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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 # This wrapper is part of IMP,
8 # Copyright 2007-2020 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_atom')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_atom')
25  _IMP_atom = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_atom', [dirname(__file__)])
34  except ImportError:
35  import _IMP_atom
36  return _IMP_atom
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_atom', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_atom = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_atom
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_ATOM_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
126  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
132  incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
133  """
134  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
140  decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
141  """
142  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
152  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
157  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
162  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
167  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
172  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
177  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
182  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
187  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
192  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
197  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
202  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
208  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
215 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_atom.IMP_DEBUG
224 IMP_RELEASE = _IMP_atom.IMP_RELEASE
225 IMP_SILENT = _IMP_atom.IMP_SILENT
226 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
227 IMP_TERSE = _IMP_atom.IMP_TERSE
228 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
229 IMP_MEMORY = _IMP_atom.IMP_MEMORY
230 IMP_NONE = _IMP_atom.IMP_NONE
231 IMP_USAGE = _IMP_atom.IMP_USAGE
232 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_atom._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_atom._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
329 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
330 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
331 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
332 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
333 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
334 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
335 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
336 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
337 import IMP.core
338 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
339 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
341 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
342 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
343 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
344 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
345 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
348 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
349 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
350 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
351 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
352 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
353 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
354 import IMP.container
355 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
356 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
357 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
358 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
359 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
360 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
361 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
362 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
363 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
364 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
372  """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class."""
373 
374  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
375  __repr__ = _swig_repr
376 
377  def __init__(self):
378  """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
379  this = _IMP_atom.new_HierarchyTree()
380  try:
381  self.this.append(this)
382  except __builtin__.Exception:
383  self.this = this
384 
385  def get_graph(self):
386  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
387  return _IMP_atom.HierarchyTree_get_graph(self)
388 
389 
390  def get_vertices(self):
391  """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
392  return _IMP_atom.HierarchyTree_get_vertices(self)
393 
394 
395  def get_vertex_name(self, i):
396  """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
397  return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
398 
399 
400  def get_in_neighbors(self, v):
401  """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"""
402  return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
403 
404 
405  def get_out_neighbors(self, v):
406  """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"""
407  return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
408 
409 
410  def show_graphviz(self, *args):
411  """
412  show_graphviz(HierarchyTree self, _ostream out)
413  show_graphviz(HierarchyTree self)
414  """
415  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
416 
417 
418  def get_graphviz_string(self):
419  """get_graphviz_string(HierarchyTree self) -> std::string"""
420  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
421 
422 
423  def add_edge(self, v0, v1):
424  """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)"""
425  return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
426 
427 
428  def add_vertex(self, l):
429  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
430  return _IMP_atom.HierarchyTree_add_vertex(self, l)
431 
432 
433  def remove_vertex(self, l):
434  """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
435  return _IMP_atom.HierarchyTree_remove_vertex(self, l)
436 
437  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
438  __del__ = lambda self: None
439 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
440 HierarchyTree_swigregister(HierarchyTree)
441 
442 
443 _value_types.append("HierarchyTree")
444 
445 
446 _object_types.append("PDBSelector")
447 
448 
449 def _object_cast_to_PDBSelector(o):
450  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
451  return _IMP_atom._object_cast_to_PDBSelector(o)
452 
453 def Angles(l=[]):
454  return [Angle(x) for x in l]
455 _plural_types.append("Angles")
456 
457 
458 _value_types.append("Angle")
459 
460 
461 def Atoms(l=[]):
462  return [Atom(x) for x in l]
463 _plural_types.append("Atoms")
464 
465 
466 _value_types.append("Atom")
467 
468 
469 def Bonds(l=[]):
470  return [Bond(x) for x in l]
471 _plural_types.append("Bonds")
472 
473 
474 _value_types.append("Bond")
475 
476 
477 def Bondeds(l=[]):
478  return [Bonded(x) for x in l]
479 _plural_types.append("Bondeds")
480 
481 
482 _value_types.append("Bonded")
483 
484 
485 def CHARMMAtomList(l=[]):
486  return [CHARMMAtom(x) for x in l]
487 _plural_types.append("CHARMMAtomList")
488 
489 
490 _value_types.append("CHARMMAtom")
491 
492 
493 def Chains(l=[]):
494  return [Chain(x) for x in l]
495 _plural_types.append("Chains")
496 
497 
498 _value_types.append("Chain")
499 
500 
501 def CenterOfMasses(l=[]):
502  return [CenterOfMass(x) for x in l]
503 _plural_types.append("CenterOfMasses")
504 
505 
506 _value_types.append("CenterOfMass")
507 
508 
509 def Chargeds(l=[]):
510  return [Charged(x) for x in l]
511 _plural_types.append("Chargeds")
512 
513 
514 _value_types.append("Charged")
515 
516 
517 def Diffusions(l=[]):
518  return [Diffusion(x) for x in l]
519 _plural_types.append("Diffusions")
520 
521 
522 _value_types.append("Diffusion")
523 
524 
525 def RigidBodyDiffusions(l=[]):
526  return [RigidBodyDiffusion(x) for x in l]
527 _plural_types.append("RigidBodyDiffusions")
528 
529 
530 _value_types.append("RigidBodyDiffusion")
531 
532 
533 def TAMDParticles(l=[]):
534  return [TAMDParticle(x) for x in l]
535 _plural_types.append("TAMDParticles")
536 
537 
538 _value_types.append("TAMDParticle")
539 
540 
541 def TAMDCentroids(l=[]):
542  return [TAMDCentroid(x) for x in l]
543 _plural_types.append("TAMDCentroids")
544 
545 
546 _value_types.append("TAMDCentroid")
547 
548 
549 def Dihedrals(l=[]):
550  return [Dihedral(x) for x in l]
551 _plural_types.append("Dihedrals")
552 
553 
554 _value_types.append("Dihedral")
555 
556 
557 def Domains(l=[]):
558  return [Domain(x) for x in l]
559 _plural_types.append("Domains")
560 
561 
562 _value_types.append("Domain")
563 
564 
565 def Fragments(l=[]):
566  return [Fragment(x) for x in l]
567 _plural_types.append("Fragments")
568 
569 
570 _value_types.append("Fragment")
571 
572 
573 def Hierarchies(l=[]):
574  return [Hierarchy(x) for x in l]
575 _plural_types.append("Hierarchies")
576 
577 
578 _value_types.append("Hierarchy")
579 
580 
581 def LennardJonesList(l=[]):
582  return [LennardJones(x) for x in l]
583 _plural_types.append("LennardJonesList")
584 
585 
586 _value_types.append("LennardJones")
587 
588 
589 def Masses(l=[]):
590  return [Mass(x) for x in l]
591 _plural_types.append("Masses")
592 
593 
594 _value_types.append("Mass")
595 
596 
597 def LinearVelocities(l=[]):
598  return [LinearVelocity(x) for x in l]
599 _plural_types.append("LinearVelocities")
600 
601 
602 _value_types.append("LinearVelocity")
603 
604 
605 def AngularVelocities(l=[]):
606  return [AngularVelocity(x) for x in l]
607 _plural_types.append("AngularVelocities")
608 
609 
610 _value_types.append("AngularVelocity")
611 
612 
613 def Molecules(l=[]):
614  return [Molecule(x) for x in l]
615 _plural_types.append("Molecules")
616 
617 
618 _value_types.append("Molecule")
619 
620 
621 def Residues(l=[]):
622  return [Residue(x) for x in l]
623 _plural_types.append("Residues")
624 
625 
626 _value_types.append("Residue")
627 
628 
629 def Representations(l=[]):
630  return [Representation(x) for x in l]
631 _plural_types.append("Representations")
632 
633 
634 _value_types.append("Representation")
635 
636 
637 def States(l=[]):
638  return [State(x) for x in l]
639 _plural_types.append("States")
640 
641 
642 _value_types.append("State")
643 
644 
645 def Copies(l=[]):
646  return [Copy(x) for x in l]
647 _plural_types.append("Copies")
648 
649 
650 _value_types.append("Copy")
651 
652 
653 def SecondaryStructureResidues(l=[]):
654  return [SecondaryStructureResidue(x) for x in l]
655 _plural_types.append("SecondaryStructureResidues")
656 
657 
658 _value_types.append("SecondaryStructureResidue")
659 
660 
661 def StructureSources(l=[]):
662  return [StructureSource(x) for x in l]
663 _plural_types.append("StructureSources")
664 
665 
666 _value_types.append("StructureSource")
667 
668 
669 _object_types.append("Simulator")
670 
671 
672 def _object_cast_to_Simulator(o):
673  """_object_cast_to_Simulator(Object o) -> Simulator"""
674  return _IMP_atom._object_cast_to_Simulator(o)
675 
676 _object_types.append("ATOMPDBSelector")
677 
678 
679 def _object_cast_to_ATOMPDBSelector(o):
680  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
681  return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
682 
683 _object_types.append("AllMol2Selector")
684 
685 
686 def _object_cast_to_AllMol2Selector(o):
687  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
688  return _IMP_atom._object_cast_to_AllMol2Selector(o)
689 
690 _object_types.append("AllPDBSelector")
691 
692 
693 def _object_cast_to_AllPDBSelector(o):
694  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
695  return _IMP_atom._object_cast_to_AllPDBSelector(o)
696 
697 _object_types.append("AndPDBSelector")
698 
699 
700 def _object_cast_to_AndPDBSelector(o):
701  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
702  return _IMP_atom._object_cast_to_AndPDBSelector(o)
703 
704 _object_types.append("XorPDBSelector")
705 
706 
707 def _object_cast_to_XorPDBSelector(o):
708  """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
709  return _IMP_atom._object_cast_to_XorPDBSelector(o)
710 
711 _object_types.append("ResidueTypePDBSelector")
712 
713 
714 def _object_cast_to_ResidueTypePDBSelector(o):
715  """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
716  return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
717 
718 _object_types.append("AtomTypePDBSelector")
719 
720 
721 def _object_cast_to_AtomTypePDBSelector(o):
722  """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
723  return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
724 
725 _object_types.append("AngleSingletonScore")
726 
727 
728 def _object_cast_to_AngleSingletonScore(o):
729  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
730  return _IMP_atom._object_cast_to_AngleSingletonScore(o)
731 
732 _object_types.append("BondEndpointsRefiner")
733 
734 
735 def _object_cast_to_BondEndpointsRefiner(o):
736  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
737  return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
738 
739 _object_types.append("BondPairContainer")
740 
741 
742 def _object_cast_to_BondPairContainer(o):
743  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
744  return _IMP_atom._object_cast_to_BondPairContainer(o)
745 
746 _object_types.append("BondSingletonScore")
747 
748 
749 def _object_cast_to_BondSingletonScore(o):
750  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
751  return _IMP_atom._object_cast_to_BondSingletonScore(o)
752 
753 _object_types.append("BondedPairFilter")
754 
755 
756 def _object_cast_to_BondedPairFilter(o):
757  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
758  return _IMP_atom._object_cast_to_BondedPairFilter(o)
759 
760 _object_types.append("BrownianDynamics")
761 
762 
763 def _object_cast_to_BrownianDynamics(o):
764  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
765  return _IMP_atom._object_cast_to_BrownianDynamics(o)
766 
767 _object_types.append("BrownianDynamicsTAMD")
768 
769 
770 def _object_cast_to_BrownianDynamicsTAMD(o):
771  """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
772  return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
773 
774 _object_types.append("CAlphaPDBSelector")
775 
776 
777 def _object_cast_to_CAlphaPDBSelector(o):
778  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
779  return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
780 
781 _object_types.append("CBetaPDBSelector")
782 
783 
784 def _object_cast_to_CBetaPDBSelector(o):
785  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
786  return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
787 
788 _object_types.append("BackbonePDBSelector")
789 
790 
791 def _object_cast_to_BackbonePDBSelector(o):
792  """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
793  return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
794 
795 _object_types.append("CHARMMParameters")
796 
797 
798 def _object_cast_to_CHARMMParameters(o):
799  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
800  return _IMP_atom._object_cast_to_CHARMMParameters(o)
801 
802 _object_types.append("CHARMMResidueTopology")
803 
804 
805 def _object_cast_to_CHARMMResidueTopology(o):
806  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
807  return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
808 
809 _object_types.append("CHARMMSegmentTopology")
810 
811 
812 def _object_cast_to_CHARMMSegmentTopology(o):
813  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
814  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
815 
816 _object_types.append("CHARMMStereochemistryRestraint")
817 
818 
819 def _object_cast_to_CHARMMStereochemistryRestraint(o):
820  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
821  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
822 
823 _object_types.append("CHARMMTopology")
824 
825 
826 def _object_cast_to_CHARMMTopology(o):
827  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
828  return _IMP_atom._object_cast_to_CHARMMTopology(o)
829 
830 _object_types.append("CPDBSelector")
831 
832 
833 def _object_cast_to_CPDBSelector(o):
834  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
835  return _IMP_atom._object_cast_to_CPDBSelector(o)
836 
837 _object_types.append("ChainPDBSelector")
838 
839 
840 def _object_cast_to_ChainPDBSelector(o):
841  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
842  return _IMP_atom._object_cast_to_ChainPDBSelector(o)
843 
844 _object_types.append("CoulombPairScore")
845 
846 
847 def _object_cast_to_CoulombPairScore(o):
848  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
849  return _IMP_atom._object_cast_to_CoulombPairScore(o)
850 
851 _object_types.append("CoverBond")
852 
853 
854 def _object_cast_to_CoverBond(o):
855  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
856  return _IMP_atom._object_cast_to_CoverBond(o)
857 
858 _object_types.append("DihedralSingletonScore")
859 
860 
861 def _object_cast_to_DihedralSingletonScore(o):
862  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
863  return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
864 
865 _object_types.append("DopePairScore")
866 
867 
868 def _object_cast_to_DopePairScore(o):
869  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
870  return _IMP_atom._object_cast_to_DopePairScore(o)
871 
872 _object_types.append("LoopStatisticalPairScore")
873 
874 
875 def _object_cast_to_LoopStatisticalPairScore(o):
876  """_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
877  return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
878 
879 _object_types.append("OrientedSoapPairScore")
880 
881 
882 def _object_cast_to_OrientedSoapPairScore(o):
883  """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
884  return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
885 
886 _object_types.append("EzRestraint")
887 
888 
889 def _object_cast_to_EzRestraint(o):
890  """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
891  return _IMP_atom._object_cast_to_EzRestraint(o)
892 
893 _object_types.append("ForceFieldParameters")
894 
895 
896 def _object_cast_to_ForceFieldParameters(o):
897  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
898  return _IMP_atom._object_cast_to_ForceFieldParameters(o)
899 
900 _object_types.append("ForceSwitch")
901 
902 
903 def _object_cast_to_ForceSwitch(o):
904  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
905  return _IMP_atom._object_cast_to_ForceSwitch(o)
906 
907 _object_types.append("HydrogenPDBSelector")
908 
909 
910 def _object_cast_to_HydrogenPDBSelector(o):
911  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
912  return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
913 
914 _object_types.append("ImproperSingletonScore")
915 
916 
917 def _object_cast_to_ImproperSingletonScore(o):
918  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
919  return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
920 
921 _object_types.append("LennardJonesPairScore")
922 
923 
924 def _object_cast_to_LennardJonesPairScore(o):
925  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
926  return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
927 
928 _object_types.append("Mol2Selector")
929 
930 
931 def _object_cast_to_Mol2Selector(o):
932  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
933  return _IMP_atom._object_cast_to_Mol2Selector(o)
934 
935 _object_types.append("MolecularDynamics")
936 
937 
938 def _object_cast_to_MolecularDynamics(o):
939  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
940  return _IMP_atom._object_cast_to_MolecularDynamics(o)
941 
942 _object_types.append("NPDBSelector")
943 
944 
945 def _object_cast_to_NPDBSelector(o):
946  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
947  return _IMP_atom._object_cast_to_NPDBSelector(o)
948 
949 _object_types.append("NonAlternativePDBSelector")
950 
951 
952 def _object_cast_to_NonAlternativePDBSelector(o):
953  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
954  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
955 
956 _object_types.append("NonHydrogenMol2Selector")
957 
958 
959 def _object_cast_to_NonHydrogenMol2Selector(o):
960  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
961  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
962 
963 _object_types.append("NonHydrogenPDBSelector")
964 
965 
966 def _object_cast_to_NonHydrogenPDBSelector(o):
967  """_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
968  return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
969 
970 _object_types.append("NonWaterNonHydrogenPDBSelector")
971 
972 
973 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
974  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
975  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
976 
977 _object_types.append("NonWaterPDBSelector")
978 
979 
980 def _object_cast_to_NonWaterPDBSelector(o):
981  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
982  return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
983 
984 _object_types.append("NotPDBSelector")
985 
986 
987 def _object_cast_to_NotPDBSelector(o):
988  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
989  return _IMP_atom._object_cast_to_NotPDBSelector(o)
990 
991 _object_types.append("OrPDBSelector")
992 
993 
994 def _object_cast_to_OrPDBSelector(o):
995  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
996  return _IMP_atom._object_cast_to_OrPDBSelector(o)
997 
998 _object_types.append("PPDBSelector")
999 
1000 
1001 def _object_cast_to_PPDBSelector(o):
1002  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1003  return _IMP_atom._object_cast_to_PPDBSelector(o)
1004 
1005 _object_types.append("ProteinLigandAtomPairScore")
1006 
1007 
1008 def _object_cast_to_ProteinLigandAtomPairScore(o):
1009  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1010  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1011 
1012 _object_types.append("ProteinLigandRestraint")
1013 
1014 
1015 def _object_cast_to_ProteinLigandRestraint(o):
1016  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1017  return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1018 
1019 _object_types.append("SameResiduePairFilter")
1020 
1021 
1022 def _object_cast_to_SameResiduePairFilter(o):
1023  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1024  return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1025 
1026 _object_types.append("SoapPairFilter")
1027 
1028 
1029 def _object_cast_to_SoapPairFilter(o):
1030  """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1031  return _IMP_atom._object_cast_to_SoapPairFilter(o)
1032 
1033 _object_types.append("SmoothingFunction")
1034 
1035 
1036 def _object_cast_to_SmoothingFunction(o):
1037  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1038  return _IMP_atom._object_cast_to_SmoothingFunction(o)
1039 
1040 _object_types.append("StereochemistryPairFilter")
1041 
1042 
1043 def _object_cast_to_StereochemistryPairFilter(o):
1044  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1045  return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1046 
1047 _object_types.append("VelocityScalingOptimizerState")
1048 
1049 
1050 def _object_cast_to_VelocityScalingOptimizerState(o):
1051  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1052  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1053 
1054 _object_types.append("WaterPDBSelector")
1055 
1056 
1057 def _object_cast_to_WaterPDBSelector(o):
1058  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1059  return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1060 
1061 _object_types.append("WritePDBOptimizerState")
1062 
1063 
1064 def _object_cast_to_WritePDBOptimizerState(o):
1065  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1066  return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1067 
1068 AtomTypes=list
1069 _plural_types.append("AtomTypes")
1070 _value_types.append("AtomType")
1071 
1072 
1073 CHARMMAtomTopologies=list
1074 _plural_types.append("CHARMMAtomTopologies")
1075 _value_types.append("CHARMMAtomTopology")
1076 
1077 
1078 CHARMMBondEndpoints=list
1079 _plural_types.append("CHARMMBondEndpoints")
1080 _value_types.append("CHARMMBondEndpoint")
1081 
1082 
1083 CHARMMBondParametersList=list
1084 _plural_types.append("CHARMMBondParametersList")
1085 _value_types.append("CHARMMBondParameters")
1086 
1087 
1088 CHARMMDihedralParametersList=list
1089 _plural_types.append("CHARMMDihedralParametersList")
1090 _value_types.append("CHARMMDihedralParameters")
1091 
1092 
1093 _object_types.append("CHARMMIdealResidueTopology")
1094 
1095 
1096 def _object_cast_to_CHARMMIdealResidueTopology(o):
1097  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1098  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1099 
1100 CHARMMInternalCoordinates=list
1101 _plural_types.append("CHARMMInternalCoordinates")
1102 _value_types.append("CHARMMInternalCoordinate")
1103 
1104 
1105 _object_types.append("CHARMMPatch")
1106 
1107 
1108 def _object_cast_to_CHARMMPatch(o):
1109  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1110  return _IMP_atom._object_cast_to_CHARMMPatch(o)
1111 
1112 _object_types.append("CHARMMResidueTopologyBase")
1113 
1114 
1115 def _object_cast_to_CHARMMResidueTopologyBase(o):
1116  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1117  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1118 
1119 ResidueTypes=list
1120 _plural_types.append("ResidueTypes")
1121 _value_types.append("ResidueType")
1122 
1123 
1124 ChainTypes=list
1125 _plural_types.append("ChainTypes")
1126 _value_types.append("ChainType")
1127 
1128 
1129 Selections=list
1130 _plural_types.append("Selections")
1131 _value_types.append("Selection")
1132 
1133 
1134 _object_types.append("RemoveRigidMotionOptimizerState")
1135 
1136 
1137 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1138  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1139  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1140 
1141 _object_types.append("BerendsenThermostatOptimizerState")
1142 
1143 
1144 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1145  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1146  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1147 
1148 _object_types.append("LangevinThermostatOptimizerState")
1149 
1150 
1151 def _object_cast_to_LangevinThermostatOptimizerState(o):
1152  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1153  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1154 
1155 _object_types.append("SelectionGeometry")
1156 
1157 
1158 def _object_cast_to_SelectionGeometry(o):
1159  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1160  return _IMP_atom._object_cast_to_SelectionGeometry(o)
1161 
1162 _object_types.append("HierarchyGeometry")
1163 
1164 
1165 def _object_cast_to_HierarchyGeometry(o):
1166  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1167  return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1168 
1169 _object_types.append("HierarchiesGeometry")
1170 
1171 
1172 def _object_cast_to_HierarchiesGeometry(o):
1173  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1174  return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1175 
1176 _object_types.append("BondGeometry")
1177 
1178 
1179 def _object_cast_to_BondGeometry(o):
1180  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1181  return _IMP_atom._object_cast_to_BondGeometry(o)
1182 
1183 _object_types.append("BondsGeometry")
1184 
1185 
1186 def _object_cast_to_BondsGeometry(o):
1187  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1188  return _IMP_atom._object_cast_to_BondsGeometry(o)
1189 
1190 _object_types.append("CAAngleRestraint")
1191 
1192 
1193 def _object_cast_to_CAAngleRestraint(o):
1194  """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1195  return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1196 
1197 _object_types.append("CADihedralRestraint")
1198 
1199 
1200 def _object_cast_to_CADihedralRestraint(o):
1201  """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1202  return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1203 
1204 _object_types.append("HelixRestraint")
1205 
1206 
1207 def _object_cast_to_HelixRestraint(o):
1208  """_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1209  return _IMP_atom._object_cast_to_HelixRestraint(o)
1210 
1211 CHARMMDihedrals=list
1212 _plural_types.append("CHARMMDihedrals")
1213 _value_types.append("CHARMMDihedral")
1214 
1215 
1216 CHARMMBonds=list
1217 _plural_types.append("CHARMMBonds")
1218 _value_types.append("CHARMMBond")
1219 
1220 
1221 CHARMMAngles=list
1222 _plural_types.append("CHARMMAngles")
1223 _value_types.append("CHARMMAngle")
1224 
1225 class Bond(IMP.Decorator):
1226  """Proxy of C++ IMP::atom::Bond class."""
1227 
1228  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1229 
1230  def __init__(self, *args):
1231  """
1232  __init__(IMP::atom::Bond self) -> Bond
1233  __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1234  __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1235  """
1236  this = _IMP_atom.new_Bond(*args)
1237  try:
1238  self.this.append(this)
1239  except __builtin__.Exception:
1240  self.this = this
1241 
1242  def show(self, *args):
1243  """
1244  show(Bond self, _ostream out)
1245  show(Bond self)
1246  """
1247  return _IMP_atom.Bond_show(self, *args)
1248 
1249 
1250  def get_is_setup(*args):
1251  """
1252  get_is_setup(_ParticleAdaptor p) -> bool
1253  get_is_setup(Model m, ParticleIndex pi) -> bool
1254  """
1255  return _IMP_atom.Bond_get_is_setup(*args)
1256 
1257  get_is_setup = staticmethod(get_is_setup)
1258  UNKNOWN = _IMP_atom.Bond_UNKNOWN
1259  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1260  SINGLE = _IMP_atom.Bond_SINGLE
1261  DOUBLE = _IMP_atom.Bond_DOUBLE
1262  TRIPLE = _IMP_atom.Bond_TRIPLE
1263  HYDROGEN = _IMP_atom.Bond_HYDROGEN
1264  SALT = _IMP_atom.Bond_SALT
1265  PEPTIDE = _IMP_atom.Bond_PEPTIDE
1266  AMIDE = _IMP_atom.Bond_AMIDE
1267  AROMATIC = _IMP_atom.Bond_AROMATIC
1268 
1269  def get_bonded(self, i):
1270  """get_bonded(Bond self, unsigned int i) -> Bonded"""
1271  return _IMP_atom.Bond_get_bonded(self, i)
1272 
1273 
1274  def get_type(self):
1275  """get_type(Bond self) -> IMP::Int"""
1276  return _IMP_atom.Bond_get_type(self)
1277 
1278 
1279  def set_type(self, t):
1280  """set_type(Bond self, IMP::Int t)"""
1281  return _IMP_atom.Bond_set_type(self, t)
1282 
1283 
1284  def get_order(self):
1285  """get_order(Bond self) -> IMP::Int"""
1286  return _IMP_atom.Bond_get_order(self)
1287 
1288 
1289  def set_order(self, t):
1290  """set_order(Bond self, IMP::Int t)"""
1291  return _IMP_atom.Bond_set_order(self, t)
1292 
1293 
1294  def get_length(self):
1295  """get_length(Bond self) -> IMP::Float"""
1296  return _IMP_atom.Bond_get_length(self)
1297 
1298 
1299  def set_length(self, t):
1300  """set_length(Bond self, IMP::Float t)"""
1301  return _IMP_atom.Bond_set_length(self, t)
1302 
1303 
1304  def get_stiffness(self):
1305  """get_stiffness(Bond self) -> IMP::Float"""
1306  return _IMP_atom.Bond_get_stiffness(self)
1307 
1308 
1309  def set_stiffness(self, t):
1310  """set_stiffness(Bond self, IMP::Float t)"""
1311  return _IMP_atom.Bond_set_stiffness(self, t)
1312 
1313 
1314  def get_length_key():
1315  """get_length_key() -> FloatKey"""
1316  return _IMP_atom.Bond_get_length_key()
1317 
1318  get_length_key = staticmethod(get_length_key)
1319 
1320  def add_attribute(self, *args):
1321  """
1322  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1323  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1324  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1325  add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1326  add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1327  add_attribute(Bond self, StringKey a0, IMP::String a1)
1328  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1329  add_attribute(Bond self, ObjectKey a0, Object a1)
1330  """
1331  return _IMP_atom.Bond_add_attribute(self, *args)
1332 
1333 
1334  def get_value(self, *args):
1335  """
1336  get_value(Bond self, FloatKey a0) -> IMP::Float
1337  get_value(Bond self, IntKey a0) -> IMP::Int
1338  get_value(Bond self, FloatsKey a0) -> IMP::Floats
1339  get_value(Bond self, IntsKey a0) -> IMP::Ints
1340  get_value(Bond self, StringKey a0) -> IMP::String
1341  get_value(Bond self, ParticleIndexKey a0) -> Particle
1342  get_value(Bond self, ObjectKey a0) -> Object
1343  """
1344  return _IMP_atom.Bond_get_value(self, *args)
1345 
1346 
1347  def set_value(self, *args):
1348  """
1349  set_value(Bond self, FloatKey a0, IMP::Float a1)
1350  set_value(Bond self, IntKey a0, IMP::Int a1)
1351  set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1352  set_value(Bond self, IntsKey a0, IMP::Ints a1)
1353  set_value(Bond self, StringKey a0, IMP::String a1)
1354  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1355  set_value(Bond self, ObjectKey a0, Object a1)
1356  """
1357  return _IMP_atom.Bond_set_value(self, *args)
1358 
1359 
1360  def remove_attribute(self, *args):
1361  """
1362  remove_attribute(Bond self, FloatKey a0)
1363  remove_attribute(Bond self, IntKey a0)
1364  remove_attribute(Bond self, FloatsKey a0)
1365  remove_attribute(Bond self, IntsKey a0)
1366  remove_attribute(Bond self, StringKey a0)
1367  remove_attribute(Bond self, ParticleIndexKey a0)
1368  remove_attribute(Bond self, ObjectKey a0)
1369  """
1370  return _IMP_atom.Bond_remove_attribute(self, *args)
1371 
1372 
1373  def has_attribute(self, *args):
1374  """
1375  has_attribute(Bond self, FloatKey a0) -> bool
1376  has_attribute(Bond self, IntKey a0) -> bool
1377  has_attribute(Bond self, FloatsKey a0) -> bool
1378  has_attribute(Bond self, IntsKey a0) -> bool
1379  has_attribute(Bond self, StringKey a0) -> bool
1380  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1381  has_attribute(Bond self, ObjectKey a0) -> bool
1382  """
1383  return _IMP_atom.Bond_has_attribute(self, *args)
1384 
1385 
1386  def get_derivative(self, a0):
1387  """get_derivative(Bond self, FloatKey a0) -> double"""
1388  return _IMP_atom.Bond_get_derivative(self, a0)
1389 
1390 
1391  def get_name(self):
1392  """get_name(Bond self) -> std::string"""
1393  return _IMP_atom.Bond_get_name(self)
1394 
1395 
1396  def clear_caches(self):
1397  """clear_caches(Bond self)"""
1398  return _IMP_atom.Bond_clear_caches(self)
1399 
1400 
1401  def set_name(self, a0):
1402  """set_name(Bond self, std::string a0)"""
1403  return _IMP_atom.Bond_set_name(self, a0)
1404 
1405 
1406  def set_check_level(self, a0):
1407  """set_check_level(Bond self, IMP::CheckLevel a0)"""
1408  return _IMP_atom.Bond_set_check_level(self, a0)
1409 
1410 
1411  def add_to_derivative(self, a0, a1, a2):
1412  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1413  return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1414 
1415 
1416  def set_is_optimized(self, a0, a1):
1417  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1418  return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1419 
1420 
1421  def get_is_optimized(self, a0):
1422  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1423  return _IMP_atom.Bond_get_is_optimized(self, a0)
1424 
1425 
1426  def get_check_level(self):
1427  """get_check_level(Bond self) -> IMP::CheckLevel"""
1428  return _IMP_atom.Bond_get_check_level(self)
1429 
1430 
1431  def __eq__(self, *args):
1432  """
1433  __eq__(Bond self, Bond o) -> bool
1434  __eq__(Bond self, Particle d) -> bool
1435  """
1436  return _IMP_atom.Bond___eq__(self, *args)
1437 
1438 
1439  def __ne__(self, *args):
1440  """
1441  __ne__(Bond self, Bond o) -> bool
1442  __ne__(Bond self, Particle d) -> bool
1443  """
1444  return _IMP_atom.Bond___ne__(self, *args)
1445 
1446 
1447  def __le__(self, *args):
1448  """
1449  __le__(Bond self, Bond o) -> bool
1450  __le__(Bond self, Particle d) -> bool
1451  """
1452  return _IMP_atom.Bond___le__(self, *args)
1453 
1454 
1455  def __lt__(self, *args):
1456  """
1457  __lt__(Bond self, Bond o) -> bool
1458  __lt__(Bond self, Particle d) -> bool
1459  """
1460  return _IMP_atom.Bond___lt__(self, *args)
1461 
1462 
1463  def __ge__(self, *args):
1464  """
1465  __ge__(Bond self, Bond o) -> bool
1466  __ge__(Bond self, Particle d) -> bool
1467  """
1468  return _IMP_atom.Bond___ge__(self, *args)
1469 
1470 
1471  def __gt__(self, *args):
1472  """
1473  __gt__(Bond self, Bond o) -> bool
1474  __gt__(Bond self, Particle d) -> bool
1475  """
1476  return _IMP_atom.Bond___gt__(self, *args)
1477 
1478 
1479  def __hash__(self):
1480  """__hash__(Bond self) -> std::size_t"""
1481  return _IMP_atom.Bond___hash__(self)
1482 
1483 
1484  def __str__(self):
1485  """__str__(Bond self) -> std::string"""
1486  return _IMP_atom.Bond___str__(self)
1487 
1488 
1489  def __repr__(self):
1490  """__repr__(Bond self) -> std::string"""
1491  return _IMP_atom.Bond___repr__(self)
1492 
1493  __swig_destroy__ = _IMP_atom.delete_Bond
1494  __del__ = lambda self: None
1495 Bond_swigregister = _IMP_atom.Bond_swigregister
1496 Bond_swigregister(Bond)
1497 
1498 def Bond_get_is_setup(*args):
1499  """
1500  get_is_setup(_ParticleAdaptor p) -> bool
1501  Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1502  """
1503  return _IMP_atom.Bond_get_is_setup(*args)
1504 
1505 def Bond_get_length_key():
1506  """Bond_get_length_key() -> FloatKey"""
1507  return _IMP_atom.Bond_get_length_key()
1508 
1509 class Bonded(IMP.Decorator):
1510  """Proxy of C++ IMP::atom::Bonded class."""
1511 
1512  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1513 
1514  def __init__(self, *args):
1515  """
1516  __init__(IMP::atom::Bonded self) -> Bonded
1517  __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1518  __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1519  """
1520  this = _IMP_atom.new_Bonded(*args)
1521  try:
1522  self.this.append(this)
1523  except __builtin__.Exception:
1524  self.this = this
1525 
1526  def show(self, *args):
1527  """
1528  show(Bonded self, _ostream out)
1529  show(Bonded self)
1530  """
1531  return _IMP_atom.Bonded_show(self, *args)
1532 
1533 
1534  def setup_particle(*args):
1535  """
1536  setup_particle(Model m, ParticleIndex pi) -> Bonded
1537  setup_particle(_ParticleAdaptor decorator) -> Bonded
1538  """
1539  return _IMP_atom.Bonded_setup_particle(*args)
1540 
1541  setup_particle = staticmethod(setup_particle)
1542 
1543  def get_is_setup(*args):
1544  """
1545  get_is_setup(_ParticleAdaptor p) -> bool
1546  get_is_setup(Model m, ParticleIndex pi) -> bool
1547  """
1548  return _IMP_atom.Bonded_get_is_setup(*args)
1549 
1550  get_is_setup = staticmethod(get_is_setup)
1551 
1552  def get_number_of_bonds(self):
1553  """get_number_of_bonds(Bonded self) -> unsigned int"""
1554  return _IMP_atom.Bonded_get_number_of_bonds(self)
1555 
1556 
1557  def get_bond_indexes(self):
1558  """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1559  return _IMP_atom.Bonded_get_bond_indexes(self)
1560 
1561 
1562  def get_bond(self, i):
1563  """get_bond(Bonded self, unsigned int i) -> Bond"""
1564  return _IMP_atom.Bonded_get_bond(self, i)
1565 
1566 
1567  def get_bonded(self, i):
1568  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1569  return _IMP_atom.Bonded_get_bonded(self, i)
1570 
1571 
1572  def add_attribute(self, *args):
1573  """
1574  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1575  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1576  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1577  add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1578  add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1579  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1580  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1581  add_attribute(Bonded self, ObjectKey a0, Object a1)
1582  """
1583  return _IMP_atom.Bonded_add_attribute(self, *args)
1584 
1585 
1586  def get_value(self, *args):
1587  """
1588  get_value(Bonded self, FloatKey a0) -> IMP::Float
1589  get_value(Bonded self, IntKey a0) -> IMP::Int
1590  get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1591  get_value(Bonded self, IntsKey a0) -> IMP::Ints
1592  get_value(Bonded self, StringKey a0) -> IMP::String
1593  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1594  get_value(Bonded self, ObjectKey a0) -> Object
1595  """
1596  return _IMP_atom.Bonded_get_value(self, *args)
1597 
1598 
1599  def set_value(self, *args):
1600  """
1601  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1602  set_value(Bonded self, IntKey a0, IMP::Int a1)
1603  set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1604  set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1605  set_value(Bonded self, StringKey a0, IMP::String a1)
1606  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1607  set_value(Bonded self, ObjectKey a0, Object a1)
1608  """
1609  return _IMP_atom.Bonded_set_value(self, *args)
1610 
1611 
1612  def remove_attribute(self, *args):
1613  """
1614  remove_attribute(Bonded self, FloatKey a0)
1615  remove_attribute(Bonded self, IntKey a0)
1616  remove_attribute(Bonded self, FloatsKey a0)
1617  remove_attribute(Bonded self, IntsKey a0)
1618  remove_attribute(Bonded self, StringKey a0)
1619  remove_attribute(Bonded self, ParticleIndexKey a0)
1620  remove_attribute(Bonded self, ObjectKey a0)
1621  """
1622  return _IMP_atom.Bonded_remove_attribute(self, *args)
1623 
1624 
1625  def has_attribute(self, *args):
1626  """
1627  has_attribute(Bonded self, FloatKey a0) -> bool
1628  has_attribute(Bonded self, IntKey a0) -> bool
1629  has_attribute(Bonded self, FloatsKey a0) -> bool
1630  has_attribute(Bonded self, IntsKey a0) -> bool
1631  has_attribute(Bonded self, StringKey a0) -> bool
1632  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1633  has_attribute(Bonded self, ObjectKey a0) -> bool
1634  """
1635  return _IMP_atom.Bonded_has_attribute(self, *args)
1636 
1637 
1638  def get_derivative(self, a0):
1639  """get_derivative(Bonded self, FloatKey a0) -> double"""
1640  return _IMP_atom.Bonded_get_derivative(self, a0)
1641 
1642 
1643  def get_name(self):
1644  """get_name(Bonded self) -> std::string"""
1645  return _IMP_atom.Bonded_get_name(self)
1646 
1647 
1648  def clear_caches(self):
1649  """clear_caches(Bonded self)"""
1650  return _IMP_atom.Bonded_clear_caches(self)
1651 
1652 
1653  def set_name(self, a0):
1654  """set_name(Bonded self, std::string a0)"""
1655  return _IMP_atom.Bonded_set_name(self, a0)
1656 
1657 
1658  def set_check_level(self, a0):
1659  """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1660  return _IMP_atom.Bonded_set_check_level(self, a0)
1661 
1662 
1663  def add_to_derivative(self, a0, a1, a2):
1664  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1665  return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1666 
1667 
1668  def set_is_optimized(self, a0, a1):
1669  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1670  return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1671 
1672 
1673  def get_is_optimized(self, a0):
1674  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1675  return _IMP_atom.Bonded_get_is_optimized(self, a0)
1676 
1677 
1678  def get_check_level(self):
1679  """get_check_level(Bonded self) -> IMP::CheckLevel"""
1680  return _IMP_atom.Bonded_get_check_level(self)
1681 
1682 
1683  def __eq__(self, *args):
1684  """
1685  __eq__(Bonded self, Bonded o) -> bool
1686  __eq__(Bonded self, Particle d) -> bool
1687  """
1688  return _IMP_atom.Bonded___eq__(self, *args)
1689 
1690 
1691  def __ne__(self, *args):
1692  """
1693  __ne__(Bonded self, Bonded o) -> bool
1694  __ne__(Bonded self, Particle d) -> bool
1695  """
1696  return _IMP_atom.Bonded___ne__(self, *args)
1697 
1698 
1699  def __le__(self, *args):
1700  """
1701  __le__(Bonded self, Bonded o) -> bool
1702  __le__(Bonded self, Particle d) -> bool
1703  """
1704  return _IMP_atom.Bonded___le__(self, *args)
1705 
1706 
1707  def __lt__(self, *args):
1708  """
1709  __lt__(Bonded self, Bonded o) -> bool
1710  __lt__(Bonded self, Particle d) -> bool
1711  """
1712  return _IMP_atom.Bonded___lt__(self, *args)
1713 
1714 
1715  def __ge__(self, *args):
1716  """
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 
1723  def __gt__(self, *args):
1724  """
1725  __gt__(Bonded self, Bonded o) -> bool
1726  __gt__(Bonded self, Particle d) -> bool
1727  """
1728  return _IMP_atom.Bonded___gt__(self, *args)
1729 
1730 
1731  def __hash__(self):
1732  """__hash__(Bonded self) -> std::size_t"""
1733  return _IMP_atom.Bonded___hash__(self)
1734 
1735 
1736  def __str__(self):
1737  """__str__(Bonded self) -> std::string"""
1738  return _IMP_atom.Bonded___str__(self)
1739 
1740 
1741  def __repr__(self):
1742  """__repr__(Bonded self) -> std::string"""
1743  return _IMP_atom.Bonded___repr__(self)
1744 
1745  __swig_destroy__ = _IMP_atom.delete_Bonded
1746  __del__ = lambda self: None
1747 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1748 Bonded_swigregister(Bonded)
1749 
1750 def Bonded_setup_particle(*args):
1751  """
1752  setup_particle(Model m, ParticleIndex pi) -> Bonded
1753  Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1754  """
1755  return _IMP_atom.Bonded_setup_particle(*args)
1756 
1757 def Bonded_get_is_setup(*args):
1758  """
1759  get_is_setup(_ParticleAdaptor p) -> bool
1760  Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1761  """
1762  return _IMP_atom.Bonded_get_is_setup(*args)
1763 
1764 
1765 def create_custom_bond(a, b, length, stiffness=-1):
1766  """
1767  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1768  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1769  """
1770  return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1771 
1772 def create_bond(*args):
1773  """
1774  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1775  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1776  """
1777  return _IMP_atom.create_bond(*args)
1778 
1779 def destroy_bond(b):
1780  """destroy_bond(Bond b)"""
1781  return _IMP_atom.destroy_bond(b)
1782 
1783 def get_bond(a, b):
1784  """get_bond(Bonded a, Bonded b) -> Bond"""
1785  return _IMP_atom.get_bond(a, b)
1786 class BondGeometry(IMP.display.SingletonGeometry):
1787  """Proxy of C++ IMP::atom::BondGeometry class."""
1788 
1789  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1790 
1791  def __init__(self, *args):
1792  """
1793  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1794  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1795  """
1796  this = _IMP_atom.new_BondGeometry(*args)
1797  try:
1798  self.this.append(this)
1799  except __builtin__.Exception:
1800  self.this = this
1801 
1802  def get_version_info(self):
1803  """get_version_info(BondGeometry self) -> VersionInfo"""
1804  return _IMP_atom.BondGeometry_get_version_info(self)
1805 
1806 
1807  def __str__(self):
1808  """__str__(BondGeometry self) -> std::string"""
1809  return _IMP_atom.BondGeometry___str__(self)
1810 
1811 
1812  def __repr__(self):
1813  """__repr__(BondGeometry self) -> std::string"""
1814  return _IMP_atom.BondGeometry___repr__(self)
1815 
1816 
1817  @staticmethod
1818  def get_from(o):
1819  return _object_cast_to_BondGeometry(o)
1820 
1821 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1822 BondGeometry_swigregister(BondGeometry)
1823 
1824 class BondsGeometry(IMP.display.SingletonsGeometry):
1825  """Proxy of C++ IMP::atom::BondsGeometry class."""
1826 
1827  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1828 
1829  def __init__(self, sc):
1830  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1831  this = _IMP_atom.new_BondsGeometry(sc)
1832  try:
1833  self.this.append(this)
1834  except __builtin__.Exception:
1835  self.this = this
1836 
1837  def get_version_info(self):
1838  """get_version_info(BondsGeometry self) -> VersionInfo"""
1839  return _IMP_atom.BondsGeometry_get_version_info(self)
1840 
1841 
1842  def __str__(self):
1843  """__str__(BondsGeometry self) -> std::string"""
1844  return _IMP_atom.BondsGeometry___str__(self)
1845 
1846 
1847  def __repr__(self):
1848  """__repr__(BondsGeometry self) -> std::string"""
1849  return _IMP_atom.BondsGeometry___repr__(self)
1850 
1851 
1852  @staticmethod
1853  def get_from(o):
1854  return _object_cast_to_BondsGeometry(o)
1855 
1856 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1857 BondsGeometry_swigregister(BondsGeometry)
1858 
1859 class Hierarchy(IMP.core.Hierarchy):
1860  """Proxy of C++ IMP::atom::Hierarchy class."""
1861 
1862  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1863 
1864  def __init__(self, *args):
1865  """
1866  __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1867  __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1868  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1869  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1870  """
1871  this = _IMP_atom.new_Hierarchy(*args)
1872  try:
1873  self.this.append(this)
1874  except __builtin__.Exception:
1875  self.this = this
1876 
1877  def setup_particle(*args):
1878  """
1879  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1880  setup_particle(Particle p) -> Hierarchy
1881  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1882  setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1883  """
1884  return _IMP_atom.Hierarchy_setup_particle(*args)
1885 
1886  setup_particle = staticmethod(setup_particle)
1887 
1888  def get_is_setup(*args):
1889  """
1890  get_is_setup(Particle p) -> bool
1891  get_is_setup(Model m, ParticleIndex p) -> bool
1892  """
1893  return _IMP_atom.Hierarchy_get_is_setup(*args)
1894 
1895  get_is_setup = staticmethod(get_is_setup)
1896 
1897  def get_is_valid(self, print_info=False):
1898  """
1899  get_is_valid(Hierarchy self, bool print_info=False) -> bool
1900  get_is_valid(Hierarchy self) -> bool
1901  """
1902  return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1903 
1904 
1905  def add_child(self, o):
1906  """add_child(Hierarchy self, Hierarchy o)"""
1907  return _IMP_atom.Hierarchy_add_child(self, o)
1908 
1909 
1910  def get_child(self, i):
1911  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1912  return _IMP_atom.Hierarchy_get_child(self, i)
1913 
1914 
1915  def get_children(self):
1916  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1917  return _IMP_atom.Hierarchy_get_children(self)
1918 
1919 
1920  def get_parent(self):
1921  """get_parent(Hierarchy self) -> Hierarchy"""
1922  return _IMP_atom.Hierarchy_get_parent(self)
1923 
1924 
1925  def get_traits():
1926  """get_traits() -> HierarchyTraits"""
1927  return _IMP_atom.Hierarchy_get_traits()
1928 
1929  get_traits = staticmethod(get_traits)
1930 
1931  def show(self, *args):
1932  """
1933  show(Hierarchy self, _ostream out, std::string delimiter)
1934  show(Hierarchy self, _ostream out)
1935  show(Hierarchy self)
1936  """
1937  return _IMP_atom.Hierarchy_show(self, *args)
1938 
1939 
1940  def add_attribute(self, *args):
1941  """
1942  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1943  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1944  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1945  add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1946  add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1947  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1948  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1949  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1950  """
1951  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1952 
1953 
1954  def get_value(self, *args):
1955  """
1956  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1957  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1958  get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1959  get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1960  get_value(Hierarchy self, StringKey a0) -> IMP::String
1961  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1962  get_value(Hierarchy self, ObjectKey a0) -> Object
1963  """
1964  return _IMP_atom.Hierarchy_get_value(self, *args)
1965 
1966 
1967  def set_value(self, *args):
1968  """
1969  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1970  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1971  set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1972  set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1973  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1974  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1975  set_value(Hierarchy self, ObjectKey a0, Object a1)
1976  """
1977  return _IMP_atom.Hierarchy_set_value(self, *args)
1978 
1979 
1980  def remove_attribute(self, *args):
1981  """
1982  remove_attribute(Hierarchy self, FloatKey a0)
1983  remove_attribute(Hierarchy self, IntKey a0)
1984  remove_attribute(Hierarchy self, FloatsKey a0)
1985  remove_attribute(Hierarchy self, IntsKey a0)
1986  remove_attribute(Hierarchy self, StringKey a0)
1987  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1988  remove_attribute(Hierarchy self, ObjectKey a0)
1989  """
1990  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1991 
1992 
1993  def has_attribute(self, *args):
1994  """
1995  has_attribute(Hierarchy self, FloatKey a0) -> bool
1996  has_attribute(Hierarchy self, IntKey a0) -> bool
1997  has_attribute(Hierarchy self, FloatsKey a0) -> bool
1998  has_attribute(Hierarchy self, IntsKey a0) -> bool
1999  has_attribute(Hierarchy self, StringKey a0) -> bool
2000  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2001  has_attribute(Hierarchy self, ObjectKey a0) -> bool
2002  """
2003  return _IMP_atom.Hierarchy_has_attribute(self, *args)
2004 
2005 
2006  def get_derivative(self, a0):
2007  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
2008  return _IMP_atom.Hierarchy_get_derivative(self, a0)
2009 
2010 
2011  def get_name(self):
2012  """get_name(Hierarchy self) -> std::string"""
2013  return _IMP_atom.Hierarchy_get_name(self)
2014 
2015 
2016  def clear_caches(self):
2017  """clear_caches(Hierarchy self)"""
2018  return _IMP_atom.Hierarchy_clear_caches(self)
2019 
2020 
2021  def set_name(self, a0):
2022  """set_name(Hierarchy self, std::string a0)"""
2023  return _IMP_atom.Hierarchy_set_name(self, a0)
2024 
2025 
2026  def set_check_level(self, a0):
2027  """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2028  return _IMP_atom.Hierarchy_set_check_level(self, a0)
2029 
2030 
2031  def add_to_derivative(self, a0, a1, a2):
2032  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2033  return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2034 
2035 
2036  def set_is_optimized(self, a0, a1):
2037  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2038  return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2039 
2040 
2041  def get_is_optimized(self, a0):
2042  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2043  return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2044 
2045 
2046  def get_check_level(self):
2047  """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2048  return _IMP_atom.Hierarchy_get_check_level(self)
2049 
2050 
2051  def __eq__(self, *args):
2052  """
2053  __eq__(Hierarchy self, Hierarchy o) -> bool
2054  __eq__(Hierarchy self, Particle d) -> bool
2055  """
2056  return _IMP_atom.Hierarchy___eq__(self, *args)
2057 
2058 
2059  def __ne__(self, *args):
2060  """
2061  __ne__(Hierarchy self, Hierarchy o) -> bool
2062  __ne__(Hierarchy self, Particle d) -> bool
2063  """
2064  return _IMP_atom.Hierarchy___ne__(self, *args)
2065 
2066 
2067  def __le__(self, *args):
2068  """
2069  __le__(Hierarchy self, Hierarchy o) -> bool
2070  __le__(Hierarchy self, Particle d) -> bool
2071  """
2072  return _IMP_atom.Hierarchy___le__(self, *args)
2073 
2074 
2075  def __lt__(self, *args):
2076  """
2077  __lt__(Hierarchy self, Hierarchy o) -> bool
2078  __lt__(Hierarchy self, Particle d) -> bool
2079  """
2080  return _IMP_atom.Hierarchy___lt__(self, *args)
2081 
2082 
2083  def __ge__(self, *args):
2084  """
2085  __ge__(Hierarchy self, Hierarchy o) -> bool
2086  __ge__(Hierarchy self, Particle d) -> bool
2087  """
2088  return _IMP_atom.Hierarchy___ge__(self, *args)
2089 
2090 
2091  def __gt__(self, *args):
2092  """
2093  __gt__(Hierarchy self, Hierarchy o) -> bool
2094  __gt__(Hierarchy self, Particle d) -> bool
2095  """
2096  return _IMP_atom.Hierarchy___gt__(self, *args)
2097 
2098 
2099  def __hash__(self):
2100  """__hash__(Hierarchy self) -> std::size_t"""
2101  return _IMP_atom.Hierarchy___hash__(self)
2102 
2103 
2104  def __str__(self):
2105  """__str__(Hierarchy self) -> std::string"""
2106  return _IMP_atom.Hierarchy___str__(self)
2107 
2108 
2109  def __repr__(self):
2110  """__repr__(Hierarchy self) -> std::string"""
2111  return _IMP_atom.Hierarchy___repr__(self)
2112 
2113  __swig_destroy__ = _IMP_atom.delete_Hierarchy
2114  __del__ = lambda self: None
2115 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2116 Hierarchy_swigregister(Hierarchy)
2117 
2118 def Hierarchy_setup_particle(*args):
2119  """
2120  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2121  setup_particle(Particle p) -> Hierarchy
2122  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2123  Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2124  """
2125  return _IMP_atom.Hierarchy_setup_particle(*args)
2126 
2127 def Hierarchy_get_is_setup(*args):
2128  """
2129  get_is_setup(Particle p) -> bool
2130  Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2131  """
2132  return _IMP_atom.Hierarchy_get_is_setup(*args)
2133 
2134 def Hierarchy_get_traits():
2135  """Hierarchy_get_traits() -> HierarchyTraits"""
2136  return _IMP_atom.Hierarchy_get_traits()
2137 
2138 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2139 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2140 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2141 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2142 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2143 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2144 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2145 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2146 MASS_TYPE = _IMP_atom.MASS_TYPE
2147 STATE_TYPE = _IMP_atom.STATE_TYPE
2148 
2149 def get_by_type(mhd, t):
2150  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2151  return _IMP_atom.get_by_type(mhd, t)
2152 
2153 def create_fragment(ps):
2154  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2155  return _IMP_atom.create_fragment(ps)
2156 
2157 def get_internal_bonds(mhd):
2158  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2159  return _IMP_atom.get_internal_bonds(mhd)
2160 
2161 def get_root(h):
2162  """get_root(Hierarchy h) -> Hierarchy"""
2163  return _IMP_atom.get_root(h)
2164 
2165 def show(*args):
2166  """
2167  show(Hierarchy h, _ostream out)
2168  show(Hierarchy h)
2169  """
2170  return _IMP_atom.show(*args)
2171 
2172 def create_rigid_body(*args):
2173  """
2174  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2175  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2176  create_rigid_body(Hierarchy h) -> RigidBody
2177  """
2178  return _IMP_atom.create_rigid_body(*args)
2179 
2180 def create_compatible_rigid_body(h, reference):
2181  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2182  return _IMP_atom.create_compatible_rigid_body(h, reference)
2183 
2184 def get_is_heterogen(h):
2185  """get_is_heterogen(Hierarchy h) -> bool"""
2186  return _IMP_atom.get_is_heterogen(h)
2187 
2188 def create_clone(d):
2189  """create_clone(Hierarchy d) -> Hierarchy"""
2190  return _IMP_atom.create_clone(d)
2191 
2192 def create_clone_one(d):
2193  """create_clone_one(Hierarchy d) -> Hierarchy"""
2194  return _IMP_atom.create_clone_one(d)
2195 
2196 def destroy(d):
2197  """destroy(Hierarchy d)"""
2198  return _IMP_atom.destroy(d)
2199 
2200 def get_bounding_box(h):
2201  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2202  return _IMP_atom.get_bounding_box(h)
2203 
2204 def get_bounding_sphere(h):
2205  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2206  return _IMP_atom.get_bounding_sphere(h)
2207 class Angle(IMP.Decorator):
2208  """Proxy of C++ IMP::atom::Angle class."""
2209 
2210  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2211 
2212  def __init__(self, *args):
2213  """
2214  __init__(IMP::atom::Angle self) -> Angle
2215  __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2216  __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2217  """
2218  this = _IMP_atom.new_Angle(*args)
2219  try:
2220  self.this.append(this)
2221  except __builtin__.Exception:
2222  self.this = this
2223 
2224  def show(self, *args):
2225  """
2226  show(Angle self, _ostream out)
2227  show(Angle self)
2228  """
2229  return _IMP_atom.Angle_show(self, *args)
2230 
2231 
2232  def setup_particle(*args):
2233  """
2234  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2235  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2236  """
2237  return _IMP_atom.Angle_setup_particle(*args)
2238 
2239  setup_particle = staticmethod(setup_particle)
2240 
2241  def get_is_setup(*args):
2242  """
2243  get_is_setup(_ParticleAdaptor p) -> bool
2244  get_is_setup(Model m, ParticleIndex pi) -> bool
2245  """
2246  return _IMP_atom.Angle_get_is_setup(*args)
2247 
2248  get_is_setup = staticmethod(get_is_setup)
2249 
2250  def get_particle(self, *args):
2251  """
2252  get_particle(Angle self) -> Particle
2253  get_particle(Angle self, unsigned int i) -> Particle
2254  """
2255  return _IMP_atom.Angle_get_particle(self, *args)
2256 
2257 
2258  def get_ideal(self):
2259  """get_ideal(Angle self) -> IMP::Float"""
2260  return _IMP_atom.Angle_get_ideal(self)
2261 
2262 
2263  def set_ideal(self, t):
2264  """set_ideal(Angle self, IMP::Float t)"""
2265  return _IMP_atom.Angle_set_ideal(self, t)
2266 
2267 
2268  def get_stiffness(self):
2269  """get_stiffness(Angle self) -> IMP::Float"""
2270  return _IMP_atom.Angle_get_stiffness(self)
2271 
2272 
2273  def set_stiffness(self, t):
2274  """set_stiffness(Angle self, IMP::Float t)"""
2275  return _IMP_atom.Angle_set_stiffness(self, t)
2276 
2277 
2278  def get_particle_key(i):
2279  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2280  return _IMP_atom.Angle_get_particle_key(i)
2281 
2282  get_particle_key = staticmethod(get_particle_key)
2283 
2284  def get_ideal_key():
2285  """get_ideal_key() -> FloatKey"""
2286  return _IMP_atom.Angle_get_ideal_key()
2287 
2288  get_ideal_key = staticmethod(get_ideal_key)
2289 
2290  def get_stiffness_key():
2291  """get_stiffness_key() -> FloatKey"""
2292  return _IMP_atom.Angle_get_stiffness_key()
2293 
2294  get_stiffness_key = staticmethod(get_stiffness_key)
2295 
2296  def add_attribute(self, *args):
2297  """
2298  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2299  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2300  add_attribute(Angle self, IntKey a0, IMP::Int a1)
2301  add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2302  add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2303  add_attribute(Angle self, StringKey a0, IMP::String a1)
2304  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2305  add_attribute(Angle self, ObjectKey a0, Object a1)
2306  """
2307  return _IMP_atom.Angle_add_attribute(self, *args)
2308 
2309 
2310  def get_value(self, *args):
2311  """
2312  get_value(Angle self, FloatKey a0) -> IMP::Float
2313  get_value(Angle self, IntKey a0) -> IMP::Int
2314  get_value(Angle self, FloatsKey a0) -> IMP::Floats
2315  get_value(Angle self, IntsKey a0) -> IMP::Ints
2316  get_value(Angle self, StringKey a0) -> IMP::String
2317  get_value(Angle self, ParticleIndexKey a0) -> Particle
2318  get_value(Angle self, ObjectKey a0) -> Object
2319  """
2320  return _IMP_atom.Angle_get_value(self, *args)
2321 
2322 
2323  def set_value(self, *args):
2324  """
2325  set_value(Angle self, FloatKey a0, IMP::Float a1)
2326  set_value(Angle self, IntKey a0, IMP::Int a1)
2327  set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2328  set_value(Angle self, IntsKey a0, IMP::Ints a1)
2329  set_value(Angle self, StringKey a0, IMP::String a1)
2330  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2331  set_value(Angle self, ObjectKey a0, Object a1)
2332  """
2333  return _IMP_atom.Angle_set_value(self, *args)
2334 
2335 
2336  def remove_attribute(self, *args):
2337  """
2338  remove_attribute(Angle self, FloatKey a0)
2339  remove_attribute(Angle self, IntKey a0)
2340  remove_attribute(Angle self, FloatsKey a0)
2341  remove_attribute(Angle self, IntsKey a0)
2342  remove_attribute(Angle self, StringKey a0)
2343  remove_attribute(Angle self, ParticleIndexKey a0)
2344  remove_attribute(Angle self, ObjectKey a0)
2345  """
2346  return _IMP_atom.Angle_remove_attribute(self, *args)
2347 
2348 
2349  def has_attribute(self, *args):
2350  """
2351  has_attribute(Angle self, FloatKey a0) -> bool
2352  has_attribute(Angle self, IntKey a0) -> bool
2353  has_attribute(Angle self, FloatsKey a0) -> bool
2354  has_attribute(Angle self, IntsKey a0) -> bool
2355  has_attribute(Angle self, StringKey a0) -> bool
2356  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2357  has_attribute(Angle self, ObjectKey a0) -> bool
2358  """
2359  return _IMP_atom.Angle_has_attribute(self, *args)
2360 
2361 
2362  def get_derivative(self, a0):
2363  """get_derivative(Angle self, FloatKey a0) -> double"""
2364  return _IMP_atom.Angle_get_derivative(self, a0)
2365 
2366 
2367  def get_name(self):
2368  """get_name(Angle self) -> std::string"""
2369  return _IMP_atom.Angle_get_name(self)
2370 
2371 
2372  def clear_caches(self):
2373  """clear_caches(Angle self)"""
2374  return _IMP_atom.Angle_clear_caches(self)
2375 
2376 
2377  def set_name(self, a0):
2378  """set_name(Angle self, std::string a0)"""
2379  return _IMP_atom.Angle_set_name(self, a0)
2380 
2381 
2382  def set_check_level(self, a0):
2383  """set_check_level(Angle self, IMP::CheckLevel a0)"""
2384  return _IMP_atom.Angle_set_check_level(self, a0)
2385 
2386 
2387  def add_to_derivative(self, a0, a1, a2):
2388  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2389  return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2390 
2391 
2392  def set_is_optimized(self, a0, a1):
2393  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2394  return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2395 
2396 
2397  def get_is_optimized(self, a0):
2398  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2399  return _IMP_atom.Angle_get_is_optimized(self, a0)
2400 
2401 
2402  def get_check_level(self):
2403  """get_check_level(Angle self) -> IMP::CheckLevel"""
2404  return _IMP_atom.Angle_get_check_level(self)
2405 
2406 
2407  def __eq__(self, *args):
2408  """
2409  __eq__(Angle self, Angle o) -> bool
2410  __eq__(Angle self, Particle d) -> bool
2411  """
2412  return _IMP_atom.Angle___eq__(self, *args)
2413 
2414 
2415  def __ne__(self, *args):
2416  """
2417  __ne__(Angle self, Angle o) -> bool
2418  __ne__(Angle self, Particle d) -> bool
2419  """
2420  return _IMP_atom.Angle___ne__(self, *args)
2421 
2422 
2423  def __le__(self, *args):
2424  """
2425  __le__(Angle self, Angle o) -> bool
2426  __le__(Angle self, Particle d) -> bool
2427  """
2428  return _IMP_atom.Angle___le__(self, *args)
2429 
2430 
2431  def __lt__(self, *args):
2432  """
2433  __lt__(Angle self, Angle o) -> bool
2434  __lt__(Angle self, Particle d) -> bool
2435  """
2436  return _IMP_atom.Angle___lt__(self, *args)
2437 
2438 
2439  def __ge__(self, *args):
2440  """
2441  __ge__(Angle self, Angle o) -> bool
2442  __ge__(Angle self, Particle d) -> bool
2443  """
2444  return _IMP_atom.Angle___ge__(self, *args)
2445 
2446 
2447  def __gt__(self, *args):
2448  """
2449  __gt__(Angle self, Angle o) -> bool
2450  __gt__(Angle self, Particle d) -> bool
2451  """
2452  return _IMP_atom.Angle___gt__(self, *args)
2453 
2454 
2455  def __hash__(self):
2456  """__hash__(Angle self) -> std::size_t"""
2457  return _IMP_atom.Angle___hash__(self)
2458 
2459 
2460  def __str__(self):
2461  """__str__(Angle self) -> std::string"""
2462  return _IMP_atom.Angle___str__(self)
2463 
2464 
2465  def __repr__(self):
2466  """__repr__(Angle self) -> std::string"""
2467  return _IMP_atom.Angle___repr__(self)
2468 
2469  __swig_destroy__ = _IMP_atom.delete_Angle
2470  __del__ = lambda self: None
2471 Angle_swigregister = _IMP_atom.Angle_swigregister
2472 Angle_swigregister(Angle)
2473 
2474 def Angle_setup_particle(*args):
2475  """
2476  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2477  Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2478  """
2479  return _IMP_atom.Angle_setup_particle(*args)
2480 
2481 def Angle_get_is_setup(*args):
2482  """
2483  get_is_setup(_ParticleAdaptor p) -> bool
2484  Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2485  """
2486  return _IMP_atom.Angle_get_is_setup(*args)
2487 
2488 def Angle_get_particle_key(i):
2489  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2490  return _IMP_atom.Angle_get_particle_key(i)
2491 
2492 def Angle_get_ideal_key():
2493  """Angle_get_ideal_key() -> FloatKey"""
2494  return _IMP_atom.Angle_get_ideal_key()
2495 
2496 def Angle_get_stiffness_key():
2497  """Angle_get_stiffness_key() -> FloatKey"""
2498  return _IMP_atom.Angle_get_stiffness_key()
2499 
2500 class Dihedral(IMP.Decorator):
2501  """Proxy of C++ IMP::atom::Dihedral class."""
2502 
2503  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2504 
2505  def __init__(self, *args):
2506  """
2507  __init__(IMP::atom::Dihedral self) -> Dihedral
2508  __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2509  __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2510  """
2511  this = _IMP_atom.new_Dihedral(*args)
2512  try:
2513  self.this.append(this)
2514  except __builtin__.Exception:
2515  self.this = this
2516 
2517  def show(self, *args):
2518  """
2519  show(Dihedral self, _ostream out)
2520  show(Dihedral self)
2521  """
2522  return _IMP_atom.Dihedral_show(self, *args)
2523 
2524 
2525  def setup_particle(*args):
2526  """
2527  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2528  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2529  """
2530  return _IMP_atom.Dihedral_setup_particle(*args)
2531 
2532  setup_particle = staticmethod(setup_particle)
2533 
2534  def get_is_setup(*args):
2535  """
2536  get_is_setup(_ParticleAdaptor p) -> bool
2537  get_is_setup(Model m, ParticleIndex pi) -> bool
2538  """
2539  return _IMP_atom.Dihedral_get_is_setup(*args)
2540 
2541  get_is_setup = staticmethod(get_is_setup)
2542 
2543  def get_particle(self, *args):
2544  """
2545  get_particle(Dihedral self) -> Particle
2546  get_particle(Dihedral self, unsigned int i) -> Particle
2547  """
2548  return _IMP_atom.Dihedral_get_particle(self, *args)
2549 
2550 
2551  def get_ideal(self):
2552  """get_ideal(Dihedral self) -> IMP::Float"""
2553  return _IMP_atom.Dihedral_get_ideal(self)
2554 
2555 
2556  def set_ideal(self, t):
2557  """set_ideal(Dihedral self, IMP::Float t)"""
2558  return _IMP_atom.Dihedral_set_ideal(self, t)
2559 
2560 
2561  def get_multiplicity(self):
2562  """get_multiplicity(Dihedral self) -> IMP::Int"""
2563  return _IMP_atom.Dihedral_get_multiplicity(self)
2564 
2565 
2566  def set_multiplicity(self, t):
2567  """set_multiplicity(Dihedral self, IMP::Int t)"""
2568  return _IMP_atom.Dihedral_set_multiplicity(self, t)
2569 
2570 
2571  def get_stiffness(self):
2572  """get_stiffness(Dihedral self) -> IMP::Float"""
2573  return _IMP_atom.Dihedral_get_stiffness(self)
2574 
2575 
2576  def set_stiffness(self, t):
2577  """set_stiffness(Dihedral self, IMP::Float t)"""
2578  return _IMP_atom.Dihedral_set_stiffness(self, t)
2579 
2580 
2581  def get_particle_key(i):
2582  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2583  return _IMP_atom.Dihedral_get_particle_key(i)
2584 
2585  get_particle_key = staticmethod(get_particle_key)
2586 
2587  def get_ideal_key():
2588  """get_ideal_key() -> FloatKey"""
2589  return _IMP_atom.Dihedral_get_ideal_key()
2590 
2591  get_ideal_key = staticmethod(get_ideal_key)
2592 
2593  def get_multiplicity_key():
2594  """get_multiplicity_key() -> IntKey"""
2595  return _IMP_atom.Dihedral_get_multiplicity_key()
2596 
2597  get_multiplicity_key = staticmethod(get_multiplicity_key)
2598 
2599  def get_stiffness_key():
2600  """get_stiffness_key() -> FloatKey"""
2601  return _IMP_atom.Dihedral_get_stiffness_key()
2602 
2603  get_stiffness_key = staticmethod(get_stiffness_key)
2604 
2605  def add_attribute(self, *args):
2606  """
2607  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2608  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2609  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2610  add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2611  add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2612  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2613  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2614  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2615  """
2616  return _IMP_atom.Dihedral_add_attribute(self, *args)
2617 
2618 
2619  def get_value(self, *args):
2620  """
2621  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2622  get_value(Dihedral self, IntKey a0) -> IMP::Int
2623  get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2624  get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2625  get_value(Dihedral self, StringKey a0) -> IMP::String
2626  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2627  get_value(Dihedral self, ObjectKey a0) -> Object
2628  """
2629  return _IMP_atom.Dihedral_get_value(self, *args)
2630 
2631 
2632  def set_value(self, *args):
2633  """
2634  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2635  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2636  set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2637  set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2638  set_value(Dihedral self, StringKey a0, IMP::String a1)
2639  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2640  set_value(Dihedral self, ObjectKey a0, Object a1)
2641  """
2642  return _IMP_atom.Dihedral_set_value(self, *args)
2643 
2644 
2645  def remove_attribute(self, *args):
2646  """
2647  remove_attribute(Dihedral self, FloatKey a0)
2648  remove_attribute(Dihedral self, IntKey a0)
2649  remove_attribute(Dihedral self, FloatsKey a0)
2650  remove_attribute(Dihedral self, IntsKey a0)
2651  remove_attribute(Dihedral self, StringKey a0)
2652  remove_attribute(Dihedral self, ParticleIndexKey a0)
2653  remove_attribute(Dihedral self, ObjectKey a0)
2654  """
2655  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2656 
2657 
2658  def has_attribute(self, *args):
2659  """
2660  has_attribute(Dihedral self, FloatKey a0) -> bool
2661  has_attribute(Dihedral self, IntKey a0) -> bool
2662  has_attribute(Dihedral self, FloatsKey a0) -> bool
2663  has_attribute(Dihedral self, IntsKey a0) -> bool
2664  has_attribute(Dihedral self, StringKey a0) -> bool
2665  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2666  has_attribute(Dihedral self, ObjectKey a0) -> bool
2667  """
2668  return _IMP_atom.Dihedral_has_attribute(self, *args)
2669 
2670 
2671  def get_derivative(self, a0):
2672  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2673  return _IMP_atom.Dihedral_get_derivative(self, a0)
2674 
2675 
2676  def get_name(self):
2677  """get_name(Dihedral self) -> std::string"""
2678  return _IMP_atom.Dihedral_get_name(self)
2679 
2680 
2681  def clear_caches(self):
2682  """clear_caches(Dihedral self)"""
2683  return _IMP_atom.Dihedral_clear_caches(self)
2684 
2685 
2686  def set_name(self, a0):
2687  """set_name(Dihedral self, std::string a0)"""
2688  return _IMP_atom.Dihedral_set_name(self, a0)
2689 
2690 
2691  def set_check_level(self, a0):
2692  """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2693  return _IMP_atom.Dihedral_set_check_level(self, a0)
2694 
2695 
2696  def add_to_derivative(self, a0, a1, a2):
2697  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2698  return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2699 
2700 
2701  def set_is_optimized(self, a0, a1):
2702  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2703  return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2704 
2705 
2706  def get_is_optimized(self, a0):
2707  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2708  return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2709 
2710 
2711  def get_check_level(self):
2712  """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2713  return _IMP_atom.Dihedral_get_check_level(self)
2714 
2715 
2716  def __eq__(self, *args):
2717  """
2718  __eq__(Dihedral self, Dihedral o) -> bool
2719  __eq__(Dihedral self, Particle d) -> bool
2720  """
2721  return _IMP_atom.Dihedral___eq__(self, *args)
2722 
2723 
2724  def __ne__(self, *args):
2725  """
2726  __ne__(Dihedral self, Dihedral o) -> bool
2727  __ne__(Dihedral self, Particle d) -> bool
2728  """
2729  return _IMP_atom.Dihedral___ne__(self, *args)
2730 
2731 
2732  def __le__(self, *args):
2733  """
2734  __le__(Dihedral self, Dihedral o) -> bool
2735  __le__(Dihedral self, Particle d) -> bool
2736  """
2737  return _IMP_atom.Dihedral___le__(self, *args)
2738 
2739 
2740  def __lt__(self, *args):
2741  """
2742  __lt__(Dihedral self, Dihedral o) -> bool
2743  __lt__(Dihedral self, Particle d) -> bool
2744  """
2745  return _IMP_atom.Dihedral___lt__(self, *args)
2746 
2747 
2748  def __ge__(self, *args):
2749  """
2750  __ge__(Dihedral self, Dihedral o) -> bool
2751  __ge__(Dihedral self, Particle d) -> bool
2752  """
2753  return _IMP_atom.Dihedral___ge__(self, *args)
2754 
2755 
2756  def __gt__(self, *args):
2757  """
2758  __gt__(Dihedral self, Dihedral o) -> bool
2759  __gt__(Dihedral self, Particle d) -> bool
2760  """
2761  return _IMP_atom.Dihedral___gt__(self, *args)
2762 
2763 
2764  def __hash__(self):
2765  """__hash__(Dihedral self) -> std::size_t"""
2766  return _IMP_atom.Dihedral___hash__(self)
2767 
2768 
2769  def __str__(self):
2770  """__str__(Dihedral self) -> std::string"""
2771  return _IMP_atom.Dihedral___str__(self)
2772 
2773 
2774  def __repr__(self):
2775  """__repr__(Dihedral self) -> std::string"""
2776  return _IMP_atom.Dihedral___repr__(self)
2777 
2778  __swig_destroy__ = _IMP_atom.delete_Dihedral
2779  __del__ = lambda self: None
2780 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2781 Dihedral_swigregister(Dihedral)
2782 
2783 def Dihedral_setup_particle(*args):
2784  """
2785  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2786  Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2787  """
2788  return _IMP_atom.Dihedral_setup_particle(*args)
2789 
2790 def Dihedral_get_is_setup(*args):
2791  """
2792  get_is_setup(_ParticleAdaptor p) -> bool
2793  Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2794  """
2795  return _IMP_atom.Dihedral_get_is_setup(*args)
2796 
2797 def Dihedral_get_particle_key(i):
2798  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2799  return _IMP_atom.Dihedral_get_particle_key(i)
2800 
2801 def Dihedral_get_ideal_key():
2802  """Dihedral_get_ideal_key() -> FloatKey"""
2803  return _IMP_atom.Dihedral_get_ideal_key()
2804 
2805 def Dihedral_get_multiplicity_key():
2806  """Dihedral_get_multiplicity_key() -> IntKey"""
2807  return _IMP_atom.Dihedral_get_multiplicity_key()
2808 
2809 def Dihedral_get_stiffness_key():
2810  """Dihedral_get_stiffness_key() -> FloatKey"""
2811  return _IMP_atom.Dihedral_get_stiffness_key()
2812 
2813 class SmoothingFunction(IMP.Object):
2814  """Proxy of C++ IMP::atom::SmoothingFunction class."""
2815 
2816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2817 
2818  def __init__(self, *args, **kwargs):
2819  raise AttributeError("No constructor defined - class is abstract")
2820 
2821  def __call__(self, *args):
2822  """
2823  __call__(SmoothingFunction self, double score, double distance) -> double
2824  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2825  """
2826  return _IMP_atom.SmoothingFunction___call__(self, *args)
2827 
2828  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2829  __del__ = lambda self: None
2830 
2831  def __str__(self):
2832  """__str__(SmoothingFunction self) -> std::string"""
2833  return _IMP_atom.SmoothingFunction___str__(self)
2834 
2835 
2836  def __repr__(self):
2837  """__repr__(SmoothingFunction self) -> std::string"""
2838  return _IMP_atom.SmoothingFunction___repr__(self)
2839 
2840 
2841  @staticmethod
2842  def get_from(o):
2843  return _object_cast_to_SmoothingFunction(o)
2844 
2845 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2846 SmoothingFunction_swigregister(SmoothingFunction)
2847 
2848 class ForceSwitch(SmoothingFunction):
2849  """Proxy of C++ IMP::atom::ForceSwitch class."""
2850 
2851  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2852 
2853  def __init__(self, min_distance, max_distance):
2854  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2855  this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2856  try:
2857  self.this.append(this)
2858  except __builtin__.Exception:
2859  self.this = this
2860 
2861  def __call__(self, *args):
2862  """
2863  __call__(ForceSwitch self, double score, double distance) -> double
2864  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2865  """
2866  return _IMP_atom.ForceSwitch___call__(self, *args)
2867 
2868 
2869  def get_version_info(self):
2870  """get_version_info(ForceSwitch self) -> VersionInfo"""
2871  return _IMP_atom.ForceSwitch_get_version_info(self)
2872 
2873 
2874  def __str__(self):
2875  """__str__(ForceSwitch self) -> std::string"""
2876  return _IMP_atom.ForceSwitch___str__(self)
2877 
2878 
2879  def __repr__(self):
2880  """__repr__(ForceSwitch self) -> std::string"""
2881  return _IMP_atom.ForceSwitch___repr__(self)
2882 
2883 
2884  @staticmethod
2885  def get_from(o):
2886  return _object_cast_to_ForceSwitch(o)
2887 
2888 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2889 ForceSwitch_swigregister(ForceSwitch)
2890 
2891 class AngleSingletonScore(IMP.SingletonScore):
2892  """Proxy of C++ IMP::atom::AngleSingletonScore class."""
2893 
2894  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2895 
2896  def __init__(self, f):
2897  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2898  this = _IMP_atom.new_AngleSingletonScore(f)
2899  try:
2900  self.this.append(this)
2901  except __builtin__.Exception:
2902  self.this = this
2903 
2904  def do_get_inputs(self, m, pis):
2905  """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2906  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2907 
2908 
2909  def get_version_info(self):
2910  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2911  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2912 
2913 
2914  def __str__(self):
2915  """__str__(AngleSingletonScore self) -> std::string"""
2916  return _IMP_atom.AngleSingletonScore___str__(self)
2917 
2918 
2919  def __repr__(self):
2920  """__repr__(AngleSingletonScore self) -> std::string"""
2921  return _IMP_atom.AngleSingletonScore___repr__(self)
2922 
2923 
2924  @staticmethod
2925  def get_from(o):
2926  return _object_cast_to_AngleSingletonScore(o)
2927 
2928 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2929 AngleSingletonScore_swigregister(AngleSingletonScore)
2930 
2931 class BondEndpointsRefiner(IMP.Refiner):
2932  """Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2933 
2934  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2935 
2936  def __init__(self):
2937  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2938  this = _IMP_atom.new_BondEndpointsRefiner()
2939  try:
2940  self.this.append(this)
2941  except __builtin__.Exception:
2942  self.this = this
2943 
2944  def do_get_inputs(self, m, pis):
2945  """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2946  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2947 
2948 
2949  def get_version_info(self):
2950  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2951  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2952 
2953 
2954  def __str__(self):
2955  """__str__(BondEndpointsRefiner self) -> std::string"""
2956  return _IMP_atom.BondEndpointsRefiner___str__(self)
2957 
2958 
2959  def __repr__(self):
2960  """__repr__(BondEndpointsRefiner self) -> std::string"""
2961  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2962 
2963 
2964  @staticmethod
2965  def get_from(o):
2966  return _object_cast_to_BondEndpointsRefiner(o)
2967 
2968 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2969 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2970 
2971 class BondPairContainer(IMP.PairContainer):
2972  """Proxy of C++ IMP::atom::BondPairContainer class."""
2973 
2974  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2975 
2976  def __init__(self, sc):
2977  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2978  this = _IMP_atom.new_BondPairContainer(sc)
2979  try:
2980  self.this.append(this)
2981  except __builtin__.Exception:
2982  self.this = this
2983 
2984  def do_get_inputs(self):
2985  """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2986  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2987 
2988 
2989  def do_apply(self, sm):
2990  """do_apply(BondPairContainer self, PairModifier sm)"""
2991  return _IMP_atom.BondPairContainer_do_apply(self, sm)
2992 
2993 
2994  def get_version_info(self):
2995  """get_version_info(BondPairContainer self) -> VersionInfo"""
2996  return _IMP_atom.BondPairContainer_get_version_info(self)
2997 
2998 
2999  def __str__(self):
3000  """__str__(BondPairContainer self) -> std::string"""
3001  return _IMP_atom.BondPairContainer___str__(self)
3002 
3003 
3004  def __repr__(self):
3005  """__repr__(BondPairContainer self) -> std::string"""
3006  return _IMP_atom.BondPairContainer___repr__(self)
3007 
3008 
3009  @staticmethod
3010  def get_from(o):
3011  return _object_cast_to_BondPairContainer(o)
3012 
3013 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
3014 BondPairContainer_swigregister(BondPairContainer)
3015 
3016 class BondSingletonScore(IMP.SingletonScore):
3017  """Proxy of C++ IMP::atom::BondSingletonScore class."""
3018 
3019  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3020 
3021  def __init__(self, f):
3022  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
3023  this = _IMP_atom.new_BondSingletonScore(f)
3024  try:
3025  self.this.append(this)
3026  except __builtin__.Exception:
3027  self.this = this
3028 
3029  def get_unary_function(self):
3030  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
3031  return _IMP_atom.BondSingletonScore_get_unary_function(self)
3032 
3033 
3034  def do_get_inputs(self, m, pis):
3035  """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3036  return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
3037 
3038 
3039  def get_version_info(self):
3040  """get_version_info(BondSingletonScore self) -> VersionInfo"""
3041  return _IMP_atom.BondSingletonScore_get_version_info(self)
3042 
3043 
3044  def __str__(self):
3045  """__str__(BondSingletonScore self) -> std::string"""
3046  return _IMP_atom.BondSingletonScore___str__(self)
3047 
3048 
3049  def __repr__(self):
3050  """__repr__(BondSingletonScore self) -> std::string"""
3051  return _IMP_atom.BondSingletonScore___repr__(self)
3052 
3053 
3054  @staticmethod
3055  def get_from(o):
3056  return _object_cast_to_BondSingletonScore(o)
3057 
3058 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
3059 BondSingletonScore_swigregister(BondSingletonScore)
3060 
3061 class DihedralSingletonScore(IMP.SingletonScore):
3062  """Proxy of C++ IMP::atom::DihedralSingletonScore class."""
3063 
3064  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3065 
3066  def __init__(self):
3067  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
3068  this = _IMP_atom.new_DihedralSingletonScore()
3069  try:
3070  self.this.append(this)
3071  except __builtin__.Exception:
3072  self.this = this
3073 
3074  def do_get_inputs(self, m, pis):
3075  """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3076  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3077 
3078 
3079  def get_version_info(self):
3080  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3081  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3082 
3083 
3084  def __str__(self):
3085  """__str__(DihedralSingletonScore self) -> std::string"""
3086  return _IMP_atom.DihedralSingletonScore___str__(self)
3087 
3088 
3089  def __repr__(self):
3090  """__repr__(DihedralSingletonScore self) -> std::string"""
3091  return _IMP_atom.DihedralSingletonScore___repr__(self)
3092 
3093 
3094  @staticmethod
3095  def get_from(o):
3096  return _object_cast_to_DihedralSingletonScore(o)
3097 
3098 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3099 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3100 
3101 class ImproperSingletonScore(IMP.SingletonScore):
3102  """Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3103 
3104  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3105 
3106  def __init__(self, f):
3107  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3108  this = _IMP_atom.new_ImproperSingletonScore(f)
3109  try:
3110  self.this.append(this)
3111  except __builtin__.Exception:
3112  self.this = this
3113 
3114  def do_get_inputs(self, m, pis):
3115  """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3116  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3117 
3118 
3119  def get_version_info(self):
3120  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3121  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3122 
3123 
3124  def __str__(self):
3125  """__str__(ImproperSingletonScore self) -> std::string"""
3126  return _IMP_atom.ImproperSingletonScore___str__(self)
3127 
3128 
3129  def __repr__(self):
3130  """__repr__(ImproperSingletonScore self) -> std::string"""
3131  return _IMP_atom.ImproperSingletonScore___repr__(self)
3132 
3133 
3134  @staticmethod
3135  def get_from(o):
3136  return _object_cast_to_ImproperSingletonScore(o)
3137 
3138 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3139 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3140 
3141 class CenterOfMass(IMP.Decorator):
3142  """Proxy of C++ IMP::atom::CenterOfMass class."""
3143 
3144  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3145 
3146  def get_constraint(self):
3147  """get_constraint(CenterOfMass self) -> Constraint"""
3148  return _IMP_atom.CenterOfMass_get_constraint(self)
3149 
3150 
3151  def get_mass(self):
3152  """get_mass(CenterOfMass self) -> IMP::Float"""
3153  return _IMP_atom.CenterOfMass_get_mass(self)
3154 
3155 
3156  def get_coordinate(self, i):
3157  """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3158  return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3159 
3160 
3161  def get_coordinates(self):
3162  """get_coordinates(CenterOfMass self) -> Vector3D"""
3163  return _IMP_atom.CenterOfMass_get_coordinates(self)
3164 
3165 
3166  def __init__(self, *args):
3167  """
3168  __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3169  __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3170  __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3171  """
3172  this = _IMP_atom.new_CenterOfMass(*args)
3173  try:
3174  self.this.append(this)
3175  except __builtin__.Exception:
3176  self.this = this
3177 
3178  def show(self, *args):
3179  """
3180  show(CenterOfMass self, _ostream out)
3181  show(CenterOfMass self)
3182  """
3183  return _IMP_atom.CenterOfMass_show(self, *args)
3184 
3185 
3186  def setup_particle(*args):
3187  """
3188  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3189  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3190  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3191  setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3192  """
3193  return _IMP_atom.CenterOfMass_setup_particle(*args)
3194 
3195  setup_particle = staticmethod(setup_particle)
3196 
3197  def get_is_setup(*args):
3198  """
3199  get_is_setup(_ParticleAdaptor p) -> bool
3200  get_is_setup(Model m, ParticleIndex pi) -> bool
3201  """
3202  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3203 
3204  get_is_setup = staticmethod(get_is_setup)
3205 
3206  def add_attribute(self, *args):
3207  """
3208  add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3209  add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3210  add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3211  add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3212  add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3213  add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3214  add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3215  add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3216  """
3217  return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3218 
3219 
3220  def get_value(self, *args):
3221  """
3222  get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3223  get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3224  get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3225  get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3226  get_value(CenterOfMass self, StringKey a0) -> IMP::String
3227  get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3228  get_value(CenterOfMass self, ObjectKey a0) -> Object
3229  """
3230  return _IMP_atom.CenterOfMass_get_value(self, *args)
3231 
3232 
3233  def set_value(self, *args):
3234  """
3235  set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3236  set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3237  set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3238  set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3239  set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3240  set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3241  set_value(CenterOfMass self, ObjectKey a0, Object a1)
3242  """
3243  return _IMP_atom.CenterOfMass_set_value(self, *args)
3244 
3245 
3246  def remove_attribute(self, *args):
3247  """
3248  remove_attribute(CenterOfMass self, FloatKey a0)
3249  remove_attribute(CenterOfMass self, IntKey a0)
3250  remove_attribute(CenterOfMass self, FloatsKey a0)
3251  remove_attribute(CenterOfMass self, IntsKey a0)
3252  remove_attribute(CenterOfMass self, StringKey a0)
3253  remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3254  remove_attribute(CenterOfMass self, ObjectKey a0)
3255  """
3256  return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3257 
3258 
3259  def has_attribute(self, *args):
3260  """
3261  has_attribute(CenterOfMass self, FloatKey a0) -> bool
3262  has_attribute(CenterOfMass self, IntKey a0) -> bool
3263  has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3264  has_attribute(CenterOfMass self, IntsKey a0) -> bool
3265  has_attribute(CenterOfMass self, StringKey a0) -> bool
3266  has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3267  has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3268  """
3269  return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3270 
3271 
3272  def get_derivative(self, a0):
3273  """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3274  return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3275 
3276 
3277  def get_name(self):
3278  """get_name(CenterOfMass self) -> std::string"""
3279  return _IMP_atom.CenterOfMass_get_name(self)
3280 
3281 
3282  def clear_caches(self):
3283  """clear_caches(CenterOfMass self)"""
3284  return _IMP_atom.CenterOfMass_clear_caches(self)
3285 
3286 
3287  def set_name(self, a0):
3288  """set_name(CenterOfMass self, std::string a0)"""
3289  return _IMP_atom.CenterOfMass_set_name(self, a0)
3290 
3291 
3292  def set_check_level(self, a0):
3293  """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3294  return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3295 
3296 
3297  def add_to_derivative(self, a0, a1, a2):
3298  """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3299  return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3300 
3301 
3302  def set_is_optimized(self, a0, a1):
3303  """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3304  return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3305 
3306 
3307  def get_is_optimized(self, a0):
3308  """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3309  return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3310 
3311 
3312  def get_check_level(self):
3313  """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3314  return _IMP_atom.CenterOfMass_get_check_level(self)
3315 
3316 
3317  def __eq__(self, *args):
3318  """
3319  __eq__(CenterOfMass self, CenterOfMass o) -> bool
3320  __eq__(CenterOfMass self, Particle d) -> bool
3321  """
3322  return _IMP_atom.CenterOfMass___eq__(self, *args)
3323 
3324 
3325  def __ne__(self, *args):
3326  """
3327  __ne__(CenterOfMass self, CenterOfMass o) -> bool
3328  __ne__(CenterOfMass self, Particle d) -> bool
3329  """
3330  return _IMP_atom.CenterOfMass___ne__(self, *args)
3331 
3332 
3333  def __le__(self, *args):
3334  """
3335  __le__(CenterOfMass self, CenterOfMass o) -> bool
3336  __le__(CenterOfMass self, Particle d) -> bool
3337  """
3338  return _IMP_atom.CenterOfMass___le__(self, *args)
3339 
3340 
3341  def __lt__(self, *args):
3342  """
3343  __lt__(CenterOfMass self, CenterOfMass o) -> bool
3344  __lt__(CenterOfMass self, Particle d) -> bool
3345  """
3346  return _IMP_atom.CenterOfMass___lt__(self, *args)
3347 
3348 
3349  def __ge__(self, *args):
3350  """
3351  __ge__(CenterOfMass self, CenterOfMass o) -> bool
3352  __ge__(CenterOfMass self, Particle d) -> bool
3353  """
3354  return _IMP_atom.CenterOfMass___ge__(self, *args)
3355 
3356 
3357  def __gt__(self, *args):
3358  """
3359  __gt__(CenterOfMass self, CenterOfMass o) -> bool
3360  __gt__(CenterOfMass self, Particle d) -> bool
3361  """
3362  return _IMP_atom.CenterOfMass___gt__(self, *args)
3363 
3364 
3365  def __hash__(self):
3366  """__hash__(CenterOfMass self) -> std::size_t"""
3367  return _IMP_atom.CenterOfMass___hash__(self)
3368 
3369 
3370  def __str__(self):
3371  """__str__(CenterOfMass self) -> std::string"""
3372  return _IMP_atom.CenterOfMass___str__(self)
3373 
3374 
3375  def __repr__(self):
3376  """__repr__(CenterOfMass self) -> std::string"""
3377  return _IMP_atom.CenterOfMass___repr__(self)
3378 
3379  __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3380  __del__ = lambda self: None
3381 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3382 CenterOfMass_swigregister(CenterOfMass)
3383 
3384 def CenterOfMass_setup_particle(*args):
3385  """
3386  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3387  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3388  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3389  CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3390  """
3391  return _IMP_atom.CenterOfMass_setup_particle(*args)
3392 
3393 def CenterOfMass_get_is_setup(*args):
3394  """
3395  get_is_setup(_ParticleAdaptor p) -> bool
3396  CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3397  """
3398  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3399 
3400 class CoverBond(IMP.SingletonModifier):
3401  """Proxy of C++ IMP::atom::CoverBond class."""
3402 
3403  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3404 
3405  def __init__(self):
3406  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3407  this = _IMP_atom.new_CoverBond()
3408  try:
3409  self.this.append(this)
3410  except __builtin__.Exception:
3411  self.this = this
3412 
3413  def do_get_inputs(self, m, pis):
3414  """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3415  return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3416 
3417 
3418  def do_get_outputs(self, m, pis):
3419  """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3420  return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3421 
3422 
3423  def get_version_info(self):
3424  """get_version_info(CoverBond self) -> VersionInfo"""
3425  return _IMP_atom.CoverBond_get_version_info(self)
3426 
3427 
3428  def __str__(self):
3429  """__str__(CoverBond self) -> std::string"""
3430  return _IMP_atom.CoverBond___str__(self)
3431 
3432 
3433  def __repr__(self):
3434  """__repr__(CoverBond self) -> std::string"""
3435  return _IMP_atom.CoverBond___repr__(self)
3436 
3437 
3438  @staticmethod
3439  def get_from(o):
3440  return _object_cast_to_CoverBond(o)
3441 
3442 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3443 CoverBond_swigregister(CoverBond)
3444 
3445 class Simulator(IMP.Optimizer):
3446  """Proxy of C++ IMP::atom::Simulator class."""
3447 
3448  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3449 
3450  def __init__(self, *args):
3451  """
3452  __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3453  __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3454  __init__(IMP::atom::Simulator self, Model m) -> Simulator
3455  """
3456  if self.__class__ == Simulator:
3457  _self = None
3458  else:
3459  _self = self
3460  this = _IMP_atom.new_Simulator(_self, *args)
3461  try:
3462  self.this.append(this)
3463  except __builtin__.Exception:
3464  self.this = this
3465 
3466  if self.__class__ != Simulator:
3467  _director_objects.register(self)
3468 
3469 
3470 
3471 
3472  def simulate(self, time_in_fs):
3473  """simulate(Simulator self, double time_in_fs) -> double"""
3474  return _IMP_atom.Simulator_simulate(self, time_in_fs)
3475 
3476 
3477  def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3478  """
3479  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3480  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3481  simulate_wave(Simulator self, double time_in_fs) -> double
3482  """
3483  return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3484 
3485 
3486  def get_temperature(self):
3487  """get_temperature(Simulator self) -> double"""
3488  return _IMP_atom.Simulator_get_temperature(self)
3489 
3490 
3491  def set_temperature(self, d):
3492  """set_temperature(Simulator self, double d)"""
3493  return _IMP_atom.Simulator_set_temperature(self, d)
3494 
3495 
3496  def set_maximum_time_step(self, ts):
3497  """set_maximum_time_step(Simulator self, double ts)"""
3498  return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3499 
3500 
3501  def get_maximum_time_step(self):
3502  """get_maximum_time_step(Simulator self) -> double"""
3503  return _IMP_atom.Simulator_get_maximum_time_step(self)
3504 
3505 
3506  def get_last_time_step(self):
3507  """get_last_time_step(Simulator self) -> double"""
3508  return _IMP_atom.Simulator_get_last_time_step(self)
3509 
3510 
3511  def set_time_step(self, ts):
3512  """set_time_step(Simulator self, double ts)"""
3513  return _IMP_atom.Simulator_set_time_step(self, ts)
3514 
3515 
3516  def get_kt(self):
3517  """get_kt(Simulator self) -> double"""
3518  return _IMP_atom.Simulator_get_kt(self)
3519 
3520 
3521  def get_current_time(self):
3522  """get_current_time(Simulator self) -> double"""
3523  return _IMP_atom.Simulator_get_current_time(self)
3524 
3525 
3526  def set_current_time(self, ct):
3527  """set_current_time(Simulator self, double ct)"""
3528  return _IMP_atom.Simulator_set_current_time(self, ct)
3529 
3530 
3531  def get_simulation_particles(self):
3532  """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3533  return _IMP_atom.Simulator_get_simulation_particles(self)
3534 
3535 
3536  def get_simulation_particle_indexes(self):
3537  """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3538  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3539 
3540 
3541  def remove_particle(self, d):
3542  """remove_particle(Simulator self, Particle d)"""
3543  return _IMP_atom.Simulator_remove_particle(self, d)
3544 
3545 
3546  def remove_particles(self, d):
3547  """remove_particles(Simulator self, IMP::Particles const & d)"""
3548  return _IMP_atom.Simulator_remove_particles(self, d)
3549 
3550 
3551  def set_particles(self, ps):
3552  """set_particles(Simulator self, IMP::Particles const & ps)"""
3553  return _IMP_atom.Simulator_set_particles(self, ps)
3554 
3555 
3556  def set_particles_order(self, objs):
3557  """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3558  return _IMP_atom.Simulator_set_particles_order(self, objs)
3559 
3560 
3561  def add_particle(self, obj):
3562  """add_particle(Simulator self, Particle obj) -> unsigned int"""
3563  return _IMP_atom.Simulator_add_particle(self, obj)
3564 
3565 
3566  def add_particles(self, objs):
3567  """add_particles(Simulator self, IMP::Particles const & objs)"""
3568  return _IMP_atom.Simulator_add_particles(self, objs)
3569 
3570 
3571  def clear_particles(self):
3572  """clear_particles(Simulator self)"""
3573  return _IMP_atom.Simulator_clear_particles(self)
3574 
3575 
3576  def get_number_of_particles(self):
3577  """get_number_of_particles(Simulator self) -> unsigned int"""
3578  return _IMP_atom.Simulator_get_number_of_particles(self)
3579 
3580 
3581  def get_has_particles(self):
3582  """get_has_particles(Simulator self) -> bool"""
3583  return _IMP_atom.Simulator_get_has_particles(self)
3584 
3585 
3586  def get_particle(self, i):
3587  """get_particle(Simulator self, unsigned int i) -> Particle"""
3588  return _IMP_atom.Simulator_get_particle(self, i)
3589 
3590 
3591  def get_particles(self):
3592  """get_particles(Simulator self) -> IMP::Particles"""
3593  return _IMP_atom.Simulator_get_particles(self)
3594 
3595 
3596  def reserve_particles(self, sz):
3597  """reserve_particles(Simulator self, unsigned int sz)"""
3598  return _IMP_atom.Simulator_reserve_particles(self, sz)
3599 
3600 
3601  def do_optimize(self, max_steps):
3602  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3603  return _IMP_atom.Simulator_do_optimize(self, max_steps)
3604 
3605 
3606  def setup(self, arg0):
3607  """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3608  return _IMP_atom.Simulator_setup(self, arg0)
3609 
3610 
3611  def do_step(self, sc, dt):
3612  """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3613  return _IMP_atom.Simulator_do_step(self, sc, dt)
3614 
3615 
3616  def get_is_simulation_particle(self, p):
3617  """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3618  return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3619 
3620 
3621  def do_simulate(self, time):
3622  """do_simulate(Simulator self, double time) -> double"""
3623  return _IMP_atom.Simulator_do_simulate(self, time)
3624 
3625 
3626  def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3627  """
3628  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3629  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3630  do_simulate_wave(Simulator self, double time_in_fs) -> double
3631  """
3632  return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3633 
3634 
3635  def __str__(self):
3636  """__str__(Simulator self) -> std::string"""
3637  return _IMP_atom.Simulator___str__(self)
3638 
3639 
3640  def __repr__(self):
3641  """__repr__(Simulator self) -> std::string"""
3642  return _IMP_atom.Simulator___repr__(self)
3643 
3644 
3645  @staticmethod
3646  def get_from(o):
3647  return _object_cast_to_Simulator(o)
3648 
3649 
3650  def get_type_name(self):
3651  return self.__class__.__name__
3652  def do_show(self, out):
3653  pass
3654  def get_version_info(self):
3655  if"IMP::atom" == "IMP":
3656  return VersionInfo(self.__module__,
3657  __import__(self.__module__).get_module_version())
3658  else:
3659  return IMP.VersionInfo(self.__module__,
3660  __import__(self.__module__).get_module_version())
3661  @staticmethod
3662  def get_from(o):
3663  return _object_cast_to_Simulator(o)
3664 
3665  __swig_destroy__ = _IMP_atom.delete_Simulator
3666  __del__ = lambda self: None
3667  def __disown__(self):
3668  self.this.disown()
3669  _IMP_atom.disown_Simulator(self)
3670  return weakref_proxy(self)
3671 
3672  def do_destroy(self):
3673  """do_destroy(Simulator self)"""
3674  return _IMP_atom.Simulator_do_destroy(self)
3675 
3676 
3677  def handle_set_has_required_score_states(self, arg0):
3678  """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3679  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3680 
3681 
3682  def do_get_inputs(self):
3683  """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3684  return _IMP_atom.Simulator_do_get_inputs(self)
3685 
3686 
3687  def do_get_outputs(self):
3688  """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3689  return _IMP_atom.Simulator_do_get_outputs(self)
3690 
3691 
3692  def do_get_interactions(self):
3693  """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3694  return _IMP_atom.Simulator_do_get_interactions(self)
3695 
3696 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3697 Simulator_swigregister(Simulator)
3698 
3699 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3700 class BrownianDynamics(Simulator):
3701  """Proxy of C++ IMP::atom::BrownianDynamics class."""
3702 
3703  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3704 
3705  def __init__(self, *args):
3706  """
3707  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics
3708  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3709  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3710  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3711  """
3712  this = _IMP_atom.new_BrownianDynamics(*args)
3713  try:
3714  self.this.append(this)
3715  except __builtin__.Exception:
3716  self.this = this
3717 
3718  def set_maximum_move(self, ms_in_A):
3719  """set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3720  return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3721 
3722 
3723  def set_use_stochastic_runge_kutta(self, tf):
3724  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3725  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3726 
3727 
3728  def get_version_info(self):
3729  """get_version_info(BrownianDynamics self) -> VersionInfo"""
3730  return _IMP_atom.BrownianDynamics_get_version_info(self)
3731 
3732 
3733  def __str__(self):
3734  """__str__(BrownianDynamics self) -> std::string"""
3735  return _IMP_atom.BrownianDynamics___str__(self)
3736 
3737 
3738  def __repr__(self):
3739  """__repr__(BrownianDynamics self) -> std::string"""
3740  return _IMP_atom.BrownianDynamics___repr__(self)
3741 
3742 
3743  @staticmethod
3744  def get_from(o):
3745  return _object_cast_to_BrownianDynamics(o)
3746 
3747 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3748 BrownianDynamics_swigregister(BrownianDynamics)
3749 
3750 
3752  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3753  return _IMP_atom.get_maximum_time_step_estimate(bd)
3754 
3755 def get_harmonic_sigma(D, f):
3756  """get_harmonic_sigma(double D, double f) -> double"""
3757  return _IMP_atom.get_harmonic_sigma(D, f)
3758 class BrownianDynamicsTAMD(BrownianDynamics):
3759  """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3760 
3761  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3762 
3763  def __init__(self, *args):
3764  """
3765  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3766  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3767  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3768  """
3769  this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3770  try:
3771  self.this.append(this)
3772  except __builtin__.Exception:
3773  self.this = this
3774 
3775  def __str__(self):
3776  """__str__(BrownianDynamicsTAMD self) -> std::string"""
3777  return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3778 
3779 
3780  def __repr__(self):
3781  """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3782  return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3783 
3784 
3785  @staticmethod
3786  def get_from(o):
3787  return _object_cast_to_BrownianDynamicsTAMD(o)
3788 
3789  __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3790  __del__ = lambda self: None
3791 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3792 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3793 
3794 class Diffusion(IMP.core.XYZ):
3795  """Proxy of C++ IMP::atom::Diffusion class."""
3796 
3797  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3798 
3799  def __init__(self, *args):
3800  """
3801  __init__(IMP::atom::Diffusion self) -> Diffusion
3802  __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3803  __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3804  """
3805  this = _IMP_atom.new_Diffusion(*args)
3806  try:
3807  self.this.append(this)
3808  except __builtin__.Exception:
3809  self.this = this
3810 
3811  def show(self, *args):
3812  """
3813  show(Diffusion self, _ostream out)
3814  show(Diffusion self)
3815  """
3816  return _IMP_atom.Diffusion_show(self, *args)
3817 
3818 
3819  def setup_particle(*args):
3820  """
3821  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3822  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3823  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3824  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3825  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3826  setup_particle(_ParticleAdaptor decorator) -> Diffusion
3827  """
3828  return _IMP_atom.Diffusion_setup_particle(*args)
3829 
3830  setup_particle = staticmethod(setup_particle)
3831 
3832  def get_is_setup(*args):
3833  """
3834  get_is_setup(_ParticleAdaptor p) -> bool
3835  get_is_setup(Model m, ParticleIndex p) -> bool
3836  """
3837  return _IMP_atom.Diffusion_get_is_setup(*args)
3838 
3839  get_is_setup = staticmethod(get_is_setup)
3840 
3841  def set_diffusion_coefficient(self, d):
3842  """set_diffusion_coefficient(Diffusion self, double d)"""
3843  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3844 
3845 
3846  def get_diffusion_coefficient(self):
3847  """get_diffusion_coefficient(Diffusion self) -> double"""
3848  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3849 
3850 
3851  def get_diffusion_coefficient_key():
3852  """get_diffusion_coefficient_key() -> FloatKey"""
3853  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3854 
3855  get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3856 
3857  def add_attribute(self, *args):
3858  """
3859  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3860  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3861  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3862  add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3863  add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3864  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3865  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3866  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3867  """
3868  return _IMP_atom.Diffusion_add_attribute(self, *args)
3869 
3870 
3871  def get_value(self, *args):
3872  """
3873  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3874  get_value(Diffusion self, IntKey a0) -> IMP::Int
3875  get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3876  get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3877  get_value(Diffusion self, StringKey a0) -> IMP::String
3878  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3879  get_value(Diffusion self, ObjectKey a0) -> Object
3880  """
3881  return _IMP_atom.Diffusion_get_value(self, *args)
3882 
3883 
3884  def set_value(self, *args):
3885  """
3886  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3887  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3888  set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3889  set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3890  set_value(Diffusion self, StringKey a0, IMP::String a1)
3891  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3892  set_value(Diffusion self, ObjectKey a0, Object a1)
3893  """
3894  return _IMP_atom.Diffusion_set_value(self, *args)
3895 
3896 
3897  def remove_attribute(self, *args):
3898  """
3899  remove_attribute(Diffusion self, FloatKey a0)
3900  remove_attribute(Diffusion self, IntKey a0)
3901  remove_attribute(Diffusion self, FloatsKey a0)
3902  remove_attribute(Diffusion self, IntsKey a0)
3903  remove_attribute(Diffusion self, StringKey a0)
3904  remove_attribute(Diffusion self, ParticleIndexKey a0)
3905  remove_attribute(Diffusion self, ObjectKey a0)
3906  """
3907  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3908 
3909 
3910  def has_attribute(self, *args):
3911  """
3912  has_attribute(Diffusion self, FloatKey a0) -> bool
3913  has_attribute(Diffusion self, IntKey a0) -> bool
3914  has_attribute(Diffusion self, FloatsKey a0) -> bool
3915  has_attribute(Diffusion self, IntsKey a0) -> bool
3916  has_attribute(Diffusion self, StringKey a0) -> bool
3917  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3918  has_attribute(Diffusion self, ObjectKey a0) -> bool
3919  """
3920  return _IMP_atom.Diffusion_has_attribute(self, *args)
3921 
3922 
3923  def get_derivative(self, a0):
3924  """get_derivative(Diffusion self, FloatKey a0) -> double"""
3925  return _IMP_atom.Diffusion_get_derivative(self, a0)
3926 
3927 
3928  def get_name(self):
3929  """get_name(Diffusion self) -> std::string"""
3930  return _IMP_atom.Diffusion_get_name(self)
3931 
3932 
3933  def clear_caches(self):
3934  """clear_caches(Diffusion self)"""
3935  return _IMP_atom.Diffusion_clear_caches(self)
3936 
3937 
3938  def set_name(self, a0):
3939  """set_name(Diffusion self, std::string a0)"""
3940  return _IMP_atom.Diffusion_set_name(self, a0)
3941 
3942 
3943  def set_check_level(self, a0):
3944  """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3945  return _IMP_atom.Diffusion_set_check_level(self, a0)
3946 
3947 
3948  def add_to_derivative(self, a0, a1, a2):
3949  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3950  return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3951 
3952 
3953  def set_is_optimized(self, a0, a1):
3954  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3955  return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3956 
3957 
3958  def get_is_optimized(self, a0):
3959  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3960  return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3961 
3962 
3963  def get_check_level(self):
3964  """get_check_level(Diffusion self) -> IMP::CheckLevel"""
3965  return _IMP_atom.Diffusion_get_check_level(self)
3966 
3967 
3968  def __eq__(self, *args):
3969  """
3970  __eq__(Diffusion self, Diffusion o) -> bool
3971  __eq__(Diffusion self, Particle d) -> bool
3972  """
3973  return _IMP_atom.Diffusion___eq__(self, *args)
3974 
3975 
3976  def __ne__(self, *args):
3977  """
3978  __ne__(Diffusion self, Diffusion o) -> bool
3979  __ne__(Diffusion self, Particle d) -> bool
3980  """
3981  return _IMP_atom.Diffusion___ne__(self, *args)
3982 
3983 
3984  def __le__(self, *args):
3985  """
3986  __le__(Diffusion self, Diffusion o) -> bool
3987  __le__(Diffusion self, Particle d) -> bool
3988  """
3989  return _IMP_atom.Diffusion___le__(self, *args)
3990 
3991 
3992  def __lt__(self, *args):
3993  """
3994  __lt__(Diffusion self, Diffusion o) -> bool
3995  __lt__(Diffusion self, Particle d) -> bool
3996  """
3997  return _IMP_atom.Diffusion___lt__(self, *args)
3998 
3999 
4000  def __ge__(self, *args):
4001  """
4002  __ge__(Diffusion self, Diffusion o) -> bool
4003  __ge__(Diffusion self, Particle d) -> bool
4004  """
4005  return _IMP_atom.Diffusion___ge__(self, *args)
4006 
4007 
4008  def __gt__(self, *args):
4009  """
4010  __gt__(Diffusion self, Diffusion o) -> bool
4011  __gt__(Diffusion self, Particle d) -> bool
4012  """
4013  return _IMP_atom.Diffusion___gt__(self, *args)
4014 
4015 
4016  def __hash__(self):
4017  """__hash__(Diffusion self) -> std::size_t"""
4018  return _IMP_atom.Diffusion___hash__(self)
4019 
4020 
4021  def __str__(self):
4022  """__str__(Diffusion self) -> std::string"""
4023  return _IMP_atom.Diffusion___str__(self)
4024 
4025 
4026  def __repr__(self):
4027  """__repr__(Diffusion self) -> std::string"""
4028  return _IMP_atom.Diffusion___repr__(self)
4029 
4030  __swig_destroy__ = _IMP_atom.delete_Diffusion
4031  __del__ = lambda self: None
4032 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
4033 Diffusion_swigregister(Diffusion)
4034 
4035 def Diffusion_setup_particle(*args):
4036  """
4037  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
4038  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
4039  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
4040  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
4041  setup_particle(Model m, ParticleIndex pi) -> Diffusion
4042  Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
4043  """
4044  return _IMP_atom.Diffusion_setup_particle(*args)
4045 
4046 def Diffusion_get_is_setup(*args):
4047  """
4048  get_is_setup(_ParticleAdaptor p) -> bool
4049  Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4050  """
4051  return _IMP_atom.Diffusion_get_is_setup(*args)
4052 
4053 def Diffusion_get_diffusion_coefficient_key():
4054  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
4055  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
4056 
4057 
4058 def get_diffusion_coefficient_from_cm2_per_second(din):
4059  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
4060  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
4061 class RigidBodyDiffusion(Diffusion):
4062  """Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
4063 
4064  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4065 
4066  def __init__(self, *args):
4067  """
4068  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
4069  __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
4070  __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
4071  """
4072  this = _IMP_atom.new_RigidBodyDiffusion(*args)
4073  try:
4074  self.this.append(this)
4075  except __builtin__.Exception:
4076  self.this = this
4077 
4078  def show(self, *args):
4079  """
4080  show(RigidBodyDiffusion self, _ostream out)
4081  show(RigidBodyDiffusion self)
4082  """
4083  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
4084 
4085 
4086  def setup_particle(*args):
4087  """
4088  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4089  setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4090  """
4091  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4092 
4093  setup_particle = staticmethod(setup_particle)
4094 
4096  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4097  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4098 
4099 
4100  def set_rotational_diffusion_coefficient(self, d):
4101  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4102  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4103 
4104 
4105  def get_is_setup(*args):
4106  """
4107  get_is_setup(_ParticleAdaptor p) -> bool
4108  get_is_setup(Model m, ParticleIndex p) -> bool
4109  """
4110  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4111 
4112  get_is_setup = staticmethod(get_is_setup)
4113 
4114  def get_rotational_diffusion_coefficient_key():
4115  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4116  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4117 
4118  get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4119 
4120  def add_attribute(self, *args):
4121  """
4122  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4123  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4124  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4125  add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4126  add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4127  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4128  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4129  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4130  """
4131  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4132 
4133 
4134  def get_value(self, *args):
4135  """
4136  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4137  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4138  get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
4139  get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
4140  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4141  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4142  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4143  """
4144  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4145 
4146 
4147  def set_value(self, *args):
4148  """
4149  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4150  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4151  set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4152  set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4153  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4154  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4155  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4156  """
4157  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4158 
4159 
4160  def remove_attribute(self, *args):
4161  """
4162  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4163  remove_attribute(RigidBodyDiffusion self, IntKey a0)
4164  remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
4165  remove_attribute(RigidBodyDiffusion self, IntsKey a0)
4166  remove_attribute(RigidBodyDiffusion self, StringKey a0)
4167  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4168  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4169  """
4170  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4171 
4172 
4173  def has_attribute(self, *args):
4174  """
4175  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4176  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4177  has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
4178  has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
4179  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4180  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4181  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4182  """
4183  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4184 
4185 
4186  def get_derivative(self, a0):
4187  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4188  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4189 
4190 
4191  def get_name(self):
4192  """get_name(RigidBodyDiffusion self) -> std::string"""
4193  return _IMP_atom.RigidBodyDiffusion_get_name(self)
4194 
4195 
4196  def clear_caches(self):
4197  """clear_caches(RigidBodyDiffusion self)"""
4198  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4199 
4200 
4201  def set_name(self, a0):
4202  """set_name(RigidBodyDiffusion self, std::string a0)"""
4203  return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4204 
4205 
4206  def set_check_level(self, a0):
4207  """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4208  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4209 
4210 
4211  def add_to_derivative(self, a0, a1, a2):
4212  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4213  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4214 
4215 
4216  def set_is_optimized(self, a0, a1):
4217  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4218  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4219 
4220 
4221  def get_is_optimized(self, a0):
4222  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4223  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4224 
4225 
4226  def get_check_level(self):
4227  """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4228  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4229 
4230 
4231  def __eq__(self, *args):
4232  """
4233  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4234  __eq__(RigidBodyDiffusion self, Particle d) -> bool
4235  """
4236  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4237 
4238 
4239  def __ne__(self, *args):
4240  """
4241  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4242  __ne__(RigidBodyDiffusion self, Particle d) -> bool
4243  """
4244  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4245 
4246 
4247  def __le__(self, *args):
4248  """
4249  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4250  __le__(RigidBodyDiffusion self, Particle d) -> bool
4251  """
4252  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4253 
4254 
4255  def __lt__(self, *args):
4256  """
4257  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4258  __lt__(RigidBodyDiffusion self, Particle d) -> bool
4259  """
4260  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4261 
4262 
4263  def __ge__(self, *args):
4264  """
4265  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4266  __ge__(RigidBodyDiffusion self, Particle d) -> bool
4267  """
4268  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4269 
4270 
4271  def __gt__(self, *args):
4272  """
4273  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4274  __gt__(RigidBodyDiffusion self, Particle d) -> bool
4275  """
4276  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4277 
4278 
4279  def __hash__(self):
4280  """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4281  return _IMP_atom.RigidBodyDiffusion___hash__(self)
4282 
4283 
4284  def __str__(self):
4285  """__str__(RigidBodyDiffusion self) -> std::string"""
4286  return _IMP_atom.RigidBodyDiffusion___str__(self)
4287 
4288 
4289  def __repr__(self):
4290  """__repr__(RigidBodyDiffusion self) -> std::string"""
4291  return _IMP_atom.RigidBodyDiffusion___repr__(self)
4292 
4293  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4294  __del__ = lambda self: None
4295 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4296 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4297 
4298 def RigidBodyDiffusion_setup_particle(*args):
4299  """
4300  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4301  RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4302  """
4303  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4304 
4305 def RigidBodyDiffusion_get_is_setup(*args):
4306  """
4307  get_is_setup(_ParticleAdaptor p) -> bool
4308  RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4309  """
4310  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4311 
4312 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4313  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4314  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4315 
4316 class TAMDParticle(IMP.Decorator):
4317  """Proxy of C++ IMP::atom::TAMDParticle class."""
4318 
4319  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4320 
4321  def __init__(self, *args):
4322  """
4323  __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4324  __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4325  __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4326  """
4327  this = _IMP_atom.new_TAMDParticle(*args)
4328  try:
4329  self.this.append(this)
4330  except __builtin__.Exception:
4331  self.this = this
4332 
4333  def show(self, *args):
4334  """
4335  show(TAMDParticle self, _ostream out)
4336  show(TAMDParticle self)
4337  """
4338  return _IMP_atom.TAMDParticle_show(self, *args)
4339 
4340 
4341  def setup_particle(*args):
4342  """
4343  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4344  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4345  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4346  setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4347  """
4348  return _IMP_atom.TAMDParticle_setup_particle(*args)
4349 
4350  setup_particle = staticmethod(setup_particle)
4351 
4352  def get_is_setup(*args):
4353  """
4354  get_is_setup(_ParticleAdaptor p) -> bool
4355  get_is_setup(Model m, ParticleIndex p) -> bool
4356  """
4357  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4358 
4359  get_is_setup = staticmethod(get_is_setup)
4360 
4361  def get_reference_particle_index(self):
4362  """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4363  return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4364 
4365 
4366  def set_temperature_scale_factor(self, tsf):
4367  """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4368  return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4369 
4370 
4371  def get_temperature_scale_factor(self):
4372  """get_temperature_scale_factor(TAMDParticle self) -> double"""
4373  return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4374 
4375 
4376  def set_friction_scale_factor(self, tsf):
4377  """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4378  return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4379 
4380 
4381  def get_friction_scale_factor(self):
4382  """get_friction_scale_factor(TAMDParticle self) -> double"""
4383  return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4384 
4385 
4386  def update_coordinates_from_ref(self):
4387  """update_coordinates_from_ref(TAMDParticle self)"""
4388  return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4389 
4390 
4391  def get_temperature_scale_factor_key():
4392  """get_temperature_scale_factor_key() -> FloatKey"""
4393  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4394 
4395  get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4396 
4397  def get_friction_scale_factor_key():
4398  """get_friction_scale_factor_key() -> FloatKey"""
4399  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4400 
4401  get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4402 
4403  def get_reference_particle_index_key():
4404  """get_reference_particle_index_key() -> ParticleIndexKey"""
4405  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4406 
4407  get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4408 
4409  def add_attribute(self, *args):
4410  """
4411  add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4412  add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4413  add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4414  add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4415  add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4416  add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4417  add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4418  add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4419  """
4420  return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4421 
4422 
4423  def get_value(self, *args):
4424  """
4425  get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4426  get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4427  get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4428  get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4429  get_value(TAMDParticle self, StringKey a0) -> IMP::String
4430  get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4431  get_value(TAMDParticle self, ObjectKey a0) -> Object
4432  """
4433  return _IMP_atom.TAMDParticle_get_value(self, *args)
4434 
4435 
4436  def set_value(self, *args):
4437  """
4438  set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4439  set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4440  set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4441  set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4442  set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4443  set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4444  set_value(TAMDParticle self, ObjectKey a0, Object a1)
4445  """
4446  return _IMP_atom.TAMDParticle_set_value(self, *args)
4447 
4448 
4449  def remove_attribute(self, *args):
4450  """
4451  remove_attribute(TAMDParticle self, FloatKey a0)
4452  remove_attribute(TAMDParticle self, IntKey a0)
4453  remove_attribute(TAMDParticle self, FloatsKey a0)
4454  remove_attribute(TAMDParticle self, IntsKey a0)
4455  remove_attribute(TAMDParticle self, StringKey a0)
4456  remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4457  remove_attribute(TAMDParticle self, ObjectKey a0)
4458  """
4459  return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4460 
4461 
4462  def has_attribute(self, *args):
4463  """
4464  has_attribute(TAMDParticle self, FloatKey a0) -> bool
4465  has_attribute(TAMDParticle self, IntKey a0) -> bool
4466  has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4467  has_attribute(TAMDParticle self, IntsKey a0) -> bool
4468  has_attribute(TAMDParticle self, StringKey a0) -> bool
4469  has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4470  has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4471  """
4472  return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4473 
4474 
4475  def get_derivative(self, a0):
4476  """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4477  return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4478 
4479 
4480  def get_name(self):
4481  """get_name(TAMDParticle self) -> std::string"""
4482  return _IMP_atom.TAMDParticle_get_name(self)
4483 
4484 
4485  def clear_caches(self):
4486  """clear_caches(TAMDParticle self)"""
4487  return _IMP_atom.TAMDParticle_clear_caches(self)
4488 
4489 
4490  def set_name(self, a0):
4491  """set_name(TAMDParticle self, std::string a0)"""
4492  return _IMP_atom.TAMDParticle_set_name(self, a0)
4493 
4494 
4495  def set_check_level(self, a0):
4496  """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4497  return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4498 
4499 
4500  def add_to_derivative(self, a0, a1, a2):
4501  """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4502  return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4503 
4504 
4505  def set_is_optimized(self, a0, a1):
4506  """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4507  return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4508 
4509 
4510  def get_is_optimized(self, a0):
4511  """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4512  return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4513 
4514 
4515  def get_check_level(self):
4516  """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4517  return _IMP_atom.TAMDParticle_get_check_level(self)
4518 
4519 
4520  def __eq__(self, *args):
4521  """
4522  __eq__(TAMDParticle self, TAMDParticle o) -> bool
4523  __eq__(TAMDParticle self, Particle d) -> bool
4524  """
4525  return _IMP_atom.TAMDParticle___eq__(self, *args)
4526 
4527 
4528  def __ne__(self, *args):
4529  """
4530  __ne__(TAMDParticle self, TAMDParticle o) -> bool
4531  __ne__(TAMDParticle self, Particle d) -> bool
4532  """
4533  return _IMP_atom.TAMDParticle___ne__(self, *args)
4534 
4535 
4536  def __le__(self, *args):
4537  """
4538  __le__(TAMDParticle self, TAMDParticle o) -> bool
4539  __le__(TAMDParticle self, Particle d) -> bool
4540  """
4541  return _IMP_atom.TAMDParticle___le__(self, *args)
4542 
4543 
4544  def __lt__(self, *args):
4545  """
4546  __lt__(TAMDParticle self, TAMDParticle o) -> bool
4547  __lt__(TAMDParticle self, Particle d) -> bool
4548  """
4549  return _IMP_atom.TAMDParticle___lt__(self, *args)
4550 
4551 
4552  def __ge__(self, *args):
4553  """
4554  __ge__(TAMDParticle self, TAMDParticle o) -> bool
4555  __ge__(TAMDParticle self, Particle d) -> bool
4556  """
4557  return _IMP_atom.TAMDParticle___ge__(self, *args)
4558 
4559 
4560  def __gt__(self, *args):
4561  """
4562  __gt__(TAMDParticle self, TAMDParticle o) -> bool
4563  __gt__(TAMDParticle self, Particle d) -> bool
4564  """
4565  return _IMP_atom.TAMDParticle___gt__(self, *args)
4566 
4567 
4568  def __hash__(self):
4569  """__hash__(TAMDParticle self) -> std::size_t"""
4570  return _IMP_atom.TAMDParticle___hash__(self)
4571 
4572 
4573  def __str__(self):
4574  """__str__(TAMDParticle self) -> std::string"""
4575  return _IMP_atom.TAMDParticle___str__(self)
4576 
4577 
4578  def __repr__(self):
4579  """__repr__(TAMDParticle self) -> std::string"""
4580  return _IMP_atom.TAMDParticle___repr__(self)
4581 
4582  __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4583  __del__ = lambda self: None
4584 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4585 TAMDParticle_swigregister(TAMDParticle)
4586 
4587 def TAMDParticle_setup_particle(*args):
4588  """
4589  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4590  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4591  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4592  TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4593  """
4594  return _IMP_atom.TAMDParticle_setup_particle(*args)
4595 
4596 def TAMDParticle_get_is_setup(*args):
4597  """
4598  get_is_setup(_ParticleAdaptor p) -> bool
4599  TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4600  """
4601  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4602 
4603 def TAMDParticle_get_temperature_scale_factor_key():
4604  """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4605  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4606 
4607 def TAMDParticle_get_friction_scale_factor_key():
4608  """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4609  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4610 
4611 def TAMDParticle_get_reference_particle_index_key():
4612  """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4613  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4614 
4615 class Chain(Hierarchy):
4616  """Proxy of C++ IMP::atom::Chain class."""
4617 
4618  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4619 
4620  def __init__(self, *args):
4621  """
4622  __init__(IMP::atom::Chain self) -> Chain
4623  __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4624  __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4625  """
4626  this = _IMP_atom.new_Chain(*args)
4627  try:
4628  self.this.append(this)
4629  except __builtin__.Exception:
4630  self.this = this
4631 
4632  def show(self, *args):
4633  """
4634  show(Chain self, _ostream out)
4635  show(Chain self)
4636  """
4637  return _IMP_atom.Chain_show(self, *args)
4638 
4639 
4640  def setup_particle(*args):
4641  """
4642  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4643  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4644  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4645  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4646  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4647  setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4648  """
4649  return _IMP_atom.Chain_setup_particle(*args)
4650 
4651  setup_particle = staticmethod(setup_particle)
4652 
4653  def get_is_setup(*args):
4654  """
4655  get_is_setup(_ParticleAdaptor p) -> bool
4656  get_is_setup(Model m, ParticleIndex pi) -> bool
4657  """
4658  return _IMP_atom.Chain_get_is_setup(*args)
4659 
4660  get_is_setup = staticmethod(get_is_setup)
4661 
4662  def get_id(self):
4663  """get_id(Chain self) -> std::string"""
4664  return _IMP_atom.Chain_get_id(self)
4665 
4666 
4667  def set_id(self, c):
4668  """set_id(Chain self, std::string c)"""
4669  return _IMP_atom.Chain_set_id(self, c)
4670 
4671 
4672  def get_sequence(self):
4673  """get_sequence(Chain self) -> std::string"""
4674  return _IMP_atom.Chain_get_sequence(self)
4675 
4676 
4677  def set_sequence(self, sequence):
4678  """set_sequence(Chain self, std::string sequence)"""
4679  return _IMP_atom.Chain_set_sequence(self, sequence)
4680 
4681 
4682  def get_chain_type(self):
4683  """get_chain_type(Chain self) -> ChainType"""
4684  return _IMP_atom.Chain_get_chain_type(self)
4685 
4686 
4687  def set_chain_type(self, t):
4688  """set_chain_type(Chain self, ChainType t)"""
4689  return _IMP_atom.Chain_set_chain_type(self, t)
4690 
4691 
4692  def get_id_key():
4693  """get_id_key() -> StringKey"""
4694  return _IMP_atom.Chain_get_id_key()
4695 
4696  get_id_key = staticmethod(get_id_key)
4697 
4698  def get_sequence_key():
4699  """get_sequence_key() -> StringKey"""
4700  return _IMP_atom.Chain_get_sequence_key()
4701 
4702  get_sequence_key = staticmethod(get_sequence_key)
4703 
4704  def get_chain_type_key():
4705  """get_chain_type_key() -> IntKey"""
4706  return _IMP_atom.Chain_get_chain_type_key()
4707 
4708  get_chain_type_key = staticmethod(get_chain_type_key)
4709 
4710  def add_attribute(self, *args):
4711  """
4712  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4713  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4714  add_attribute(Chain self, IntKey a0, IMP::Int a1)
4715  add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
4716  add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
4717  add_attribute(Chain self, StringKey a0, IMP::String a1)
4718  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4719  add_attribute(Chain self, ObjectKey a0, Object a1)
4720  """
4721  return _IMP_atom.Chain_add_attribute(self, *args)
4722 
4723 
4724  def get_value(self, *args):
4725  """
4726  get_value(Chain self, FloatKey a0) -> IMP::Float
4727  get_value(Chain self, IntKey a0) -> IMP::Int
4728  get_value(Chain self, FloatsKey a0) -> IMP::Floats
4729  get_value(Chain self, IntsKey a0) -> IMP::Ints
4730  get_value(Chain self, StringKey a0) -> IMP::String
4731  get_value(Chain self, ParticleIndexKey a0) -> Particle
4732  get_value(Chain self, ObjectKey a0) -> Object
4733  """
4734  return _IMP_atom.Chain_get_value(self, *args)
4735 
4736 
4737  def set_value(self, *args):
4738  """
4739  set_value(Chain self, FloatKey a0, IMP::Float a1)
4740  set_value(Chain self, IntKey a0, IMP::Int a1)
4741  set_value(Chain self, FloatsKey a0, IMP::Floats a1)
4742  set_value(Chain self, IntsKey a0, IMP::Ints a1)
4743  set_value(Chain self, StringKey a0, IMP::String a1)
4744  set_value(Chain self, ParticleIndexKey a0, Particle a1)
4745  set_value(Chain self, ObjectKey a0, Object a1)
4746  """
4747  return _IMP_atom.Chain_set_value(self, *args)
4748 
4749 
4750  def remove_attribute(self, *args):
4751  """
4752  remove_attribute(Chain self, FloatKey a0)
4753  remove_attribute(Chain self, IntKey a0)
4754  remove_attribute(Chain self, FloatsKey a0)
4755  remove_attribute(Chain self, IntsKey a0)
4756  remove_attribute(Chain self, StringKey a0)
4757  remove_attribute(Chain self, ParticleIndexKey a0)
4758  remove_attribute(Chain self, ObjectKey a0)
4759  """
4760  return _IMP_atom.Chain_remove_attribute(self, *args)
4761 
4762 
4763  def has_attribute(self, *args):
4764  """
4765  has_attribute(Chain self, FloatKey a0) -> bool
4766  has_attribute(Chain self, IntKey a0) -> bool
4767  has_attribute(Chain self, FloatsKey a0) -> bool
4768  has_attribute(Chain self, IntsKey a0) -> bool
4769  has_attribute(Chain self, StringKey a0) -> bool
4770  has_attribute(Chain self, ParticleIndexKey a0) -> bool
4771  has_attribute(Chain self, ObjectKey a0) -> bool
4772  """
4773  return _IMP_atom.Chain_has_attribute(self, *args)
4774 
4775 
4776  def get_derivative(self, a0):
4777  """get_derivative(Chain self, FloatKey a0) -> double"""
4778  return _IMP_atom.Chain_get_derivative(self, a0)
4779 
4780 
4781  def get_name(self):
4782  """get_name(Chain self) -> std::string"""
4783  return _IMP_atom.Chain_get_name(self)
4784 
4785 
4786  def clear_caches(self):
4787  """clear_caches(Chain self)"""
4788  return _IMP_atom.Chain_clear_caches(self)
4789 
4790 
4791  def set_name(self, a0):
4792  """set_name(Chain self, std::string a0)"""
4793  return _IMP_atom.Chain_set_name(self, a0)
4794 
4795 
4796  def set_check_level(self, a0):
4797  """set_check_level(Chain self, IMP::CheckLevel a0)"""
4798  return _IMP_atom.Chain_set_check_level(self, a0)
4799 
4800 
4801  def add_to_derivative(self, a0, a1, a2):
4802  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4803  return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4804 
4805 
4806  def set_is_optimized(self, a0, a1):
4807  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4808  return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4809 
4810 
4811  def get_is_optimized(self, a0):
4812  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4813  return _IMP_atom.Chain_get_is_optimized(self, a0)
4814 
4815 
4816  def get_check_level(self):
4817  """get_check_level(Chain self) -> IMP::CheckLevel"""
4818  return _IMP_atom.Chain_get_check_level(self)
4819 
4820 
4821  def __eq__(self, *args):
4822  """
4823  __eq__(Chain self, Chain o) -> bool
4824  __eq__(Chain self, Particle d) -> bool
4825  """
4826  return _IMP_atom.Chain___eq__(self, *args)
4827 
4828 
4829  def __ne__(self, *args):
4830  """
4831  __ne__(Chain self, Chain o) -> bool
4832  __ne__(Chain self, Particle d) -> bool
4833  """
4834  return _IMP_atom.Chain___ne__(self, *args)
4835 
4836 
4837  def __le__(self, *args):
4838  """
4839  __le__(Chain self, Chain o) -> bool
4840  __le__(Chain self, Particle d) -> bool
4841  """
4842  return _IMP_atom.Chain___le__(self, *args)
4843 
4844 
4845  def __lt__(self, *args):
4846  """
4847  __lt__(Chain self, Chain o) -> bool
4848  __lt__(Chain self, Particle d) -> bool
4849  """
4850  return _IMP_atom.Chain___lt__(self, *args)
4851 
4852 
4853  def __ge__(self, *args):
4854  """
4855  __ge__(Chain self, Chain o) -> bool
4856  __ge__(Chain self, Particle d) -> bool
4857  """
4858  return _IMP_atom.Chain___ge__(self, *args)
4859 
4860 
4861  def __gt__(self, *args):
4862  """
4863  __gt__(Chain self, Chain o) -> bool
4864  __gt__(Chain self, Particle d) -> bool
4865  """
4866  return _IMP_atom.Chain___gt__(self, *args)
4867 
4868 
4869  def __hash__(self):
4870  """__hash__(Chain self) -> std::size_t"""
4871  return _IMP_atom.Chain___hash__(self)
4872 
4873 
4874  def __str__(self):
4875  """__str__(Chain self) -> std::string"""
4876  return _IMP_atom.Chain___str__(self)
4877 
4878 
4879  def __repr__(self):
4880  """__repr__(Chain self) -> std::string"""
4881  return _IMP_atom.Chain___repr__(self)
4882 
4883  __swig_destroy__ = _IMP_atom.delete_Chain
4884  __del__ = lambda self: None
4885 Chain_swigregister = _IMP_atom.Chain_swigregister
4886 Chain_swigregister(Chain)
4887 cvar = _IMP_atom.cvar
4888 UnknownChainType = cvar.UnknownChainType
4889 DPolypeptide = cvar.DPolypeptide
4890 LPolypeptide = cvar.LPolypeptide
4891 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
4892 Polyribonucleotide = cvar.Polyribonucleotide
4893 DPolysaccharide = cvar.DPolysaccharide
4894 LPolysaccharide = cvar.LPolysaccharide
4895 Protein = cvar.Protein
4896 DNA = cvar.DNA
4897 RNA = cvar.RNA
4898 
4899 def Chain_setup_particle(*args):
4900  """
4901  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4902  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4903  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4904  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4905  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4906  Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4907  """
4908  return _IMP_atom.Chain_setup_particle(*args)
4909 
4910 def Chain_get_is_setup(*args):
4911  """
4912  get_is_setup(_ParticleAdaptor p) -> bool
4913  Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4914  """
4915  return _IMP_atom.Chain_get_is_setup(*args)
4916 
4917 def Chain_get_id_key():
4918  """Chain_get_id_key() -> StringKey"""
4919  return _IMP_atom.Chain_get_id_key()
4920 
4921 def Chain_get_sequence_key():
4922  """Chain_get_sequence_key() -> StringKey"""
4923  return _IMP_atom.Chain_get_sequence_key()
4924 
4925 def Chain_get_chain_type_key():
4926  """Chain_get_chain_type_key() -> IntKey"""
4927  return _IMP_atom.Chain_get_chain_type_key()
4928 
4929 
4930 def get_chain(h):
4931  """get_chain(Hierarchy h) -> Chain"""
4932  return _IMP_atom.get_chain(h)
4933 
4934 def get_chain_id(h):
4935  """get_chain_id(Hierarchy h) -> std::string"""
4936  return _IMP_atom.get_chain_id(h)
4937 class Charged(IMP.core.XYZ):
4938  """Proxy of C++ IMP::atom::Charged class."""
4939 
4940  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4941 
4942  def __init__(self, *args):
4943  """
4944  __init__(IMP::atom::Charged self) -> Charged
4945  __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4946  __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4947  """
4948  this = _IMP_atom.new_Charged(*args)
4949  try:
4950  self.this.append(this)
4951  except __builtin__.Exception:
4952  self.this = this
4953 
4954  def show(self, *args):
4955  """
4956  show(Charged self, _ostream out)
4957  show(Charged self)
4958  """
4959  return _IMP_atom.Charged_show(self, *args)
4960 
4961 
4962  def setup_particle(*args):
4963  """
4964  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4965  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4966  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4967  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4968  """
4969  return _IMP_atom.Charged_setup_particle(*args)
4970 
4971  setup_particle = staticmethod(setup_particle)
4972 
4973  def get_charge(self):
4974  """get_charge(Charged self) -> IMP::Float"""
4975  return _IMP_atom.Charged_get_charge(self)
4976 
4977 
4978  def set_charge(self, t):
4979  """set_charge(Charged self, IMP::Float t)"""
4980  return _IMP_atom.Charged_set_charge(self, t)
4981 
4982 
4983  def get_is_setup(*args):
4984  """
4985  get_is_setup(_ParticleAdaptor p) -> bool
4986  get_is_setup(Model m, ParticleIndex pi) -> bool
4987  """
4988  return _IMP_atom.Charged_get_is_setup(*args)
4989 
4990  get_is_setup = staticmethod(get_is_setup)
4991 
4992  def get_charge_key():
4993  """get_charge_key() -> FloatKey"""
4994  return _IMP_atom.Charged_get_charge_key()
4995 
4996  get_charge_key = staticmethod(get_charge_key)
4997 
4998  def add_attribute(self, *args):
4999  """
5000  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
5001  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
5002  add_attribute(Charged self, IntKey a0, IMP::Int a1)
5003  add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
5004  add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
5005  add_attribute(Charged self, StringKey a0, IMP::String a1)
5006  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
5007  add_attribute(Charged self, ObjectKey a0, Object a1)
5008  """
5009  return _IMP_atom.Charged_add_attribute(self, *args)
5010 
5011 
5012  def get_value(self, *args):
5013  """
5014  get_value(Charged self, FloatKey a0) -> IMP::Float
5015  get_value(Charged self, IntKey a0) -> IMP::Int
5016  get_value(Charged self, FloatsKey a0) -> IMP::Floats
5017  get_value(Charged self, IntsKey a0) -> IMP::Ints
5018  get_value(Charged self, StringKey a0) -> IMP::String
5019  get_value(Charged self, ParticleIndexKey a0) -> Particle
5020  get_value(Charged self, ObjectKey a0) -> Object
5021  """
5022  return _IMP_atom.Charged_get_value(self, *args)
5023 
5024 
5025  def set_value(self, *args):
5026  """
5027  set_value(Charged self, FloatKey a0, IMP::Float a1)
5028  set_value(Charged self, IntKey a0, IMP::Int a1)
5029  set_value(Charged self, FloatsKey a0, IMP::Floats a1)
5030  set_value(Charged self, IntsKey a0, IMP::Ints a1)
5031  set_value(Charged self, StringKey a0, IMP::String a1)
5032  set_value(Charged self, ParticleIndexKey a0, Particle a1)
5033  set_value(Charged self, ObjectKey a0, Object a1)
5034  """
5035  return _IMP_atom.Charged_set_value(self, *args)
5036 
5037 
5038  def remove_attribute(self, *args):
5039  """
5040  remove_attribute(Charged self, FloatKey a0)
5041  remove_attribute(Charged self, IntKey a0)
5042  remove_attribute(Charged self, FloatsKey a0)
5043  remove_attribute(Charged self, IntsKey a0)
5044  remove_attribute(Charged self, StringKey a0)
5045  remove_attribute(Charged self, ParticleIndexKey a0)
5046  remove_attribute(Charged self, ObjectKey a0)
5047  """
5048  return _IMP_atom.Charged_remove_attribute(self, *args)
5049 
5050 
5051  def has_attribute(self, *args):
5052  """
5053  has_attribute(Charged self, FloatKey a0) -> bool
5054  has_attribute(Charged self, IntKey a0) -> bool
5055  has_attribute(Charged self, FloatsKey a0) -> bool
5056  has_attribute(Charged self, IntsKey a0) -> bool
5057  has_attribute(Charged self, StringKey a0) -> bool
5058  has_attribute(Charged self, ParticleIndexKey a0) -> bool
5059  has_attribute(Charged self, ObjectKey a0) -> bool
5060  """
5061  return _IMP_atom.Charged_has_attribute(self, *args)
5062 
5063 
5064  def get_derivative(self, a0):
5065  """get_derivative(Charged self, FloatKey a0) -> double"""
5066  return _IMP_atom.Charged_get_derivative(self, a0)
5067 
5068 
5069  def get_name(self):
5070  """get_name(Charged self) -> std::string"""
5071  return _IMP_atom.Charged_get_name(self)
5072 
5073 
5074  def clear_caches(self):
5075  """clear_caches(Charged self)"""
5076  return _IMP_atom.Charged_clear_caches(self)
5077 
5078 
5079  def set_name(self, a0):
5080  """set_name(Charged self, std::string a0)"""
5081  return _IMP_atom.Charged_set_name(self, a0)
5082 
5083 
5084  def set_check_level(self, a0):
5085  """set_check_level(Charged self, IMP::CheckLevel a0)"""
5086  return _IMP_atom.Charged_set_check_level(self, a0)
5087 
5088 
5089  def add_to_derivative(self, a0, a1, a2):
5090  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5091  return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
5092 
5093 
5094  def set_is_optimized(self, a0, a1):
5095  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
5096  return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
5097 
5098 
5099  def get_is_optimized(self, a0):
5100  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
5101  return _IMP_atom.Charged_get_is_optimized(self, a0)
5102 
5103 
5104  def get_check_level(self):
5105  """get_check_level(Charged self) -> IMP::CheckLevel"""
5106  return _IMP_atom.Charged_get_check_level(self)
5107 
5108 
5109  def __eq__(self, *args):
5110  """
5111  __eq__(Charged self, Charged o) -> bool
5112  __eq__(Charged self, Particle d) -> bool
5113  """
5114  return _IMP_atom.Charged___eq__(self, *args)
5115 
5116 
5117  def __ne__(self, *args):
5118  """
5119  __ne__(Charged self, Charged o) -> bool
5120  __ne__(Charged self, Particle d) -> bool
5121  """
5122  return _IMP_atom.Charged___ne__(self, *args)
5123 
5124 
5125  def __le__(self, *args):
5126  """
5127  __le__(Charged self, Charged o) -> bool
5128  __le__(Charged self, Particle d) -> bool
5129  """
5130  return _IMP_atom.Charged___le__(self, *args)
5131 
5132 
5133  def __lt__(self, *args):
5134  """
5135  __lt__(Charged self, Charged o) -> bool
5136  __lt__(Charged self, Particle d) -> bool
5137  """
5138  return _IMP_atom.Charged___lt__(self, *args)
5139 
5140 
5141  def __ge__(self, *args):
5142  """
5143  __ge__(Charged self, Charged o) -> bool
5144  __ge__(Charged self, Particle d) -> bool
5145  """
5146  return _IMP_atom.Charged___ge__(self, *args)
5147 
5148 
5149  def __gt__(self, *args):
5150  """
5151  __gt__(Charged self, Charged o) -> bool
5152  __gt__(Charged self, Particle d) -> bool
5153  """
5154  return _IMP_atom.Charged___gt__(self, *args)
5155 
5156 
5157  def __hash__(self):
5158  """__hash__(Charged self) -> std::size_t"""
5159  return _IMP_atom.Charged___hash__(self)
5160 
5161 
5162  def __str__(self):
5163  """__str__(Charged self) -> std::string"""
5164  return _IMP_atom.Charged___str__(self)
5165 
5166 
5167  def __repr__(self):
5168  """__repr__(Charged self) -> std::string"""
5169  return _IMP_atom.Charged___repr__(self)
5170 
5171  __swig_destroy__ = _IMP_atom.delete_Charged
5172  __del__ = lambda self: None
5173 Charged_swigregister = _IMP_atom.Charged_swigregister
5174 Charged_swigregister(Charged)
5175 
5176 def Charged_setup_particle(*args):
5177  """
5178  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5179  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5180  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5181  Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5182  """
5183  return _IMP_atom.Charged_setup_particle(*args)
5184 
5185 def Charged_get_is_setup(*args):
5186  """
5187  get_is_setup(_ParticleAdaptor p) -> bool
5188  Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5189  """
5190  return _IMP_atom.Charged_get_is_setup(*args)
5191 
5192 def Charged_get_charge_key():
5193  """Charged_get_charge_key() -> FloatKey"""
5194  return _IMP_atom.Charged_get_charge_key()
5195 
5196 class CoulombPairScore(IMP.PairScore):
5197  """Proxy of C++ IMP::atom::CoulombPairScore class."""
5198 
5199  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5200 
5201  def __init__(self, f):
5202  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5203  this = _IMP_atom.new_CoulombPairScore(f)
5204  try:
5205  self.this.append(this)
5206  except __builtin__.Exception:
5207  self.this = this
5208 
5209  def set_relative_dielectric(self, relative_dielectric):
5210  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5211  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5212 
5213 
5214  def get_relative_dielectric(self):
5215  """get_relative_dielectric(CoulombPairScore self) -> double"""
5216  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5217 
5218 
5219  def do_get_inputs(self, m, pis):
5220  """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5221  return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5222 
5223 
5224  def get_version_info(self):
5225  """get_version_info(CoulombPairScore self) -> VersionInfo"""
5226  return _IMP_atom.CoulombPairScore_get_version_info(self)
5227 
5228 
5229  def __str__(self):
5230  """__str__(CoulombPairScore self) -> std::string"""
5231  return _IMP_atom.CoulombPairScore___str__(self)
5232 
5233 
5234  def __repr__(self):
5235  """__repr__(CoulombPairScore self) -> std::string"""
5236  return _IMP_atom.CoulombPairScore___repr__(self)
5237 
5238 
5239  @staticmethod
5240  def get_from(o):
5241  return _object_cast_to_CoulombPairScore(o)
5242 
5243 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5244 CoulombPairScore_swigregister(CoulombPairScore)
5245 
5246 class Domain(Hierarchy):
5247  """Proxy of C++ IMP::atom::Domain class."""
5248 
5249  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5250 
5251  def set_index_range(self, ir):
5252  """set_index_range(Domain self, IMP::IntRange ir)"""
5253  return _IMP_atom.Domain_set_index_range(self, ir)
5254 
5255 
5256  def get_index_range(self):
5257  """get_index_range(Domain self) -> IMP::IntRange"""
5258  return _IMP_atom.Domain_get_index_range(self)
5259 
5260 
5261  def __init__(self, *args):
5262  """
5263  __init__(IMP::atom::Domain self) -> Domain
5264  __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5265  __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5266  """
5267  this = _IMP_atom.new_Domain(*args)
5268  try:
5269  self.this.append(this)
5270  except __builtin__.Exception:
5271  self.this = this
5272 
5273  def get_is_setup(*args):
5274  """
5275  get_is_setup(Model m, ParticleIndex pi) -> bool
5276  get_is_setup(_ParticleAdaptor p) -> bool
5277  """
5278  return _IMP_atom.Domain_get_is_setup(*args)
5279 
5280  get_is_setup = staticmethod(get_is_setup)
5281 
5282  def show(self, *args):
5283  """
5284  show(Domain self, _ostream out)
5285  show(Domain self)
5286  """
5287  return _IMP_atom.Domain_show(self, *args)
5288 
5289 
5290  def setup_particle(*args):
5291  """
5292  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5293  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5294  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5295  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5296  """
5297  return _IMP_atom.Domain_setup_particle(*args)
5298 
5299  setup_particle = staticmethod(setup_particle)
5300 
5301  def add_attribute(self, *args):
5302  """
5303  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5304  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5305  add_attribute(Domain self, IntKey a0, IMP::Int a1)
5306  add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
5307  add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
5308  add_attribute(Domain self, StringKey a0, IMP::String a1)
5309  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5310  add_attribute(Domain self, ObjectKey a0, Object a1)
5311  """
5312  return _IMP_atom.Domain_add_attribute(self, *args)
5313 
5314 
5315  def get_value(self, *args):
5316  """
5317  get_value(Domain self, FloatKey a0) -> IMP::Float
5318  get_value(Domain self, IntKey a0) -> IMP::Int
5319  get_value(Domain self, FloatsKey a0) -> IMP::Floats
5320  get_value(Domain self, IntsKey a0) -> IMP::Ints
5321  get_value(Domain self, StringKey a0) -> IMP::String
5322  get_value(Domain self, ParticleIndexKey a0) -> Particle
5323  get_value(Domain self, ObjectKey a0) -> Object
5324  """
5325  return _IMP_atom.Domain_get_value(self, *args)
5326 
5327 
5328  def set_value(self, *args):
5329  """
5330  set_value(Domain self, FloatKey a0, IMP::Float a1)
5331  set_value(Domain self, IntKey a0, IMP::Int a1)
5332  set_value(Domain self, FloatsKey a0, IMP::Floats a1)
5333  set_value(Domain self, IntsKey a0, IMP::Ints a1)
5334  set_value(Domain self, StringKey a0, IMP::String a1)
5335  set_value(Domain self, ParticleIndexKey a0, Particle a1)
5336  set_value(Domain self, ObjectKey a0, Object a1)
5337  """
5338  return _IMP_atom.Domain_set_value(self, *args)
5339 
5340 
5341  def remove_attribute(self, *args):
5342  """
5343  remove_attribute(Domain self, FloatKey a0)
5344  remove_attribute(Domain self, IntKey a0)
5345  remove_attribute(Domain self, FloatsKey a0)
5346  remove_attribute(Domain self, IntsKey a0)
5347  remove_attribute(Domain self, StringKey a0)
5348  remove_attribute(Domain self, ParticleIndexKey a0)
5349  remove_attribute(Domain self, ObjectKey a0)
5350  """
5351  return _IMP_atom.Domain_remove_attribute(self, *args)
5352 
5353 
5354  def has_attribute(self, *args):
5355  """
5356  has_attribute(Domain self, FloatKey a0) -> bool
5357  has_attribute(Domain self, IntKey a0) -> bool
5358  has_attribute(Domain self, FloatsKey a0) -> bool
5359  has_attribute(Domain self, IntsKey a0) -> bool
5360  has_attribute(Domain self, StringKey a0) -> bool
5361  has_attribute(Domain self, ParticleIndexKey a0) -> bool
5362  has_attribute(Domain self, ObjectKey a0) -> bool
5363  """
5364  return _IMP_atom.Domain_has_attribute(self, *args)
5365 
5366 
5367  def get_derivative(self, a0):
5368  """get_derivative(Domain self, FloatKey a0) -> double"""
5369  return _IMP_atom.Domain_get_derivative(self, a0)
5370 
5371 
5372  def get_name(self):
5373  """get_name(Domain self) -> std::string"""
5374  return _IMP_atom.Domain_get_name(self)
5375 
5376 
5377  def clear_caches(self):
5378  """clear_caches(Domain self)"""
5379  return _IMP_atom.Domain_clear_caches(self)
5380 
5381 
5382  def set_name(self, a0):
5383  """set_name(Domain self, std::string a0)"""
5384  return _IMP_atom.Domain_set_name(self, a0)
5385 
5386 
5387  def set_check_level(self, a0):
5388  """set_check_level(Domain self, IMP::CheckLevel a0)"""
5389  return _IMP_atom.Domain_set_check_level(self, a0)
5390 
5391 
5392  def add_to_derivative(self, a0, a1, a2):
5393  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5394  return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5395 
5396 
5397  def set_is_optimized(self, a0, a1):
5398  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5399  return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5400 
5401 
5402  def get_is_optimized(self, a0):
5403  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5404  return _IMP_atom.Domain_get_is_optimized(self, a0)
5405 
5406 
5407  def get_check_level(self):
5408  """get_check_level(Domain self) -> IMP::CheckLevel"""
5409  return _IMP_atom.Domain_get_check_level(self)
5410 
5411 
5412  def __eq__(self, *args):
5413  """
5414  __eq__(Domain self, Domain o) -> bool
5415  __eq__(Domain self, Particle d) -> bool
5416  """
5417  return _IMP_atom.Domain___eq__(self, *args)
5418 
5419 
5420  def __ne__(self, *args):
5421  """
5422  __ne__(Domain self, Domain o) -> bool
5423  __ne__(Domain self, Particle d) -> bool
5424  """
5425  return _IMP_atom.Domain___ne__(self, *args)
5426 
5427 
5428  def __le__(self, *args):
5429  """
5430  __le__(Domain self, Domain o) -> bool
5431  __le__(Domain self, Particle d) -> bool
5432  """
5433  return _IMP_atom.Domain___le__(self, *args)
5434 
5435 
5436  def __lt__(self, *args):
5437  """
5438  __lt__(Domain self, Domain o) -> bool
5439  __lt__(Domain self, Particle d) -> bool
5440  """
5441  return _IMP_atom.Domain___lt__(self, *args)
5442 
5443 
5444  def __ge__(self, *args):
5445  """
5446  __ge__(Domain self, Domain o) -> bool
5447  __ge__(Domain self, Particle d) -> bool
5448  """
5449  return _IMP_atom.Domain___ge__(self, *args)
5450 
5451 
5452  def __gt__(self, *args):
5453  """
5454  __gt__(Domain self, Domain o) -> bool
5455  __gt__(Domain self, Particle d) -> bool
5456  """
5457  return _IMP_atom.Domain___gt__(self, *args)
5458 
5459 
5460  def __hash__(self):
5461  """__hash__(Domain self) -> std::size_t"""
5462  return _IMP_atom.Domain___hash__(self)
5463 
5464 
5465  def __str__(self):
5466  """__str__(Domain self) -> std::string"""
5467  return _IMP_atom.Domain___str__(self)
5468 
5469 
5470  def __repr__(self):
5471  """__repr__(Domain self) -> std::string"""
5472  return _IMP_atom.Domain___repr__(self)
5473 
5474  __swig_destroy__ = _IMP_atom.delete_Domain
5475  __del__ = lambda self: None
5476 Domain_swigregister = _IMP_atom.Domain_swigregister
5477 Domain_swigregister(Domain)
5478 
5479 def Domain_get_is_setup(*args):
5480  """
5481  get_is_setup(Model m, ParticleIndex pi) -> bool
5482  Domain_get_is_setup(_ParticleAdaptor p) -> bool
5483  """
5484  return _IMP_atom.Domain_get_is_setup(*args)
5485 
5486 def Domain_setup_particle(*args):
5487  """
5488  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5489  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5490  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5491  Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5492  """
5493  return _IMP_atom.Domain_setup_particle(*args)
5494 
5495 class LennardJones(IMP.core.XYZR):
5496  """Proxy of C++ IMP::atom::LennardJones class."""
5497 
5498  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5499 
5500  def __init__(self, *args):
5501  """
5502  __init__(IMP::atom::LennardJones self) -> LennardJones
5503  __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5504  __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5505  """
5506  this = _IMP_atom.new_LennardJones(*args)
5507  try:
5508  self.this.append(this)
5509  except __builtin__.Exception:
5510  self.this = this
5511 
5512  def show(self, *args):
5513  """
5514  show(LennardJones self, _ostream out)
5515  show(LennardJones self)
5516  """
5517  return _IMP_atom.LennardJones_show(self, *args)
5518 
5519 
5520  def setup_particle(*args):
5521  """
5522  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5523  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5524  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5525  setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5526  """
5527  return _IMP_atom.LennardJones_setup_particle(*args)
5528 
5529  setup_particle = staticmethod(setup_particle)
5530 
5531  def get_well_depth(self):
5532  """get_well_depth(LennardJones self) -> IMP::Float"""
5533  return _IMP_atom.LennardJones_get_well_depth(self)
5534 
5535 
5536  def set_well_depth(self, well_depth):
5537  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5538  return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5539 
5540 
5541  def get_is_setup(*args):
5542  """
5543  get_is_setup(_ParticleAdaptor p) -> bool
5544  get_is_setup(Model m, ParticleIndex pi) -> bool
5545  """
5546  return _IMP_atom.LennardJones_get_is_setup(*args)
5547 
5548  get_is_setup = staticmethod(get_is_setup)
5549 
5550  def get_well_depth_key():
5551  """get_well_depth_key() -> FloatKey"""
5552  return _IMP_atom.LennardJones_get_well_depth_key()
5553 
5554  get_well_depth_key = staticmethod(get_well_depth_key)
5555 
5556  def add_attribute(self, *args):
5557  """
5558  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5559  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5560  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5561  add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
5562  add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
5563  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5564  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5565  add_attribute(LennardJones self, ObjectKey a0, Object a1)
5566  """
5567  return _IMP_atom.LennardJones_add_attribute(self, *args)
5568 
5569 
5570  def get_value(self, *args):
5571  """
5572  get_value(LennardJones self, FloatKey a0) -> IMP::Float
5573  get_value(LennardJones self, IntKey a0) -> IMP::Int
5574  get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
5575  get_value(LennardJones self, IntsKey a0) -> IMP::Ints
5576  get_value(LennardJones self, StringKey a0) -> IMP::String
5577  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5578  get_value(LennardJones self, ObjectKey a0) -> Object
5579  """
5580  return _IMP_atom.LennardJones_get_value(self, *args)
5581 
5582 
5583  def set_value(self, *args):
5584  """
5585  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5586  set_value(LennardJones self, IntKey a0, IMP::Int a1)
5587  set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5588  set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5589  set_value(LennardJones self, StringKey a0, IMP::String a1)
5590  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5591  set_value(LennardJones self, ObjectKey a0, Object a1)
5592  """
5593  return _IMP_atom.LennardJones_set_value(self, *args)
5594 
5595 
5596  def remove_attribute(self, *args):
5597  """
5598  remove_attribute(LennardJones self, FloatKey a0)
5599  remove_attribute(LennardJones self, IntKey a0)
5600  remove_attribute(LennardJones self, FloatsKey a0)
5601  remove_attribute(LennardJones self, IntsKey a0)
5602  remove_attribute(LennardJones self, StringKey a0)
5603  remove_attribute(LennardJones self, ParticleIndexKey a0)
5604  remove_attribute(LennardJones self, ObjectKey a0)
5605  """
5606  return _IMP_atom.LennardJones_remove_attribute(self, *args)
5607 
5608 
5609  def has_attribute(self, *args):
5610  """
5611  has_attribute(LennardJones self, FloatKey a0) -> bool
5612  has_attribute(LennardJones self, IntKey a0) -> bool
5613  has_attribute(LennardJones self, FloatsKey a0) -> bool
5614  has_attribute(LennardJones self, IntsKey a0) -> bool
5615  has_attribute(LennardJones self, StringKey a0) -> bool
5616  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5617  has_attribute(LennardJones self, ObjectKey a0) -> bool
5618  """
5619  return _IMP_atom.LennardJones_has_attribute(self, *args)
5620 
5621 
5622  def get_derivative(self, a0):
5623  """get_derivative(LennardJones self, FloatKey a0) -> double"""
5624  return _IMP_atom.LennardJones_get_derivative(self, a0)
5625 
5626 
5627  def get_name(self):
5628  """get_name(LennardJones self) -> std::string"""
5629  return _IMP_atom.LennardJones_get_name(self)
5630 
5631 
5632  def clear_caches(self):
5633  """clear_caches(LennardJones self)"""
5634  return _IMP_atom.LennardJones_clear_caches(self)
5635 
5636 
5637  def set_name(self, a0):
5638  """set_name(LennardJones self, std::string a0)"""
5639  return _IMP_atom.LennardJones_set_name(self, a0)
5640 
5641 
5642  def set_check_level(self, a0):
5643  """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5644  return _IMP_atom.LennardJones_set_check_level(self, a0)
5645 
5646 
5647  def add_to_derivative(self, a0, a1, a2):
5648  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5649  return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5650 
5651 
5652  def set_is_optimized(self, a0, a1):
5653  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5654  return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5655 
5656 
5657  def get_is_optimized(self, a0):
5658  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5659  return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5660 
5661 
5662  def get_check_level(self):
5663  """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5664  return _IMP_atom.LennardJones_get_check_level(self)
5665 
5666 
5667  def __eq__(self, *args):
5668  """
5669  __eq__(LennardJones self, LennardJones o) -> bool
5670  __eq__(LennardJones self, Particle d) -> bool
5671  """
5672  return _IMP_atom.LennardJones___eq__(self, *args)
5673 
5674 
5675  def __ne__(self, *args):
5676  """
5677  __ne__(LennardJones self, LennardJones o) -> bool
5678  __ne__(LennardJones self, Particle d) -> bool
5679  """
5680  return _IMP_atom.LennardJones___ne__(self, *args)
5681 
5682 
5683  def __le__(self, *args):
5684  """
5685  __le__(LennardJones self, LennardJones o) -> bool
5686  __le__(LennardJones self, Particle d) -> bool
5687  """
5688  return _IMP_atom.LennardJones___le__(self, *args)
5689 
5690 
5691  def __lt__(self, *args):
5692  """
5693  __lt__(LennardJones self, LennardJones o) -> bool
5694  __lt__(LennardJones self, Particle d) -> bool
5695  """
5696  return _IMP_atom.LennardJones___lt__(self, *args)
5697 
5698 
5699  def __ge__(self, *args):
5700  """
5701  __ge__(LennardJones self, LennardJones o) -> bool
5702  __ge__(LennardJones self, Particle d) -> bool
5703  """
5704  return _IMP_atom.LennardJones___ge__(self, *args)
5705 
5706 
5707  def __gt__(self, *args):
5708  """
5709  __gt__(LennardJones self, LennardJones o) -> bool
5710  __gt__(LennardJones self, Particle d) -> bool
5711  """
5712  return _IMP_atom.LennardJones___gt__(self, *args)
5713 
5714 
5715  def __hash__(self):
5716  """__hash__(LennardJones self) -> std::size_t"""
5717  return _IMP_atom.LennardJones___hash__(self)
5718 
5719 
5720  def __str__(self):
5721  """__str__(LennardJones self) -> std::string"""
5722  return _IMP_atom.LennardJones___str__(self)
5723 
5724 
5725  def __repr__(self):
5726  """__repr__(LennardJones self) -> std::string"""
5727  return _IMP_atom.LennardJones___repr__(self)
5728 
5729  __swig_destroy__ = _IMP_atom.delete_LennardJones
5730  __del__ = lambda self: None
5731 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5732 LennardJones_swigregister(LennardJones)
5733 
5734 def LennardJones_setup_particle(*args):
5735  """
5736  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5737  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5738  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5739  LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5740  """
5741  return _IMP_atom.LennardJones_setup_particle(*args)
5742 
5743 def LennardJones_get_is_setup(*args):
5744  """
5745  get_is_setup(_ParticleAdaptor p) -> bool
5746  LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5747  """
5748  return _IMP_atom.LennardJones_get_is_setup(*args)
5749 
5750 def LennardJones_get_well_depth_key():
5751  """LennardJones_get_well_depth_key() -> FloatKey"""
5752  return _IMP_atom.LennardJones_get_well_depth_key()
5753 
5754 class LennardJonesPairScore(IMP.PairScore):
5755  """Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5756 
5757  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5758 
5759  def __init__(self, f):
5760  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5761  this = _IMP_atom.new_LennardJonesPairScore(f)
5762  try:
5763  self.this.append(this)
5764  except __builtin__.Exception:
5765  self.this = this
5766 
5767  def set_repulsive_weight(self, repulsive_weight):
5768  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5769  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5770 
5771 
5772  def get_repulsive_weight(self):
5773  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5774  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5775 
5776 
5777  def set_attractive_weight(self, attractive_weight):
5778  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5779  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5780 
5781 
5782  def get_attractive_weight(self):
5783  """get_attractive_weight(LennardJonesPairScore self) -> double"""
5784  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5785 
5786 
5787  def do_get_inputs(self, m, pis):
5788  """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5789  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5790 
5791 
5792  def get_version_info(self):
5793  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5794  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5795 
5796 
5797  def __str__(self):
5798  """__str__(LennardJonesPairScore self) -> std::string"""
5799  return _IMP_atom.LennardJonesPairScore___str__(self)
5800 
5801 
5802  def __repr__(self):
5803  """__repr__(LennardJonesPairScore self) -> std::string"""
5804  return _IMP_atom.LennardJonesPairScore___repr__(self)
5805 
5806 
5807  @staticmethod
5808  def get_from(o):
5809  return _object_cast_to_LennardJonesPairScore(o)
5810 
5811 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5812 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5813 
5814 class LinearVelocity(IMP.Decorator):
5815  """Proxy of C++ IMP::atom::LinearVelocity class."""
5816 
5817  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5818 
5819  def __init__(self, *args):
5820  """
5821  __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5822  __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5823  __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5824  """
5825  this = _IMP_atom.new_LinearVelocity(*args)
5826  try:
5827  self.this.append(this)
5828  except __builtin__.Exception:
5829  self.this = this
5830 
5831  def get_is_setup(*args):
5832  """
5833  get_is_setup(Model m, ParticleIndex pi) -> bool
5834  get_is_setup(_ParticleAdaptor p) -> bool
5835  """
5836  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5837 
5838  get_is_setup = staticmethod(get_is_setup)
5839 
5840  def show(self, *args):
5841  """
5842  show(LinearVelocity self, _ostream out)
5843  show(LinearVelocity self)
5844  """
5845  return _IMP_atom.LinearVelocity_show(self, *args)
5846 
5847 
5848  def setup_particle(*args):
5849  """
5850  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5851  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5852  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5853  setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5854  """
5855  return _IMP_atom.LinearVelocity_setup_particle(*args)
5856 
5857  setup_particle = staticmethod(setup_particle)
5858 
5859  def set_velocity(self, v):
5860  """set_velocity(LinearVelocity self, Vector3D v)"""
5861  return _IMP_atom.LinearVelocity_set_velocity(self, v)
5862 
5863 
5864  def get_velocity(self):
5865  """get_velocity(LinearVelocity self) -> Vector3D"""
5866  return _IMP_atom.LinearVelocity_get_velocity(self)
5867 
5868 
5869  def add_attribute(self, *args):
5870  """
5871  add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5872  add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5873  add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5874  add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5875  add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5876  add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5877  add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5878  add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5879  """
5880  return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5881 
5882 
5883  def get_value(self, *args):
5884  """
5885  get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5886  get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5887  get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5888  get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5889  get_value(LinearVelocity self, StringKey a0) -> IMP::String
5890  get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5891  get_value(LinearVelocity self, ObjectKey a0) -> Object
5892  """
5893  return _IMP_atom.LinearVelocity_get_value(self, *args)
5894 
5895 
5896  def set_value(self, *args):
5897  """
5898  set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5899  set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5900  set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5901  set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5902  set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5903  set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5904  set_value(LinearVelocity self, ObjectKey a0, Object a1)
5905  """
5906  return _IMP_atom.LinearVelocity_set_value(self, *args)
5907 
5908 
5909  def remove_attribute(self, *args):
5910  """
5911  remove_attribute(LinearVelocity self, FloatKey a0)
5912  remove_attribute(LinearVelocity self, IntKey a0)
5913  remove_attribute(LinearVelocity self, FloatsKey a0)
5914  remove_attribute(LinearVelocity self, IntsKey a0)
5915  remove_attribute(LinearVelocity self, StringKey a0)
5916  remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5917  remove_attribute(LinearVelocity self, ObjectKey a0)
5918  """
5919  return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5920 
5921 
5922  def has_attribute(self, *args):
5923  """
5924  has_attribute(LinearVelocity self, FloatKey a0) -> bool
5925  has_attribute(LinearVelocity self, IntKey a0) -> bool
5926  has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5927  has_attribute(LinearVelocity self, IntsKey a0) -> bool
5928  has_attribute(LinearVelocity self, StringKey a0) -> bool
5929  has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5930  has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5931  """
5932  return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5933 
5934 
5935  def get_derivative(self, a0):
5936  """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5937  return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5938 
5939 
5940  def get_name(self):
5941  """get_name(LinearVelocity self) -> std::string"""
5942  return _IMP_atom.LinearVelocity_get_name(self)
5943 
5944 
5945  def clear_caches(self):
5946  """clear_caches(LinearVelocity self)"""
5947  return _IMP_atom.LinearVelocity_clear_caches(self)
5948 
5949 
5950  def set_name(self, a0):
5951  """set_name(LinearVelocity self, std::string a0)"""
5952  return _IMP_atom.LinearVelocity_set_name(self, a0)
5953 
5954 
5955  def set_check_level(self, a0):
5956  """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5957  return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5958 
5959 
5960  def add_to_derivative(self, a0, a1, a2):
5961  """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5962  return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5963 
5964 
5965  def set_is_optimized(self, a0, a1):
5966  """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5967  return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5968 
5969 
5970  def get_is_optimized(self, a0):
5971  """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5972  return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5973 
5974 
5975  def get_check_level(self):
5976  """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5977  return _IMP_atom.LinearVelocity_get_check_level(self)
5978 
5979 
5980  def __eq__(self, *args):
5981  """
5982  __eq__(LinearVelocity self, LinearVelocity o) -> bool
5983  __eq__(LinearVelocity self, Particle d) -> bool
5984  """
5985  return _IMP_atom.LinearVelocity___eq__(self, *args)
5986 
5987 
5988  def __ne__(self, *args):
5989  """
5990  __ne__(LinearVelocity self, LinearVelocity o) -> bool
5991  __ne__(LinearVelocity self, Particle d) -> bool
5992  """
5993  return _IMP_atom.LinearVelocity___ne__(self, *args)
5994 
5995 
5996  def __le__(self, *args):
5997  """
5998  __le__(LinearVelocity self, LinearVelocity o) -> bool
5999  __le__(LinearVelocity self, Particle d) -> bool
6000  """
6001  return _IMP_atom.LinearVelocity___le__(self, *args)
6002 
6003 
6004  def __lt__(self, *args):
6005  """
6006  __lt__(LinearVelocity self, LinearVelocity o) -> bool
6007  __lt__(LinearVelocity self, Particle d) -> bool
6008  """
6009  return _IMP_atom.LinearVelocity___lt__(self, *args)
6010 
6011 
6012  def __ge__(self, *args):
6013  """
6014  __ge__(LinearVelocity self, LinearVelocity o) -> bool
6015  __ge__(LinearVelocity self, Particle d) -> bool
6016  """
6017  return _IMP_atom.LinearVelocity___ge__(self, *args)
6018 
6019 
6020  def __gt__(self, *args):
6021  """
6022  __gt__(LinearVelocity self, LinearVelocity o) -> bool
6023  __gt__(LinearVelocity self, Particle d) -> bool
6024  """
6025  return _IMP_atom.LinearVelocity___gt__(self, *args)
6026 
6027 
6028  def __hash__(self):
6029  """__hash__(LinearVelocity self) -> std::size_t"""
6030  return _IMP_atom.LinearVelocity___hash__(self)
6031 
6032 
6033  def __str__(self):
6034  """__str__(LinearVelocity self) -> std::string"""
6035  return _IMP_atom.LinearVelocity___str__(self)
6036 
6037 
6038  def __repr__(self):
6039  """__repr__(LinearVelocity self) -> std::string"""
6040  return _IMP_atom.LinearVelocity___repr__(self)
6041 
6042  __swig_destroy__ = _IMP_atom.delete_LinearVelocity
6043  __del__ = lambda self: None
6044 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
6045 LinearVelocity_swigregister(LinearVelocity)
6046 
6047 def LinearVelocity_get_is_setup(*args):
6048  """
6049  get_is_setup(Model m, ParticleIndex pi) -> bool
6050  LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6051  """
6052  return _IMP_atom.LinearVelocity_get_is_setup(*args)
6053 
6054 def LinearVelocity_setup_particle(*args):
6055  """
6056  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
6057  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
6058  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
6059  LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
6060  """
6061  return _IMP_atom.LinearVelocity_setup_particle(*args)
6062 
6063 class AngularVelocity(IMP.Decorator):
6064  """Proxy of C++ IMP::atom::AngularVelocity class."""
6065 
6066  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6067 
6068  def __init__(self, *args):
6069  """
6070  __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
6071  __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
6072  __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
6073  """
6074  this = _IMP_atom.new_AngularVelocity(*args)
6075  try:
6076  self.this.append(this)
6077  except __builtin__.Exception:
6078  self.this = this
6079 
6080  def get_is_setup(*args):
6081  """
6082  get_is_setup(Model m, ParticleIndex pi) -> bool
6083  get_is_setup(_ParticleAdaptor p) -> bool
6084  """
6085  return _IMP_atom.AngularVelocity_get_is_setup(*args)
6086 
6087  get_is_setup = staticmethod(get_is_setup)
6088 
6089  def show(self, *args):
6090  """
6091  show(AngularVelocity self, _ostream out)
6092  show(AngularVelocity self)
6093  """
6094  return _IMP_atom.AngularVelocity_show(self, *args)
6095 
6096 
6097  def setup_particle(*args):
6098  """
6099  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6100  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6101  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6102  setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6103  """
6104  return _IMP_atom.AngularVelocity_setup_particle(*args)
6105 
6106  setup_particle = staticmethod(setup_particle)
6107 
6108  def set_velocity(self, v):
6109  """set_velocity(AngularVelocity self, Vector4D v)"""
6110  return _IMP_atom.AngularVelocity_set_velocity(self, v)
6111 
6112 
6113  def get_velocity(self):
6114  """get_velocity(AngularVelocity self) -> Vector4D"""
6115  return _IMP_atom.AngularVelocity_get_velocity(self)
6116 
6117 
6118  def add_attribute(self, *args):
6119  """
6120  add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
6121  add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
6122  add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
6123  add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
6124  add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
6125  add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
6126  add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6127  add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
6128  """
6129  return _IMP_atom.AngularVelocity_add_attribute(self, *args)
6130 
6131 
6132  def get_value(self, *args):
6133  """
6134  get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
6135  get_value(AngularVelocity self, IntKey a0) -> IMP::Int
6136  get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
6137  get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
6138  get_value(AngularVelocity self, StringKey a0) -> IMP::String
6139  get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
6140  get_value(AngularVelocity self, ObjectKey a0) -> Object
6141  """
6142  return _IMP_atom.AngularVelocity_get_value(self, *args)
6143 
6144 
6145  def set_value(self, *args):
6146  """
6147  set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
6148  set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
6149  set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
6150  set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
6151  set_value(AngularVelocity self, StringKey a0, IMP::String a1)
6152  set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6153  set_value(AngularVelocity self, ObjectKey a0, Object a1)
6154  """
6155  return _IMP_atom.AngularVelocity_set_value(self, *args)
6156 
6157 
6158  def remove_attribute(self, *args):
6159  """
6160  remove_attribute(AngularVelocity self, FloatKey a0)
6161  remove_attribute(AngularVelocity self, IntKey a0)
6162  remove_attribute(AngularVelocity self, FloatsKey a0)
6163  remove_attribute(AngularVelocity self, IntsKey a0)
6164  remove_attribute(AngularVelocity self, StringKey a0)
6165  remove_attribute(AngularVelocity self, ParticleIndexKey a0)
6166  remove_attribute(AngularVelocity self, ObjectKey a0)
6167  """
6168  return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
6169 
6170 
6171  def has_attribute(self, *args):
6172  """
6173  has_attribute(AngularVelocity self, FloatKey a0) -> bool
6174  has_attribute(AngularVelocity self, IntKey a0) -> bool
6175  has_attribute(AngularVelocity self, FloatsKey a0) -> bool
6176  has_attribute(AngularVelocity self, IntsKey a0) -> bool
6177  has_attribute(AngularVelocity self, StringKey a0) -> bool
6178  has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6179  has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6180  """
6181  return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6182 
6183 
6184  def get_derivative(self, a0):
6185  """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6186  return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6187 
6188 
6189  def get_name(self):
6190  """get_name(AngularVelocity self) -> std::string"""
6191  return _IMP_atom.AngularVelocity_get_name(self)
6192 
6193 
6194  def clear_caches(self):
6195  """clear_caches(AngularVelocity self)"""
6196  return _IMP_atom.AngularVelocity_clear_caches(self)
6197 
6198 
6199  def set_name(self, a0):
6200  """set_name(AngularVelocity self, std::string a0)"""
6201  return _IMP_atom.AngularVelocity_set_name(self, a0)
6202 
6203 
6204  def set_check_level(self, a0):
6205  """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6206  return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6207 
6208 
6209  def add_to_derivative(self, a0, a1, a2):
6210  """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6211  return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6212 
6213 
6214  def set_is_optimized(self, a0, a1):
6215  """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6216  return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6217 
6218 
6219  def get_is_optimized(self, a0):
6220  """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6221  return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6222 
6223 
6224  def get_check_level(self):
6225  """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6226  return _IMP_atom.AngularVelocity_get_check_level(self)
6227 
6228 
6229  def __eq__(self, *args):
6230  """
6231  __eq__(AngularVelocity self, AngularVelocity o) -> bool
6232  __eq__(AngularVelocity self, Particle d) -> bool
6233  """
6234  return _IMP_atom.AngularVelocity___eq__(self, *args)
6235 
6236 
6237  def __ne__(self, *args):
6238  """
6239  __ne__(AngularVelocity self, AngularVelocity o) -> bool
6240  __ne__(AngularVelocity self, Particle d) -> bool
6241  """
6242  return _IMP_atom.AngularVelocity___ne__(self, *args)
6243 
6244 
6245  def __le__(self, *args):
6246  """
6247  __le__(AngularVelocity self, AngularVelocity o) -> bool
6248  __le__(AngularVelocity self, Particle d) -> bool
6249  """
6250  return _IMP_atom.AngularVelocity___le__(self, *args)
6251 
6252 
6253  def __lt__(self, *args):
6254  """
6255  __lt__(AngularVelocity self, AngularVelocity o) -> bool
6256  __lt__(AngularVelocity self, Particle d) -> bool
6257  """
6258  return _IMP_atom.AngularVelocity___lt__(self, *args)
6259 
6260 
6261  def __ge__(self, *args):
6262  """
6263  __ge__(AngularVelocity self, AngularVelocity o) -> bool
6264  __ge__(AngularVelocity self, Particle d) -> bool
6265  """
6266  return _IMP_atom.AngularVelocity___ge__(self, *args)
6267 
6268 
6269  def __gt__(self, *args):
6270  """
6271  __gt__(AngularVelocity self, AngularVelocity o) -> bool
6272  __gt__(AngularVelocity self, Particle d) -> bool
6273  """
6274  return _IMP_atom.AngularVelocity___gt__(self, *args)
6275 
6276 
6277  def __hash__(self):
6278  """__hash__(AngularVelocity self) -> std::size_t"""
6279  return _IMP_atom.AngularVelocity___hash__(self)
6280 
6281 
6282  def __str__(self):
6283  """__str__(AngularVelocity self) -> std::string"""
6284  return _IMP_atom.AngularVelocity___str__(self)
6285 
6286 
6287  def __repr__(self):
6288  """__repr__(AngularVelocity self) -> std::string"""
6289  return _IMP_atom.AngularVelocity___repr__(self)
6290 
6291  __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6292  __del__ = lambda self: None
6293 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6294 AngularVelocity_swigregister(AngularVelocity)
6295 
6296 def AngularVelocity_get_is_setup(*args):
6297  """
6298  get_is_setup(Model m, ParticleIndex pi) -> bool
6299  AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6300  """
6301  return _IMP_atom.AngularVelocity_get_is_setup(*args)
6302 
6303 def AngularVelocity_setup_particle(*args):
6304  """
6305  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6306  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6307  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6308  AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6309  """
6310  return _IMP_atom.AngularVelocity_setup_particle(*args)
6311 
6312 class MolecularDynamics(Simulator):
6313  """Proxy of C++ IMP::atom::MolecularDynamics class."""
6314 
6315  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6316 
6317  def __init__(self, m):
6318  """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6319  this = _IMP_atom.new_MolecularDynamics(m)
6320  try:
6321  self.this.append(this)
6322  except __builtin__.Exception:
6323  self.this = this
6324 
6325  def get_kinetic_energy(self):
6326  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6327  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6328 
6329 
6330  def get_kinetic_temperature(self, ekinetic):
6331  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6332  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6333 
6334 
6335  def set_velocity_cap(self, velocity_cap):
6336  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6337  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6338 
6339 
6340  def assign_velocities(self, temperature):
6341  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6342  return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6343 
6344 
6345  def setup(self, ps):
6346  """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6347  return _IMP_atom.MolecularDynamics_setup(self, ps)
6348 
6349 
6350  def do_step(self, sc, dt):
6351  """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6352  return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6353 
6354 
6355  def get_is_simulation_particle(self, p):
6356  """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6357  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6358 
6359 
6360  def get_version_info(self):
6361  """get_version_info(MolecularDynamics self) -> VersionInfo"""
6362  return _IMP_atom.MolecularDynamics_get_version_info(self)
6363 
6364 
6365  def __str__(self):
6366  """__str__(MolecularDynamics self) -> std::string"""
6367  return _IMP_atom.MolecularDynamics___str__(self)
6368 
6369 
6370  def __repr__(self):
6371  """__repr__(MolecularDynamics self) -> std::string"""
6372  return _IMP_atom.MolecularDynamics___repr__(self)
6373 
6374 
6375  @staticmethod
6376  def get_from(o):
6377  return _object_cast_to_MolecularDynamics(o)
6378 
6379 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6380 MolecularDynamics_swigregister(MolecularDynamics)
6381 
6382 class VelocityScalingOptimizerState(IMP.OptimizerState):
6383  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6384 
6385  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6386 
6387  def __init__(self, m, pis, temperature):
6388  """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6389  this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6390  try:
6391  self.this.append(this)
6392  except __builtin__.Exception:
6393  self.this = this
6394 
6395  def set_particles(self, pis):
6396  """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6397  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6398 
6399 
6400  def set_temperature(self, temperature):
6401  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6402  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6403 
6404 
6405  def rescale_velocities(self):
6406  """rescale_velocities(VelocityScalingOptimizerState self)"""
6407  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6408 
6409 
6410  def get_version_info(self):
6411  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6412  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6413 
6414 
6415  def __str__(self):
6416  """__str__(VelocityScalingOptimizerState self) -> std::string"""
6417  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6418 
6419 
6420  def __repr__(self):
6421  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6422  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6423 
6424 
6425  @staticmethod
6426  def get_from(o):
6427  return _object_cast_to_VelocityScalingOptimizerState(o)
6428 
6429 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6430 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6431 
6432 class Fragment(Hierarchy):
6433  """Proxy of C++ IMP::atom::Fragment class."""
6434 
6435  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6436 
6437  def set_residue_indexes(self, o):
6438  """set_residue_indexes(Fragment self, IMP::Ints o)"""
6439  return _IMP_atom.Fragment_set_residue_indexes(self, o)
6440 
6441 
6442  def get_residue_indexes(self):
6443  """get_residue_indexes(Fragment self) -> IMP::Ints"""
6444  return _IMP_atom.Fragment_get_residue_indexes(self)
6445 
6446 
6447  def get_contains_residue(self, rindex):
6448  """get_contains_residue(Fragment self, int rindex) -> bool"""
6449  return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6450 
6451 
6452  def __init__(self, *args):
6453  """
6454  __init__(IMP::atom::Fragment self) -> Fragment
6455  __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6456  __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6457  """
6458  this = _IMP_atom.new_Fragment(*args)
6459  try:
6460  self.this.append(this)
6461  except __builtin__.Exception:
6462  self.this = this
6463 
6464  def get_is_setup(*args):
6465  """
6466  get_is_setup(Model m, ParticleIndex pi) -> bool
6467  get_is_setup(_ParticleAdaptor p) -> bool
6468  """
6469  return _IMP_atom.Fragment_get_is_setup(*args)
6470 
6471  get_is_setup = staticmethod(get_is_setup)
6472 
6473  def show(self, *args):
6474  """
6475  show(Fragment self, _ostream out)
6476  show(Fragment self)
6477  """
6478  return _IMP_atom.Fragment_show(self, *args)
6479 
6480 
6481  def setup_particle(*args):
6482  """
6483  setup_particle(Model m, ParticleIndex pi) -> Fragment
6484  setup_particle(_ParticleAdaptor decorator) -> Fragment
6485  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6486  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6487  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6488  setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6489  """
6490  return _IMP_atom.Fragment_setup_particle(*args)
6491 
6492  setup_particle = staticmethod(setup_particle)
6493 
6494  def add_attribute(self, *args):
6495  """
6496  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6497  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6498  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6499  add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
6500  add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
6501  add_attribute(Fragment self, StringKey a0, IMP::String a1)
6502  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6503  add_attribute(Fragment self, ObjectKey a0, Object a1)
6504  """
6505  return _IMP_atom.Fragment_add_attribute(self, *args)
6506 
6507 
6508  def get_value(self, *args):
6509  """
6510  get_value(Fragment self, FloatKey a0) -> IMP::Float
6511  get_value(Fragment self, IntKey a0) -> IMP::Int
6512  get_value(Fragment self, FloatsKey a0) -> IMP::Floats
6513  get_value(Fragment self, IntsKey a0) -> IMP::Ints
6514  get_value(Fragment self, StringKey a0) -> IMP::String
6515  get_value(Fragment self, ParticleIndexKey a0) -> Particle
6516  get_value(Fragment self, ObjectKey a0) -> Object
6517  """
6518  return _IMP_atom.Fragment_get_value(self, *args)
6519 
6520 
6521  def set_value(self, *args):
6522  """
6523  set_value(Fragment self, FloatKey a0, IMP::Float a1)
6524  set_value(Fragment self, IntKey a0, IMP::Int a1)
6525  set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
6526  set_value(Fragment self, IntsKey a0, IMP::Ints a1)
6527  set_value(Fragment self, StringKey a0, IMP::String a1)
6528  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6529  set_value(Fragment self, ObjectKey a0, Object a1)
6530  """
6531  return _IMP_atom.Fragment_set_value(self, *args)
6532 
6533 
6534  def remove_attribute(self, *args):
6535  """
6536  remove_attribute(Fragment self, FloatKey a0)
6537  remove_attribute(Fragment self, IntKey a0)
6538  remove_attribute(Fragment self, FloatsKey a0)
6539  remove_attribute(Fragment self, IntsKey a0)
6540  remove_attribute(Fragment self, StringKey a0)
6541  remove_attribute(Fragment self, ParticleIndexKey a0)
6542  remove_attribute(Fragment self, ObjectKey a0)
6543  """
6544  return _IMP_atom.Fragment_remove_attribute(self, *args)
6545 
6546 
6547  def has_attribute(self, *args):
6548  """
6549  has_attribute(Fragment self, FloatKey a0) -> bool
6550  has_attribute(Fragment self, IntKey a0) -> bool
6551  has_attribute(Fragment self, FloatsKey a0) -> bool
6552  has_attribute(Fragment self, IntsKey a0) -> bool
6553  has_attribute(Fragment self, StringKey a0) -> bool
6554  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6555  has_attribute(Fragment self, ObjectKey a0) -> bool
6556  """
6557  return _IMP_atom.Fragment_has_attribute(self, *args)
6558 
6559 
6560  def get_derivative(self, a0):
6561  """get_derivative(Fragment self, FloatKey a0) -> double"""
6562  return _IMP_atom.Fragment_get_derivative(self, a0)
6563 
6564 
6565  def get_name(self):
6566  """get_name(Fragment self) -> std::string"""
6567  return _IMP_atom.Fragment_get_name(self)
6568 
6569 
6570  def clear_caches(self):
6571  """clear_caches(Fragment self)"""
6572  return _IMP_atom.Fragment_clear_caches(self)
6573 
6574 
6575  def set_name(self, a0):
6576  """set_name(Fragment self, std::string a0)"""
6577  return _IMP_atom.Fragment_set_name(self, a0)
6578 
6579 
6580  def set_check_level(self, a0):
6581  """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6582  return _IMP_atom.Fragment_set_check_level(self, a0)
6583 
6584 
6585  def add_to_derivative(self, a0, a1, a2):
6586  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6587  return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6588 
6589 
6590  def set_is_optimized(self, a0, a1):
6591  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6592  return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6593 
6594 
6595  def get_is_optimized(self, a0):
6596  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6597  return _IMP_atom.Fragment_get_is_optimized(self, a0)
6598 
6599 
6600  def get_check_level(self):
6601  """get_check_level(Fragment self) -> IMP::CheckLevel"""
6602  return _IMP_atom.Fragment_get_check_level(self)
6603 
6604 
6605  def __eq__(self, *args):
6606  """
6607  __eq__(Fragment self, Fragment o) -> bool
6608  __eq__(Fragment self, Particle d) -> bool
6609  """
6610  return _IMP_atom.Fragment___eq__(self, *args)
6611 
6612 
6613  def __ne__(self, *args):
6614  """
6615  __ne__(Fragment self, Fragment o) -> bool
6616  __ne__(Fragment self, Particle d) -> bool
6617  """
6618  return _IMP_atom.Fragment___ne__(self, *args)
6619 
6620 
6621  def __le__(self, *args):
6622  """
6623  __le__(Fragment self, Fragment o) -> bool
6624  __le__(Fragment self, Particle d) -> bool
6625  """
6626  return _IMP_atom.Fragment___le__(self, *args)
6627 
6628 
6629  def __lt__(self, *args):
6630  """
6631  __lt__(Fragment self, Fragment o) -> bool
6632  __lt__(Fragment self, Particle d) -> bool
6633  """
6634  return _IMP_atom.Fragment___lt__(self, *args)
6635 
6636 
6637  def __ge__(self, *args):
6638  """
6639  __ge__(Fragment self, Fragment o) -> bool
6640  __ge__(Fragment self, Particle d) -> bool
6641  """
6642  return _IMP_atom.Fragment___ge__(self, *args)
6643 
6644 
6645  def __gt__(self, *args):
6646  """
6647  __gt__(Fragment self, Fragment o) -> bool
6648  __gt__(Fragment self, Particle d) -> bool
6649  """
6650  return _IMP_atom.Fragment___gt__(self, *args)
6651 
6652 
6653  def __hash__(self):
6654  """__hash__(Fragment self) -> std::size_t"""
6655  return _IMP_atom.Fragment___hash__(self)
6656 
6657 
6658  def __str__(self):
6659  """__str__(Fragment self) -> std::string"""
6660  return _IMP_atom.Fragment___str__(self)
6661 
6662 
6663  def __repr__(self):
6664  """__repr__(Fragment self) -> std::string"""
6665  return _IMP_atom.Fragment___repr__(self)
6666 
6667  __swig_destroy__ = _IMP_atom.delete_Fragment
6668  __del__ = lambda self: None
6669 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6670 Fragment_swigregister(Fragment)
6671 
6672 def Fragment_get_is_setup(*args):
6673  """
6674  get_is_setup(Model m, ParticleIndex pi) -> bool
6675  Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6676  """
6677  return _IMP_atom.Fragment_get_is_setup(*args)
6678 
6679 def Fragment_setup_particle(*args):
6680  """
6681  setup_particle(Model m, ParticleIndex pi) -> Fragment
6682  setup_particle(_ParticleAdaptor decorator) -> Fragment
6683  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6684  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6685  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6686  Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6687  """
6688  return _IMP_atom.Fragment_setup_particle(*args)
6689 
6690 class StereochemistryPairFilter(IMP.PairPredicate):
6691  """Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6692 
6693  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6694 
6695  def __init__(self):
6696  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6697  this = _IMP_atom.new_StereochemistryPairFilter()
6698  try:
6699  self.this.append(this)
6700  except __builtin__.Exception:
6701  self.this = this
6702 
6703  def set_bonds(self, bonds):
6704  """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6705  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6706 
6707 
6708  def set_angles(self, angles):
6709  """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6710  return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6711 
6712 
6713  def set_dihedrals(self, dihedrals):
6714  """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6715  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6716 
6717 
6718  def do_get_inputs(self, m, pis):
6719  """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6720  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6721 
6722 
6723  def get_value(self, *args):
6724  """
6725  get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6726  get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6727  """
6728  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6729 
6730 
6731  def get_value_index(self, *args):
6732  """
6733  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6734  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6735  """
6736  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6737 
6738 
6739  def get_version_info(self):
6740  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6741  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6742 
6743 
6744  def __str__(self):
6745  """__str__(StereochemistryPairFilter self) -> std::string"""
6746  return _IMP_atom.StereochemistryPairFilter___str__(self)
6747 
6748 
6749  def __repr__(self):
6750  """__repr__(StereochemistryPairFilter self) -> std::string"""
6751  return _IMP_atom.StereochemistryPairFilter___repr__(self)
6752 
6753 
6754  @staticmethod
6755  def get_from(o):
6756  return _object_cast_to_StereochemistryPairFilter(o)
6757 
6758 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6759 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6760 
6761 class SoapPairFilter(IMP.PairPredicate):
6762  """Proxy of C++ IMP::atom::SoapPairFilter class."""
6763 
6764  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6765 
6766  def __init__(self, library):
6767  """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6768  this = _IMP_atom.new_SoapPairFilter(library)
6769  try:
6770  self.this.append(this)
6771  except __builtin__.Exception:
6772  self.this = this
6773 
6774  def do_get_inputs(self, m, pis):
6775  """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6776  return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6777 
6778 
6779  def get_value(self, *args):
6780  """
6781  get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6782  get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6783  """
6784  return _IMP_atom.SoapPairFilter_get_value(self, *args)
6785 
6786 
6787  def get_value_index(self, *args):
6788  """
6789  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6790  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6791  """
6792  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6793 
6794 
6795  def get_version_info(self):
6796  """get_version_info(SoapPairFilter self) -> VersionInfo"""
6797  return _IMP_atom.SoapPairFilter_get_version_info(self)
6798 
6799 
6800  def __str__(self):
6801  """__str__(SoapPairFilter self) -> std::string"""
6802  return _IMP_atom.SoapPairFilter___str__(self)
6803 
6804 
6805  def __repr__(self):
6806  """__repr__(SoapPairFilter self) -> std::string"""
6807  return _IMP_atom.SoapPairFilter___repr__(self)
6808 
6809 
6810  @staticmethod
6811  def get_from(o):
6812  return _object_cast_to_SoapPairFilter(o)
6813 
6814 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6815 SoapPairFilter_swigregister(SoapPairFilter)
6816 
6817 class Mass(IMP.Decorator):
6818  """Proxy of C++ IMP::atom::Mass class."""
6819 
6820  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6821 
6822  def get_mass(self):
6823  """get_mass(Mass self) -> IMP::Float"""
6824  return _IMP_atom.Mass_get_mass(self)
6825 
6826 
6827  def set_mass(self, d):
6828  """set_mass(Mass self, IMP::Float d)"""
6829  return _IMP_atom.Mass_set_mass(self, d)
6830 
6831 
6832  def __init__(self, *args):
6833  """
6834  __init__(IMP::atom::Mass self) -> Mass
6835  __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6836  __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6837  """
6838  this = _IMP_atom.new_Mass(*args)
6839  try:
6840  self.this.append(this)
6841  except __builtin__.Exception:
6842  self.this = this
6843 
6844  def get_is_setup(*args):
6845  """
6846  get_is_setup(Model m, ParticleIndex pi) -> bool
6847  get_is_setup(_ParticleAdaptor p) -> bool
6848  """
6849  return _IMP_atom.Mass_get_is_setup(*args)
6850 
6851  get_is_setup = staticmethod(get_is_setup)
6852 
6853  def show(self, *args):
6854  """
6855  show(Mass self, _ostream out)
6856  show(Mass self)
6857  """
6858  return _IMP_atom.Mass_show(self, *args)
6859 
6860 
6861  def setup_particle(*args):
6862  """
6863  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6864  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6865  setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6866  setup_particle(_ParticleAdaptor decorator, Mass other) -> Mass
6867  """
6868  return _IMP_atom.Mass_setup_particle(*args)
6869 
6870  setup_particle = staticmethod(setup_particle)
6871 
6872  def get_mass_key():
6873  """get_mass_key() -> FloatKey"""
6874  return _IMP_atom.Mass_get_mass_key()
6875 
6876  get_mass_key = staticmethod(get_mass_key)
6877 
6878  def add_attribute(self, *args):
6879  """
6880  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6881  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6882  add_attribute(Mass self, IntKey a0, IMP::Int a1)
6883  add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6884  add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6885  add_attribute(Mass self, StringKey a0, IMP::String a1)
6886  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6887  add_attribute(Mass self, ObjectKey a0, Object a1)
6888  """
6889  return _IMP_atom.Mass_add_attribute(self, *args)
6890 
6891 
6892  def get_value(self, *args):
6893  """
6894  get_value(Mass self, FloatKey a0) -> IMP::Float
6895  get_value(Mass self, IntKey a0) -> IMP::Int
6896  get_value(Mass self, FloatsKey a0) -> IMP::Floats
6897  get_value(Mass self, IntsKey a0) -> IMP::Ints
6898  get_value(Mass self, StringKey a0) -> IMP::String
6899  get_value(Mass self, ParticleIndexKey a0) -> Particle
6900  get_value(Mass self, ObjectKey a0) -> Object
6901  """
6902  return _IMP_atom.Mass_get_value(self, *args)
6903 
6904 
6905  def set_value(self, *args):
6906  """
6907  set_value(Mass self, FloatKey a0, IMP::Float a1)
6908  set_value(Mass self, IntKey a0, IMP::Int a1)
6909  set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6910  set_value(Mass self, IntsKey a0, IMP::Ints a1)
6911  set_value(Mass self, StringKey a0, IMP::String a1)
6912  set_value(Mass self, ParticleIndexKey a0, Particle a1)
6913  set_value(Mass self, ObjectKey a0, Object a1)
6914  """
6915  return _IMP_atom.Mass_set_value(self, *args)
6916 
6917 
6918  def remove_attribute(self, *args):
6919  """
6920  remove_attribute(Mass self, FloatKey a0)
6921  remove_attribute(Mass self, IntKey a0)
6922  remove_attribute(Mass self, FloatsKey a0)
6923  remove_attribute(Mass self, IntsKey a0)
6924  remove_attribute(Mass self, StringKey a0)
6925  remove_attribute(Mass self, ParticleIndexKey a0)
6926  remove_attribute(Mass self, ObjectKey a0)
6927  """
6928  return _IMP_atom.Mass_remove_attribute(self, *args)
6929 
6930 
6931  def has_attribute(self, *args):
6932  """
6933  has_attribute(Mass self, FloatKey a0) -> bool
6934  has_attribute(Mass self, IntKey a0) -> bool
6935  has_attribute(Mass self, FloatsKey a0) -> bool
6936  has_attribute(Mass self, IntsKey a0) -> bool
6937  has_attribute(Mass self, StringKey a0) -> bool
6938  has_attribute(Mass self, ParticleIndexKey a0) -> bool
6939  has_attribute(Mass self, ObjectKey a0) -> bool
6940  """
6941  return _IMP_atom.Mass_has_attribute(self, *args)
6942 
6943 
6944  def get_derivative(self, a0):
6945  """get_derivative(Mass self, FloatKey a0) -> double"""
6946  return _IMP_atom.Mass_get_derivative(self, a0)
6947 
6948 
6949  def get_name(self):
6950  """get_name(Mass self) -> std::string"""
6951  return _IMP_atom.Mass_get_name(self)
6952 
6953 
6954  def clear_caches(self):
6955  """clear_caches(Mass self)"""
6956  return _IMP_atom.Mass_clear_caches(self)
6957 
6958 
6959  def set_name(self, a0):
6960  """set_name(Mass self, std::string a0)"""
6961  return _IMP_atom.Mass_set_name(self, a0)
6962 
6963 
6964  def set_check_level(self, a0):
6965  """set_check_level(Mass self, IMP::CheckLevel a0)"""
6966  return _IMP_atom.Mass_set_check_level(self, a0)
6967 
6968 
6969  def add_to_derivative(self, a0, a1, a2):
6970  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6971  return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6972 
6973 
6974  def set_is_optimized(self, a0, a1):
6975  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6976  return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6977 
6978 
6979  def get_is_optimized(self, a0):
6980  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6981  return _IMP_atom.Mass_get_is_optimized(self, a0)
6982 
6983 
6984  def get_check_level(self):
6985  """get_check_level(Mass self) -> IMP::CheckLevel"""
6986  return _IMP_atom.Mass_get_check_level(self)
6987 
6988 
6989  def __eq__(self, *args):
6990  """
6991  __eq__(Mass self, Mass o) -> bool
6992  __eq__(Mass self, Particle d) -> bool
6993  """
6994  return _IMP_atom.Mass___eq__(self, *args)
6995 
6996 
6997  def __ne__(self, *args):
6998  """
6999  __ne__(Mass self, Mass o) -> bool
7000  __ne__(Mass self, Particle d) -> bool
7001  """
7002  return _IMP_atom.Mass___ne__(self, *args)
7003 
7004 
7005  def __le__(self, *args):
7006  """
7007  __le__(Mass self, Mass o) -> bool
7008  __le__(Mass self, Particle d) -> bool
7009  """
7010  return _IMP_atom.Mass___le__(self, *args)
7011 
7012 
7013  def __lt__(self, *args):
7014  """
7015  __lt__(Mass self, Mass o) -> bool
7016  __lt__(Mass self, Particle d) -> bool
7017  """
7018  return _IMP_atom.Mass___lt__(self, *args)
7019 
7020 
7021  def __ge__(self, *args):
7022  """
7023  __ge__(Mass self, Mass o) -> bool
7024  __ge__(Mass self, Particle d) -> bool
7025  """
7026  return _IMP_atom.Mass___ge__(self, *args)
7027 
7028 
7029  def __gt__(self, *args):
7030  """
7031  __gt__(Mass self, Mass o) -> bool
7032  __gt__(Mass self, Particle d) -> bool
7033  """
7034  return _IMP_atom.Mass___gt__(self, *args)
7035 
7036 
7037  def __hash__(self):
7038  """__hash__(Mass self) -> std::size_t"""
7039  return _IMP_atom.Mass___hash__(self)
7040 
7041 
7042  def __str__(self):
7043  """__str__(Mass self) -> std::string"""
7044  return _IMP_atom.Mass___str__(self)
7045 
7046 
7047  def __repr__(self):
7048  """__repr__(Mass self) -> std::string"""
7049  return _IMP_atom.Mass___repr__(self)
7050 
7051  __swig_destroy__ = _IMP_atom.delete_Mass
7052  __del__ = lambda self: None
7053 Mass_swigregister = _IMP_atom.Mass_swigregister
7054 Mass_swigregister(Mass)
7055 
7056 def Mass_get_is_setup(*args):
7057  """
7058  get_is_setup(Model m, ParticleIndex pi) -> bool
7059  Mass_get_is_setup(_ParticleAdaptor p) -> bool
7060  """
7061  return _IMP_atom.Mass_get_is_setup(*args)
7062 
7063 def Mass_setup_particle(*args):
7064  """
7065  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
7066  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
7067  setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
7068  Mass_setup_particle(_ParticleAdaptor decorator, Mass other) -> Mass
7069  """
7070  return _IMP_atom.Mass_setup_particle(*args)
7071 
7072 def Mass_get_mass_key():
7073  """Mass_get_mass_key() -> FloatKey"""
7074  return _IMP_atom.Mass_get_mass_key()
7075 
7076 class BondedPairFilter(IMP.PairPredicate):
7077  """Proxy of C++ IMP::atom::BondedPairFilter class."""
7078 
7079  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7080 
7081  def __init__(self):
7082  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
7083  this = _IMP_atom.new_BondedPairFilter()
7084  try:
7085  self.this.append(this)
7086  except __builtin__.Exception:
7087  self.this = this
7088 
7089  def do_get_inputs(self, m, pis):
7090  """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7091  return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
7092 
7093 
7094  def get_value(self, *args):
7095  """
7096  get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
7097  get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
7098  """
7099  return _IMP_atom.BondedPairFilter_get_value(self, *args)
7100 
7101 
7102  def get_value_index(self, *args):
7103  """
7104  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
7105  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
7106  """
7107  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
7108 
7109 
7110  def get_version_info(self):
7111  """get_version_info(BondedPairFilter self) -> VersionInfo"""
7112  return _IMP_atom.BondedPairFilter_get_version_info(self)
7113 
7114 
7115  def __str__(self):
7116  """__str__(BondedPairFilter self) -> std::string"""
7117  return _IMP_atom.BondedPairFilter___str__(self)
7118 
7119 
7120  def __repr__(self):
7121  """__repr__(BondedPairFilter self) -> std::string"""
7122  return _IMP_atom.BondedPairFilter___repr__(self)
7123 
7124 
7125  @staticmethod
7126  def get_from(o):
7127  return _object_cast_to_BondedPairFilter(o)
7128 
7129 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
7130 BondedPairFilter_swigregister(BondedPairFilter)
7131 
7132 class Mol2Selector(IMP.Object):
7133  """Proxy of C++ IMP::atom::Mol2Selector class."""
7134 
7135  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7136 
7137  def __init__(self, *args, **kwargs):
7138  raise AttributeError("No constructor defined - class is abstract")
7139 
7140  def get_is_selected(self, atom_line):
7141  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
7142  return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
7143 
7144  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
7145  __del__ = lambda self: None
7146 
7147  def __str__(self):
7148  """__str__(Mol2Selector self) -> std::string"""
7149  return _IMP_atom.Mol2Selector___str__(self)
7150 
7151 
7152  def __repr__(self):
7153  """__repr__(Mol2Selector self) -> std::string"""
7154  return _IMP_atom.Mol2Selector___repr__(self)
7155 
7156 
7157  @staticmethod
7158  def get_from(o):
7159  return _object_cast_to_Mol2Selector(o)
7160 
7161 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
7162 Mol2Selector_swigregister(Mol2Selector)
7163 
7164 class AllMol2Selector(Mol2Selector):
7165  """Proxy of C++ IMP::atom::AllMol2Selector class."""
7166 
7167  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7168 
7169  def __str__(self):
7170  """__str__(AllMol2Selector self) -> std::string"""
7171  return _IMP_atom.AllMol2Selector___str__(self)
7172 
7173 
7174  def __repr__(self):
7175  """__repr__(AllMol2Selector self) -> std::string"""
7176  return _IMP_atom.AllMol2Selector___repr__(self)
7177 
7178 
7179  @staticmethod
7180  def get_from(o):
7181  return _object_cast_to_AllMol2Selector(o)
7182 
7183 
7184  def __init__(self):
7185  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
7186  this = _IMP_atom.new_AllMol2Selector()
7187  try:
7188  self.this.append(this)
7189  except __builtin__.Exception:
7190  self.this = this
7191  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
7192  __del__ = lambda self: None
7193 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
7194 AllMol2Selector_swigregister(AllMol2Selector)
7195 
7196 class NonHydrogenMol2Selector(Mol2Selector):
7197  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
7198 
7199  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7200 
7201  def __str__(self):
7202  """__str__(NonHydrogenMol2Selector self) -> std::string"""
7203  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
7204 
7205 
7206  def __repr__(self):
7207  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
7208  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
7209 
7210 
7211  @staticmethod
7212  def get_from(o):
7213  return _object_cast_to_NonHydrogenMol2Selector(o)
7214 
7215 
7216  def __init__(self):
7217  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
7218  this = _IMP_atom.new_NonHydrogenMol2Selector()
7219  try:
7220  self.this.append(this)
7221  except __builtin__.Exception:
7222  self.this = this
7223  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
7224  __del__ = lambda self: None
7225 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
7226 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7227 
7228 
7229 def read_mol2(mol2_file, model, mol2sel=None):
7230  """
7231  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7232  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7233  """
7234  return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7235 
7236 def write_mol2(rhd, file_name):
7237  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7238  return _IMP_atom.write_mol2(rhd, file_name)
7239 class SecondaryStructureResidue(IMP.Decorator):
7240  """Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
7241 
7242  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7243 
7244  def __init__(self, *args):
7245  """
7246  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7247  __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7248  __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7249  """
7250  this = _IMP_atom.new_SecondaryStructureResidue(*args)
7251  try:
7252  self.this.append(this)
7253  except __builtin__.Exception:
7254  self.this = this
7255 
7256  def show(self, *args):
7257  """
7258  show(SecondaryStructureResidue self, _ostream out)
7259  show(SecondaryStructureResidue self)
7260  """
7261  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7262 
7263 
7264  def setup_particle(*args):
7265  """
7266  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7267  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7268  setup_particle(Particle res_p) -> SecondaryStructureResidue
7269  """
7270  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7271 
7272  setup_particle = staticmethod(setup_particle)
7273 
7274  def get_is_setup(*args):
7275  """
7276  get_is_setup(_ParticleAdaptor p) -> bool
7277  get_is_setup(Model m, ParticleIndex pi) -> bool
7278  """
7279  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7280 
7281  get_is_setup = staticmethod(get_is_setup)
7282 
7283  def get_particle(self):
7284  """get_particle(SecondaryStructureResidue self) -> Particle"""
7285  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7286 
7287 
7288  def get_all_probabilities(self):
7289  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7290  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7291 
7292 
7293  def get_prob_helix(self):
7294  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7295  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7296 
7297 
7298  def set_prob_helix(self, t):
7299  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7300  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7301 
7302 
7303  def get_prob_strand(self):
7304  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7305  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7306 
7307 
7308  def set_prob_strand(self, t):
7309  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7310  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7311 
7312 
7313  def get_prob_coil(self):
7314  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7315  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7316 
7317 
7318  def set_prob_coil(self, t):
7319  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7320  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7321 
7322 
7323  def get_prob_helix_key():
7324  """get_prob_helix_key() -> FloatKey"""
7325  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7326 
7327  get_prob_helix_key = staticmethod(get_prob_helix_key)
7328 
7329  def get_prob_strand_key():
7330  """get_prob_strand_key() -> FloatKey"""
7331  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7332 
7333  get_prob_strand_key = staticmethod(get_prob_strand_key)
7334 
7335  def get_prob_coil_key():
7336  """get_prob_coil_key() -> FloatKey"""
7337  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7338 
7339  get_prob_coil_key = staticmethod(get_prob_coil_key)
7340 
7341  def add_attribute(self, *args):
7342  """
7343  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7344  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7345  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7346  add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7347  add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7348  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7349  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7350  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7351  """
7352  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7353 
7354 
7355  def get_value(self, *args):
7356  """
7357  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7358  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7359  get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
7360  get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
7361  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7362  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7363  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7364  """
7365  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7366 
7367 
7368  def set_value(self, *args):
7369  """
7370  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7371  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7372  set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7373  set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7374  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7375  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7376  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7377  """
7378  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7379 
7380 
7381  def remove_attribute(self, *args):
7382  """
7383  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7384  remove_attribute(SecondaryStructureResidue self, IntKey a0)
7385  remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
7386  remove_attribute(SecondaryStructureResidue self, IntsKey a0)
7387  remove_attribute(SecondaryStructureResidue self, StringKey a0)
7388  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7389  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7390  """
7391  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7392 
7393 
7394  def has_attribute(self, *args):
7395  """
7396  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7397  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7398  has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
7399  has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
7400  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7401  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7402  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7403  """
7404  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7405 
7406 
7407  def get_derivative(self, a0):
7408  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7409  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7410 
7411 
7412  def get_name(self):
7413  """get_name(SecondaryStructureResidue self) -> std::string"""
7414  return _IMP_atom.SecondaryStructureResidue_get_name(self)
7415 
7416 
7417  def clear_caches(self):
7418  """clear_caches(SecondaryStructureResidue self)"""
7419  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7420 
7421 
7422  def set_name(self, a0):
7423  """set_name(SecondaryStructureResidue self, std::string a0)"""
7424  return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7425 
7426 
7427  def set_check_level(self, a0):
7428  """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7429  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7430 
7431 
7432  def add_to_derivative(self, a0, a1, a2):
7433  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7434  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7435 
7436 
7437  def set_is_optimized(self, a0, a1):
7438  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7439  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7440 
7441 
7442  def get_is_optimized(self, a0):
7443  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7444  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7445 
7446 
7447  def get_check_level(self):
7448  """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7449  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7450 
7451 
7452  def __eq__(self, *args):
7453  """
7454  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7455  __eq__(SecondaryStructureResidue self, Particle d) -> bool
7456  """
7457  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7458 
7459 
7460  def __ne__(self, *args):
7461  """
7462  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7463  __ne__(SecondaryStructureResidue self, Particle d) -> bool
7464  """
7465  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7466 
7467 
7468  def __le__(self, *args):
7469  """
7470  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7471  __le__(SecondaryStructureResidue self, Particle d) -> bool
7472  """
7473  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7474 
7475 
7476  def __lt__(self, *args):
7477  """
7478  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7479  __lt__(SecondaryStructureResidue self, Particle d) -> bool
7480  """
7481  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7482 
7483 
7484  def __ge__(self, *args):
7485  """
7486  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7487  __ge__(SecondaryStructureResidue self, Particle d) -> bool
7488  """
7489  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7490 
7491 
7492  def __gt__(self, *args):
7493  """
7494  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7495  __gt__(SecondaryStructureResidue self, Particle d) -> bool
7496  """
7497  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7498 
7499 
7500  def __hash__(self):
7501  """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7502  return _IMP_atom.SecondaryStructureResidue___hash__(self)
7503 
7504 
7505  def __str__(self):
7506  """__str__(SecondaryStructureResidue self) -> std::string"""
7507  return _IMP_atom.SecondaryStructureResidue___str__(self)
7508 
7509 
7510  def __repr__(self):
7511  """__repr__(SecondaryStructureResidue self) -> std::string"""
7512  return _IMP_atom.SecondaryStructureResidue___repr__(self)
7513 
7514  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7515  __del__ = lambda self: None
7516 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7517 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7518 
7519 def SecondaryStructureResidue_setup_particle(*args):
7520  """
7521  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7522  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7523  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7524  """
7525  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7526 
7527 def SecondaryStructureResidue_get_is_setup(*args):
7528  """
7529  get_is_setup(_ParticleAdaptor p) -> bool
7530  SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7531  """
7532  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7533 
7534 def SecondaryStructureResidue_get_prob_helix_key():
7535  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7536  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7537 
7538 def SecondaryStructureResidue_get_prob_strand_key():
7539  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7540  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7541 
7542 def SecondaryStructureResidue_get_prob_coil_key():
7543  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7544  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7545 
7546 
7547 def setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res=False):
7548  """
7549  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7550  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7551  """
7552  return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7553 
7554 def setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res=False):
7555  """
7556  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
7557  setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7558  """
7559  return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7560 
7561 def get_secondary_structure_match_score(ssr1, ssr2):
7562  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7563  return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7564 
7565 def read_psipred(*args):
7566  """
7567  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7568  read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7569  """
7570  return _IMP_atom.read_psipred(*args)
7571 class _ADopeBase(IMP.PairScore):
7572  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class."""
7573 
7574  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7575  __repr__ = _swig_repr
7576 
7577  def __init__(self, *args):
7578  """
7579  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7580  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7581  """
7582  this = _IMP_atom.new__ADopeBase(*args)
7583  try:
7584  self.this.append(this)
7585  except __builtin__.Exception:
7586  self.this = this
7587 
7588  def do_get_inputs(self, m, pis):
7589  """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7590  return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7591 
7592 
7593  def get_score_functor(self):
7594  """get_score_functor(_ADopeBase self) -> Dope"""
7595  return _IMP_atom._ADopeBase_get_score_functor(self)
7596 
7597 
7598  def get_version_info(self):
7599  """get_version_info(_ADopeBase self) -> VersionInfo"""
7600  return _IMP_atom._ADopeBase_get_version_info(self)
7601 
7602 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7603 _ADopeBase_swigregister(_ADopeBase)
7604 
7605 class _BDopeBase(IMP.PairScore):
7606  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class."""
7607 
7608  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7609  __repr__ = _swig_repr
7610 
7611  def __init__(self, *args):
7612  """
7613  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BDopeBase
7614  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0) -> _BDopeBase
7615  """
7616  this = _IMP_atom.new__BDopeBase(*args)
7617  try:
7618  self.this.append(this)
7619  except __builtin__.Exception:
7620  self.this = this
7621 
7622  def do_get_inputs(self, m, pis):
7623  """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7624  return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7625 
7626 
7627  def get_score_functor(self):
7628  """get_score_functor(_BDopeBase self) -> _DopeBase"""
7629  return _IMP_atom._BDopeBase_get_score_functor(self)
7630 
7631 
7632  def get_version_info(self):
7633  """get_version_info(_BDopeBase self) -> VersionInfo"""
7634  return _IMP_atom._BDopeBase_get_version_info(self)
7635 
7636 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7637 _BDopeBase_swigregister(_BDopeBase)
7638 
7639 class _ALoopStatisticalBase(IMP.PairScore):
7640  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> class."""
7641 
7642  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7643  __repr__ = _swig_repr
7644 
7645  def __init__(self, *args):
7646  """
7647  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> self, LoopStatistical t0, std::string name) -> _ALoopStatisticalBase
7648  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> self, LoopStatistical t0) -> _ALoopStatisticalBase
7649  """
7650  this = _IMP_atom.new__ALoopStatisticalBase(*args)
7651  try:
7652  self.this.append(this)
7653  except __builtin__.Exception:
7654  self.this = this
7655 
7656  def do_get_inputs(self, m, pis):
7657  """do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7658  return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
7659 
7660 
7661  def get_score_functor(self):
7662  """get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
7663  return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
7664 
7665 
7666  def get_version_info(self):
7667  """get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
7668  return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
7669 
7670 _ALoopStatisticalBase_swigregister = _IMP_atom._ALoopStatisticalBase_swigregister
7671 _ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
7672 
7673 class _BLoopStatisticalBase(IMP.PairScore):
7674  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> class."""
7675 
7676  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7677  __repr__ = _swig_repr
7678 
7679  def __init__(self, *args):
7680  """
7681  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BLoopStatisticalBase
7682  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0) -> _BLoopStatisticalBase
7683  """
7684  this = _IMP_atom.new__BLoopStatisticalBase(*args)
7685  try:
7686  self.this.append(this)
7687  except __builtin__.Exception:
7688  self.this = this
7689 
7690  def do_get_inputs(self, m, pis):
7691  """do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7692  return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
7693 
7694 
7695  def get_score_functor(self):
7696  """get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
7697  return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
7698 
7699 
7700  def get_version_info(self):
7701  """get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
7702  return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
7703 
7704 _BLoopStatisticalBase_swigregister = _IMP_atom._BLoopStatisticalBase_swigregister
7705 _BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
7706 
7707 class _OrientedSoapBase(IMP.PairScore):
7708  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class."""
7709 
7710  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7711  __repr__ = _swig_repr
7712 
7713  def __init__(self, *args):
7714  """
7715  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name) -> _OrientedSoapBase
7716  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7717  """
7718  this = _IMP_atom.new__OrientedSoapBase(*args)
7719  try:
7720  self.this.append(this)
7721  except __builtin__.Exception:
7722  self.this = this
7723 
7724  def do_get_inputs(self, m, pis):
7725  """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7726  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7727 
7728 
7729  def get_score_functor(self):
7730  """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7731  return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7732 
7733 
7734  def get_version_info(self):
7735  """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7736  return _IMP_atom._OrientedSoapBase_get_version_info(self)
7737 
7738 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7739 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7740 
7741 class _SPSFTB(IMP.PairScore):
7742  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class."""
7743 
7744  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7745  __repr__ = _swig_repr
7746 
7747  def __init__(self, *args):
7748  """
7749  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name) -> _SPSFTB
7750  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0) -> _SPSFTB
7751  """
7752  this = _IMP_atom.new__SPSFTB(*args)
7753  try:
7754  self.this.append(this)
7755  except __builtin__.Exception:
7756  self.this = this
7757 
7758  def do_get_inputs(self, m, pis):
7759  """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7760  return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7761 
7762 
7763  def get_score_functor(self):
7764  """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7765  return _IMP_atom._SPSFTB_get_score_functor(self)
7766 
7767 
7768  def get_version_info(self):
7769  """get_version_info(_SPSFTB self) -> VersionInfo"""
7770  return _IMP_atom._SPSFTB_get_version_info(self)
7771 
7772 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7773 _SPSFTB_swigregister(_SPSFTB)
7774 
7775 class _SPSTF(_SPSFTB):
7776  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class."""
7777 
7778  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7779  __repr__ = _swig_repr
7780 
7781  def __init__(self, *args):
7782  """
7783  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7784  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7785  """
7786  this = _IMP_atom.new__SPSTF(*args)
7787  try:
7788  self.this.append(this)
7789  except __builtin__.Exception:
7790  self.this = this
7791  __swig_destroy__ = _IMP_atom.delete__SPSTF
7792  __del__ = lambda self: None
7793 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7794 _SPSTF_swigregister(_SPSTF)
7795 
7796 class _SPSFT(_BDopeBase):
7797  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class."""
7798 
7799  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7800  __repr__ = _swig_repr
7801 
7802  def __init__(self, *args):
7803  """
7804  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7805  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7806  """
7807  this = _IMP_atom.new__SPSFT(*args)
7808  try:
7809  self.this.append(this)
7810  except __builtin__.Exception:
7811  self.this = this
7812  __swig_destroy__ = _IMP_atom.delete__SPSFT
7813  __del__ = lambda self: None
7814 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7815 _SPSFT_swigregister(_SPSFT)
7816 
7817 class _SPSFTL(_BLoopStatisticalBase):
7818  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> class."""
7819 
7820  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7821  __repr__ = _swig_repr
7822 
7823  def __init__(self, *args):
7824  """
7825  __init__(IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7826  __init__(IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7827  """
7828  this = _IMP_atom.new__SPSFTL(*args)
7829  try:
7830  self.this.append(this)
7831  except __builtin__.Exception:
7832  self.this = this
7833  __swig_destroy__ = _IMP_atom.delete__SPSFTL
7834  __del__ = lambda self: None
7835 _SPSFTL_swigregister = _IMP_atom._SPSFTL_swigregister
7836 _SPSFTL_swigregister(_SPSFTL)
7837 
7838 class ProteinLigandAtomPairScore(_SPSTF):
7839  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7840 
7841  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7842 
7843  def __init__(self, *args):
7844  """
7845  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7846  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7847  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7848  """
7849  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7850  try:
7851  self.this.append(this)
7852  except __builtin__.Exception:
7853  self.this = this
7854 
7855  def get_maximum_distance(self):
7856  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7857  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7858 
7859 
7860  def __str__(self):
7861  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7862  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7863 
7864 
7865  def __repr__(self):
7866  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7867  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7868 
7869 
7870  @staticmethod
7871  def get_from(o):
7872  return _object_cast_to_ProteinLigandAtomPairScore(o)
7873 
7874  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7875  __del__ = lambda self: None
7876 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7877 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7878 
7879 class ProteinLigandRestraint(IMP.container.PairsRestraint):
7880  """Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7881 
7882  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7883 
7884  def __init__(self, *args):
7885  """
7886  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7887  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7888  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7889  """
7890  this = _IMP_atom.new_ProteinLigandRestraint(*args)
7891  try:
7892  self.this.append(this)
7893  except __builtin__.Exception:
7894  self.this = this
7895 
7896  def __str__(self):
7897  """__str__(ProteinLigandRestraint self) -> std::string"""
7898  return _IMP_atom.ProteinLigandRestraint___str__(self)
7899 
7900 
7901  def __repr__(self):
7902  """__repr__(ProteinLigandRestraint self) -> std::string"""
7903  return _IMP_atom.ProteinLigandRestraint___repr__(self)
7904 
7905 
7906  @staticmethod
7907  def get_from(o):
7908  return _object_cast_to_ProteinLigandRestraint(o)
7909 
7910  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7911  __del__ = lambda self: None
7912 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7913 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7914 
7915 
7917  """add_protein_ligand_score_data(Hierarchy h)"""
7918  return _IMP_atom.add_protein_ligand_score_data(h)
7919 class AtomType(IMP._Value):
7920  """Proxy of C++ IMP::Key<(8974343)> class."""
7921 
7922  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7923 
7924  def __init__(self, *args):
7925  """
7926  __init__(IMP::Key<(8974343)> self) -> AtomType
7927  __init__(IMP::Key<(8974343)> self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7928  __init__(IMP::Key<(8974343)> self, std::string const & c) -> AtomType
7929  __init__(IMP::Key<(8974343)> self, unsigned int i) -> AtomType
7930  """
7931  this = _IMP_atom.new_AtomType(*args)
7932  try:
7933  self.this.append(this)
7934  except __builtin__.Exception:
7935  self.this = this
7936 
7937  def add_key(sc):
7938  """add_key(std::string sc) -> unsigned int"""
7939  return _IMP_atom.AtomType_add_key(sc)
7940 
7941  add_key = staticmethod(add_key)
7942 
7943  def get_key_exists(sc):
7944  """get_key_exists(std::string sc) -> bool"""
7945  return _IMP_atom.AtomType_get_key_exists(sc)
7946 
7947  get_key_exists = staticmethod(get_key_exists)
7948 
7949  def get_string(self):
7950  """get_string(AtomType self) -> std::string const"""
7951  return _IMP_atom.AtomType_get_string(self)
7952 
7953 
7954  def __cmp__(self, o):
7955  """__cmp__(AtomType self, AtomType o) -> int"""
7956  return _IMP_atom.AtomType___cmp__(self, o)
7957 
7958 
7959  def __eq__(self, o):
7960  """__eq__(AtomType self, AtomType o) -> bool"""
7961  return _IMP_atom.AtomType___eq__(self, o)
7962 
7963 
7964  def __ne__(self, o):
7965  """__ne__(AtomType self, AtomType o) -> bool"""
7966  return _IMP_atom.AtomType___ne__(self, o)
7967 
7968 
7969  def __lt__(self, o):
7970  """__lt__(AtomType self, AtomType o) -> bool"""
7971  return _IMP_atom.AtomType___lt__(self, o)
7972 
7973 
7974  def __gt__(self, o):
7975  """__gt__(AtomType self, AtomType o) -> bool"""
7976  return _IMP_atom.AtomType___gt__(self, o)
7977 
7978 
7979  def __ge__(self, o):
7980  """__ge__(AtomType self, AtomType o) -> bool"""
7981  return _IMP_atom.AtomType___ge__(self, o)
7982 
7983 
7984  def __le__(self, o):
7985  """__le__(AtomType self, AtomType o) -> bool"""
7986  return _IMP_atom.AtomType___le__(self, o)
7987 
7988 
7989  def __hash__(self):
7990  """__hash__(AtomType self) -> std::size_t"""
7991  return _IMP_atom.AtomType___hash__(self)
7992 
7993 
7994  def show(self, *args):
7995  """
7996  show(AtomType self, _ostream out)
7997  show(AtomType self)
7998  """
7999  return _IMP_atom.AtomType_show(self, *args)
8000 
8001 
8002  def add_alias(old_key, new_name):
8003  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
8004  return _IMP_atom.AtomType_add_alias(old_key, new_name)
8005 
8006  add_alias = staticmethod(add_alias)
8007 
8008  def get_number_of_keys():
8009  """get_number_of_keys() -> unsigned int"""
8010  return _IMP_atom.AtomType_get_number_of_keys()
8011 
8012  get_number_of_keys = staticmethod(get_number_of_keys)
8013 
8014  def get_index(self):
8015  """get_index(AtomType self) -> unsigned int"""
8016  return _IMP_atom.AtomType_get_index(self)
8017 
8018 
8019  def show_all(out):
8020  """show_all(_ostream out)"""
8021  return _IMP_atom.AtomType_show_all(out)
8022 
8023  show_all = staticmethod(show_all)
8024 
8025  def get_all_strings():
8026  """get_all_strings() -> IMP::Vector< std::string >"""
8027  return _IMP_atom.AtomType_get_all_strings()
8028 
8029  get_all_strings = staticmethod(get_all_strings)
8030 
8031  def get_number_unique():
8032  """get_number_unique() -> unsigned int"""
8033  return _IMP_atom.AtomType_get_number_unique()
8034 
8035  get_number_unique = staticmethod(get_number_unique)
8036 
8037  def __str__(self):
8038  """__str__(AtomType self) -> std::string"""
8039  return _IMP_atom.AtomType___str__(self)
8040 
8041 
8042  def __repr__(self):
8043  """__repr__(AtomType self) -> std::string"""
8044  return _IMP_atom.AtomType___repr__(self)
8045 
8046  __swig_destroy__ = _IMP_atom.delete_AtomType
8047  __del__ = lambda self: None
8048 AtomType_swigregister = _IMP_atom.AtomType_swigregister
8049 AtomType_swigregister(AtomType)
8050 
8051 def AtomType_add_key(sc):
8052  """AtomType_add_key(std::string sc) -> unsigned int"""
8053  return _IMP_atom.AtomType_add_key(sc)
8054 
8055 def AtomType_get_key_exists(sc):
8056  """AtomType_get_key_exists(std::string sc) -> bool"""
8057  return _IMP_atom.AtomType_get_key_exists(sc)
8058 
8059 def AtomType_add_alias(old_key, new_name):
8060  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
8061  return _IMP_atom.AtomType_add_alias(old_key, new_name)
8062 
8063 def AtomType_get_number_of_keys():
8064  """AtomType_get_number_of_keys() -> unsigned int"""
8065  return _IMP_atom.AtomType_get_number_of_keys()
8066 
8067 def AtomType_show_all(out):
8068  """AtomType_show_all(_ostream out)"""
8069  return _IMP_atom.AtomType_show_all(out)
8070 
8071 def AtomType_get_all_strings():
8072  """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
8073  return _IMP_atom.AtomType_get_all_strings()
8074 
8075 def AtomType_get_number_unique():
8076  """AtomType_get_number_unique() -> unsigned int"""
8077  return _IMP_atom.AtomType_get_number_unique()
8078 
8079 class ResidueType(IMP._Value):
8080  """Proxy of C++ IMP::Key<(90784334)> class."""
8081 
8082  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8083 
8084  def __init__(self, *args):
8085  """
8086  __init__(IMP::Key<(90784334)> self) -> ResidueType
8087  __init__(IMP::Key<(90784334)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
8088  __init__(IMP::Key<(90784334)> self, std::string const & c) -> ResidueType
8089  __init__(IMP::Key<(90784334)> self, unsigned int i) -> ResidueType
8090  """
8091  this = _IMP_atom.new_ResidueType(*args)
8092  try:
8093  self.this.append(this)
8094  except __builtin__.Exception:
8095  self.this = this
8096 
8097  def add_key(sc):
8098  """add_key(std::string sc) -> unsigned int"""
8099  return _IMP_atom.ResidueType_add_key(sc)
8100 
8101  add_key = staticmethod(add_key)
8102 
8103  def get_key_exists(sc):
8104  """get_key_exists(std::string sc) -> bool"""
8105  return _IMP_atom.ResidueType_get_key_exists(sc)
8106 
8107  get_key_exists = staticmethod(get_key_exists)
8108 
8109  def get_string(self):
8110  """get_string(ResidueType self) -> std::string const"""
8111  return _IMP_atom.ResidueType_get_string(self)
8112 
8113 
8114  def __cmp__(self, o):
8115  """__cmp__(ResidueType self, ResidueType o) -> int"""
8116  return _IMP_atom.ResidueType___cmp__(self, o)
8117 
8118 
8119  def __eq__(self, o):
8120  """__eq__(ResidueType self, ResidueType o) -> bool"""
8121  return _IMP_atom.ResidueType___eq__(self, o)
8122 
8123 
8124  def __ne__(self, o):
8125  """__ne__(ResidueType self, ResidueType o) -> bool"""
8126  return _IMP_atom.ResidueType___ne__(self, o)
8127 
8128 
8129  def __lt__(self, o):
8130  """__lt__(ResidueType self, ResidueType o) -> bool"""
8131  return _IMP_atom.ResidueType___lt__(self, o)
8132 
8133 
8134  def __gt__(self, o):
8135  """__gt__(ResidueType self, ResidueType o) -> bool"""
8136  return _IMP_atom.ResidueType___gt__(self, o)
8137 
8138 
8139  def __ge__(self, o):
8140  """__ge__(ResidueType self, ResidueType o) -> bool"""
8141  return _IMP_atom.ResidueType___ge__(self, o)
8142 
8143 
8144  def __le__(self, o):
8145  """__le__(ResidueType self, ResidueType o) -> bool"""
8146  return _IMP_atom.ResidueType___le__(self, o)
8147 
8148 
8149  def __hash__(self):
8150  """__hash__(ResidueType self) -> std::size_t"""
8151  return _IMP_atom.ResidueType___hash__(self)
8152 
8153 
8154  def show(self, *args):
8155  """
8156  show(ResidueType self, _ostream out)
8157  show(ResidueType self)
8158  """
8159  return _IMP_atom.ResidueType_show(self, *args)
8160 
8161 
8162  def add_alias(old_key, new_name):
8163  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8164  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8165 
8166  add_alias = staticmethod(add_alias)
8167 
8168  def get_number_of_keys():
8169  """get_number_of_keys() -> unsigned int"""
8170  return _IMP_atom.ResidueType_get_number_of_keys()
8171 
8172  get_number_of_keys = staticmethod(get_number_of_keys)
8173 
8174  def get_index(self):
8175  """get_index(ResidueType self) -> unsigned int"""
8176  return _IMP_atom.ResidueType_get_index(self)
8177 
8178 
8179  def show_all(out):
8180  """show_all(_ostream out)"""
8181  return _IMP_atom.ResidueType_show_all(out)
8182 
8183  show_all = staticmethod(show_all)
8184 
8185  def get_all_strings():
8186  """get_all_strings() -> IMP::Vector< std::string >"""
8187  return _IMP_atom.ResidueType_get_all_strings()
8188 
8189  get_all_strings = staticmethod(get_all_strings)
8190 
8191  def get_number_unique():
8192  """get_number_unique() -> unsigned int"""
8193  return _IMP_atom.ResidueType_get_number_unique()
8194 
8195  get_number_unique = staticmethod(get_number_unique)
8196 
8197  def __str__(self):
8198  """__str__(ResidueType self) -> std::string"""
8199  return _IMP_atom.ResidueType___str__(self)
8200 
8201 
8202  def __repr__(self):
8203  """__repr__(ResidueType self) -> std::string"""
8204  return _IMP_atom.ResidueType___repr__(self)
8205 
8206  __swig_destroy__ = _IMP_atom.delete_ResidueType
8207  __del__ = lambda self: None
8208 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
8209 ResidueType_swigregister(ResidueType)
8210 
8211 def ResidueType_add_key(sc):
8212  """ResidueType_add_key(std::string sc) -> unsigned int"""
8213  return _IMP_atom.ResidueType_add_key(sc)
8214 
8215 def ResidueType_get_key_exists(sc):
8216  """ResidueType_get_key_exists(std::string sc) -> bool"""
8217  return _IMP_atom.ResidueType_get_key_exists(sc)
8218 
8219 def ResidueType_add_alias(old_key, new_name):
8220  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8221  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8222 
8223 def ResidueType_get_number_of_keys():
8224  """ResidueType_get_number_of_keys() -> unsigned int"""
8225  return _IMP_atom.ResidueType_get_number_of_keys()
8226 
8227 def ResidueType_show_all(out):
8228  """ResidueType_show_all(_ostream out)"""
8229  return _IMP_atom.ResidueType_show_all(out)
8230 
8231 def ResidueType_get_all_strings():
8232  """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
8233  return _IMP_atom.ResidueType_get_all_strings()
8234 
8235 def ResidueType_get_number_unique():
8236  """ResidueType_get_number_unique() -> unsigned int"""
8237  return _IMP_atom.ResidueType_get_number_unique()
8238 
8239 class ChainType(IMP._Value):
8240  """Proxy of C++ IMP::Key<(90784336)> class."""
8241 
8242  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8243 
8244  def __init__(self, *args):
8245  """
8246  __init__(IMP::Key<(90784336)> self) -> ChainType
8247  __init__(IMP::Key<(90784336)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
8248  __init__(IMP::Key<(90784336)> self, std::string const & c) -> ChainType
8249  __init__(IMP::Key<(90784336)> self, unsigned int i) -> ChainType
8250  """
8251  this = _IMP_atom.new_ChainType(*args)
8252  try:
8253  self.this.append(this)
8254  except __builtin__.Exception:
8255  self.this = this
8256 
8257  def add_key(sc):
8258  """add_key(std::string sc) -> unsigned int"""
8259  return _IMP_atom.ChainType_add_key(sc)
8260 
8261  add_key = staticmethod(add_key)
8262 
8263  def get_key_exists(sc):
8264  """get_key_exists(std::string sc) -> bool"""
8265  return _IMP_atom.ChainType_get_key_exists(sc)
8266 
8267  get_key_exists = staticmethod(get_key_exists)
8268 
8269  def get_string(self):
8270  """get_string(ChainType self) -> std::string const"""
8271  return _IMP_atom.ChainType_get_string(self)
8272 
8273 
8274  def __cmp__(self, o):
8275  """__cmp__(ChainType self, ChainType o) -> int"""
8276  return _IMP_atom.ChainType___cmp__(self, o)
8277 
8278 
8279  def __eq__(self, o):
8280  """__eq__(ChainType self, ChainType o) -> bool"""
8281  return _IMP_atom.ChainType___eq__(self, o)
8282 
8283 
8284  def __ne__(self, o):
8285  """__ne__(ChainType self, ChainType o) -> bool"""
8286  return _IMP_atom.ChainType___ne__(self, o)
8287 
8288 
8289  def __lt__(self, o):
8290  """__lt__(ChainType self, ChainType o) -> bool"""
8291  return _IMP_atom.ChainType___lt__(self, o)
8292 
8293 
8294  def __gt__(self, o):
8295  """__gt__(ChainType self, ChainType o) -> bool"""
8296  return _IMP_atom.ChainType___gt__(self, o)
8297 
8298 
8299  def __ge__(self, o):
8300  """__ge__(ChainType self, ChainType o) -> bool"""
8301  return _IMP_atom.ChainType___ge__(self, o)
8302 
8303 
8304  def __le__(self, o):
8305  """__le__(ChainType self, ChainType o) -> bool"""
8306  return _IMP_atom.ChainType___le__(self, o)
8307 
8308 
8309  def __hash__(self):
8310  """__hash__(ChainType self) -> std::size_t"""
8311  return _IMP_atom.ChainType___hash__(self)
8312 
8313 
8314  def show(self, *args):
8315  """
8316  show(ChainType self, _ostream out)
8317  show(ChainType self)
8318  """
8319  return _IMP_atom.ChainType_show(self, *args)
8320 
8321 
8322  def add_alias(old_key, new_name):
8323  """add_alias(ChainType old_key, std::string new_name) -> ChainType"""
8324  return _IMP_atom.ChainType_add_alias(old_key, new_name)
8325 
8326  add_alias = staticmethod(add_alias)
8327 
8328  def get_number_of_keys():
8329  """get_number_of_keys() -> unsigned int"""
8330  return _IMP_atom.ChainType_get_number_of_keys()
8331 
8332  get_number_of_keys = staticmethod(get_number_of_keys)
8333 
8334  def get_index(self):
8335  """get_index(ChainType self) -> unsigned int"""
8336  return _IMP_atom.ChainType_get_index(self)
8337 
8338 
8339  def show_all(out):
8340  """show_all(_ostream out)"""
8341  return _IMP_atom.ChainType_show_all(out)
8342 
8343  show_all = staticmethod(show_all)
8344 
8345  def get_all_strings():
8346  """get_all_strings() -> IMP::Vector< std::string >"""
8347  return _IMP_atom.ChainType_get_all_strings()
8348 
8349  get_all_strings = staticmethod(get_all_strings)
8350 
8351  def get_number_unique():
8352  """get_number_unique() -> unsigned int"""
8353  return _IMP_atom.ChainType_get_number_unique()
8354 
8355  get_number_unique = staticmethod(get_number_unique)
8356 
8357  def __str__(self):
8358  """__str__(ChainType self) -> std::string"""
8359  return _IMP_atom.ChainType___str__(self)
8360 
8361 
8362  def __repr__(self):
8363  """__repr__(ChainType self) -> std::string"""
8364  return _IMP_atom.ChainType___repr__(self)
8365 
8366  __swig_destroy__ = _IMP_atom.delete_ChainType
8367  __del__ = lambda self: None
8368 ChainType_swigregister = _IMP_atom.ChainType_swigregister
8369 ChainType_swigregister(ChainType)
8370 
8371 def ChainType_add_key(sc):
8372  """ChainType_add_key(std::string sc) -> unsigned int"""
8373  return _IMP_atom.ChainType_add_key(sc)
8374 
8375 def ChainType_get_key_exists(sc):
8376  """ChainType_get_key_exists(std::string sc) -> bool"""
8377  return _IMP_atom.ChainType_get_key_exists(sc)
8378 
8379 def ChainType_add_alias(old_key, new_name):
8380  """ChainType_add_alias(ChainType old_key, std::string new_name) -> ChainType"""
8381  return _IMP_atom.ChainType_add_alias(old_key, new_name)
8382 
8383 def ChainType_get_number_of_keys():
8384  """ChainType_get_number_of_keys() -> unsigned int"""
8385  return _IMP_atom.ChainType_get_number_of_keys()
8386 
8387 def ChainType_show_all(out):
8388  """ChainType_show_all(_ostream out)"""
8389  return _IMP_atom.ChainType_show_all(out)
8390 
8391 def ChainType_get_all_strings():
8392  """ChainType_get_all_strings() -> IMP::Vector< std::string >"""
8393  return _IMP_atom.ChainType_get_all_strings()
8394 
8395 def ChainType_get_number_unique():
8396  """ChainType_get_number_unique() -> unsigned int"""
8397  return _IMP_atom.ChainType_get_number_unique()
8398 
8399 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8400 OH = _IMP_atom.OH
8401 H2O = _IMP_atom.H2O
8402 H = _IMP_atom.H
8403 He = _IMP_atom.He
8404 Li = _IMP_atom.Li
8405 Be = _IMP_atom.Be
8406 B = _IMP_atom.B
8407 C = _IMP_atom.C
8408 N = _IMP_atom.N
8409 O = _IMP_atom.O
8410 F = _IMP_atom.F
8411 Ne = _IMP_atom.Ne
8412 Na = _IMP_atom.Na
8413 Mg = _IMP_atom.Mg
8414 Al = _IMP_atom.Al
8415 Si = _IMP_atom.Si
8416 P = _IMP_atom.P
8417 S = _IMP_atom.S
8418 Cl = _IMP_atom.Cl
8419 Ar = _IMP_atom.Ar
8420 K = _IMP_atom.K
8421 Ca = _IMP_atom.Ca
8422 Sc = _IMP_atom.Sc
8423 Ti = _IMP_atom.Ti
8424 V = _IMP_atom.V
8425 Cr = _IMP_atom.Cr
8426 Mn = _IMP_atom.Mn
8427 Fe = _IMP_atom.Fe
8428 Co = _IMP_atom.Co
8429 Ni = _IMP_atom.Ni
8430 Cu = _IMP_atom.Cu
8431 Zn = _IMP_atom.Zn
8432 Ga = _IMP_atom.Ga
8433 Ge = _IMP_atom.Ge
8434 As = _IMP_atom.As
8435 Se = _IMP_atom.Se
8436 Br = _IMP_atom.Br
8437 Kr = _IMP_atom.Kr
8438 Rb = _IMP_atom.Rb
8439 Sr = _IMP_atom.Sr
8440 Y = _IMP_atom.Y
8441 Zr = _IMP_atom.Zr
8442 Nb = _IMP_atom.Nb
8443 Mo = _IMP_atom.Mo
8444 Tc = _IMP_atom.Tc
8445 Ru = _IMP_atom.Ru
8446 Rh = _IMP_atom.Rh
8447 Pd = _IMP_atom.Pd
8448 Ag = _IMP_atom.Ag
8449 Cd = _IMP_atom.Cd
8450 In = _IMP_atom.In
8451 Sn = _IMP_atom.Sn
8452 Sb = _IMP_atom.Sb
8453 Te = _IMP_atom.Te
8454 I = _IMP_atom.I
8455 Xe = _IMP_atom.Xe
8456 Cs = _IMP_atom.Cs
8457 Ba = _IMP_atom.Ba
8458 La = _IMP_atom.La
8459 Ce = _IMP_atom.Ce
8460 Pr = _IMP_atom.Pr
8461 Nd = _IMP_atom.Nd
8462 Pm = _IMP_atom.Pm
8463 Sm = _IMP_atom.Sm
8464 Eu = _IMP_atom.Eu
8465 Gd = _IMP_atom.Gd
8466 Tb = _IMP_atom.Tb
8467 Dy = _IMP_atom.Dy
8468 Ho = _IMP_atom.Ho
8469 Er = _IMP_atom.Er
8470 Tm = _IMP_atom.Tm
8471 Yb = _IMP_atom.Yb
8472 Lu = _IMP_atom.Lu
8473 Hf = _IMP_atom.Hf
8474 Ta = _IMP_atom.Ta
8475 W = _IMP_atom.W
8476 Re = _IMP_atom.Re
8477 Os = _IMP_atom.Os
8478 Ir = _IMP_atom.Ir
8479 Pt = _IMP_atom.Pt
8480 Au = _IMP_atom.Au
8481 Hg = _IMP_atom.Hg
8482 Tl = _IMP_atom.Tl
8483 Pb = _IMP_atom.Pb
8484 Bi = _IMP_atom.Bi
8485 Po = _IMP_atom.Po
8486 At = _IMP_atom.At
8487 Rn = _IMP_atom.Rn
8488 Fr = _IMP_atom.Fr
8489 Ra = _IMP_atom.Ra
8490 Ac = _IMP_atom.Ac
8491 Th = _IMP_atom.Th
8492 Pa = _IMP_atom.Pa
8493 U = _IMP_atom.U
8494 Np = _IMP_atom.Np
8495 Pu = _IMP_atom.Pu
8496 Am = _IMP_atom.Am
8497 Cm = _IMP_atom.Cm
8498 Bk = _IMP_atom.Bk
8499 Cf = _IMP_atom.Cf
8500 Es = _IMP_atom.Es
8501 Fm = _IMP_atom.Fm
8502 Md = _IMP_atom.Md
8503 No = _IMP_atom.No
8504 Lr = _IMP_atom.Lr
8505 Db = _IMP_atom.Db
8506 Jl = _IMP_atom.Jl
8507 Rf = _IMP_atom.Rf
8508 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8509 
8510 def hash_value(e):
8511  """hash_value(IMP::atom::Element e) -> size_t"""
8512  return _IMP_atom.hash_value(e)
8513 class ElementTable(object):
8514  """Proxy of C++ IMP::atom::ElementTable class."""
8515 
8516  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8517  __repr__ = _swig_repr
8518 
8519  def __init__(self):
8520  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8521  this = _IMP_atom.new_ElementTable()
8522  try:
8523  self.this.append(this)
8524  except __builtin__.Exception:
8525  self.this = this
8526 
8527  def get_element(self, s):
8528  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8529  return _IMP_atom.ElementTable_get_element(self, s)
8530 
8531 
8532  def get_name(self, e):
8533  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8534  return _IMP_atom.ElementTable_get_name(self, e)
8535 
8536 
8537  def get_mass(self, e):
8538  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8539  return _IMP_atom.ElementTable_get_mass(self, e)
8540 
8541  __swig_destroy__ = _IMP_atom.delete_ElementTable
8542  __del__ = lambda self: None
8543 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8544 ElementTable_swigregister(ElementTable)
8545 
8546 
8547 def get_element_table():
8548  """get_element_table() -> ElementTable"""
8549  return _IMP_atom.get_element_table()
8550 class Atom(Hierarchy):
8551  """Proxy of C++ IMP::atom::Atom class."""
8552 
8553  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8554 
8555  def __init__(self, *args):
8556  """
8557  __init__(IMP::atom::Atom self) -> Atom
8558  __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8559  __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8560  """
8561  this = _IMP_atom.new_Atom(*args)
8562  try:
8563  self.this.append(this)
8564  except __builtin__.Exception:
8565  self.this = this
8566 
8567  def show(self, *args):
8568  """
8569  show(Atom self, _ostream out)
8570  show(Atom self)
8571  """
8572  return _IMP_atom.Atom_show(self, *args)
8573 
8574 
8575  def setup_particle(*args):
8576  """
8577  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8578  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8579  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8580  setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8581  """
8582  return _IMP_atom.Atom_setup_particle(*args)
8583 
8584  setup_particle = staticmethod(setup_particle)
8585 
8586  def get_is_setup(*args):
8587  """
8588  get_is_setup(_ParticleAdaptor p) -> bool
8589  get_is_setup(Model m, ParticleIndex pi) -> bool
8590  """
8591  return _IMP_atom.Atom_get_is_setup(*args)
8592 
8593  get_is_setup = staticmethod(get_is_setup)
8594 
8595  def get_atom_type(self):
8596  """get_atom_type(Atom self) -> AtomType"""
8597  return _IMP_atom.Atom_get_atom_type(self)
8598 
8599 
8600  def set_atom_type(self, t):
8601  """set_atom_type(Atom self, AtomType t)"""
8602  return _IMP_atom.Atom_set_atom_type(self, t)
8603 
8604 
8605  def get_element(self):
8606  """get_element(Atom self) -> IMP::atom::Element"""
8607  return _IMP_atom.Atom_get_element(self)
8608 
8609 
8610  def set_element(self, e):
8611  """set_element(Atom self, IMP::atom::Element e)"""
8612  return _IMP_atom.Atom_set_element(self, e)
8613 
8614 
8615  def get_occupancy(self):
8616  """get_occupancy(Atom self) -> double"""
8617  return _IMP_atom.Atom_get_occupancy(self)
8618 
8619 
8620  def set_occupancy(self, occupancy):
8621  """set_occupancy(Atom self, double occupancy)"""
8622  return _IMP_atom.Atom_set_occupancy(self, occupancy)
8623 
8624 
8625  def get_temperature_factor(self):
8626  """get_temperature_factor(Atom self) -> double"""
8627  return _IMP_atom.Atom_get_temperature_factor(self)
8628 
8629 
8630  def set_temperature_factor(self, tempFactor):
8631  """set_temperature_factor(Atom self, double tempFactor)"""
8632  return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8633 
8634 
8635  def get_input_index(self):
8636  """get_input_index(Atom self) -> IMP::Int"""
8637  return _IMP_atom.Atom_get_input_index(self)
8638 
8639 
8640  def set_input_index(self, t):
8641  """set_input_index(Atom self, IMP::Int t)"""
8642  return _IMP_atom.Atom_set_input_index(self, t)
8643 
8644 
8645  def get_atom_type_key():
8646  """get_atom_type_key() -> IntKey"""
8647  return _IMP_atom.Atom_get_atom_type_key()
8648 
8649  get_atom_type_key = staticmethod(get_atom_type_key)
8650 
8651  def get_element_key():
8652  """get_element_key() -> IntKey"""
8653  return _IMP_atom.Atom_get_element_key()
8654 
8655  get_element_key = staticmethod(get_element_key)
8656 
8657  def get_input_index_key():
8658  """get_input_index_key() -> IntKey"""
8659  return _IMP_atom.Atom_get_input_index_key()
8660 
8661  get_input_index_key = staticmethod(get_input_index_key)
8662 
8663  def get_occupancy_key():
8664  """get_occupancy_key() -> FloatKey"""
8665  return _IMP_atom.Atom_get_occupancy_key()
8666 
8667  get_occupancy_key = staticmethod(get_occupancy_key)
8668 
8669  def get_temperature_factor_key():
8670  """get_temperature_factor_key() -> FloatKey"""
8671  return _IMP_atom.Atom_get_temperature_factor_key()
8672 
8673  get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8674 
8675  def add_attribute(self, *args):
8676  """
8677  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8678  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8679  add_attribute(Atom self, IntKey a0, IMP::Int a1)
8680  add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
8681  add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
8682  add_attribute(Atom self, StringKey a0, IMP::String a1)
8683  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8684  add_attribute(Atom self, ObjectKey a0, Object a1)
8685  """
8686  return _IMP_atom.Atom_add_attribute(self, *args)
8687 
8688 
8689  def get_value(self, *args):
8690  """
8691  get_value(Atom self, FloatKey a0) -> IMP::Float
8692  get_value(Atom self, IntKey a0) -> IMP::Int
8693  get_value(Atom self, FloatsKey a0) -> IMP::Floats
8694  get_value(Atom self, IntsKey a0) -> IMP::Ints
8695  get_value(Atom self, StringKey a0) -> IMP::String
8696  get_value(Atom self, ParticleIndexKey a0) -> Particle
8697  get_value(Atom self, ObjectKey a0) -> Object
8698  """
8699  return _IMP_atom.Atom_get_value(self, *args)
8700 
8701 
8702  def set_value(self, *args):
8703  """
8704  set_value(Atom self, FloatKey a0, IMP::Float a1)
8705  set_value(Atom self, IntKey a0, IMP::Int a1)
8706  set_value(Atom self, FloatsKey a0, IMP::Floats a1)
8707  set_value(Atom self, IntsKey a0, IMP::Ints a1)
8708  set_value(Atom self, StringKey a0, IMP::String a1)
8709  set_value(Atom self, ParticleIndexKey a0, Particle a1)
8710  set_value(Atom self, ObjectKey a0, Object a1)
8711  """
8712  return _IMP_atom.Atom_set_value(self, *args)
8713 
8714 
8715  def remove_attribute(self, *args):
8716  """
8717  remove_attribute(Atom self, FloatKey a0)
8718  remove_attribute(Atom self, IntKey a0)
8719  remove_attribute(Atom self, FloatsKey a0)
8720  remove_attribute(Atom self, IntsKey a0)
8721  remove_attribute(Atom self, StringKey a0)
8722  remove_attribute(Atom self, ParticleIndexKey a0)
8723  remove_attribute(Atom self, ObjectKey a0)
8724  """
8725  return _IMP_atom.Atom_remove_attribute(self, *args)
8726 
8727 
8728  def has_attribute(self, *args):
8729  """
8730  has_attribute(Atom self, FloatKey a0) -> bool
8731  has_attribute(Atom self, IntKey a0) -> bool
8732  has_attribute(Atom self, FloatsKey a0) -> bool
8733  has_attribute(Atom self, IntsKey a0) -> bool
8734  has_attribute(Atom self, StringKey a0) -> bool
8735  has_attribute(Atom self, ParticleIndexKey a0) -> bool
8736  has_attribute(Atom self, ObjectKey a0) -> bool
8737  """
8738  return _IMP_atom.Atom_has_attribute(self, *args)
8739 
8740 
8741  def get_derivative(self, a0):
8742  """get_derivative(Atom self, FloatKey a0) -> double"""
8743  return _IMP_atom.Atom_get_derivative(self, a0)
8744 
8745 
8746  def get_name(self):
8747  """get_name(Atom self) -> std::string"""
8748  return _IMP_atom.Atom_get_name(self)
8749 
8750 
8751  def clear_caches(self):
8752  """clear_caches(Atom self)"""
8753  return _IMP_atom.Atom_clear_caches(self)
8754 
8755 
8756  def set_name(self, a0):
8757  """set_name(Atom self, std::string a0)"""
8758  return _IMP_atom.Atom_set_name(self, a0)
8759 
8760 
8761  def set_check_level(self, a0):
8762  """set_check_level(Atom self, IMP::CheckLevel a0)"""
8763  return _IMP_atom.Atom_set_check_level(self, a0)
8764 
8765 
8766  def add_to_derivative(self, a0, a1, a2):
8767  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8768  return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8769 
8770 
8771  def set_is_optimized(self, a0, a1):
8772  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8773  return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8774 
8775 
8776  def get_is_optimized(self, a0):
8777  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8778  return _IMP_atom.Atom_get_is_optimized(self, a0)
8779 
8780 
8781  def get_check_level(self):
8782  """get_check_level(Atom self) -> IMP::CheckLevel"""
8783  return _IMP_atom.Atom_get_check_level(self)
8784 
8785 
8786  def __eq__(self, *args):
8787  """
8788  __eq__(Atom self, Atom o) -> bool
8789  __eq__(Atom self, Particle d) -> bool
8790  """
8791  return _IMP_atom.Atom___eq__(self, *args)
8792 
8793 
8794  def __ne__(self, *args):
8795  """
8796  __ne__(Atom self, Atom o) -> bool
8797  __ne__(Atom self, Particle d) -> bool
8798  """
8799  return _IMP_atom.Atom___ne__(self, *args)
8800 
8801 
8802  def __le__(self, *args):
8803  """
8804  __le__(Atom self, Atom o) -> bool
8805  __le__(Atom self, Particle d) -> bool
8806  """
8807  return _IMP_atom.Atom___le__(self, *args)
8808 
8809 
8810  def __lt__(self, *args):
8811  """
8812  __lt__(Atom self, Atom o) -> bool
8813  __lt__(Atom self, Particle d) -> bool
8814  """
8815  return _IMP_atom.Atom___lt__(self, *args)
8816 
8817 
8818  def __ge__(self, *args):
8819  """
8820  __ge__(Atom self, Atom o) -> bool
8821  __ge__(Atom self, Particle d) -> bool
8822  """
8823  return _IMP_atom.Atom___ge__(self, *args)
8824 
8825 
8826  def __gt__(self, *args):
8827  """
8828  __gt__(Atom self, Atom o) -> bool
8829  __gt__(Atom self, Particle d) -> bool
8830  """
8831  return _IMP_atom.Atom___gt__(self, *args)
8832 
8833 
8834  def __hash__(self):
8835  """__hash__(Atom self) -> std::size_t"""
8836  return _IMP_atom.Atom___hash__(self)
8837 
8838 
8839  def __str__(self):
8840  """__str__(Atom self) -> std::string"""
8841  return _IMP_atom.Atom___str__(self)
8842 
8843 
8844  def __repr__(self):
8845  """__repr__(Atom self) -> std::string"""
8846  return _IMP_atom.Atom___repr__(self)
8847 
8848  __swig_destroy__ = _IMP_atom.delete_Atom
8849  __del__ = lambda self: None
8850 Atom_swigregister = _IMP_atom.Atom_swigregister
8851 Atom_swigregister(Atom)
8852 AT_UNKNOWN = cvar.AT_UNKNOWN
8853 AT_N = cvar.AT_N
8854 AT_CA = cvar.AT_CA
8855 AT_C = cvar.AT_C
8856 AT_O = cvar.AT_O
8857 AT_H = cvar.AT_H
8858 AT_H1 = cvar.AT_H1
8859 AT_H2 = cvar.AT_H2
8860 AT_H3 = cvar.AT_H3
8861 AT_HA = cvar.AT_HA
8862 AT_HA1 = cvar.AT_HA1
8863 AT_HA2 = cvar.AT_HA2
8864 AT_HA3 = cvar.AT_HA3
8865 AT_CB = cvar.AT_CB
8866 AT_HB = cvar.AT_HB
8867 AT_HB1 = cvar.AT_HB1
8868 AT_HB2 = cvar.AT_HB2
8869 AT_HB3 = cvar.AT_HB3
8870 AT_OXT = cvar.AT_OXT
8871 AT_CH3 = cvar.AT_CH3
8872 AT_CH = cvar.AT_CH
8873 AT_CG = cvar.AT_CG
8874 AT_CG1 = cvar.AT_CG1
8875 AT_CG2 = cvar.AT_CG2
8876 AT_HG = cvar.AT_HG
8877 AT_HG1 = cvar.AT_HG1
8878 AT_HG2 = cvar.AT_HG2
8879 AT_HG3 = cvar.AT_HG3
8880 AT_HG11 = cvar.AT_HG11
8881 AT_HG21 = cvar.AT_HG21
8882 AT_HG31 = cvar.AT_HG31
8883 AT_HG12 = cvar.AT_HG12
8884 AT_HG13 = cvar.AT_HG13
8885 AT_HG22 = cvar.AT_HG22
8886 AT_HG23 = cvar.AT_HG23
8887 AT_HG32 = cvar.AT_HG32
8888 AT_OG = cvar.AT_OG
8889 AT_OG1 = cvar.AT_OG1
8890 AT_SG = cvar.AT_SG
8891 AT_CD = cvar.AT_CD
8892 AT_CD1 = cvar.AT_CD1
8893 AT_CD2 = cvar.AT_CD2
8894 AT_HD = cvar.AT_HD
8895 AT_HD1 = cvar.AT_HD1
8896 AT_HD2 = cvar.AT_HD2
8897 AT_HD3 = cvar.AT_HD3
8898 AT_HD11 = cvar.AT_HD11
8899 AT_HD21 = cvar.AT_HD21
8900 AT_HD31 = cvar.AT_HD31
8901 AT_HD12 = cvar.AT_HD12
8902 AT_HD13 = cvar.AT_HD13
8903 AT_HD22 = cvar.AT_HD22
8904 AT_HD23 = cvar.AT_HD23
8905 AT_HD32 = cvar.AT_HD32
8906 AT_SD = cvar.AT_SD
8907 AT_OD1 = cvar.AT_OD1
8908 AT_OD2 = cvar.AT_OD2
8909 AT_ND1 = cvar.AT_ND1
8910 AT_ND2 = cvar.AT_ND2
8911 AT_CE = cvar.AT_CE
8912 AT_CE1 = cvar.AT_CE1
8913 AT_CE2 = cvar.AT_CE2
8914 AT_CE3 = cvar.AT_CE3
8915 AT_HE = cvar.AT_HE
8916 AT_HE1 = cvar.AT_HE1
8917 AT_HE2 = cvar.AT_HE2
8918 AT_HE3 = cvar.AT_HE3
8919 AT_HE21 = cvar.AT_HE21
8920 AT_HE22 = cvar.AT_HE22
8921 AT_OE1 = cvar.AT_OE1
8922 AT_OE2 = cvar.AT_OE2
8923 AT_NE = cvar.AT_NE
8924 AT_NE1 = cvar.AT_NE1
8925 AT_NE2 = cvar.AT_NE2
8926 AT_CZ = cvar.AT_CZ
8927 AT_CZ2 = cvar.AT_CZ2
8928 AT_CZ3 = cvar.AT_CZ3
8929 AT_NZ = cvar.AT_NZ
8930 AT_HZ = cvar.AT_HZ
8931 AT_HZ1 = cvar.AT_HZ1
8932 AT_HZ2 = cvar.AT_HZ2
8933 AT_HZ3 = cvar.AT_HZ3
8934 AT_CH2 = cvar.AT_CH2
8935 AT_NH1 = cvar.AT_NH1
8936 AT_NH2 = cvar.AT_NH2
8937 AT_OH = cvar.AT_OH
8938 AT_HH = cvar.AT_HH
8939 AT_HH11 = cvar.AT_HH11
8940 AT_HH21 = cvar.AT_HH21
8941 AT_HH2 = cvar.AT_HH2
8942 AT_HH12 = cvar.AT_HH12
8943 AT_HH22 = cvar.AT_HH22
8944 AT_HH13 = cvar.AT_HH13
8945 AT_HH23 = cvar.AT_HH23
8946 AT_HH33 = cvar.AT_HH33
8947 AT_P = cvar.AT_P
8948 AT_OP1 = cvar.AT_OP1
8949 AT_OP2 = cvar.AT_OP2
8950 AT_OP3 = cvar.AT_OP3
8951 AT_O5p = cvar.AT_O5p
8952 AT_C5p = cvar.AT_C5p
8953 AT_H5p = cvar.AT_H5p
8954 AT_H5pp = cvar.AT_H5pp
8955 AT_C4p = cvar.AT_C4p
8956 AT_H4p = cvar.AT_H4p
8957 AT_O4p = cvar.AT_O4p
8958 AT_C1p = cvar.AT_C1p
8959 AT_H1p = cvar.AT_H1p
8960 AT_C3p = cvar.AT_C3p
8961 AT_H3p = cvar.AT_H3p
8962 AT_O3p = cvar.AT_O3p
8963 AT_C2p = cvar.AT_C2p
8964 AT_H2p = cvar.AT_H2p
8965 AT_H2pp = cvar.AT_H2pp
8966 AT_O2p = cvar.AT_O2p
8967 AT_HO2p = cvar.AT_HO2p
8968 AT_N9 = cvar.AT_N9
8969 AT_C8 = cvar.AT_C8
8970 AT_H8 = cvar.AT_H8
8971 AT_N7 = cvar.AT_N7
8972 AT_C5 = cvar.AT_C5
8973 AT_C4 = cvar.AT_C4
8974 AT_N3 = cvar.AT_N3
8975 AT_C2 = cvar.AT_C2
8976 AT_N1 = cvar.AT_N1
8977 AT_C6 = cvar.AT_C6
8978 AT_N6 = cvar.AT_N6
8979 AT_H61 = cvar.AT_H61
8980 AT_H62 = cvar.AT_H62
8981 AT_O6 = cvar.AT_O6
8982 AT_N2 = cvar.AT_N2
8983 AT_NT = cvar.AT_NT
8984 AT_H21 = cvar.AT_H21
8985 AT_H22 = cvar.AT_H22
8986 AT_H6 = cvar.AT_H6
8987 AT_H5 = cvar.AT_H5
8988 AT_O2 = cvar.AT_O2
8989 AT_N4 = cvar.AT_N4
8990 AT_H41 = cvar.AT_H41
8991 AT_H42 = cvar.AT_H42
8992 AT_O4 = cvar.AT_O4
8993 AT_C7 = cvar.AT_C7
8994 AT_H71 = cvar.AT_H71
8995 AT_H72 = cvar.AT_H72
8996 AT_H73 = cvar.AT_H73
8997 AT_O1A = cvar.AT_O1A
8998 AT_O2A = cvar.AT_O2A
8999 AT_O3A = cvar.AT_O3A
9000 AT_O1B = cvar.AT_O1B
9001 AT_O2B = cvar.AT_O2B
9002 AT_O3B = cvar.AT_O3B
9003 
9004 def Atom_setup_particle(*args):
9005  """
9006  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
9007  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
9008  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
9009  Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
9010  """
9011  return _IMP_atom.Atom_setup_particle(*args)
9012 
9013 def Atom_get_is_setup(*args):
9014  """
9015  get_is_setup(_ParticleAdaptor p) -> bool
9016  Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
9017  """
9018  return _IMP_atom.Atom_get_is_setup(*args)
9019 
9020 def Atom_get_atom_type_key():
9021  """Atom_get_atom_type_key() -> IntKey"""
9022  return _IMP_atom.Atom_get_atom_type_key()
9023 
9024 def Atom_get_element_key():
9025  """Atom_get_element_key() -> IntKey"""
9026  return _IMP_atom.Atom_get_element_key()
9027 
9028 def Atom_get_input_index_key():
9029  """Atom_get_input_index_key() -> IntKey"""
9030  return _IMP_atom.Atom_get_input_index_key()
9031 
9032 def Atom_get_occupancy_key():
9033  """Atom_get_occupancy_key() -> FloatKey"""
9034  return _IMP_atom.Atom_get_occupancy_key()
9035 
9036 def Atom_get_temperature_factor_key():
9037  """Atom_get_temperature_factor_key() -> FloatKey"""
9038  return _IMP_atom.Atom_get_temperature_factor_key()
9039 
9040 
9041 def get_residue(*args):
9042  """
9043  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
9044  get_residue(Atom d, bool nothrow=False) -> Residue
9045  get_residue(Atom d) -> Residue
9046  """
9047  return _IMP_atom.get_residue(*args)
9048 
9049 def get_atom(rd, at):
9050  """get_atom(Residue rd, AtomType at) -> Atom"""
9051  return _IMP_atom.get_atom(rd, at)
9052 
9053 def add_atom_type(name, e):
9054  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
9055  return _IMP_atom.add_atom_type(name, e)
9056 
9057 def get_element_for_atom_type(at):
9058  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
9059  return _IMP_atom.get_element_for_atom_type(at)
9060 
9061 def get_atom_type_exists(name):
9062  """get_atom_type_exists(std::string name) -> bool"""
9063  return _IMP_atom.get_atom_type_exists(name)
9064 class Residue(Hierarchy):
9065  """Proxy of C++ IMP::atom::Residue class."""
9066 
9067  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9068 
9069  def __init__(self, *args):
9070  """
9071  __init__(IMP::atom::Residue self) -> Residue
9072  __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
9073  __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
9074  """
9075  this = _IMP_atom.new_Residue(*args)
9076  try:
9077  self.this.append(this)
9078  except __builtin__.Exception:
9079  self.this = this
9080 
9081  def show(self, *args):
9082  """
9083  show(Residue self, _ostream out)
9084  show(Residue self)
9085  """
9086  return _IMP_atom.Residue_show(self, *args)
9087 
9088 
9089  def setup_particle(*args):
9090  """
9091  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9092  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9093  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9094  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9095  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9096  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9097  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9098  setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9099  """
9100  return _IMP_atom.Residue_setup_particle(*args)
9101 
9102  setup_particle = staticmethod(setup_particle)
9103 
9104  def get_is_setup(*args):
9105  """
9106  get_is_setup(_ParticleAdaptor p) -> bool
9107  get_is_setup(Model m, ParticleIndex pi) -> bool
9108  """
9109  return _IMP_atom.Residue_get_is_setup(*args)
9110 
9111  get_is_setup = staticmethod(get_is_setup)
9112 
9113  def get_residue_type(self):
9114  """get_residue_type(Residue self) -> ResidueType"""
9115  return _IMP_atom.Residue_get_residue_type(self)
9116 
9117 
9118  def set_residue_type(self, t):
9119  """set_residue_type(Residue self, ResidueType t)"""
9120  return _IMP_atom.Residue_set_residue_type(self, t)
9121 
9122 
9123  def get_is_protein(self):
9124  """get_is_protein(Residue self) -> bool"""
9125  return _IMP_atom.Residue_get_is_protein(self)
9126 
9127 
9128  def get_is_dna(self):
9129  """get_is_dna(Residue self) -> bool"""
9130  return _IMP_atom.Residue_get_is_dna(self)
9131 
9132 
9133  def get_is_rna(self):
9134  """get_is_rna(Residue self) -> bool"""
9135  return _IMP_atom.Residue_get_is_rna(self)
9136 
9137 
9138  def get_index(self):
9139  """get_index(Residue self) -> IMP::Int"""
9140  return _IMP_atom.Residue_get_index(self)
9141 
9142 
9143  def set_index(self, t):
9144  """set_index(Residue self, IMP::Int t)"""
9145  return _IMP_atom.Residue_set_index(self, t)
9146 
9147 
9148  def get_insertion_code(self):
9149  """get_insertion_code(Residue self) -> char"""
9150  return _IMP_atom.Residue_get_insertion_code(self)
9151 
9152 
9153  def set_insertion_code(self, insertion_code):
9154  """set_insertion_code(Residue self, char insertion_code)"""
9155  return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
9156 
9157 
9158  def get_index_key():
9159  """get_index_key() -> IntKey"""
9160  return _IMP_atom.Residue_get_index_key()
9161 
9162  get_index_key = staticmethod(get_index_key)
9163 
9164  def get_residue_type_key():
9165  """get_residue_type_key() -> IntKey"""
9166  return _IMP_atom.Residue_get_residue_type_key()
9167 
9168  get_residue_type_key = staticmethod(get_residue_type_key)
9169 
9170  def get_insertion_code_key():
9171  """get_insertion_code_key() -> IntKey"""
9172  return _IMP_atom.Residue_get_insertion_code_key()
9173 
9174  get_insertion_code_key = staticmethod(get_insertion_code_key)
9175 
9176  def add_attribute(self, *args):
9177  """
9178  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
9179  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
9180  add_attribute(Residue self, IntKey a0, IMP::Int a1)
9181  add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
9182  add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
9183  add_attribute(Residue self, StringKey a0, IMP::String a1)
9184  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
9185  add_attribute(Residue self, ObjectKey a0, Object a1)
9186  """
9187  return _IMP_atom.Residue_add_attribute(self, *args)
9188 
9189 
9190  def get_value(self, *args):
9191  """
9192  get_value(Residue self, FloatKey a0) -> IMP::Float
9193  get_value(Residue self, IntKey a0) -> IMP::Int
9194  get_value(Residue self, FloatsKey a0) -> IMP::Floats
9195  get_value(Residue self, IntsKey a0) -> IMP::Ints
9196  get_value(Residue self, StringKey a0) -> IMP::String
9197  get_value(Residue self, ParticleIndexKey a0) -> Particle
9198  get_value(Residue self, ObjectKey a0) -> Object
9199  """
9200  return _IMP_atom.Residue_get_value(self, *args)
9201 
9202 
9203  def set_value(self, *args):
9204  """
9205  set_value(Residue self, FloatKey a0, IMP::Float a1)
9206  set_value(Residue self, IntKey a0, IMP::Int a1)
9207  set_value(Residue self, FloatsKey a0, IMP::Floats a1)
9208  set_value(Residue self, IntsKey a0, IMP::Ints a1)
9209  set_value(Residue self, StringKey a0, IMP::String a1)
9210  set_value(Residue self, ParticleIndexKey a0, Particle a1)
9211  set_value(Residue self, ObjectKey a0, Object a1)
9212  """
9213  return _IMP_atom.Residue_set_value(self, *args)
9214 
9215 
9216  def remove_attribute(self, *args):
9217  """
9218  remove_attribute(Residue self, FloatKey a0)
9219  remove_attribute(Residue self, IntKey a0)
9220  remove_attribute(Residue self, FloatsKey a0)
9221  remove_attribute(Residue self, IntsKey a0)
9222  remove_attribute(Residue self, StringKey a0)
9223  remove_attribute(Residue self, ParticleIndexKey a0)
9224  remove_attribute(Residue self, ObjectKey a0)
9225  """
9226  return _IMP_atom.Residue_remove_attribute(self, *args)
9227 
9228 
9229  def has_attribute(self, *args):
9230  """
9231  has_attribute(Residue self, FloatKey a0) -> bool
9232  has_attribute(Residue self, IntKey a0) -> bool
9233  has_attribute(Residue self, FloatsKey a0) -> bool
9234  has_attribute(Residue self, IntsKey a0) -> bool
9235  has_attribute(Residue self, StringKey a0) -> bool
9236  has_attribute(Residue self, ParticleIndexKey a0) -> bool
9237  has_attribute(Residue self, ObjectKey a0) -> bool
9238  """
9239  return _IMP_atom.Residue_has_attribute(self, *args)
9240 
9241 
9242  def get_derivative(self, a0):
9243  """get_derivative(Residue self, FloatKey a0) -> double"""
9244  return _IMP_atom.Residue_get_derivative(self, a0)
9245 
9246 
9247  def get_name(self):
9248  """get_name(Residue self) -> std::string"""
9249  return _IMP_atom.Residue_get_name(self)
9250 
9251 
9252  def clear_caches(self):
9253  """clear_caches(Residue self)"""
9254  return _IMP_atom.Residue_clear_caches(self)
9255 
9256 
9257  def set_name(self, a0):
9258  """set_name(Residue self, std::string a0)"""
9259  return _IMP_atom.Residue_set_name(self, a0)
9260 
9261 
9262  def set_check_level(self, a0):
9263  """set_check_level(Residue self, IMP::CheckLevel a0)"""
9264  return _IMP_atom.Residue_set_check_level(self, a0)
9265 
9266 
9267  def add_to_derivative(self, a0, a1, a2):
9268  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9269  return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
9270 
9271 
9272  def set_is_optimized(self, a0, a1):
9273  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
9274  return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
9275 
9276 
9277  def get_is_optimized(self, a0):
9278  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
9279  return _IMP_atom.Residue_get_is_optimized(self, a0)
9280 
9281 
9282  def get_check_level(self):
9283  """get_check_level(Residue self) -> IMP::CheckLevel"""
9284  return _IMP_atom.Residue_get_check_level(self)
9285 
9286 
9287  def __eq__(self, *args):
9288  """
9289  __eq__(Residue self, Residue o) -> bool
9290  __eq__(Residue self, Particle d) -> bool
9291  """
9292  return _IMP_atom.Residue___eq__(self, *args)
9293 
9294 
9295  def __ne__(self, *args):
9296  """
9297  __ne__(Residue self, Residue o) -> bool
9298  __ne__(Residue self, Particle d) -> bool
9299  """
9300  return _IMP_atom.Residue___ne__(self, *args)
9301 
9302 
9303  def __le__(self, *args):
9304  """
9305  __le__(Residue self, Residue o) -> bool
9306  __le__(Residue self, Particle d) -> bool
9307  """
9308  return _IMP_atom.Residue___le__(self, *args)
9309 
9310 
9311  def __lt__(self, *args):
9312  """
9313  __lt__(Residue self, Residue o) -> bool
9314  __lt__(Residue self, Particle d) -> bool
9315  """
9316  return _IMP_atom.Residue___lt__(self, *args)
9317 
9318 
9319  def __ge__(self, *args):
9320  """
9321  __ge__(Residue self, Residue o) -> bool
9322  __ge__(Residue self, Particle d) -> bool
9323  """
9324  return _IMP_atom.Residue___ge__(self, *args)
9325 
9326 
9327  def __gt__(self, *args):
9328  """
9329  __gt__(Residue self, Residue o) -> bool
9330  __gt__(Residue self, Particle d) -> bool
9331  """
9332  return _IMP_atom.Residue___gt__(self, *args)
9333 
9334 
9335  def __hash__(self):
9336  """__hash__(Residue self) -> std::size_t"""
9337  return _IMP_atom.Residue___hash__(self)
9338 
9339 
9340  def __str__(self):
9341  """__str__(Residue self) -> std::string"""
9342  return _IMP_atom.Residue___str__(self)
9343 
9344 
9345  def __repr__(self):
9346  """__repr__(Residue self) -> std::string"""
9347  return _IMP_atom.Residue___repr__(self)
9348 
9349  __swig_destroy__ = _IMP_atom.delete_Residue
9350  __del__ = lambda self: None
9351 Residue_swigregister = _IMP_atom.Residue_swigregister
9352 Residue_swigregister(Residue)
9353 UNK = cvar.UNK
9354 GLY = cvar.GLY
9355 ALA = cvar.ALA
9356 VAL = cvar.VAL
9357 LEU = cvar.LEU
9358 ILE = cvar.ILE
9359 SER = cvar.SER
9360 THR = cvar.THR
9361 CYS = cvar.CYS
9362 MET = cvar.MET
9363 PRO = cvar.PRO
9364 ASP = cvar.ASP
9365 ASN = cvar.ASN
9366 GLU = cvar.GLU
9367 GLN = cvar.GLN
9368 LYS = cvar.LYS
9369 ARG = cvar.ARG
9370 HIS = cvar.HIS
9371 PHE = cvar.PHE
9372 TYR = cvar.TYR
9373 TRP = cvar.TRP
9374 ACE = cvar.ACE
9375 NH2 = cvar.NH2
9376 ADE = cvar.ADE
9377 URA = cvar.URA
9378 CYT = cvar.CYT
9379 GUA = cvar.GUA
9380 THY = cvar.THY
9381 DADE = cvar.DADE
9382 DURA = cvar.DURA
9383 DCYT = cvar.DCYT
9384 DGUA = cvar.DGUA
9385 DTHY = cvar.DTHY
9386 HOH = cvar.HOH
9387 HEME = cvar.HEME
9388 POP = cvar.POP
9389 
9390 def Residue_setup_particle(*args):
9391  """
9392  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9393  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9394  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9395  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9396  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9397  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9398  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9399  Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9400  """
9401  return _IMP_atom.Residue_setup_particle(*args)
9402 
9403 def Residue_get_is_setup(*args):
9404  """
9405  get_is_setup(_ParticleAdaptor p) -> bool
9406  Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
9407  """
9408  return _IMP_atom.Residue_get_is_setup(*args)
9409 
9410 def Residue_get_index_key():
9411  """Residue_get_index_key() -> IntKey"""
9412  return _IMP_atom.Residue_get_index_key()
9413 
9414 def Residue_get_residue_type_key():
9415  """Residue_get_residue_type_key() -> IntKey"""
9416  return _IMP_atom.Residue_get_residue_type_key()
9417 
9418 def Residue_get_insertion_code_key():
9419  """Residue_get_insertion_code_key() -> IntKey"""
9420  return _IMP_atom.Residue_get_insertion_code_key()
9421 
9422 
9423 def get_next_residue(rd):
9424  """get_next_residue(Residue rd) -> Hierarchy"""
9425  return _IMP_atom.get_next_residue(rd)
9426 
9427 def get_previous_residue(rd):
9428  """get_previous_residue(Residue rd) -> Hierarchy"""
9429  return _IMP_atom.get_previous_residue(rd)
9430 
9431 def get_one_letter_code(c):
9432  """get_one_letter_code(ResidueType c) -> char"""
9433  return _IMP_atom.get_one_letter_code(c)
9434 BALLS = _IMP_atom.BALLS
9435 DENSITIES = _IMP_atom.DENSITIES
9436 class Representation(Hierarchy):
9437  """Proxy of C++ IMP::atom::Representation class."""
9438 
9439  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9440 
9441  def setup_particle(*args):
9442  """
9443  setup_particle(Model m, ParticleIndex pi) -> Representation
9444  setup_particle(_ParticleAdaptor decorator) -> Representation
9445  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9446  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9447  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9448  setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9449  """
9450  return _IMP_atom.Representation_setup_particle(*args)
9451 
9452  setup_particle = staticmethod(setup_particle)
9453 
9454  def __init__(self, *args):
9455  """
9456  __init__(IMP::atom::Representation self) -> Representation
9457  __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
9458  __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
9459  """
9460  this = _IMP_atom.new_Representation(*args)
9461  try:
9462  self.this.append(this)
9463  except __builtin__.Exception:
9464  self.this = this
9465 
9466  def show(self, *args):
9467  """
9468  show(Representation self, _ostream out)
9469  show(Representation self)
9470  """
9471  return _IMP_atom.Representation_show(self, *args)
9472 
9473 
9474  def get_is_setup(*args):
9475  """
9476  get_is_setup(_ParticleAdaptor p) -> bool
9477  get_is_setup(Model m, ParticleIndex pi) -> bool
9478  """
9479  return _IMP_atom.Representation_get_is_setup(*args)
9480 
9481  get_is_setup = staticmethod(get_is_setup)
9482 
9483  def get_representation(self, *args):
9484  """
9485  get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
9486  get_representation(Representation self, double resolution) -> Hierarchy
9487  """
9488  return _IMP_atom.Representation_get_representation(self, *args)
9489 
9490 
9491  def get_representations(self, *args):
9492  """
9493  get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
9494  get_representations(Representation self) -> IMP::atom::Hierarchies
9495  """
9496  return _IMP_atom.Representation_get_representations(self, *args)
9497 
9498 
9499  def add_representation(self, *args):
9500  """
9501  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
9502  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
9503  add_representation(Representation self, _ParticleIndexAdaptor rep)
9504  """
9505  return _IMP_atom.Representation_add_representation(self, *args)
9506 
9507 
9508  def get_resolutions(self, *args):
9509  """
9510  get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9511  get_resolutions(Representation self) -> IMP::Floats
9512  """
9513  return _IMP_atom.Representation_get_resolutions(self, *args)
9514 
9515 
9516  def remove_representation(self, rep):
9517  """remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
9518  return _IMP_atom.Representation_remove_representation(self, rep)
9519 
9520 
9521  def update_parents(self):
9522  """update_parents(Representation self)"""
9523  return _IMP_atom.Representation_update_parents(self)
9524 
9525 
9526  def add_attribute(self, *args):
9527  """
9528  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9529  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9530  add_attribute(Representation self, IntKey a0, IMP::Int a1)
9531  add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
9532  add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
9533  add_attribute(Representation self, StringKey a0, IMP::String a1)
9534  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9535  add_attribute(Representation self, ObjectKey a0, Object a1)
9536  """
9537  return _IMP_atom.Representation_add_attribute(self, *args)
9538 
9539 
9540  def get_value(self, *args):
9541  """
9542  get_value(Representation self, FloatKey a0) -> IMP::Float
9543  get_value(Representation self, IntKey a0) -> IMP::Int
9544  get_value(Representation self, FloatsKey a0) -> IMP::Floats
9545  get_value(Representation self, IntsKey a0) -> IMP::Ints
9546  get_value(Representation self, StringKey a0) -> IMP::String
9547  get_value(Representation self, ParticleIndexKey a0) -> Particle
9548  get_value(Representation self, ObjectKey a0) -> Object
9549  """
9550  return _IMP_atom.Representation_get_value(self, *args)
9551 
9552 
9553  def set_value(self, *args):
9554  """
9555  set_value(Representation self, FloatKey a0, IMP::Float a1)
9556  set_value(Representation self, IntKey a0, IMP::Int a1)
9557  set_value(Representation self, FloatsKey a0, IMP::Floats a1)
9558  set_value(Representation self, IntsKey a0, IMP::Ints a1)
9559  set_value(Representation self, StringKey a0, IMP::String a1)
9560  set_value(Representation self, ParticleIndexKey a0, Particle a1)
9561  set_value(Representation self, ObjectKey a0, Object a1)
9562  """
9563  return _IMP_atom.Representation_set_value(self, *args)
9564 
9565 
9566  def remove_attribute(self, *args):
9567  """
9568  remove_attribute(Representation self, FloatKey a0)
9569  remove_attribute(Representation self, IntKey a0)
9570  remove_attribute(Representation self, FloatsKey a0)
9571  remove_attribute(Representation self, IntsKey a0)
9572  remove_attribute(Representation self, StringKey a0)
9573  remove_attribute(Representation self, ParticleIndexKey a0)
9574  remove_attribute(Representation self, ObjectKey a0)
9575  """
9576  return _IMP_atom.Representation_remove_attribute(self, *args)
9577 
9578 
9579  def has_attribute(self, *args):
9580  """
9581  has_attribute(Representation self, FloatKey a0) -> bool
9582  has_attribute(Representation self, IntKey a0) -> bool
9583  has_attribute(Representation self, FloatsKey a0) -> bool
9584  has_attribute(Representation self, IntsKey a0) -> bool
9585  has_attribute(Representation self, StringKey a0) -> bool
9586  has_attribute(Representation self, ParticleIndexKey a0) -> bool
9587  has_attribute(Representation self, ObjectKey a0) -> bool
9588  """
9589  return _IMP_atom.Representation_has_attribute(self, *args)
9590 
9591 
9592  def get_derivative(self, a0):
9593  """get_derivative(Representation self, FloatKey a0) -> double"""
9594  return _IMP_atom.Representation_get_derivative(self, a0)
9595 
9596 
9597  def get_name(self):
9598  """get_name(Representation self) -> std::string"""
9599  return _IMP_atom.Representation_get_name(self)
9600 
9601 
9602  def clear_caches(self):
9603  """clear_caches(Representation self)"""
9604  return _IMP_atom.Representation_clear_caches(self)
9605 
9606 
9607  def set_name(self, a0):
9608  """set_name(Representation self, std::string a0)"""
9609  return _IMP_atom.Representation_set_name(self, a0)
9610 
9611 
9612  def set_check_level(self, a0):
9613  """set_check_level(Representation self, IMP::CheckLevel a0)"""
9614  return _IMP_atom.Representation_set_check_level(self, a0)
9615 
9616 
9617  def add_to_derivative(self, a0, a1, a2):
9618  """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9619  return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9620 
9621 
9622  def set_is_optimized(self, a0, a1):
9623  """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9624  return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9625 
9626 
9627  def get_is_optimized(self, a0):
9628  """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9629  return _IMP_atom.Representation_get_is_optimized(self, a0)
9630 
9631 
9632  def get_check_level(self):
9633  """get_check_level(Representation self) -> IMP::CheckLevel"""
9634  return _IMP_atom.Representation_get_check_level(self)
9635 
9636 
9637  def __eq__(self, *args):
9638  """
9639  __eq__(Representation self, Representation o) -> bool
9640  __eq__(Representation self, Particle d) -> bool
9641  """
9642  return _IMP_atom.Representation___eq__(self, *args)
9643 
9644 
9645  def __ne__(self, *args):
9646  """
9647  __ne__(Representation self, Representation o) -> bool
9648  __ne__(Representation self, Particle d) -> bool
9649  """
9650  return _IMP_atom.Representation___ne__(self, *args)
9651 
9652 
9653  def __le__(self, *args):
9654  """
9655  __le__(Representation self, Representation o) -> bool
9656  __le__(Representation self, Particle d) -> bool
9657  """
9658  return _IMP_atom.Representation___le__(self, *args)
9659 
9660 
9661  def __lt__(self, *args):
9662  """
9663  __lt__(Representation self, Representation o) -> bool
9664  __lt__(Representation self, Particle d) -> bool
9665  """
9666  return _IMP_atom.Representation___lt__(self, *args)
9667 
9668 
9669  def __ge__(self, *args):
9670  """
9671  __ge__(Representation self, Representation o) -> bool
9672  __ge__(Representation self, Particle d) -> bool
9673  """
9674  return _IMP_atom.Representation___ge__(self, *args)
9675 
9676 
9677  def __gt__(self, *args):
9678  """
9679  __gt__(Representation self, Representation o) -> bool
9680  __gt__(Representation self, Particle d) -> bool
9681  """
9682  return _IMP_atom.Representation___gt__(self, *args)
9683 
9684 
9685  def __hash__(self):
9686  """__hash__(Representation self) -> std::size_t"""
9687  return _IMP_atom.Representation___hash__(self)
9688 
9689 
9690  def __str__(self):
9691  """__str__(Representation self) -> std::string"""
9692  return _IMP_atom.Representation___str__(self)
9693 
9694 
9695  def __repr__(self):
9696  """__repr__(Representation self) -> std::string"""
9697  return _IMP_atom.Representation___repr__(self)
9698 
9699  __swig_destroy__ = _IMP_atom.delete_Representation
9700  __del__ = lambda self: None
9701 Representation_swigregister = _IMP_atom.Representation_swigregister
9702 Representation_swigregister(Representation)
9703 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9704 
9705 def Representation_setup_particle(*args):
9706  """
9707  setup_particle(Model m, ParticleIndex pi) -> Representation
9708  setup_particle(_ParticleAdaptor decorator) -> Representation
9709  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9710  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9711  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9712  Representation_setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9713  """
9714  return _IMP_atom.Representation_setup_particle(*args)
9715 
9716 def Representation_get_is_setup(*args):
9717  """
9718  get_is_setup(_ParticleAdaptor p) -> bool
9719  Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9720  """
9721  return _IMP_atom.Representation_get_is_setup(*args)
9722 
9723 
9724 def get_resolution(*args):
9725  """
9726  get_resolution(Model m, ParticleIndex pi) -> double
9727  get_resolution(Hierarchy h) -> double
9728  """
9729  return _IMP_atom.get_resolution(*args)
9730 
9731 def get_representation(h, nothrow=False):
9732  """
9733  get_representation(Hierarchy h, bool nothrow=False) -> Representation
9734  get_representation(Hierarchy h) -> Representation
9735  """
9736  return _IMP_atom.get_representation(h, nothrow)
9737 
9738 def show_with_representations(*args):
9739  """
9740  show_with_representations(Hierarchy h, _ostream out)
9741  show_with_representations(Hierarchy h)
9742  """
9743  return _IMP_atom.show_with_representations(*args)
9744 class State(Hierarchy):
9745  """Proxy of C++ IMP::atom::State class."""
9746 
9747  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9748 
9749  def setup_particle(*args):
9750  """
9751  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9752  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9753  setup_particle(Model m, ParticleIndex pi, State other) -> State
9754  setup_particle(_ParticleAdaptor decorator, State other) -> State
9755  """
9756  return _IMP_atom.State_setup_particle(*args)
9757 
9758  setup_particle = staticmethod(setup_particle)
9759 
9760  def __init__(self, *args):
9761  """
9762  __init__(IMP::atom::State self) -> State
9763  __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9764  __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9765  """
9766  this = _IMP_atom.new_State(*args)
9767  try:
9768  self.this.append(this)
9769  except __builtin__.Exception:
9770  self.this = this
9771 
9772  def show(self, *args):
9773  """
9774  show(State self, _ostream out)
9775  show(State self)
9776  """
9777  return _IMP_atom.State_show(self, *args)
9778 
9779 
9780  def get_is_setup(*args):
9781  """
9782  get_is_setup(_ParticleAdaptor p) -> bool
9783  get_is_setup(Model m, ParticleIndex pi) -> bool
9784  """
9785  return _IMP_atom.State_get_is_setup(*args)
9786 
9787  get_is_setup = staticmethod(get_is_setup)
9788 
9789  def get_state_index(self):
9790  """get_state_index(State self) -> unsigned int"""
9791  return _IMP_atom.State_get_state_index(self)
9792 
9793 
9794  def add_attribute(self, *args):
9795  """
9796  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9797  add_attribute(State self, FloatKey a0, IMP::Float a1)
9798  add_attribute(State self, IntKey a0, IMP::Int a1)
9799  add_attribute(State self, FloatsKey a0, IMP::Floats a1)
9800  add_attribute(State self, IntsKey a0, IMP::Ints a1)
9801  add_attribute(State self, StringKey a0, IMP::String a1)
9802  add_attribute(State self, ParticleIndexKey a0, Particle a1)
9803  add_attribute(State self, ObjectKey a0, Object a1)
9804  """
9805  return _IMP_atom.State_add_attribute(self, *args)
9806 
9807 
9808  def get_value(self, *args):
9809  """
9810  get_value(State self, FloatKey a0) -> IMP::Float
9811  get_value(State self, IntKey a0) -> IMP::Int
9812  get_value(State self, FloatsKey a0) -> IMP::Floats
9813  get_value(State self, IntsKey a0) -> IMP::Ints
9814  get_value(State self, StringKey a0) -> IMP::String
9815  get_value(State self, ParticleIndexKey a0) -> Particle
9816  get_value(State self, ObjectKey a0) -> Object
9817  """
9818  return _IMP_atom.State_get_value(self, *args)
9819 
9820 
9821  def set_value(self, *args):
9822  """
9823  set_value(State self, FloatKey a0, IMP::Float a1)
9824  set_value(State self, IntKey a0, IMP::Int a1)
9825  set_value(State self, FloatsKey a0, IMP::Floats a1)
9826  set_value(State self, IntsKey a0, IMP::Ints a1)
9827  set_value(State self, StringKey a0, IMP::String a1)
9828  set_value(State self, ParticleIndexKey a0, Particle a1)
9829  set_value(State self, ObjectKey a0, Object a1)
9830  """
9831  return _IMP_atom.State_set_value(self, *args)
9832 
9833 
9834  def remove_attribute(self, *args):
9835  """
9836  remove_attribute(State self, FloatKey a0)
9837  remove_attribute(State self, IntKey a0)
9838  remove_attribute(State self, FloatsKey a0)
9839  remove_attribute(State self, IntsKey a0)
9840  remove_attribute(State self, StringKey a0)
9841  remove_attribute(State self, ParticleIndexKey a0)
9842  remove_attribute(State self, ObjectKey a0)
9843  """
9844  return _IMP_atom.State_remove_attribute(self, *args)
9845 
9846 
9847  def has_attribute(self, *args):
9848  """
9849  has_attribute(State self, FloatKey a0) -> bool
9850  has_attribute(State self, IntKey a0) -> bool
9851  has_attribute(State self, FloatsKey a0) -> bool
9852  has_attribute(State self, IntsKey a0) -> bool
9853  has_attribute(State self, StringKey a0) -> bool
9854  has_attribute(State self, ParticleIndexKey a0) -> bool
9855  has_attribute(State self, ObjectKey a0) -> bool
9856  """
9857  return _IMP_atom.State_has_attribute(self, *args)
9858 
9859 
9860  def get_derivative(self, a0):
9861  """get_derivative(State self, FloatKey a0) -> double"""
9862  return _IMP_atom.State_get_derivative(self, a0)
9863 
9864 
9865  def get_name(self):
9866  """get_name(State self) -> std::string"""
9867  return _IMP_atom.State_get_name(self)
9868 
9869 
9870  def clear_caches(self):
9871  """clear_caches(State self)"""
9872  return _IMP_atom.State_clear_caches(self)
9873 
9874 
9875  def set_name(self, a0):
9876  """set_name(State self, std::string a0)"""
9877  return _IMP_atom.State_set_name(self, a0)
9878 
9879 
9880  def set_check_level(self, a0):
9881  """set_check_level(State self, IMP::CheckLevel a0)"""
9882  return _IMP_atom.State_set_check_level(self, a0)
9883 
9884 
9885  def add_to_derivative(self, a0, a1, a2):
9886  """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9887  return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9888 
9889 
9890  def set_is_optimized(self, a0, a1):
9891  """set_is_optimized(State self, FloatKey a0, bool a1)"""
9892  return _IMP_atom.State_set_is_optimized(self, a0, a1)
9893 
9894 
9895  def get_is_optimized(self, a0):
9896  """get_is_optimized(State self, FloatKey a0) -> bool"""
9897  return _IMP_atom.State_get_is_optimized(self, a0)
9898 
9899 
9900  def get_check_level(self):
9901  """get_check_level(State self) -> IMP::CheckLevel"""
9902  return _IMP_atom.State_get_check_level(self)
9903 
9904 
9905  def __eq__(self, *args):
9906  """
9907  __eq__(State self, State o) -> bool
9908  __eq__(State self, Particle d) -> bool
9909  """
9910  return _IMP_atom.State___eq__(self, *args)
9911 
9912 
9913  def __ne__(self, *args):
9914  """
9915  __ne__(State self, State o) -> bool
9916  __ne__(State self, Particle d) -> bool
9917  """
9918  return _IMP_atom.State___ne__(self, *args)
9919 
9920 
9921  def __le__(self, *args):
9922  """
9923  __le__(State self, State o) -> bool
9924  __le__(State self, Particle d) -> bool
9925  """
9926  return _IMP_atom.State___le__(self, *args)
9927 
9928 
9929  def __lt__(self, *args):
9930  """
9931  __lt__(State self, State o) -> bool
9932  __lt__(State self, Particle d) -> bool
9933  """
9934  return _IMP_atom.State___lt__(self, *args)
9935 
9936 
9937  def __ge__(self, *args):
9938  """
9939  __ge__(State self, State o) -> bool
9940  __ge__(State self, Particle d) -> bool
9941  """
9942  return _IMP_atom.State___ge__(self, *args)
9943 
9944 
9945  def __gt__(self, *args):
9946  """
9947  __gt__(State self, State o) -> bool
9948  __gt__(State self, Particle d) -> bool
9949  """
9950  return _IMP_atom.State___gt__(self, *args)
9951 
9952 
9953  def __hash__(self):
9954  """__hash__(State self) -> std::size_t"""
9955  return _IMP_atom.State___hash__(self)
9956 
9957 
9958  def __str__(self):
9959  """__str__(State self) -> std::string"""
9960  return _IMP_atom.State___str__(self)
9961 
9962 
9963  def __repr__(self):
9964  """__repr__(State self) -> std::string"""
9965  return _IMP_atom.State___repr__(self)
9966 
9967  __swig_destroy__ = _IMP_atom.delete_State
9968  __del__ = lambda self: None
9969 State_swigregister = _IMP_atom.State_swigregister
9970 State_swigregister(State)
9971 
9972 def State_setup_particle(*args):
9973  """
9974  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9975  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9976  setup_particle(Model m, ParticleIndex pi, State other) -> State
9977  State_setup_particle(_ParticleAdaptor decorator, State other) -> State
9978  """
9979  return _IMP_atom.State_setup_particle(*args)
9980 
9981 def State_get_is_setup(*args):
9982  """
9983  get_is_setup(_ParticleAdaptor p) -> bool
9984  State_get_is_setup(Model m, ParticleIndex pi) -> bool
9985  """
9986  return _IMP_atom.State_get_is_setup(*args)
9987 
9988 
9989 def get_state_index(h):
9990  """get_state_index(Hierarchy h) -> int"""
9991  return _IMP_atom.get_state_index(h)
9992 
9993 def get_phi_dihedral_atoms(rd):
9994  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9995  return _IMP_atom.get_phi_dihedral_atoms(rd)
9996 
9997 def get_psi_dihedral_atoms(rd):
9998  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9999  return _IMP_atom.get_psi_dihedral_atoms(rd)
10000 
10001 def get_omega_dihedral_atoms(rd):
10002  """get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
10003  return _IMP_atom.get_omega_dihedral_atoms(rd)
10004 
10006  """get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
10007  return _IMP_atom.get_chi_dihedral_atom_types(rt)
10008 
10009 def get_chi_dihedral_atoms(rd):
10010  """get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
10011  return _IMP_atom.get_chi_dihedral_atoms(rd)
10012 
10014  """get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
10015  return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
10016 class Molecule(Hierarchy):
10017  """Proxy of C++ IMP::atom::Molecule class."""
10018 
10019  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10020 
10021  def __init__(self, *args):
10022  """
10023  __init__(IMP::atom::Molecule self) -> Molecule
10024  __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
10025  __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
10026  """
10027  this = _IMP_atom.new_Molecule(*args)
10028  try:
10029  self.this.append(this)
10030  except __builtin__.Exception:
10031  self.this = this
10032 
10033  def show(self, *args):
10034  """
10035  show(Molecule self, _ostream out)
10036  show(Molecule self)
10037  """
10038  return _IMP_atom.Molecule_show(self, *args)
10039 
10040 
10041  def setup_particle(*args):
10042  """
10043  setup_particle(Model m, ParticleIndex pi) -> Molecule
10044  setup_particle(_ParticleAdaptor decorator) -> Molecule
10045  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10046  setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10047  """
10048  return _IMP_atom.Molecule_setup_particle(*args)
10049 
10050  setup_particle = staticmethod(setup_particle)
10051 
10052  def get_is_setup(*args):
10053  """
10054  get_is_setup(_ParticleAdaptor p) -> bool
10055  get_is_setup(Model m, ParticleIndex pi) -> bool
10056  """
10057  return _IMP_atom.Molecule_get_is_setup(*args)
10058 
10059  get_is_setup = staticmethod(get_is_setup)
10060 
10061  def add_attribute(self, *args):
10062  """
10063  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
10064  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
10065  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
10066  add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
10067  add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
10068  add_attribute(Molecule self, StringKey a0, IMP::String a1)
10069  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
10070  add_attribute(Molecule self, ObjectKey a0, Object a1)
10071  """
10072  return _IMP_atom.Molecule_add_attribute(self, *args)
10073 
10074 
10075  def get_value(self, *args):
10076  """
10077  get_value(Molecule self, FloatKey a0) -> IMP::Float
10078  get_value(Molecule self, IntKey a0) -> IMP::Int
10079  get_value(Molecule self, FloatsKey a0) -> IMP::Floats
10080  get_value(Molecule self, IntsKey a0) -> IMP::Ints
10081  get_value(Molecule self, StringKey a0) -> IMP::String
10082  get_value(Molecule self, ParticleIndexKey a0) -> Particle
10083  get_value(Molecule self, ObjectKey a0) -> Object
10084  """
10085  return _IMP_atom.Molecule_get_value(self, *args)
10086 
10087 
10088  def set_value(self, *args):
10089  """
10090  set_value(Molecule self, FloatKey a0, IMP::Float a1)
10091  set_value(Molecule self, IntKey a0, IMP::Int a1)
10092  set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
10093  set_value(Molecule self, IntsKey a0, IMP::Ints a1)
10094  set_value(Molecule self, StringKey a0, IMP::String a1)
10095  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
10096  set_value(Molecule self, ObjectKey a0, Object a1)
10097  """
10098  return _IMP_atom.Molecule_set_value(self, *args)
10099 
10100 
10101  def remove_attribute(self, *args):
10102  """
10103  remove_attribute(Molecule self, FloatKey a0)
10104  remove_attribute(Molecule self, IntKey a0)
10105  remove_attribute(Molecule self, FloatsKey a0)
10106  remove_attribute(Molecule self, IntsKey a0)
10107  remove_attribute(Molecule self, StringKey a0)
10108  remove_attribute(Molecule self, ParticleIndexKey a0)
10109  remove_attribute(Molecule self, ObjectKey a0)
10110  """
10111  return _IMP_atom.Molecule_remove_attribute(self, *args)
10112 
10113 
10114  def has_attribute(self, *args):
10115  """
10116  has_attribute(Molecule self, FloatKey a0) -> bool
10117  has_attribute(Molecule self, IntKey a0) -> bool
10118  has_attribute(Molecule self, FloatsKey a0) -> bool
10119  has_attribute(Molecule self, IntsKey a0) -> bool
10120  has_attribute(Molecule self, StringKey a0) -> bool
10121  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
10122  has_attribute(Molecule self, ObjectKey a0) -> bool
10123  """
10124  return _IMP_atom.Molecule_has_attribute(self, *args)
10125 
10126 
10127  def get_derivative(self, a0):
10128  """get_derivative(Molecule self, FloatKey a0) -> double"""
10129  return _IMP_atom.Molecule_get_derivative(self, a0)
10130 
10131 
10132  def get_name(self):
10133  """get_name(Molecule self) -> std::string"""
10134  return _IMP_atom.Molecule_get_name(self)
10135 
10136 
10137  def clear_caches(self):
10138  """clear_caches(Molecule self)"""
10139  return _IMP_atom.Molecule_clear_caches(self)
10140 
10141 
10142  def set_name(self, a0):
10143  """set_name(Molecule self, std::string a0)"""
10144  return _IMP_atom.Molecule_set_name(self, a0)
10145 
10146 
10147  def set_check_level(self, a0):
10148  """set_check_level(Molecule self, IMP::CheckLevel a0)"""
10149  return _IMP_atom.Molecule_set_check_level(self, a0)
10150 
10151 
10152  def add_to_derivative(self, a0, a1, a2):
10153  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10154  return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
10155 
10156 
10157  def set_is_optimized(self, a0, a1):
10158  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
10159  return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
10160 
10161 
10162  def get_is_optimized(self, a0):
10163  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
10164  return _IMP_atom.Molecule_get_is_optimized(self, a0)
10165 
10166 
10167  def get_check_level(self):
10168  """get_check_level(Molecule self) -> IMP::CheckLevel"""
10169  return _IMP_atom.Molecule_get_check_level(self)
10170 
10171 
10172  def __eq__(self, *args):
10173  """
10174  __eq__(Molecule self, Molecule o) -> bool
10175  __eq__(Molecule self, Particle d) -> bool
10176  """
10177  return _IMP_atom.Molecule___eq__(self, *args)
10178 
10179 
10180  def __ne__(self, *args):
10181  """
10182  __ne__(Molecule self, Molecule o) -> bool
10183  __ne__(Molecule self, Particle d) -> bool
10184  """
10185  return _IMP_atom.Molecule___ne__(self, *args)
10186 
10187 
10188  def __le__(self, *args):
10189  """
10190  __le__(Molecule self, Molecule o) -> bool
10191  __le__(Molecule self, Particle d) -> bool
10192  """
10193  return _IMP_atom.Molecule___le__(self, *args)
10194 
10195 
10196  def __lt__(self, *args):
10197  """
10198  __lt__(Molecule self, Molecule o) -> bool
10199  __lt__(Molecule self, Particle d) -> bool
10200  """
10201  return _IMP_atom.Molecule___lt__(self, *args)
10202 
10203 
10204  def __ge__(self, *args):
10205  """
10206  __ge__(Molecule self, Molecule o) -> bool
10207  __ge__(Molecule self, Particle d) -> bool
10208  """
10209  return _IMP_atom.Molecule___ge__(self, *args)
10210 
10211 
10212  def __gt__(self, *args):
10213  """
10214  __gt__(Molecule self, Molecule o) -> bool
10215  __gt__(Molecule self, Particle d) -> bool
10216  """
10217  return _IMP_atom.Molecule___gt__(self, *args)
10218 
10219 
10220  def __hash__(self):
10221  """__hash__(Molecule self) -> std::size_t"""
10222  return _IMP_atom.Molecule___hash__(self)
10223 
10224 
10225  def __str__(self):
10226  """__str__(Molecule self) -> std::string"""
10227  return _IMP_atom.Molecule___str__(self)
10228 
10229 
10230  def __repr__(self):
10231  """__repr__(Molecule self) -> std::string"""
10232  return _IMP_atom.Molecule___repr__(self)
10233 
10234  __swig_destroy__ = _IMP_atom.delete_Molecule
10235  __del__ = lambda self: None
10236 Molecule_swigregister = _IMP_atom.Molecule_swigregister
10237 Molecule_swigregister(Molecule)
10238 
10239 def Molecule_setup_particle(*args):
10240  """
10241  setup_particle(Model m, ParticleIndex pi) -> Molecule
10242  setup_particle(_ParticleAdaptor decorator) -> Molecule
10243  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10244  Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10245  """
10246  return _IMP_atom.Molecule_setup_particle(*args)
10247 
10248 def Molecule_get_is_setup(*args):
10249  """
10250  get_is_setup(_ParticleAdaptor p) -> bool
10251  Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
10252  """
10253  return _IMP_atom.Molecule_get_is_setup(*args)
10254 
10255 
10256 def get_molecule_name(h):
10257  """get_molecule_name(Hierarchy h) -> std::string"""
10258  return _IMP_atom.get_molecule_name(h)
10259 class Copy(Molecule):
10260  """Proxy of C++ IMP::atom::Copy class."""
10261 
10262  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10263 
10264  def get_copy_index_key():
10265  """get_copy_index_key() -> IntKey"""
10266  return _IMP_atom.Copy_get_copy_index_key()
10267 
10268  get_copy_index_key = staticmethod(get_copy_index_key)
10269 
10270  def __init__(self, *args):
10271  """
10272  __init__(IMP::atom::Copy self) -> Copy
10273  __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
10274  __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
10275  """
10276  this = _IMP_atom.new_Copy(*args)
10277  try:
10278  self.this.append(this)
10279  except __builtin__.Exception:
10280  self.this = this
10281 
10282  def show(self, *args):
10283  """
10284  show(Copy self, _ostream out)
10285  show(Copy self)
10286  """
10287  return _IMP_atom.Copy_show(self, *args)
10288 
10289 
10290  def setup_particle(*args):
10291  """
10292  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10293  setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10294  """
10295  return _IMP_atom.Copy_setup_particle(*args)
10296 
10297  setup_particle = staticmethod(setup_particle)
10298 
10299  def get_is_setup(*args):
10300  """
10301  get_is_setup(_ParticleAdaptor p) -> bool
10302  get_is_setup(Model m, ParticleIndex pi) -> bool
10303  """
10304  return _IMP_atom.Copy_get_is_setup(*args)
10305 
10306  get_is_setup = staticmethod(get_is_setup)
10307 
10308  def get_copy_index(self):
10309  """get_copy_index(Copy self) -> int"""
10310  return _IMP_atom.Copy_get_copy_index(self)
10311 
10312 
10313  def add_attribute(self, *args):
10314  """
10315  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
10316  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
10317  add_attribute(Copy self, IntKey a0, IMP::Int a1)
10318  add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
10319  add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
10320  add_attribute(Copy self, StringKey a0, IMP::String a1)
10321  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
10322  add_attribute(Copy self, ObjectKey a0, Object a1)
10323  """
10324  return _IMP_atom.Copy_add_attribute(self, *args)
10325 
10326 
10327  def get_value(self, *args):
10328  """
10329  get_value(Copy self, FloatKey a0) -> IMP::Float
10330  get_value(Copy self, IntKey a0) -> IMP::Int
10331  get_value(Copy self, FloatsKey a0) -> IMP::Floats
10332  get_value(Copy self, IntsKey a0) -> IMP::Ints
10333  get_value(Copy self, StringKey a0) -> IMP::String
10334  get_value(Copy self, ParticleIndexKey a0) -> Particle
10335  get_value(Copy self, ObjectKey a0) -> Object
10336  """
10337  return _IMP_atom.Copy_get_value(self, *args)
10338 
10339 
10340  def set_value(self, *args):
10341  """
10342  set_value(Copy self, FloatKey a0, IMP::Float a1)
10343  set_value(Copy self, IntKey a0, IMP::Int a1)
10344  set_value(Copy self, FloatsKey a0, IMP::Floats a1)
10345  set_value(Copy self, IntsKey a0, IMP::Ints a1)
10346  set_value(Copy self, StringKey a0, IMP::String a1)
10347  set_value(Copy self, ParticleIndexKey a0, Particle a1)
10348  set_value(Copy self, ObjectKey a0, Object a1)
10349  """
10350  return _IMP_atom.Copy_set_value(self, *args)
10351 
10352 
10353  def remove_attribute(self, *args):
10354  """
10355  remove_attribute(Copy self, FloatKey a0)
10356  remove_attribute(Copy self, IntKey a0)
10357  remove_attribute(Copy self, FloatsKey a0)
10358  remove_attribute(Copy self, IntsKey a0)
10359  remove_attribute(Copy self, StringKey a0)
10360  remove_attribute(Copy self, ParticleIndexKey a0)
10361  remove_attribute(Copy self, ObjectKey a0)
10362  """
10363  return _IMP_atom.Copy_remove_attribute(self, *args)
10364 
10365 
10366  def has_attribute(self, *args):
10367  """
10368  has_attribute(Copy self, FloatKey a0) -> bool
10369  has_attribute(Copy self, IntKey a0) -> bool
10370  has_attribute(Copy self, FloatsKey a0) -> bool
10371  has_attribute(Copy self, IntsKey a0) -> bool
10372  has_attribute(Copy self, StringKey a0) -> bool
10373  has_attribute(Copy self, ParticleIndexKey a0) -> bool
10374  has_attribute(Copy self, ObjectKey a0) -> bool
10375  """
10376  return _IMP_atom.Copy_has_attribute(self, *args)
10377 
10378 
10379  def get_derivative(self, a0):
10380  """get_derivative(Copy self, FloatKey a0) -> double"""
10381  return _IMP_atom.Copy_get_derivative(self, a0)
10382 
10383 
10384  def get_name(self):
10385  """get_name(Copy self) -> std::string"""
10386  return _IMP_atom.Copy_get_name(self)
10387 
10388 
10389  def clear_caches(self):
10390  """clear_caches(Copy self)"""
10391  return _IMP_atom.Copy_clear_caches(self)
10392 
10393 
10394  def set_name(self, a0):
10395  """set_name(Copy self, std::string a0)"""
10396  return _IMP_atom.Copy_set_name(self, a0)
10397 
10398 
10399  def set_check_level(self, a0):
10400  """set_check_level(Copy self, IMP::CheckLevel a0)"""
10401  return _IMP_atom.Copy_set_check_level(self, a0)
10402 
10403 
10404  def add_to_derivative(self, a0, a1, a2):
10405  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10406  return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
10407 
10408 
10409  def set_is_optimized(self, a0, a1):
10410  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
10411  return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
10412 
10413 
10414  def get_is_optimized(self, a0):
10415  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
10416  return _IMP_atom.Copy_get_is_optimized(self, a0)
10417 
10418 
10419  def get_check_level(self):
10420  """get_check_level(Copy self) -> IMP::CheckLevel"""
10421  return _IMP_atom.Copy_get_check_level(self)
10422 
10423 
10424  def __eq__(self, *args):
10425  """
10426  __eq__(Copy self, Copy o) -> bool
10427  __eq__(Copy self, Particle d) -> bool
10428  """
10429  return _IMP_atom.Copy___eq__(self, *args)
10430 
10431 
10432  def __ne__(self, *args):
10433  """
10434  __ne__(Copy self, Copy o) -> bool
10435  __ne__(Copy self, Particle d) -> bool
10436  """
10437  return _IMP_atom.Copy___ne__(self, *args)
10438 
10439 
10440  def __le__(self, *args):
10441  """
10442  __le__(Copy self, Copy o) -> bool
10443  __le__(Copy self, Particle d) -> bool
10444  """
10445  return _IMP_atom.Copy___le__(self, *args)
10446 
10447 
10448  def __lt__(self, *args):
10449  """
10450  __lt__(Copy self, Copy o) -> bool
10451  __lt__(Copy self, Particle d) -> bool
10452  """
10453  return _IMP_atom.Copy___lt__(self, *args)
10454 
10455 
10456  def __ge__(self, *args):
10457  """
10458  __ge__(Copy self, Copy o) -> bool
10459  __ge__(Copy self, Particle d) -> bool
10460  """
10461  return _IMP_atom.Copy___ge__(self, *args)
10462 
10463 
10464  def __gt__(self, *args):
10465  """
10466  __gt__(Copy self, Copy o) -> bool
10467  __gt__(Copy self, Particle d) -> bool
10468  """
10469  return _IMP_atom.Copy___gt__(self, *args)
10470 
10471 
10472  def __hash__(self):
10473  """__hash__(Copy self) -> std::size_t"""
10474  return _IMP_atom.Copy___hash__(self)
10475 
10476 
10477  def __str__(self):
10478  """__str__(Copy self) -> std::string"""
10479  return _IMP_atom.Copy___str__(self)
10480 
10481 
10482  def __repr__(self):
10483  """__repr__(Copy self) -> std::string"""
10484  return _IMP_atom.Copy___repr__(self)
10485 
10486  __swig_destroy__ = _IMP_atom.delete_Copy
10487  __del__ = lambda self: None
10488 Copy_swigregister = _IMP_atom.Copy_swigregister
10489 Copy_swigregister(Copy)
10490 
10491 def Copy_get_copy_index_key():
10492  """Copy_get_copy_index_key() -> IntKey"""
10493  return _IMP_atom.Copy_get_copy_index_key()
10494 
10495 def Copy_setup_particle(*args):
10496  """
10497  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10498  Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10499  """
10500  return _IMP_atom.Copy_setup_particle(*args)
10501 
10502 def Copy_get_is_setup(*args):
10503  """
10504  get_is_setup(_ParticleAdaptor p) -> bool
10505  Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
10506  """
10507  return _IMP_atom.Copy_get_is_setup(*args)
10508 
10509 
10510 def get_copy_index(h):
10511  """get_copy_index(Hierarchy h) -> int"""
10512  return _IMP_atom.get_copy_index(h)
10513 class Selection(IMP._ParticleIndexesAdaptor):
10514  """Proxy of C++ IMP::atom::Selection class."""
10515 
10516  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10517  NONE = _IMP_atom.Selection_NONE
10518  C = _IMP_atom.Selection_C
10519  N = _IMP_atom.Selection_N
10520 
10521  def __init__(self, *args):
10522  """
10523  __init__(IMP::atom::Selection self) -> Selection
10524  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
10525  __init__(IMP::atom::Selection self, Particle h) -> Selection
10526  __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10527  __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
10528  """
10529  this = _IMP_atom.new_Selection(*args)
10530  try:
10531  self.this.append(this)
10532  except __builtin__.Exception:
10533  self.this = this
10534 
10535  def create_clone(self):
10536  """create_clone(Selection self) -> Selection"""
10537  return _IMP_atom.Selection_create_clone(self)
10538 
10539 
10540  def get_hierarchies(self):
10541  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10542  return _IMP_atom.Selection_get_hierarchies(self)
10543 
10544 
10545  def set_molecules(self, mols):
10546  """set_molecules(Selection self, IMP::Strings mols)"""
10547  return _IMP_atom.Selection_set_molecules(self, mols)
10548 
10549 
10550  def set_resolution(self, r):
10551  """set_resolution(Selection self, double r)"""
10552  return _IMP_atom.Selection_set_resolution(self, r)
10553 
10554 
10555  def set_representation_type(self, t):
10556  """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10557  return _IMP_atom.Selection_set_representation_type(self, t)
10558 
10559 
10560  def set_state_index(self, state):
10561  """set_state_index(Selection self, int state)"""
10562  return _IMP_atom.Selection_set_state_index(self, state)
10563 
10564 
10565  def set_state_indexes(self, states):
10566  """set_state_indexes(Selection self, IMP::Ints states)"""
10567  return _IMP_atom.Selection_set_state_indexes(self, states)
10568 
10569 
10570  def set_terminus(self, t):
10571  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10572  return _IMP_atom.Selection_set_terminus(self, t)
10573 
10574 
10575  def set_element(self, e):
10576  """set_element(Selection self, IMP::atom::Element e)"""
10577  return _IMP_atom.Selection_set_element(self, e)
10578 
10579 
10580  def set_chain_ids(self, chains):
10581  """set_chain_ids(Selection self, IMP::Strings chains)"""
10582  return _IMP_atom.Selection_set_chain_ids(self, chains)
10583 
10584 
10585  def set_chains(self, chains):
10586  """set_chains(Selection self, IMP::Strings chains)"""
10587  return _IMP_atom.Selection_set_chains(self, chains)
10588 
10589 
10590  def set_residue_indexes(self, indexes):
10591  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10592  return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10593 
10594 
10595  def set_atom_types(self, types):
10596  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10597  return _IMP_atom.Selection_set_atom_types(self, types)
10598 
10599 
10600  def set_residue_types(self, types):
10601  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10602  return _IMP_atom.Selection_set_residue_types(self, types)
10603 
10604 
10605  def set_domains(self, names):
10606  """set_domains(Selection self, IMP::Strings names)"""
10607  return _IMP_atom.Selection_set_domains(self, names)
10608 
10609 
10610  def set_molecule(self, mol):
10611  """set_molecule(Selection self, std::string mol)"""
10612  return _IMP_atom.Selection_set_molecule(self, mol)
10613 
10614 
10615  def set_chain_id(self, c):
10616  """set_chain_id(Selection self, std::string c)"""
10617  return _IMP_atom.Selection_set_chain_id(self, c)
10618 
10619 
10620  def set_chain(self, c):
10621  """set_chain(Selection self, std::string c)"""
10622  return _IMP_atom.Selection_set_chain(self, c)
10623 
10624 
10625  def set_residue_index(self, i):
10626  """set_residue_index(Selection self, int i)"""
10627  return _IMP_atom.Selection_set_residue_index(self, i)
10628 
10629 
10630  def set_atom_type(self, types):
10631  """set_atom_type(Selection self, AtomType types)"""
10632  return _IMP_atom.Selection_set_atom_type(self, types)
10633 
10634 
10635  def set_residue_type(self, type):
10636  """set_residue_type(Selection self, ResidueType type)"""
10637  return _IMP_atom.Selection_set_residue_type(self, type)
10638 
10639 
10640  def set_domain(self, name):
10641  """set_domain(Selection self, std::string name)"""
10642  return _IMP_atom.Selection_set_domain(self, name)
10643 
10644 
10645  def set_copy_index(self, copy):
10646  """set_copy_index(Selection self, unsigned int copy)"""
10647  return _IMP_atom.Selection_set_copy_index(self, copy)
10648 
10649 
10650  def set_copy_indexes(self, copies):
10651  """set_copy_indexes(Selection self, IMP::Ints copies)"""
10652  return _IMP_atom.Selection_set_copy_indexes(self, copies)
10653 
10654 
10655  def set_particle_type(self, t):
10656  """set_particle_type(Selection self, ParticleType t)"""
10657  return _IMP_atom.Selection_set_particle_type(self, t)
10658 
10659 
10660  def set_particle_types(self, t):
10661  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10662  return _IMP_atom.Selection_set_particle_types(self, t)
10663 
10664 
10665  def set_hierarchy_types(self, types):
10666  """set_hierarchy_types(Selection self, IMP::Ints types)"""
10667  return _IMP_atom.Selection_set_hierarchy_types(self, types)
10668 
10669 
10670  def set_intersection(self, s):
10671  """set_intersection(Selection self, Selection s)"""
10672  return _IMP_atom.Selection_set_intersection(self, s)
10673 
10674 
10675  def set_union(self, s):
10676  """set_union(Selection self, Selection s)"""
10677  return _IMP_atom.Selection_set_union(self, s)
10678 
10679 
10680  def set_symmetric_difference(self, s):
10681  """set_symmetric_difference(Selection self, Selection s)"""
10682  return _IMP_atom.Selection_set_symmetric_difference(self, s)
10683 
10684 
10685  def set_difference(self, s):
10686  """set_difference(Selection self, Selection s)"""
10687  return _IMP_atom.Selection_set_difference(self, s)
10688 
10689 
10690  def get_selected_particles(self, with_representation=True):
10691  """
10692  get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10693  get_selected_particles(Selection self) -> IMP::ParticlesTemp
10694  """
10695  return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10696 
10697 
10698  def get_selected_particle_indexes(self, with_representation=True):
10699  """
10700  get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10701  get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10702  """
10703  return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10704 
10705 
10706  def show(self, *args):
10707  """
10708  show(Selection self, _ostream out)
10709  show(Selection self)
10710  """
10711  return _IMP_atom.Selection_show(self, *args)
10712 
10713 
10714  def __str__(self):
10715  """__str__(Selection self) -> std::string"""
10716  return _IMP_atom.Selection___str__(self)
10717 
10718 
10719  def __repr__(self):
10720  """__repr__(Selection self) -> std::string"""
10721  return _IMP_atom.Selection___repr__(self)
10722 
10723 
10724  def __init__(self, hierarchy=None,
10725  hierarchies=None, **params):
10726  if hierarchy and hierarchies:
10727  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
10728  if hierarchy:
10729  this = _IMP_atom.new_Selection(hierarchy)
10730  try: self.this.append(this)
10731  except: self.this = this
10732  elif hierarchies:
10733  this = _IMP_atom.new_Selection(hierarchies)
10734  try: self.this.append(this)
10735  except: self.this = this
10736  else:
10737  raise ValueError("Either hierarchy or hierarchies must be provided.")
10738  for k in params.keys():
10739  eval("self.set_%s(params[k])"%k)
10740 
10741  def union(self, s):
10742  news = self.create_clone()
10743  news.union_update(s)
10744  return news
10745  def intersection(self, s):
10746  news = self.create_clone()
10747  news.intersection_update(s)
10748  return news
10749  def symmetric_difference(self, s):
10750  news = self.create_clone()
10751  news.symmetric_difference_update(s)
10752  return news
10753  def difference(self, s):
10754  news = self.create_clone()
10755  news.difference_update(s)
10756  return news
10757  def union_update(self, s):
10758  self.set_union(s)
10759  return self
10760  def intersection_update(self, s):
10761  self.set_intersection(s)
10762  return self
10763  def symmetric_difference_update(self, s):
10764  self.set_symmetric_difference(s)
10765  return self
10766  def difference_update(self, s):
10767  self.set_difference(s)
10768  return self
10769  __or__ = union
10770  __and__ = intersection
10771  __xor__ = symmetric_difference
10772  __sub__ = difference
10773  __ior__ = union_update
10774  __iand__ = intersection_update
10775  __ixor__ = symmetric_difference_update
10776  __isub__ = difference_update
10777 
10778  __swig_destroy__ = _IMP_atom.delete_Selection
10779  __del__ = lambda self: None
10780 Selection_swigregister = _IMP_atom.Selection_swigregister
10781 Selection_swigregister(Selection)
10782 
10783 
10784 def create_distance_restraint(*args):
10785  """
10786  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10787  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10788  """
10789  return _IMP_atom.create_distance_restraint(*args)
10790 
10792  """
10793  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10794  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10795  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10796  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10797  """
10798  return _IMP_atom.create_connectivity_restraint(*args)
10799 
10801  """
10802  create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10803  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10804  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10805  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10806  """
10807  return _IMP_atom.create_internal_connectivity_restraint(*args)
10808 
10809 def create_cover(*args):
10810  """
10811  create_cover(Selection s, std::string name) -> XYZR
10812  create_cover(Selection s) -> XYZR
10813  """
10814  return _IMP_atom.create_cover(*args)
10815 
10816 def get_mass(*args):
10817  """
10818  get_mass(ResidueType c) -> double
10819  get_mass(Selection s) -> double
10820  """
10821  return _IMP_atom.get_mass(*args)
10822 
10823 def get_volume(s):
10824  """get_volume(Selection s) -> double"""
10825  return _IMP_atom.get_volume(s)
10826 
10827 def get_surface_area(s):
10828  """get_surface_area(Selection s) -> double"""
10829  return _IMP_atom.get_surface_area(s)
10830 
10831 def get_leaves(*args):
10832  """
10833  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10834  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10835  get_leaves(Selection h) -> IMP::atom::Hierarchies
10836  """
10837  return _IMP_atom.get_leaves(*args)
10838 class SelectionGeometry(IMP.display.Geometry):
10839  """Proxy of C++ IMP::atom::SelectionGeometry class."""
10840 
10841  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10842 
10843  def __init__(self, *args):
10844  """
10845  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10846  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10847  """
10848  this = _IMP_atom.new_SelectionGeometry(*args)
10849  try:
10850  self.this.append(this)
10851  except __builtin__.Exception:
10852  self.this = this
10853 
10854  def get_version_info(self):
10855  """get_version_info(SelectionGeometry self) -> VersionInfo"""
10856  return _IMP_atom.SelectionGeometry_get_version_info(self)
10857 
10858 
10859  def __str__(self):
10860  """__str__(SelectionGeometry self) -> std::string"""
10861  return _IMP_atom.SelectionGeometry___str__(self)
10862 
10863 
10864  def __repr__(self):
10865  """__repr__(SelectionGeometry self) -> std::string"""
10866  return _IMP_atom.SelectionGeometry___repr__(self)
10867 
10868 
10869  @staticmethod
10870  def get_from(o):
10871  return _object_cast_to_SelectionGeometry(o)
10872 
10873 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10874 SelectionGeometry_swigregister(SelectionGeometry)
10875 
10876 
10877 def get_rmsd(*args):
10878  """
10879  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10880  get_rmsd(Selection s0, Selection s1) -> double
10881  """
10882  return _IMP_atom.get_rmsd(*args)
10883 
10884 def get_rmsd_transforming_first(*args):
10885  """
10886  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10887  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10888  """
10889  return _IMP_atom.get_rmsd_transforming_first(*args)
10890 
10891 def get_placement_score(source, target):
10892  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10893  return _IMP_atom.get_placement_score(source, target)
10894 
10895 def get_component_placement_score(ref1, ref2, mdl1, mdl2):
10896  """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"""
10897  return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10898 
10899 def get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2):
10900  """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"""
10901  return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10902 
10903 def get_radius_of_gyration(*args):
10904  """
10905  get_radius_of_gyration(Selection s) -> double
10906  get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10907  get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10908  """
10909  return _IMP_atom.get_radius_of_gyration(*args)
10910 class ForceFieldParameters(IMP.Object):
10911  """Proxy of C++ IMP::atom::ForceFieldParameters class."""
10912 
10913  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10914 
10915  def __init__(self):
10916  """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10917  this = _IMP_atom.new_ForceFieldParameters()
10918  try:
10919  self.this.append(this)
10920  except __builtin__.Exception:
10921  self.this = this
10922 
10923  def get_radius(self, atom):
10924  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10925  return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10926 
10927 
10928  def get_epsilon(self, atom):
10929  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10930  return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10931 
10932 
10933  def add_radii(self, *args):
10934  """
10935  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10936  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10937  add_radii(ForceFieldParameters self, Hierarchy mhd)
10938  """
10939  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10940 
10941 
10942  def add_well_depths(self, mhd):
10943  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10944  return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10945 
10946 
10947  def add_bonds(self, mhd):
10948  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10949  return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10950 
10951  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10952  __del__ = lambda self: None
10953 
10954  def __str__(self):
10955  """__str__(ForceFieldParameters self) -> std::string"""
10956  return _IMP_atom.ForceFieldParameters___str__(self)
10957 
10958 
10959  def __repr__(self):
10960  """__repr__(ForceFieldParameters self) -> std::string"""
10961  return _IMP_atom.ForceFieldParameters___repr__(self)
10962 
10963 
10964  @staticmethod
10965  def get_from(o):
10966  return _object_cast_to_ForceFieldParameters(o)
10967 
10968 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10969 ForceFieldParameters_swigregister(ForceFieldParameters)
10970 
10971 class CHARMMAtomTopology(object):
10972  """Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10973 
10974  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10975 
10976  def __init__(self, *args):
10977  """
10978  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10979  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10980  """
10981  this = _IMP_atom.new_CHARMMAtomTopology(*args)
10982  try:
10983  self.this.append(this)
10984  except __builtin__.Exception:
10985  self.this = this
10986 
10987  def get_name(self):
10988  """get_name(CHARMMAtomTopology self) -> std::string"""
10989  return _IMP_atom.CHARMMAtomTopology_get_name(self)
10990 
10991 
10992  def get_charmm_type(self):
10993  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10994  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10995 
10996 
10997  def get_charge(self):
10998  """get_charge(CHARMMAtomTopology self) -> double"""
10999  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
11000 
11001 
11002  def set_charmm_type(self, charmm_type):
11003  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
11004  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
11005 
11006 
11007  def set_charge(self, charge):
11008  """set_charge(CHARMMAtomTopology self, double charge)"""
11009  return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
11010 
11011 
11012  def show(self, *args):
11013  """
11014  show(CHARMMAtomTopology self, _ostream out)
11015  show(CHARMMAtomTopology self)
11016  """
11017  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
11018 
11019 
11020  def __str__(self):
11021  """__str__(CHARMMAtomTopology self) -> std::string"""
11022  return _IMP_atom.CHARMMAtomTopology___str__(self)
11023 
11024 
11025  def __repr__(self):
11026  """__repr__(CHARMMAtomTopology self) -> std::string"""
11027  return _IMP_atom.CHARMMAtomTopology___repr__(self)
11028 
11029  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
11030  __del__ = lambda self: None
11031 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
11032 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
11033 
11034 class CHARMMBondEndpoint(object):
11035  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
11036 
11037  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11038 
11039  def __init__(self, atom_name, residue=None):
11040  """
11041  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
11042  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
11043  """
11044  this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
11045  try:
11046  self.this.append(this)
11047  except __builtin__.Exception:
11048  self.this = this
11049 
11050  def get_atom_name(self):
11051  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
11052  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
11053 
11054 
11055  def get_atom(self, current_residue, previous_residue, next_residue, resmap):
11056  """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"""
11057  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
11058 
11059 
11060  def show(self, *args):
11061  """
11062  show(CHARMMBondEndpoint self, _ostream out)
11063  show(CHARMMBondEndpoint self)
11064  """
11065  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
11066 
11067 
11068  def __str__(self):
11069  """__str__(CHARMMBondEndpoint self) -> std::string"""
11070  return _IMP_atom.CHARMMBondEndpoint___str__(self)
11071 
11072 
11073  def __repr__(self):
11074  """__repr__(CHARMMBondEndpoint self) -> std::string"""
11075  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
11076 
11077  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
11078  __del__ = lambda self: None
11079 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
11080 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
11081 
11082 class CHARMMDihedral(object):
11083  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class."""
11084 
11085  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11086  __repr__ = _swig_repr
11087 
11088  def __init__(self, atoms):
11089  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
11090  this = _IMP_atom.new_CHARMMDihedral(atoms)
11091  try:
11092  self.this.append(this)
11093  except __builtin__.Exception:
11094  self.this = this
11095 
11096  def get_endpoint(self, i):
11097  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
11098  return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
11099 
11100 
11101  def get_contains_atom(self, name):
11102  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
11103  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
11104 
11105 
11106  def show(self, *args):
11107  """
11108  show(CHARMMDihedral self, _ostream out)
11109  show(CHARMMDihedral self)
11110  """
11111  return _IMP_atom.CHARMMDihedral_show(self, *args)
11112 
11113  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
11114  __del__ = lambda self: None
11115 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
11116 CHARMMDihedral_swigregister(CHARMMDihedral)
11117 
11118 class CHARMMInternalCoordinate(CHARMMDihedral):
11119  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
11120 
11121  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11122 
11123  def __init__(self, *args):
11124  """
11125  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
11126  __init__(IMP::atom::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
11127  """
11128  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
11129  try:
11130  self.this.append(this)
11131  except __builtin__.Exception:
11132  self.this = this
11133 
11134  def get_first_distance(self):
11135  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
11136  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
11137 
11138 
11139  def get_second_distance(self):
11140  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
11141  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
11142 
11143 
11144  def get_first_angle(self):
11145  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
11146  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
11147 
11148 
11149  def get_second_angle(self):
11150  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
11151  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
11152 
11153 
11154  def get_dihedral(self):
11155  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
11156  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
11157 
11158 
11159  def get_improper(self):
11160  """get_improper(CHARMMInternalCoordinate self) -> bool"""
11161  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
11162 
11163 
11164  def show(self, *args):
11165  """
11166  show(CHARMMInternalCoordinate self, _ostream out)
11167  show(CHARMMInternalCoordinate self)
11168  """
11169  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
11170 
11171 
11172  def __str__(self):
11173  """__str__(CHARMMInternalCoordinate self) -> std::string"""
11174  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
11175 
11176 
11177  def __repr__(self):
11178  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
11179  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
11180 
11181  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
11182  __del__ = lambda self: None
11183 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
11184 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
11185 
11186 class CHARMMResidueTopologyBase(IMP.Object):
11187  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
11188 
11189  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11190 
11191  def __init__(self, *args, **kwargs):
11192  raise AttributeError("No constructor defined")
11193 
11194  def get_type(self):
11195  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
11196  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
11197 
11198 
11199  def get_number_of_atoms(self):
11200  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
11201  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
11202 
11203 
11204  def add_atom(self, atom):
11205  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
11206  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
11207 
11208 
11209  def get_atom(self, *args):
11210  """
11211  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
11212  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
11213  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
11214  """
11215  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
11216 
11217 
11218  def get_number_of_bonds(self):
11219  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
11220  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
11221 
11222 
11223  def add_bond(self, bond):
11224  """add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
11225  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
11226 
11227 
11228  def get_number_of_angles(self):
11229  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
11230  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
11231 
11232 
11233  def add_angle(self, bond):
11234  """add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
11235  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
11236 
11237 
11238  def get_number_of_dihedrals(self):
11239  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
11240  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
11241 
11242 
11243  def add_dihedral(self, bond):
11244  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11245  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
11246 
11247 
11248  def get_number_of_impropers(self):
11249  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
11250  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
11251 
11252 
11253  def add_improper(self, bond):
11254  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11255  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
11256 
11257 
11258  def get_number_of_internal_coordinates(self):
11259  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11260  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11261 
11262 
11263  def add_internal_coordinate(self, ic):
11264  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11265  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11266 
11267 
11268  def get_internal_coordinate(self, index):
11269  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11270  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11271 
11272 
11273  def get_bond(self, index):
11274  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
11275  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11276 
11277 
11278  def get_angle(self, index):
11279  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
11280  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11281 
11282 
11283  def get_dihedral(self, index):
11284  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11285  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11286 
11287 
11288  def get_improper(self, index):
11289  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11290  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11291 
11292 
11293  def get_version_info(self):
11294  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11295  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11296 
11297 
11298  def __str__(self):
11299  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
11300  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11301 
11302 
11303  def __repr__(self):
11304  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11305  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11306 
11307 
11308  @staticmethod
11309  def get_from(o):
11310  return _object_cast_to_CHARMMResidueTopologyBase(o)
11311 
11312 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
11313 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11314 
11315 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11316  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
11317 
11318  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11319 
11320  def __init__(self, *args):
11321  """
11322  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11323  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11324  """
11325  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
11326  try:
11327  self.this.append(this)
11328  except __builtin__.Exception:
11329  self.this = this
11330 
11331  def remove_atom(self, name):
11332  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11333  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11334 
11335 
11336  def set_default_first_patch(self, patch):
11337  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11338  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11339 
11340 
11341  def set_default_last_patch(self, patch):
11342  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11343  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11344 
11345 
11346  def get_default_first_patch(self):
11347  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11348  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11349 
11350 
11351  def get_default_last_patch(self):
11352  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11353  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11354 
11355 
11356  def __str__(self):
11357  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
11358  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11359 
11360 
11361  def __repr__(self):
11362  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11363  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11364 
11365 
11366  @staticmethod
11367  def get_from(o):
11368  return _object_cast_to_CHARMMIdealResidueTopology(o)
11369 
11370 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
11371 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11372 
11373 class CHARMMPatch(CHARMMResidueTopologyBase):
11374  """Proxy of C++ IMP::atom::CHARMMPatch class."""
11375 
11376  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11377 
11378  def __init__(self, type):
11379  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
11380  this = _IMP_atom.new_CHARMMPatch(type)
11381  try:
11382  self.this.append(this)
11383  except __builtin__.Exception:
11384  self.this = this
11385 
11386  def add_removed_atom(self, name):
11387  """add_removed_atom(CHARMMPatch self, std::string name)"""
11388  return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11389 
11390 
11391  def get_number_of_removed_atoms(self):
11392  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11393  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11394 
11395 
11396  def get_removed_atom(self, i):
11397  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11398  return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11399 
11400 
11401  def apply(self, *args):
11402  """
11403  apply(CHARMMPatch self, CHARMMResidueTopology res)
11404  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11405  """
11406  return _IMP_atom.CHARMMPatch_apply(self, *args)
11407 
11408 
11409  def __str__(self):
11410  """__str__(CHARMMPatch self) -> std::string"""
11411  return _IMP_atom.CHARMMPatch___str__(self)
11412 
11413 
11414  def __repr__(self):
11415  """__repr__(CHARMMPatch self) -> std::string"""
11416  return _IMP_atom.CHARMMPatch___repr__(self)
11417 
11418 
11419  @staticmethod
11420  def get_from(o):
11421  return _object_cast_to_CHARMMPatch(o)
11422 
11423 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
11424 CHARMMPatch_swigregister(CHARMMPatch)
11425 
11426 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11427  """Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
11428 
11429  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11430 
11431  def __init__(self, *args):
11432  """
11433  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11434  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11435  """
11436  this = _IMP_atom.new_CHARMMResidueTopology(*args)
11437  try:
11438  self.this.append(this)
11439  except __builtin__.Exception:
11440  self.this = this
11441 
11442  def get_patched(self):
11443  """get_patched(CHARMMResidueTopology self) -> bool"""
11444  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11445 
11446 
11447  def set_patched(self, patched):
11448  """set_patched(CHARMMResidueTopology self, bool patched)"""
11449  return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11450 
11451 
11452  def __str__(self):
11453  """__str__(CHARMMResidueTopology self) -> std::string"""
11454  return _IMP_atom.CHARMMResidueTopology___str__(self)
11455 
11456 
11457  def __repr__(self):
11458  """__repr__(CHARMMResidueTopology self) -> std::string"""
11459  return _IMP_atom.CHARMMResidueTopology___repr__(self)
11460 
11461 
11462  @staticmethod
11463  def get_from(o):
11464  return _object_cast_to_CHARMMResidueTopology(o)
11465 
11466 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
11467 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11468 
11469 class CHARMMAtom(Atom):
11470  """Proxy of C++ IMP::atom::CHARMMAtom class."""
11471 
11472  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11473 
11474  def __init__(self, *args):
11475  """
11476  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
11477  __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11478  __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11479  """
11480  this = _IMP_atom.new_CHARMMAtom(*args)
11481  try:
11482  self.this.append(this)
11483  except __builtin__.Exception:
11484  self.this = this
11485 
11486  def show(self, *args):
11487  """
11488  show(CHARMMAtom self, _ostream out)
11489  show(CHARMMAtom self)
11490  """
11491  return _IMP_atom.CHARMMAtom_show(self, *args)
11492 
11493 
11494  def setup_particle(*args):
11495  """
11496  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11497  setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11498  """
11499  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11500 
11501  setup_particle = staticmethod(setup_particle)
11502 
11503  def get_charmm_type(self):
11504  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
11505  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11506 
11507 
11508  def set_charmm_type(self, t):
11509  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
11510  return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11511 
11512 
11513  def get_is_setup(*args):
11514  """
11515  get_is_setup(_ParticleAdaptor p) -> bool
11516  get_is_setup(Model m, ParticleIndex pi) -> bool
11517  """
11518  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11519 
11520  get_is_setup = staticmethod(get_is_setup)
11521 
11522  def get_charmm_type_key():
11523  """get_charmm_type_key() -> StringKey"""
11524  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11525 
11526  get_charmm_type_key = staticmethod(get_charmm_type_key)
11527 
11528  def add_attribute(self, *args):
11529  """
11530  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11531  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11532  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11533  add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11534  add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11535  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11536  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11537  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11538  """
11539  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11540 
11541 
11542  def get_value(self, *args):
11543  """
11544  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11545  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11546  get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
11547  get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
11548  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11549  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11550  get_value(CHARMMAtom self, ObjectKey a0) -> Object
11551  """
11552  return _IMP_atom.CHARMMAtom_get_value(self, *args)
11553 
11554 
11555  def set_value(self, *args):
11556  """
11557  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11558  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11559  set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11560  set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11561  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11562  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11563  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11564  """
11565  return _IMP_atom.CHARMMAtom_set_value(self, *args)
11566 
11567 
11568  def remove_attribute(self, *args):
11569  """
11570  remove_attribute(CHARMMAtom self, FloatKey a0)
11571  remove_attribute(CHARMMAtom self, IntKey a0)
11572  remove_attribute(CHARMMAtom self, FloatsKey a0)
11573  remove_attribute(CHARMMAtom self, IntsKey a0)
11574  remove_attribute(CHARMMAtom self, StringKey a0)
11575  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11576  remove_attribute(CHARMMAtom self, ObjectKey a0)
11577  """
11578  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11579 
11580 
11581  def has_attribute(self, *args):
11582  """
11583  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11584  has_attribute(CHARMMAtom self, IntKey a0) -> bool
11585  has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
11586  has_attribute(CHARMMAtom self, IntsKey a0) -> bool
11587  has_attribute(CHARMMAtom self, StringKey a0) -> bool
11588  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11589  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11590  """
11591  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11592 
11593 
11594  def get_derivative(self, a0):
11595  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11596  return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11597 
11598 
11599  def get_name(self):
11600  """get_name(CHARMMAtom self) -> std::string"""
11601  return _IMP_atom.CHARMMAtom_get_name(self)
11602 
11603 
11604  def clear_caches(self):
11605  """clear_caches(CHARMMAtom self)"""
11606  return _IMP_atom.CHARMMAtom_clear_caches(self)
11607 
11608 
11609  def set_name(self, a0):
11610  """set_name(CHARMMAtom self, std::string a0)"""
11611  return _IMP_atom.CHARMMAtom_set_name(self, a0)
11612 
11613 
11614  def set_check_level(self, a0):
11615  """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11616  return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11617 
11618 
11619  def add_to_derivative(self, a0, a1, a2):
11620  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11621  return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11622 
11623 
11624  def set_is_optimized(self, a0, a1):
11625  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11626  return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11627 
11628 
11629  def get_is_optimized(self, a0):
11630  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11631  return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11632 
11633 
11634  def get_check_level(self):
11635  """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11636  return _IMP_atom.CHARMMAtom_get_check_level(self)
11637 
11638 
11639  def __eq__(self, *args):
11640  """
11641  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11642  __eq__(CHARMMAtom self, Particle d) -> bool
11643  """
11644  return _IMP_atom.CHARMMAtom___eq__(self, *args)
11645 
11646 
11647  def __ne__(self, *args):
11648  """
11649  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11650  __ne__(CHARMMAtom self, Particle d) -> bool
11651  """
11652  return _IMP_atom.CHARMMAtom___ne__(self, *args)
11653 
11654 
11655  def __le__(self, *args):
11656  """
11657  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11658  __le__(CHARMMAtom self, Particle d) -> bool
11659  """
11660  return _IMP_atom.CHARMMAtom___le__(self, *args)
11661 
11662 
11663  def __lt__(self, *args):
11664  """
11665  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11666  __lt__(CHARMMAtom self, Particle d) -> bool
11667  """
11668  return _IMP_atom.CHARMMAtom___lt__(self, *args)
11669 
11670 
11671  def __ge__(self, *args):
11672  """
11673  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11674  __ge__(CHARMMAtom self, Particle d) -> bool
11675  """
11676  return _IMP_atom.CHARMMAtom___ge__(self, *args)
11677 
11678 
11679  def __gt__(self, *args):
11680  """
11681  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11682  __gt__(CHARMMAtom self, Particle d) -> bool
11683  """
11684  return _IMP_atom.CHARMMAtom___gt__(self, *args)
11685 
11686 
11687  def __hash__(self):
11688  """__hash__(CHARMMAtom self) -> std::size_t"""
11689  return _IMP_atom.CHARMMAtom___hash__(self)
11690 
11691 
11692  def __str__(self):
11693  """__str__(CHARMMAtom self) -> std::string"""
11694  return _IMP_atom.CHARMMAtom___str__(self)
11695 
11696 
11697  def __repr__(self):
11698  """__repr__(CHARMMAtom self) -> std::string"""
11699  return _IMP_atom.CHARMMAtom___repr__(self)
11700 
11701  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11702  __del__ = lambda self: None
11703 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11704 CHARMMAtom_swigregister(CHARMMAtom)
11705 
11706 def CHARMMAtom_setup_particle(*args):
11707  """
11708  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11709  CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11710  """
11711  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11712 
11713 def CHARMMAtom_get_is_setup(*args):
11714  """
11715  get_is_setup(_ParticleAdaptor p) -> bool
11716  CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11717  """
11718  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11719 
11720 def CHARMMAtom_get_charmm_type_key():
11721  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11722  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11723 
11724 
11725 def get_charmm_untyped_atoms(hierarchy):
11726  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11727  return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11728 
11729 def remove_charmm_untyped_atoms(hierarchy):
11730  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11731  return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11732 class CHARMMBondParameters(object):
11733  """Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11734 
11735  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11736  force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11737  ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11738 
11739  def __init__(self):
11740  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11741  this = _IMP_atom.new_CHARMMBondParameters()
11742  try:
11743  self.this.append(this)
11744  except __builtin__.Exception:
11745  self.this = this
11746 
11747  def show(self, *args):
11748  """
11749  show(CHARMMBondParameters self, _ostream out)
11750  show(CHARMMBondParameters self)
11751  """
11752  return _IMP_atom.CHARMMBondParameters_show(self, *args)
11753 
11754 
11755  def __str__(self):
11756  """__str__(CHARMMBondParameters self) -> std::string"""
11757  return _IMP_atom.CHARMMBondParameters___str__(self)
11758 
11759 
11760  def __repr__(self):
11761  """__repr__(CHARMMBondParameters self) -> std::string"""
11762  return _IMP_atom.CHARMMBondParameters___repr__(self)
11763 
11764  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11765  __del__ = lambda self: None
11766 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11767 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11768 
11769 class CHARMMDihedralParameters(object):
11770  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11771 
11772  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11773  force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11774  multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11775  ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11776 
11777  def __init__(self):
11778  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11779  this = _IMP_atom.new_CHARMMDihedralParameters()
11780  try:
11781  self.this.append(this)
11782  except __builtin__.Exception:
11783  self.this = this
11784 
11785  def show(self, *args):
11786  """
11787  show(CHARMMDihedralParameters self, _ostream out)
11788  show(CHARMMDihedralParameters self)
11789  """
11790  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11791 
11792 
11793  def __str__(self):
11794  """__str__(CHARMMDihedralParameters self) -> std::string"""
11795  return _IMP_atom.CHARMMDihedralParameters___str__(self)
11796 
11797 
11798  def __repr__(self):
11799  """__repr__(CHARMMDihedralParameters self) -> std::string"""
11800  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11801 
11802  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11803  __del__ = lambda self: None
11804 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11805 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11806 
11807 class CHARMMParameters(ForceFieldParameters):
11808  """Proxy of C++ IMP::atom::CHARMMParameters class."""
11809 
11810  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11811 
11812  def __init__(self, *args):
11813  """
11814  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11815  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11816  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11817  """
11818  this = _IMP_atom.new_CHARMMParameters(*args)
11819  try:
11820  self.this.append(this)
11821  except __builtin__.Exception:
11822  self.this = this
11823 
11824  def add_residue_topology(self, res):
11825  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11826  return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11827 
11828 
11829  def get_residue_topology(self, type):
11830  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11831  return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11832 
11833 
11834  def add_patch(self, patch):
11835  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11836  return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11837 
11838 
11839  def get_patch(self, name):
11840  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11841  return _IMP_atom.CHARMMParameters_get_patch(self, name)
11842 
11843 
11844  def create_topology(self, hierarchy):
11845  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11846  return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11847 
11848 
11849  def get_bond_parameters(self, type1, type2):
11850  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11851  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11852 
11853 
11854  def get_angle_parameters(self, type1, type2, type3):
11855  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11856  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11857 
11858 
11859  def get_dihedral_parameters(self, type1, type2, type3, type4):
11860  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11861  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11862 
11863 
11864  def get_improper_parameters(self, type1, type2, type3, type4):
11865  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11866  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11867 
11868 
11869  def create_angles(self, bonds):
11870  """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11871  return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11872 
11873 
11874  def create_dihedrals(self, bonds):
11875  """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11876  return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11877 
11878 
11879  def get_version_info(self):
11880  """get_version_info(CHARMMParameters self) -> VersionInfo"""
11881  return _IMP_atom.CHARMMParameters_get_version_info(self)
11882 
11883 
11884  def __str__(self):
11885  """__str__(CHARMMParameters self) -> std::string"""
11886  return _IMP_atom.CHARMMParameters___str__(self)
11887 
11888 
11889  def __repr__(self):
11890  """__repr__(CHARMMParameters self) -> std::string"""
11891  return _IMP_atom.CHARMMParameters___repr__(self)
11892 
11893 
11894  @staticmethod
11895  def get_from(o):
11896  return _object_cast_to_CHARMMParameters(o)
11897 
11898 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11899 CHARMMParameters_swigregister(CHARMMParameters)
11900 
11901 
11903  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11904  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11905 
11907  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11908  return _IMP_atom.get_all_atom_CHARMM_parameters()
11909 class CHARMMSegmentTopology(IMP.Object):
11910  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11911 
11912  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11913 
11914  def remove_residue(self, d):
11915  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11916  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11917 
11918 
11919  def remove_residues(self, d):
11920  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11921  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11922 
11923 
11924  def set_residues(self, ps):
11925  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11926  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11927 
11928 
11929  def set_residues_order(self, objs):
11930  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11931  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11932 
11933 
11934  def add_residue(self, obj):
11935  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11936  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11937 
11938 
11939  def add_residues(self, objs):
11940  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11941  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11942 
11943 
11944  def clear_residues(self):
11945  """clear_residues(CHARMMSegmentTopology self)"""
11946  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11947 
11948 
11949  def get_number_of_residues(self):
11950  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11951  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11952 
11953 
11954  def get_has_residues(self):
11955  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11956  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11957 
11958 
11959  def get_residue(self, i):
11960  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11961  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11962 
11963 
11964  def get_residues(self):
11965  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11966  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11967 
11968 
11969  def reserve_residues(self, sz):
11970  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11971  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11972 
11973 
11974  def get_version_info(self):
11975  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11976  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11977 
11978 
11979  def __init__(self, *args):
11980  """
11981  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11982  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11983  """
11984  this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11985  try:
11986  self.this.append(this)
11987  except __builtin__.Exception:
11988  self.this = this
11989 
11990  def apply_default_patches(self, ff):
11991  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11992  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11993 
11994 
11995  def __str__(self):
11996  """__str__(CHARMMSegmentTopology self) -> std::string"""
11997  return _IMP_atom.CHARMMSegmentTopology___str__(self)
11998 
11999 
12000  def __repr__(self):
12001  """__repr__(CHARMMSegmentTopology self) -> std::string"""
12002  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
12003 
12004 
12005  @staticmethod
12006  def get_from(o):
12007  return _object_cast_to_CHARMMSegmentTopology(o)
12008 
12009 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
12010 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
12011 
12012 class CHARMMTopology(IMP.Object):
12013  """Proxy of C++ IMP::atom::CHARMMTopology class."""
12014 
12015  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12016 
12017  def __init__(self, *args):
12018  """
12019  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
12020  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
12021  """
12022  this = _IMP_atom.new_CHARMMTopology(*args)
12023  try:
12024  self.this.append(this)
12025  except __builtin__.Exception:
12026  self.this = this
12027 
12028  def get_parameters(self):
12029  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
12030  return _IMP_atom.CHARMMTopology_get_parameters(self)
12031 
12032 
12033  def add_sequence(self, sequence):
12034  """add_sequence(CHARMMTopology self, std::string sequence)"""
12035  return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
12036 
12037 
12038  def apply_default_patches(self):
12039  """apply_default_patches(CHARMMTopology self)"""
12040  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
12041 
12042 
12043  def create_hierarchy(self, model):
12044  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
12045  return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
12046 
12047 
12048  def add_atom_types(self, hierarchy):
12049  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
12050  return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
12051 
12052 
12053  def add_coordinates(self, hierarchy):
12054  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
12055  return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
12056 
12057 
12058  def add_missing_atoms(self, hierarchy):
12059  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
12060  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
12061 
12062 
12063  def setup_hierarchy(self, hierarchy):
12064  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
12065  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
12066 
12067 
12068  def add_charges(self, hierarchy):
12069  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
12070  return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
12071 
12072 
12073  def add_bonds(self, hierarchy):
12074  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12075  return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
12076 
12077 
12078  def add_dihedrals(self, hierarchy):
12079  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12080  return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
12081 
12082 
12083  def add_impropers(self, hierarchy):
12084  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12085  return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
12086 
12087 
12088  def remove_segment(self, d):
12089  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
12090  return _IMP_atom.CHARMMTopology_remove_segment(self, d)
12091 
12092 
12093  def remove_segments(self, d):
12094  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
12095  return _IMP_atom.CHARMMTopology_remove_segments(self, d)
12096 
12097 
12098  def set_segments(self, ps):
12099  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
12100  return _IMP_atom.CHARMMTopology_set_segments(self, ps)
12101 
12102 
12103  def set_segments_order(self, objs):
12104  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
12105  return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
12106 
12107 
12108  def add_segment(self, obj):
12109  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
12110  return _IMP_atom.CHARMMTopology_add_segment(self, obj)
12111 
12112 
12113  def add_segments(self, objs):
12114  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
12115  return _IMP_atom.CHARMMTopology_add_segments(self, objs)
12116 
12117 
12118  def clear_segments(self):
12119  """clear_segments(CHARMMTopology self)"""
12120  return _IMP_atom.CHARMMTopology_clear_segments(self)
12121 
12122 
12123  def get_number_of_segments(self):
12124  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
12125  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
12126 
12127 
12128  def get_has_segments(self):
12129  """get_has_segments(CHARMMTopology self) -> bool"""
12130  return _IMP_atom.CHARMMTopology_get_has_segments(self)
12131 
12132 
12133  def get_segment(self, i):
12134  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
12135  return _IMP_atom.CHARMMTopology_get_segment(self, i)
12136 
12137 
12138  def get_segments(self):
12139  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
12140  return _IMP_atom.CHARMMTopology_get_segments(self)
12141 
12142 
12143  def reserve_segments(self, sz):
12144  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
12145  return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
12146 
12147 
12148  def get_version_info(self):
12149  """get_version_info(CHARMMTopology self) -> VersionInfo"""
12150  return _IMP_atom.CHARMMTopology_get_version_info(self)
12151 
12152 
12153  def __str__(self):
12154  """__str__(CHARMMTopology self) -> std::string"""
12155  return _IMP_atom.CHARMMTopology___str__(self)
12156 
12157 
12158  def __repr__(self):
12159  """__repr__(CHARMMTopology self) -> std::string"""
12160  return _IMP_atom.CHARMMTopology___repr__(self)
12161 
12162 
12163  @staticmethod
12164  def get_from(o):
12165  return _object_cast_to_CHARMMTopology(o)
12166 
12167 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
12168 CHARMMTopology_swigregister(CHARMMTopology)
12169 
12170 class CHARMMStereochemistryRestraint(IMP.Restraint):
12171  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
12172 
12173  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12174 
12175  def __init__(self, *args):
12176  """
12177  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
12178  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
12179  """
12180  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
12181  try:
12182  self.this.append(this)
12183  except __builtin__.Exception:
12184  self.this = this
12185 
12186  def get_pair_filter(self):
12187  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
12188  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
12189 
12190 
12191  def get_full_pair_filter(self):
12192  """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
12193  return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
12194 
12195 
12196  def do_get_inputs(self):
12197  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
12198  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
12199 
12200 
12201  def get_version_info(self):
12202  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
12203  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
12204 
12205 
12206  def __str__(self):
12207  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
12208  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
12209 
12210 
12211  def __repr__(self):
12212  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
12213  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
12214 
12215 
12216  @staticmethod
12217  def get_from(o):
12218  return _object_cast_to_CHARMMStereochemistryRestraint(o)
12219 
12220 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
12221 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
12222 
12223 
12224 def add_bonds(*args):
12225  """
12226  add_bonds(Hierarchy d, ForceFieldParameters ffp)
12227  add_bonds(Hierarchy d)
12228  """
12229  return _IMP_atom.add_bonds(*args)
12230 
12231 def add_radii(*args):
12232  """
12233  add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
12234  add_radii(Hierarchy d, ForceFieldParameters ffp)
12235  add_radii(Hierarchy d)
12236  """
12237  return _IMP_atom.add_radii(*args)
12238 ALBER = _IMP_atom.ALBER
12239 HARPAZ = _IMP_atom.HARPAZ
12240 ANDERSSON = _IMP_atom.ANDERSSON
12241 TSAI = _IMP_atom.TSAI
12242 QUILLIN = _IMP_atom.QUILLIN
12243 SQUIRE = _IMP_atom.SQUIRE
12244 
12245 def get_protein_density_from_reference(densityReference):
12246  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
12247  return _IMP_atom.get_protein_density_from_reference(densityReference)
12248 
12249 def get_volume_from_mass(*args):
12250  """
12251  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
12252  get_volume_from_mass(double m) -> double
12253  """
12254  return _IMP_atom.get_volume_from_mass(*args)
12255 
12256 def get_mass_from_volume(*args):
12257  """
12258  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
12259  get_mass_from_volume(double v) -> double
12260  """
12261  return _IMP_atom.get_mass_from_volume(*args)
12262 
12264  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
12265  return _IMP_atom.get_mass_from_number_of_residues(num_aa)
12266 
12268  """get_volume_from_residue_type(ResidueType rt) -> double"""
12269  return _IMP_atom.get_volume_from_residue_type(rt)
12270 
12271 def get_molarity(n, volume):
12272  """get_molarity(double n, double volume) -> double"""
12273  return _IMP_atom.get_molarity(n, volume)
12274 
12275 def get_kd(na, nb, nab, volume):
12276  """get_kd(double na, double nb, double nab, double volume) -> double"""
12277  return _IMP_atom.get_kd(na, nb, nab, volume)
12278 
12279 def get_einstein_diffusion_coefficient(r, temp=-1):
12280  """
12281  get_einstein_diffusion_coefficient(double r, double temp=-1) -> double
12282  get_einstein_diffusion_coefficient(double r) -> double
12283  """
12284  return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
12285 
12287  """
12288  get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double
12289  get_einstein_rotational_diffusion_coefficient(double r) -> double
12290  """
12291  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
12292 
12293 def get_diffusion_length(*args):
12294  """
12295  get_diffusion_length(double D, double t) -> double
12296  get_diffusion_length(double D, double force, double t, double temp=-1) -> double
12297  get_diffusion_length(double D, double force, double t) -> double
12298  """
12299  return _IMP_atom.get_diffusion_length(*args)
12300 
12301 def get_diffusion_angle(D, dtfs):
12302  """get_diffusion_angle(double D, double dtfs) -> double"""
12303  return _IMP_atom.get_diffusion_angle(D, dtfs)
12304 
12305 def get_diffusion_coefficient(*args):
12306  """
12307  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
12308  get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
12309  """
12310  return _IMP_atom.get_diffusion_coefficient(*args)
12311 
12312 def get_rotational_diffusion_coefficient(orientations, dt):
12313  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
12314  return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
12315 
12316 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
12317  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
12318  return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
12319 
12320 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
12321  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
12322  return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
12323 
12324 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
12325  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
12326  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
12327 class EzRestraint(IMP.Restraint):
12328  """Proxy of C++ IMP::atom::EzRestraint class."""
12329 
12330  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12331 
12332  def __init__(self, m, ps):
12333  """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
12334  this = _IMP_atom.new_EzRestraint(m, ps)
12335  try:
12336  self.this.append(this)
12337  except __builtin__.Exception:
12338  self.this = this
12339 
12340  def get_version_info(self):
12341  """get_version_info(EzRestraint self) -> VersionInfo"""
12342  return _IMP_atom.EzRestraint_get_version_info(self)
12343 
12344 
12345  def __str__(self):
12346  """__str__(EzRestraint self) -> std::string"""
12347  return _IMP_atom.EzRestraint___str__(self)
12348 
12349 
12350  def __repr__(self):
12351  """__repr__(EzRestraint self) -> std::string"""
12352  return _IMP_atom.EzRestraint___repr__(self)
12353 
12354 
12355  @staticmethod
12356  def get_from(o):
12357  return _object_cast_to_EzRestraint(o)
12358 
12359 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
12360 EzRestraint_swigregister(EzRestraint)
12361 
12362 
12363 def create_protein(*args):
12364  """
12365  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
12366  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
12367  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
12368  create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
12369  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12370  """
12371  return _IMP_atom.create_protein(*args)
12372 
12374  """
12375  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12376  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
12377  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12378  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
12379  """
12380  return _IMP_atom.create_simplified_along_backbone(*args)
12381 
12382 def create_simplified_from_volume(h, resolution):
12383  """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12384  return _IMP_atom.create_simplified_from_volume(h, resolution)
12385 
12386 def create_simplified_assembly_from_volume(h, resolution):
12387  """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12388  return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12389 
12390 def get_residue_indexes(h):
12391  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12392  return _IMP_atom.get_residue_indexes(h)
12393 
12394 def get_residue_type(*args):
12395  """
12396  get_residue_type(char c) -> ResidueType
12397  get_residue_type(Hierarchy h) -> ResidueType
12398  """
12399  return _IMP_atom.get_residue_type(*args)
12400 
12401 def get_atom_type(h):
12402  """get_atom_type(Hierarchy h) -> AtomType"""
12403  return _IMP_atom.get_atom_type(h)
12404 
12405 def get_domain_name(h):
12406  """get_domain_name(Hierarchy h) -> std::string"""
12407  return _IMP_atom.get_domain_name(h)
12408 
12410  """
12411  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12412  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12413  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
12414  """
12415  return _IMP_atom.create_excluded_volume_restraint(*args)
12416 
12417 def setup_as_approximation(*args):
12418  """
12419  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12420  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
12421  setup_as_approximation(Hierarchy h, double resolution=-1)
12422  setup_as_approximation(Hierarchy h)
12423  """
12424  return _IMP_atom.setup_as_approximation(*args)
12425 class _HierarchyTreeVertexIndex(object):
12426  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
12427 
12428  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12429  __repr__ = _swig_repr
12430 
12431  def __init__(self):
12432  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12433  this = _IMP_atom.new__HierarchyTreeVertexIndex()
12434  try:
12435  self.this.append(this)
12436  except __builtin__.Exception:
12437  self.this = this
12438  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12439  __del__ = lambda self: None
12440 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
12441 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12442 
12443 
12444 def show_as_graphviz(name, out):
12445  """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12446  return _IMP_atom.show_as_graphviz(name, out)
12447 
12448 def get_vertex_index(g):
12449  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12450  return _IMP_atom.get_vertex_index(g)
12451 
12452 def get_hierarchy_tree(h):
12453  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12454  return _IMP_atom.get_hierarchy_tree(h)
12455 class HierarchyGeometry(IMP.display.SingletonGeometry):
12456  """Proxy of C++ IMP::atom::HierarchyGeometry class."""
12457 
12458  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12459 
12460  def __init__(self, d, resolution=0):
12461  """
12462  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
12463  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
12464  """
12465  this = _IMP_atom.new_HierarchyGeometry(d, resolution)
12466  try:
12467  self.this.append(this)
12468  except __builtin__.Exception:
12469  self.this = this
12470 
12471  def get_version_info(self):
12472  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
12473  return _IMP_atom.HierarchyGeometry_get_version_info(self)
12474 
12475 
12476  def __str__(self):
12477  """__str__(HierarchyGeometry self) -> std::string"""
12478  return _IMP_atom.HierarchyGeometry___str__(self)
12479 
12480 
12481  def __repr__(self):
12482  """__repr__(HierarchyGeometry self) -> std::string"""
12483  return _IMP_atom.HierarchyGeometry___repr__(self)
12484 
12485 
12486  @staticmethod
12487  def get_from(o):
12488  return _object_cast_to_HierarchyGeometry(o)
12489 
12490 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
12491 HierarchyGeometry_swigregister(HierarchyGeometry)
12492 
12493 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
12494  """Proxy of C++ IMP::atom::HierarchiesGeometry class."""
12495 
12496  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12497 
12498  def __init__(self, sc, resolution=-1):
12499  """
12500  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
12501  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
12502  """
12503  this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
12504  try:
12505  self.this.append(this)
12506  except __builtin__.Exception:
12507  self.this = this
12508 
12509  def get_version_info(self):
12510  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12511  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12512 
12513 
12514  def __str__(self):
12515  """__str__(HierarchiesGeometry self) -> std::string"""
12516  return _IMP_atom.HierarchiesGeometry___str__(self)
12517 
12518 
12519  def __repr__(self):
12520  """__repr__(HierarchiesGeometry self) -> std::string"""
12521  return _IMP_atom.HierarchiesGeometry___repr__(self)
12522 
12523 
12524  @staticmethod
12525  def get_from(o):
12526  return _object_cast_to_HierarchiesGeometry(o)
12527 
12528 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
12529 HierarchiesGeometry_swigregister(HierarchiesGeometry)
12530 
12531 
12532 def transform(*args):
12533  """
12534  transform(Hierarchy h, Transformation3D tr)
12535  transform(Hierarchy h, Transformation3D tr)
12536  """
12537  return _IMP_atom.transform(*args)
12538 class DopePairScore(_ADopeBase):
12539  """Proxy of C++ IMP::atom::DopePairScore class."""
12540 
12541  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12542 
12543  def __init__(self, *args):
12544  """
12545  __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
12546  __init__(IMP::atom::DopePairScore self) -> DopePairScore
12547  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12548  """
12549  this = _IMP_atom.new_DopePairScore(*args)
12550  try:
12551  self.this.append(this)
12552  except __builtin__.Exception:
12553  self.this = this
12554 
12555  def __str__(self):
12556  """__str__(DopePairScore self) -> std::string"""
12557  return _IMP_atom.DopePairScore___str__(self)
12558 
12559 
12560  def __repr__(self):
12561  """__repr__(DopePairScore self) -> std::string"""
12562  return _IMP_atom.DopePairScore___repr__(self)
12563 
12564 
12565  @staticmethod
12566  def get_from(o):
12567  return _object_cast_to_DopePairScore(o)
12568 
12569  __swig_destroy__ = _IMP_atom.delete_DopePairScore
12570  __del__ = lambda self: None
12571 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
12572 DopePairScore_swigregister(DopePairScore)
12573 
12574 
12575 def add_dope_score_data(h):
12576  """add_dope_score_data(Hierarchy h)"""
12577  return _IMP_atom.add_dope_score_data(h)
12578 class LoopStatisticalPairScore(_ALoopStatisticalBase):
12579  """Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
12580 
12581  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12582 
12583  def __init__(self, *args):
12584  """
12585  __init__(IMP::atom::LoopStatisticalPairScore self, double threshold) -> LoopStatisticalPairScore
12586  __init__(IMP::atom::LoopStatisticalPairScore self) -> LoopStatisticalPairScore
12587  __init__(IMP::atom::LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
12588  """
12589  this = _IMP_atom.new_LoopStatisticalPairScore(*args)
12590  try:
12591  self.this.append(this)
12592  except __builtin__.Exception:
12593  self.this = this
12594 
12595  def __str__(self):
12596  """__str__(LoopStatisticalPairScore self) -> std::string"""
12597  return _IMP_atom.LoopStatisticalPairScore___str__(self)
12598 
12599 
12600  def __repr__(self):
12601  """__repr__(LoopStatisticalPairScore self) -> std::string"""
12602  return _IMP_atom.LoopStatisticalPairScore___repr__(self)
12603 
12604 
12605  @staticmethod
12606  def get_from(o):
12607  return _object_cast_to_LoopStatisticalPairScore(o)
12608 
12609  __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
12610  __del__ = lambda self: None
12611 LoopStatisticalPairScore_swigregister = _IMP_atom.LoopStatisticalPairScore_swigregister
12612 LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
12613 
12614 
12616  """add_loop_statistical_score_data(Hierarchy h)"""
12617  return _IMP_atom.add_loop_statistical_score_data(h)
12618 class OrientedSoapPairScore(_OrientedSoapBase):
12619  """Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
12620 
12621  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12622 
12623  def __init__(self, library):
12624  """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12625  this = _IMP_atom.new_OrientedSoapPairScore(library)
12626  try:
12627  self.this.append(this)
12628  except __builtin__.Exception:
12629  self.this = this
12630 
12631  def get_pair_filter(self):
12632  """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12633  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12634 
12635 
12636  def __str__(self):
12637  """__str__(OrientedSoapPairScore self) -> std::string"""
12638  return _IMP_atom.OrientedSoapPairScore___str__(self)
12639 
12640 
12641  def __repr__(self):
12642  """__repr__(OrientedSoapPairScore self) -> std::string"""
12643  return _IMP_atom.OrientedSoapPairScore___repr__(self)
12644 
12645 
12646  @staticmethod
12647  def get_from(o):
12648  return _object_cast_to_OrientedSoapPairScore(o)
12649 
12650  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12651  __del__ = lambda self: None
12652 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12653 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12654 
12655 class SameResiduePairFilter(IMP.PairPredicate):
12656  """Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12657 
12658  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12659 
12660  def __init__(self):
12661  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12662  this = _IMP_atom.new_SameResiduePairFilter()
12663  try:
12664  self.this.append(this)
12665  except __builtin__.Exception:
12666  self.this = this
12667 
12668  def do_get_inputs(self, m, pis):
12669  """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12670  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12671 
12672 
12673  def get_value(self, *args):
12674  """
12675  get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12676  get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12677  """
12678  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12679 
12680 
12681  def get_value_index(self, *args):
12682  """
12683  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12684  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12685  """
12686  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12687 
12688 
12689  def get_version_info(self):
12690  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12691  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12692 
12693 
12694  def __str__(self):
12695  """__str__(SameResiduePairFilter self) -> std::string"""
12696  return _IMP_atom.SameResiduePairFilter___str__(self)
12697 
12698 
12699  def __repr__(self):
12700  """__repr__(SameResiduePairFilter self) -> std::string"""
12701  return _IMP_atom.SameResiduePairFilter___repr__(self)
12702 
12703 
12704  @staticmethod
12705  def get_from(o):
12706  return _object_cast_to_SameResiduePairFilter(o)
12707 
12708 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12709 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12710 
12711 class RemoveRigidMotionOptimizerState(IMP.OptimizerState):
12712  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12713 
12714  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12715 
12716  def __init__(self, m, pis):
12717  """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12718  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12719  try:
12720  self.this.append(this)
12721  except __builtin__.Exception:
12722  self.this = this
12723 
12724  def set_particles(self, pis):
12725  """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12726  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12727 
12728 
12729  def remove_rigid_motion(self):
12730  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12731  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12732 
12733 
12734  def get_version_info(self):
12735  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12736  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12737 
12738 
12739  def __str__(self):
12740  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12741  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12742 
12743 
12744  def __repr__(self):
12745  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12746  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12747 
12748 
12749  @staticmethod
12750  def get_from(o):
12751  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12752 
12753 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12754 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12755 
12756 class BerendsenThermostatOptimizerState(IMP.OptimizerState):
12757  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12758 
12759  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12760 
12761  def __init__(self, pis, temperature, tau):
12762  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12763  this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12764  try:
12765  self.this.append(this)
12766  except __builtin__.Exception:
12767  self.this = this
12768 
12769  def set_particles(self, pis):
12770  """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12771  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12772 
12773 
12774  def get_temperature(self):
12775  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12776  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12777 
12778 
12779  def get_tau(self):
12780  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12781  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12782 
12783 
12784  def set_temperature(self, temperature):
12785  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12786  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12787 
12788 
12789  def set_tau(self, tau):
12790  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12791  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12792 
12793 
12794  def rescale_velocities(self):
12795  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12796  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12797 
12798 
12799  def get_version_info(self):
12800  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12801  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12802 
12803 
12804  def __str__(self):
12805  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12806  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12807 
12808 
12809  def __repr__(self):
12810  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12811  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12812 
12813 
12814  @staticmethod
12815  def get_from(o):
12816  return _object_cast_to_BerendsenThermostatOptimizerState(o)
12817 
12818 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12819 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12820 
12821 class LangevinThermostatOptimizerState(IMP.OptimizerState):
12822  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12823 
12824  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12825 
12826  def __init__(self, m, pis, temperature, gamma):
12827  """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12828  this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12829  try:
12830  self.this.append(this)
12831  except __builtin__.Exception:
12832  self.this = this
12833 
12834  def set_particles(self, pis):
12835  """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12836  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12837 
12838 
12839  def get_temperature(self):
12840  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12841  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12842 
12843 
12844  def get_gamma(self):
12845  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12846  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12847 
12848 
12849  def set_temperature(self, temperature):
12850  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12851  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12852 
12853 
12854  def set_gamma(self, gamma):
12855  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12856  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12857 
12858 
12859  def rescale_velocities(self):
12860  """rescale_velocities(LangevinThermostatOptimizerState self)"""
12861  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12862 
12863 
12864  def get_version_info(self):
12865  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12866  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12867 
12868 
12869  def __str__(self):
12870  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12871  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12872 
12873 
12874  def __repr__(self):
12875  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12876  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12877 
12878 
12879  @staticmethod
12880  def get_from(o):
12881  return _object_cast_to_LangevinThermostatOptimizerState(o)
12882 
12883 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12884 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12885 
12886 class PDBSelector(IMP.Object):
12887  """Proxy of C++ IMP::atom::PDBSelector class."""
12888 
12889  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12890 
12891  def __init__(self, name):
12892  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12893  if self.__class__ == PDBSelector:
12894  _self = None
12895  else:
12896  _self = self
12897  this = _IMP_atom.new_PDBSelector(_self, name)
12898  try:
12899  self.this.append(this)
12900  except __builtin__.Exception:
12901  self.this = this
12902 
12903  if self.__class__ != PDBSelector:
12904  _director_objects.register(self)
12905 
12906 
12907 
12908 
12909  def get_is_selected(self, pdb_line):
12910  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12911  return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12912 
12913  __swig_destroy__ = _IMP_atom.delete_PDBSelector
12914  __del__ = lambda self: None
12915 
12916  def __str__(self):
12917  """__str__(PDBSelector self) -> std::string"""
12918  return _IMP_atom.PDBSelector___str__(self)
12919 
12920 
12921  def __repr__(self):
12922  """__repr__(PDBSelector self) -> std::string"""
12923  return _IMP_atom.PDBSelector___repr__(self)
12924 
12925 
12926  @staticmethod
12927  def get_from(o):
12928  return _object_cast_to_PDBSelector(o)
12929 
12930 
12931  def get_type_name(self):
12932  return self.__class__.__name__
12933  def do_show(self, out):
12934  pass
12935  def get_version_info(self):
12936  if"IMP::atom" == "IMP":
12937  return VersionInfo(self.__module__,
12938  __import__(self.__module__).get_module_version())
12939  else:
12940  return IMP.VersionInfo(self.__module__,
12941  __import__(self.__module__).get_module_version())
12942  @staticmethod
12943  def get_from(o):
12944  return _object_cast_to_PDBSelector(o)
12945 
12946 
12947  def __and__(self, s):
12948  return AndPDBSelector(self, s)
12949  def __or__(self, s):
12950  return OrPDBSelector(self, s)
12951  def __xor__(self, s):
12952  return XorPDBSelector(self, s)
12953  def __invert__(self):
12954  return NotPDBSelector(self)
12955  def __sub__(self, s):
12956  return AndPDBSelector(self, NotPDBSelector(s))
12957 
12958  def __disown__(self):
12959  self.this.disown()
12960  _IMP_atom.disown_PDBSelector(self)
12961  return weakref_proxy(self)
12962 
12963  def do_destroy(self):
12964  """do_destroy(PDBSelector self)"""
12965  return _IMP_atom.PDBSelector_do_destroy(self)
12966 
12967 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12968 PDBSelector_swigregister(PDBSelector)
12969 
12970 class NonAlternativePDBSelector(PDBSelector):
12971  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12972 
12973  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12974 
12975  def __init__(self, *args):
12976  """
12977  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12978  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12979  """
12980  this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12981  try:
12982  self.this.append(this)
12983  except __builtin__.Exception:
12984  self.this = this
12985 
12986  def get_version_info(self):
12987  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12988  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12989 
12990 
12991  def __str__(self):
12992  """__str__(NonAlternativePDBSelector self) -> std::string"""
12993  return _IMP_atom.NonAlternativePDBSelector___str__(self)
12994 
12995 
12996  def __repr__(self):
12997  """__repr__(NonAlternativePDBSelector self) -> std::string"""
12998  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12999 
13000 
13001  @staticmethod
13002  def get_from(o):
13003  return _object_cast_to_NonAlternativePDBSelector(o)
13004 
13005 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
13006 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
13007 
13008 class ATOMPDBSelector(NonAlternativePDBSelector):
13009  """Proxy of C++ IMP::atom::ATOMPDBSelector class."""
13010 
13011  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13012 
13013  def __init__(self, *args):
13014  """
13015  __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
13016  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
13017  """
13018  this = _IMP_atom.new_ATOMPDBSelector(*args)
13019  try:
13020  self.this.append(this)
13021  except __builtin__.Exception:
13022  self.this = this
13023 
13024  def __str__(self):
13025  """__str__(ATOMPDBSelector self) -> std::string"""
13026  return _IMP_atom.ATOMPDBSelector___str__(self)
13027 
13028 
13029  def __repr__(self):
13030  """__repr__(ATOMPDBSelector self) -> std::string"""
13031  return _IMP_atom.ATOMPDBSelector___repr__(self)
13032 
13033 
13034  @staticmethod
13035  def get_from(o):
13036  return _object_cast_to_ATOMPDBSelector(o)
13037 
13038 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
13039 ATOMPDBSelector_swigregister(ATOMPDBSelector)
13040 
13041 class CAlphaPDBSelector(NonAlternativePDBSelector):
13042  """Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
13043 
13044  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13045 
13046  def __init__(self, *args):
13047  """
13048  __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
13049  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
13050  """
13051  this = _IMP_atom.new_CAlphaPDBSelector(*args)
13052  try:
13053  self.this.append(this)
13054  except __builtin__.Exception:
13055  self.this = this
13056 
13057  def __str__(self):
13058  """__str__(CAlphaPDBSelector self) -> std::string"""
13059  return _IMP_atom.CAlphaPDBSelector___str__(self)
13060 
13061 
13062  def __repr__(self):
13063  """__repr__(CAlphaPDBSelector self) -> std::string"""
13064  return _IMP_atom.CAlphaPDBSelector___repr__(self)
13065 
13066 
13067  @staticmethod
13068  def get_from(o):
13069  return _object_cast_to_CAlphaPDBSelector(o)
13070 
13071 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
13072 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
13073 
13074 class CBetaPDBSelector(NonAlternativePDBSelector):
13075  """Proxy of C++ IMP::atom::CBetaPDBSelector class."""
13076 
13077  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13078 
13079  def __init__(self, *args):
13080  """
13081  __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
13082  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
13083  """
13084  this = _IMP_atom.new_CBetaPDBSelector(*args)
13085  try:
13086  self.this.append(this)
13087  except __builtin__.Exception:
13088  self.this = this
13089 
13090  def __str__(self):
13091  """__str__(CBetaPDBSelector self) -> std::string"""
13092  return _IMP_atom.CBetaPDBSelector___str__(self)
13093 
13094 
13095  def __repr__(self):
13096  """__repr__(CBetaPDBSelector self) -> std::string"""
13097  return _IMP_atom.CBetaPDBSelector___repr__(self)
13098 
13099 
13100  @staticmethod
13101  def get_from(o):
13102  return _object_cast_to_CBetaPDBSelector(o)
13103 
13104 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
13105 CBetaPDBSelector_swigregister(CBetaPDBSelector)
13106 
13107 class AtomTypePDBSelector(PDBSelector):
13108  """Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
13109 
13110  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13111 
13112  def __init__(self, *args):
13113  """
13114  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
13115  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
13116  """
13117  this = _IMP_atom.new_AtomTypePDBSelector(*args)
13118  try:
13119  self.this.append(this)
13120  except __builtin__.Exception:
13121  self.this = this
13122 
13123  def get_version_info(self):
13124  """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
13125  return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
13126 
13127 
13128  def __str__(self):
13129  """__str__(AtomTypePDBSelector self) -> std::string"""
13130  return _IMP_atom.AtomTypePDBSelector___str__(self)
13131 
13132 
13133  def __repr__(self):
13134  """__repr__(AtomTypePDBSelector self) -> std::string"""
13135  return _IMP_atom.AtomTypePDBSelector___repr__(self)
13136 
13137 
13138  @staticmethod
13139  def get_from(o):
13140  return _object_cast_to_AtomTypePDBSelector(o)
13141 
13142 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
13143 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
13144 
13145 class ResidueTypePDBSelector(PDBSelector):
13146  """Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
13147 
13148  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13149 
13150  def __init__(self, *args):
13151  """
13152  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
13153  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
13154  """
13155  this = _IMP_atom.new_ResidueTypePDBSelector(*args)
13156  try:
13157  self.this.append(this)
13158  except __builtin__.Exception:
13159  self.this = this
13160 
13161  def get_version_info(self):
13162  """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
13163  return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
13164 
13165 
13166  def __str__(self):
13167  """__str__(ResidueTypePDBSelector self) -> std::string"""
13168  return _IMP_atom.ResidueTypePDBSelector___str__(self)
13169 
13170 
13171  def __repr__(self):
13172  """__repr__(ResidueTypePDBSelector self) -> std::string"""
13173  return _IMP_atom.ResidueTypePDBSelector___repr__(self)
13174 
13175 
13176  @staticmethod
13177  def get_from(o):
13178  return _object_cast_to_ResidueTypePDBSelector(o)
13179 
13180 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
13181 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
13182 
13183 class CPDBSelector(NonAlternativePDBSelector):
13184  """Proxy of C++ IMP::atom::CPDBSelector class."""
13185 
13186  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13187 
13188  def __init__(self, *args):
13189  """
13190  __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
13191  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
13192  """
13193  this = _IMP_atom.new_CPDBSelector(*args)
13194  try:
13195  self.this.append(this)
13196  except __builtin__.Exception:
13197  self.this = this
13198 
13199  def __str__(self):
13200  """__str__(CPDBSelector self) -> std::string"""
13201  return _IMP_atom.CPDBSelector___str__(self)
13202 
13203 
13204  def __repr__(self):
13205  """__repr__(CPDBSelector self) -> std::string"""
13206  return _IMP_atom.CPDBSelector___repr__(self)
13207 
13208 
13209  @staticmethod
13210  def get_from(o):
13211  return _object_cast_to_CPDBSelector(o)
13212 
13213 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
13214 CPDBSelector_swigregister(CPDBSelector)
13215 
13216 class NPDBSelector(NonAlternativePDBSelector):
13217  """Proxy of C++ IMP::atom::NPDBSelector class."""
13218 
13219  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13220 
13221  def __init__(self, *args):
13222  """
13223  __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
13224  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
13225  """
13226  this = _IMP_atom.new_NPDBSelector(*args)
13227  try:
13228  self.this.append(this)
13229  except __builtin__.Exception:
13230  self.this = this
13231 
13232  def __str__(self):
13233  """__str__(NPDBSelector self) -> std::string"""
13234  return _IMP_atom.NPDBSelector___str__(self)
13235 
13236 
13237  def __repr__(self):
13238  """__repr__(NPDBSelector self) -> std::string"""
13239  return _IMP_atom.NPDBSelector___repr__(self)
13240 
13241 
13242  @staticmethod
13243  def get_from(o):
13244  return _object_cast_to_NPDBSelector(o)
13245 
13246 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
13247 NPDBSelector_swigregister(NPDBSelector)
13248 
13249 class AllPDBSelector(PDBSelector):
13250  """Proxy of C++ IMP::atom::AllPDBSelector class."""
13251 
13252  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13253 
13254  def __init__(self, *args):
13255  """
13256  __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
13257  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
13258  """
13259  this = _IMP_atom.new_AllPDBSelector(*args)
13260  try:
13261  self.this.append(this)
13262  except __builtin__.Exception:
13263  self.this = this
13264 
13265  def get_version_info(self):
13266  """get_version_info(AllPDBSelector self) -> VersionInfo"""
13267  return _IMP_atom.AllPDBSelector_get_version_info(self)
13268 
13269 
13270  def __str__(self):
13271  """__str__(AllPDBSelector self) -> std::string"""
13272  return _IMP_atom.AllPDBSelector___str__(self)
13273 
13274 
13275  def __repr__(self):
13276  """__repr__(AllPDBSelector self) -> std::string"""
13277  return _IMP_atom.AllPDBSelector___repr__(self)
13278 
13279 
13280  @staticmethod
13281  def get_from(o):
13282  return _object_cast_to_AllPDBSelector(o)
13283 
13284 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
13285 AllPDBSelector_swigregister(AllPDBSelector)
13286 
13287 class ChainPDBSelector(NonAlternativePDBSelector):
13288  """Proxy of C++ IMP::atom::ChainPDBSelector class."""
13289 
13290  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13291 
13292  def __init__(self, *args):
13293  """
13294  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
13295  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
13296  """
13297  this = _IMP_atom.new_ChainPDBSelector(*args)
13298  try:
13299  self.this.append(this)
13300  except __builtin__.Exception:
13301  self.this = this
13302 
13303  def __str__(self):
13304  """__str__(ChainPDBSelector self) -> std::string"""
13305  return _IMP_atom.ChainPDBSelector___str__(self)
13306 
13307 
13308  def __repr__(self):
13309  """__repr__(ChainPDBSelector self) -> std::string"""
13310  return _IMP_atom.ChainPDBSelector___repr__(self)
13311 
13312 
13313  @staticmethod
13314  def get_from(o):
13315  return _object_cast_to_ChainPDBSelector(o)
13316 
13317 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
13318 ChainPDBSelector_swigregister(ChainPDBSelector)
13319 
13320 class WaterPDBSelector(NonAlternativePDBSelector):
13321  """Proxy of C++ IMP::atom::WaterPDBSelector class."""
13322 
13323  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13324 
13325  def __init__(self, *args):
13326  """
13327  __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
13328  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
13329  """
13330  this = _IMP_atom.new_WaterPDBSelector(*args)
13331  try:
13332  self.this.append(this)
13333  except __builtin__.Exception:
13334  self.this = this
13335 
13336  def __str__(self):
13337  """__str__(WaterPDBSelector self) -> std::string"""
13338  return _IMP_atom.WaterPDBSelector___str__(self)
13339 
13340 
13341  def __repr__(self):
13342  """__repr__(WaterPDBSelector self) -> std::string"""
13343  return _IMP_atom.WaterPDBSelector___repr__(self)
13344 
13345 
13346  @staticmethod
13347  def get_from(o):
13348  return _object_cast_to_WaterPDBSelector(o)
13349 
13350 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
13351 WaterPDBSelector_swigregister(WaterPDBSelector)
13352 
13353 class HydrogenPDBSelector(NonAlternativePDBSelector):
13354  """Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
13355 
13356  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13357 
13358  def __init__(self, *args):
13359  """
13360  __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
13361  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
13362  """
13363  this = _IMP_atom.new_HydrogenPDBSelector(*args)
13364  try:
13365  self.this.append(this)
13366  except __builtin__.Exception:
13367  self.this = this
13368 
13369  def __str__(self):
13370  """__str__(HydrogenPDBSelector self) -> std::string"""
13371  return _IMP_atom.HydrogenPDBSelector___str__(self)
13372 
13373 
13374  def __repr__(self):
13375  """__repr__(HydrogenPDBSelector self) -> std::string"""
13376  return _IMP_atom.HydrogenPDBSelector___repr__(self)
13377 
13378 
13379  @staticmethod
13380  def get_from(o):
13381  return _object_cast_to_HydrogenPDBSelector(o)
13382 
13383 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
13384 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
13385 
13386 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
13387  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
13388 
13389  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13390 
13391  def __init__(self, *args):
13392  """
13393  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
13394  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
13395  """
13396  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
13397  try:
13398  self.this.append(this)
13399  except __builtin__.Exception:
13400  self.this = this
13401 
13402  def __str__(self):
13403  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13404  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
13405 
13406 
13407  def __repr__(self):
13408  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13409  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
13410 
13411 
13412  @staticmethod
13413  def get_from(o):
13414  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
13415 
13416 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
13417 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
13418 
13419 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
13420  """Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
13421 
13422  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13423 
13424  def __init__(self, *args):
13425  """
13426  __init__(IMP::atom::NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
13427  __init__(IMP::atom::NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
13428  """
13429  this = _IMP_atom.new_NonHydrogenPDBSelector(*args)
13430  try:
13431  self.this.append(this)
13432  except __builtin__.Exception:
13433  self.this = this
13434 
13435  def __str__(self):
13436  """__str__(NonHydrogenPDBSelector self) -> std::string"""
13437  return _IMP_atom.NonHydrogenPDBSelector___str__(self)
13438 
13439 
13440  def __repr__(self):
13441  """__repr__(NonHydrogenPDBSelector self) -> std::string"""
13442  return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
13443 
13444 
13445  @staticmethod
13446  def get_from(o):
13447  return _object_cast_to_NonHydrogenPDBSelector(o)
13448 
13449 NonHydrogenPDBSelector_swigregister = _IMP_atom.NonHydrogenPDBSelector_swigregister
13450 NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
13451 
13452 class NonWaterPDBSelector(NonAlternativePDBSelector):
13453  """Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
13454 
13455  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13456 
13457  def __init__(self, *args):
13458  """
13459  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
13460  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
13461  """
13462  this = _IMP_atom.new_NonWaterPDBSelector(*args)
13463  try:
13464  self.this.append(this)
13465  except __builtin__.Exception:
13466  self.this = this
13467 
13468  def __str__(self):
13469  """__str__(NonWaterPDBSelector self) -> std::string"""
13470  return _IMP_atom.NonWaterPDBSelector___str__(self)
13471 
13472 
13473  def __repr__(self):
13474  """__repr__(NonWaterPDBSelector self) -> std::string"""
13475  return _IMP_atom.NonWaterPDBSelector___repr__(self)
13476 
13477 
13478  @staticmethod
13479  def get_from(o):
13480  return _object_cast_to_NonWaterPDBSelector(o)
13481 
13482 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
13483 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
13484 
13485 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
13486  """Proxy of C++ IMP::atom::BackbonePDBSelector class."""
13487 
13488  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13489 
13490  def __init__(self, *args):
13491  """
13492  __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
13493  __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
13494  """
13495  this = _IMP_atom.new_BackbonePDBSelector(*args)
13496  try:
13497  self.this.append(this)
13498  except __builtin__.Exception:
13499  self.this = this
13500 
13501  def __str__(self):
13502  """__str__(BackbonePDBSelector self) -> std::string"""
13503  return _IMP_atom.BackbonePDBSelector___str__(self)
13504 
13505 
13506  def __repr__(self):
13507  """__repr__(BackbonePDBSelector self) -> std::string"""
13508  return _IMP_atom.BackbonePDBSelector___repr__(self)
13509 
13510 
13511  @staticmethod
13512  def get_from(o):
13513  return _object_cast_to_BackbonePDBSelector(o)
13514 
13515 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
13516 BackbonePDBSelector_swigregister(BackbonePDBSelector)
13517 
13518 class PPDBSelector(NonAlternativePDBSelector):
13519  """Proxy of C++ IMP::atom::PPDBSelector class."""
13520 
13521  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13522 
13523  def __init__(self, *args):
13524  """
13525  __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
13526  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
13527  """
13528  this = _IMP_atom.new_PPDBSelector(*args)
13529  try:
13530  self.this.append(this)
13531  except __builtin__.Exception:
13532  self.this = this
13533 
13534  def __str__(self):
13535  """__str__(PPDBSelector self) -> std::string"""
13536  return _IMP_atom.PPDBSelector___str__(self)
13537 
13538 
13539  def __repr__(self):
13540  """__repr__(PPDBSelector self) -> std::string"""
13541  return _IMP_atom.PPDBSelector___repr__(self)
13542 
13543 
13544  @staticmethod
13545  def get_from(o):
13546  return _object_cast_to_PPDBSelector(o)
13547 
13548 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
13549 PPDBSelector_swigregister(PPDBSelector)
13550 
13551 class AndPDBSelector(PDBSelector):
13552  """Proxy of C++ IMP::atom::AndPDBSelector class."""
13553 
13554  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13555 
13556  def get_version_info(self):
13557  """get_version_info(AndPDBSelector self) -> VersionInfo"""
13558  return _IMP_atom.AndPDBSelector_get_version_info(self)
13559 
13560 
13561  def __init__(self, a, b):
13562  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13563  this = _IMP_atom.new_AndPDBSelector(a, b)
13564  try:
13565  self.this.append(this)
13566  except __builtin__.Exception:
13567  self.this = this
13568 
13569  def __str__(self):
13570  """__str__(AndPDBSelector self) -> std::string"""
13571  return _IMP_atom.AndPDBSelector___str__(self)
13572 
13573 
13574  def __repr__(self):
13575  """__repr__(AndPDBSelector self) -> std::string"""
13576  return _IMP_atom.AndPDBSelector___repr__(self)
13577 
13578 
13579  @staticmethod
13580  def get_from(o):
13581  return _object_cast_to_AndPDBSelector(o)
13582 
13583 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
13584 AndPDBSelector_swigregister(AndPDBSelector)
13585 
13586 class OrPDBSelector(PDBSelector):
13587  """Proxy of C++ IMP::atom::OrPDBSelector class."""
13588 
13589  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13590 
13591  def get_version_info(self):
13592  """get_version_info(OrPDBSelector self) -> VersionInfo"""
13593  return _IMP_atom.OrPDBSelector_get_version_info(self)
13594 
13595 
13596  def __init__(self, a, b):
13597  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13598  this = _IMP_atom.new_OrPDBSelector(a, b)
13599  try:
13600  self.this.append(this)
13601  except __builtin__.Exception:
13602  self.this = this
13603 
13604  def __str__(self):
13605  """__str__(OrPDBSelector self) -> std::string"""
13606  return _IMP_atom.OrPDBSelector___str__(self)
13607 
13608 
13609  def __repr__(self):
13610  """__repr__(OrPDBSelector self) -> std::string"""
13611  return _IMP_atom.OrPDBSelector___repr__(self)
13612 
13613 
13614  @staticmethod
13615  def get_from(o):
13616  return _object_cast_to_OrPDBSelector(o)
13617 
13618 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
13619 OrPDBSelector_swigregister(OrPDBSelector)
13620 
13621 class XorPDBSelector(PDBSelector):
13622  """Proxy of C++ IMP::atom::XorPDBSelector class."""
13623 
13624  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13625 
13626  def get_version_info(self):
13627  """get_version_info(XorPDBSelector self) -> VersionInfo"""
13628  return _IMP_atom.XorPDBSelector_get_version_info(self)
13629 
13630 
13631  def __init__(self, a, b):
13632  """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13633  this = _IMP_atom.new_XorPDBSelector(a, b)
13634  try:
13635  self.this.append(this)
13636  except __builtin__.Exception:
13637  self.this = this
13638 
13639  def __str__(self):
13640  """__str__(XorPDBSelector self) -> std::string"""
13641  return _IMP_atom.XorPDBSelector___str__(self)
13642 
13643 
13644  def __repr__(self):
13645  """__repr__(XorPDBSelector self) -> std::string"""
13646  return _IMP_atom.XorPDBSelector___repr__(self)
13647 
13648 
13649  @staticmethod
13650  def get_from(o):
13651  return _object_cast_to_XorPDBSelector(o)
13652 
13653 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13654 XorPDBSelector_swigregister(XorPDBSelector)
13655 
13656 class NotPDBSelector(PDBSelector):
13657  """Proxy of C++ IMP::atom::NotPDBSelector class."""
13658 
13659  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13660 
13661  def get_version_info(self):
13662  """get_version_info(NotPDBSelector self) -> VersionInfo"""
13663  return _IMP_atom.NotPDBSelector_get_version_info(self)
13664 
13665 
13666  def __init__(self, a):
13667  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13668  this = _IMP_atom.new_NotPDBSelector(a)
13669  try:
13670  self.this.append(this)
13671  except __builtin__.Exception:
13672  self.this = this
13673 
13674  def __str__(self):
13675  """__str__(NotPDBSelector self) -> std::string"""
13676  return _IMP_atom.NotPDBSelector___str__(self)
13677 
13678 
13679  def __repr__(self):
13680  """__repr__(NotPDBSelector self) -> std::string"""
13681  return _IMP_atom.NotPDBSelector___repr__(self)
13682 
13683 
13684  @staticmethod
13685  def get_from(o):
13686  return _object_cast_to_NotPDBSelector(o)
13687 
13688 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13689 NotPDBSelector_swigregister(NotPDBSelector)
13690 
13691 
13692 def get_default_pdb_selector():
13693  """get_default_pdb_selector() -> PDBSelector"""
13694  return _IMP_atom.get_default_pdb_selector()
13695 
13696 def read_pdb(*args):
13697  """
13698  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13699  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13700  read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13701  read_pdb(TextInput input, Model model) -> Hierarchy
13702  read_pdb(TextInput input, int model, Hierarchy h)
13703  """
13704  return _IMP_atom.read_pdb(*args)
13705 
13706 def read_multimodel_pdb(*args):
13707  """
13708  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13709  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13710  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13711  """
13712  return _IMP_atom.read_multimodel_pdb(*args)
13713 
13714 def write_pdb(mhd, out, model=1):
13715  """
13716  write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13717  write_pdb(Selection mhd, TextOutput out)
13718  """
13719  return _IMP_atom.write_pdb(mhd, out, model)
13720 
13721 def write_pdb_of_c_alphas(mhd, out, model=1):
13722  """
13723  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13724  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13725  """
13726  return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13727 
13728 def write_multimodel_pdb(mhd, out):
13729  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13730  return _IMP_atom.write_multimodel_pdb(mhd, out)
13731 
13732 def get_pdb_string(*args):
13733  """
13734  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00, double tempFactor=0.00, IMP::atom::Element e) -> std::string
13735  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00, double tempFactor=0.00) -> std::string
13736  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00) -> std::string
13737  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13738  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13739  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13740  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13741  get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13742  get_pdb_string(Vector3D v, int index=-1) -> std::string
13743  get_pdb_string(Vector3D v) -> std::string
13744  """
13745  return _IMP_atom.get_pdb_string(*args)
13746 
13747 def get_pdb_conect_record_string(arg1, arg2):
13748  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13749  return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13750 class WritePDBOptimizerState(IMP.OptimizerState):
13751  """Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13752 
13753  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13754 
13755  def __init__(self, *args):
13756  """
13757  __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13758  __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13759  """
13760  this = _IMP_atom.new_WritePDBOptimizerState(*args)
13761  try:
13762  self.this.append(this)
13763  except __builtin__.Exception:
13764  self.this = this
13765 
13766  def get_version_info(self):
13767  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13768  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13769 
13770 
13771  def __str__(self):
13772  """__str__(WritePDBOptimizerState self) -> std::string"""
13773  return _IMP_atom.WritePDBOptimizerState___str__(self)
13774 
13775 
13776  def __repr__(self):
13777  """__repr__(WritePDBOptimizerState self) -> std::string"""
13778  return _IMP_atom.WritePDBOptimizerState___repr__(self)
13779 
13780 
13781  @staticmethod
13782  def get_from(o):
13783  return _object_cast_to_WritePDBOptimizerState(o)
13784 
13785 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13786 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13787 
13788 
13789 def read_multimodel_mmcif(*args):
13790  """
13791  read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13792  read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13793  read_multimodel_mmcif(TextInput input, Model model) -> IMP::atom::Hierarchies
13794  """
13795  return _IMP_atom.read_multimodel_mmcif(*args)
13796 
13797 def read_mmcif(*args):
13798  """
13799  read_mmcif(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> Hierarchy
13800  read_mmcif(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13801  read_mmcif(TextInput input, Model model) -> Hierarchy
13802  """
13803  return _IMP_atom.read_mmcif(*args)
13804 
13805 def get_kt(T):
13806  """get_kt(double T) -> double"""
13807  return _IMP_atom.get_kt(T)
13808 class CAAngleRestraint(IMP.Restraint):
13809  """Proxy of C++ IMP::atom::CAAngleRestraint class."""
13810 
13811  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13812 
13813  def __init__(self, m, p1, p2, p3, phi0, score):
13814  """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13815  this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13816  try:
13817  self.this.append(this)
13818  except __builtin__.Exception:
13819  self.this = this
13820 
13821  def do_get_inputs(self):
13822  """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13823  return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13824 
13825 
13826  def get_version_info(self):
13827  """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13828  return _IMP_atom.CAAngleRestraint_get_version_info(self)
13829 
13830 
13831  def __str__(self):
13832  """__str__(CAAngleRestraint self) -> std::string"""
13833  return _IMP_atom.CAAngleRestraint___str__(self)
13834 
13835 
13836  def __repr__(self):
13837  """__repr__(CAAngleRestraint self) -> std::string"""
13838  return _IMP_atom.CAAngleRestraint___repr__(self)
13839 
13840 
13841  @staticmethod
13842  def get_from(o):
13843  return _object_cast_to_CAAngleRestraint(o)
13844 
13845 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13846 CAAngleRestraint_swigregister(CAAngleRestraint)
13847 
13848 class CADihedralRestraint(IMP.Restraint):
13849  """Proxy of C++ IMP::atom::CADihedralRestraint class."""
13850 
13851  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13852 
13853  def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13854  """__init__(IMP::atom::CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
13855  this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13856  try:
13857  self.this.append(this)
13858  except __builtin__.Exception:
13859  self.this = this
13860 
13861  def do_get_inputs(self):
13862  """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13863  return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13864 
13865 
13866  def get_version_info(self):
13867  """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13868  return _IMP_atom.CADihedralRestraint_get_version_info(self)
13869 
13870 
13871  def __str__(self):
13872  """__str__(CADihedralRestraint self) -> std::string"""
13873  return _IMP_atom.CADihedralRestraint___str__(self)
13874 
13875 
13876  def __repr__(self):
13877  """__repr__(CADihedralRestraint self) -> std::string"""
13878  return _IMP_atom.CADihedralRestraint___repr__(self)
13879 
13880 
13881  @staticmethod
13882  def get_from(o):
13883  return _object_cast_to_CADihedralRestraint(o)
13884 
13885 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13886 CADihedralRestraint_swigregister(CADihedralRestraint)
13887 
13888 class StructureSource(IMP.Decorator):
13889  """Proxy of C++ IMP::atom::StructureSource class."""
13890 
13891  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13892 
13893  def get_source_id(self):
13894  """get_source_id(StructureSource self) -> std::string"""
13895  return _IMP_atom.StructureSource_get_source_id(self)
13896 
13897 
13898  def get_source_chain_id(self):
13899  """get_source_chain_id(StructureSource self) -> std::string"""
13900  return _IMP_atom.StructureSource_get_source_chain_id(self)
13901 
13902 
13903  def set_source_id(self, source_id):
13904  """set_source_id(StructureSource self, std::string source_id)"""
13905  return _IMP_atom.StructureSource_set_source_id(self, source_id)
13906 
13907 
13908  def set_source_chain_id(self, source_chain_id):
13909  """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13910  return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13911 
13912 
13913  def __init__(self, *args):
13914  """
13915  __init__(IMP::atom::StructureSource self) -> StructureSource
13916  __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13917  __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13918  """
13919  this = _IMP_atom.new_StructureSource(*args)
13920  try:
13921  self.this.append(this)
13922  except __builtin__.Exception:
13923  self.this = this
13924 
13925  def get_is_setup(*args):
13926  """
13927  get_is_setup(Model m, ParticleIndex pi) -> bool
13928  get_is_setup(_ParticleAdaptor p) -> bool
13929  """
13930  return _IMP_atom.StructureSource_get_is_setup(*args)
13931 
13932  get_is_setup = staticmethod(get_is_setup)
13933 
13934  def show(self, *args):
13935  """
13936  show(StructureSource self, _ostream out)
13937  show(StructureSource self)
13938  """
13939  return _IMP_atom.StructureSource_show(self, *args)
13940 
13941 
13942  def setup_particle(*args):
13943  """
13944  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13945  setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13946  """
13947  return _IMP_atom.StructureSource_setup_particle(*args)
13948 
13949  setup_particle = staticmethod(setup_particle)
13950 
13951  def add_attribute(self, *args):
13952  """
13953  add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13954  add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13955  add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13956  add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
13957  add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
13958  add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13959  add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13960  add_attribute(StructureSource self, ObjectKey a0, Object a1)
13961  """
13962  return _IMP_atom.StructureSource_add_attribute(self, *args)
13963 
13964 
13965  def get_value(self, *args):
13966  """
13967  get_value(StructureSource self, FloatKey a0) -> IMP::Float
13968  get_value(StructureSource self, IntKey a0) -> IMP::Int
13969  get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
13970  get_value(StructureSource self, IntsKey a0) -> IMP::Ints
13971  get_value(StructureSource self, StringKey a0) -> IMP::String
13972  get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13973  get_value(StructureSource self, ObjectKey a0) -> Object
13974  """
13975  return _IMP_atom.StructureSource_get_value(self, *args)
13976 
13977 
13978  def set_value(self, *args):
13979  """
13980  set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13981  set_value(StructureSource self, IntKey a0, IMP::Int a1)
13982  set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
13983  set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
13984  set_value(StructureSource self, StringKey a0, IMP::String a1)
13985  set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13986  set_value(StructureSource self, ObjectKey a0, Object a1)
13987  """
13988  return _IMP_atom.StructureSource_set_value(self, *args)
13989 
13990 
13991  def remove_attribute(self, *args):
13992  """
13993  remove_attribute(StructureSource self, FloatKey a0)
13994  remove_attribute(StructureSource self, IntKey a0)
13995  remove_attribute(StructureSource self, FloatsKey a0)
13996  remove_attribute(StructureSource self, IntsKey a0)
13997  remove_attribute(StructureSource self, StringKey a0)
13998  remove_attribute(StructureSource self, ParticleIndexKey a0)
13999  remove_attribute(StructureSource self, ObjectKey a0)
14000  """
14001  return _IMP_atom.StructureSource_remove_attribute(self, *args)
14002 
14003 
14004  def has_attribute(self, *args):
14005  """
14006  has_attribute(StructureSource self, FloatKey a0) -> bool
14007  has_attribute(StructureSource self, IntKey a0) -> bool
14008  has_attribute(StructureSource self, FloatsKey a0) -> bool
14009  has_attribute(StructureSource self, IntsKey a0) -> bool
14010  has_attribute(StructureSource self, StringKey a0) -> bool
14011  has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
14012  has_attribute(StructureSource self, ObjectKey a0) -> bool
14013  """
14014  return _IMP_atom.StructureSource_has_attribute(self, *args)
14015 
14016 
14017  def get_derivative(self, a0):
14018  """get_derivative(StructureSource self, FloatKey a0) -> double"""
14019  return _IMP_atom.StructureSource_get_derivative(self, a0)
14020 
14021 
14022  def get_name(self):
14023  """get_name(StructureSource self) -> std::string"""
14024  return _IMP_atom.StructureSource_get_name(self)
14025 
14026 
14027  def clear_caches(self):
14028  """clear_caches(StructureSource self)"""
14029  return _IMP_atom.StructureSource_clear_caches(self)
14030 
14031 
14032  def set_name(self, a0):
14033  """set_name(StructureSource self, std::string a0)"""
14034  return _IMP_atom.StructureSource_set_name(self, a0)
14035 
14036 
14037  def set_check_level(self, a0):
14038  """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
14039  return _IMP_atom.StructureSource_set_check_level(self, a0)
14040 
14041 
14042  def add_to_derivative(self, a0, a1, a2):
14043  """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
14044  return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
14045 
14046 
14047  def set_is_optimized(self, a0, a1):
14048  """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
14049  return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
14050 
14051 
14052  def get_is_optimized(self, a0):
14053  """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
14054  return _IMP_atom.StructureSource_get_is_optimized(self, a0)
14055 
14056 
14057  def get_check_level(self):
14058  """get_check_level(StructureSource self) -> IMP::CheckLevel"""
14059  return _IMP_atom.StructureSource_get_check_level(self)
14060 
14061 
14062  def __eq__(self, *args):
14063  """
14064  __eq__(StructureSource self, StructureSource o) -> bool
14065  __eq__(StructureSource self, Particle d) -> bool
14066  """
14067  return _IMP_atom.StructureSource___eq__(self, *args)
14068 
14069 
14070  def __ne__(self, *args):
14071  """
14072  __ne__(StructureSource self, StructureSource o) -> bool
14073  __ne__(StructureSource self, Particle d) -> bool
14074  """
14075  return _IMP_atom.StructureSource___ne__(self, *args)
14076 
14077 
14078  def __le__(self, *args):
14079  """
14080  __le__(StructureSource self, StructureSource o) -> bool
14081  __le__(StructureSource self, Particle d) -> bool
14082  """
14083  return _IMP_atom.StructureSource___le__(self, *args)
14084 
14085 
14086  def __lt__(self, *args):
14087  """
14088  __lt__(StructureSource self, StructureSource o) -> bool
14089  __lt__(StructureSource self, Particle d) -> bool
14090  """
14091  return _IMP_atom.StructureSource___lt__(self, *args)
14092 
14093 
14094  def __ge__(self, *args):
14095  """
14096  __ge__(StructureSource self, StructureSource o) -> bool
14097  __ge__(StructureSource self, Particle d) -> bool
14098  """
14099  return _IMP_atom.StructureSource___ge__(self, *args)
14100 
14101 
14102  def __gt__(self, *args):
14103  """
14104  __gt__(StructureSource self, StructureSource o) -> bool
14105  __gt__(StructureSource self, Particle d) -> bool
14106  """
14107  return _IMP_atom.StructureSource___gt__(self, *args)
14108 
14109 
14110  def __hash__(self):
14111  """__hash__(StructureSource self) -> std::size_t"""
14112  return _IMP_atom.StructureSource___hash__(self)
14113 
14114 
14115  def __str__(self):
14116  """__str__(StructureSource self) -> std::string"""
14117  return _IMP_atom.StructureSource___str__(self)
14118 
14119 
14120  def __repr__(self):
14121  """__repr__(StructureSource self) -> std::string"""
14122  return _IMP_atom.StructureSource___repr__(self)
14123 
14124  __swig_destroy__ = _IMP_atom.delete_StructureSource
14125  __del__ = lambda self: None
14126 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
14127 StructureSource_swigregister(StructureSource)
14128 
14129 def StructureSource_get_is_setup(*args):
14130  """
14131  get_is_setup(Model m, ParticleIndex pi) -> bool
14132  StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
14133  """
14134  return _IMP_atom.StructureSource_get_is_setup(*args)
14135 
14136 def StructureSource_setup_particle(*args):
14137  """
14138  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
14139  StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
14140  """
14141  return _IMP_atom.StructureSource_setup_particle(*args)
14142 
14143 
14144 def __lshift__(*args):
14145  """
14146  __lshift__(_ostream out, Bonded n) -> _ostream
14147  __lshift__(_ostream out, Bond n) -> _ostream
14148  __lshift__(_ostream out, Hierarchy n) -> _ostream
14149  __lshift__(_ostream out, Angle n) -> _ostream
14150  __lshift__(_ostream out, Dihedral n) -> _ostream
14151  __lshift__(_ostream out, CenterOfMass n) -> _ostream
14152  __lshift__(_ostream out, Diffusion n) -> _ostream
14153  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
14154  __lshift__(_ostream out, TAMDParticle n) -> _ostream
14155  __lshift__(_ostream out, Chain n) -> _ostream
14156  __lshift__(_ostream out, Charged n) -> _ostream
14157  __lshift__(_ostream out, Domain n) -> _ostream
14158  __lshift__(_ostream out, LennardJones n) -> _ostream
14159  __lshift__(_ostream out, Fragment n) -> _ostream
14160  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
14161  __lshift__(_ostream out, Atom n) -> _ostream
14162  __lshift__(_ostream out, Residue n) -> _ostream
14163  __lshift__(_ostream out, Representation n) -> _ostream
14164  __lshift__(_ostream out, State n) -> _ostream
14165  __lshift__(_ostream out, Molecule n) -> _ostream
14166  __lshift__(_ostream out, Copy n) -> _ostream
14167  __lshift__(_ostream out, StructureSource n) -> _ostream
14168  """
14169  return _IMP_atom.__lshift__(*args)
14170 class HelixRestraint(IMP.Restraint):
14171  """Proxy of C++ IMP::atom::HelixRestraint class."""
14172 
14173  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
14174 
14175  def __init__(self, rs, ideal=True):
14176  """
14177  __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint
14178  __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs) -> HelixRestraint
14179  """
14180  this = _IMP_atom.new_HelixRestraint(rs, ideal)
14181  try:
14182  self.this.append(this)
14183  except __builtin__.Exception:
14184  self.this = this
14185 
14186  def get_number_of_bonds(self):
14187  """get_number_of_bonds(HelixRestraint self) -> int"""
14188  return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
14189 
14190 
14191  def get_number_of_dihedrals(self):
14192  """get_number_of_dihedrals(HelixRestraint self) -> int"""
14193  return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
14194 
14195 
14196  def do_get_inputs(self):
14197  """do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
14198  return _IMP_atom.HelixRestraint_do_get_inputs(self)
14199 
14200 
14201  def get_version_info(self):
14202  """get_version_info(HelixRestraint self) -> VersionInfo"""
14203  return _IMP_atom.HelixRestraint_get_version_info(self)
14204 
14205 
14206  def __str__(self):
14207  """__str__(HelixRestraint self) -> std::string"""
14208  return _IMP_atom.HelixRestraint___str__(self)
14209 
14210 
14211  def __repr__(self):
14212  """__repr__(HelixRestraint self) -> std::string"""
14213  return _IMP_atom.HelixRestraint___repr__(self)
14214 
14215 
14216  @staticmethod
14217  def get_from(o):
14218  return _object_cast_to_HelixRestraint(o)
14219 
14220 HelixRestraint_swigregister = _IMP_atom.HelixRestraint_swigregister
14221 HelixRestraint_swigregister(HelixRestraint)
14222 
14223 
14225  """get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
14226  return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
14227 
14228 def show_molecular_hierarchy(*args):
14229  """
14230  show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
14231  show_molecular_hierarchy(Hierarchy h) -> _ostream
14232  """
14233  return _IMP_atom.show_molecular_hierarchy(*args)
14234 class CHARMMBond(object):
14235  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class."""
14236 
14237  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
14238  __repr__ = _swig_repr
14239 
14240  def __init__(self, atoms):
14241  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
14242  this = _IMP_atom.new_CHARMMBond(atoms)
14243  try:
14244  self.this.append(this)
14245  except __builtin__.Exception:
14246  self.this = this
14247 
14248  def get_endpoint(self, i):
14249  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
14250  return _IMP_atom.CHARMMBond_get_endpoint(self, i)
14251 
14252 
14253  def get_contains_atom(self, name):
14254  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
14255  return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
14256 
14257 
14258  def show(self, *args):
14259  """
14260  show(CHARMMBond self, _ostream out)
14261  show(CHARMMBond self)
14262  """
14263  return _IMP_atom.CHARMMBond_show(self, *args)
14264 
14265  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
14266  __del__ = lambda self: None
14267 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
14268 CHARMMBond_swigregister(CHARMMBond)
14269 
14270 class CHARMMAngle(object):
14271  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class."""
14272 
14273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
14274  __repr__ = _swig_repr
14275 
14276  def __init__(self, atoms):
14277  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
14278  this = _IMP_atom.new_CHARMMAngle(atoms)
14279  try:
14280  self.this.append(this)
14281  except __builtin__.Exception:
14282  self.this = this
14283 
14284  def get_endpoint(self, i):
14285  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
14286  return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
14287 
14288 
14289  def get_contains_atom(self, name):
14290  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
14291  return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
14292 
14293 
14294  def show(self, *args):
14295  """
14296  show(CHARMMAngle self, _ostream out)
14297  show(CHARMMAngle self)
14298  """
14299  return _IMP_atom.CHARMMAngle_show(self, *args)
14300 
14301  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
14302  __del__ = lambda self: None
14303 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
14304 CHARMMAngle_swigregister(CHARMMAngle)
14305 
14306 
14307 def _get_native_overlap_cpp(m1, m2, threshold):
14308  """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
14309  return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
14310 
14311 def _get_drmsd_cpp(m0, m1):
14312  """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
14313  return _IMP_atom._get_drmsd_cpp(m0, m1)
14314 
14315 def _get_drmsd_Q_cpp(m0, m1, threshold):
14316  """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
14317  return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
14318 
14319 def _get_drms_cpp(m1, m2):
14320  """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
14321  return _IMP_atom._get_drms_cpp(m1, m2)
14322 
14323 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
14324  """_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"""
14325  return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
14326 
14327 def get_native_overlap(a, b, d):
14328  va= [IMP.algebra.get_vector(x) for x in a]
14329  vb= [IMP.algebra.get_vector(x) for x in b]
14330  return _get_native_overlap_cpp(va, vb, d)
14331 
14332 def get_drmsd(a, b):
14333  va= [IMP.algebra.get_vector(x) for x in a]
14334  vb= [IMP.algebra.get_vector(x) for x in b]
14335  return _get_drmsd_cpp(va, vb)
14336 
14337 def get_drms(a, b):
14338  va= [IMP.algebra.get_vector(x) for x in a]
14339  vb= [IMP.algebra.get_vector(x) for x in b]
14340  return _get_drms_cpp(va, vb)
14341 
14342 def get_drmsd_Q(a, b, t):
14343  va= [IMP.algebra.get_vector(x) for x in a]
14344  vb= [IMP.algebra.get_vector(x) for x in b]
14345  return _get_drmsd_Q_cpp(va, vb, t)
14346 
14347 def get_rigid_bodies_drms(a, b, ranges):
14348  va= [IMP.algebra.get_vector(x) for x in a]
14349  vb= [IMP.algebra.get_vector(x) for x in b]
14350 #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
14351  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
14352 
14353 
14354 
14355 def get_module_version():
14356  """get_module_version() -> std::string const"""
14357  return _IMP_atom.get_module_version()
14358 
14359 def get_example_path(fname):
14360  """get_example_path(std::string fname) -> std::string"""
14361  return _IMP_atom.get_example_path(fname)
14362 
14363 def get_data_path(fname):
14364  """get_data_path(std::string fname) -> std::string"""
14365  return _IMP_atom.get_data_path(fname)
14366 
14367 from . import _version_check
14368 _version_check.check_version(get_module_version())
14369 __version__ = get_module_version()
14370 
14371 
14372 
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:37
A shared container for Pairs.
Definition: PairContainer.h:37
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
double get_einstein_rotational_diffusion_coefficient(double r, double temp=-1)
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:81
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:274
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"))
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)
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:163
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:106
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)
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all the molecules in the first model of the mmCIF file.
Base class for all optimizers.
Definition: Optimizer.h:46
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:28
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:118
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom)
Convert force from kcal/mol/A to femtonewtons.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:31
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
Definition: Refiner.h:34
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
Definition: atom/distance.h:85
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
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:54
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27