self, SparseIntKey a0) -> IMP::Int
9654  get_value(Chain self, SparseStringKey a0) -> IMP::String
9655  get_value(Chain self, SparseParticleIndexKey a0) -> ParticleIndex
9656  """
9657  return _IMP_atom.Chain_get_value(self, *args)
9658 
9659  def set_value(self, *args):
9660  r"""
9661  set_value(Chain self, FloatKey a0, IMP::Float a1)
9662  set_value(Chain self, IntKey a0, IMP::Int a1)
9663  set_value(Chain self, FloatsKey a0, IMP::Floats a1)
9664  set_value(Chain self, IntsKey a0, IMP::Ints a1)
9665  set_value(Chain self, StringKey a0, IMP::String a1)
9666  set_value(Chain self, ParticleIndexKey a0, Particle a1)
9667  set_value(Chain self, ObjectKey a0, Object a1)
9668  set_value(Chain self, SparseFloatKey a0, IMP::Float a1)
9669  set_value(Chain self, SparseIntKey a0, IMP::Int a1)
9670  set_value(Chain self, SparseStringKey a0, IMP::String a1)
9671  set_value(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
9672  """
9673  return _IMP_atom.Chain_set_value(self, *args)
9674 
9675  def remove_attribute(self, *args):
9676  r"""
9677  remove_attribute(Chain self, FloatKey a0)
9678  remove_attribute(Chain self, IntKey a0)
9679  remove_attribute(Chain self, FloatsKey a0)
9680  remove_attribute(Chain self, IntsKey a0)
9681  remove_attribute(Chain self, StringKey a0)
9682  remove_attribute(Chain self, ParticleIndexKey a0)
9683  remove_attribute(Chain self, ObjectKey a0)
9684  remove_attribute(Chain self, SparseFloatKey a0)
9685  remove_attribute(Chain self, SparseIntKey a0)
9686  remove_attribute(Chain self, SparseStringKey a0)
9687  remove_attribute(Chain self, SparseParticleIndexKey a0)
9688  """
9689  return _IMP_atom.Chain_remove_attribute(self, *args)
9690 
9691  def has_attribute(self, *args):
9692  r"""
9693  has_attribute(Chain self, FloatKey a0) -> bool
9694  has_attribute(Chain self, IntKey a0) -> bool
9695  has_attribute(Chain self, FloatsKey a0) -> bool
9696  has_attribute(Chain self, IntsKey a0) -> bool
9697  has_attribute(Chain self, StringKey a0) -> bool
9698  has_attribute(Chain self, ParticleIndexKey a0) -> bool
9699  has_attribute(Chain self, ObjectKey a0) -> bool
9700  has_attribute(Chain self, SparseFloatKey a0) -> bool
9701  has_attribute(Chain self, SparseIntKey a0) -> bool
9702  has_attribute(Chain self, SparseStringKey a0) -> bool
9703  has_attribute(Chain self, SparseParticleIndexKey a0) -> bool
9704  """
9705  return _IMP_atom.Chain_has_attribute(self, *args)
9706 
9707  def get_derivative(self, a0):
9708  r"""get_derivative(Chain self, FloatKey a0) -> double"""
9709  return _IMP_atom.Chain_get_derivative(self, a0)
9710 
9711  def get_name(self):
9712  r"""get_name(Chain self) -> std::string"""
9713  return _IMP_atom.Chain_get_name(self)
9714 
9715  def clear_caches(self):
9716  r"""clear_caches(Chain self)"""
9717  return _IMP_atom.Chain_clear_caches(self)
9718 
9719  def set_name(self, a0):
9720  r"""set_name(Chain self, std::string a0)"""
9721  return _IMP_atom.Chain_set_name(self, a0)
9722 
9723  def set_check_level(self, a0):
9724  r"""set_check_level(Chain self, IMP::CheckLevel a0)"""
9725  return _IMP_atom.Chain_set_check_level(self, a0)
9726 
9727  def add_to_derivative(self, a0, a1, a2):
9728  r"""add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9729  return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
9730 
9731  def set_is_optimized(self, a0, a1):
9732  r"""set_is_optimized(Chain self, FloatKey a0, bool a1)"""
9733  return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
9734 
9735  def get_is_optimized(self, a0):
9736  r"""get_is_optimized(Chain self, FloatKey a0) -> bool"""
9737  return _IMP_atom.Chain_get_is_optimized(self, a0)
9738 
9739  def get_check_level(self):
9740  r"""get_check_level(Chain self) -> IMP::CheckLevel"""
9741  return _IMP_atom.Chain_get_check_level(self)
9742 
9743  def __eq__(self, *args):
9744  r"""
9745  __eq__(Chain self, Chain o) -> bool
9746  __eq__(Chain self, Particle d) -> bool
9747  """
9748  return _IMP_atom.Chain___eq__(self, *args)
9749 
9750  def __ne__(self, *args):
9751  r"""
9752  __ne__(Chain self, Chain o) -> bool
9753  __ne__(Chain self, Particle d) -> bool
9754  """
9755  return _IMP_atom.Chain___ne__(self, *args)
9756 
9757  def __le__(self, *args):
9758  r"""
9759  __le__(Chain self, Chain o) -> bool
9760  __le__(Chain self, Particle d) -> bool
9761  """
9762  return _IMP_atom.Chain___le__(self, *args)
9763 
9764  def __lt__(self, *args):
9765  r"""
9766  __lt__(Chain self, Chain o) -> bool
9767  __lt__(Chain self, Particle d) -> bool
9768  """
9769  return _IMP_atom.Chain___lt__(self, *args)
9770 
9771  def __ge__(self, *args):
9772  r"""
9773  __ge__(Chain self, Chain o) -> bool
9774  __ge__(Chain self, Particle d) -> bool
9775  """
9776  return _IMP_atom.Chain___ge__(self, *args)
9777 
9778  def __gt__(self, *args):
9779  r"""
9780  __gt__(Chain self, Chain o) -> bool
9781  __gt__(Chain self, Particle d) -> bool
9782  """
9783  return _IMP_atom.Chain___gt__(self, *args)
9784 
9785  def __hash__(self):
9786  r"""__hash__(Chain self) -> std::size_t"""
9787  return _IMP_atom.Chain___hash__(self)
9788 
9789  def __str__(self):
9790  r"""__str__(Chain self) -> std::string"""
9791  return _IMP_atom.Chain___str__(self)
9792 
9793  def __repr__(self):
9794  r"""__repr__(Chain self) -> std::string"""
9795  return _IMP_atom.Chain___repr__(self)
9796 
9797  def _get_as_binary(self):
9798  r"""_get_as_binary(Chain self) -> PyObject *"""
9799  return _IMP_atom.Chain__get_as_binary(self)
9800 
9801  def _set_from_binary(self, p):
9802  r"""_set_from_binary(Chain self, PyObject * p)"""
9803  return _IMP_atom.Chain__set_from_binary(self, p)
9804 
9805  def __getstate__(self):
9806  p = self._get_as_binary()
9807  if len(self.__dict__) > 1:
9808  d = self.__dict__.copy()
9809  del d['this']
9810  p = (d, p)
9811  return p
9812 
9813  def __setstate__(self, p):
9814  if not hasattr(self, 'this'):
9815  self.__init__()
9816  if isinstance(p, tuple):
9817  d, p = p
9818  self.__dict__.update(d)
9819  return self._set_from_binary(p)
9820 
9821  __swig_destroy__ = _IMP_atom.delete_Chain
9822 
9823 # Register Chain in _IMP_atom:
9824 _IMP_atom.Chain_swigregister(Chain)
9825 UnknownChainType = cvar.UnknownChainType
9826 DPolypeptide = cvar.DPolypeptide
9827 LPolypeptide = cvar.LPolypeptide
9828 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
9829 Polyribonucleotide = cvar.Polyribonucleotide
9830 DPolysaccharide = cvar.DPolysaccharide
9831 LPolysaccharide = cvar.LPolysaccharide
9832 Protein = cvar.Protein
9833 DNA = cvar.DNA
9834 RNA = cvar.RNA
9835 
9836 
9837 def get_chain(h):
9838  r"""get_chain(Hierarchy h) -> Chain"""
9839  return _IMP_atom.get_chain(h)
9840 
9841 def get_chain_id(h):
9842  r"""get_chain_id(Hierarchy h) -> std::string"""
9843  return _IMP_atom.get_chain_id(h)
9844 class Selection(IMP._ParticleIndexesAdaptor):
9845  r"""Proxy of C++ IMP::atom::Selection class."""
9846 
9847  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
9848  NONE = _IMP_atom.Selection_NONE
9849 
9850  C = _IMP_atom.Selection_C
9851 
9852  N = _IMP_atom.Selection_N
9853 
9854 
9855  def __init__(self, *args):
9856  r"""
9857  __init__(Selection self) -> Selection
9858  __init__(Selection self, Hierarchy h) -> Selection
9859  __init__(Selection self, Particle h) -> Selection
9860  __init__(Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
9861  __init__(Selection self, IMP::ParticlesTemp const & h) -> Selection
9862  """
9863  _IMP_atom.Selection_swiginit(self, _IMP_atom.new_Selection(*args))
9864 
9865  def create_clone(self):
9866  r"""create_clone(Selection self) -> Selection"""
9867  return _IMP_atom.Selection_create_clone(self)
9868 
9869  def get_hierarchies(self):
9870  r"""get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
9871  return _IMP_atom.Selection_get_hierarchies(self)
9872 
9873  def set_molecules(self, mols):
9874  r"""set_molecules(Selection self, IMP::Strings mols)"""
9875  return _IMP_atom.Selection_set_molecules(self, mols)
9876 
9877  def set_resolution(self, r):
9878  r"""set_resolution(Selection self, double r)"""
9879  return _IMP_atom.Selection_set_resolution(self, r)
9880 
9881  def set_representation_type(self, t):
9882  r"""set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
9883  return _IMP_atom.Selection_set_representation_type(self, t)
9884 
9885  def set_state_index(self, state):
9886  r"""set_state_index(Selection self, int state)"""
9887  return _IMP_atom.Selection_set_state_index(self, state)
9888 
9889  def set_state_indexes(self, states):
9890  r"""set_state_indexes(Selection self, IMP::Ints states)"""
9891  return _IMP_atom.Selection_set_state_indexes(self, states)
9892 
9893  def set_terminus(self, t):
9894  r"""set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
9895  return _IMP_atom.Selection_set_terminus(self, t)
9896 
9897  def set_element(self, e):
9898  r"""set_element(Selection self, IMP::atom::Element e)"""
9899  return _IMP_atom.Selection_set_element(self, e)
9900 
9901  def set_chain_ids(self, chains):
9902  r"""set_chain_ids(Selection self, IMP::Strings chains)"""
9903  return _IMP_atom.Selection_set_chain_ids(self, chains)
9904 
9905  def set_chains(self, chains):
9906  r"""set_chains(Selection self, IMP::Strings chains)"""
9907  return _IMP_atom.Selection_set_chains(self, chains)
9908 
9909  def set_residue_indexes(self, indexes):
9910  r"""set_residue_indexes(Selection self, IMP::Ints indexes)"""
9911  return _IMP_atom.Selection_set_residue_indexes(self, indexes)
9912 
9913  def set_atom_types(self, types):
9914  r"""set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
9915  return _IMP_atom.Selection_set_atom_types(self, types)
9916 
9917  def set_residue_types(self, types):
9918  r"""set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
9919  return _IMP_atom.Selection_set_residue_types(self, types)
9920 
9921  def set_domains(self, names):
9922  r"""set_domains(Selection self, IMP::Strings names)"""
9923  return _IMP_atom.Selection_set_domains(self, names)
9924 
9925  def set_molecule(self, mol):
9926  r"""set_molecule(Selection self, std::string mol)"""
9927  return _IMP_atom.Selection_set_molecule(self, mol)
9928 
9929  def set_chain_id(self, c):
9930  r"""set_chain_id(Selection self, std::string c)"""
9931  return _IMP_atom.Selection_set_chain_id(self, c)
9932 
9933  def set_chain(self, c):
9934  r"""set_chain(Selection self, std::string c)"""
9935  return _IMP_atom.Selection_set_chain(self, c)
9936 
9937  def set_residue_index(self, i):
9938  r"""set_residue_index(Selection self, int i)"""
9939  return _IMP_atom.Selection_set_residue_index(self, i)
9940 
9941  def set_atom_type(self, types):
9942  r"""set_atom_type(Selection self, AtomType types)"""
9943  return _IMP_atom.Selection_set_atom_type(self, types)
9944 
9945  def set_residue_type(self, type):
9946  r"""set_residue_type(Selection self, ResidueType type)"""
9947  return _IMP_atom.Selection_set_residue_type(self, type)
9948 
9949  def set_domain(self, name):
9950  r"""set_domain(Selection self, std::string name)"""
9951  return _IMP_atom.Selection_set_domain(self, name)
9952 
9953  def set_copy_index(self, copy):
9954  r"""set_copy_index(Selection self, unsigned int copy)"""
9955  return _IMP_atom.Selection_set_copy_index(self, copy)
9956 
9957  def set_copy_indexes(self, copies):
9958  r"""set_copy_indexes(Selection self, IMP::Ints copies)"""
9959  return _IMP_atom.Selection_set_copy_indexes(self, copies)
9960 
9961  def set_particle_type(self, t):
9962  r"""set_particle_type(Selection self, ParticleType t)"""
9963  return _IMP_atom.Selection_set_particle_type(self, t)
9964 
9965  def set_particle_types(self, t):
9966  r"""set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
9967  return _IMP_atom.Selection_set_particle_types(self, t)
9968 
9969  def set_hierarchy_types(self, types):
9970  r"""set_hierarchy_types(Selection self, IMP::Ints types)"""
9971  return _IMP_atom.Selection_set_hierarchy_types(self, types)
9972 
9973  def set_intersection(self, s):
9974  r"""set_intersection(Selection self, Selection s)"""
9975  return _IMP_atom.Selection_set_intersection(self, s)
9976 
9977  def set_union(self, s):
9978  r"""set_union(Selection self, Selection s)"""
9979  return _IMP_atom.Selection_set_union(self, s)
9980 
9981  def set_symmetric_difference(self, s):
9982  r"""set_symmetric_difference(Selection self, Selection s)"""
9983  return _IMP_atom.Selection_set_symmetric_difference(self, s)
9984 
9985  def set_difference(self, s):
9986  r"""set_difference(Selection self, Selection s)"""
9987  return _IMP_atom.Selection_set_difference(self, s)
9988 
9989  def get_selected_particles(self, with_representation=True):
9990  r"""get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp"""
9991  return _IMP_atom.Selection_get_selected_particles(self, with_representation)
9992 
9993  def get_selected_particle_indexes(self, with_representation=True):
9994  r"""get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes"""
9995  return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
9996 
9997  def show(self, *args):
9998  r"""show(Selection self, _ostream out=std::cout)"""
9999  return _IMP_atom.Selection_show(self, *args)
10000 
10001  def __str__(self):
10002  r"""__str__(Selection self) -> std::string"""
10003  return _IMP_atom.Selection___str__(self)
10004 
10005  def __repr__(self):
10006  r"""__repr__(Selection self) -> std::string"""
10007  return _IMP_atom.Selection___repr__(self)
10008 
10009  def __init__(self, hierarchy=None,
10010  hierarchies=None, **params):
10011  if hierarchy and hierarchies:
10012  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
10013  if hierarchy:
10014  this = _IMP_atom.new_Selection(hierarchy)
10015  try: self.this.append(this)
10016  except: self.this = this
10017  elif hierarchies:
10018  this = _IMP_atom.new_Selection(hierarchies)
10019  try: self.this.append(this)
10020  except: self.this = this
10021  else:
10022  raise ValueError("Either hierarchy or hierarchies must be provided.")
10023  for k in params.keys():
10024  eval("self.set_%s(params[k])"%k)
10025 
10026  def union(self, s):
10027  news = self.create_clone()
10028  news.union_update(s)
10029  return news
10030  def intersection(self, s):
10031  news = self.create_clone()
10032  news.intersection_update(s)
10033  return news
10034  def symmetric_difference(self, s):
10035  news = self.create_clone()
10036  news.symmetric_difference_update(s)
10037  return news
10038  def difference(self, s):
10039  news = self.create_clone()
10040  news.difference_update(s)
10041  return news
10042  def union_update(self, s):
10043  self.set_union(s)
10044  return self
10045  def intersection_update(self, s):
10046  self.set_intersection(s)
10047  return self
10048  def symmetric_difference_update(self, s):
10049  self.set_symmetric_difference(s)
10050  return self
10051  def difference_update(self, s):
10052  self.set_difference(s)
10053  return self
10054  __or__ = union
10055  __and__ = intersection
10056  __xor__ = symmetric_difference
10057  __sub__ = difference
10058  __ior__ = union_update
10059  __iand__ = intersection_update
10060  __ixor__ = symmetric_difference_update
10061  __isub__ = difference_update
10062 
10063  __swig_destroy__ = _IMP_atom.delete_Selection
10064 
10065 # Register Selection in _IMP_atom:
10066 _IMP_atom.Selection_swigregister(Selection)
10067 
10068 def create_distance_restraint(*args):
10069  r"""create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint"""
10070  return _IMP_atom.create_distance_restraint(*args)
10071 
10073  r"""
10074  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
10075  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10076  """
10077  return _IMP_atom.create_connectivity_restraint(*args)
10078 
10080  r"""
10081  create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
10082  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10083  """
10084  return _IMP_atom.create_internal_connectivity_restraint(*args)
10085 
10086 def create_cover(*args):
10087  r"""create_cover(Selection s, std::string name=std::string()) -> XYZR"""
10088  return _IMP_atom.create_cover(*args)
10089 
10090 def get_mass(*args):
10091  r"""
10092  get_mass(ResidueType c) -> double
10093  get_mass(Selection s) -> double
10094  """
10095  return _IMP_atom.get_mass(*args)
10096 
10097 def get_volume(s):
10098  r"""get_volume(Selection s) -> double"""
10099  return _IMP_atom.get_volume(s)
10100 
10101 def get_surface_area(s):
10102  r"""get_surface_area(Selection s) -> double"""
10103  return _IMP_atom.get_surface_area(s)
10104 
10105 def get_leaves(*args):
10106  r"""
10107  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10108  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10109  get_leaves(Selection h) -> IMP::atom::Hierarchies
10110  """
10111  return _IMP_atom.get_leaves(*args)
10112 class SelectionGeometry(IMP.display.Geometry):
10113  r"""Proxy of C++ IMP::atom::SelectionGeometry class."""
10114 
10115  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10116 
10117  def __init__(self, *args):
10118  r"""__init__(SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry"""
10119  _IMP_atom.SelectionGeometry_swiginit(self, _IMP_atom.new_SelectionGeometry(*args))
10120 
10121  def get_version_info(self):
10122  r"""get_version_info(SelectionGeometry self) -> VersionInfo"""
10123  return _IMP_atom.SelectionGeometry_get_version_info(self)
10124  __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
10125 
10126  def __str__(self):
10127  r"""__str__(SelectionGeometry self) -> std::string"""
10128  return _IMP_atom.SelectionGeometry___str__(self)
10129 
10130  def __repr__(self):
10131  r"""__repr__(SelectionGeometry self) -> std::string"""
10132  return _IMP_atom.SelectionGeometry___repr__(self)
10133 
10134  @staticmethod
10135  def get_from(o):
10136  return _object_cast_to_SelectionGeometry(o)
10137 
10138 
10139 # Register SelectionGeometry in _IMP_atom:
10140 _IMP_atom.SelectionGeometry_swigregister(SelectionGeometry)
10141 
10142 def get_rmsd(*args):
10143  r"""
10144  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10145  get_rmsd(Selection s0, Selection s1) -> double
10146  """
10147  return _IMP_atom.get_rmsd(*args)
10148 
10149 def get_rmsd_transforming_first(*args):
10150  r"""
10151  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10152  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10153  """
10154  return _IMP_atom.get_rmsd_transforming_first(*args)
10155 
10156 def get_placement_score(source, target):
10157  r"""get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10158  return _IMP_atom.get_placement_score(source, target)
10159 
10160 def get_component_placement_score(ref1, ref2, mdl1, mdl2):
10161  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"""
10162  return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10163 
10164 def get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2):
10165  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"""
10166  return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10167 
10168 def get_radius_of_gyration(*args):
10169  r"""
10170  get_radius_of_gyration(Selection s) -> double
10171  get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10172  """
10173  return _IMP_atom.get_radius_of_gyration(*args)
10174 class ForceFieldParameters(IMP.Object):
10175  r"""Proxy of C++ IMP::atom::ForceFieldParameters class."""
10176 
10177  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10178 
10179  def __init__(self):
10180  r"""__init__(ForceFieldParameters self) -> ForceFieldParameters"""
10181  _IMP_atom.ForceFieldParameters_swiginit(self, _IMP_atom.new_ForceFieldParameters())
10182 
10183  def get_radius(self, atom):
10184  r"""get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10185  return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10186 
10187  def get_epsilon(self, atom):
10188  r"""get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10189  return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10190 
10191  def add_radii(self, *args):
10192  r"""add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=IMP::FloatKey("radius"))"""
10193  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10194 
10195  def add_well_depths(self, mhd):
10196  r"""add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10197  return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10198 
10199  def add_bonds(self, mhd):
10200  r"""add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10201  return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10202  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10203 
10204  def __str__(self):
10205  r"""__str__(ForceFieldParameters self) -> std::string"""
10206  return _IMP_atom.ForceFieldParameters___str__(self)
10207 
10208  def __repr__(self):
10209  r"""__repr__(ForceFieldParameters self) -> std::string"""
10210  return _IMP_atom.ForceFieldParameters___repr__(self)
10211 
10212  @staticmethod
10213  def get_from(o):
10214  return _object_cast_to_ForceFieldParameters(o)
10215 
10216 
10217 # Register ForceFieldParameters in _IMP_atom:
10218 _IMP_atom.ForceFieldParameters_swigregister(ForceFieldParameters)
10219 class CHARMMAtomTopology(object):
10220  r"""Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10221 
10222  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10223 
10224  def __init__(self, *args):
10225  r"""
10226  __init__(CHARMMAtomTopology self) -> CHARMMAtomTopology
10227  __init__(CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10228  __init__(CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10229  """
10230  _IMP_atom.CHARMMAtomTopology_swiginit(self, _IMP_atom.new_CHARMMAtomTopology(*args))
10231 
10232  def get_name(self):
10233  r"""get_name(CHARMMAtomTopology self) -> std::string"""
10234  return _IMP_atom.CHARMMAtomTopology_get_name(self)
10235 
10236  def get_charmm_type(self):
10237  r"""get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10238  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10239 
10240  def get_charge(self):
10241  r"""get_charge(CHARMMAtomTopology self) -> double"""
10242  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10243 
10244  def set_charmm_type(self, charmm_type):
10245  r"""set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10246  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10247 
10248  def set_charge(self, charge):
10249  r"""set_charge(CHARMMAtomTopology self, double charge)"""
10250  return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10251 
10252  def show(self, *args):
10253  r"""show(CHARMMAtomTopology self, _ostream out=std::cout)"""
10254  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10255 
10256  def __str__(self):
10257  r"""__str__(CHARMMAtomTopology self) -> std::string"""
10258  return _IMP_atom.CHARMMAtomTopology___str__(self)
10259 
10260  def __repr__(self):
10261  r"""__repr__(CHARMMAtomTopology self) -> std::string"""
10262  return _IMP_atom.CHARMMAtomTopology___repr__(self)
10263 
10264  def _get_as_binary(self):
10265  r"""_get_as_binary(CHARMMAtomTopology self) -> PyObject *"""
10266  return _IMP_atom.CHARMMAtomTopology__get_as_binary(self)
10267 
10268  def _set_from_binary(self, p):
10269  r"""_set_from_binary(CHARMMAtomTopology self, PyObject * p)"""
10270  return _IMP_atom.CHARMMAtomTopology__set_from_binary(self, p)
10271 
10272  def __getstate__(self):
10273  p = self._get_as_binary()
10274  if len(self.__dict__) > 1:
10275  d = self.__dict__.copy()
10276  del d['this']
10277  p = (d, p)
10278  return p
10279 
10280  def __setstate__(self, p):
10281  if not hasattr(self, 'this'):
10282  self.__init__()
10283  if isinstance(p, tuple):
10284  d, p = p
10285  self.__dict__.update(d)
10286  return self._set_from_binary(p)
10287 
10288  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10289 
10290 # Register CHARMMAtomTopology in _IMP_atom:
10291 _IMP_atom.CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10292 class CHARMMBondEndpoint(object):
10293  r"""Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10294 
10295  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10296 
10297  def __init__(self, atom_name, residue=None):
10298  r"""__init__(CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint"""
10299  _IMP_atom.CHARMMBondEndpoint_swiginit(self, _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue))
10300 
10301  def get_atom_name(self):
10302  r"""get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10303  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10304 
10305  def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10306  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"""
10307  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10308 
10309  def show(self, *args):
10310  r"""show(CHARMMBondEndpoint self, _ostream out=std::cout)"""
10311  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10312 
10313  def __str__(self):
10314  r"""__str__(CHARMMBondEndpoint self) -> std::string"""
10315  return _IMP_atom.CHARMMBondEndpoint___str__(self)
10316 
10317  def __repr__(self):
10318  r"""__repr__(CHARMMBondEndpoint self) -> std::string"""
10319  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10320  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10321 
10322 # Register CHARMMBondEndpoint in _IMP_atom:
10323 _IMP_atom.CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10324 class CHARMMDihedral(object):
10325  r"""Proxy of C++ IMP::atom::CHARMMConnection< 4 > class."""
10326 
10327  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10328  __repr__ = _swig_repr
10329 
10330  def __init__(self, atoms):
10331  r"""__init__(CHARMMDihedral self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10332  _IMP_atom.CHARMMDihedral_swiginit(self, _IMP_atom.new_CHARMMDihedral(atoms))
10333 
10334  def get_endpoint(self, i):
10335  r"""get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10336  return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10337 
10338  def get_contains_atom(self, name):
10339  r"""get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10340  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10341 
10342  def show(self, *args):
10343  r"""show(CHARMMDihedral self, _ostream out=std::cout)"""
10344  return _IMP_atom.CHARMMDihedral_show(self, *args)
10345  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10346 
10347 # Register CHARMMDihedral in _IMP_atom:
10348 _IMP_atom.CHARMMDihedral_swigregister(CHARMMDihedral)
10349 class CHARMMInternalCoordinate(CHARMMDihedral):
10350  r"""Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10351 
10352  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10353 
10354  def __init__(self, *args):
10355  r"""
10356  __init__(CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10357  __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
10358  """
10359  _IMP_atom.CHARMMInternalCoordinate_swiginit(self, _IMP_atom.new_CHARMMInternalCoordinate(*args))
10360 
10361  def get_first_distance(self):
10362  r"""get_first_distance(CHARMMInternalCoordinate self) -> float"""
10363  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10364 
10365  def get_second_distance(self):
10366  r"""get_second_distance(CHARMMInternalCoordinate self) -> float"""
10367  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10368 
10369  def get_first_angle(self):
10370  r"""get_first_angle(CHARMMInternalCoordinate self) -> float"""
10371  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10372 
10373  def get_second_angle(self):
10374  r"""get_second_angle(CHARMMInternalCoordinate self) -> float"""
10375  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10376 
10377  def get_dihedral(self):
10378  r"""get_dihedral(CHARMMInternalCoordinate self) -> float"""
10379  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10380 
10381  def get_improper(self):
10382  r"""get_improper(CHARMMInternalCoordinate self) -> bool"""
10383  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10384 
10385  def show(self, *args):
10386  r"""show(CHARMMInternalCoordinate self, _ostream out=std::cout)"""
10387  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10388 
10389  def __str__(self):
10390  r"""__str__(CHARMMInternalCoordinate self) -> std::string"""
10391  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10392 
10393  def __repr__(self):
10394  r"""__repr__(CHARMMInternalCoordinate self) -> std::string"""
10395  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10396  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10397 
10398 # Register CHARMMInternalCoordinate in _IMP_atom:
10399 _IMP_atom.CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10400 class CHARMMResidueTopologyBase(IMP.Object):
10401  r"""Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10402 
10403  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10404 
10405  def __init__(self, *args, **kwargs):
10406  raise AttributeError("No constructor defined")
10407 
10408  def get_type(self):
10409  r"""get_type(CHARMMResidueTopologyBase self) -> std::string"""
10410  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10411 
10412  def get_number_of_atoms(self):
10413  r"""get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10414  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10415 
10416  def add_atom(self, atom):
10417  r"""add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10418  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10419 
10420  def get_atom(self, *args):
10421  r"""
10422  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10423  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10424  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10425  """
10426  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10427 
10428  def get_number_of_bonds(self):
10429  r"""get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10430  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10431 
10432  def add_bond(self, bond):
10433  r"""add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
10434  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10435 
10436  def get_number_of_angles(self):
10437  r"""get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10438  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10439 
10440  def add_angle(self, bond):
10441  r"""add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
10442  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10443 
10444  def get_number_of_dihedrals(self):
10445  r"""get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10446  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10447 
10448  def add_dihedral(self, bond):
10449  r"""add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10450  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10451 
10452  def get_number_of_impropers(self):
10453  r"""get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10454  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10455 
10456  def add_improper(self, bond):
10457  r"""add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10458  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10459 
10460  def get_number_of_internal_coordinates(self):
10461  r"""get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
10462  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
10463 
10464  def add_internal_coordinate(self, ic):
10465  r"""add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
10466  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
10467 
10468  def get_internal_coordinate(self, index):
10469  r"""get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
10470  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
10471 
10472  def get_bond(self, index):
10473  r"""get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
10474  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
10475 
10476  def get_angle(self, index):
10477  r"""get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
10478  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
10479 
10480  def get_dihedral(self, index):
10481  r"""get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10482  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
10483 
10484  def get_improper(self, index):
10485  r"""get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10486  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
10487 
10488  def get_version_info(self):
10489  r"""get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
10490  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
10491  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
10492 
10493  def __str__(self):
10494  r"""__str__(CHARMMResidueTopologyBase self) -> std::string"""
10495  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
10496 
10497  def __repr__(self):
10498  r"""__repr__(CHARMMResidueTopologyBase self) -> std::string"""
10499  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
10500 
10501  @staticmethod
10502  def get_from(o):
10503  return _object_cast_to_CHARMMResidueTopologyBase(o)
10504 
10505 
10506 # Register CHARMMResidueTopologyBase in _IMP_atom:
10507 _IMP_atom.CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
10508 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
10509  r"""Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
10510 
10511  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10512 
10513  def __init__(self, *args):
10514  r"""
10515  __init__(CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
10516  __init__(CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
10517  """
10518  _IMP_atom.CHARMMIdealResidueTopology_swiginit(self, _IMP_atom.new_CHARMMIdealResidueTopology(*args))
10519 
10520  def remove_atom(self, name):
10521  r"""remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
10522  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
10523 
10524  def set_default_first_patch(self, patch):
10525  r"""set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10526  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
10527 
10528  def set_default_last_patch(self, patch):
10529  r"""set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10530  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
10531 
10532  def get_default_first_patch(self):
10533  r"""get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
10534  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
10535 
10536  def get_default_last_patch(self):
10537  r"""get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
10538  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
10539  __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
10540 
10541  def __str__(self):
10542  r"""__str__(CHARMMIdealResidueTopology self) -> std::string"""
10543  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
10544 
10545  def __repr__(self):
10546  r"""__repr__(CHARMMIdealResidueTopology self) -> std::string"""
10547  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
10548 
10549  @staticmethod
10550  def get_from(o):
10551  return _object_cast_to_CHARMMIdealResidueTopology(o)
10552 
10553 
10554 # Register CHARMMIdealResidueTopology in _IMP_atom:
10555 _IMP_atom.CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
10556 class CHARMMPatch(CHARMMResidueTopologyBase):
10557  r"""Proxy of C++ IMP::atom::CHARMMPatch class."""
10558 
10559  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10560 
10561  def __init__(self, type):
10562  r"""__init__(CHARMMPatch self, std::string type) -> CHARMMPatch"""
10563  _IMP_atom.CHARMMPatch_swiginit(self, _IMP_atom.new_CHARMMPatch(type))
10564 
10565  def add_removed_atom(self, name):
10566  r"""add_removed_atom(CHARMMPatch self, std::string name)"""
10567  return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
10568 
10569  def get_number_of_removed_atoms(self):
10570  r"""get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
10571  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
10572 
10573  def get_removed_atom(self, i):
10574  r"""get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
10575  return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
10576 
10577  def apply(self, *args):
10578  r"""
10579  apply(CHARMMPatch self, CHARMMResidueTopology res)
10580  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
10581  """
10582  return _IMP_atom.CHARMMPatch_apply(self, *args)
10583  __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
10584 
10585  def __str__(self):
10586  r"""__str__(CHARMMPatch self) -> std::string"""
10587  return _IMP_atom.CHARMMPatch___str__(self)
10588 
10589  def __repr__(self):
10590  r"""__repr__(CHARMMPatch self) -> std::string"""
10591  return _IMP_atom.CHARMMPatch___repr__(self)
10592 
10593  @staticmethod
10594  def get_from(o):
10595  return _object_cast_to_CHARMMPatch(o)
10596 
10597 
10598 # Register CHARMMPatch in _IMP_atom:
10599 _IMP_atom.CHARMMPatch_swigregister(CHARMMPatch)
10600 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
10601  r"""Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
10602 
10603  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10604 
10605  def __init__(self, *args):
10606  r"""
10607  __init__(CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
10608  __init__(CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
10609  """
10610  _IMP_atom.CHARMMResidueTopology_swiginit(self, _IMP_atom.new_CHARMMResidueTopology(*args))
10611 
10612  def get_patched(self):
10613  r"""get_patched(CHARMMResidueTopology self) -> bool"""
10614  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
10615 
10616  def set_patched(self, patched):
10617  r"""set_patched(CHARMMResidueTopology self, bool patched)"""
10618  return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
10619  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
10620 
10621  def __str__(self):
10622  r"""__str__(CHARMMResidueTopology self) -> std::string"""
10623  return _IMP_atom.CHARMMResidueTopology___str__(self)
10624 
10625  def __repr__(self):
10626  r"""__repr__(CHARMMResidueTopology self) -> std::string"""
10627  return _IMP_atom.CHARMMResidueTopology___repr__(self)
10628 
10629  @staticmethod
10630  def get_from(o):
10631  return _object_cast_to_CHARMMResidueTopology(o)
10632 
10633 
10634 # Register CHARMMResidueTopology in _IMP_atom:
10635 _IMP_atom.CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
10636 class CHARMMAtom(Atom):
10637  r"""Proxy of C++ IMP::atom::CHARMMAtom class."""
10638 
10639  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10640 
10641  def __init__(self, *args):
10642  r"""
10643  __init__(CHARMMAtom self) -> CHARMMAtom
10644  __init__(CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
10645  __init__(CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
10646  """
10647  _IMP_atom.CHARMMAtom_swiginit(self, _IMP_atom.new_CHARMMAtom(*args))
10648 
10649  def show(self, *args):
10650  r"""show(CHARMMAtom self, _ostream out=std::cout)"""
10651  return _IMP_atom.CHARMMAtom_show(self, *args)
10652 
10653  @staticmethod
10654  def setup_particle(*args):
10655  r"""
10656  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
10657  setup_particle(_ParticleAdaptor pa, IMP::String charmm_type) -> CHARMMAtom
10658  """
10659  return _IMP_atom.CHARMMAtom_setup_particle(*args)
10660 
10661  def get_charmm_type(self):
10662  r"""get_charmm_type(CHARMMAtom self) -> IMP::String"""
10663  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
10664 
10665  def set_charmm_type(self, t):
10666  r"""set_charmm_type(CHARMMAtom self, IMP::String t)"""
10667  return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
10668 
10669  @staticmethod
10670  def get_is_setup(*args):
10671  r"""
10672  get_is_setup(_ParticleAdaptor p) -> bool
10673  get_is_setup(Model m, ParticleIndex pi) -> bool
10674  """
10675  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
10676 
10677  @staticmethod
10678  def get_charmm_type_key():
10679  r"""get_charmm_type_key() -> StringKey"""
10680  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
10681 
10682  def add_attribute(self, *args):
10683  r"""
10684  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
10685  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10686  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
10687  add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10688  add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10689  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
10690  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10691  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
10692  add_attribute(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
10693  add_attribute(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
10694  add_attribute(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
10695  add_attribute(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
10696  """
10697  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
10698 
10699  def get_value(self, *args):
10700  r"""
10701  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
10702  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
10703  get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
10704  get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
10705  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
10706  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
10707  get_value(CHARMMAtom self, ObjectKey a0) -> Object
10708  get_value(CHARMMAtom self, SparseFloatKey a0) -> IMP::Float
10709  get_value(CHARMMAtom self, SparseIntKey a0) -> IMP::Int
10710  get_value(CHARMMAtom self, SparseStringKey a0) -> IMP::String
10711  get_value(CHARMMAtom self, SparseParticleIndexKey a0) -> ParticleIndex
10712  """
10713  return _IMP_atom.CHARMMAtom_get_value(self, *args)
10714 
10715  def set_value(self, *args):
10716  r"""
10717  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10718  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
10719  set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10720  set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10721  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
10722  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10723  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
10724  set_value(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
10725  set_value(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
10726  set_value(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
10727  set_value(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
10728  """
10729  return _IMP_atom.CHARMMAtom_set_value(self, *args)
10730 
10731  def remove_attribute(self, *args):
10732  r"""
10733  remove_attribute(CHARMMAtom self, FloatKey a0)
10734  remove_attribute(CHARMMAtom self, IntKey a0)
10735  remove_attribute(CHARMMAtom self, FloatsKey a0)
10736  remove_attribute(CHARMMAtom self, IntsKey a0)
10737  remove_attribute(CHARMMAtom self, StringKey a0)
10738  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
10739  remove_attribute(CHARMMAtom self, ObjectKey a0)
10740  remove_attribute(CHARMMAtom self, SparseFloatKey a0)
10741  remove_attribute(CHARMMAtom self, SparseIntKey a0)
10742  remove_attribute(CHARMMAtom self, SparseStringKey a0)
10743  remove_attribute(CHARMMAtom self, SparseParticleIndexKey a0)
10744  """
10745  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
10746 
10747  def has_attribute(self, *args):
10748  r"""
10749  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
10750  has_attribute(CHARMMAtom self, IntKey a0) -> bool
10751  has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
10752  has_attribute(CHARMMAtom self, IntsKey a0) -> bool
10753  has_attribute(CHARMMAtom self, StringKey a0) -> bool
10754  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
10755  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
10756  has_attribute(CHARMMAtom self, SparseFloatKey a0) -> bool
10757  has_attribute(CHARMMAtom self, SparseIntKey a0) -> bool
10758  has_attribute(CHARMMAtom self, SparseStringKey a0) -> bool
10759  has_attribute(CHARMMAtom self, SparseParticleIndexKey a0) -> bool
10760  """
10761  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
10762 
10763  def get_derivative(self, a0):
10764  r"""get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
10765  return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
10766 
10767  def get_name(self):
10768  r"""get_name(CHARMMAtom self) -> std::string"""
10769  return _IMP_atom.CHARMMAtom_get_name(self)
10770 
10771  def clear_caches(self):
10772  r"""clear_caches(CHARMMAtom self)"""
10773  return _IMP_atom.CHARMMAtom_clear_caches(self)
10774 
10775  def set_name(self, a0):
10776  r"""set_name(CHARMMAtom self, std::string a0)"""
10777  return _IMP_atom.CHARMMAtom_set_name(self, a0)
10778 
10779  def set_check_level(self, a0):
10780  r"""set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
10781  return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
10782 
10783  def add_to_derivative(self, a0, a1, a2):
10784  r"""add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10785  return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
10786 
10787  def set_is_optimized(self, a0, a1):
10788  r"""set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
10789  return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
10790 
10791  def get_is_optimized(self, a0):
10792  r"""get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
10793  return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
10794 
10795  def get_check_level(self):
10796  r"""get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
10797  return _IMP_atom.CHARMMAtom_get_check_level(self)
10798 
10799  def __eq__(self, *args):
10800  r"""
10801  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
10802  __eq__(CHARMMAtom self, Particle d) -> bool
10803  """
10804  return _IMP_atom.CHARMMAtom___eq__(self, *args)
10805 
10806  def __ne__(self, *args):
10807  r"""
10808  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
10809  __ne__(CHARMMAtom self, Particle d) -> bool
10810  """
10811  return _IMP_atom.CHARMMAtom___ne__(self, *args)
10812 
10813  def __le__(self, *args):
10814  r"""
10815  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
10816  __le__(CHARMMAtom self, Particle d) -> bool
10817  """
10818  return _IMP_atom.CHARMMAtom___le__(self, *args)
10819 
10820  def __lt__(self, *args):
10821  r"""
10822  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
10823  __lt__(CHARMMAtom self, Particle d) -> bool
10824  """
10825  return _IMP_atom.CHARMMAtom___lt__(self, *args)
10826 
10827  def __ge__(self, *args):
10828  r"""
10829  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
10830  __ge__(CHARMMAtom self, Particle d) -> bool
10831  """
10832  return _IMP_atom.CHARMMAtom___ge__(self, *args)
10833 
10834  def __gt__(self, *args):
10835  r"""
10836  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
10837  __gt__(CHARMMAtom self, Particle d) -> bool
10838  """
10839  return _IMP_atom.CHARMMAtom___gt__(self, *args)
10840 
10841  def __hash__(self):
10842  r"""__hash__(CHARMMAtom self) -> std::size_t"""
10843  return _IMP_atom.CHARMMAtom___hash__(self)
10844 
10845  def __str__(self):
10846  r"""__str__(CHARMMAtom self) -> std::string"""
10847  return _IMP_atom.CHARMMAtom___str__(self)
10848 
10849  def __repr__(self):
10850  r"""__repr__(CHARMMAtom self) -> std::string"""
10851  return _IMP_atom.CHARMMAtom___repr__(self)
10852 
10853  def _get_as_binary(self):
10854  r"""_get_as_binary(CHARMMAtom self) -> PyObject *"""
10855  return _IMP_atom.CHARMMAtom__get_as_binary(self)
10856 
10857  def _set_from_binary(self, p):
10858  r"""_set_from_binary(CHARMMAtom self, PyObject * p)"""
10859  return _IMP_atom.CHARMMAtom__set_from_binary(self, p)
10860 
10861  def __getstate__(self):
10862  p = self._get_as_binary()
10863  if len(self.__dict__) > 1:
10864  d = self.__dict__.copy()
10865  del d['this']
10866  p = (d, p)
10867  return p
10868 
10869  def __setstate__(self, p):
10870  if not hasattr(self, 'this'):
10871  self.__init__()
10872  if isinstance(p, tuple):
10873  d, p = p
10874  self.__dict__.update(d)
10875  return self._set_from_binary(p)
10876 
10877  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
10878 
10879 # Register CHARMMAtom in _IMP_atom:
10880 _IMP_atom.CHARMMAtom_swigregister(CHARMMAtom)
10881 
10882 def get_charmm_untyped_atoms(hierarchy):
10883  r"""get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
10884  return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
10885 
10886 def remove_charmm_untyped_atoms(hierarchy):
10887  r"""remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
10888  return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
10889 class CHARMMBondParameters(object):
10890  r"""Proxy of C++ IMP::atom::CHARMMBondParameters class."""
10891 
10892  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10893  force_constant = property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set, doc=r"""force_constant : double""")
10894  ideal = property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set, doc=r"""ideal : double""")
10895 
10896  def __init__(self):
10897  r"""__init__(CHARMMBondParameters self) -> CHARMMBondParameters"""
10898  _IMP_atom.CHARMMBondParameters_swiginit(self, _IMP_atom.new_CHARMMBondParameters())
10899 
10900  def show(self, *args):
10901  r"""show(CHARMMBondParameters self, _ostream out=std::cout)"""
10902  return _IMP_atom.CHARMMBondParameters_show(self, *args)
10903 
10904  def __str__(self):
10905  r"""__str__(CHARMMBondParameters self) -> std::string"""
10906  return _IMP_atom.CHARMMBondParameters___str__(self)
10907 
10908  def __repr__(self):
10909  r"""__repr__(CHARMMBondParameters self) -> std::string"""
10910  return _IMP_atom.CHARMMBondParameters___repr__(self)
10911 
10912  def _get_as_binary(self):
10913  r"""_get_as_binary(CHARMMBondParameters self) -> PyObject *"""
10914  return _IMP_atom.CHARMMBondParameters__get_as_binary(self)
10915 
10916  def _set_from_binary(self, p):
10917  r"""_set_from_binary(CHARMMBondParameters self, PyObject * p)"""
10918  return _IMP_atom.CHARMMBondParameters__set_from_binary(self, p)
10919 
10920  def __getstate__(self):
10921  p = self._get_as_binary()
10922  if len(self.__dict__) > 1:
10923  d = self.__dict__.copy()
10924  del d['this']
10925  p = (d, p)
10926  return p
10927 
10928  def __setstate__(self, p):
10929  if not hasattr(self, 'this'):
10930  self.__init__()
10931  if isinstance(p, tuple):
10932  d, p = p
10933  self.__dict__.update(d)
10934  return self._set_from_binary(p)
10935 
10936  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
10937 
10938 # Register CHARMMBondParameters in _IMP_atom:
10939 _IMP_atom.CHARMMBondParameters_swigregister(CHARMMBondParameters)
10940 class CHARMMDihedralParameters(object):
10941  r"""Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
10942 
10943  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10944  force_constant = property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set, doc=r"""force_constant : double""")
10945  multiplicity = property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set, doc=r"""multiplicity : int""")
10946  ideal = property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set, doc=r"""ideal : double""")
10947 
10948  def __init__(self):
10949  r"""__init__(CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
10950  _IMP_atom.CHARMMDihedralParameters_swiginit(self, _IMP_atom.new_CHARMMDihedralParameters())
10951 
10952  def show(self, *args):
10953  r"""show(CHARMMDihedralParameters self, _ostream out=std::cout)"""
10954  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
10955 
10956  def __str__(self):
10957  r"""__str__(CHARMMDihedralParameters self) -> std::string"""
10958  return _IMP_atom.CHARMMDihedralParameters___str__(self)
10959 
10960  def __repr__(self):
10961  r"""__repr__(CHARMMDihedralParameters self) -> std::string"""
10962  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
10963 
10964  def _get_as_binary(self):
10965  r"""_get_as_binary(CHARMMDihedralParameters self) -> PyObject *"""
10966  return _IMP_atom.CHARMMDihedralParameters__get_as_binary(self)
10967 
10968  def _set_from_binary(self, p):
10969  r"""_set_from_binary(CHARMMDihedralParameters self, PyObject * p)"""
10970  return _IMP_atom.CHARMMDihedralParameters__set_from_binary(self, p)
10971 
10972  def __getstate__(self):
10973  p = self._get_as_binary()
10974  if len(self.__dict__) > 1:
10975  d = self.__dict__.copy()
10976  del d['this']
10977  p = (d, p)
10978  return p
10979 
10980  def __setstate__(self, p):
10981  if not hasattr(self, 'this'):
10982  self.__init__()
10983  if isinstance(p, tuple):
10984  d, p = p
10985  self.__dict__.update(d)
10986  return self._set_from_binary(p)
10987 
10988  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
10989 
10990 # Register CHARMMDihedralParameters in _IMP_atom:
10991 _IMP_atom.CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
10992 class CHARMMParameters(ForceFieldParameters):
10993  r"""Proxy of C++ IMP::atom::CHARMMParameters class."""
10994 
10995  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
10996 
10997  def __init__(self, *args):
10998  r"""__init__(CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters"""
10999  _IMP_atom.CHARMMParameters_swiginit(self, _IMP_atom.new_CHARMMParameters(*args))
11000 
11001  def add_residue_topology(self, res):
11002  r"""add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11003  return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11004 
11005  def get_residue_topology(self, type):
11006  r"""get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11007  return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11008 
11009  def add_patch(self, patch):
11010  r"""add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11011  return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11012 
11013  def get_patch(self, name):
11014  r"""get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11015  return _IMP_atom.CHARMMParameters_get_patch(self, name)
11016 
11017  def create_topology(self, hierarchy):
11018  r"""create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11019  return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11020 
11021  def get_bond_parameters(self, type1, type2):
11022  r"""get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11023  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11024 
11025  def get_angle_parameters(self, type1, type2, type3):
11026  r"""get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11027  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11028 
11029  def get_dihedral_parameters(self, type1, type2, type3, type4):
11030  r"""get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11031  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11032 
11033  def get_improper_parameters(self, type1, type2, type3, type4):
11034  r"""get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11035  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11036 
11037  def create_angles(self, bonds):
11038  r"""create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11039  return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11040 
11041  def create_dihedrals(self, bonds):
11042  r"""create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11043  return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11044 
11045  def get_version_info(self):
11046  r"""get_version_info(CHARMMParameters self) -> VersionInfo"""
11047  return _IMP_atom.CHARMMParameters_get_version_info(self)
11048  __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
11049 
11050  def __str__(self):
11051  r"""__str__(CHARMMParameters self) -> std::string"""
11052  return _IMP_atom.CHARMMParameters___str__(self)
11053 
11054  def __repr__(self):
11055  r"""__repr__(CHARMMParameters self) -> std::string"""
11056  return _IMP_atom.CHARMMParameters___repr__(self)
11057 
11058  @staticmethod
11059  def get_from(o):
11060  return _object_cast_to_CHARMMParameters(o)
11061 
11062 
11063 # Register CHARMMParameters in _IMP_atom:
11064 _IMP_atom.CHARMMParameters_swigregister(CHARMMParameters)
11065 
11067  r"""get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11068  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11069 
11071  r"""get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11072  return _IMP_atom.get_all_atom_CHARMM_parameters()
11073 class CHARMMSegmentTopology(IMP.Object):
11074  r"""Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11075 
11076  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11077  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)
11078  def __set_residues(self, obj): IMP._list_util.set_varlist(self.residues, obj)
11079  def __del_residues(self): IMP._list_util.del_varlist(self.residues)
11080  residues = property(__get_residues, __set_residues, __del_residues, doc="List of ##ucnames")
11081 
11082  def remove_residue(self, d):
11083  r"""remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11084  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11085 
11086  def _python_index_residue(self, d, start, stop):
11087  r"""_python_index_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11088  return _IMP_atom.CHARMMSegmentTopology__python_index_residue(self, d, start, stop)
11089 
11090  def remove_residues(self, d):
11091  r"""remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11092  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11093 
11094  def set_residues(self, ps):
11095  r"""set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11096  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11097 
11098  def set_residues_order(self, objs):
11099  r"""set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11100  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11101 
11102  def add_residue(self, obj):
11103  r"""add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11104  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11105 
11106  def add_residues(self, objs):
11107  r"""add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11108  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11109 
11110  def clear_residues(self):
11111  r"""clear_residues(CHARMMSegmentTopology self)"""
11112  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11113 
11114  def get_number_of_residues(self):
11115  r"""get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11116  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11117 
11118  def get_has_residues(self):
11119  r"""get_has_residues(CHARMMSegmentTopology self) -> bool"""
11120  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11121 
11122  def get_residue(self, i):
11123  r"""get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11124  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11125 
11126  def get_residues(self):
11127  r"""get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11128  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11129 
11130  def erase_residue(self, i):
11131  r"""erase_residue(CHARMMSegmentTopology self, unsigned int i)"""
11132  return _IMP_atom.CHARMMSegmentTopology_erase_residue(self, i)
11133 
11134  def reserve_residues(self, sz):
11135  r"""reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11136  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11137 
11138  def get_version_info(self):
11139  r"""get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11140  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11141  __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
11142 
11143  def __init__(self, *args):
11144  r"""__init__(CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology"""
11145  _IMP_atom.CHARMMSegmentTopology_swiginit(self, _IMP_atom.new_CHARMMSegmentTopology(*args))
11146 
11147  def apply_default_patches(self, ff):
11148  r"""apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11149  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11150 
11151  def __str__(self):
11152  r"""__str__(CHARMMSegmentTopology self) -> std::string"""
11153  return _IMP_atom.CHARMMSegmentTopology___str__(self)
11154 
11155  def __repr__(self):
11156  r"""__repr__(CHARMMSegmentTopology self) -> std::string"""
11157  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11158 
11159  @staticmethod
11160  def get_from(o):
11161  return _object_cast_to_CHARMMSegmentTopology(o)
11162 
11163 
11164 # Register CHARMMSegmentTopology in _IMP_atom:
11165 _IMP_atom.CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11166 class CHARMMTopology(IMP.Object):
11167  r"""Proxy of C++ IMP::atom::CHARMMTopology class."""
11168 
11169  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11170 
11171  def __init__(self, *args):
11172  r"""__init__(CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology"""
11173  _IMP_atom.CHARMMTopology_swiginit(self, _IMP_atom.new_CHARMMTopology(*args))
11174 
11175  def get_parameters(self):
11176  r"""get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11177  return _IMP_atom.CHARMMTopology_get_parameters(self)
11178 
11179  def add_sequence(self, sequence):
11180  r"""add_sequence(CHARMMTopology self, std::string sequence)"""
11181  return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11182 
11183  def apply_default_patches(self):
11184  r"""apply_default_patches(CHARMMTopology self)"""
11185  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11186 
11187  def create_hierarchy(self, model):
11188  r"""create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11189  return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11190 
11191  def add_atom_types(self, hierarchy):
11192  r"""add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11193  return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11194 
11195  def add_coordinates(self, hierarchy):
11196  r"""add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11197  return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11198 
11199  def add_missing_atoms(self, hierarchy):
11200  r"""add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11201  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11202 
11203  def setup_hierarchy(self, hierarchy):
11204  r"""setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11205  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11206 
11207  def add_charges(self, hierarchy):
11208  r"""add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11209  return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11210 
11211  def add_bonds(self, hierarchy):
11212  r"""add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11213  return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11214 
11215  def add_dihedrals(self, hierarchy):
11216  r"""add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11217  return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11218 
11219  def add_impropers(self, hierarchy):
11220  r"""add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11221  return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11222  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)
11223  def __set_segments(self, obj): IMP._list_util.set_varlist(self.segments, obj)
11224  def __del_segments(self): IMP._list_util.del_varlist(self.segments)
11225  segments = property(__get_segments, __set_segments, __del_segments, doc="List of ##ucnames")
11226 
11227  def remove_segment(self, d):
11228  r"""remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11229  return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11230 
11231  def _python_index_segment(self, d, start, stop):
11232  r"""_python_index_segment(CHARMMTopology self, CHARMMSegmentTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11233  return _IMP_atom.CHARMMTopology__python_index_segment(self, d, start, stop)
11234 
11235  def remove_segments(self, d):
11236  r"""remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11237  return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11238 
11239  def set_segments(self, ps):
11240  r"""set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11241  return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11242 
11243  def set_segments_order(self, objs):
11244  r"""set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11245  return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11246 
11247  def add_segment(self, obj):
11248  r"""add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11249  return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11250 
11251  def add_segments(self, objs):
11252  r"""add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11253  return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11254 
11255  def clear_segments(self):
11256  r"""clear_segments(CHARMMTopology self)"""
11257  return _IMP_atom.CHARMMTopology_clear_segments(self)
11258 
11259  def get_number_of_segments(self):
11260  r"""get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11261  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11262 
11263  def get_has_segments(self):
11264  r"""get_has_segments(CHARMMTopology self) -> bool"""
11265  return _IMP_atom.CHARMMTopology_get_has_segments(self)
11266 
11267  def get_segment(self, i):
11268  r"""get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11269  return _IMP_atom.CHARMMTopology_get_segment(self, i)
11270 
11271  def get_segments(self):
11272  r"""get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11273  return _IMP_atom.CHARMMTopology_get_segments(self)
11274 
11275  def erase_segment(self, i):
11276  r"""erase_segment(CHARMMTopology self, unsigned int i)"""
11277  return _IMP_atom.CHARMMTopology_erase_segment(self, i)
11278 
11279  def reserve_segments(self, sz):
11280  r"""reserve_segments(CHARMMTopology self, unsigned int sz)"""
11281  return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11282 
11283  def get_version_info(self):
11284  r"""get_version_info(CHARMMTopology self) -> VersionInfo"""
11285  return _IMP_atom.CHARMMTopology_get_version_info(self)
11286  __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
11287 
11288  def __str__(self):
11289  r"""__str__(CHARMMTopology self) -> std::string"""
11290  return _IMP_atom.CHARMMTopology___str__(self)
11291 
11292  def __repr__(self):
11293  r"""__repr__(CHARMMTopology self) -> std::string"""
11294  return _IMP_atom.CHARMMTopology___repr__(self)
11295 
11296  @staticmethod
11297  def get_from(o):
11298  return _object_cast_to_CHARMMTopology(o)
11299 
11300 
11301 # Register CHARMMTopology in _IMP_atom:
11302 _IMP_atom.CHARMMTopology_swigregister(CHARMMTopology)
11303 class CHARMMStereochemistryRestraint(IMP.Restraint):
11304  r"""Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11305 
11306  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11307 
11308  def __init__(self, *args):
11309  r"""
11310  __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11311  __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11312  """
11313  _IMP_atom.CHARMMStereochemistryRestraint_swiginit(self, _IMP_atom.new_CHARMMStereochemistryRestraint(*args))
11314 
11315  def get_pair_filter(self):
11316  r"""get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11317  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11318 
11319  def get_full_pair_filter(self):
11320  r"""get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11321  return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11322 
11323  def do_get_inputs(self):
11324  r"""do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11325  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11326 
11327  def get_version_info(self):
11328  r"""get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11329  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11330  __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
11331 
11332  def __str__(self):
11333  r"""__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11334  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11335 
11336  def __repr__(self):
11337  r"""__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11338  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11339 
11340  @staticmethod
11341  def get_from(o):
11342  return _object_cast_to_CHARMMStereochemistryRestraint(o)
11343 
11344 
11345 # Register CHARMMStereochemistryRestraint in _IMP_atom:
11346 _IMP_atom.CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11347 
11348 def add_bonds(*args):
11349  r"""add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())"""
11350  return _IMP_atom.add_bonds(*args)
11351 
11352 def add_radii(*args):
11353  r"""add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(), FloatKey radius_key=IMP::FloatKey("radius"))"""
11354  return _IMP_atom.add_radii(*args)
11355 ALBER = _IMP_atom.ALBER
11356 
11357 HARPAZ = _IMP_atom.HARPAZ
11358 
11359 ANDERSSON = _IMP_atom.ANDERSSON
11360 
11361 TSAI = _IMP_atom.TSAI
11362 
11363 QUILLIN = _IMP_atom.QUILLIN
11364 
11365 SQUIRE = _IMP_atom.SQUIRE
11366 
11367 
11368 def get_protein_density_from_reference(densityReference):
11369  r"""get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11370  return _IMP_atom.get_protein_density_from_reference(densityReference)
11371 
11372 def get_volume_from_mass(*args):
11373  r"""get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11374  return _IMP_atom.get_volume_from_mass(*args)
11375 
11376 def get_mass_from_volume(*args):
11377  r"""get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11378  return _IMP_atom.get_mass_from_volume(*args)
11379 
11381  r"""get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11382  return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11383 
11385  r"""get_volume_from_residue_type(ResidueType rt) -> double"""
11386  return _IMP_atom.get_volume_from_residue_type(rt)
11387 
11388 def get_molarity(n, volume):
11389  r"""get_molarity(double n, double volume) -> double"""
11390  return _IMP_atom.get_molarity(n, volume)
11391 
11392 def get_kd(na, nb, nab, volume):
11393  r"""get_kd(double na, double nb, double nab, double volume) -> double"""
11394  return _IMP_atom.get_kd(na, nb, nab, volume)
11395 
11396 def get_einstein_diffusion_coefficient(r, temp=-1):
11397  r"""get_einstein_diffusion_coefficient(double r, double temp=-1) -> double"""
11398  return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
11399 
11401  r"""get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double"""
11402  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
11403 
11404 def get_diffusion_length(*args):
11405  r"""
11406  get_diffusion_length(double D, double t) -> double
11407  get_diffusion_length(double D, double force, double t, double temp=-1) -> double
11408  """
11409  return _IMP_atom.get_diffusion_length(*args)
11410 
11411 def get_diffusion_angle(D, dtfs):
11412  r"""get_diffusion_angle(double D, double dtfs) -> double"""
11413  return _IMP_atom.get_diffusion_angle(D, dtfs)
11414 
11415 def get_diffusion_coefficient(*args):
11416  r"""
11417  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
11418  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
11419  """
11420  return _IMP_atom.get_diffusion_coefficient(*args)
11421 
11422 def get_rotational_diffusion_coefficient(orientations, dt):
11423  r"""get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
11424  return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
11425 
11426 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11427  r"""get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11428  return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11429 
11430 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
11431  r"""get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11432  return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11433 
11434 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
11435  r"""get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11436  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11437 class EzRestraint(IMP.Restraint):
11438  r"""Proxy of C++ IMP::atom::EzRestraint class."""
11439 
11440  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11441 
11442  def __init__(self, m, ps):
11443  r"""__init__(EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11444  _IMP_atom.EzRestraint_swiginit(self, _IMP_atom.new_EzRestraint(m, ps))
11445 
11446  def get_version_info(self):
11447  r"""get_version_info(EzRestraint self) -> VersionInfo"""
11448  return _IMP_atom.EzRestraint_get_version_info(self)
11449  __swig_destroy__ = _IMP_atom.delete_EzRestraint
11450 
11451  def __str__(self):
11452  r"""__str__(EzRestraint self) -> std::string"""
11453  return _IMP_atom.EzRestraint___str__(self)
11454 
11455  def __repr__(self):
11456  r"""__repr__(EzRestraint self) -> std::string"""
11457  return _IMP_atom.EzRestraint___repr__(self)
11458 
11459  @staticmethod
11460  def get_from(o):
11461  return _object_cast_to_EzRestraint(o)
11462 
11463 
11464 # Register EzRestraint in _IMP_atom:
11465 _IMP_atom.EzRestraint_swigregister(EzRestraint)
11466 
11467 def create_protein(*args):
11468  r"""
11469  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
11470  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
11471  """
11472  return _IMP_atom.create_protein(*args)
11473 
11475  r"""
11476  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
11477  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
11478  """
11479  return _IMP_atom.create_simplified_along_backbone(*args)
11480 
11481 def create_simplified_from_volume(h, resolution):
11482  r"""create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11483  return _IMP_atom.create_simplified_from_volume(h, resolution)
11484 
11485 def create_simplified_assembly_from_volume(h, resolution):
11486  r"""create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11487  return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
11488 
11489 def get_residue_indexes(h):
11490  r"""get_residue_indexes(Hierarchy h) -> IMP::Ints"""
11491  return _IMP_atom.get_residue_indexes(h)
11492 
11493 def get_residue_type(*args):
11494  r"""
11495  get_residue_type(char c) -> ResidueType
11496  get_residue_type(Hierarchy h) -> ResidueType
11497  """
11498  return _IMP_atom.get_residue_type(*args)
11499 
11500 def get_atom_type(h):
11501  r"""get_atom_type(Hierarchy h) -> AtomType"""
11502  return _IMP_atom.get_atom_type(h)
11503 
11504 def get_domain_name(h):
11505  r"""get_domain_name(Hierarchy h) -> std::string"""
11506  return _IMP_atom.get_domain_name(h)
11507 
11509  r"""
11510  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
11511  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
11512  """
11513  return _IMP_atom.create_excluded_volume_restraint(*args)
11514 
11515 def setup_as_approximation(*args):
11516  r"""
11517  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
11518  setup_as_approximation(Hierarchy h, double resolution=-1)
11519  """
11520  return _IMP_atom.setup_as_approximation(*args)
11521 class _HierarchyTreeVertexIndex(object):
11522  r"""Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
11523 
11524  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11525  __repr__ = _swig_repr
11526 
11527  def __init__(self):
11528  r"""__init__(_HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
11529  _IMP_atom._HierarchyTreeVertexIndex_swiginit(self, _IMP_atom.new__HierarchyTreeVertexIndex())
11530  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
11531 
11532 # Register _HierarchyTreeVertexIndex in _IMP_atom:
11533 _IMP_atom._HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
11534 
11535 def show_as_graphviz(name, out):
11536  r"""show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
11537  return _IMP_atom.show_as_graphviz(name, out)
11538 
11539 def get_vertex_index(g):
11540  r"""get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
11541  return _IMP_atom.get_vertex_index(g)
11542 
11543 def get_hierarchy_tree(h):
11544  r"""get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
11545  return _IMP_atom.get_hierarchy_tree(h)
11546 class HierarchyGeometry(IMP.display.SingletonGeometry):
11547  r"""Proxy of C++ IMP::atom::HierarchyGeometry class."""
11548 
11549  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11550 
11551  def __init__(self, d, resolution=0):
11552  r"""__init__(HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry"""
11553  _IMP_atom.HierarchyGeometry_swiginit(self, _IMP_atom.new_HierarchyGeometry(d, resolution))
11554 
11555  def get_version_info(self):
11556  r"""get_version_info(HierarchyGeometry self) -> VersionInfo"""
11557  return _IMP_atom.HierarchyGeometry_get_version_info(self)
11558  __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
11559 
11560  def __str__(self):
11561  r"""__str__(HierarchyGeometry self) -> std::string"""
11562  return _IMP_atom.HierarchyGeometry___str__(self)
11563 
11564  def __repr__(self):
11565  r"""__repr__(HierarchyGeometry self) -> std::string"""
11566  return _IMP_atom.HierarchyGeometry___repr__(self)
11567 
11568  @staticmethod
11569  def get_from(o):
11570  return _object_cast_to_HierarchyGeometry(o)
11571 
11572 
11573 # Register HierarchyGeometry in _IMP_atom:
11574 _IMP_atom.HierarchyGeometry_swigregister(HierarchyGeometry)
11575 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
11576  r"""Proxy of C++ IMP::atom::HierarchiesGeometry class."""
11577 
11578  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11579 
11580  def __init__(self, sc, resolution=-1):
11581  r"""__init__(HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry"""
11582  _IMP_atom.HierarchiesGeometry_swiginit(self, _IMP_atom.new_HierarchiesGeometry(sc, resolution))
11583 
11584  def get_version_info(self):
11585  r"""get_version_info(HierarchiesGeometry self) -> VersionInfo"""
11586  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
11587  __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
11588 
11589  def __str__(self):
11590  r"""__str__(HierarchiesGeometry self) -> std::string"""
11591  return _IMP_atom.HierarchiesGeometry___str__(self)
11592 
11593  def __repr__(self):
11594  r"""__repr__(HierarchiesGeometry self) -> std::string"""
11595  return _IMP_atom.HierarchiesGeometry___repr__(self)
11596 
11597  @staticmethod
11598  def get_from(o):
11599  return _object_cast_to_HierarchiesGeometry(o)
11600 
11601 
11602 # Register HierarchiesGeometry in _IMP_atom:
11603 _IMP_atom.HierarchiesGeometry_swigregister(HierarchiesGeometry)
11604 
11605 def transform(*args):
11606  r"""
11607  transform(Hierarchy h, Transformation3D tr)
11608  transform(Hierarchy h, Transformation3D tr)
11609  """
11610  return _IMP_atom.transform(*args)
11611 class DopePairScore(_ADopeBase):
11612  r"""Proxy of C++ IMP::atom::DopePairScore class."""
11613 
11614  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11615 
11616  def __init__(self, *args):
11617  r"""
11618  __init__(DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
11619  __init__(DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
11620  """
11621  _IMP_atom.DopePairScore_swiginit(self, _IMP_atom.new_DopePairScore(*args))
11622 
11623  def __str__(self):
11624  r"""__str__(DopePairScore self) -> std::string"""
11625  return _IMP_atom.DopePairScore___str__(self)
11626 
11627  def __repr__(self):
11628  r"""__repr__(DopePairScore self) -> std::string"""
11629  return _IMP_atom.DopePairScore___repr__(self)
11630 
11631  @staticmethod
11632  def get_from(o):
11633  return _object_cast_to_DopePairScore(o)
11634 
11635  __swig_destroy__ = _IMP_atom.delete_DopePairScore
11636 
11637 # Register DopePairScore in _IMP_atom:
11638 _IMP_atom.DopePairScore_swigregister(DopePairScore)
11639 
11640 def add_dope_score_data(h):
11641  r"""add_dope_score_data(Hierarchy h)"""
11642  return _IMP_atom.add_dope_score_data(h)
11643 class LoopStatisticalPairScore(_ALoopStatisticalBase):
11644  r"""Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
11645 
11646  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11647 
11648  def __init__(self, *args):
11649  r"""
11650  __init__(LoopStatisticalPairScore self, double threshold=std::numeric_limits< double >::max()) -> LoopStatisticalPairScore
11651  __init__(LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
11652  """
11653  _IMP_atom.LoopStatisticalPairScore_swiginit(self, _IMP_atom.new_LoopStatisticalPairScore(*args))
11654 
11655  def __str__(self):
11656  r"""__str__(LoopStatisticalPairScore self) -> std::string"""
11657  return _IMP_atom.LoopStatisticalPairScore___str__(self)
11658 
11659  def __repr__(self):
11660  r"""__repr__(LoopStatisticalPairScore self) -> std::string"""
11661  return _IMP_atom.LoopStatisticalPairScore___repr__(self)
11662 
11663  @staticmethod
11664  def get_from(o):
11665  return _object_cast_to_LoopStatisticalPairScore(o)
11666 
11667  __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
11668 
11669 # Register LoopStatisticalPairScore in _IMP_atom:
11670 _IMP_atom.LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
11671 
11673  r"""add_loop_statistical_score_data(Hierarchy h)"""
11674  return _IMP_atom.add_loop_statistical_score_data(h)
11675 class OrientedSoapPairScore(_OrientedSoapBase):
11676  r"""Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
11677 
11678  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11679 
11680  def __init__(self, library):
11681  r"""__init__(OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
11682  _IMP_atom.OrientedSoapPairScore_swiginit(self, _IMP_atom.new_OrientedSoapPairScore(library))
11683 
11684  def get_pair_filter(self):
11685  r"""get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
11686  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
11687 
11688  def __str__(self):
11689  r"""__str__(OrientedSoapPairScore self) -> std::string"""
11690  return _IMP_atom.OrientedSoapPairScore___str__(self)
11691 
11692  def __repr__(self):
11693  r"""__repr__(OrientedSoapPairScore self) -> std::string"""
11694  return _IMP_atom.OrientedSoapPairScore___repr__(self)
11695 
11696  @staticmethod
11697  def get_from(o):
11698  return _object_cast_to_OrientedSoapPairScore(o)
11699 
11700  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
11701 
11702 # Register OrientedSoapPairScore in _IMP_atom:
11703 _IMP_atom.OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
11704 class SameResiduePairFilter(IMP.PairPredicate):
11705  r"""Proxy of C++ IMP::atom::SameResiduePairFilter class."""
11706 
11707  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11708 
11709  def __init__(self):
11710  r"""__init__(SameResiduePairFilter self) -> SameResiduePairFilter"""
11711  _IMP_atom.SameResiduePairFilter_swiginit(self, _IMP_atom.new_SameResiduePairFilter())
11712 
11713  def do_get_inputs(self, m, pis):
11714  r"""do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
11715  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
11716 
11717  def get_value(self, *args):
11718  r"""
11719  get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
11720  get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
11721  """
11722  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
11723 
11724  def get_value_index(self, *args):
11725  r"""
11726  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
11727  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
11728  """
11729  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
11730 
11731  def get_version_info(self):
11732  r"""get_version_info(SameResiduePairFilter self) -> VersionInfo"""
11733  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
11734  __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
11735 
11736  def __str__(self):
11737  r"""__str__(SameResiduePairFilter self) -> std::string"""
11738  return _IMP_atom.SameResiduePairFilter___str__(self)
11739 
11740  def __repr__(self):
11741  r"""__repr__(SameResiduePairFilter self) -> std::string"""
11742  return _IMP_atom.SameResiduePairFilter___repr__(self)
11743 
11744  @staticmethod
11745  def get_from(o):
11746  return _object_cast_to_SameResiduePairFilter(o)
11747 
11748 
11749 # Register SameResiduePairFilter in _IMP_atom:
11750 _IMP_atom.SameResiduePairFilter_swigregister(SameResiduePairFilter)
11751 class RemoveRigidMotionOptimizerState(IMP.OptimizerState):
11752  r"""Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
11753 
11754  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11755 
11756  def __init__(self, m, pis):
11757  r"""__init__(RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
11758  _IMP_atom.RemoveRigidMotionOptimizerState_swiginit(self, _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis))
11759 
11760  def set_particles(self, pis):
11761  r"""set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
11762  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
11763 
11764  def remove_rigid_motion(self):
11765  r"""remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
11766  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
11767 
11768  def get_version_info(self):
11769  r"""get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
11770  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
11771  __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
11772 
11773  def __str__(self):
11774  r"""__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
11775  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
11776 
11777  def __repr__(self):
11778  r"""__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
11779  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
11780 
11781  @staticmethod
11782  def get_from(o):
11783  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
11784 
11785 
11786 # Register RemoveRigidMotionOptimizerState in _IMP_atom:
11787 _IMP_atom.RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
11788 class BerendsenThermostatOptimizerState(IMP.OptimizerState):
11789  r"""Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
11790 
11791  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11792 
11793  def __init__(self, pis, temperature, tau):
11794  r"""__init__(BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
11795  _IMP_atom.BerendsenThermostatOptimizerState_swiginit(self, _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau))
11796 
11797  def set_particles(self, pis):
11798  r"""set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
11799  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
11800 
11801  def get_temperature(self):
11802  r"""get_temperature(BerendsenThermostatOptimizerState self) -> double"""
11803  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
11804 
11805  def get_tau(self):
11806  r"""get_tau(BerendsenThermostatOptimizerState self) -> double"""
11807  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
11808 
11809  def set_temperature(self, temperature):
11810  r"""set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
11811  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
11812 
11813  def set_tau(self, tau):
11814  r"""set_tau(BerendsenThermostatOptimizerState self, double tau)"""
11815  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
11816 
11817  def rescale_velocities(self):
11818  r"""rescale_velocities(BerendsenThermostatOptimizerState self)"""
11819  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
11820 
11821  def get_version_info(self):
11822  r"""get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
11823  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
11824  __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
11825 
11826  def __str__(self):
11827  r"""__str__(BerendsenThermostatOptimizerState self) -> std::string"""
11828  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
11829 
11830  def __repr__(self):
11831  r"""__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
11832  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
11833 
11834  @staticmethod
11835  def get_from(o):
11836  return _object_cast_to_BerendsenThermostatOptimizerState(o)
11837 
11838 
11839 # Register BerendsenThermostatOptimizerState in _IMP_atom:
11840 _IMP_atom.BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
11841 class LangevinThermostatOptimizerState(IMP.OptimizerState):
11842  r"""Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
11843 
11844  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11845 
11846  def __init__(self, m, pis, temperature, gamma):
11847  r"""__init__(LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
11848  _IMP_atom.LangevinThermostatOptimizerState_swiginit(self, _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma))
11849 
11850  def set_particles(self, pis):
11851  r"""set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
11852  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
11853 
11854  def get_temperature(self):
11855  r"""get_temperature(LangevinThermostatOptimizerState self) -> double"""
11856  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
11857 
11858  def get_gamma(self):
11859  r"""get_gamma(LangevinThermostatOptimizerState self) -> double"""
11860  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
11861 
11862  def set_temperature(self, temperature):
11863  r"""set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
11864  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
11865 
11866  def set_gamma(self, gamma):
11867  r"""set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
11868  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
11869 
11870  def rescale_velocities(self):
11871  r"""rescale_velocities(LangevinThermostatOptimizerState self)"""
11872  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
11873 
11874  def get_version_info(self):
11875  r"""get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
11876  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
11877  __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
11878 
11879  def __str__(self):
11880  r"""__str__(LangevinThermostatOptimizerState self) -> std::string"""
11881  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
11882 
11883  def __repr__(self):
11884  r"""__repr__(LangevinThermostatOptimizerState self) -> std::string"""
11885  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
11886 
11887  @staticmethod
11888  def get_from(o):
11889  return _object_cast_to_LangevinThermostatOptimizerState(o)
11890 
11891 
11892 # Register LangevinThermostatOptimizerState in _IMP_atom:
11893 _IMP_atom.LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
11894 class PDBRecord(IMP._Value):
11895  r"""Proxy of C++ IMP::atom::PDBRecord class."""
11896 
11897  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11898 
11899  def __init__(self):
11900  r"""__init__(PDBRecord self) -> PDBRecord"""
11901  _IMP_atom.PDBRecord_swiginit(self, _IMP_atom.new_PDBRecord())
11902 
11903  def get_alt_loc_indicator(self):
11904  r"""get_alt_loc_indicator(PDBRecord self) -> std::string"""
11905  return _IMP_atom.PDBRecord_get_alt_loc_indicator(self)
11906 
11907  def get_is_atom(self):
11908  r"""get_is_atom(PDBRecord self) -> bool"""
11909  return _IMP_atom.PDBRecord_get_is_atom(self)
11910 
11911  def get_trimmed_atom_name(self):
11912  r"""get_trimmed_atom_name(PDBRecord self) -> std::string"""
11913  return _IMP_atom.PDBRecord_get_trimmed_atom_name(self)
11914 
11915  def get_padded_atom_name(self):
11916  r"""get_padded_atom_name(PDBRecord self) -> std::string"""
11917  return _IMP_atom.PDBRecord_get_padded_atom_name(self)
11918 
11919  def get_residue_name(self):
11920  r"""get_residue_name(PDBRecord self) -> std::string"""
11921  return _IMP_atom.PDBRecord_get_residue_name(self)
11922 
11923  def get_chain_id(self):
11924  r"""get_chain_id(PDBRecord self) -> std::string"""
11925  return _IMP_atom.PDBRecord_get_chain_id(self)
11926 
11927  def get_element(self):
11928  r"""get_element(PDBRecord self) -> std::string"""
11929  return _IMP_atom.PDBRecord_get_element(self)
11930 
11931  def show(self, *args):
11932  r"""show(PDBRecord self, _ostream out=std::cout)"""
11933  return _IMP_atom.PDBRecord_show(self, *args)
11934 
11935  def __str__(self):
11936  r"""__str__(PDBRecord self) -> std::string"""
11937  return _IMP_atom.PDBRecord___str__(self)
11938 
11939  def __repr__(self):
11940  r"""__repr__(PDBRecord self) -> std::string"""
11941  return _IMP_atom.PDBRecord___repr__(self)
11942  __swig_destroy__ = _IMP_atom.delete_PDBRecord
11943 
11944 # Register PDBRecord in _IMP_atom:
11945 _IMP_atom.PDBRecord_swigregister(PDBRecord)
11946 class PDBSelector(IMP.Object):
11947  r"""Proxy of C++ IMP::atom::PDBSelector class."""
11948 
11949  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
11950 
11951  def __init__(self, name):
11952  r"""__init__(PDBSelector self, std::string name) -> PDBSelector"""
11953  if self.__class__ == PDBSelector:
11954  _self = None
11955  else:
11956  _self = self
11957  _IMP_atom.PDBSelector_swiginit(self, _IMP_atom.new_PDBSelector(_self, name))
11958 
11959  if self.__class__ != PDBSelector:
11960  _director_objects.register(self)
11961 
11962 
11963 
11964 
11965  def get_is_selected(self, record):
11966  r"""get_is_selected(PDBSelector self, PDBRecord record) -> bool"""
11967  return _IMP_atom.PDBSelector_get_is_selected(self, record)
11968  __swig_destroy__ = _IMP_atom.delete_PDBSelector
11969 
11970  def __str__(self):
11971  r"""__str__(PDBSelector self) -> std::string"""
11972  return _IMP_atom.PDBSelector___str__(self)
11973 
11974  def __repr__(self):
11975  r"""__repr__(PDBSelector self) -> std::string"""
11976  return _IMP_atom.PDBSelector___repr__(self)
11977 
11978  @staticmethod
11979  def get_from(o):
11980  return _object_cast_to_PDBSelector(o)
11981 
11982 
11983  def get_type_name(self):
11984  return self.__class__.__name__
11985  def do_show(self, out):
11986  pass
11987  def get_version_info(self):
11988  if"IMP::atom" == "IMP":
11989  return VersionInfo(self.__module__,
11990  __import__(self.__module__).get_module_version())
11991  else:
11992  return IMP.VersionInfo(self.__module__,
11993  __import__(self.__module__).get_module_version())
11994  @staticmethod
11995  def get_from(o):
11996  return _object_cast_to_PDBSelector(o)
11997 
11998 
11999  def __and__(self, s):
12000  return AndPDBSelector(self, s)
12001  def __or__(self, s):
12002  return OrPDBSelector(self, s)
12003  def __xor__(self, s):
12004  return XorPDBSelector(self, s)
12005  def __invert__(self):
12006  return NotPDBSelector(self)
12007  def __sub__(self, s):
12008  return AndPDBSelector(self, NotPDBSelector(s))
12009 
12010  def __disown__(self):
12011  self.this.disown()
12012  _IMP_atom.disown_PDBSelector(self)
12013  return weakref.proxy(self)
12014 
12015  def do_destroy(self):
12016  r"""do_destroy(PDBSelector self)"""
12017  return _IMP_atom.PDBSelector_do_destroy(self)
12018 
12019 # Register PDBSelector in _IMP_atom:
12020 _IMP_atom.PDBSelector_swigregister(PDBSelector)
12021 class NonAlternativePDBSelector(PDBSelector):
12022  r"""Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12023 
12024  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12025 
12026  def __init__(self, *args):
12027  r"""__init__(NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector"""
12028  _IMP_atom.NonAlternativePDBSelector_swiginit(self, _IMP_atom.new_NonAlternativePDBSelector(*args))
12029 
12030  def get_version_info(self):
12031  r"""get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12032  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12033  __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
12034 
12035  def __str__(self):
12036  r"""__str__(NonAlternativePDBSelector self) -> std::string"""
12037  return _IMP_atom.NonAlternativePDBSelector___str__(self)
12038 
12039  def __repr__(self):
12040  r"""__repr__(NonAlternativePDBSelector self) -> std::string"""
12041  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12042 
12043  @staticmethod
12044  def get_from(o):
12045  return _object_cast_to_NonAlternativePDBSelector(o)
12046 
12047 
12048 # Register NonAlternativePDBSelector in _IMP_atom:
12049 _IMP_atom.NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12050 class ATOMPDBSelector(NonAlternativePDBSelector):
12051  r"""Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12052 
12053  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12054 
12055  def __init__(self, *args):
12056  r"""__init__(ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector"""
12057  _IMP_atom.ATOMPDBSelector_swiginit(self, _IMP_atom.new_ATOMPDBSelector(*args))
12058  __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
12059 
12060  def __str__(self):
12061  r"""__str__(ATOMPDBSelector self) -> std::string"""
12062  return _IMP_atom.ATOMPDBSelector___str__(self)
12063 
12064  def __repr__(self):
12065  r"""__repr__(ATOMPDBSelector self) -> std::string"""
12066  return _IMP_atom.ATOMPDBSelector___repr__(self)
12067 
12068  @staticmethod
12069  def get_from(o):
12070  return _object_cast_to_ATOMPDBSelector(o)
12071 
12072 
12073 # Register ATOMPDBSelector in _IMP_atom:
12074 _IMP_atom.ATOMPDBSelector_swigregister(ATOMPDBSelector)
12075 class CAlphaPDBSelector(NonAlternativePDBSelector):
12076  r"""Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12077 
12078  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12079 
12080  def __init__(self, *args):
12081  r"""__init__(CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector"""
12082  _IMP_atom.CAlphaPDBSelector_swiginit(self, _IMP_atom.new_CAlphaPDBSelector(*args))
12083  __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
12084 
12085  def __str__(self):
12086  r"""__str__(CAlphaPDBSelector self) -> std::string"""
12087  return _IMP_atom.CAlphaPDBSelector___str__(self)
12088 
12089  def __repr__(self):
12090  r"""__repr__(CAlphaPDBSelector self) -> std::string"""
12091  return _IMP_atom.CAlphaPDBSelector___repr__(self)
12092 
12093  @staticmethod
12094  def get_from(o):
12095  return _object_cast_to_CAlphaPDBSelector(o)
12096 
12097 
12098 # Register CAlphaPDBSelector in _IMP_atom:
12099 _IMP_atom.CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12100 class CBetaPDBSelector(NonAlternativePDBSelector):
12101  r"""Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12102 
12103  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12104 
12105  def __init__(self, *args):
12106  r"""__init__(CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector"""
12107  _IMP_atom.CBetaPDBSelector_swiginit(self, _IMP_atom.new_CBetaPDBSelector(*args))
12108  __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
12109 
12110  def __str__(self):
12111  r"""__str__(CBetaPDBSelector self) -> std::string"""
12112  return _IMP_atom.CBetaPDBSelector___str__(self)
12113 
12114  def __repr__(self):
12115  r"""__repr__(CBetaPDBSelector self) -> std::string"""
12116  return _IMP_atom.CBetaPDBSelector___repr__(self)
12117 
12118  @staticmethod
12119  def get_from(o):
12120  return _object_cast_to_CBetaPDBSelector(o)
12121 
12122 
12123 # Register CBetaPDBSelector in _IMP_atom:
12124 _IMP_atom.CBetaPDBSelector_swigregister(CBetaPDBSelector)
12125 class AtomTypePDBSelector(PDBSelector):
12126  r"""Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12127 
12128  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12129 
12130  def __init__(self, *args):
12131  r"""__init__(AtomTypePDBSelector self, IMP::Strings atom_types, std::string name="AtomTypePDBSelector%1%") -> AtomTypePDBSelector"""
12132  _IMP_atom.AtomTypePDBSelector_swiginit(self, _IMP_atom.new_AtomTypePDBSelector(*args))
12133 
12134  def get_version_info(self):
12135  r"""get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12136  return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12137  __swig_destroy__ = _IMP_atom.delete_AtomTypePDBSelector
12138 
12139  def __str__(self):
12140  r"""__str__(AtomTypePDBSelector self) -> std::string"""
12141  return _IMP_atom.AtomTypePDBSelector___str__(self)
12142 
12143  def __repr__(self):
12144  r"""__repr__(AtomTypePDBSelector self) -> std::string"""
12145  return _IMP_atom.AtomTypePDBSelector___repr__(self)
12146 
12147  @staticmethod
12148  def get_from(o):
12149  return _object_cast_to_AtomTypePDBSelector(o)
12150 
12151 
12152 # Register AtomTypePDBSelector in _IMP_atom:
12153 _IMP_atom.AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12154 class ResidueTypePDBSelector(PDBSelector):
12155  r"""Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12156 
12157  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12158 
12159  def __init__(self, *args):
12160  r"""__init__(ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name="ResidueTypePDBSelector%1%") -> ResidueTypePDBSelector"""
12161  _IMP_atom.ResidueTypePDBSelector_swiginit(self, _IMP_atom.new_ResidueTypePDBSelector(*args))
12162 
12163  def get_version_info(self):
12164  r"""get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12165  return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12166  __swig_destroy__ = _IMP_atom.delete_ResidueTypePDBSelector
12167 
12168  def __str__(self):
12169  r"""__str__(ResidueTypePDBSelector self) -> std::string"""
12170  return _IMP_atom.ResidueTypePDBSelector___str__(self)
12171 
12172  def __repr__(self):
12173  r"""__repr__(ResidueTypePDBSelector self) -> std::string"""
12174  return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12175 
12176  @staticmethod
12177  def get_from(o):
12178  return _object_cast_to_ResidueTypePDBSelector(o)
12179 
12180 
12181 # Register ResidueTypePDBSelector in _IMP_atom:
12182 _IMP_atom.ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12183 class CPDBSelector(NonAlternativePDBSelector):
12184  r"""Proxy of C++ IMP::atom::CPDBSelector class."""
12185 
12186  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12187 
12188  def __init__(self, *args):
12189  r"""__init__(CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector"""
12190  _IMP_atom.CPDBSelector_swiginit(self, _IMP_atom.new_CPDBSelector(*args))
12191  __swig_destroy__ = _IMP_atom.delete_CPDBSelector
12192 
12193  def __str__(self):
12194  r"""__str__(CPDBSelector self) -> std::string"""
12195  return _IMP_atom.CPDBSelector___str__(self)
12196 
12197  def __repr__(self):
12198  r"""__repr__(CPDBSelector self) -> std::string"""
12199  return _IMP_atom.CPDBSelector___repr__(self)
12200 
12201  @staticmethod
12202  def get_from(o):
12203  return _object_cast_to_CPDBSelector(o)
12204 
12205 
12206 # Register CPDBSelector in _IMP_atom:
12207 _IMP_atom.CPDBSelector_swigregister(CPDBSelector)
12208 class NPDBSelector(NonAlternativePDBSelector):
12209  r"""Proxy of C++ IMP::atom::NPDBSelector class."""
12210 
12211  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12212 
12213  def __init__(self, *args):
12214  r"""__init__(NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector"""
12215  _IMP_atom.NPDBSelector_swiginit(self, _IMP_atom.new_NPDBSelector(*args))
12216  __swig_destroy__ = _IMP_atom.delete_NPDBSelector
12217 
12218  def __str__(self):
12219  r"""__str__(NPDBSelector self) -> std::string"""
12220  return _IMP_atom.NPDBSelector___str__(self)
12221 
12222  def __repr__(self):
12223  r"""__repr__(NPDBSelector self) -> std::string"""
12224  return _IMP_atom.NPDBSelector___repr__(self)
12225 
12226  @staticmethod
12227  def get_from(o):
12228  return _object_cast_to_NPDBSelector(o)
12229 
12230 
12231 # Register NPDBSelector in _IMP_atom:
12232 _IMP_atom.NPDBSelector_swigregister(NPDBSelector)
12233 class AllPDBSelector(PDBSelector):
12234  r"""Proxy of C++ IMP::atom::AllPDBSelector class."""
12235 
12236  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12237 
12238  def __init__(self, *args):
12239  r"""__init__(AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector"""
12240  _IMP_atom.AllPDBSelector_swiginit(self, _IMP_atom.new_AllPDBSelector(*args))
12241 
12242  def get_version_info(self):
12243  r"""get_version_info(AllPDBSelector self) -> VersionInfo"""
12244  return _IMP_atom.AllPDBSelector_get_version_info(self)
12245  __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
12246 
12247  def __str__(self):
12248  r"""__str__(AllPDBSelector self) -> std::string"""
12249  return _IMP_atom.AllPDBSelector___str__(self)
12250 
12251  def __repr__(self):
12252  r"""__repr__(AllPDBSelector self) -> std::string"""
12253  return _IMP_atom.AllPDBSelector___repr__(self)
12254 
12255  @staticmethod
12256  def get_from(o):
12257  return _object_cast_to_AllPDBSelector(o)
12258 
12259 
12260 # Register AllPDBSelector in _IMP_atom:
12261 _IMP_atom.AllPDBSelector_swigregister(AllPDBSelector)
12262 class ChainPDBSelector(NonAlternativePDBSelector):
12263  r"""Proxy of C++ IMP::atom::ChainPDBSelector class."""
12264 
12265  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12266  __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
12267 
12268  def __init__(self, *args):
12269  r"""
12270  __init__(ChainPDBSelector self, IMP::Strings chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
12271  __init__(ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
12272  """
12273  _IMP_atom.ChainPDBSelector_swiginit(self, _IMP_atom.new_ChainPDBSelector(*args))
12274 
12275  def __str__(self):
12276  r"""__str__(ChainPDBSelector self) -> std::string"""
12277  return _IMP_atom.ChainPDBSelector___str__(self)
12278 
12279  def __repr__(self):
12280  r"""__repr__(ChainPDBSelector self) -> std::string"""
12281  return _IMP_atom.ChainPDBSelector___repr__(self)
12282 
12283  @staticmethod
12284  def get_from(o):
12285  return _object_cast_to_ChainPDBSelector(o)
12286 
12287 
12288 # Register ChainPDBSelector in _IMP_atom:
12289 _IMP_atom.ChainPDBSelector_swigregister(ChainPDBSelector)
12290 class WaterPDBSelector(NonAlternativePDBSelector):
12291  r"""Proxy of C++ IMP::atom::WaterPDBSelector 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, *args):
12296  r"""__init__(WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector"""
12297  _IMP_atom.WaterPDBSelector_swiginit(self, _IMP_atom.new_WaterPDBSelector(*args))
12298  __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
12299 
12300  def __str__(self):
12301  r"""__str__(WaterPDBSelector self) -> std::string"""
12302  return _IMP_atom.WaterPDBSelector___str__(self)
12303 
12304  def __repr__(self):
12305  r"""__repr__(WaterPDBSelector self) -> std::string"""
12306  return _IMP_atom.WaterPDBSelector___repr__(self)
12307 
12308  @staticmethod
12309  def get_from(o):
12310  return _object_cast_to_WaterPDBSelector(o)
12311 
12312 
12313 # Register WaterPDBSelector in _IMP_atom:
12314 _IMP_atom.WaterPDBSelector_swigregister(WaterPDBSelector)
12315 class HydrogenPDBSelector(NonAlternativePDBSelector):
12316  r"""Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12317 
12318  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12319 
12320  def __init__(self, *args):
12321  r"""__init__(HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector"""
12322  _IMP_atom.HydrogenPDBSelector_swiginit(self, _IMP_atom.new_HydrogenPDBSelector(*args))
12323  __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
12324 
12325  def __str__(self):
12326  r"""__str__(HydrogenPDBSelector self) -> std::string"""
12327  return _IMP_atom.HydrogenPDBSelector___str__(self)
12328 
12329  def __repr__(self):
12330  r"""__repr__(HydrogenPDBSelector self) -> std::string"""
12331  return _IMP_atom.HydrogenPDBSelector___repr__(self)
12332 
12333  @staticmethod
12334  def get_from(o):
12335  return _object_cast_to_HydrogenPDBSelector(o)
12336 
12337 
12338 # Register HydrogenPDBSelector in _IMP_atom:
12339 _IMP_atom.HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12340 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12341  r"""Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12342 
12343  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12344  __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
12345 
12346  def __init__(self, *args):
12347  r"""
12348  __init__(NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12349  __init__(NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12350  """
12351  _IMP_atom.NonWaterNonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args))
12352 
12353  def __str__(self):
12354  r"""__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12355  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12356 
12357  def __repr__(self):
12358  r"""__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12359  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12360 
12361  @staticmethod
12362  def get_from(o):
12363  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12364 
12365 
12366 # Register NonWaterNonHydrogenPDBSelector in _IMP_atom:
12367 _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12368 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12369  r"""Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12370 
12371  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12372  __swig_destroy__ = _IMP_atom.delete_NonHydrogenPDBSelector
12373 
12374  def __init__(self, *args):
12375  r"""
12376  __init__(NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12377  __init__(NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12378  """
12379  _IMP_atom.NonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonHydrogenPDBSelector(*args))
12380 
12381  def __str__(self):
12382  r"""__str__(NonHydrogenPDBSelector self) -> std::string"""
12383  return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12384 
12385  def __repr__(self):
12386  r"""__repr__(NonHydrogenPDBSelector self) -> std::string"""
12387  return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12388 
12389  @staticmethod
12390  def get_from(o):
12391  return _object_cast_to_NonHydrogenPDBSelector(o)
12392 
12393 
12394 # Register NonHydrogenPDBSelector in _IMP_atom:
12395 _IMP_atom.NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12396 class NonWaterPDBSelector(NonAlternativePDBSelector):
12397  r"""Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12398 
12399  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12400  __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
12401 
12402  def __init__(self, *args):
12403  r"""
12404  __init__(NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12405  __init__(NonWaterPDBSelector self) -> NonWaterPDBSelector
12406  """
12407  _IMP_atom.NonWaterPDBSelector_swiginit(self, _IMP_atom.new_NonWaterPDBSelector(*args))
12408 
12409  def __str__(self):
12410  r"""__str__(NonWaterPDBSelector self) -> std::string"""
12411  return _IMP_atom.NonWaterPDBSelector___str__(self)
12412 
12413  def __repr__(self):
12414  r"""__repr__(NonWaterPDBSelector self) -> std::string"""
12415  return _IMP_atom.NonWaterPDBSelector___repr__(self)
12416 
12417  @staticmethod
12418  def get_from(o):
12419  return _object_cast_to_NonWaterPDBSelector(o)
12420 
12421 
12422 # Register NonWaterPDBSelector in _IMP_atom:
12423 _IMP_atom.NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12424 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12425  r"""Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12426 
12427  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12428 
12429  def __init__(self, *args):
12430  r"""__init__(BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector"""
12431  _IMP_atom.BackbonePDBSelector_swiginit(self, _IMP_atom.new_BackbonePDBSelector(*args))
12432  __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
12433 
12434  def __str__(self):
12435  r"""__str__(BackbonePDBSelector self) -> std::string"""
12436  return _IMP_atom.BackbonePDBSelector___str__(self)
12437 
12438  def __repr__(self):
12439  r"""__repr__(BackbonePDBSelector self) -> std::string"""
12440  return _IMP_atom.BackbonePDBSelector___repr__(self)
12441 
12442  @staticmethod
12443  def get_from(o):
12444  return _object_cast_to_BackbonePDBSelector(o)
12445 
12446 
12447 # Register BackbonePDBSelector in _IMP_atom:
12448 _IMP_atom.BackbonePDBSelector_swigregister(BackbonePDBSelector)
12449 class PPDBSelector(NonAlternativePDBSelector):
12450  r"""Proxy of C++ IMP::atom::PPDBSelector class."""
12451 
12452  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12453 
12454  def __init__(self, *args):
12455  r"""__init__(PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector"""
12456  _IMP_atom.PPDBSelector_swiginit(self, _IMP_atom.new_PPDBSelector(*args))
12457  __swig_destroy__ = _IMP_atom.delete_PPDBSelector
12458 
12459  def __str__(self):
12460  r"""__str__(PPDBSelector self) -> std::string"""
12461  return _IMP_atom.PPDBSelector___str__(self)
12462 
12463  def __repr__(self):
12464  r"""__repr__(PPDBSelector self) -> std::string"""
12465  return _IMP_atom.PPDBSelector___repr__(self)
12466 
12467  @staticmethod
12468  def get_from(o):
12469  return _object_cast_to_PPDBSelector(o)
12470 
12471 
12472 # Register PPDBSelector in _IMP_atom:
12473 _IMP_atom.PPDBSelector_swigregister(PPDBSelector)
12474 class AndPDBSelector(PDBSelector):
12475  r"""Proxy of C++ IMP::atom::AndPDBSelector class."""
12476 
12477  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12478 
12479  def get_version_info(self):
12480  r"""get_version_info(AndPDBSelector self) -> VersionInfo"""
12481  return _IMP_atom.AndPDBSelector_get_version_info(self)
12482  __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
12483 
12484  def __init__(self, a, b):
12485  r"""__init__(AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
12486  _IMP_atom.AndPDBSelector_swiginit(self, _IMP_atom.new_AndPDBSelector(a, b))
12487 
12488  def __str__(self):
12489  r"""__str__(AndPDBSelector self) -> std::string"""
12490  return _IMP_atom.AndPDBSelector___str__(self)
12491 
12492  def __repr__(self):
12493  r"""__repr__(AndPDBSelector self) -> std::string"""
12494  return _IMP_atom.AndPDBSelector___repr__(self)
12495 
12496  @staticmethod
12497  def get_from(o):
12498  return _object_cast_to_AndPDBSelector(o)
12499 
12500 
12501 # Register AndPDBSelector in _IMP_atom:
12502 _IMP_atom.AndPDBSelector_swigregister(AndPDBSelector)
12503 class OrPDBSelector(PDBSelector):
12504  r"""Proxy of C++ IMP::atom::OrPDBSelector class."""
12505 
12506  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12507 
12508  def get_version_info(self):
12509  r"""get_version_info(OrPDBSelector self) -> VersionInfo"""
12510  return _IMP_atom.OrPDBSelector_get_version_info(self)
12511  __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
12512 
12513  def __init__(self, a, b):
12514  r"""__init__(OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
12515  _IMP_atom.OrPDBSelector_swiginit(self, _IMP_atom.new_OrPDBSelector(a, b))
12516 
12517  def __str__(self):
12518  r"""__str__(OrPDBSelector self) -> std::string"""
12519  return _IMP_atom.OrPDBSelector___str__(self)
12520 
12521  def __repr__(self):
12522  r"""__repr__(OrPDBSelector self) -> std::string"""
12523  return _IMP_atom.OrPDBSelector___repr__(self)
12524 
12525  @staticmethod
12526  def get_from(o):
12527  return _object_cast_to_OrPDBSelector(o)
12528 
12529 
12530 # Register OrPDBSelector in _IMP_atom:
12531 _IMP_atom.OrPDBSelector_swigregister(OrPDBSelector)
12532 class XorPDBSelector(PDBSelector):
12533  r"""Proxy of C++ IMP::atom::XorPDBSelector class."""
12534 
12535  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12536 
12537  def get_version_info(self):
12538  r"""get_version_info(XorPDBSelector self) -> VersionInfo"""
12539  return _IMP_atom.XorPDBSelector_get_version_info(self)
12540  __swig_destroy__ = _IMP_atom.delete_XorPDBSelector
12541 
12542  def __init__(self, a, b):
12543  r"""__init__(XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
12544  _IMP_atom.XorPDBSelector_swiginit(self, _IMP_atom.new_XorPDBSelector(a, b))
12545 
12546  def __str__(self):
12547  r"""__str__(XorPDBSelector self) -> std::string"""
12548  return _IMP_atom.XorPDBSelector___str__(self)
12549 
12550  def __repr__(self):
12551  r"""__repr__(XorPDBSelector self) -> std::string"""
12552  return _IMP_atom.XorPDBSelector___repr__(self)
12553 
12554  @staticmethod
12555  def get_from(o):
12556  return _object_cast_to_XorPDBSelector(o)
12557 
12558 
12559 # Register XorPDBSelector in _IMP_atom:
12560 _IMP_atom.XorPDBSelector_swigregister(XorPDBSelector)
12561 class NotPDBSelector(PDBSelector):
12562  r"""Proxy of C++ IMP::atom::NotPDBSelector class."""
12563 
12564  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12565 
12566  def get_version_info(self):
12567  r"""get_version_info(NotPDBSelector self) -> VersionInfo"""
12568  return _IMP_atom.NotPDBSelector_get_version_info(self)
12569  __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
12570 
12571  def __init__(self, a):
12572  r"""__init__(NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
12573  _IMP_atom.NotPDBSelector_swiginit(self, _IMP_atom.new_NotPDBSelector(a))
12574 
12575  def __str__(self):
12576  r"""__str__(NotPDBSelector self) -> std::string"""
12577  return _IMP_atom.NotPDBSelector___str__(self)
12578 
12579  def __repr__(self):
12580  r"""__repr__(NotPDBSelector self) -> std::string"""
12581  return _IMP_atom.NotPDBSelector___repr__(self)
12582 
12583  @staticmethod
12584  def get_from(o):
12585  return _object_cast_to_NotPDBSelector(o)
12586 
12587 
12588 # Register NotPDBSelector in _IMP_atom:
12589 _IMP_atom.NotPDBSelector_swigregister(NotPDBSelector)
12590 
12591 def get_default_pdb_selector():
12592  r"""get_default_pdb_selector() -> PDBSelector"""
12593  return _IMP_atom.get_default_pdb_selector()
12594 
12595 def read_pdb(*args):
12596  r"""
12597  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool no_radii=False) -> Hierarchy
12598  read_pdb(TextInput input, int model, Hierarchy h)
12599  """
12600  return _IMP_atom.read_pdb(*args)
12601 
12602 def read_multimodel_pdb(*args):
12603  r"""read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12604  return _IMP_atom.read_multimodel_pdb(*args)
12605 
12606 def write_pdb(mhd, out, model=1):
12607  r"""write_pdb(Selection mhd, TextOutput out, unsigned int model=1)"""
12608  return _IMP_atom.write_pdb(mhd, out, model)
12609 
12610 def write_pdb_of_c_alphas(mhd, out, model=1):
12611  r"""write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)"""
12612  return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
12613 
12614 def write_multimodel_pdb(mhd, out):
12615  r"""write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
12616  return _IMP_atom.write_multimodel_pdb(mhd, out)
12617 
12618 def get_pdb_string(*args):
12619  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"""
12620  return _IMP_atom.get_pdb_string(*args)
12621 
12622 def get_pdb_conect_record_string(arg1, arg2):
12623  r"""get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
12624  return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
12625 class WritePDBOptimizerState(IMP.OptimizerState):
12626  r"""Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
12627 
12628  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12629 
12630  def __init__(self, *args):
12631  r"""
12632  __init__(WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
12633  __init__(WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
12634  __init__(WritePDBOptimizerState self) -> WritePDBOptimizerState
12635  """
12636  _IMP_atom.WritePDBOptimizerState_swiginit(self, _IMP_atom.new_WritePDBOptimizerState(*args))
12637 
12638  def get_version_info(self):
12639  r"""get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
12640  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
12641  __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
12642 
12643  def __str__(self):
12644  r"""__str__(WritePDBOptimizerState self) -> std::string"""
12645  return _IMP_atom.WritePDBOptimizerState___str__(self)
12646 
12647  def __repr__(self):
12648  r"""__repr__(WritePDBOptimizerState self) -> std::string"""
12649  return _IMP_atom.WritePDBOptimizerState___repr__(self)
12650 
12651  @staticmethod
12652  def get_from(o):
12653  return _object_cast_to_WritePDBOptimizerState(o)
12654 
12655 
12656  def _get_as_binary(self):
12657  r"""_get_as_binary(WritePDBOptimizerState self) -> PyObject *"""
12658  return _IMP_atom.WritePDBOptimizerState__get_as_binary(self)
12659 
12660  def _set_from_binary(self, p):
12661  r"""_set_from_binary(WritePDBOptimizerState self, PyObject * p)"""
12662  return _IMP_atom.WritePDBOptimizerState__set_from_binary(self, p)
12663 
12664  def __getstate__(self):
12665  p = self._get_as_binary()
12666  if len(self.__dict__) > 1:
12667  d = self.__dict__.copy()
12668  del d['this']
12669  p = (d, p)
12670  return p
12671 
12672  def __setstate__(self, p):
12673  if not hasattr(self, 'this'):
12674  self.__init__()
12675  if isinstance(p, tuple):
12676  d, p = p
12677  self.__dict__.update(d)
12678  return self._set_from_binary(p)
12679 
12680 
12681 # Register WritePDBOptimizerState in _IMP_atom:
12682 _IMP_atom.WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
12683 
12684 def read_multimodel_mmcif(*args):
12685  r"""read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12686  return _IMP_atom.read_multimodel_mmcif(*args)
12687 
12688 def read_mmcif(*args):
12689  r"""read_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
12690  return _IMP_atom.read_mmcif(*args)
12691 
12692 def read_pdb_or_mmcif(*args):
12693  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"""
12694  return _IMP_atom.read_pdb_or_mmcif(*args)
12695 
12696 def read_multimodel_pdb_or_mmcif(*args):
12697  r"""read_multimodel_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12698  return _IMP_atom.read_multimodel_pdb_or_mmcif(*args)
12699 
12700 def get_kt(T):
12701  r"""get_kt(double T) -> double"""
12702  return _IMP_atom.get_kt(T)
12703 class CAAngleRestraint(IMP.Restraint):
12704  r"""Proxy of C++ IMP::atom::CAAngleRestraint class."""
12705 
12706  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12707 
12708  def __init__(self, m, p1, p2, p3, phi0, score):
12709  r"""__init__(CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
12710  _IMP_atom.CAAngleRestraint_swiginit(self, _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score))
12711 
12712  def do_get_inputs(self):
12713  r"""do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
12714  return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
12715 
12716  def get_version_info(self):
12717  r"""get_version_info(CAAngleRestraint self) -> VersionInfo"""
12718  return _IMP_atom.CAAngleRestraint_get_version_info(self)
12719  __swig_destroy__ = _IMP_atom.delete_CAAngleRestraint
12720 
12721  def __str__(self):
12722  r"""__str__(CAAngleRestraint self) -> std::string"""
12723  return _IMP_atom.CAAngleRestraint___str__(self)
12724 
12725  def __repr__(self):
12726  r"""__repr__(CAAngleRestraint self) -> std::string"""
12727  return _IMP_atom.CAAngleRestraint___repr__(self)
12728 
12729  @staticmethod
12730  def get_from(o):
12731  return _object_cast_to_CAAngleRestraint(o)
12732 
12733 
12734 # Register CAAngleRestraint in _IMP_atom:
12735 _IMP_atom.CAAngleRestraint_swigregister(CAAngleRestraint)
12736 class CADihedralRestraint(IMP.Restraint):
12737  r"""Proxy of C++ IMP::atom::CADihedralRestraint class."""
12738 
12739  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12740 
12741  def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
12742  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"""
12743  _IMP_atom.CADihedralRestraint_swiginit(self, _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score))
12744 
12745  def do_get_inputs(self):
12746  r"""do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
12747  return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
12748 
12749  def get_version_info(self):
12750  r"""get_version_info(CADihedralRestraint self) -> VersionInfo"""
12751  return _IMP_atom.CADihedralRestraint_get_version_info(self)
12752  __swig_destroy__ = _IMP_atom.delete_CADihedralRestraint
12753 
12754  def __str__(self):
12755  r"""__str__(CADihedralRestraint self) -> std::string"""
12756  return _IMP_atom.CADihedralRestraint___str__(self)
12757 
12758  def __repr__(self):
12759  r"""__repr__(CADihedralRestraint self) -> std::string"""
12760  return _IMP_atom.CADihedralRestraint___repr__(self)
12761 
12762  @staticmethod
12763  def get_from(o):
12764  return _object_cast_to_CADihedralRestraint(o)
12765 
12766 
12767 # Register CADihedralRestraint in _IMP_atom:
12768 _IMP_atom.CADihedralRestraint_swigregister(CADihedralRestraint)
12769 class StructureSource(IMP.Decorator):
12770  r"""Proxy of C++ IMP::atom::StructureSource class."""
12771 
12772  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
12773 
12774  def get_source_id(self):
12775  r"""get_source_id(StructureSource self) -> std::string"""
12776  return _IMP_atom.StructureSource_get_source_id(self)
12777 
12778  def get_source_chain_id(self):
12779  r"""get_source_chain_id(StructureSource self) -> std::string"""
12780  return _IMP_atom.StructureSource_get_source_chain_id(self)
12781 
12782  def set_source_id(self, source_id):
12783  r"""set_source_id(StructureSource self, std::string source_id)"""
12784  return _IMP_atom.StructureSource_set_source_id(self, source_id)
12785 
12786  def set_source_chain_id(self, source_chain_id):
12787  r"""set_source_chain_id(StructureSource self, std::string source_chain_id)"""
12788  return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
12789 
12790  def __init__(self, *args):
12791  r"""
12792  __init__(StructureSource self) -> StructureSource
12793  __init__(StructureSource self, Model m, ParticleIndex id) -> StructureSource
12794  __init__(StructureSource self, _ParticleAdaptor d) -> StructureSource
12795  """
12796  _IMP_atom.StructureSource_swiginit(self, _IMP_atom.new_StructureSource(*args))
12797 
12798  @staticmethod
12799  def get_is_setup(*args):
12800  r"""
12801  get_is_setup(Model m, ParticleIndex pi) -> bool
12802  get_is_setup(_ParticleAdaptor p) -> bool
12803  """
12804  return _IMP_atom.StructureSource_get_is_setup(*args)
12805 
12806  def show(self, *args):
12807  r"""show(StructureSource self, _ostream out=std::cout)"""
12808  return _IMP_atom.StructureSource_show(self, *args)
12809 
12810  @staticmethod
12811  def setup_particle(*args):
12812  r"""
12813  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
12814  setup_particle(_ParticleAdaptor pa, std::string source_id, std::string source_chain_id) -> StructureSource
12815  """
12816  return _IMP_atom.StructureSource_setup_particle(*args)
12817 
12818  def add_attribute(self, *args):
12819  r"""
12820  add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
12821  add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
12822  add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
12823  add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
12824  add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
12825  add_attribute(StructureSource self, StringKey a0, IMP::String a1)
12826  add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
12827  add_attribute(StructureSource self, ObjectKey a0, Object a1)
12828  add_attribute(StructureSource self, SparseFloatKey a0, IMP::Float a1)
12829  add_attribute(StructureSource self, SparseIntKey a0, IMP::Int a1)
12830  add_attribute(StructureSource self, SparseStringKey a0, IMP::String a1)
12831  add_attribute(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
12832  """
12833  return _IMP_atom.StructureSource_add_attribute(self, *args)
12834 
12835  def get_value(self, *args):
12836  r"""
12837  get_value(StructureSource self, FloatKey a0) -> IMP::Float
12838  get_value(StructureSource self, IntKey a0) -> IMP::Int
12839  get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
12840  get_value(StructureSource self, IntsKey a0) -> IMP::Ints
12841  get_value(StructureSource self, StringKey a0) -> IMP::String
12842  get_value(StructureSource self, ParticleIndexKey a0) -> Particle
12843  get_value(StructureSource self, ObjectKey a0) -> Object
12844  get_value(StructureSource self, SparseFloatKey a0) -> IMP::Float
12845  get_value(StructureSource self, SparseIntKey a0) -> IMP::Int
12846  get_value(StructureSource self, SparseStringKey a0) -> IMP::String
12847  get_value(StructureSource self, SparseParticleIndexKey a0) -> ParticleIndex
12848  """
12849  return _IMP_atom.StructureSource_get_value(self, *args)
12850 
12851  def set_value(self, *args):
12852  r"""
12853  set_value(StructureSource self, FloatKey a0, IMP::Float a1)
12854  set_value(StructureSource self, IntKey a0, IMP::Int a1)
12855  set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
12856  set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
12857  set_value(StructureSource self, StringKey a0, IMP::String a1)
12858  set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
12859  set_value(StructureSource self, ObjectKey a0, Object a1)
12860  set_value(StructureSource self, SparseFloatKey a0, IMP::Float a1)
12861  set_value(StructureSource self, SparseIntKey a0, IMP::Int a1)
12862  set_value(StructureSource self, SparseStringKey a0, IMP::String a1)
12863  set_value(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
12864  """
12865  return _IMP_atom.StructureSource_set_value(self, *args)
12866 
12867  def remove_attribute(self, *args):
12868  r"""
12869  remove_attribute(StructureSource self, FloatKey a0)
12870  remove_attribute(StructureSource self, IntKey a0)
12871  remove_attribute(StructureSource self, FloatsKey a0)
12872  remove_attribute(StructureSource self, IntsKey a0)
12873  remove_attribute(StructureSource self, StringKey a0)
12874  remove_attribute(StructureSource self, ParticleIndexKey a0)
12875  remove_attribute(StructureSource self, ObjectKey a0)
12876  remove_attribute(StructureSource self, SparseFloatKey a0)
12877  remove_attribute(StructureSource self, SparseIntKey a0)
12878  remove_attribute(StructureSource self, SparseStringKey a0)
12879  remove_attribute(StructureSource self, SparseParticleIndexKey a0)
12880  """
12881  return _IMP_atom.StructureSource_remove_attribute(self, *args)
12882 
12883  def has_attribute(self, *args):
12884  r"""
12885  has_attribute(StructureSource self, FloatKey a0) -> bool
12886  has_attribute(StructureSource self, IntKey a0) -> bool
12887  has_attribute(StructureSource self, FloatsKey a0) -> bool
12888  has_attribute(StructureSource self, IntsKey a0) -> bool
12889  has_attribute(StructureSource self, StringKey a0) -> bool
12890  has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
12891  has_attribute(StructureSource self, ObjectKey a0) -> bool
12892  has_attribute(StructureSource self, SparseFloatKey a0) -> bool
12893  has_attribute(StructureSource self, SparseIntKey a0) -> bool
12894  has_attribute(StructureSource self, SparseStringKey a0) -> bool
12895  has_attribute(StructureSource self, SparseParticleIndexKey a0) -> bool
12896  """
12897  return _IMP_atom.StructureSource_has_attribute(self, *args)
12898 
12899  def get_derivative(self, a0):
12900  r"""get_derivative(StructureSource self, FloatKey a0) -> double"""
12901  return _IMP_atom.StructureSource_get_derivative(self, a0)
12902 
12903  def get_name(self):
12904  r"""get_name(StructureSource self) -> std::string"""
12905  return _IMP_atom.StructureSource_get_name(self)
12906 
12907  def clear_caches(self):
12908  r"""clear_caches(StructureSource self)"""
12909  return _IMP_atom.StructureSource_clear_caches(self)
12910 
12911  def set_name(self, a0):
12912  r"""set_name(StructureSource self, std::string a0)"""
12913  return _IMP_atom.StructureSource_set_name(self, a0)
12914 
12915  def set_check_level(self, a0):
12916  r"""set_check_level(StructureSource self, IMP::CheckLevel a0)"""
12917  return _IMP_atom.StructureSource_set_check_level(self, a0)
12918 
12919  def add_to_derivative(self, a0, a1, a2):
12920  r"""add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
12921  return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
12922 
12923  def set_is_optimized(self, a0, a1):
12924  r"""set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
12925  return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
12926 
12927  def get_is_optimized(self, a0):
12928  r"""get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
12929  return _IMP_atom.StructureSource_get_is_optimized(self, a0)
12930 
12931  def get_check_level(self):
12932  r"""get_check_level(StructureSource self) -> IMP::CheckLevel"""
12933  return _IMP_atom.StructureSource_get_check_level(self)
12934 
12935  def __eq__(self, *args):
12936  r"""
12937  __eq__(StructureSource self, StructureSource o) -> bool
12938  __eq__(StructureSource self, Particle d) -> bool
12939  """
12940  return _IMP_atom.StructureSource___eq__(self, *args)
12941 
12942  def __ne__(self, *args):
12943  r"""
12944  __ne__(StructureSource self, StructureSource o) -> bool
12945  __ne__(StructureSource self, Particle d) -> bool
12946  """
12947  return _IMP_atom.StructureSource___ne__(self, *args)
12948 
12949  def __le__(self, *args):
12950  r"""
12951  __le__(StructureSource self, StructureSource o) -> bool
12952  __le__(StructureSource self, Particle d) -> bool
12953  """
12954  return _IMP_atom.StructureSource___le__(self, *args)
12955 
12956  def __lt__(self, *args):
12957  r"""
12958  __lt__(StructureSource self, StructureSource o) -> bool
12959  __lt__(StructureSource self, Particle d) -> bool
12960  """
12961  return _IMP_atom.StructureSource___lt__(self, *args)
12962 
12963  def __ge__(self, *args):
12964  r"""
12965  __ge__(StructureSource self, StructureSource o) -> bool
12966  __ge__(StructureSource self, Particle d) -> bool
12967  """
12968  return _IMP_atom.StructureSource___ge__(self, *args)
12969 
12970  def __gt__(self, *args):
12971  r"""
12972  __gt__(StructureSource self, StructureSource o) -> bool
12973  __gt__(StructureSource self, Particle d) -> bool
12974  """
12975  return _IMP_atom.StructureSource___gt__(self, *args)
12976 
12977  def __hash__(self):
12978  r"""__hash__(StructureSource self) -> std::size_t"""
12979  return _IMP_atom.StructureSource___hash__(self)
12980 
12981  def __str__(self):
12982  r"""__str__(StructureSource self) -> std::string"""
12983  return _IMP_atom.StructureSource___str__(self)
12984 
12985  def __repr__(self):
12986  r"""__repr__(StructureSource self) -> std::string"""
12987  return _IMP_atom.StructureSource___repr__(self)
12988 
12989  def _get_as_binary(self):
12990  r"""_get_as_binary(StructureSource self) -> PyObject *"""
12991  return _IMP_atom.StructureSource__get_as_binary(self)
12992 
12993  def _set_from_binary(self, p):
12994  r"""_set_from_binary(StructureSource self, PyObject * p)"""
12995  return _IMP_atom.StructureSource__set_from_binary(self, p)
12996 
12997  def __getstate__(self):
12998  p = self._get_as_binary()
12999  if len(self.__dict__) > 1:
13000  d = self.__dict__.copy()
13001  del d['this']
13002  p = (d, p)
13003  return p
13004 
13005  def __setstate__(self, p):
13006  if not hasattr(self, 'this'):
13007  self.__init__()
13008  if isinstance(p, tuple):
13009  d, p = p
13010  self.__dict__.update(d)
13011  return self._set_from_binary(p)
13012 
13013  __swig_destroy__ = _IMP_atom.delete_StructureSource
13014 
13015 # Register StructureSource in _IMP_atom:
13016 _IMP_atom.StructureSource_swigregister(StructureSource)
13017 
13018 def __lshift__(*args):
13019  r"""
13020  __lshift__(_ostream out, Bonded n) -> _ostream
13021  __lshift__(_ostream out, Bond n) -> _ostream
13022  __lshift__(_ostream out, Hierarchy n) -> _ostream
13023  __lshift__(_ostream out, Angle n) -> _ostream
13024  __lshift__(_ostream out, Dihedral n) -> _ostream
13025  __lshift__(_ostream out, CenterOfMass n) -> _ostream
13026  __lshift__(_ostream out, Diffusion n) -> _ostream
13027  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13028  __lshift__(_ostream out, TAMDParticle n) -> _ostream
13029  __lshift__(_ostream out, Charged n) -> _ostream
13030  __lshift__(_ostream out, Domain n) -> _ostream
13031  __lshift__(_ostream out, LennardJones n) -> _ostream
13032  __lshift__(_ostream out, Fragment n) -> _ostream
13033  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13034  __lshift__(_ostream out, Atom n) -> _ostream
13035  __lshift__(_ostream out, Residue n) -> _ostream
13036  __lshift__(_ostream out, Representation n) -> _ostream
13037  __lshift__(_ostream out, State n) -> _ostream
13038  __lshift__(_ostream out, Molecule n) -> _ostream
13039  __lshift__(_ostream out, Copy n) -> _ostream
13040  __lshift__(_ostream out, Chain n) -> _ostream
13041  __lshift__(_ostream out, StructureSource n) -> _ostream
13042  """
13043  return _IMP_atom.__lshift__(*args)
13044 class HelixRestraint(IMP.Restraint):
13045  r"""Proxy of C++ IMP::atom::HelixRestraint class."""
13046 
13047  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13048 
13049  def __init__(self, rs, ideal=True):
13050  r"""__init__(HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint"""
13051  _IMP_atom.HelixRestraint_swiginit(self, _IMP_atom.new_HelixRestraint(rs, ideal))
13052 
13053  def get_number_of_bonds(self):
13054  r"""get_number_of_bonds(HelixRestraint self) -> int"""
13055  return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13056 
13057  def get_number_of_dihedrals(self):
13058  r"""get_number_of_dihedrals(HelixRestraint self) -> int"""
13059  return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13060 
13061  def do_get_inputs(self):
13062  r"""do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13063  return _IMP_atom.HelixRestraint_do_get_inputs(self)
13064 
13065  def get_version_info(self):
13066  r"""get_version_info(HelixRestraint self) -> VersionInfo"""
13067  return _IMP_atom.HelixRestraint_get_version_info(self)
13068  __swig_destroy__ = _IMP_atom.delete_HelixRestraint
13069 
13070  def __str__(self):
13071  r"""__str__(HelixRestraint self) -> std::string"""
13072  return _IMP_atom.HelixRestraint___str__(self)
13073 
13074  def __repr__(self):
13075  r"""__repr__(HelixRestraint self) -> std::string"""
13076  return _IMP_atom.HelixRestraint___repr__(self)
13077 
13078  @staticmethod
13079  def get_from(o):
13080  return _object_cast_to_HelixRestraint(o)
13081 
13082 
13083 # Register HelixRestraint in _IMP_atom:
13084 _IMP_atom.HelixRestraint_swigregister(HelixRestraint)
13085 
13087  r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
13088  return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
13089 
13090 def show_molecular_hierarchy(*args):
13091  r"""show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream"""
13092  return _IMP_atom.show_molecular_hierarchy(*args)
13093 class CHARMMBond(object):
13094  r"""Proxy of C++ IMP::atom::CHARMMConnection< 2 > class."""
13095 
13096  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13097  __repr__ = _swig_repr
13098 
13099  def __init__(self, atoms):
13100  r"""__init__(CHARMMBond self, IMP::Strings const & atoms) -> CHARMMBond"""
13101  _IMP_atom.CHARMMBond_swiginit(self, _IMP_atom.new_CHARMMBond(atoms))
13102 
13103  def get_endpoint(self, i):
13104  r"""get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13105  return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13106 
13107  def get_contains_atom(self, name):
13108  r"""get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13109  return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13110 
13111  def show(self, *args):
13112  r"""show(CHARMMBond self, _ostream out=std::cout)"""
13113  return _IMP_atom.CHARMMBond_show(self, *args)
13114  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13115 
13116 # Register CHARMMBond in _IMP_atom:
13117 _IMP_atom.CHARMMBond_swigregister(CHARMMBond)
13118 class CHARMMAngle(object):
13119  r"""Proxy of C++ IMP::atom::CHARMMConnection< 3 > class."""
13120 
13121  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
13122  __repr__ = _swig_repr
13123 
13124  def __init__(self, atoms):
13125  r"""__init__(CHARMMAngle self, IMP::Strings const & atoms) -> CHARMMAngle"""
13126  _IMP_atom.CHARMMAngle_swiginit(self, _IMP_atom.new_CHARMMAngle(atoms))
13127 
13128  def get_endpoint(self, i):
13129  r"""get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13130  return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13131 
13132  def get_contains_atom(self, name):
13133  r"""get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13134  return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13135 
13136  def show(self, *args):
13137  r"""show(CHARMMAngle self, _ostream out=std::cout)"""
13138  return _IMP_atom.CHARMMAngle_show(self, *args)
13139  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13140 
13141 # Register CHARMMAngle in _IMP_atom:
13142 _IMP_atom.CHARMMAngle_swigregister(CHARMMAngle)
13143 
13144 def _get_native_overlap_cpp(m1, m2, threshold):
13145  r"""_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13146  return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13147 
13148 def _get_drmsd_cpp(m0, m1):
13149  r"""_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13150  return _IMP_atom._get_drmsd_cpp(m0, m1)
13151 
13152 def _get_drmsd_Q_cpp(m0, m1, threshold):
13153  r"""_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13154  return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13155 
13156 def _get_drms_cpp(m1, m2):
13157  r"""_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13158  return _IMP_atom._get_drms_cpp(m1, m2)
13159 
13160 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13161  r"""_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, IMP::IntRanges const & ranges) -> double"""
13162  return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13163 
13164 def get_native_overlap(a, b, d):
13165  va= [IMP.algebra.get_vector(x) for x in a]
13166  vb= [IMP.algebra.get_vector(x) for x in b]
13167  return _get_native_overlap_cpp(va, vb, d)
13168 
13169 def get_drmsd(a, b):
13170  va= [IMP.algebra.get_vector(x) for x in a]
13171  vb= [IMP.algebra.get_vector(x) for x in b]
13172  return _get_drmsd_cpp(va, vb)
13173 
13174 def get_drms(a, b):
13175  va= [IMP.algebra.get_vector(x) for x in a]
13176  vb= [IMP.algebra.get_vector(x) for x in b]
13177  return _get_drms_cpp(va, vb)
13178 
13179 def get_drmsd_Q(a, b, t):
13180  va= [IMP.algebra.get_vector(x) for x in a]
13181  vb= [IMP.algebra.get_vector(x) for x in b]
13182  return _get_drmsd_Q_cpp(va, vb, t)
13183 
13184 def get_rigid_bodies_drms(a, b, ranges):
13185  va= [IMP.algebra.get_vector(x) for x in a]
13186  vb= [IMP.algebra.get_vector(x) for x in b]
13187 #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
13188  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13189 
13190 
13191 
13192 def get_module_version():
13193  r"""get_module_version() -> std::string const"""
13194  return _IMP_atom.get_module_version()
13195 
13196 def get_example_path(fname):
13197  r"""get_example_path(std::string fname) -> std::string"""
13198  return _IMP_atom.get_example_path(fname)
13199 
13200 def get_data_path(fname):
13201  r"""get_data_path(std::string fname) -> std::string"""
13202  return _IMP_atom.get_data_path(fname)
13203 
13204 from . import _version_check
13205 _version_check.check_version(get_module_version())
13206 __version__ = get_module_version()
13207 
13208 
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.
Hierarchy read_pdb_or_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 PDB or mmCIF file.
Definition: mmcif.h:40
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)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
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.
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.
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)
Hierarchies read_multimodel_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB or mmCIF file.
Definition: mmcif.h:60
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