IMP logo
IMP Reference Guide  2.8.0
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 2007-2017 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_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_atom._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_atom._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
330 import IMP.core
331 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
334 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
335 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
336 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
337 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
339 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
340 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
341 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
342 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
343 import IMP.container
344 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
345 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
346 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
347 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
348 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
349 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
350 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
351 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
352 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
353 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
354 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
355 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
356 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
358  """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class."""
359 
360  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
361  __repr__ = _swig_repr
362 
363  def __init__(self):
364  """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
365  this = _IMP_atom.new_HierarchyTree()
366  try:
367  self.this.append(this)
368  except __builtin__.Exception:
369  self.this = this
370 
371  def get_graph(self):
372  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
373  return _IMP_atom.HierarchyTree_get_graph(self)
374 
375 
376  def get_vertices(self):
377  """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
378  return _IMP_atom.HierarchyTree_get_vertices(self)
379 
380 
381  def get_vertex_name(self, i):
382  """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
383  return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
384 
385 
386  def get_in_neighbors(self, v):
387  """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"""
388  return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
389 
390 
391  def get_out_neighbors(self, v):
392  """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"""
393  return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
394 
395 
396  def show_graphviz(self, *args):
397  """
398  show_graphviz(HierarchyTree self, _ostream out)
399  show_graphviz(HierarchyTree self)
400  """
401  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
402 
403 
404  def get_graphviz_string(self):
405  """get_graphviz_string(HierarchyTree self) -> std::string"""
406  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
407 
408 
409  def add_edge(self, v0, v1):
410  """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)"""
411  return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
412 
413 
414  def add_vertex(self, l):
415  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
416  return _IMP_atom.HierarchyTree_add_vertex(self, l)
417 
418 
419  def remove_vertex(self, l):
420  """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
421  return _IMP_atom.HierarchyTree_remove_vertex(self, l)
422 
423  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
424  __del__ = lambda self: None
425 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
426 HierarchyTree_swigregister(HierarchyTree)
427 
428 
429 _value_types.append("HierarchyTree")
430 
431 
432 _object_types.append("PDBSelector")
433 
434 
435 def _object_cast_to_PDBSelector(o):
436  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
437  return _IMP_atom._object_cast_to_PDBSelector(o)
438 
439 def Angles(l=[]):
440  return [Angle(x) for x in l]
441 _plural_types.append("Angles")
442 
443 
444 _value_types.append("Angle")
445 
446 
447 def Atoms(l=[]):
448  return [Atom(x) for x in l]
449 _plural_types.append("Atoms")
450 
451 
452 _value_types.append("Atom")
453 
454 
455 def Bonds(l=[]):
456  return [Bond(x) for x in l]
457 _plural_types.append("Bonds")
458 
459 
460 _value_types.append("Bond")
461 
462 
463 def Bondeds(l=[]):
464  return [Bonded(x) for x in l]
465 _plural_types.append("Bondeds")
466 
467 
468 _value_types.append("Bonded")
469 
470 
471 def CHARMMAtomList(l=[]):
472  return [CHARMMAtom(x) for x in l]
473 _plural_types.append("CHARMMAtomList")
474 
475 
476 _value_types.append("CHARMMAtom")
477 
478 
479 def Chains(l=[]):
480  return [Chain(x) for x in l]
481 _plural_types.append("Chains")
482 
483 
484 _value_types.append("Chain")
485 
486 
487 def CenterOfMasses(l=[]):
488  return [CenterOfMass(x) for x in l]
489 _plural_types.append("CenterOfMasses")
490 
491 
492 _value_types.append("CenterOfMass")
493 
494 
495 def Chargeds(l=[]):
496  return [Charged(x) for x in l]
497 _plural_types.append("Chargeds")
498 
499 
500 _value_types.append("Charged")
501 
502 
503 def Diffusions(l=[]):
504  return [Diffusion(x) for x in l]
505 _plural_types.append("Diffusions")
506 
507 
508 _value_types.append("Diffusion")
509 
510 
511 def RigidBodyDiffusions(l=[]):
512  return [RigidBodyDiffusion(x) for x in l]
513 _plural_types.append("RigidBodyDiffusions")
514 
515 
516 _value_types.append("RigidBodyDiffusion")
517 
518 
519 def TAMDParticles(l=[]):
520  return [TAMDParticle(x) for x in l]
521 _plural_types.append("TAMDParticles")
522 
523 
524 _value_types.append("TAMDParticle")
525 
526 
527 def TAMDCentroids(l=[]):
528  return [TAMDCentroid(x) for x in l]
529 _plural_types.append("TAMDCentroids")
530 
531 
532 _value_types.append("TAMDCentroid")
533 
534 
535 def Dihedrals(l=[]):
536  return [Dihedral(x) for x in l]
537 _plural_types.append("Dihedrals")
538 
539 
540 _value_types.append("Dihedral")
541 
542 
543 def Domains(l=[]):
544  return [Domain(x) for x in l]
545 _plural_types.append("Domains")
546 
547 
548 _value_types.append("Domain")
549 
550 
551 def Fragments(l=[]):
552  return [Fragment(x) for x in l]
553 _plural_types.append("Fragments")
554 
555 
556 _value_types.append("Fragment")
557 
558 
559 def Hierarchies(l=[]):
560  return [Hierarchy(x) for x in l]
561 _plural_types.append("Hierarchies")
562 
563 
564 _value_types.append("Hierarchy")
565 
566 
567 def LennardJonesList(l=[]):
568  return [LennardJones(x) for x in l]
569 _plural_types.append("LennardJonesList")
570 
571 
572 _value_types.append("LennardJones")
573 
574 
575 def Masses(l=[]):
576  return [Mass(x) for x in l]
577 _plural_types.append("Masses")
578 
579 
580 _value_types.append("Mass")
581 
582 
583 def LinearVelocities(l=[]):
584  return [LinearVelocity(x) for x in l]
585 _plural_types.append("LinearVelocities")
586 
587 
588 _value_types.append("LinearVelocity")
589 
590 
591 def AngularVelocities(l=[]):
592  return [AngularVelocity(x) for x in l]
593 _plural_types.append("AngularVelocities")
594 
595 
596 _value_types.append("AngularVelocity")
597 
598 
599 def Molecules(l=[]):
600  return [Molecule(x) for x in l]
601 _plural_types.append("Molecules")
602 
603 
604 _value_types.append("Molecule")
605 
606 
607 def Residues(l=[]):
608  return [Residue(x) for x in l]
609 _plural_types.append("Residues")
610 
611 
612 _value_types.append("Residue")
613 
614 
615 def Representations(l=[]):
616  return [Representation(x) for x in l]
617 _plural_types.append("Representations")
618 
619 
620 _value_types.append("Representation")
621 
622 
623 def States(l=[]):
624  return [State(x) for x in l]
625 _plural_types.append("States")
626 
627 
628 _value_types.append("State")
629 
630 
631 def Copies(l=[]):
632  return [Copy(x) for x in l]
633 _plural_types.append("Copies")
634 
635 
636 _value_types.append("Copy")
637 
638 
639 def SecondaryStructureResidues(l=[]):
640  return [SecondaryStructureResidue(x) for x in l]
641 _plural_types.append("SecondaryStructureResidues")
642 
643 
644 _value_types.append("SecondaryStructureResidue")
645 
646 
647 def StructureSources(l=[]):
648  return [StructureSource(x) for x in l]
649 _plural_types.append("StructureSources")
650 
651 
652 _value_types.append("StructureSource")
653 
654 
655 _object_types.append("Simulator")
656 
657 
658 def _object_cast_to_Simulator(o):
659  """_object_cast_to_Simulator(Object o) -> Simulator"""
660  return _IMP_atom._object_cast_to_Simulator(o)
661 
662 _object_types.append("ATOMPDBSelector")
663 
664 
665 def _object_cast_to_ATOMPDBSelector(o):
666  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
667  return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
668 
669 _object_types.append("AllMol2Selector")
670 
671 
672 def _object_cast_to_AllMol2Selector(o):
673  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
674  return _IMP_atom._object_cast_to_AllMol2Selector(o)
675 
676 _object_types.append("AllPDBSelector")
677 
678 
679 def _object_cast_to_AllPDBSelector(o):
680  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
681  return _IMP_atom._object_cast_to_AllPDBSelector(o)
682 
683 _object_types.append("AndPDBSelector")
684 
685 
686 def _object_cast_to_AndPDBSelector(o):
687  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
688  return _IMP_atom._object_cast_to_AndPDBSelector(o)
689 
690 _object_types.append("XorPDBSelector")
691 
692 
693 def _object_cast_to_XorPDBSelector(o):
694  """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
695  return _IMP_atom._object_cast_to_XorPDBSelector(o)
696 
697 _object_types.append("ResidueTypePDBSelector")
698 
699 
700 def _object_cast_to_ResidueTypePDBSelector(o):
701  """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
702  return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
703 
704 _object_types.append("AtomTypePDBSelector")
705 
706 
707 def _object_cast_to_AtomTypePDBSelector(o):
708  """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
709  return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
710 
711 _object_types.append("AngleSingletonScore")
712 
713 
714 def _object_cast_to_AngleSingletonScore(o):
715  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
716  return _IMP_atom._object_cast_to_AngleSingletonScore(o)
717 
718 _object_types.append("BondEndpointsRefiner")
719 
720 
721 def _object_cast_to_BondEndpointsRefiner(o):
722  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
723  return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
724 
725 _object_types.append("BondPairContainer")
726 
727 
728 def _object_cast_to_BondPairContainer(o):
729  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
730  return _IMP_atom._object_cast_to_BondPairContainer(o)
731 
732 _object_types.append("BondSingletonScore")
733 
734 
735 def _object_cast_to_BondSingletonScore(o):
736  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
737  return _IMP_atom._object_cast_to_BondSingletonScore(o)
738 
739 _object_types.append("BondedPairFilter")
740 
741 
742 def _object_cast_to_BondedPairFilter(o):
743  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
744  return _IMP_atom._object_cast_to_BondedPairFilter(o)
745 
746 _object_types.append("BrownianDynamics")
747 
748 
749 def _object_cast_to_BrownianDynamics(o):
750  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
751  return _IMP_atom._object_cast_to_BrownianDynamics(o)
752 
753 _object_types.append("BrownianDynamicsTAMD")
754 
755 
756 def _object_cast_to_BrownianDynamicsTAMD(o):
757  """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
758  return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
759 
760 _object_types.append("CAlphaPDBSelector")
761 
762 
763 def _object_cast_to_CAlphaPDBSelector(o):
764  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
765  return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
766 
767 _object_types.append("CBetaPDBSelector")
768 
769 
770 def _object_cast_to_CBetaPDBSelector(o):
771  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
772  return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
773 
774 _object_types.append("BackbonePDBSelector")
775 
776 
777 def _object_cast_to_BackbonePDBSelector(o):
778  """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
779  return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
780 
781 _object_types.append("CHARMMParameters")
782 
783 
784 def _object_cast_to_CHARMMParameters(o):
785  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
786  return _IMP_atom._object_cast_to_CHARMMParameters(o)
787 
788 _object_types.append("CHARMMResidueTopology")
789 
790 
791 def _object_cast_to_CHARMMResidueTopology(o):
792  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
793  return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
794 
795 _object_types.append("CHARMMSegmentTopology")
796 
797 
798 def _object_cast_to_CHARMMSegmentTopology(o):
799  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
800  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
801 
802 _object_types.append("CHARMMStereochemistryRestraint")
803 
804 
805 def _object_cast_to_CHARMMStereochemistryRestraint(o):
806  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
807  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
808 
809 _object_types.append("CHARMMTopology")
810 
811 
812 def _object_cast_to_CHARMMTopology(o):
813  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
814  return _IMP_atom._object_cast_to_CHARMMTopology(o)
815 
816 _object_types.append("CPDBSelector")
817 
818 
819 def _object_cast_to_CPDBSelector(o):
820  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
821  return _IMP_atom._object_cast_to_CPDBSelector(o)
822 
823 _object_types.append("ChainPDBSelector")
824 
825 
826 def _object_cast_to_ChainPDBSelector(o):
827  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
828  return _IMP_atom._object_cast_to_ChainPDBSelector(o)
829 
830 _object_types.append("CoulombPairScore")
831 
832 
833 def _object_cast_to_CoulombPairScore(o):
834  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
835  return _IMP_atom._object_cast_to_CoulombPairScore(o)
836 
837 _object_types.append("CoverBond")
838 
839 
840 def _object_cast_to_CoverBond(o):
841  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
842  return _IMP_atom._object_cast_to_CoverBond(o)
843 
844 _object_types.append("DihedralSingletonScore")
845 
846 
847 def _object_cast_to_DihedralSingletonScore(o):
848  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
849  return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
850 
851 _object_types.append("DopePairScore")
852 
853 
854 def _object_cast_to_DopePairScore(o):
855  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
856  return _IMP_atom._object_cast_to_DopePairScore(o)
857 
858 _object_types.append("OrientedSoapPairScore")
859 
860 
861 def _object_cast_to_OrientedSoapPairScore(o):
862  """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
863  return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
864 
865 _object_types.append("EzRestraint")
866 
867 
868 def _object_cast_to_EzRestraint(o):
869  """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
870  return _IMP_atom._object_cast_to_EzRestraint(o)
871 
872 _object_types.append("ForceFieldParameters")
873 
874 
875 def _object_cast_to_ForceFieldParameters(o):
876  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
877  return _IMP_atom._object_cast_to_ForceFieldParameters(o)
878 
879 _object_types.append("ForceSwitch")
880 
881 
882 def _object_cast_to_ForceSwitch(o):
883  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
884  return _IMP_atom._object_cast_to_ForceSwitch(o)
885 
886 _object_types.append("HydrogenPDBSelector")
887 
888 
889 def _object_cast_to_HydrogenPDBSelector(o):
890  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
891  return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
892 
893 _object_types.append("ImproperSingletonScore")
894 
895 
896 def _object_cast_to_ImproperSingletonScore(o):
897  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
898  return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
899 
900 _object_types.append("LennardJonesPairScore")
901 
902 
903 def _object_cast_to_LennardJonesPairScore(o):
904  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
905  return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
906 
907 _object_types.append("Mol2Selector")
908 
909 
910 def _object_cast_to_Mol2Selector(o):
911  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
912  return _IMP_atom._object_cast_to_Mol2Selector(o)
913 
914 _object_types.append("MolecularDynamics")
915 
916 
917 def _object_cast_to_MolecularDynamics(o):
918  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
919  return _IMP_atom._object_cast_to_MolecularDynamics(o)
920 
921 _object_types.append("NPDBSelector")
922 
923 
924 def _object_cast_to_NPDBSelector(o):
925  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
926  return _IMP_atom._object_cast_to_NPDBSelector(o)
927 
928 _object_types.append("NonAlternativePDBSelector")
929 
930 
931 def _object_cast_to_NonAlternativePDBSelector(o):
932  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
933  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
934 
935 _object_types.append("NonHydrogenMol2Selector")
936 
937 
938 def _object_cast_to_NonHydrogenMol2Selector(o):
939  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
940  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
941 
942 _object_types.append("NonHydrogenPDBSelector")
943 
944 
945 def _object_cast_to_NonHydrogenPDBSelector(o):
946  """_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
947  return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
948 
949 _object_types.append("NonWaterNonHydrogenPDBSelector")
950 
951 
952 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
953  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
954  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
955 
956 _object_types.append("NonWaterPDBSelector")
957 
958 
959 def _object_cast_to_NonWaterPDBSelector(o):
960  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
961  return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
962 
963 _object_types.append("NotPDBSelector")
964 
965 
966 def _object_cast_to_NotPDBSelector(o):
967  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
968  return _IMP_atom._object_cast_to_NotPDBSelector(o)
969 
970 _object_types.append("OrPDBSelector")
971 
972 
973 def _object_cast_to_OrPDBSelector(o):
974  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
975  return _IMP_atom._object_cast_to_OrPDBSelector(o)
976 
977 _object_types.append("PPDBSelector")
978 
979 
980 def _object_cast_to_PPDBSelector(o):
981  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
982  return _IMP_atom._object_cast_to_PPDBSelector(o)
983 
984 _object_types.append("ProteinLigandAtomPairScore")
985 
986 
987 def _object_cast_to_ProteinLigandAtomPairScore(o):
988  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
989  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
990 
991 _object_types.append("ProteinLigandRestraint")
992 
993 
994 def _object_cast_to_ProteinLigandRestraint(o):
995  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
996  return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
997 
998 _object_types.append("SameResiduePairFilter")
999 
1000 
1001 def _object_cast_to_SameResiduePairFilter(o):
1002  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1003  return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1004 
1005 _object_types.append("SoapPairFilter")
1006 
1007 
1008 def _object_cast_to_SoapPairFilter(o):
1009  """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1010  return _IMP_atom._object_cast_to_SoapPairFilter(o)
1011 
1012 _object_types.append("SmoothingFunction")
1013 
1014 
1015 def _object_cast_to_SmoothingFunction(o):
1016  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1017  return _IMP_atom._object_cast_to_SmoothingFunction(o)
1018 
1019 _object_types.append("StereochemistryPairFilter")
1020 
1021 
1022 def _object_cast_to_StereochemistryPairFilter(o):
1023  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1024  return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1025 
1026 _object_types.append("VelocityScalingOptimizerState")
1027 
1028 
1029 def _object_cast_to_VelocityScalingOptimizerState(o):
1030  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1031  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1032 
1033 _object_types.append("WaterPDBSelector")
1034 
1035 
1036 def _object_cast_to_WaterPDBSelector(o):
1037  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1038  return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1039 
1040 _object_types.append("WritePDBOptimizerState")
1041 
1042 
1043 def _object_cast_to_WritePDBOptimizerState(o):
1044  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1045  return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1046 
1047 AtomTypes=list
1048 _plural_types.append("AtomTypes")
1049 _value_types.append("AtomType")
1050 
1051 
1052 CHARMMAtomTopologies=list
1053 _plural_types.append("CHARMMAtomTopologies")
1054 _value_types.append("CHARMMAtomTopology")
1055 
1056 
1057 CHARMMBondEndpoints=list
1058 _plural_types.append("CHARMMBondEndpoints")
1059 _value_types.append("CHARMMBondEndpoint")
1060 
1061 
1062 CHARMMBondParametersList=list
1063 _plural_types.append("CHARMMBondParametersList")
1064 _value_types.append("CHARMMBondParameters")
1065 
1066 
1067 CHARMMDihedralParametersList=list
1068 _plural_types.append("CHARMMDihedralParametersList")
1069 _value_types.append("CHARMMDihedralParameters")
1070 
1071 
1072 _object_types.append("CHARMMIdealResidueTopology")
1073 
1074 
1075 def _object_cast_to_CHARMMIdealResidueTopology(o):
1076  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1077  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1078 
1079 CHARMMInternalCoordinates=list
1080 _plural_types.append("CHARMMInternalCoordinates")
1081 _value_types.append("CHARMMInternalCoordinate")
1082 
1083 
1084 _object_types.append("CHARMMPatch")
1085 
1086 
1087 def _object_cast_to_CHARMMPatch(o):
1088  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1089  return _IMP_atom._object_cast_to_CHARMMPatch(o)
1090 
1091 _object_types.append("CHARMMResidueTopologyBase")
1092 
1093 
1094 def _object_cast_to_CHARMMResidueTopologyBase(o):
1095  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1096  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1097 
1098 ResidueTypes=list
1099 _plural_types.append("ResidueTypes")
1100 _value_types.append("ResidueType")
1101 
1102 
1103 Selections=list
1104 _plural_types.append("Selections")
1105 _value_types.append("Selection")
1106 
1107 
1108 _object_types.append("RemoveRigidMotionOptimizerState")
1109 
1110 
1111 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1112  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1113  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1114 
1115 _object_types.append("BerendsenThermostatOptimizerState")
1116 
1117 
1118 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1119  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1120  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1121 
1122 _object_types.append("LangevinThermostatOptimizerState")
1123 
1124 
1125 def _object_cast_to_LangevinThermostatOptimizerState(o):
1126  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1127  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1128 
1129 _object_types.append("SelectionGeometry")
1130 
1131 
1132 def _object_cast_to_SelectionGeometry(o):
1133  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1134  return _IMP_atom._object_cast_to_SelectionGeometry(o)
1135 
1136 _object_types.append("HierarchyGeometry")
1137 
1138 
1139 def _object_cast_to_HierarchyGeometry(o):
1140  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1141  return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1142 
1143 _object_types.append("HierarchiesGeometry")
1144 
1145 
1146 def _object_cast_to_HierarchiesGeometry(o):
1147  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1148  return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1149 
1150 _object_types.append("BondGeometry")
1151 
1152 
1153 def _object_cast_to_BondGeometry(o):
1154  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1155  return _IMP_atom._object_cast_to_BondGeometry(o)
1156 
1157 _object_types.append("BondsGeometry")
1158 
1159 
1160 def _object_cast_to_BondsGeometry(o):
1161  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1162  return _IMP_atom._object_cast_to_BondsGeometry(o)
1163 
1164 _object_types.append("CAAngleRestraint")
1165 
1166 
1167 def _object_cast_to_CAAngleRestraint(o):
1168  """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1169  return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1170 
1171 _object_types.append("CADihedralRestraint")
1172 
1173 
1174 def _object_cast_to_CADihedralRestraint(o):
1175  """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1176  return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1177 
1178 _object_types.append("HelixRestraint")
1179 
1180 
1181 def _object_cast_to_HelixRestraint(o):
1182  """_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1183  return _IMP_atom._object_cast_to_HelixRestraint(o)
1184 
1185 CHARMMDihedrals=list
1186 _plural_types.append("CHARMMDihedrals")
1187 _value_types.append("CHARMMDihedral")
1188 
1189 
1190 CHARMMBonds=list
1191 _plural_types.append("CHARMMBonds")
1192 _value_types.append("CHARMMBond")
1193 
1194 
1195 CHARMMAngles=list
1196 _plural_types.append("CHARMMAngles")
1197 _value_types.append("CHARMMAngle")
1198 
1199 class Bond(IMP.Decorator):
1200  """Proxy of C++ IMP::atom::Bond class."""
1201 
1202  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1203 
1204  def __init__(self, *args):
1205  """
1206  __init__(IMP::atom::Bond self) -> Bond
1207  __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1208  __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1209  """
1210  this = _IMP_atom.new_Bond(*args)
1211  try:
1212  self.this.append(this)
1213  except __builtin__.Exception:
1214  self.this = this
1215 
1216  def show(self, *args):
1217  """
1218  show(Bond self, _ostream out)
1219  show(Bond self)
1220  """
1221  return _IMP_atom.Bond_show(self, *args)
1222 
1223 
1224  def get_is_setup(*args):
1225  """
1226  get_is_setup(_ParticleAdaptor p) -> bool
1227  get_is_setup(Model m, ParticleIndex pi) -> bool
1228  """
1229  return _IMP_atom.Bond_get_is_setup(*args)
1230 
1231  get_is_setup = staticmethod(get_is_setup)
1232  UNKNOWN = _IMP_atom.Bond_UNKNOWN
1233  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1234  SINGLE = _IMP_atom.Bond_SINGLE
1235  DOUBLE = _IMP_atom.Bond_DOUBLE
1236  TRIPLE = _IMP_atom.Bond_TRIPLE
1237  HYDROGEN = _IMP_atom.Bond_HYDROGEN
1238  SALT = _IMP_atom.Bond_SALT
1239  PEPTIDE = _IMP_atom.Bond_PEPTIDE
1240  AMIDE = _IMP_atom.Bond_AMIDE
1241  AROMATIC = _IMP_atom.Bond_AROMATIC
1242 
1243  def get_bonded(self, i):
1244  """get_bonded(Bond self, unsigned int i) -> Bonded"""
1245  return _IMP_atom.Bond_get_bonded(self, i)
1246 
1247 
1248  def get_type(self):
1249  """get_type(Bond self) -> IMP::Int"""
1250  return _IMP_atom.Bond_get_type(self)
1251 
1252 
1253  def set_type(self, t):
1254  """set_type(Bond self, IMP::Int t)"""
1255  return _IMP_atom.Bond_set_type(self, t)
1256 
1257 
1258  def get_order(self):
1259  """get_order(Bond self) -> IMP::Int"""
1260  return _IMP_atom.Bond_get_order(self)
1261 
1262 
1263  def set_order(self, t):
1264  """set_order(Bond self, IMP::Int t)"""
1265  return _IMP_atom.Bond_set_order(self, t)
1266 
1267 
1268  def get_length(self):
1269  """get_length(Bond self) -> IMP::Float"""
1270  return _IMP_atom.Bond_get_length(self)
1271 
1272 
1273  def set_length(self, t):
1274  """set_length(Bond self, IMP::Float t)"""
1275  return _IMP_atom.Bond_set_length(self, t)
1276 
1277 
1278  def get_stiffness(self):
1279  """get_stiffness(Bond self) -> IMP::Float"""
1280  return _IMP_atom.Bond_get_stiffness(self)
1281 
1282 
1283  def set_stiffness(self, t):
1284  """set_stiffness(Bond self, IMP::Float t)"""
1285  return _IMP_atom.Bond_set_stiffness(self, t)
1286 
1287 
1288  def get_length_key():
1289  """get_length_key() -> FloatKey"""
1290  return _IMP_atom.Bond_get_length_key()
1291 
1292  get_length_key = staticmethod(get_length_key)
1293 
1294  def add_attribute(self, *args):
1295  """
1296  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1297  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1298  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1299  add_attribute(Bond self, StringKey a0, IMP::String a1)
1300  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1301  add_attribute(Bond self, ObjectKey a0, Object a1)
1302  """
1303  return _IMP_atom.Bond_add_attribute(self, *args)
1304 
1305 
1306  def get_value(self, *args):
1307  """
1308  get_value(Bond self, FloatKey a0) -> IMP::Float
1309  get_value(Bond self, IntKey a0) -> IMP::Int
1310  get_value(Bond self, StringKey a0) -> IMP::String
1311  get_value(Bond self, ParticleIndexKey a0) -> Particle
1312  get_value(Bond self, ObjectKey a0) -> Object
1313  """
1314  return _IMP_atom.Bond_get_value(self, *args)
1315 
1316 
1317  def set_value(self, *args):
1318  """
1319  set_value(Bond self, FloatKey a0, IMP::Float a1)
1320  set_value(Bond self, IntKey a0, IMP::Int a1)
1321  set_value(Bond self, StringKey a0, IMP::String a1)
1322  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1323  set_value(Bond self, ObjectKey a0, Object a1)
1324  """
1325  return _IMP_atom.Bond_set_value(self, *args)
1326 
1327 
1328  def remove_attribute(self, *args):
1329  """
1330  remove_attribute(Bond self, FloatKey a0)
1331  remove_attribute(Bond self, IntKey a0)
1332  remove_attribute(Bond self, StringKey a0)
1333  remove_attribute(Bond self, ParticleIndexKey a0)
1334  remove_attribute(Bond self, ObjectKey a0)
1335  """
1336  return _IMP_atom.Bond_remove_attribute(self, *args)
1337 
1338 
1339  def has_attribute(self, *args):
1340  """
1341  has_attribute(Bond self, FloatKey a0) -> bool
1342  has_attribute(Bond self, IntKey a0) -> bool
1343  has_attribute(Bond self, StringKey a0) -> bool
1344  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1345  has_attribute(Bond self, ObjectKey a0) -> bool
1346  """
1347  return _IMP_atom.Bond_has_attribute(self, *args)
1348 
1349 
1350  def get_derivative(self, a0):
1351  """get_derivative(Bond self, FloatKey a0) -> double"""
1352  return _IMP_atom.Bond_get_derivative(self, a0)
1353 
1354 
1355  def get_name(self):
1356  """get_name(Bond self) -> std::string"""
1357  return _IMP_atom.Bond_get_name(self)
1358 
1359 
1360  def clear_caches(self):
1361  """clear_caches(Bond self)"""
1362  return _IMP_atom.Bond_clear_caches(self)
1363 
1364 
1365  def set_name(self, a0):
1366  """set_name(Bond self, std::string a0)"""
1367  return _IMP_atom.Bond_set_name(self, a0)
1368 
1369 
1370  def set_check_level(self, a0):
1371  """set_check_level(Bond self, IMP::CheckLevel a0)"""
1372  return _IMP_atom.Bond_set_check_level(self, a0)
1373 
1374 
1375  def add_to_derivative(self, a0, a1, a2):
1376  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1377  return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1378 
1379 
1380  def set_is_optimized(self, a0, a1):
1381  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1382  return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1383 
1384 
1385  def get_is_optimized(self, a0):
1386  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1387  return _IMP_atom.Bond_get_is_optimized(self, a0)
1388 
1389 
1390  def get_check_level(self):
1391  """get_check_level(Bond self) -> IMP::CheckLevel"""
1392  return _IMP_atom.Bond_get_check_level(self)
1393 
1394 
1395  def __eq__(self, *args):
1396  """
1397  __eq__(Bond self, Bond o) -> bool
1398  __eq__(Bond self, Particle d) -> bool
1399  """
1400  return _IMP_atom.Bond___eq__(self, *args)
1401 
1402 
1403  def __ne__(self, *args):
1404  """
1405  __ne__(Bond self, Bond o) -> bool
1406  __ne__(Bond self, Particle d) -> bool
1407  """
1408  return _IMP_atom.Bond___ne__(self, *args)
1409 
1410 
1411  def __le__(self, *args):
1412  """
1413  __le__(Bond self, Bond o) -> bool
1414  __le__(Bond self, Particle d) -> bool
1415  """
1416  return _IMP_atom.Bond___le__(self, *args)
1417 
1418 
1419  def __lt__(self, *args):
1420  """
1421  __lt__(Bond self, Bond o) -> bool
1422  __lt__(Bond self, Particle d) -> bool
1423  """
1424  return _IMP_atom.Bond___lt__(self, *args)
1425 
1426 
1427  def __ge__(self, *args):
1428  """
1429  __ge__(Bond self, Bond o) -> bool
1430  __ge__(Bond self, Particle d) -> bool
1431  """
1432  return _IMP_atom.Bond___ge__(self, *args)
1433 
1434 
1435  def __gt__(self, *args):
1436  """
1437  __gt__(Bond self, Bond o) -> bool
1438  __gt__(Bond self, Particle d) -> bool
1439  """
1440  return _IMP_atom.Bond___gt__(self, *args)
1441 
1442 
1443  def __hash__(self):
1444  """__hash__(Bond self) -> std::size_t"""
1445  return _IMP_atom.Bond___hash__(self)
1446 
1447 
1448  def __str__(self):
1449  """__str__(Bond self) -> std::string"""
1450  return _IMP_atom.Bond___str__(self)
1451 
1452 
1453  def __repr__(self):
1454  """__repr__(Bond self) -> std::string"""
1455  return _IMP_atom.Bond___repr__(self)
1456 
1457  __swig_destroy__ = _IMP_atom.delete_Bond
1458  __del__ = lambda self: None
1459 Bond_swigregister = _IMP_atom.Bond_swigregister
1460 Bond_swigregister(Bond)
1461 
1462 def Bond_get_is_setup(*args):
1463  """
1464  get_is_setup(_ParticleAdaptor p) -> bool
1465  Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1466  """
1467  return _IMP_atom.Bond_get_is_setup(*args)
1468 
1469 def Bond_get_length_key():
1470  """Bond_get_length_key() -> FloatKey"""
1471  return _IMP_atom.Bond_get_length_key()
1472 
1473 class Bonded(IMP.Decorator):
1474  """Proxy of C++ IMP::atom::Bonded class."""
1475 
1476  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1477 
1478  def __init__(self, *args):
1479  """
1480  __init__(IMP::atom::Bonded self) -> Bonded
1481  __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1482  __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1483  """
1484  this = _IMP_atom.new_Bonded(*args)
1485  try:
1486  self.this.append(this)
1487  except __builtin__.Exception:
1488  self.this = this
1489 
1490  def show(self, *args):
1491  """
1492  show(Bonded self, _ostream out)
1493  show(Bonded self)
1494  """
1495  return _IMP_atom.Bonded_show(self, *args)
1496 
1497 
1498  def setup_particle(*args):
1499  """
1500  setup_particle(Model m, ParticleIndex pi) -> Bonded
1501  setup_particle(_ParticleAdaptor decorator) -> Bonded
1502  """
1503  return _IMP_atom.Bonded_setup_particle(*args)
1504 
1505  setup_particle = staticmethod(setup_particle)
1506 
1507  def get_is_setup(*args):
1508  """
1509  get_is_setup(_ParticleAdaptor p) -> bool
1510  get_is_setup(Model m, ParticleIndex pi) -> bool
1511  """
1512  return _IMP_atom.Bonded_get_is_setup(*args)
1513 
1514  get_is_setup = staticmethod(get_is_setup)
1515 
1516  def get_number_of_bonds(self):
1517  """get_number_of_bonds(Bonded self) -> unsigned int"""
1518  return _IMP_atom.Bonded_get_number_of_bonds(self)
1519 
1520 
1521  def get_bond_indexes(self):
1522  """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1523  return _IMP_atom.Bonded_get_bond_indexes(self)
1524 
1525 
1526  def get_bond(self, i):
1527  """get_bond(Bonded self, unsigned int i) -> Bond"""
1528  return _IMP_atom.Bonded_get_bond(self, i)
1529 
1530 
1531  def get_bonded(self, i):
1532  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1533  return _IMP_atom.Bonded_get_bonded(self, i)
1534 
1535 
1536  def add_attribute(self, *args):
1537  """
1538  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1539  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1540  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1541  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1542  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1543  add_attribute(Bonded self, ObjectKey a0, Object a1)
1544  """
1545  return _IMP_atom.Bonded_add_attribute(self, *args)
1546 
1547 
1548  def get_value(self, *args):
1549  """
1550  get_value(Bonded self, FloatKey a0) -> IMP::Float
1551  get_value(Bonded self, IntKey a0) -> IMP::Int
1552  get_value(Bonded self, StringKey a0) -> IMP::String
1553  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1554  get_value(Bonded self, ObjectKey a0) -> Object
1555  """
1556  return _IMP_atom.Bonded_get_value(self, *args)
1557 
1558 
1559  def set_value(self, *args):
1560  """
1561  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1562  set_value(Bonded self, IntKey a0, IMP::Int a1)
1563  set_value(Bonded self, StringKey a0, IMP::String a1)
1564  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1565  set_value(Bonded self, ObjectKey a0, Object a1)
1566  """
1567  return _IMP_atom.Bonded_set_value(self, *args)
1568 
1569 
1570  def remove_attribute(self, *args):
1571  """
1572  remove_attribute(Bonded self, FloatKey a0)
1573  remove_attribute(Bonded self, IntKey a0)
1574  remove_attribute(Bonded self, StringKey a0)
1575  remove_attribute(Bonded self, ParticleIndexKey a0)
1576  remove_attribute(Bonded self, ObjectKey a0)
1577  """
1578  return _IMP_atom.Bonded_remove_attribute(self, *args)
1579 
1580 
1581  def has_attribute(self, *args):
1582  """
1583  has_attribute(Bonded self, FloatKey a0) -> bool
1584  has_attribute(Bonded self, IntKey a0) -> bool
1585  has_attribute(Bonded self, StringKey a0) -> bool
1586  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1587  has_attribute(Bonded self, ObjectKey a0) -> bool
1588  """
1589  return _IMP_atom.Bonded_has_attribute(self, *args)
1590 
1591 
1592  def get_derivative(self, a0):
1593  """get_derivative(Bonded self, FloatKey a0) -> double"""
1594  return _IMP_atom.Bonded_get_derivative(self, a0)
1595 
1596 
1597  def get_name(self):
1598  """get_name(Bonded self) -> std::string"""
1599  return _IMP_atom.Bonded_get_name(self)
1600 
1601 
1602  def clear_caches(self):
1603  """clear_caches(Bonded self)"""
1604  return _IMP_atom.Bonded_clear_caches(self)
1605 
1606 
1607  def set_name(self, a0):
1608  """set_name(Bonded self, std::string a0)"""
1609  return _IMP_atom.Bonded_set_name(self, a0)
1610 
1611 
1612  def set_check_level(self, a0):
1613  """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1614  return _IMP_atom.Bonded_set_check_level(self, a0)
1615 
1616 
1617  def add_to_derivative(self, a0, a1, a2):
1618  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1619  return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1620 
1621 
1622  def set_is_optimized(self, a0, a1):
1623  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1624  return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1625 
1626 
1627  def get_is_optimized(self, a0):
1628  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1629  return _IMP_atom.Bonded_get_is_optimized(self, a0)
1630 
1631 
1632  def get_check_level(self):
1633  """get_check_level(Bonded self) -> IMP::CheckLevel"""
1634  return _IMP_atom.Bonded_get_check_level(self)
1635 
1636 
1637  def __eq__(self, *args):
1638  """
1639  __eq__(Bonded self, Bonded o) -> bool
1640  __eq__(Bonded self, Particle d) -> bool
1641  """
1642  return _IMP_atom.Bonded___eq__(self, *args)
1643 
1644 
1645  def __ne__(self, *args):
1646  """
1647  __ne__(Bonded self, Bonded o) -> bool
1648  __ne__(Bonded self, Particle d) -> bool
1649  """
1650  return _IMP_atom.Bonded___ne__(self, *args)
1651 
1652 
1653  def __le__(self, *args):
1654  """
1655  __le__(Bonded self, Bonded o) -> bool
1656  __le__(Bonded self, Particle d) -> bool
1657  """
1658  return _IMP_atom.Bonded___le__(self, *args)
1659 
1660 
1661  def __lt__(self, *args):
1662  """
1663  __lt__(Bonded self, Bonded o) -> bool
1664  __lt__(Bonded self, Particle d) -> bool
1665  """
1666  return _IMP_atom.Bonded___lt__(self, *args)
1667 
1668 
1669  def __ge__(self, *args):
1670  """
1671  __ge__(Bonded self, Bonded o) -> bool
1672  __ge__(Bonded self, Particle d) -> bool
1673  """
1674  return _IMP_atom.Bonded___ge__(self, *args)
1675 
1676 
1677  def __gt__(self, *args):
1678  """
1679  __gt__(Bonded self, Bonded o) -> bool
1680  __gt__(Bonded self, Particle d) -> bool
1681  """
1682  return _IMP_atom.Bonded___gt__(self, *args)
1683 
1684 
1685  def __hash__(self):
1686  """__hash__(Bonded self) -> std::size_t"""
1687  return _IMP_atom.Bonded___hash__(self)
1688 
1689 
1690  def __str__(self):
1691  """__str__(Bonded self) -> std::string"""
1692  return _IMP_atom.Bonded___str__(self)
1693 
1694 
1695  def __repr__(self):
1696  """__repr__(Bonded self) -> std::string"""
1697  return _IMP_atom.Bonded___repr__(self)
1698 
1699  __swig_destroy__ = _IMP_atom.delete_Bonded
1700  __del__ = lambda self: None
1701 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1702 Bonded_swigregister(Bonded)
1703 
1704 def Bonded_setup_particle(*args):
1705  """
1706  setup_particle(Model m, ParticleIndex pi) -> Bonded
1707  Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1708  """
1709  return _IMP_atom.Bonded_setup_particle(*args)
1710 
1711 def Bonded_get_is_setup(*args):
1712  """
1713  get_is_setup(_ParticleAdaptor p) -> bool
1714  Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1715  """
1716  return _IMP_atom.Bonded_get_is_setup(*args)
1717 
1718 
1719 def create_custom_bond(a, b, length, stiffness=-1):
1720  """
1721  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1722  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1723  """
1724  return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1725 
1726 def create_bond(*args):
1727  """
1728  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1729  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1730  """
1731  return _IMP_atom.create_bond(*args)
1732 
1733 def destroy_bond(b):
1734  """destroy_bond(Bond b)"""
1735  return _IMP_atom.destroy_bond(b)
1736 
1737 def get_bond(a, b):
1738  """get_bond(Bonded a, Bonded b) -> Bond"""
1739  return _IMP_atom.get_bond(a, b)
1740 class BondGeometry(IMP.display.SingletonGeometry):
1741  """Proxy of C++ IMP::atom::BondGeometry class."""
1742 
1743  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1744 
1745  def __init__(self, *args):
1746  """
1747  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1748  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1749  """
1750  this = _IMP_atom.new_BondGeometry(*args)
1751  try:
1752  self.this.append(this)
1753  except __builtin__.Exception:
1754  self.this = this
1755 
1756  def get_version_info(self):
1757  """get_version_info(BondGeometry self) -> VersionInfo"""
1758  return _IMP_atom.BondGeometry_get_version_info(self)
1759 
1760 
1761  def __str__(self):
1762  """__str__(BondGeometry self) -> std::string"""
1763  return _IMP_atom.BondGeometry___str__(self)
1764 
1765 
1766  def __repr__(self):
1767  """__repr__(BondGeometry self) -> std::string"""
1768  return _IMP_atom.BondGeometry___repr__(self)
1769 
1770 
1771  @staticmethod
1772  def get_from(o):
1773  return _object_cast_to_BondGeometry(o)
1774 
1775 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1776 BondGeometry_swigregister(BondGeometry)
1777 
1778 class BondsGeometry(IMP.display.SingletonsGeometry):
1779  """Proxy of C++ IMP::atom::BondsGeometry class."""
1780 
1781  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1782 
1783  def __init__(self, sc):
1784  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1785  this = _IMP_atom.new_BondsGeometry(sc)
1786  try:
1787  self.this.append(this)
1788  except __builtin__.Exception:
1789  self.this = this
1790 
1791  def get_version_info(self):
1792  """get_version_info(BondsGeometry self) -> VersionInfo"""
1793  return _IMP_atom.BondsGeometry_get_version_info(self)
1794 
1795 
1796  def __str__(self):
1797  """__str__(BondsGeometry self) -> std::string"""
1798  return _IMP_atom.BondsGeometry___str__(self)
1799 
1800 
1801  def __repr__(self):
1802  """__repr__(BondsGeometry self) -> std::string"""
1803  return _IMP_atom.BondsGeometry___repr__(self)
1804 
1805 
1806  @staticmethod
1807  def get_from(o):
1808  return _object_cast_to_BondsGeometry(o)
1809 
1810 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1811 BondsGeometry_swigregister(BondsGeometry)
1812 
1813 class Hierarchy(IMP.core.Hierarchy):
1814  """Proxy of C++ IMP::atom::Hierarchy class."""
1815 
1816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1817 
1818  def __init__(self, *args):
1819  """
1820  __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1821  __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1822  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1823  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1824  """
1825  this = _IMP_atom.new_Hierarchy(*args)
1826  try:
1827  self.this.append(this)
1828  except __builtin__.Exception:
1829  self.this = this
1830 
1831  def setup_particle(*args):
1832  """
1833  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1834  setup_particle(Particle p) -> Hierarchy
1835  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1836  setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1837  """
1838  return _IMP_atom.Hierarchy_setup_particle(*args)
1839 
1840  setup_particle = staticmethod(setup_particle)
1841 
1842  def get_is_setup(*args):
1843  """
1844  get_is_setup(Particle p) -> bool
1845  get_is_setup(Model m, ParticleIndex p) -> bool
1846  """
1847  return _IMP_atom.Hierarchy_get_is_setup(*args)
1848 
1849  get_is_setup = staticmethod(get_is_setup)
1850 
1851  def get_is_valid(self, print_info=False):
1852  """
1853  get_is_valid(Hierarchy self, bool print_info=False) -> bool
1854  get_is_valid(Hierarchy self) -> bool
1855  """
1856  return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1857 
1858 
1859  def add_child(self, o):
1860  """add_child(Hierarchy self, Hierarchy o)"""
1861  return _IMP_atom.Hierarchy_add_child(self, o)
1862 
1863 
1864  def get_child(self, i):
1865  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1866  return _IMP_atom.Hierarchy_get_child(self, i)
1867 
1868 
1869  def get_children(self):
1870  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1871  return _IMP_atom.Hierarchy_get_children(self)
1872 
1873 
1874  def get_parent(self):
1875  """get_parent(Hierarchy self) -> Hierarchy"""
1876  return _IMP_atom.Hierarchy_get_parent(self)
1877 
1878 
1879  def get_traits():
1880  """get_traits() -> HierarchyTraits"""
1881  return _IMP_atom.Hierarchy_get_traits()
1882 
1883  get_traits = staticmethod(get_traits)
1884 
1885  def show(self, *args):
1886  """
1887  show(Hierarchy self, _ostream out, std::string delimiter)
1888  show(Hierarchy self, _ostream out)
1889  show(Hierarchy self)
1890  """
1891  return _IMP_atom.Hierarchy_show(self, *args)
1892 
1893 
1894  def add_attribute(self, *args):
1895  """
1896  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1897  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1898  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1899  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1900  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1901  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1902  """
1903  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1904 
1905 
1906  def get_value(self, *args):
1907  """
1908  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1909  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1910  get_value(Hierarchy self, StringKey a0) -> IMP::String
1911  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1912  get_value(Hierarchy self, ObjectKey a0) -> Object
1913  """
1914  return _IMP_atom.Hierarchy_get_value(self, *args)
1915 
1916 
1917  def set_value(self, *args):
1918  """
1919  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1920  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1921  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1922  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1923  set_value(Hierarchy self, ObjectKey a0, Object a1)
1924  """
1925  return _IMP_atom.Hierarchy_set_value(self, *args)
1926 
1927 
1928  def remove_attribute(self, *args):
1929  """
1930  remove_attribute(Hierarchy self, FloatKey a0)
1931  remove_attribute(Hierarchy self, IntKey a0)
1932  remove_attribute(Hierarchy self, StringKey a0)
1933  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1934  remove_attribute(Hierarchy self, ObjectKey a0)
1935  """
1936  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1937 
1938 
1939  def has_attribute(self, *args):
1940  """
1941  has_attribute(Hierarchy self, FloatKey a0) -> bool
1942  has_attribute(Hierarchy self, IntKey a0) -> bool
1943  has_attribute(Hierarchy self, StringKey a0) -> bool
1944  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1945  has_attribute(Hierarchy self, ObjectKey a0) -> bool
1946  """
1947  return _IMP_atom.Hierarchy_has_attribute(self, *args)
1948 
1949 
1950  def get_derivative(self, a0):
1951  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
1952  return _IMP_atom.Hierarchy_get_derivative(self, a0)
1953 
1954 
1955  def get_name(self):
1956  """get_name(Hierarchy self) -> std::string"""
1957  return _IMP_atom.Hierarchy_get_name(self)
1958 
1959 
1960  def clear_caches(self):
1961  """clear_caches(Hierarchy self)"""
1962  return _IMP_atom.Hierarchy_clear_caches(self)
1963 
1964 
1965  def set_name(self, a0):
1966  """set_name(Hierarchy self, std::string a0)"""
1967  return _IMP_atom.Hierarchy_set_name(self, a0)
1968 
1969 
1970  def set_check_level(self, a0):
1971  """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
1972  return _IMP_atom.Hierarchy_set_check_level(self, a0)
1973 
1974 
1975  def add_to_derivative(self, a0, a1, a2):
1976  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1977  return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
1978 
1979 
1980  def set_is_optimized(self, a0, a1):
1981  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1982  return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
1983 
1984 
1985  def get_is_optimized(self, a0):
1986  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1987  return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
1988 
1989 
1990  def get_check_level(self):
1991  """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
1992  return _IMP_atom.Hierarchy_get_check_level(self)
1993 
1994 
1995  def __eq__(self, *args):
1996  """
1997  __eq__(Hierarchy self, Hierarchy o) -> bool
1998  __eq__(Hierarchy self, Particle d) -> bool
1999  """
2000  return _IMP_atom.Hierarchy___eq__(self, *args)
2001 
2002 
2003  def __ne__(self, *args):
2004  """
2005  __ne__(Hierarchy self, Hierarchy o) -> bool
2006  __ne__(Hierarchy self, Particle d) -> bool
2007  """
2008  return _IMP_atom.Hierarchy___ne__(self, *args)
2009 
2010 
2011  def __le__(self, *args):
2012  """
2013  __le__(Hierarchy self, Hierarchy o) -> bool
2014  __le__(Hierarchy self, Particle d) -> bool
2015  """
2016  return _IMP_atom.Hierarchy___le__(self, *args)
2017 
2018 
2019  def __lt__(self, *args):
2020  """
2021  __lt__(Hierarchy self, Hierarchy o) -> bool
2022  __lt__(Hierarchy self, Particle d) -> bool
2023  """
2024  return _IMP_atom.Hierarchy___lt__(self, *args)
2025 
2026 
2027  def __ge__(self, *args):
2028  """
2029  __ge__(Hierarchy self, Hierarchy o) -> bool
2030  __ge__(Hierarchy self, Particle d) -> bool
2031  """
2032  return _IMP_atom.Hierarchy___ge__(self, *args)
2033 
2034 
2035  def __gt__(self, *args):
2036  """
2037  __gt__(Hierarchy self, Hierarchy o) -> bool
2038  __gt__(Hierarchy self, Particle d) -> bool
2039  """
2040  return _IMP_atom.Hierarchy___gt__(self, *args)
2041 
2042 
2043  def __hash__(self):
2044  """__hash__(Hierarchy self) -> std::size_t"""
2045  return _IMP_atom.Hierarchy___hash__(self)
2046 
2047 
2048  def __str__(self):
2049  """__str__(Hierarchy self) -> std::string"""
2050  return _IMP_atom.Hierarchy___str__(self)
2051 
2052 
2053  def __repr__(self):
2054  """__repr__(Hierarchy self) -> std::string"""
2055  return _IMP_atom.Hierarchy___repr__(self)
2056 
2057  __swig_destroy__ = _IMP_atom.delete_Hierarchy
2058  __del__ = lambda self: None
2059 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2060 Hierarchy_swigregister(Hierarchy)
2061 
2062 def Hierarchy_setup_particle(*args):
2063  """
2064  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2065  setup_particle(Particle p) -> Hierarchy
2066  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2067  Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2068  """
2069  return _IMP_atom.Hierarchy_setup_particle(*args)
2070 
2071 def Hierarchy_get_is_setup(*args):
2072  """
2073  get_is_setup(Particle p) -> bool
2074  Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2075  """
2076  return _IMP_atom.Hierarchy_get_is_setup(*args)
2077 
2078 def Hierarchy_get_traits():
2079  """Hierarchy_get_traits() -> HierarchyTraits"""
2080  return _IMP_atom.Hierarchy_get_traits()
2081 
2082 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2083 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2084 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2085 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2086 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2087 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2088 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2089 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2090 MASS_TYPE = _IMP_atom.MASS_TYPE
2091 STATE_TYPE = _IMP_atom.STATE_TYPE
2092 
2093 def get_by_type(mhd, t):
2094  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2095  return _IMP_atom.get_by_type(mhd, t)
2096 
2097 def create_fragment(ps):
2098  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2099  return _IMP_atom.create_fragment(ps)
2100 
2101 def get_internal_bonds(mhd):
2102  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2103  return _IMP_atom.get_internal_bonds(mhd)
2104 
2105 def get_root(h):
2106  """get_root(Hierarchy h) -> Hierarchy"""
2107  return _IMP_atom.get_root(h)
2108 
2109 def show(*args):
2110  """
2111  show(Hierarchy h, _ostream out)
2112  show(Hierarchy h)
2113  """
2114  return _IMP_atom.show(*args)
2115 
2116 def create_rigid_body(*args):
2117  """
2118  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2119  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2120  create_rigid_body(Hierarchy h) -> RigidBody
2121  """
2122  return _IMP_atom.create_rigid_body(*args)
2123 
2124 def create_compatible_rigid_body(h, reference):
2125  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2126  return _IMP_atom.create_compatible_rigid_body(h, reference)
2127 
2128 def setup_as_rigid_body(h):
2129  """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
2130  return _IMP_atom.setup_as_rigid_body(h)
2131 
2132 def get_is_heterogen(h):
2133  """get_is_heterogen(Hierarchy h) -> bool"""
2134  return _IMP_atom.get_is_heterogen(h)
2135 
2136 def create_clone(d):
2137  """create_clone(Hierarchy d) -> Hierarchy"""
2138  return _IMP_atom.create_clone(d)
2139 
2140 def create_clone_one(d):
2141  """create_clone_one(Hierarchy d) -> Hierarchy"""
2142  return _IMP_atom.create_clone_one(d)
2143 
2144 def destroy(d):
2145  """destroy(Hierarchy d)"""
2146  return _IMP_atom.destroy(d)
2147 
2148 def get_bounding_box(h):
2149  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2150  return _IMP_atom.get_bounding_box(h)
2151 
2152 def get_bounding_sphere(h):
2153  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2154  return _IMP_atom.get_bounding_sphere(h)
2155 class Angle(IMP.Decorator):
2156  """Proxy of C++ IMP::atom::Angle class."""
2157 
2158  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2159 
2160  def __init__(self, *args):
2161  """
2162  __init__(IMP::atom::Angle self) -> Angle
2163  __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2164  __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2165  """
2166  this = _IMP_atom.new_Angle(*args)
2167  try:
2168  self.this.append(this)
2169  except __builtin__.Exception:
2170  self.this = this
2171 
2172  def show(self, *args):
2173  """
2174  show(Angle self, _ostream out)
2175  show(Angle self)
2176  """
2177  return _IMP_atom.Angle_show(self, *args)
2178 
2179 
2180  def setup_particle(*args):
2181  """
2182  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2183  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2184  """
2185  return _IMP_atom.Angle_setup_particle(*args)
2186 
2187  setup_particle = staticmethod(setup_particle)
2188 
2189  def get_is_setup(*args):
2190  """
2191  get_is_setup(_ParticleAdaptor p) -> bool
2192  get_is_setup(Model m, ParticleIndex pi) -> bool
2193  """
2194  return _IMP_atom.Angle_get_is_setup(*args)
2195 
2196  get_is_setup = staticmethod(get_is_setup)
2197 
2198  def get_particle(self, *args):
2199  """
2200  get_particle(Angle self) -> Particle
2201  get_particle(Angle self, unsigned int i) -> Particle
2202  """
2203  return _IMP_atom.Angle_get_particle(self, *args)
2204 
2205 
2206  def get_ideal(self):
2207  """get_ideal(Angle self) -> IMP::Float"""
2208  return _IMP_atom.Angle_get_ideal(self)
2209 
2210 
2211  def set_ideal(self, t):
2212  """set_ideal(Angle self, IMP::Float t)"""
2213  return _IMP_atom.Angle_set_ideal(self, t)
2214 
2215 
2216  def get_stiffness(self):
2217  """get_stiffness(Angle self) -> IMP::Float"""
2218  return _IMP_atom.Angle_get_stiffness(self)
2219 
2220 
2221  def set_stiffness(self, t):
2222  """set_stiffness(Angle self, IMP::Float t)"""
2223  return _IMP_atom.Angle_set_stiffness(self, t)
2224 
2225 
2226  def get_particle_key(i):
2227  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2228  return _IMP_atom.Angle_get_particle_key(i)
2229 
2230  get_particle_key = staticmethod(get_particle_key)
2231 
2232  def get_ideal_key():
2233  """get_ideal_key() -> FloatKey"""
2234  return _IMP_atom.Angle_get_ideal_key()
2235 
2236  get_ideal_key = staticmethod(get_ideal_key)
2237 
2238  def get_stiffness_key():
2239  """get_stiffness_key() -> FloatKey"""
2240  return _IMP_atom.Angle_get_stiffness_key()
2241 
2242  get_stiffness_key = staticmethod(get_stiffness_key)
2243 
2244  def add_attribute(self, *args):
2245  """
2246  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2247  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2248  add_attribute(Angle self, IntKey a0, IMP::Int a1)
2249  add_attribute(Angle self, StringKey a0, IMP::String a1)
2250  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2251  add_attribute(Angle self, ObjectKey a0, Object a1)
2252  """
2253  return _IMP_atom.Angle_add_attribute(self, *args)
2254 
2255 
2256  def get_value(self, *args):
2257  """
2258  get_value(Angle self, FloatKey a0) -> IMP::Float
2259  get_value(Angle self, IntKey a0) -> IMP::Int
2260  get_value(Angle self, StringKey a0) -> IMP::String
2261  get_value(Angle self, ParticleIndexKey a0) -> Particle
2262  get_value(Angle self, ObjectKey a0) -> Object
2263  """
2264  return _IMP_atom.Angle_get_value(self, *args)
2265 
2266 
2267  def set_value(self, *args):
2268  """
2269  set_value(Angle self, FloatKey a0, IMP::Float a1)
2270  set_value(Angle self, IntKey a0, IMP::Int a1)
2271  set_value(Angle self, StringKey a0, IMP::String a1)
2272  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2273  set_value(Angle self, ObjectKey a0, Object a1)
2274  """
2275  return _IMP_atom.Angle_set_value(self, *args)
2276 
2277 
2278  def remove_attribute(self, *args):
2279  """
2280  remove_attribute(Angle self, FloatKey a0)
2281  remove_attribute(Angle self, IntKey a0)
2282  remove_attribute(Angle self, StringKey a0)
2283  remove_attribute(Angle self, ParticleIndexKey a0)
2284  remove_attribute(Angle self, ObjectKey a0)
2285  """
2286  return _IMP_atom.Angle_remove_attribute(self, *args)
2287 
2288 
2289  def has_attribute(self, *args):
2290  """
2291  has_attribute(Angle self, FloatKey a0) -> bool
2292  has_attribute(Angle self, IntKey a0) -> bool
2293  has_attribute(Angle self, StringKey a0) -> bool
2294  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2295  has_attribute(Angle self, ObjectKey a0) -> bool
2296  """
2297  return _IMP_atom.Angle_has_attribute(self, *args)
2298 
2299 
2300  def get_derivative(self, a0):
2301  """get_derivative(Angle self, FloatKey a0) -> double"""
2302  return _IMP_atom.Angle_get_derivative(self, a0)
2303 
2304 
2305  def get_name(self):
2306  """get_name(Angle self) -> std::string"""
2307  return _IMP_atom.Angle_get_name(self)
2308 
2309 
2310  def clear_caches(self):
2311  """clear_caches(Angle self)"""
2312  return _IMP_atom.Angle_clear_caches(self)
2313 
2314 
2315  def set_name(self, a0):
2316  """set_name(Angle self, std::string a0)"""
2317  return _IMP_atom.Angle_set_name(self, a0)
2318 
2319 
2320  def set_check_level(self, a0):
2321  """set_check_level(Angle self, IMP::CheckLevel a0)"""
2322  return _IMP_atom.Angle_set_check_level(self, a0)
2323 
2324 
2325  def add_to_derivative(self, a0, a1, a2):
2326  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2327  return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2328 
2329 
2330  def set_is_optimized(self, a0, a1):
2331  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2332  return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2333 
2334 
2335  def get_is_optimized(self, a0):
2336  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2337  return _IMP_atom.Angle_get_is_optimized(self, a0)
2338 
2339 
2340  def get_check_level(self):
2341  """get_check_level(Angle self) -> IMP::CheckLevel"""
2342  return _IMP_atom.Angle_get_check_level(self)
2343 
2344 
2345  def __eq__(self, *args):
2346  """
2347  __eq__(Angle self, Angle o) -> bool
2348  __eq__(Angle self, Particle d) -> bool
2349  """
2350  return _IMP_atom.Angle___eq__(self, *args)
2351 
2352 
2353  def __ne__(self, *args):
2354  """
2355  __ne__(Angle self, Angle o) -> bool
2356  __ne__(Angle self, Particle d) -> bool
2357  """
2358  return _IMP_atom.Angle___ne__(self, *args)
2359 
2360 
2361  def __le__(self, *args):
2362  """
2363  __le__(Angle self, Angle o) -> bool
2364  __le__(Angle self, Particle d) -> bool
2365  """
2366  return _IMP_atom.Angle___le__(self, *args)
2367 
2368 
2369  def __lt__(self, *args):
2370  """
2371  __lt__(Angle self, Angle o) -> bool
2372  __lt__(Angle self, Particle d) -> bool
2373  """
2374  return _IMP_atom.Angle___lt__(self, *args)
2375 
2376 
2377  def __ge__(self, *args):
2378  """
2379  __ge__(Angle self, Angle o) -> bool
2380  __ge__(Angle self, Particle d) -> bool
2381  """
2382  return _IMP_atom.Angle___ge__(self, *args)
2383 
2384 
2385  def __gt__(self, *args):
2386  """
2387  __gt__(Angle self, Angle o) -> bool
2388  __gt__(Angle self, Particle d) -> bool
2389  """
2390  return _IMP_atom.Angle___gt__(self, *args)
2391 
2392 
2393  def __hash__(self):
2394  """__hash__(Angle self) -> std::size_t"""
2395  return _IMP_atom.Angle___hash__(self)
2396 
2397 
2398  def __str__(self):
2399  """__str__(Angle self) -> std::string"""
2400  return _IMP_atom.Angle___str__(self)
2401 
2402 
2403  def __repr__(self):
2404  """__repr__(Angle self) -> std::string"""
2405  return _IMP_atom.Angle___repr__(self)
2406 
2407  __swig_destroy__ = _IMP_atom.delete_Angle
2408  __del__ = lambda self: None
2409 Angle_swigregister = _IMP_atom.Angle_swigregister
2410 Angle_swigregister(Angle)
2411 
2412 def Angle_setup_particle(*args):
2413  """
2414  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2415  Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2416  """
2417  return _IMP_atom.Angle_setup_particle(*args)
2418 
2419 def Angle_get_is_setup(*args):
2420  """
2421  get_is_setup(_ParticleAdaptor p) -> bool
2422  Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2423  """
2424  return _IMP_atom.Angle_get_is_setup(*args)
2425 
2426 def Angle_get_particle_key(i):
2427  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2428  return _IMP_atom.Angle_get_particle_key(i)
2429 
2430 def Angle_get_ideal_key():
2431  """Angle_get_ideal_key() -> FloatKey"""
2432  return _IMP_atom.Angle_get_ideal_key()
2433 
2434 def Angle_get_stiffness_key():
2435  """Angle_get_stiffness_key() -> FloatKey"""
2436  return _IMP_atom.Angle_get_stiffness_key()
2437 
2438 class Dihedral(IMP.Decorator):
2439  """Proxy of C++ IMP::atom::Dihedral class."""
2440 
2441  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2442 
2443  def __init__(self, *args):
2444  """
2445  __init__(IMP::atom::Dihedral self) -> Dihedral
2446  __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2447  __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2448  """
2449  this = _IMP_atom.new_Dihedral(*args)
2450  try:
2451  self.this.append(this)
2452  except __builtin__.Exception:
2453  self.this = this
2454 
2455  def show(self, *args):
2456  """
2457  show(Dihedral self, _ostream out)
2458  show(Dihedral self)
2459  """
2460  return _IMP_atom.Dihedral_show(self, *args)
2461 
2462 
2463  def setup_particle(*args):
2464  """
2465  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2466  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2467  """
2468  return _IMP_atom.Dihedral_setup_particle(*args)
2469 
2470  setup_particle = staticmethod(setup_particle)
2471 
2472  def get_is_setup(*args):
2473  """
2474  get_is_setup(_ParticleAdaptor p) -> bool
2475  get_is_setup(Model m, ParticleIndex pi) -> bool
2476  """
2477  return _IMP_atom.Dihedral_get_is_setup(*args)
2478 
2479  get_is_setup = staticmethod(get_is_setup)
2480 
2481  def get_particle(self, *args):
2482  """
2483  get_particle(Dihedral self) -> Particle
2484  get_particle(Dihedral self, unsigned int i) -> Particle
2485  """
2486  return _IMP_atom.Dihedral_get_particle(self, *args)
2487 
2488 
2489  def get_ideal(self):
2490  """get_ideal(Dihedral self) -> IMP::Float"""
2491  return _IMP_atom.Dihedral_get_ideal(self)
2492 
2493 
2494  def set_ideal(self, t):
2495  """set_ideal(Dihedral self, IMP::Float t)"""
2496  return _IMP_atom.Dihedral_set_ideal(self, t)
2497 
2498 
2499  def get_multiplicity(self):
2500  """get_multiplicity(Dihedral self) -> IMP::Int"""
2501  return _IMP_atom.Dihedral_get_multiplicity(self)
2502 
2503 
2504  def set_multiplicity(self, t):
2505  """set_multiplicity(Dihedral self, IMP::Int t)"""
2506  return _IMP_atom.Dihedral_set_multiplicity(self, t)
2507 
2508 
2509  def get_stiffness(self):
2510  """get_stiffness(Dihedral self) -> IMP::Float"""
2511  return _IMP_atom.Dihedral_get_stiffness(self)
2512 
2513 
2514  def set_stiffness(self, t):
2515  """set_stiffness(Dihedral self, IMP::Float t)"""
2516  return _IMP_atom.Dihedral_set_stiffness(self, t)
2517 
2518 
2519  def get_particle_key(i):
2520  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2521  return _IMP_atom.Dihedral_get_particle_key(i)
2522 
2523  get_particle_key = staticmethod(get_particle_key)
2524 
2525  def get_ideal_key():
2526  """get_ideal_key() -> FloatKey"""
2527  return _IMP_atom.Dihedral_get_ideal_key()
2528 
2529  get_ideal_key = staticmethod(get_ideal_key)
2530 
2531  def get_multiplicity_key():
2532  """get_multiplicity_key() -> IntKey"""
2533  return _IMP_atom.Dihedral_get_multiplicity_key()
2534 
2535  get_multiplicity_key = staticmethod(get_multiplicity_key)
2536 
2537  def get_stiffness_key():
2538  """get_stiffness_key() -> FloatKey"""
2539  return _IMP_atom.Dihedral_get_stiffness_key()
2540 
2541  get_stiffness_key = staticmethod(get_stiffness_key)
2542 
2543  def add_attribute(self, *args):
2544  """
2545  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2546  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2547  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2548  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2549  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2550  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2551  """
2552  return _IMP_atom.Dihedral_add_attribute(self, *args)
2553 
2554 
2555  def get_value(self, *args):
2556  """
2557  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2558  get_value(Dihedral self, IntKey a0) -> IMP::Int
2559  get_value(Dihedral self, StringKey a0) -> IMP::String
2560  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2561  get_value(Dihedral self, ObjectKey a0) -> Object
2562  """
2563  return _IMP_atom.Dihedral_get_value(self, *args)
2564 
2565 
2566  def set_value(self, *args):
2567  """
2568  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2569  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2570  set_value(Dihedral self, StringKey a0, IMP::String a1)
2571  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2572  set_value(Dihedral self, ObjectKey a0, Object a1)
2573  """
2574  return _IMP_atom.Dihedral_set_value(self, *args)
2575 
2576 
2577  def remove_attribute(self, *args):
2578  """
2579  remove_attribute(Dihedral self, FloatKey a0)
2580  remove_attribute(Dihedral self, IntKey a0)
2581  remove_attribute(Dihedral self, StringKey a0)
2582  remove_attribute(Dihedral self, ParticleIndexKey a0)
2583  remove_attribute(Dihedral self, ObjectKey a0)
2584  """
2585  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2586 
2587 
2588  def has_attribute(self, *args):
2589  """
2590  has_attribute(Dihedral self, FloatKey a0) -> bool
2591  has_attribute(Dihedral self, IntKey a0) -> bool
2592  has_attribute(Dihedral self, StringKey a0) -> bool
2593  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2594  has_attribute(Dihedral self, ObjectKey a0) -> bool
2595  """
2596  return _IMP_atom.Dihedral_has_attribute(self, *args)
2597 
2598 
2599  def get_derivative(self, a0):
2600  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2601  return _IMP_atom.Dihedral_get_derivative(self, a0)
2602 
2603 
2604  def get_name(self):
2605  """get_name(Dihedral self) -> std::string"""
2606  return _IMP_atom.Dihedral_get_name(self)
2607 
2608 
2609  def clear_caches(self):
2610  """clear_caches(Dihedral self)"""
2611  return _IMP_atom.Dihedral_clear_caches(self)
2612 
2613 
2614  def set_name(self, a0):
2615  """set_name(Dihedral self, std::string a0)"""
2616  return _IMP_atom.Dihedral_set_name(self, a0)
2617 
2618 
2619  def set_check_level(self, a0):
2620  """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2621  return _IMP_atom.Dihedral_set_check_level(self, a0)
2622 
2623 
2624  def add_to_derivative(self, a0, a1, a2):
2625  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2626  return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2627 
2628 
2629  def set_is_optimized(self, a0, a1):
2630  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2631  return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2632 
2633 
2634  def get_is_optimized(self, a0):
2635  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2636  return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2637 
2638 
2639  def get_check_level(self):
2640  """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2641  return _IMP_atom.Dihedral_get_check_level(self)
2642 
2643 
2644  def __eq__(self, *args):
2645  """
2646  __eq__(Dihedral self, Dihedral o) -> bool
2647  __eq__(Dihedral self, Particle d) -> bool
2648  """
2649  return _IMP_atom.Dihedral___eq__(self, *args)
2650 
2651 
2652  def __ne__(self, *args):
2653  """
2654  __ne__(Dihedral self, Dihedral o) -> bool
2655  __ne__(Dihedral self, Particle d) -> bool
2656  """
2657  return _IMP_atom.Dihedral___ne__(self, *args)
2658 
2659 
2660  def __le__(self, *args):
2661  """
2662  __le__(Dihedral self, Dihedral o) -> bool
2663  __le__(Dihedral self, Particle d) -> bool
2664  """
2665  return _IMP_atom.Dihedral___le__(self, *args)
2666 
2667 
2668  def __lt__(self, *args):
2669  """
2670  __lt__(Dihedral self, Dihedral o) -> bool
2671  __lt__(Dihedral self, Particle d) -> bool
2672  """
2673  return _IMP_atom.Dihedral___lt__(self, *args)
2674 
2675 
2676  def __ge__(self, *args):
2677  """
2678  __ge__(Dihedral self, Dihedral o) -> bool
2679  __ge__(Dihedral self, Particle d) -> bool
2680  """
2681  return _IMP_atom.Dihedral___ge__(self, *args)
2682 
2683 
2684  def __gt__(self, *args):
2685  """
2686  __gt__(Dihedral self, Dihedral o) -> bool
2687  __gt__(Dihedral self, Particle d) -> bool
2688  """
2689  return _IMP_atom.Dihedral___gt__(self, *args)
2690 
2691 
2692  def __hash__(self):
2693  """__hash__(Dihedral self) -> std::size_t"""
2694  return _IMP_atom.Dihedral___hash__(self)
2695 
2696 
2697  def __str__(self):
2698  """__str__(Dihedral self) -> std::string"""
2699  return _IMP_atom.Dihedral___str__(self)
2700 
2701 
2702  def __repr__(self):
2703  """__repr__(Dihedral self) -> std::string"""
2704  return _IMP_atom.Dihedral___repr__(self)
2705 
2706  __swig_destroy__ = _IMP_atom.delete_Dihedral
2707  __del__ = lambda self: None
2708 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2709 Dihedral_swigregister(Dihedral)
2710 
2711 def Dihedral_setup_particle(*args):
2712  """
2713  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2714  Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2715  """
2716  return _IMP_atom.Dihedral_setup_particle(*args)
2717 
2718 def Dihedral_get_is_setup(*args):
2719  """
2720  get_is_setup(_ParticleAdaptor p) -> bool
2721  Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2722  """
2723  return _IMP_atom.Dihedral_get_is_setup(*args)
2724 
2725 def Dihedral_get_particle_key(i):
2726  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2727  return _IMP_atom.Dihedral_get_particle_key(i)
2728 
2729 def Dihedral_get_ideal_key():
2730  """Dihedral_get_ideal_key() -> FloatKey"""
2731  return _IMP_atom.Dihedral_get_ideal_key()
2732 
2733 def Dihedral_get_multiplicity_key():
2734  """Dihedral_get_multiplicity_key() -> IntKey"""
2735  return _IMP_atom.Dihedral_get_multiplicity_key()
2736 
2737 def Dihedral_get_stiffness_key():
2738  """Dihedral_get_stiffness_key() -> FloatKey"""
2739  return _IMP_atom.Dihedral_get_stiffness_key()
2740 
2741 class SmoothingFunction(IMP.Object):
2742  """Proxy of C++ IMP::atom::SmoothingFunction class."""
2743 
2744  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2745 
2746  def __init__(self, *args, **kwargs):
2747  raise AttributeError("No constructor defined - class is abstract")
2748 
2749  def __call__(self, *args):
2750  """
2751  __call__(SmoothingFunction self, double score, double distance) -> double
2752  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2753  """
2754  return _IMP_atom.SmoothingFunction___call__(self, *args)
2755 
2756  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2757  __del__ = lambda self: None
2758 
2759  def __str__(self):
2760  """__str__(SmoothingFunction self) -> std::string"""
2761  return _IMP_atom.SmoothingFunction___str__(self)
2762 
2763 
2764  def __repr__(self):
2765  """__repr__(SmoothingFunction self) -> std::string"""
2766  return _IMP_atom.SmoothingFunction___repr__(self)
2767 
2768 
2769  @staticmethod
2770  def get_from(o):
2771  return _object_cast_to_SmoothingFunction(o)
2772 
2773 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2774 SmoothingFunction_swigregister(SmoothingFunction)
2775 
2776 class ForceSwitch(SmoothingFunction):
2777  """Proxy of C++ IMP::atom::ForceSwitch class."""
2778 
2779  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2780 
2781  def __init__(self, min_distance, max_distance):
2782  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2783  this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2784  try:
2785  self.this.append(this)
2786  except __builtin__.Exception:
2787  self.this = this
2788 
2789  def __call__(self, *args):
2790  """
2791  __call__(ForceSwitch self, double score, double distance) -> double
2792  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2793  """
2794  return _IMP_atom.ForceSwitch___call__(self, *args)
2795 
2796 
2797  def get_version_info(self):
2798  """get_version_info(ForceSwitch self) -> VersionInfo"""
2799  return _IMP_atom.ForceSwitch_get_version_info(self)
2800 
2801 
2802  def __str__(self):
2803  """__str__(ForceSwitch self) -> std::string"""
2804  return _IMP_atom.ForceSwitch___str__(self)
2805 
2806 
2807  def __repr__(self):
2808  """__repr__(ForceSwitch self) -> std::string"""
2809  return _IMP_atom.ForceSwitch___repr__(self)
2810 
2811 
2812  @staticmethod
2813  def get_from(o):
2814  return _object_cast_to_ForceSwitch(o)
2815 
2816 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2817 ForceSwitch_swigregister(ForceSwitch)
2818 
2819 class AngleSingletonScore(IMP.SingletonScore):
2820  """Proxy of C++ IMP::atom::AngleSingletonScore class."""
2821 
2822  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2823 
2824  def __init__(self, f):
2825  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2826  this = _IMP_atom.new_AngleSingletonScore(f)
2827  try:
2828  self.this.append(this)
2829  except __builtin__.Exception:
2830  self.this = this
2831 
2832  def do_get_inputs(self, m, pis):
2833  """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2834  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2835 
2836 
2837  def get_version_info(self):
2838  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2839  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2840 
2841 
2842  def __str__(self):
2843  """__str__(AngleSingletonScore self) -> std::string"""
2844  return _IMP_atom.AngleSingletonScore___str__(self)
2845 
2846 
2847  def __repr__(self):
2848  """__repr__(AngleSingletonScore self) -> std::string"""
2849  return _IMP_atom.AngleSingletonScore___repr__(self)
2850 
2851 
2852  @staticmethod
2853  def get_from(o):
2854  return _object_cast_to_AngleSingletonScore(o)
2855 
2856 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2857 AngleSingletonScore_swigregister(AngleSingletonScore)
2858 
2859 class BondEndpointsRefiner(IMP.Refiner):
2860  """Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2861 
2862  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2863 
2864  def __init__(self):
2865  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2866  this = _IMP_atom.new_BondEndpointsRefiner()
2867  try:
2868  self.this.append(this)
2869  except __builtin__.Exception:
2870  self.this = this
2871 
2872  def do_get_inputs(self, m, pis):
2873  """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2874  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2875 
2876 
2877  def get_version_info(self):
2878  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2879  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2880 
2881 
2882  def __str__(self):
2883  """__str__(BondEndpointsRefiner self) -> std::string"""
2884  return _IMP_atom.BondEndpointsRefiner___str__(self)
2885 
2886 
2887  def __repr__(self):
2888  """__repr__(BondEndpointsRefiner self) -> std::string"""
2889  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2890 
2891 
2892  @staticmethod
2893  def get_from(o):
2894  return _object_cast_to_BondEndpointsRefiner(o)
2895 
2896 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2897 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2898 
2899 class BondPairContainer(IMP.PairContainer):
2900  """Proxy of C++ IMP::atom::BondPairContainer class."""
2901 
2902  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2903 
2904  def __init__(self, sc):
2905  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2906  this = _IMP_atom.new_BondPairContainer(sc)
2907  try:
2908  self.this.append(this)
2909  except __builtin__.Exception:
2910  self.this = this
2911 
2912  def do_get_inputs(self):
2913  """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2914  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2915 
2916 
2917  def do_apply(self, sm):
2918  """do_apply(BondPairContainer self, PairModifier sm)"""
2919  return _IMP_atom.BondPairContainer_do_apply(self, sm)
2920 
2921 
2922  def get_version_info(self):
2923  """get_version_info(BondPairContainer self) -> VersionInfo"""
2924  return _IMP_atom.BondPairContainer_get_version_info(self)
2925 
2926 
2927  def __str__(self):
2928  """__str__(BondPairContainer self) -> std::string"""
2929  return _IMP_atom.BondPairContainer___str__(self)
2930 
2931 
2932  def __repr__(self):
2933  """__repr__(BondPairContainer self) -> std::string"""
2934  return _IMP_atom.BondPairContainer___repr__(self)
2935 
2936 
2937  @staticmethod
2938  def get_from(o):
2939  return _object_cast_to_BondPairContainer(o)
2940 
2941 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
2942 BondPairContainer_swigregister(BondPairContainer)
2943 
2944 class BondSingletonScore(IMP.SingletonScore):
2945  """Proxy of C++ IMP::atom::BondSingletonScore class."""
2946 
2947  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2948 
2949  def __init__(self, f):
2950  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2951  this = _IMP_atom.new_BondSingletonScore(f)
2952  try:
2953  self.this.append(this)
2954  except __builtin__.Exception:
2955  self.this = this
2956 
2957  def get_unary_function(self):
2958  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2959  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2960 
2961 
2962  def do_get_inputs(self, m, pis):
2963  """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2964  return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2965 
2966 
2967  def get_version_info(self):
2968  """get_version_info(BondSingletonScore self) -> VersionInfo"""
2969  return _IMP_atom.BondSingletonScore_get_version_info(self)
2970 
2971 
2972  def __str__(self):
2973  """__str__(BondSingletonScore self) -> std::string"""
2974  return _IMP_atom.BondSingletonScore___str__(self)
2975 
2976 
2977  def __repr__(self):
2978  """__repr__(BondSingletonScore self) -> std::string"""
2979  return _IMP_atom.BondSingletonScore___repr__(self)
2980 
2981 
2982  @staticmethod
2983  def get_from(o):
2984  return _object_cast_to_BondSingletonScore(o)
2985 
2986 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
2987 BondSingletonScore_swigregister(BondSingletonScore)
2988 
2989 class DihedralSingletonScore(IMP.SingletonScore):
2990  """Proxy of C++ IMP::atom::DihedralSingletonScore class."""
2991 
2992  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2993 
2994  def __init__(self):
2995  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
2996  this = _IMP_atom.new_DihedralSingletonScore()
2997  try:
2998  self.this.append(this)
2999  except __builtin__.Exception:
3000  self.this = this
3001 
3002  def do_get_inputs(self, m, pis):
3003  """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3004  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3005 
3006 
3007  def get_version_info(self):
3008  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3009  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3010 
3011 
3012  def __str__(self):
3013  """__str__(DihedralSingletonScore self) -> std::string"""
3014  return _IMP_atom.DihedralSingletonScore___str__(self)
3015 
3016 
3017  def __repr__(self):
3018  """__repr__(DihedralSingletonScore self) -> std::string"""
3019  return _IMP_atom.DihedralSingletonScore___repr__(self)
3020 
3021 
3022  @staticmethod
3023  def get_from(o):
3024  return _object_cast_to_DihedralSingletonScore(o)
3025 
3026 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3027 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3028 
3029 class ImproperSingletonScore(IMP.SingletonScore):
3030  """Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3031 
3032  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3033 
3034  def __init__(self, f):
3035  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3036  this = _IMP_atom.new_ImproperSingletonScore(f)
3037  try:
3038  self.this.append(this)
3039  except __builtin__.Exception:
3040  self.this = this
3041 
3042  def do_get_inputs(self, m, pis):
3043  """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3044  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3045 
3046 
3047  def get_version_info(self):
3048  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3049  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3050 
3051 
3052  def __str__(self):
3053  """__str__(ImproperSingletonScore self) -> std::string"""
3054  return _IMP_atom.ImproperSingletonScore___str__(self)
3055 
3056 
3057  def __repr__(self):
3058  """__repr__(ImproperSingletonScore self) -> std::string"""
3059  return _IMP_atom.ImproperSingletonScore___repr__(self)
3060 
3061 
3062  @staticmethod
3063  def get_from(o):
3064  return _object_cast_to_ImproperSingletonScore(o)
3065 
3066 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3067 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3068 
3069 class CenterOfMass(IMP.Decorator):
3070  """Proxy of C++ IMP::atom::CenterOfMass class."""
3071 
3072  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3073 
3074  def get_constraint(self):
3075  """get_constraint(CenterOfMass self) -> Constraint"""
3076  return _IMP_atom.CenterOfMass_get_constraint(self)
3077 
3078 
3079  def get_mass(self):
3080  """get_mass(CenterOfMass self) -> IMP::Float"""
3081  return _IMP_atom.CenterOfMass_get_mass(self)
3082 
3083 
3084  def get_coordinate(self, i):
3085  """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3086  return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3087 
3088 
3089  def get_coordinates(self):
3090  """get_coordinates(CenterOfMass self) -> Vector3D"""
3091  return _IMP_atom.CenterOfMass_get_coordinates(self)
3092 
3093 
3094  def __init__(self, *args):
3095  """
3096  __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3097  __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3098  __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3099  """
3100  this = _IMP_atom.new_CenterOfMass(*args)
3101  try:
3102  self.this.append(this)
3103  except __builtin__.Exception:
3104  self.this = this
3105 
3106  def show(self, *args):
3107  """
3108  show(CenterOfMass self, _ostream out)
3109  show(CenterOfMass self)
3110  """
3111  return _IMP_atom.CenterOfMass_show(self, *args)
3112 
3113 
3114  def setup_particle(*args):
3115  """
3116  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3117  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3118  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3119  setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3120  """
3121  return _IMP_atom.CenterOfMass_setup_particle(*args)
3122 
3123  setup_particle = staticmethod(setup_particle)
3124 
3125  def get_is_setup(*args):
3126  """
3127  get_is_setup(_ParticleAdaptor p) -> bool
3128  get_is_setup(Model m, ParticleIndex pi) -> bool
3129  """
3130  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3131 
3132  get_is_setup = staticmethod(get_is_setup)
3133 
3134  def add_attribute(self, *args):
3135  """
3136  add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3137  add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3138  add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3139  add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3140  add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3141  add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3142  """
3143  return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3144 
3145 
3146  def get_value(self, *args):
3147  """
3148  get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3149  get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3150  get_value(CenterOfMass self, StringKey a0) -> IMP::String
3151  get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3152  get_value(CenterOfMass self, ObjectKey a0) -> Object
3153  """
3154  return _IMP_atom.CenterOfMass_get_value(self, *args)
3155 
3156 
3157  def set_value(self, *args):
3158  """
3159  set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3160  set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3161  set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3162  set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3163  set_value(CenterOfMass self, ObjectKey a0, Object a1)
3164  """
3165  return _IMP_atom.CenterOfMass_set_value(self, *args)
3166 
3167 
3168  def remove_attribute(self, *args):
3169  """
3170  remove_attribute(CenterOfMass self, FloatKey a0)
3171  remove_attribute(CenterOfMass self, IntKey a0)
3172  remove_attribute(CenterOfMass self, StringKey a0)
3173  remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3174  remove_attribute(CenterOfMass self, ObjectKey a0)
3175  """
3176  return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3177 
3178 
3179  def has_attribute(self, *args):
3180  """
3181  has_attribute(CenterOfMass self, FloatKey a0) -> bool
3182  has_attribute(CenterOfMass self, IntKey a0) -> bool
3183  has_attribute(CenterOfMass self, StringKey a0) -> bool
3184  has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3185  has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3186  """
3187  return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3188 
3189 
3190  def get_derivative(self, a0):
3191  """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3192  return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3193 
3194 
3195  def get_name(self):
3196  """get_name(CenterOfMass self) -> std::string"""
3197  return _IMP_atom.CenterOfMass_get_name(self)
3198 
3199 
3200  def clear_caches(self):
3201  """clear_caches(CenterOfMass self)"""
3202  return _IMP_atom.CenterOfMass_clear_caches(self)
3203 
3204 
3205  def set_name(self, a0):
3206  """set_name(CenterOfMass self, std::string a0)"""
3207  return _IMP_atom.CenterOfMass_set_name(self, a0)
3208 
3209 
3210  def set_check_level(self, a0):
3211  """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3212  return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3213 
3214 
3215  def add_to_derivative(self, a0, a1, a2):
3216  """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3217  return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3218 
3219 
3220  def set_is_optimized(self, a0, a1):
3221  """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3222  return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3223 
3224 
3225  def get_is_optimized(self, a0):
3226  """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3227  return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3228 
3229 
3230  def get_check_level(self):
3231  """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3232  return _IMP_atom.CenterOfMass_get_check_level(self)
3233 
3234 
3235  def __eq__(self, *args):
3236  """
3237  __eq__(CenterOfMass self, CenterOfMass o) -> bool
3238  __eq__(CenterOfMass self, Particle d) -> bool
3239  """
3240  return _IMP_atom.CenterOfMass___eq__(self, *args)
3241 
3242 
3243  def __ne__(self, *args):
3244  """
3245  __ne__(CenterOfMass self, CenterOfMass o) -> bool
3246  __ne__(CenterOfMass self, Particle d) -> bool
3247  """
3248  return _IMP_atom.CenterOfMass___ne__(self, *args)
3249 
3250 
3251  def __le__(self, *args):
3252  """
3253  __le__(CenterOfMass self, CenterOfMass o) -> bool
3254  __le__(CenterOfMass self, Particle d) -> bool
3255  """
3256  return _IMP_atom.CenterOfMass___le__(self, *args)
3257 
3258 
3259  def __lt__(self, *args):
3260  """
3261  __lt__(CenterOfMass self, CenterOfMass o) -> bool
3262  __lt__(CenterOfMass self, Particle d) -> bool
3263  """
3264  return _IMP_atom.CenterOfMass___lt__(self, *args)
3265 
3266 
3267  def __ge__(self, *args):
3268  """
3269  __ge__(CenterOfMass self, CenterOfMass o) -> bool
3270  __ge__(CenterOfMass self, Particle d) -> bool
3271  """
3272  return _IMP_atom.CenterOfMass___ge__(self, *args)
3273 
3274 
3275  def __gt__(self, *args):
3276  """
3277  __gt__(CenterOfMass self, CenterOfMass o) -> bool
3278  __gt__(CenterOfMass self, Particle d) -> bool
3279  """
3280  return _IMP_atom.CenterOfMass___gt__(self, *args)
3281 
3282 
3283  def __hash__(self):
3284  """__hash__(CenterOfMass self) -> std::size_t"""
3285  return _IMP_atom.CenterOfMass___hash__(self)
3286 
3287 
3288  def __str__(self):
3289  """__str__(CenterOfMass self) -> std::string"""
3290  return _IMP_atom.CenterOfMass___str__(self)
3291 
3292 
3293  def __repr__(self):
3294  """__repr__(CenterOfMass self) -> std::string"""
3295  return _IMP_atom.CenterOfMass___repr__(self)
3296 
3297  __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3298  __del__ = lambda self: None
3299 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3300 CenterOfMass_swigregister(CenterOfMass)
3301 
3302 def CenterOfMass_setup_particle(*args):
3303  """
3304  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3305  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3306  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3307  CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3308  """
3309  return _IMP_atom.CenterOfMass_setup_particle(*args)
3310 
3311 def CenterOfMass_get_is_setup(*args):
3312  """
3313  get_is_setup(_ParticleAdaptor p) -> bool
3314  CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3315  """
3316  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3317 
3318 class CoverBond(IMP.SingletonModifier):
3319  """Proxy of C++ IMP::atom::CoverBond class."""
3320 
3321  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3322 
3323  def __init__(self):
3324  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3325  this = _IMP_atom.new_CoverBond()
3326  try:
3327  self.this.append(this)
3328  except __builtin__.Exception:
3329  self.this = this
3330 
3331  def do_get_inputs(self, m, pis):
3332  """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3333  return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3334 
3335 
3336  def do_get_outputs(self, m, pis):
3337  """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3338  return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3339 
3340 
3341  def get_version_info(self):
3342  """get_version_info(CoverBond self) -> VersionInfo"""
3343  return _IMP_atom.CoverBond_get_version_info(self)
3344 
3345 
3346  def __str__(self):
3347  """__str__(CoverBond self) -> std::string"""
3348  return _IMP_atom.CoverBond___str__(self)
3349 
3350 
3351  def __repr__(self):
3352  """__repr__(CoverBond self) -> std::string"""
3353  return _IMP_atom.CoverBond___repr__(self)
3354 
3355 
3356  @staticmethod
3357  def get_from(o):
3358  return _object_cast_to_CoverBond(o)
3359 
3360 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3361 CoverBond_swigregister(CoverBond)
3362 
3363 class Simulator(IMP.Optimizer):
3364  """Proxy of C++ IMP::atom::Simulator class."""
3365 
3366  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3367 
3368  def __init__(self, *args):
3369  """
3370  __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3371  __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3372  __init__(IMP::atom::Simulator self, Model m) -> Simulator
3373  """
3374  if self.__class__ == Simulator:
3375  _self = None
3376  else:
3377  _self = self
3378  this = _IMP_atom.new_Simulator(_self, *args)
3379  try:
3380  self.this.append(this)
3381  except __builtin__.Exception:
3382  self.this = this
3383 
3384  if self.__class__ != Simulator:
3385  _director_objects.register(self)
3386 
3387 
3388 
3389 
3390  def simulate(self, time_in_fs):
3391  """simulate(Simulator self, double time_in_fs) -> double"""
3392  return _IMP_atom.Simulator_simulate(self, time_in_fs)
3393 
3394 
3395  def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3396  """
3397  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3398  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3399  simulate_wave(Simulator self, double time_in_fs) -> double
3400  """
3401  return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3402 
3403 
3404  def get_temperature(self):
3405  """get_temperature(Simulator self) -> double"""
3406  return _IMP_atom.Simulator_get_temperature(self)
3407 
3408 
3409  def set_temperature(self, d):
3410  """set_temperature(Simulator self, double d)"""
3411  return _IMP_atom.Simulator_set_temperature(self, d)
3412 
3413 
3414  def set_maximum_time_step(self, ts):
3415  """set_maximum_time_step(Simulator self, double ts)"""
3416  return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3417 
3418 
3419  def get_maximum_time_step(self):
3420  """get_maximum_time_step(Simulator self) -> double"""
3421  return _IMP_atom.Simulator_get_maximum_time_step(self)
3422 
3423 
3424  def get_last_time_step(self):
3425  """get_last_time_step(Simulator self) -> double"""
3426  return _IMP_atom.Simulator_get_last_time_step(self)
3427 
3428 
3429  def set_time_step(self, ts):
3430  """set_time_step(Simulator self, double ts)"""
3431  return _IMP_atom.Simulator_set_time_step(self, ts)
3432 
3433 
3434  def get_kt(self):
3435  """get_kt(Simulator self) -> double"""
3436  return _IMP_atom.Simulator_get_kt(self)
3437 
3438 
3439  def get_current_time(self):
3440  """get_current_time(Simulator self) -> double"""
3441  return _IMP_atom.Simulator_get_current_time(self)
3442 
3443 
3444  def set_current_time(self, ct):
3445  """set_current_time(Simulator self, double ct)"""
3446  return _IMP_atom.Simulator_set_current_time(self, ct)
3447 
3448 
3449  def get_simulation_particles(self):
3450  """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3451  return _IMP_atom.Simulator_get_simulation_particles(self)
3452 
3453 
3454  def get_simulation_particle_indexes(self):
3455  """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3456  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3457 
3458 
3459  def remove_particle(self, d):
3460  """remove_particle(Simulator self, Particle d)"""
3461  return _IMP_atom.Simulator_remove_particle(self, d)
3462 
3463 
3464  def remove_particles(self, d):
3465  """remove_particles(Simulator self, IMP::Particles const & d)"""
3466  return _IMP_atom.Simulator_remove_particles(self, d)
3467 
3468 
3469  def set_particles(self, ps):
3470  """set_particles(Simulator self, IMP::Particles const & ps)"""
3471  return _IMP_atom.Simulator_set_particles(self, ps)
3472 
3473 
3474  def set_particles_order(self, objs):
3475  """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3476  return _IMP_atom.Simulator_set_particles_order(self, objs)
3477 
3478 
3479  def add_particle(self, obj):
3480  """add_particle(Simulator self, Particle obj) -> unsigned int"""
3481  return _IMP_atom.Simulator_add_particle(self, obj)
3482 
3483 
3484  def add_particles(self, objs):
3485  """add_particles(Simulator self, IMP::Particles const & objs)"""
3486  return _IMP_atom.Simulator_add_particles(self, objs)
3487 
3488 
3489  def clear_particles(self):
3490  """clear_particles(Simulator self)"""
3491  return _IMP_atom.Simulator_clear_particles(self)
3492 
3493 
3494  def get_number_of_particles(self):
3495  """get_number_of_particles(Simulator self) -> unsigned int"""
3496  return _IMP_atom.Simulator_get_number_of_particles(self)
3497 
3498 
3499  def get_has_particles(self):
3500  """get_has_particles(Simulator self) -> bool"""
3501  return _IMP_atom.Simulator_get_has_particles(self)
3502 
3503 
3504  def get_particle(self, i):
3505  """get_particle(Simulator self, unsigned int i) -> Particle"""
3506  return _IMP_atom.Simulator_get_particle(self, i)
3507 
3508 
3509  def get_particles(self):
3510  """get_particles(Simulator self) -> IMP::Particles"""
3511  return _IMP_atom.Simulator_get_particles(self)
3512 
3513 
3514  def reserve_particles(self, sz):
3515  """reserve_particles(Simulator self, unsigned int sz)"""
3516  return _IMP_atom.Simulator_reserve_particles(self, sz)
3517 
3518 
3519  def do_optimize(self, max_steps):
3520  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3521  return _IMP_atom.Simulator_do_optimize(self, max_steps)
3522 
3523 
3524  def setup(self, arg0):
3525  """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3526  return _IMP_atom.Simulator_setup(self, arg0)
3527 
3528 
3529  def do_step(self, sc, dt):
3530  """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3531  return _IMP_atom.Simulator_do_step(self, sc, dt)
3532 
3533 
3534  def get_is_simulation_particle(self, p):
3535  """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3536  return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3537 
3538 
3539  def do_simulate(self, time):
3540  """do_simulate(Simulator self, double time) -> double"""
3541  return _IMP_atom.Simulator_do_simulate(self, time)
3542 
3543 
3544  def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3545  """
3546  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3547  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3548  do_simulate_wave(Simulator self, double time_in_fs) -> double
3549  """
3550  return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3551 
3552 
3553  def __str__(self):
3554  """__str__(Simulator self) -> std::string"""
3555  return _IMP_atom.Simulator___str__(self)
3556 
3557 
3558  def __repr__(self):
3559  """__repr__(Simulator self) -> std::string"""
3560  return _IMP_atom.Simulator___repr__(self)
3561 
3562 
3563  @staticmethod
3564  def get_from(o):
3565  return _object_cast_to_Simulator(o)
3566 
3567 
3568  def get_type_name(self):
3569  return self.__class__.__name__
3570  def do_show(self, out):
3571  pass
3572  def get_version_info(self):
3573  if"IMP::atom" == "IMP":
3574  return VersionInfo(self.__module__,
3575  __import__(self.__module__).get_module_version())
3576  else:
3577  return IMP.VersionInfo(self.__module__,
3578  __import__(self.__module__).get_module_version())
3579  @staticmethod
3580  def get_from(o):
3581  return _object_cast_to_Simulator(o)
3582 
3583  __swig_destroy__ = _IMP_atom.delete_Simulator
3584  __del__ = lambda self: None
3585  def __disown__(self):
3586  self.this.disown()
3587  _IMP_atom.disown_Simulator(self)
3588  return weakref_proxy(self)
3589 
3590  def do_destroy(self):
3591  """do_destroy(Simulator self)"""
3592  return _IMP_atom.Simulator_do_destroy(self)
3593 
3594 
3595  def handle_set_has_required_score_states(self, arg0):
3596  """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3597  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3598 
3599 
3600  def do_get_inputs(self):
3601  """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3602  return _IMP_atom.Simulator_do_get_inputs(self)
3603 
3604 
3605  def do_get_outputs(self):
3606  """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3607  return _IMP_atom.Simulator_do_get_outputs(self)
3608 
3609 
3610  def do_get_interactions(self):
3611  """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3612  return _IMP_atom.Simulator_do_get_interactions(self)
3613 
3614 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3615 Simulator_swigregister(Simulator)
3616 
3617 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3618 class BrownianDynamics(Simulator):
3619  """Proxy of C++ IMP::atom::BrownianDynamics class."""
3620 
3621  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3622 
3623  def __init__(self, *args):
3624  """
3625  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics
3626  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3627  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3628  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3629  """
3630  this = _IMP_atom.new_BrownianDynamics(*args)
3631  try:
3632  self.this.append(this)
3633  except __builtin__.Exception:
3634  self.this = this
3635 
3636  def set_maximum_move(self, ms):
3637  """set_maximum_move(BrownianDynamics self, double ms)"""
3638  return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms)
3639 
3640 
3641  def set_use_stochastic_runge_kutta(self, tf):
3642  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3643  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3644 
3645 
3646  def get_version_info(self):
3647  """get_version_info(BrownianDynamics self) -> VersionInfo"""
3648  return _IMP_atom.BrownianDynamics_get_version_info(self)
3649 
3650 
3651  def __str__(self):
3652  """__str__(BrownianDynamics self) -> std::string"""
3653  return _IMP_atom.BrownianDynamics___str__(self)
3654 
3655 
3656  def __repr__(self):
3657  """__repr__(BrownianDynamics self) -> std::string"""
3658  return _IMP_atom.BrownianDynamics___repr__(self)
3659 
3660 
3661  @staticmethod
3662  def get_from(o):
3663  return _object_cast_to_BrownianDynamics(o)
3664 
3665 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3666 BrownianDynamics_swigregister(BrownianDynamics)
3667 
3668 
3670  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3671  return _IMP_atom.get_maximum_time_step_estimate(bd)
3672 
3673 def get_harmonic_sigma(D, f):
3674  """get_harmonic_sigma(double D, double f) -> double"""
3675  return _IMP_atom.get_harmonic_sigma(D, f)
3676 class BrownianDynamicsTAMD(BrownianDynamics):
3677  """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3678 
3679  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3680 
3681  def __init__(self, *args):
3682  """
3683  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3684  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3685  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3686  """
3687  this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3688  try:
3689  self.this.append(this)
3690  except __builtin__.Exception:
3691  self.this = this
3692 
3693  def __str__(self):
3694  """__str__(BrownianDynamicsTAMD self) -> std::string"""
3695  return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3696 
3697 
3698  def __repr__(self):
3699  """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3700  return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3701 
3702 
3703  @staticmethod
3704  def get_from(o):
3705  return _object_cast_to_BrownianDynamicsTAMD(o)
3706 
3707  __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3708  __del__ = lambda self: None
3709 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3710 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3711 
3712 class Diffusion(IMP.core.XYZ):
3713  """Proxy of C++ IMP::atom::Diffusion class."""
3714 
3715  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3716 
3717  def __init__(self, *args):
3718  """
3719  __init__(IMP::atom::Diffusion self) -> Diffusion
3720  __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3721  __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3722  """
3723  this = _IMP_atom.new_Diffusion(*args)
3724  try:
3725  self.this.append(this)
3726  except __builtin__.Exception:
3727  self.this = this
3728 
3729  def show(self, *args):
3730  """
3731  show(Diffusion self, _ostream out)
3732  show(Diffusion self)
3733  """
3734  return _IMP_atom.Diffusion_show(self, *args)
3735 
3736 
3737  def setup_particle(*args):
3738  """
3739  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3740  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3741  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3742  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3743  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3744  setup_particle(_ParticleAdaptor decorator) -> Diffusion
3745  """
3746  return _IMP_atom.Diffusion_setup_particle(*args)
3747 
3748  setup_particle = staticmethod(setup_particle)
3749 
3750  def get_is_setup(*args):
3751  """
3752  get_is_setup(_ParticleAdaptor p) -> bool
3753  get_is_setup(Model m, ParticleIndex p) -> bool
3754  """
3755  return _IMP_atom.Diffusion_get_is_setup(*args)
3756 
3757  get_is_setup = staticmethod(get_is_setup)
3758 
3759  def set_diffusion_coefficient(self, d):
3760  """set_diffusion_coefficient(Diffusion self, double d)"""
3761  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3762 
3763 
3764  def get_diffusion_coefficient(self):
3765  """get_diffusion_coefficient(Diffusion self) -> double"""
3766  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3767 
3768 
3769  def get_diffusion_coefficient_key():
3770  """get_diffusion_coefficient_key() -> FloatKey"""
3771  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3772 
3773  get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3774 
3775  def add_attribute(self, *args):
3776  """
3777  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3778  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3779  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3780  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3781  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3782  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3783  """
3784  return _IMP_atom.Diffusion_add_attribute(self, *args)
3785 
3786 
3787  def get_value(self, *args):
3788  """
3789  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3790  get_value(Diffusion self, IntKey a0) -> IMP::Int
3791  get_value(Diffusion self, StringKey a0) -> IMP::String
3792  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3793  get_value(Diffusion self, ObjectKey a0) -> Object
3794  """
3795  return _IMP_atom.Diffusion_get_value(self, *args)
3796 
3797 
3798  def set_value(self, *args):
3799  """
3800  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3801  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3802  set_value(Diffusion self, StringKey a0, IMP::String a1)
3803  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3804  set_value(Diffusion self, ObjectKey a0, Object a1)
3805  """
3806  return _IMP_atom.Diffusion_set_value(self, *args)
3807 
3808 
3809  def remove_attribute(self, *args):
3810  """
3811  remove_attribute(Diffusion self, FloatKey a0)
3812  remove_attribute(Diffusion self, IntKey a0)
3813  remove_attribute(Diffusion self, StringKey a0)
3814  remove_attribute(Diffusion self, ParticleIndexKey a0)
3815  remove_attribute(Diffusion self, ObjectKey a0)
3816  """
3817  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3818 
3819 
3820  def has_attribute(self, *args):
3821  """
3822  has_attribute(Diffusion self, FloatKey a0) -> bool
3823  has_attribute(Diffusion self, IntKey a0) -> bool
3824  has_attribute(Diffusion self, StringKey a0) -> bool
3825  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3826  has_attribute(Diffusion self, ObjectKey a0) -> bool
3827  """
3828  return _IMP_atom.Diffusion_has_attribute(self, *args)
3829 
3830 
3831  def get_derivative(self, a0):
3832  """get_derivative(Diffusion self, FloatKey a0) -> double"""
3833  return _IMP_atom.Diffusion_get_derivative(self, a0)
3834 
3835 
3836  def get_name(self):
3837  """get_name(Diffusion self) -> std::string"""
3838  return _IMP_atom.Diffusion_get_name(self)
3839 
3840 
3841  def clear_caches(self):
3842  """clear_caches(Diffusion self)"""
3843  return _IMP_atom.Diffusion_clear_caches(self)
3844 
3845 
3846  def set_name(self, a0):
3847  """set_name(Diffusion self, std::string a0)"""
3848  return _IMP_atom.Diffusion_set_name(self, a0)
3849 
3850 
3851  def set_check_level(self, a0):
3852  """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3853  return _IMP_atom.Diffusion_set_check_level(self, a0)
3854 
3855 
3856  def add_to_derivative(self, a0, a1, a2):
3857  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3858  return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3859 
3860 
3861  def set_is_optimized(self, a0, a1):
3862  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3863  return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3864 
3865 
3866  def get_is_optimized(self, a0):
3867  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3868  return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3869 
3870 
3871  def get_check_level(self):
3872  """get_check_level(Diffusion self) -> IMP::CheckLevel"""
3873  return _IMP_atom.Diffusion_get_check_level(self)
3874 
3875 
3876  def __eq__(self, *args):
3877  """
3878  __eq__(Diffusion self, Diffusion o) -> bool
3879  __eq__(Diffusion self, Particle d) -> bool
3880  """
3881  return _IMP_atom.Diffusion___eq__(self, *args)
3882 
3883 
3884  def __ne__(self, *args):
3885  """
3886  __ne__(Diffusion self, Diffusion o) -> bool
3887  __ne__(Diffusion self, Particle d) -> bool
3888  """
3889  return _IMP_atom.Diffusion___ne__(self, *args)
3890 
3891 
3892  def __le__(self, *args):
3893  """
3894  __le__(Diffusion self, Diffusion o) -> bool
3895  __le__(Diffusion self, Particle d) -> bool
3896  """
3897  return _IMP_atom.Diffusion___le__(self, *args)
3898 
3899 
3900  def __lt__(self, *args):
3901  """
3902  __lt__(Diffusion self, Diffusion o) -> bool
3903  __lt__(Diffusion self, Particle d) -> bool
3904  """
3905  return _IMP_atom.Diffusion___lt__(self, *args)
3906 
3907 
3908  def __ge__(self, *args):
3909  """
3910  __ge__(Diffusion self, Diffusion o) -> bool
3911  __ge__(Diffusion self, Particle d) -> bool
3912  """
3913  return _IMP_atom.Diffusion___ge__(self, *args)
3914 
3915 
3916  def __gt__(self, *args):
3917  """
3918  __gt__(Diffusion self, Diffusion o) -> bool
3919  __gt__(Diffusion self, Particle d) -> bool
3920  """
3921  return _IMP_atom.Diffusion___gt__(self, *args)
3922 
3923 
3924  def __hash__(self):
3925  """__hash__(Diffusion self) -> std::size_t"""
3926  return _IMP_atom.Diffusion___hash__(self)
3927 
3928 
3929  def __str__(self):
3930  """__str__(Diffusion self) -> std::string"""
3931  return _IMP_atom.Diffusion___str__(self)
3932 
3933 
3934  def __repr__(self):
3935  """__repr__(Diffusion self) -> std::string"""
3936  return _IMP_atom.Diffusion___repr__(self)
3937 
3938  __swig_destroy__ = _IMP_atom.delete_Diffusion
3939  __del__ = lambda self: None
3940 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
3941 Diffusion_swigregister(Diffusion)
3942 
3943 def Diffusion_setup_particle(*args):
3944  """
3945  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3946  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3947  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3948  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3949  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3950  Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
3951  """
3952  return _IMP_atom.Diffusion_setup_particle(*args)
3953 
3954 def Diffusion_get_is_setup(*args):
3955  """
3956  get_is_setup(_ParticleAdaptor p) -> bool
3957  Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
3958  """
3959  return _IMP_atom.Diffusion_get_is_setup(*args)
3960 
3961 def Diffusion_get_diffusion_coefficient_key():
3962  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
3963  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3964 
3965 
3966 def get_diffusion_coefficient_from_cm2_per_second(din):
3967  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3968  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3969 class RigidBodyDiffusion(Diffusion):
3970  """Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3971 
3972  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3973 
3974  def __init__(self, *args):
3975  """
3976  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
3977  __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3978  __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3979  """
3980  this = _IMP_atom.new_RigidBodyDiffusion(*args)
3981  try:
3982  self.this.append(this)
3983  except __builtin__.Exception:
3984  self.this = this
3985 
3986  def show(self, *args):
3987  """
3988  show(RigidBodyDiffusion self, _ostream out)
3989  show(RigidBodyDiffusion self)
3990  """
3991  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3992 
3993 
3994  def setup_particle(*args):
3995  """
3996  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3997  setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3998  """
3999  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4000 
4001  setup_particle = staticmethod(setup_particle)
4002 
4004  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4005  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4006 
4007 
4008  def set_rotational_diffusion_coefficient(self, d):
4009  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4010  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4011 
4012 
4013  def get_is_setup(*args):
4014  """
4015  get_is_setup(_ParticleAdaptor p) -> bool
4016  get_is_setup(Model m, ParticleIndex p) -> bool
4017  """
4018  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4019 
4020  get_is_setup = staticmethod(get_is_setup)
4021 
4022  def get_rotational_diffusion_coefficient_key():
4023  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4024  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4025 
4026  get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4027 
4028  def add_attribute(self, *args):
4029  """
4030  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4031  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4032  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4033  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4034  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4035  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4036  """
4037  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4038 
4039 
4040  def get_value(self, *args):
4041  """
4042  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4043  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4044  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4045  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4046  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4047  """
4048  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4049 
4050 
4051  def set_value(self, *args):
4052  """
4053  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4054  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4055  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4056  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4057  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4058  """
4059  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4060 
4061 
4062  def remove_attribute(self, *args):
4063  """
4064  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4065  remove_attribute(RigidBodyDiffusion self, IntKey a0)
4066  remove_attribute(RigidBodyDiffusion self, StringKey a0)
4067  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4068  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4069  """
4070  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4071 
4072 
4073  def has_attribute(self, *args):
4074  """
4075  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4076  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4077  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4078  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4079  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4080  """
4081  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4082 
4083 
4084  def get_derivative(self, a0):
4085  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4086  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4087 
4088 
4089  def get_name(self):
4090  """get_name(RigidBodyDiffusion self) -> std::string"""
4091  return _IMP_atom.RigidBodyDiffusion_get_name(self)
4092 
4093 
4094  def clear_caches(self):
4095  """clear_caches(RigidBodyDiffusion self)"""
4096  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4097 
4098 
4099  def set_name(self, a0):
4100  """set_name(RigidBodyDiffusion self, std::string a0)"""
4101  return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4102 
4103 
4104  def set_check_level(self, a0):
4105  """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4106  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4107 
4108 
4109  def add_to_derivative(self, a0, a1, a2):
4110  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4111  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4112 
4113 
4114  def set_is_optimized(self, a0, a1):
4115  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4116  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4117 
4118 
4119  def get_is_optimized(self, a0):
4120  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4121  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4122 
4123 
4124  def get_check_level(self):
4125  """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4126  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4127 
4128 
4129  def __eq__(self, *args):
4130  """
4131  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4132  __eq__(RigidBodyDiffusion self, Particle d) -> bool
4133  """
4134  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4135 
4136 
4137  def __ne__(self, *args):
4138  """
4139  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4140  __ne__(RigidBodyDiffusion self, Particle d) -> bool
4141  """
4142  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4143 
4144 
4145  def __le__(self, *args):
4146  """
4147  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4148  __le__(RigidBodyDiffusion self, Particle d) -> bool
4149  """
4150  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4151 
4152 
4153  def __lt__(self, *args):
4154  """
4155  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4156  __lt__(RigidBodyDiffusion self, Particle d) -> bool
4157  """
4158  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4159 
4160 
4161  def __ge__(self, *args):
4162  """
4163  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4164  __ge__(RigidBodyDiffusion self, Particle d) -> bool
4165  """
4166  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4167 
4168 
4169  def __gt__(self, *args):
4170  """
4171  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4172  __gt__(RigidBodyDiffusion self, Particle d) -> bool
4173  """
4174  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4175 
4176 
4177  def __hash__(self):
4178  """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4179  return _IMP_atom.RigidBodyDiffusion___hash__(self)
4180 
4181 
4182  def __str__(self):
4183  """__str__(RigidBodyDiffusion self) -> std::string"""
4184  return _IMP_atom.RigidBodyDiffusion___str__(self)
4185 
4186 
4187  def __repr__(self):
4188  """__repr__(RigidBodyDiffusion self) -> std::string"""
4189  return _IMP_atom.RigidBodyDiffusion___repr__(self)
4190 
4191  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4192  __del__ = lambda self: None
4193 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4194 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4195 
4196 def RigidBodyDiffusion_setup_particle(*args):
4197  """
4198  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4199  RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4200  """
4201  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4202 
4203 def RigidBodyDiffusion_get_is_setup(*args):
4204  """
4205  get_is_setup(_ParticleAdaptor p) -> bool
4206  RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4207  """
4208  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4209 
4210 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4211  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4212  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4213 
4214 class TAMDParticle(IMP.Decorator):
4215  """Proxy of C++ IMP::atom::TAMDParticle class."""
4216 
4217  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4218 
4219  def __init__(self, *args):
4220  """
4221  __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4222  __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4223  __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4224  """
4225  this = _IMP_atom.new_TAMDParticle(*args)
4226  try:
4227  self.this.append(this)
4228  except __builtin__.Exception:
4229  self.this = this
4230 
4231  def show(self, *args):
4232  """
4233  show(TAMDParticle self, _ostream out)
4234  show(TAMDParticle self)
4235  """
4236  return _IMP_atom.TAMDParticle_show(self, *args)
4237 
4238 
4239  def setup_particle(*args):
4240  """
4241  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4242  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4243  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4244  setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4245  """
4246  return _IMP_atom.TAMDParticle_setup_particle(*args)
4247 
4248  setup_particle = staticmethod(setup_particle)
4249 
4250  def get_is_setup(*args):
4251  """
4252  get_is_setup(_ParticleAdaptor p) -> bool
4253  get_is_setup(Model m, ParticleIndex p) -> bool
4254  """
4255  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4256 
4257  get_is_setup = staticmethod(get_is_setup)
4258 
4259  def get_reference_particle_index(self):
4260  """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4261  return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4262 
4263 
4264  def set_temperature_scale_factor(self, tsf):
4265  """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4266  return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4267 
4268 
4269  def get_temperature_scale_factor(self):
4270  """get_temperature_scale_factor(TAMDParticle self) -> double"""
4271  return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4272 
4273 
4274  def set_friction_scale_factor(self, tsf):
4275  """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4276  return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4277 
4278 
4279  def get_friction_scale_factor(self):
4280  """get_friction_scale_factor(TAMDParticle self) -> double"""
4281  return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4282 
4283 
4284  def update_coordinates_from_ref(self):
4285  """update_coordinates_from_ref(TAMDParticle self)"""
4286  return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4287 
4288 
4289  def get_temperature_scale_factor_key():
4290  """get_temperature_scale_factor_key() -> FloatKey"""
4291  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4292 
4293  get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4294 
4295  def get_friction_scale_factor_key():
4296  """get_friction_scale_factor_key() -> FloatKey"""
4297  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4298 
4299  get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4300 
4301  def get_reference_particle_index_key():
4302  """get_reference_particle_index_key() -> ParticleIndexKey"""
4303  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4304 
4305  get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4306 
4307  def add_attribute(self, *args):
4308  """
4309  add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4310  add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4311  add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4312  add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4313  add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4314  add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4315  """
4316  return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4317 
4318 
4319  def get_value(self, *args):
4320  """
4321  get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4322  get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4323  get_value(TAMDParticle self, StringKey a0) -> IMP::String
4324  get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4325  get_value(TAMDParticle self, ObjectKey a0) -> Object
4326  """
4327  return _IMP_atom.TAMDParticle_get_value(self, *args)
4328 
4329 
4330  def set_value(self, *args):
4331  """
4332  set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4333  set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4334  set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4335  set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4336  set_value(TAMDParticle self, ObjectKey a0, Object a1)
4337  """
4338  return _IMP_atom.TAMDParticle_set_value(self, *args)
4339 
4340 
4341  def remove_attribute(self, *args):
4342  """
4343  remove_attribute(TAMDParticle self, FloatKey a0)
4344  remove_attribute(TAMDParticle self, IntKey a0)
4345  remove_attribute(TAMDParticle self, StringKey a0)
4346  remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4347  remove_attribute(TAMDParticle self, ObjectKey a0)
4348  """
4349  return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4350 
4351 
4352  def has_attribute(self, *args):
4353  """
4354  has_attribute(TAMDParticle self, FloatKey a0) -> bool
4355  has_attribute(TAMDParticle self, IntKey a0) -> bool
4356  has_attribute(TAMDParticle self, StringKey a0) -> bool
4357  has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4358  has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4359  """
4360  return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4361 
4362 
4363  def get_derivative(self, a0):
4364  """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4365  return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4366 
4367 
4368  def get_name(self):
4369  """get_name(TAMDParticle self) -> std::string"""
4370  return _IMP_atom.TAMDParticle_get_name(self)
4371 
4372 
4373  def clear_caches(self):
4374  """clear_caches(TAMDParticle self)"""
4375  return _IMP_atom.TAMDParticle_clear_caches(self)
4376 
4377 
4378  def set_name(self, a0):
4379  """set_name(TAMDParticle self, std::string a0)"""
4380  return _IMP_atom.TAMDParticle_set_name(self, a0)
4381 
4382 
4383  def set_check_level(self, a0):
4384  """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4385  return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4386 
4387 
4388  def add_to_derivative(self, a0, a1, a2):
4389  """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4390  return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4391 
4392 
4393  def set_is_optimized(self, a0, a1):
4394  """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4395  return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4396 
4397 
4398  def get_is_optimized(self, a0):
4399  """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4400  return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4401 
4402 
4403  def get_check_level(self):
4404  """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4405  return _IMP_atom.TAMDParticle_get_check_level(self)
4406 
4407 
4408  def __eq__(self, *args):
4409  """
4410  __eq__(TAMDParticle self, TAMDParticle o) -> bool
4411  __eq__(TAMDParticle self, Particle d) -> bool
4412  """
4413  return _IMP_atom.TAMDParticle___eq__(self, *args)
4414 
4415 
4416  def __ne__(self, *args):
4417  """
4418  __ne__(TAMDParticle self, TAMDParticle o) -> bool
4419  __ne__(TAMDParticle self, Particle d) -> bool
4420  """
4421  return _IMP_atom.TAMDParticle___ne__(self, *args)
4422 
4423 
4424  def __le__(self, *args):
4425  """
4426  __le__(TAMDParticle self, TAMDParticle o) -> bool
4427  __le__(TAMDParticle self, Particle d) -> bool
4428  """
4429  return _IMP_atom.TAMDParticle___le__(self, *args)
4430 
4431 
4432  def __lt__(self, *args):
4433  """
4434  __lt__(TAMDParticle self, TAMDParticle o) -> bool
4435  __lt__(TAMDParticle self, Particle d) -> bool
4436  """
4437  return _IMP_atom.TAMDParticle___lt__(self, *args)
4438 
4439 
4440  def __ge__(self, *args):
4441  """
4442  __ge__(TAMDParticle self, TAMDParticle o) -> bool
4443  __ge__(TAMDParticle self, Particle d) -> bool
4444  """
4445  return _IMP_atom.TAMDParticle___ge__(self, *args)
4446 
4447 
4448  def __gt__(self, *args):
4449  """
4450  __gt__(TAMDParticle self, TAMDParticle o) -> bool
4451  __gt__(TAMDParticle self, Particle d) -> bool
4452  """
4453  return _IMP_atom.TAMDParticle___gt__(self, *args)
4454 
4455 
4456  def __hash__(self):
4457  """__hash__(TAMDParticle self) -> std::size_t"""
4458  return _IMP_atom.TAMDParticle___hash__(self)
4459 
4460 
4461  def __str__(self):
4462  """__str__(TAMDParticle self) -> std::string"""
4463  return _IMP_atom.TAMDParticle___str__(self)
4464 
4465 
4466  def __repr__(self):
4467  """__repr__(TAMDParticle self) -> std::string"""
4468  return _IMP_atom.TAMDParticle___repr__(self)
4469 
4470  __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4471  __del__ = lambda self: None
4472 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4473 TAMDParticle_swigregister(TAMDParticle)
4474 
4475 def TAMDParticle_setup_particle(*args):
4476  """
4477  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4478  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4479  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4480  TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4481  """
4482  return _IMP_atom.TAMDParticle_setup_particle(*args)
4483 
4484 def TAMDParticle_get_is_setup(*args):
4485  """
4486  get_is_setup(_ParticleAdaptor p) -> bool
4487  TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4488  """
4489  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4490 
4491 def TAMDParticle_get_temperature_scale_factor_key():
4492  """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4493  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4494 
4495 def TAMDParticle_get_friction_scale_factor_key():
4496  """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4497  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4498 
4499 def TAMDParticle_get_reference_particle_index_key():
4500  """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4501  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4502 
4503 class Chain(Hierarchy):
4504  """Proxy of C++ IMP::atom::Chain class."""
4505 
4506  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4507 
4508  def __init__(self, *args):
4509  """
4510  __init__(IMP::atom::Chain self) -> Chain
4511  __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4512  __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4513  """
4514  this = _IMP_atom.new_Chain(*args)
4515  try:
4516  self.this.append(this)
4517  except __builtin__.Exception:
4518  self.this = this
4519 
4520  def show(self, *args):
4521  """
4522  show(Chain self, _ostream out)
4523  show(Chain self)
4524  """
4525  return _IMP_atom.Chain_show(self, *args)
4526 
4527 
4528  def setup_particle(*args):
4529  """
4530  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4531  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4532  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4533  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4534  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4535  setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4536  """
4537  return _IMP_atom.Chain_setup_particle(*args)
4538 
4539  setup_particle = staticmethod(setup_particle)
4540 
4541  def get_is_setup(*args):
4542  """
4543  get_is_setup(_ParticleAdaptor p) -> bool
4544  get_is_setup(Model m, ParticleIndex pi) -> bool
4545  """
4546  return _IMP_atom.Chain_get_is_setup(*args)
4547 
4548  get_is_setup = staticmethod(get_is_setup)
4549 
4550  def get_id(self):
4551  """get_id(Chain self) -> std::string"""
4552  return _IMP_atom.Chain_get_id(self)
4553 
4554 
4555  def set_id(self, c):
4556  """set_id(Chain self, std::string c)"""
4557  return _IMP_atom.Chain_set_id(self, c)
4558 
4559 
4560  def get_id_key():
4561  """get_id_key() -> StringKey"""
4562  return _IMP_atom.Chain_get_id_key()
4563 
4564  get_id_key = staticmethod(get_id_key)
4565 
4566  def add_attribute(self, *args):
4567  """
4568  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4569  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4570  add_attribute(Chain self, IntKey a0, IMP::Int a1)
4571  add_attribute(Chain self, StringKey a0, IMP::String a1)
4572  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4573  add_attribute(Chain self, ObjectKey a0, Object a1)
4574  """
4575  return _IMP_atom.Chain_add_attribute(self, *args)
4576 
4577 
4578  def get_value(self, *args):
4579  """
4580  get_value(Chain self, FloatKey a0) -> IMP::Float
4581  get_value(Chain self, IntKey a0) -> IMP::Int
4582  get_value(Chain self, StringKey a0) -> IMP::String
4583  get_value(Chain self, ParticleIndexKey a0) -> Particle
4584  get_value(Chain self, ObjectKey a0) -> Object
4585  """
4586  return _IMP_atom.Chain_get_value(self, *args)
4587 
4588 
4589  def set_value(self, *args):
4590  """
4591  set_value(Chain self, FloatKey a0, IMP::Float a1)
4592  set_value(Chain self, IntKey a0, IMP::Int a1)
4593  set_value(Chain self, StringKey a0, IMP::String a1)
4594  set_value(Chain self, ParticleIndexKey a0, Particle a1)
4595  set_value(Chain self, ObjectKey a0, Object a1)
4596  """
4597  return _IMP_atom.Chain_set_value(self, *args)
4598 
4599 
4600  def remove_attribute(self, *args):
4601  """
4602  remove_attribute(Chain self, FloatKey a0)
4603  remove_attribute(Chain self, IntKey a0)
4604  remove_attribute(Chain self, StringKey a0)
4605  remove_attribute(Chain self, ParticleIndexKey a0)
4606  remove_attribute(Chain self, ObjectKey a0)
4607  """
4608  return _IMP_atom.Chain_remove_attribute(self, *args)
4609 
4610 
4611  def has_attribute(self, *args):
4612  """
4613  has_attribute(Chain self, FloatKey a0) -> bool
4614  has_attribute(Chain self, IntKey a0) -> bool
4615  has_attribute(Chain self, StringKey a0) -> bool
4616  has_attribute(Chain self, ParticleIndexKey a0) -> bool
4617  has_attribute(Chain self, ObjectKey a0) -> bool
4618  """
4619  return _IMP_atom.Chain_has_attribute(self, *args)
4620 
4621 
4622  def get_derivative(self, a0):
4623  """get_derivative(Chain self, FloatKey a0) -> double"""
4624  return _IMP_atom.Chain_get_derivative(self, a0)
4625 
4626 
4627  def get_name(self):
4628  """get_name(Chain self) -> std::string"""
4629  return _IMP_atom.Chain_get_name(self)
4630 
4631 
4632  def clear_caches(self):
4633  """clear_caches(Chain self)"""
4634  return _IMP_atom.Chain_clear_caches(self)
4635 
4636 
4637  def set_name(self, a0):
4638  """set_name(Chain self, std::string a0)"""
4639  return _IMP_atom.Chain_set_name(self, a0)
4640 
4641 
4642  def set_check_level(self, a0):
4643  """set_check_level(Chain self, IMP::CheckLevel a0)"""
4644  return _IMP_atom.Chain_set_check_level(self, a0)
4645 
4646 
4647  def add_to_derivative(self, a0, a1, a2):
4648  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4649  return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4650 
4651 
4652  def set_is_optimized(self, a0, a1):
4653  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4654  return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4655 
4656 
4657  def get_is_optimized(self, a0):
4658  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4659  return _IMP_atom.Chain_get_is_optimized(self, a0)
4660 
4661 
4662  def get_check_level(self):
4663  """get_check_level(Chain self) -> IMP::CheckLevel"""
4664  return _IMP_atom.Chain_get_check_level(self)
4665 
4666 
4667  def __eq__(self, *args):
4668  """
4669  __eq__(Chain self, Chain o) -> bool
4670  __eq__(Chain self, Particle d) -> bool
4671  """
4672  return _IMP_atom.Chain___eq__(self, *args)
4673 
4674 
4675  def __ne__(self, *args):
4676  """
4677  __ne__(Chain self, Chain o) -> bool
4678  __ne__(Chain self, Particle d) -> bool
4679  """
4680  return _IMP_atom.Chain___ne__(self, *args)
4681 
4682 
4683  def __le__(self, *args):
4684  """
4685  __le__(Chain self, Chain o) -> bool
4686  __le__(Chain self, Particle d) -> bool
4687  """
4688  return _IMP_atom.Chain___le__(self, *args)
4689 
4690 
4691  def __lt__(self, *args):
4692  """
4693  __lt__(Chain self, Chain o) -> bool
4694  __lt__(Chain self, Particle d) -> bool
4695  """
4696  return _IMP_atom.Chain___lt__(self, *args)
4697 
4698 
4699  def __ge__(self, *args):
4700  """
4701  __ge__(Chain self, Chain o) -> bool
4702  __ge__(Chain self, Particle d) -> bool
4703  """
4704  return _IMP_atom.Chain___ge__(self, *args)
4705 
4706 
4707  def __gt__(self, *args):
4708  """
4709  __gt__(Chain self, Chain o) -> bool
4710  __gt__(Chain self, Particle d) -> bool
4711  """
4712  return _IMP_atom.Chain___gt__(self, *args)
4713 
4714 
4715  def __hash__(self):
4716  """__hash__(Chain self) -> std::size_t"""
4717  return _IMP_atom.Chain___hash__(self)
4718 
4719 
4720  def __str__(self):
4721  """__str__(Chain self) -> std::string"""
4722  return _IMP_atom.Chain___str__(self)
4723 
4724 
4725  def __repr__(self):
4726  """__repr__(Chain self) -> std::string"""
4727  return _IMP_atom.Chain___repr__(self)
4728 
4729  __swig_destroy__ = _IMP_atom.delete_Chain
4730  __del__ = lambda self: None
4731 Chain_swigregister = _IMP_atom.Chain_swigregister
4732 Chain_swigregister(Chain)
4733 
4734 def Chain_setup_particle(*args):
4735  """
4736  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4737  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4738  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4739  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4740  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4741  Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4742  """
4743  return _IMP_atom.Chain_setup_particle(*args)
4744 
4745 def Chain_get_is_setup(*args):
4746  """
4747  get_is_setup(_ParticleAdaptor p) -> bool
4748  Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4749  """
4750  return _IMP_atom.Chain_get_is_setup(*args)
4751 
4752 def Chain_get_id_key():
4753  """Chain_get_id_key() -> StringKey"""
4754  return _IMP_atom.Chain_get_id_key()
4755 
4756 
4757 def get_chain(h):
4758  """get_chain(Hierarchy h) -> Chain"""
4759  return _IMP_atom.get_chain(h)
4760 
4761 def get_chain_id(h):
4762  """get_chain_id(Hierarchy h) -> std::string"""
4763  return _IMP_atom.get_chain_id(h)
4764 class Charged(IMP.core.XYZ):
4765  """Proxy of C++ IMP::atom::Charged class."""
4766 
4767  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4768 
4769  def __init__(self, *args):
4770  """
4771  __init__(IMP::atom::Charged self) -> Charged
4772  __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4773  __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4774  """
4775  this = _IMP_atom.new_Charged(*args)
4776  try:
4777  self.this.append(this)
4778  except __builtin__.Exception:
4779  self.this = this
4780 
4781  def show(self, *args):
4782  """
4783  show(Charged self, _ostream out)
4784  show(Charged self)
4785  """
4786  return _IMP_atom.Charged_show(self, *args)
4787 
4788 
4789  def setup_particle(*args):
4790  """
4791  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4792  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4793  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4794  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4795  """
4796  return _IMP_atom.Charged_setup_particle(*args)
4797 
4798  setup_particle = staticmethod(setup_particle)
4799 
4800  def get_charge(self):
4801  """get_charge(Charged self) -> IMP::Float"""
4802  return _IMP_atom.Charged_get_charge(self)
4803 
4804 
4805  def set_charge(self, t):
4806  """set_charge(Charged self, IMP::Float t)"""
4807  return _IMP_atom.Charged_set_charge(self, t)
4808 
4809 
4810  def get_is_setup(*args):
4811  """
4812  get_is_setup(_ParticleAdaptor p) -> bool
4813  get_is_setup(Model m, ParticleIndex pi) -> bool
4814  """
4815  return _IMP_atom.Charged_get_is_setup(*args)
4816 
4817  get_is_setup = staticmethod(get_is_setup)
4818 
4819  def get_charge_key():
4820  """get_charge_key() -> FloatKey"""
4821  return _IMP_atom.Charged_get_charge_key()
4822 
4823  get_charge_key = staticmethod(get_charge_key)
4824 
4825  def add_attribute(self, *args):
4826  """
4827  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4828  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4829  add_attribute(Charged self, IntKey a0, IMP::Int a1)
4830  add_attribute(Charged self, StringKey a0, IMP::String a1)
4831  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4832  add_attribute(Charged self, ObjectKey a0, Object a1)
4833  """
4834  return _IMP_atom.Charged_add_attribute(self, *args)
4835 
4836 
4837  def get_value(self, *args):
4838  """
4839  get_value(Charged self, FloatKey a0) -> IMP::Float
4840  get_value(Charged self, IntKey a0) -> IMP::Int
4841  get_value(Charged self, StringKey a0) -> IMP::String
4842  get_value(Charged self, ParticleIndexKey a0) -> Particle
4843  get_value(Charged self, ObjectKey a0) -> Object
4844  """
4845  return _IMP_atom.Charged_get_value(self, *args)
4846 
4847 
4848  def set_value(self, *args):
4849  """
4850  set_value(Charged self, FloatKey a0, IMP::Float a1)
4851  set_value(Charged self, IntKey a0, IMP::Int a1)
4852  set_value(Charged self, StringKey a0, IMP::String a1)
4853  set_value(Charged self, ParticleIndexKey a0, Particle a1)
4854  set_value(Charged self, ObjectKey a0, Object a1)
4855  """
4856  return _IMP_atom.Charged_set_value(self, *args)
4857 
4858 
4859  def remove_attribute(self, *args):
4860  """
4861  remove_attribute(Charged self, FloatKey a0)
4862  remove_attribute(Charged self, IntKey a0)
4863  remove_attribute(Charged self, StringKey a0)
4864  remove_attribute(Charged self, ParticleIndexKey a0)
4865  remove_attribute(Charged self, ObjectKey a0)
4866  """
4867  return _IMP_atom.Charged_remove_attribute(self, *args)
4868 
4869 
4870  def has_attribute(self, *args):
4871  """
4872  has_attribute(Charged self, FloatKey a0) -> bool
4873  has_attribute(Charged self, IntKey a0) -> bool
4874  has_attribute(Charged self, StringKey a0) -> bool
4875  has_attribute(Charged self, ParticleIndexKey a0) -> bool
4876  has_attribute(Charged self, ObjectKey a0) -> bool
4877  """
4878  return _IMP_atom.Charged_has_attribute(self, *args)
4879 
4880 
4881  def get_derivative(self, a0):
4882  """get_derivative(Charged self, FloatKey a0) -> double"""
4883  return _IMP_atom.Charged_get_derivative(self, a0)
4884 
4885 
4886  def get_name(self):
4887  """get_name(Charged self) -> std::string"""
4888  return _IMP_atom.Charged_get_name(self)
4889 
4890 
4891  def clear_caches(self):
4892  """clear_caches(Charged self)"""
4893  return _IMP_atom.Charged_clear_caches(self)
4894 
4895 
4896  def set_name(self, a0):
4897  """set_name(Charged self, std::string a0)"""
4898  return _IMP_atom.Charged_set_name(self, a0)
4899 
4900 
4901  def set_check_level(self, a0):
4902  """set_check_level(Charged self, IMP::CheckLevel a0)"""
4903  return _IMP_atom.Charged_set_check_level(self, a0)
4904 
4905 
4906  def add_to_derivative(self, a0, a1, a2):
4907  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4908  return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4909 
4910 
4911  def set_is_optimized(self, a0, a1):
4912  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4913  return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4914 
4915 
4916  def get_is_optimized(self, a0):
4917  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
4918  return _IMP_atom.Charged_get_is_optimized(self, a0)
4919 
4920 
4921  def get_check_level(self):
4922  """get_check_level(Charged self) -> IMP::CheckLevel"""
4923  return _IMP_atom.Charged_get_check_level(self)
4924 
4925 
4926  def __eq__(self, *args):
4927  """
4928  __eq__(Charged self, Charged o) -> bool
4929  __eq__(Charged self, Particle d) -> bool
4930  """
4931  return _IMP_atom.Charged___eq__(self, *args)
4932 
4933 
4934  def __ne__(self, *args):
4935  """
4936  __ne__(Charged self, Charged o) -> bool
4937  __ne__(Charged self, Particle d) -> bool
4938  """
4939  return _IMP_atom.Charged___ne__(self, *args)
4940 
4941 
4942  def __le__(self, *args):
4943  """
4944  __le__(Charged self, Charged o) -> bool
4945  __le__(Charged self, Particle d) -> bool
4946  """
4947  return _IMP_atom.Charged___le__(self, *args)
4948 
4949 
4950  def __lt__(self, *args):
4951  """
4952  __lt__(Charged self, Charged o) -> bool
4953  __lt__(Charged self, Particle d) -> bool
4954  """
4955  return _IMP_atom.Charged___lt__(self, *args)
4956 
4957 
4958  def __ge__(self, *args):
4959  """
4960  __ge__(Charged self, Charged o) -> bool
4961  __ge__(Charged self, Particle d) -> bool
4962  """
4963  return _IMP_atom.Charged___ge__(self, *args)
4964 
4965 
4966  def __gt__(self, *args):
4967  """
4968  __gt__(Charged self, Charged o) -> bool
4969  __gt__(Charged self, Particle d) -> bool
4970  """
4971  return _IMP_atom.Charged___gt__(self, *args)
4972 
4973 
4974  def __hash__(self):
4975  """__hash__(Charged self) -> std::size_t"""
4976  return _IMP_atom.Charged___hash__(self)
4977 
4978 
4979  def __str__(self):
4980  """__str__(Charged self) -> std::string"""
4981  return _IMP_atom.Charged___str__(self)
4982 
4983 
4984  def __repr__(self):
4985  """__repr__(Charged self) -> std::string"""
4986  return _IMP_atom.Charged___repr__(self)
4987 
4988  __swig_destroy__ = _IMP_atom.delete_Charged
4989  __del__ = lambda self: None
4990 Charged_swigregister = _IMP_atom.Charged_swigregister
4991 Charged_swigregister(Charged)
4992 
4993 def Charged_setup_particle(*args):
4994  """
4995  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4996  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4997  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4998  Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4999  """
5000  return _IMP_atom.Charged_setup_particle(*args)
5001 
5002 def Charged_get_is_setup(*args):
5003  """
5004  get_is_setup(_ParticleAdaptor p) -> bool
5005  Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5006  """
5007  return _IMP_atom.Charged_get_is_setup(*args)
5008 
5009 def Charged_get_charge_key():
5010  """Charged_get_charge_key() -> FloatKey"""
5011  return _IMP_atom.Charged_get_charge_key()
5012 
5013 class CoulombPairScore(IMP.PairScore):
5014  """Proxy of C++ IMP::atom::CoulombPairScore class."""
5015 
5016  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5017 
5018  def __init__(self, f):
5019  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5020  this = _IMP_atom.new_CoulombPairScore(f)
5021  try:
5022  self.this.append(this)
5023  except __builtin__.Exception:
5024  self.this = this
5025 
5026  def set_relative_dielectric(self, relative_dielectric):
5027  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5028  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5029 
5030 
5031  def get_relative_dielectric(self):
5032  """get_relative_dielectric(CoulombPairScore self) -> double"""
5033  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5034 
5035 
5036  def do_get_inputs(self, m, pis):
5037  """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5038  return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5039 
5040 
5041  def get_version_info(self):
5042  """get_version_info(CoulombPairScore self) -> VersionInfo"""
5043  return _IMP_atom.CoulombPairScore_get_version_info(self)
5044 
5045 
5046  def __str__(self):
5047  """__str__(CoulombPairScore self) -> std::string"""
5048  return _IMP_atom.CoulombPairScore___str__(self)
5049 
5050 
5051  def __repr__(self):
5052  """__repr__(CoulombPairScore self) -> std::string"""
5053  return _IMP_atom.CoulombPairScore___repr__(self)
5054 
5055 
5056  @staticmethod
5057  def get_from(o):
5058  return _object_cast_to_CoulombPairScore(o)
5059 
5060 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5061 CoulombPairScore_swigregister(CoulombPairScore)
5062 
5063 class Domain(Hierarchy):
5064  """Proxy of C++ IMP::atom::Domain class."""
5065 
5066  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5067 
5068  def set_index_range(self, ir):
5069  """set_index_range(Domain self, IMP::IntRange ir)"""
5070  return _IMP_atom.Domain_set_index_range(self, ir)
5071 
5072 
5073  def get_index_range(self):
5074  """get_index_range(Domain self) -> IMP::IntRange"""
5075  return _IMP_atom.Domain_get_index_range(self)
5076 
5077 
5078  def __init__(self, *args):
5079  """
5080  __init__(IMP::atom::Domain self) -> Domain
5081  __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5082  __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5083  """
5084  this = _IMP_atom.new_Domain(*args)
5085  try:
5086  self.this.append(this)
5087  except __builtin__.Exception:
5088  self.this = this
5089 
5090  def get_is_setup(*args):
5091  """
5092  get_is_setup(Model m, ParticleIndex pi) -> bool
5093  get_is_setup(_ParticleAdaptor p) -> bool
5094  """
5095  return _IMP_atom.Domain_get_is_setup(*args)
5096 
5097  get_is_setup = staticmethod(get_is_setup)
5098 
5099  def show(self, *args):
5100  """
5101  show(Domain self, _ostream out)
5102  show(Domain self)
5103  """
5104  return _IMP_atom.Domain_show(self, *args)
5105 
5106 
5107  def setup_particle(*args):
5108  """
5109  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5110  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5111  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5112  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5113  """
5114  return _IMP_atom.Domain_setup_particle(*args)
5115 
5116  setup_particle = staticmethod(setup_particle)
5117 
5118  def add_attribute(self, *args):
5119  """
5120  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5121  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5122  add_attribute(Domain self, IntKey a0, IMP::Int a1)
5123  add_attribute(Domain self, StringKey a0, IMP::String a1)
5124  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5125  add_attribute(Domain self, ObjectKey a0, Object a1)
5126  """
5127  return _IMP_atom.Domain_add_attribute(self, *args)
5128 
5129 
5130  def get_value(self, *args):
5131  """
5132  get_value(Domain self, FloatKey a0) -> IMP::Float
5133  get_value(Domain self, IntKey a0) -> IMP::Int
5134  get_value(Domain self, StringKey a0) -> IMP::String
5135  get_value(Domain self, ParticleIndexKey a0) -> Particle
5136  get_value(Domain self, ObjectKey a0) -> Object
5137  """
5138  return _IMP_atom.Domain_get_value(self, *args)
5139 
5140 
5141  def set_value(self, *args):
5142  """
5143  set_value(Domain self, FloatKey a0, IMP::Float a1)
5144  set_value(Domain self, IntKey a0, IMP::Int a1)
5145  set_value(Domain self, StringKey a0, IMP::String a1)
5146  set_value(Domain self, ParticleIndexKey a0, Particle a1)
5147  set_value(Domain self, ObjectKey a0, Object a1)
5148  """
5149  return _IMP_atom.Domain_set_value(self, *args)
5150 
5151 
5152  def remove_attribute(self, *args):
5153  """
5154  remove_attribute(Domain self, FloatKey a0)
5155  remove_attribute(Domain self, IntKey a0)
5156  remove_attribute(Domain self, StringKey a0)
5157  remove_attribute(Domain self, ParticleIndexKey a0)
5158  remove_attribute(Domain self, ObjectKey a0)
5159  """
5160  return _IMP_atom.Domain_remove_attribute(self, *args)
5161 
5162 
5163  def has_attribute(self, *args):
5164  """
5165  has_attribute(Domain self, FloatKey a0) -> bool
5166  has_attribute(Domain self, IntKey a0) -> bool
5167  has_attribute(Domain self, StringKey a0) -> bool
5168  has_attribute(Domain self, ParticleIndexKey a0) -> bool
5169  has_attribute(Domain self, ObjectKey a0) -> bool
5170  """
5171  return _IMP_atom.Domain_has_attribute(self, *args)
5172 
5173 
5174  def get_derivative(self, a0):
5175  """get_derivative(Domain self, FloatKey a0) -> double"""
5176  return _IMP_atom.Domain_get_derivative(self, a0)
5177 
5178 
5179  def get_name(self):
5180  """get_name(Domain self) -> std::string"""
5181  return _IMP_atom.Domain_get_name(self)
5182 
5183 
5184  def clear_caches(self):
5185  """clear_caches(Domain self)"""
5186  return _IMP_atom.Domain_clear_caches(self)
5187 
5188 
5189  def set_name(self, a0):
5190  """set_name(Domain self, std::string a0)"""
5191  return _IMP_atom.Domain_set_name(self, a0)
5192 
5193 
5194  def set_check_level(self, a0):
5195  """set_check_level(Domain self, IMP::CheckLevel a0)"""
5196  return _IMP_atom.Domain_set_check_level(self, a0)
5197 
5198 
5199  def add_to_derivative(self, a0, a1, a2):
5200  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5201  return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5202 
5203 
5204  def set_is_optimized(self, a0, a1):
5205  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5206  return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5207 
5208 
5209  def get_is_optimized(self, a0):
5210  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5211  return _IMP_atom.Domain_get_is_optimized(self, a0)
5212 
5213 
5214  def get_check_level(self):
5215  """get_check_level(Domain self) -> IMP::CheckLevel"""
5216  return _IMP_atom.Domain_get_check_level(self)
5217 
5218 
5219  def __eq__(self, *args):
5220  """
5221  __eq__(Domain self, Domain o) -> bool
5222  __eq__(Domain self, Particle d) -> bool
5223  """
5224  return _IMP_atom.Domain___eq__(self, *args)
5225 
5226 
5227  def __ne__(self, *args):
5228  """
5229  __ne__(Domain self, Domain o) -> bool
5230  __ne__(Domain self, Particle d) -> bool
5231  """
5232  return _IMP_atom.Domain___ne__(self, *args)
5233 
5234 
5235  def __le__(self, *args):
5236  """
5237  __le__(Domain self, Domain o) -> bool
5238  __le__(Domain self, Particle d) -> bool
5239  """
5240  return _IMP_atom.Domain___le__(self, *args)
5241 
5242 
5243  def __lt__(self, *args):
5244  """
5245  __lt__(Domain self, Domain o) -> bool
5246  __lt__(Domain self, Particle d) -> bool
5247  """
5248  return _IMP_atom.Domain___lt__(self, *args)
5249 
5250 
5251  def __ge__(self, *args):
5252  """
5253  __ge__(Domain self, Domain o) -> bool
5254  __ge__(Domain self, Particle d) -> bool
5255  """
5256  return _IMP_atom.Domain___ge__(self, *args)
5257 
5258 
5259  def __gt__(self, *args):
5260  """
5261  __gt__(Domain self, Domain o) -> bool
5262  __gt__(Domain self, Particle d) -> bool
5263  """
5264  return _IMP_atom.Domain___gt__(self, *args)
5265 
5266 
5267  def __hash__(self):
5268  """__hash__(Domain self) -> std::size_t"""
5269  return _IMP_atom.Domain___hash__(self)
5270 
5271 
5272  def __str__(self):
5273  """__str__(Domain self) -> std::string"""
5274  return _IMP_atom.Domain___str__(self)
5275 
5276 
5277  def __repr__(self):
5278  """__repr__(Domain self) -> std::string"""
5279  return _IMP_atom.Domain___repr__(self)
5280 
5281  __swig_destroy__ = _IMP_atom.delete_Domain
5282  __del__ = lambda self: None
5283 Domain_swigregister = _IMP_atom.Domain_swigregister
5284 Domain_swigregister(Domain)
5285 
5286 def Domain_get_is_setup(*args):
5287  """
5288  get_is_setup(Model m, ParticleIndex pi) -> bool
5289  Domain_get_is_setup(_ParticleAdaptor p) -> bool
5290  """
5291  return _IMP_atom.Domain_get_is_setup(*args)
5292 
5293 def Domain_setup_particle(*args):
5294  """
5295  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5296  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5297  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5298  Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5299  """
5300  return _IMP_atom.Domain_setup_particle(*args)
5301 
5302 class LennardJones(IMP.core.XYZR):
5303  """Proxy of C++ IMP::atom::LennardJones class."""
5304 
5305  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5306 
5307  def __init__(self, *args):
5308  """
5309  __init__(IMP::atom::LennardJones self) -> LennardJones
5310  __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5311  __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5312  """
5313  this = _IMP_atom.new_LennardJones(*args)
5314  try:
5315  self.this.append(this)
5316  except __builtin__.Exception:
5317  self.this = this
5318 
5319  def show(self, *args):
5320  """
5321  show(LennardJones self, _ostream out)
5322  show(LennardJones self)
5323  """
5324  return _IMP_atom.LennardJones_show(self, *args)
5325 
5326 
5327  def setup_particle(*args):
5328  """
5329  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5330  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5331  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5332  setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5333  """
5334  return _IMP_atom.LennardJones_setup_particle(*args)
5335 
5336  setup_particle = staticmethod(setup_particle)
5337 
5338  def get_well_depth(self):
5339  """get_well_depth(LennardJones self) -> IMP::Float"""
5340  return _IMP_atom.LennardJones_get_well_depth(self)
5341 
5342 
5343  def set_well_depth(self, well_depth):
5344  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5345  return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5346 
5347 
5348  def get_is_setup(*args):
5349  """
5350  get_is_setup(_ParticleAdaptor p) -> bool
5351  get_is_setup(Model m, ParticleIndex pi) -> bool
5352  """
5353  return _IMP_atom.LennardJones_get_is_setup(*args)
5354 
5355  get_is_setup = staticmethod(get_is_setup)
5356 
5357  def get_well_depth_key():
5358  """get_well_depth_key() -> FloatKey"""
5359  return _IMP_atom.LennardJones_get_well_depth_key()
5360 
5361  get_well_depth_key = staticmethod(get_well_depth_key)
5362 
5363  def add_attribute(self, *args):
5364  """
5365  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5366  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5367  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5368  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5369  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5370  add_attribute(LennardJones self, ObjectKey a0, Object a1)
5371  """
5372  return _IMP_atom.LennardJones_add_attribute(self, *args)
5373 
5374 
5375  def get_value(self, *args):
5376  """
5377  get_value(LennardJones self, FloatKey a0) -> IMP::Float
5378  get_value(LennardJones self, IntKey a0) -> IMP::Int
5379  get_value(LennardJones self, StringKey a0) -> IMP::String
5380  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5381  get_value(LennardJones self, ObjectKey a0) -> Object
5382  """
5383  return _IMP_atom.LennardJones_get_value(self, *args)
5384 
5385 
5386  def set_value(self, *args):
5387  """
5388  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5389  set_value(LennardJones self, IntKey a0, IMP::Int a1)
5390  set_value(LennardJones self, StringKey a0, IMP::String a1)
5391  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5392  set_value(LennardJones self, ObjectKey a0, Object a1)
5393  """
5394  return _IMP_atom.LennardJones_set_value(self, *args)
5395 
5396 
5397  def remove_attribute(self, *args):
5398  """
5399  remove_attribute(LennardJones self, FloatKey a0)
5400  remove_attribute(LennardJones self, IntKey a0)
5401  remove_attribute(LennardJones self, StringKey a0)
5402  remove_attribute(LennardJones self, ParticleIndexKey a0)
5403  remove_attribute(LennardJones self, ObjectKey a0)
5404  """
5405  return _IMP_atom.LennardJones_remove_attribute(self, *args)
5406 
5407 
5408  def has_attribute(self, *args):
5409  """
5410  has_attribute(LennardJones self, FloatKey a0) -> bool
5411  has_attribute(LennardJones self, IntKey a0) -> bool
5412  has_attribute(LennardJones self, StringKey a0) -> bool
5413  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5414  has_attribute(LennardJones self, ObjectKey a0) -> bool
5415  """
5416  return _IMP_atom.LennardJones_has_attribute(self, *args)
5417 
5418 
5419  def get_derivative(self, a0):
5420  """get_derivative(LennardJones self, FloatKey a0) -> double"""
5421  return _IMP_atom.LennardJones_get_derivative(self, a0)
5422 
5423 
5424  def get_name(self):
5425  """get_name(LennardJones self) -> std::string"""
5426  return _IMP_atom.LennardJones_get_name(self)
5427 
5428 
5429  def clear_caches(self):
5430  """clear_caches(LennardJones self)"""
5431  return _IMP_atom.LennardJones_clear_caches(self)
5432 
5433 
5434  def set_name(self, a0):
5435  """set_name(LennardJones self, std::string a0)"""
5436  return _IMP_atom.LennardJones_set_name(self, a0)
5437 
5438 
5439  def set_check_level(self, a0):
5440  """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5441  return _IMP_atom.LennardJones_set_check_level(self, a0)
5442 
5443 
5444  def add_to_derivative(self, a0, a1, a2):
5445  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5446  return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5447 
5448 
5449  def set_is_optimized(self, a0, a1):
5450  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5451  return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5452 
5453 
5454  def get_is_optimized(self, a0):
5455  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5456  return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5457 
5458 
5459  def get_check_level(self):
5460  """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5461  return _IMP_atom.LennardJones_get_check_level(self)
5462 
5463 
5464  def __eq__(self, *args):
5465  """
5466  __eq__(LennardJones self, LennardJones o) -> bool
5467  __eq__(LennardJones self, Particle d) -> bool
5468  """
5469  return _IMP_atom.LennardJones___eq__(self, *args)
5470 
5471 
5472  def __ne__(self, *args):
5473  """
5474  __ne__(LennardJones self, LennardJones o) -> bool
5475  __ne__(LennardJones self, Particle d) -> bool
5476  """
5477  return _IMP_atom.LennardJones___ne__(self, *args)
5478 
5479 
5480  def __le__(self, *args):
5481  """
5482  __le__(LennardJones self, LennardJones o) -> bool
5483  __le__(LennardJones self, Particle d) -> bool
5484  """
5485  return _IMP_atom.LennardJones___le__(self, *args)
5486 
5487 
5488  def __lt__(self, *args):
5489  """
5490  __lt__(LennardJones self, LennardJones o) -> bool
5491  __lt__(LennardJones self, Particle d) -> bool
5492  """
5493  return _IMP_atom.LennardJones___lt__(self, *args)
5494 
5495 
5496  def __ge__(self, *args):
5497  """
5498  __ge__(LennardJones self, LennardJones o) -> bool
5499  __ge__(LennardJones self, Particle d) -> bool
5500  """
5501  return _IMP_atom.LennardJones___ge__(self, *args)
5502 
5503 
5504  def __gt__(self, *args):
5505  """
5506  __gt__(LennardJones self, LennardJones o) -> bool
5507  __gt__(LennardJones self, Particle d) -> bool
5508  """
5509  return _IMP_atom.LennardJones___gt__(self, *args)
5510 
5511 
5512  def __hash__(self):
5513  """__hash__(LennardJones self) -> std::size_t"""
5514  return _IMP_atom.LennardJones___hash__(self)
5515 
5516 
5517  def __str__(self):
5518  """__str__(LennardJones self) -> std::string"""
5519  return _IMP_atom.LennardJones___str__(self)
5520 
5521 
5522  def __repr__(self):
5523  """__repr__(LennardJones self) -> std::string"""
5524  return _IMP_atom.LennardJones___repr__(self)
5525 
5526  __swig_destroy__ = _IMP_atom.delete_LennardJones
5527  __del__ = lambda self: None
5528 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5529 LennardJones_swigregister(LennardJones)
5530 
5531 def LennardJones_setup_particle(*args):
5532  """
5533  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5534  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5535  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5536  LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5537  """
5538  return _IMP_atom.LennardJones_setup_particle(*args)
5539 
5540 def LennardJones_get_is_setup(*args):
5541  """
5542  get_is_setup(_ParticleAdaptor p) -> bool
5543  LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5544  """
5545  return _IMP_atom.LennardJones_get_is_setup(*args)
5546 
5547 def LennardJones_get_well_depth_key():
5548  """LennardJones_get_well_depth_key() -> FloatKey"""
5549  return _IMP_atom.LennardJones_get_well_depth_key()
5550 
5551 class LennardJonesPairScore(IMP.PairScore):
5552  """Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5553 
5554  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5555 
5556  def __init__(self, f):
5557  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5558  this = _IMP_atom.new_LennardJonesPairScore(f)
5559  try:
5560  self.this.append(this)
5561  except __builtin__.Exception:
5562  self.this = this
5563 
5564  def set_repulsive_weight(self, repulsive_weight):
5565  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5566  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5567 
5568 
5569  def get_repulsive_weight(self):
5570  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5571  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5572 
5573 
5574  def set_attractive_weight(self, attractive_weight):
5575  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5576  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5577 
5578 
5579  def get_attractive_weight(self):
5580  """get_attractive_weight(LennardJonesPairScore self) -> double"""
5581  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5582 
5583 
5584  def do_get_inputs(self, m, pis):
5585  """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5586  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5587 
5588 
5589  def get_version_info(self):
5590  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5591  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5592 
5593 
5594  def __str__(self):
5595  """__str__(LennardJonesPairScore self) -> std::string"""
5596  return _IMP_atom.LennardJonesPairScore___str__(self)
5597 
5598 
5599  def __repr__(self):
5600  """__repr__(LennardJonesPairScore self) -> std::string"""
5601  return _IMP_atom.LennardJonesPairScore___repr__(self)
5602 
5603 
5604  @staticmethod
5605  def get_from(o):
5606  return _object_cast_to_LennardJonesPairScore(o)
5607 
5608 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5609 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5610 
5611 class LinearVelocity(IMP.Decorator):
5612  """Proxy of C++ IMP::atom::LinearVelocity class."""
5613 
5614  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5615 
5616  def get_velocity_key(i):
5617  """get_velocity_key(unsigned int i) -> FloatKey"""
5618  return _IMP_atom.LinearVelocity_get_velocity_key(i)
5619 
5620  get_velocity_key = staticmethod(get_velocity_key)
5621 
5622  def __init__(self, *args):
5623  """
5624  __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5625  __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5626  __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5627  """
5628  this = _IMP_atom.new_LinearVelocity(*args)
5629  try:
5630  self.this.append(this)
5631  except __builtin__.Exception:
5632  self.this = this
5633 
5634  def get_is_setup(*args):
5635  """
5636  get_is_setup(Model m, ParticleIndex pi) -> bool
5637  get_is_setup(_ParticleAdaptor p) -> bool
5638  """
5639  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5640 
5641  get_is_setup = staticmethod(get_is_setup)
5642 
5643  def show(self, *args):
5644  """
5645  show(LinearVelocity self, _ostream out)
5646  show(LinearVelocity self)
5647  """
5648  return _IMP_atom.LinearVelocity_show(self, *args)
5649 
5650 
5651  def setup_particle(*args):
5652  """
5653  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5654  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5655  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5656  setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5657  """
5658  return _IMP_atom.LinearVelocity_setup_particle(*args)
5659 
5660  setup_particle = staticmethod(setup_particle)
5661 
5662  def set_velocity(self, v):
5663  """set_velocity(LinearVelocity self, Vector3D v)"""
5664  return _IMP_atom.LinearVelocity_set_velocity(self, v)
5665 
5666 
5667  def get_velocity(self):
5668  """get_velocity(LinearVelocity self) -> Vector3D"""
5669  return _IMP_atom.LinearVelocity_get_velocity(self)
5670 
5671 
5672  def add_attribute(self, *args):
5673  """
5674  add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5675  add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5676  add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5677  add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5678  add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5679  add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5680  """
5681  return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5682 
5683 
5684  def get_value(self, *args):
5685  """
5686  get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5687  get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5688  get_value(LinearVelocity self, StringKey a0) -> IMP::String
5689  get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5690  get_value(LinearVelocity self, ObjectKey a0) -> Object
5691  """
5692  return _IMP_atom.LinearVelocity_get_value(self, *args)
5693 
5694 
5695  def set_value(self, *args):
5696  """
5697  set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5698  set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5699  set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5700  set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5701  set_value(LinearVelocity self, ObjectKey a0, Object a1)
5702  """
5703  return _IMP_atom.LinearVelocity_set_value(self, *args)
5704 
5705 
5706  def remove_attribute(self, *args):
5707  """
5708  remove_attribute(LinearVelocity self, FloatKey a0)
5709  remove_attribute(LinearVelocity self, IntKey a0)
5710  remove_attribute(LinearVelocity self, StringKey a0)
5711  remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5712  remove_attribute(LinearVelocity self, ObjectKey a0)
5713  """
5714  return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5715 
5716 
5717  def has_attribute(self, *args):
5718  """
5719  has_attribute(LinearVelocity self, FloatKey a0) -> bool
5720  has_attribute(LinearVelocity self, IntKey a0) -> bool
5721  has_attribute(LinearVelocity self, StringKey a0) -> bool
5722  has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5723  has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5724  """
5725  return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5726 
5727 
5728  def get_derivative(self, a0):
5729  """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5730  return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5731 
5732 
5733  def get_name(self):
5734  """get_name(LinearVelocity self) -> std::string"""
5735  return _IMP_atom.LinearVelocity_get_name(self)
5736 
5737 
5738  def clear_caches(self):
5739  """clear_caches(LinearVelocity self)"""
5740  return _IMP_atom.LinearVelocity_clear_caches(self)
5741 
5742 
5743  def set_name(self, a0):
5744  """set_name(LinearVelocity self, std::string a0)"""
5745  return _IMP_atom.LinearVelocity_set_name(self, a0)
5746 
5747 
5748  def set_check_level(self, a0):
5749  """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5750  return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5751 
5752 
5753  def add_to_derivative(self, a0, a1, a2):
5754  """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5755  return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5756 
5757 
5758  def set_is_optimized(self, a0, a1):
5759  """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5760  return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5761 
5762 
5763  def get_is_optimized(self, a0):
5764  """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5765  return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5766 
5767 
5768  def get_check_level(self):
5769  """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5770  return _IMP_atom.LinearVelocity_get_check_level(self)
5771 
5772 
5773  def __eq__(self, *args):
5774  """
5775  __eq__(LinearVelocity self, LinearVelocity o) -> bool
5776  __eq__(LinearVelocity self, Particle d) -> bool
5777  """
5778  return _IMP_atom.LinearVelocity___eq__(self, *args)
5779 
5780 
5781  def __ne__(self, *args):
5782  """
5783  __ne__(LinearVelocity self, LinearVelocity o) -> bool
5784  __ne__(LinearVelocity self, Particle d) -> bool
5785  """
5786  return _IMP_atom.LinearVelocity___ne__(self, *args)
5787 
5788 
5789  def __le__(self, *args):
5790  """
5791  __le__(LinearVelocity self, LinearVelocity o) -> bool
5792  __le__(LinearVelocity self, Particle d) -> bool
5793  """
5794  return _IMP_atom.LinearVelocity___le__(self, *args)
5795 
5796 
5797  def __lt__(self, *args):
5798  """
5799  __lt__(LinearVelocity self, LinearVelocity o) -> bool
5800  __lt__(LinearVelocity self, Particle d) -> bool
5801  """
5802  return _IMP_atom.LinearVelocity___lt__(self, *args)
5803 
5804 
5805  def __ge__(self, *args):
5806  """
5807  __ge__(LinearVelocity self, LinearVelocity o) -> bool
5808  __ge__(LinearVelocity self, Particle d) -> bool
5809  """
5810  return _IMP_atom.LinearVelocity___ge__(self, *args)
5811 
5812 
5813  def __gt__(self, *args):
5814  """
5815  __gt__(LinearVelocity self, LinearVelocity o) -> bool
5816  __gt__(LinearVelocity self, Particle d) -> bool
5817  """
5818  return _IMP_atom.LinearVelocity___gt__(self, *args)
5819 
5820 
5821  def __hash__(self):
5822  """__hash__(LinearVelocity self) -> std::size_t"""
5823  return _IMP_atom.LinearVelocity___hash__(self)
5824 
5825 
5826  def __str__(self):
5827  """__str__(LinearVelocity self) -> std::string"""
5828  return _IMP_atom.LinearVelocity___str__(self)
5829 
5830 
5831  def __repr__(self):
5832  """__repr__(LinearVelocity self) -> std::string"""
5833  return _IMP_atom.LinearVelocity___repr__(self)
5834 
5835  __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5836  __del__ = lambda self: None
5837 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
5838 LinearVelocity_swigregister(LinearVelocity)
5839 
5840 def LinearVelocity_get_velocity_key(i):
5841  """LinearVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
5842  return _IMP_atom.LinearVelocity_get_velocity_key(i)
5843 
5844 def LinearVelocity_get_is_setup(*args):
5845  """
5846  get_is_setup(Model m, ParticleIndex pi) -> bool
5847  LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
5848  """
5849  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5850 
5851 def LinearVelocity_setup_particle(*args):
5852  """
5853  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5854  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5855  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5856  LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5857  """
5858  return _IMP_atom.LinearVelocity_setup_particle(*args)
5859 
5860 class AngularVelocity(IMP.Decorator):
5861  """Proxy of C++ IMP::atom::AngularVelocity class."""
5862 
5863  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5864 
5865  def get_velocity_key(i):
5866  """get_velocity_key(unsigned int i) -> FloatKey"""
5867  return _IMP_atom.AngularVelocity_get_velocity_key(i)
5868 
5869  get_velocity_key = staticmethod(get_velocity_key)
5870 
5871  def __init__(self, *args):
5872  """
5873  __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
5874  __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5875  __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5876  """
5877  this = _IMP_atom.new_AngularVelocity(*args)
5878  try:
5879  self.this.append(this)
5880  except __builtin__.Exception:
5881  self.this = this
5882 
5883  def get_is_setup(*args):
5884  """
5885  get_is_setup(Model m, ParticleIndex pi) -> bool
5886  get_is_setup(_ParticleAdaptor p) -> bool
5887  """
5888  return _IMP_atom.AngularVelocity_get_is_setup(*args)
5889 
5890  get_is_setup = staticmethod(get_is_setup)
5891 
5892  def show(self, *args):
5893  """
5894  show(AngularVelocity self, _ostream out)
5895  show(AngularVelocity self)
5896  """
5897  return _IMP_atom.AngularVelocity_show(self, *args)
5898 
5899 
5900  def setup_particle(*args):
5901  """
5902  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5903  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
5904  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5905  setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
5906  """
5907  return _IMP_atom.AngularVelocity_setup_particle(*args)
5908 
5909  setup_particle = staticmethod(setup_particle)
5910 
5911  def set_velocity(self, v):
5912  """set_velocity(AngularVelocity self, Vector4D v)"""
5913  return _IMP_atom.AngularVelocity_set_velocity(self, v)
5914 
5915 
5916  def get_velocity(self):
5917  """get_velocity(AngularVelocity self) -> Vector4D"""
5918  return _IMP_atom.AngularVelocity_get_velocity(self)
5919 
5920 
5921  def add_attribute(self, *args):
5922  """
5923  add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5924  add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5925  add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5926  add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5927  add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5928  add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5929  """
5930  return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5931 
5932 
5933  def get_value(self, *args):
5934  """
5935  get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5936  get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5937  get_value(AngularVelocity self, StringKey a0) -> IMP::String
5938  get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5939  get_value(AngularVelocity self, ObjectKey a0) -> Object
5940  """
5941  return _IMP_atom.AngularVelocity_get_value(self, *args)
5942 
5943 
5944  def set_value(self, *args):
5945  """
5946  set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5947  set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5948  set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5949  set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5950  set_value(AngularVelocity self, ObjectKey a0, Object a1)
5951  """
5952  return _IMP_atom.AngularVelocity_set_value(self, *args)
5953 
5954 
5955  def remove_attribute(self, *args):
5956  """
5957  remove_attribute(AngularVelocity self, FloatKey a0)
5958  remove_attribute(AngularVelocity self, IntKey a0)
5959  remove_attribute(AngularVelocity self, StringKey a0)
5960  remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5961  remove_attribute(AngularVelocity self, ObjectKey a0)
5962  """
5963  return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5964 
5965 
5966  def has_attribute(self, *args):
5967  """
5968  has_attribute(AngularVelocity self, FloatKey a0) -> bool
5969  has_attribute(AngularVelocity self, IntKey a0) -> bool
5970  has_attribute(AngularVelocity self, StringKey a0) -> bool
5971  has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
5972  has_attribute(AngularVelocity self, ObjectKey a0) -> bool
5973  """
5974  return _IMP_atom.AngularVelocity_has_attribute(self, *args)
5975 
5976 
5977  def get_derivative(self, a0):
5978  """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
5979  return _IMP_atom.AngularVelocity_get_derivative(self, a0)
5980 
5981 
5982  def get_name(self):
5983  """get_name(AngularVelocity self) -> std::string"""
5984  return _IMP_atom.AngularVelocity_get_name(self)
5985 
5986 
5987  def clear_caches(self):
5988  """clear_caches(AngularVelocity self)"""
5989  return _IMP_atom.AngularVelocity_clear_caches(self)
5990 
5991 
5992  def set_name(self, a0):
5993  """set_name(AngularVelocity self, std::string a0)"""
5994  return _IMP_atom.AngularVelocity_set_name(self, a0)
5995 
5996 
5997  def set_check_level(self, a0):
5998  """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
5999  return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6000 
6001 
6002  def add_to_derivative(self, a0, a1, a2):
6003  """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6004  return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6005 
6006 
6007  def set_is_optimized(self, a0, a1):
6008  """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6009  return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6010 
6011 
6012  def get_is_optimized(self, a0):
6013  """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6014  return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6015 
6016 
6017  def get_check_level(self):
6018  """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6019  return _IMP_atom.AngularVelocity_get_check_level(self)
6020 
6021 
6022  def __eq__(self, *args):
6023  """
6024  __eq__(AngularVelocity self, AngularVelocity o) -> bool
6025  __eq__(AngularVelocity self, Particle d) -> bool
6026  """
6027  return _IMP_atom.AngularVelocity___eq__(self, *args)
6028 
6029 
6030  def __ne__(self, *args):
6031  """
6032  __ne__(AngularVelocity self, AngularVelocity o) -> bool
6033  __ne__(AngularVelocity self, Particle d) -> bool
6034  """
6035  return _IMP_atom.AngularVelocity___ne__(self, *args)
6036 
6037 
6038  def __le__(self, *args):
6039  """
6040  __le__(AngularVelocity self, AngularVelocity o) -> bool
6041  __le__(AngularVelocity self, Particle d) -> bool
6042  """
6043  return _IMP_atom.AngularVelocity___le__(self, *args)
6044 
6045 
6046  def __lt__(self, *args):
6047  """
6048  __lt__(AngularVelocity self, AngularVelocity o) -> bool
6049  __lt__(AngularVelocity self, Particle d) -> bool
6050  """
6051  return _IMP_atom.AngularVelocity___lt__(self, *args)
6052 
6053 
6054  def __ge__(self, *args):
6055  """
6056  __ge__(AngularVelocity self, AngularVelocity o) -> bool
6057  __ge__(AngularVelocity self, Particle d) -> bool
6058  """
6059  return _IMP_atom.AngularVelocity___ge__(self, *args)
6060 
6061 
6062  def __gt__(self, *args):
6063  """
6064  __gt__(AngularVelocity self, AngularVelocity o) -> bool
6065  __gt__(AngularVelocity self, Particle d) -> bool
6066  """
6067  return _IMP_atom.AngularVelocity___gt__(self, *args)
6068 
6069 
6070  def __hash__(self):
6071  """__hash__(AngularVelocity self) -> std::size_t"""
6072  return _IMP_atom.AngularVelocity___hash__(self)
6073 
6074 
6075  def __str__(self):
6076  """__str__(AngularVelocity self) -> std::string"""
6077  return _IMP_atom.AngularVelocity___str__(self)
6078 
6079 
6080  def __repr__(self):
6081  """__repr__(AngularVelocity self) -> std::string"""
6082  return _IMP_atom.AngularVelocity___repr__(self)
6083 
6084  __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6085  __del__ = lambda self: None
6086 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6087 AngularVelocity_swigregister(AngularVelocity)
6088 
6089 def AngularVelocity_get_velocity_key(i):
6090  """AngularVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6091  return _IMP_atom.AngularVelocity_get_velocity_key(i)
6092 
6093 def AngularVelocity_get_is_setup(*args):
6094  """
6095  get_is_setup(Model m, ParticleIndex pi) -> bool
6096  AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6097  """
6098  return _IMP_atom.AngularVelocity_get_is_setup(*args)
6099 
6100 def AngularVelocity_setup_particle(*args):
6101  """
6102  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6103  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6104  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6105  AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6106  """
6107  return _IMP_atom.AngularVelocity_setup_particle(*args)
6108 
6109 class MolecularDynamics(Simulator):
6110  """Proxy of C++ IMP::atom::MolecularDynamics class."""
6111 
6112  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6113 
6114  def __init__(self, m):
6115  """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6116  this = _IMP_atom.new_MolecularDynamics(m)
6117  try:
6118  self.this.append(this)
6119  except __builtin__.Exception:
6120  self.this = this
6121 
6122  def get_kinetic_energy(self):
6123  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6124  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6125 
6126 
6127  def get_kinetic_temperature(self, ekinetic):
6128  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6129  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6130 
6131 
6132  def set_velocity_cap(self, velocity_cap):
6133  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6134  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6135 
6136 
6137  def assign_velocities(self, temperature):
6138  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6139  return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6140 
6141 
6142  def setup(self, ps):
6143  """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6144  return _IMP_atom.MolecularDynamics_setup(self, ps)
6145 
6146 
6147  def do_step(self, sc, dt):
6148  """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6149  return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6150 
6151 
6152  def get_is_simulation_particle(self, p):
6153  """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6154  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6155 
6156 
6157  def get_version_info(self):
6158  """get_version_info(MolecularDynamics self) -> VersionInfo"""
6159  return _IMP_atom.MolecularDynamics_get_version_info(self)
6160 
6161 
6162  def __str__(self):
6163  """__str__(MolecularDynamics self) -> std::string"""
6164  return _IMP_atom.MolecularDynamics___str__(self)
6165 
6166 
6167  def __repr__(self):
6168  """__repr__(MolecularDynamics self) -> std::string"""
6169  return _IMP_atom.MolecularDynamics___repr__(self)
6170 
6171 
6172  @staticmethod
6173  def get_from(o):
6174  return _object_cast_to_MolecularDynamics(o)
6175 
6176 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6177 MolecularDynamics_swigregister(MolecularDynamics)
6178 
6179 class VelocityScalingOptimizerState(IMP.OptimizerState):
6180  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6181 
6182  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6183 
6184  def __init__(self, m, pis, temperature):
6185  """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6186  this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6187  try:
6188  self.this.append(this)
6189  except __builtin__.Exception:
6190  self.this = this
6191 
6192  def set_particles(self, pis):
6193  """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6194  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6195 
6196 
6197  def set_temperature(self, temperature):
6198  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6199  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6200 
6201 
6202  def rescale_velocities(self):
6203  """rescale_velocities(VelocityScalingOptimizerState self)"""
6204  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6205 
6206 
6207  def get_version_info(self):
6208  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6209  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6210 
6211 
6212  def __str__(self):
6213  """__str__(VelocityScalingOptimizerState self) -> std::string"""
6214  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6215 
6216 
6217  def __repr__(self):
6218  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6219  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6220 
6221 
6222  @staticmethod
6223  def get_from(o):
6224  return _object_cast_to_VelocityScalingOptimizerState(o)
6225 
6226 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6227 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6228 
6229 class Fragment(Hierarchy):
6230  """Proxy of C++ IMP::atom::Fragment class."""
6231 
6232  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6233 
6234  def set_residue_indexes(self, o):
6235  """set_residue_indexes(Fragment self, IMP::Ints o)"""
6236  return _IMP_atom.Fragment_set_residue_indexes(self, o)
6237 
6238 
6239  def get_residue_indexes(self):
6240  """get_residue_indexes(Fragment self) -> IMP::Ints"""
6241  return _IMP_atom.Fragment_get_residue_indexes(self)
6242 
6243 
6244  def get_contains_residue(self, rindex):
6245  """get_contains_residue(Fragment self, int rindex) -> bool"""
6246  return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6247 
6248 
6249  def __init__(self, *args):
6250  """
6251  __init__(IMP::atom::Fragment self) -> Fragment
6252  __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6253  __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6254  """
6255  this = _IMP_atom.new_Fragment(*args)
6256  try:
6257  self.this.append(this)
6258  except __builtin__.Exception:
6259  self.this = this
6260 
6261  def get_is_setup(*args):
6262  """
6263  get_is_setup(Model m, ParticleIndex pi) -> bool
6264  get_is_setup(_ParticleAdaptor p) -> bool
6265  """
6266  return _IMP_atom.Fragment_get_is_setup(*args)
6267 
6268  get_is_setup = staticmethod(get_is_setup)
6269 
6270  def show(self, *args):
6271  """
6272  show(Fragment self, _ostream out)
6273  show(Fragment self)
6274  """
6275  return _IMP_atom.Fragment_show(self, *args)
6276 
6277 
6278  def setup_particle(*args):
6279  """
6280  setup_particle(Model m, ParticleIndex pi) -> Fragment
6281  setup_particle(_ParticleAdaptor decorator) -> Fragment
6282  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6283  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6284  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6285  setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6286  """
6287  return _IMP_atom.Fragment_setup_particle(*args)
6288 
6289  setup_particle = staticmethod(setup_particle)
6290 
6291  def add_attribute(self, *args):
6292  """
6293  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6294  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6295  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6296  add_attribute(Fragment self, StringKey a0, IMP::String a1)
6297  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6298  add_attribute(Fragment self, ObjectKey a0, Object a1)
6299  """
6300  return _IMP_atom.Fragment_add_attribute(self, *args)
6301 
6302 
6303  def get_value(self, *args):
6304  """
6305  get_value(Fragment self, FloatKey a0) -> IMP::Float
6306  get_value(Fragment self, IntKey a0) -> IMP::Int
6307  get_value(Fragment self, StringKey a0) -> IMP::String
6308  get_value(Fragment self, ParticleIndexKey a0) -> Particle
6309  get_value(Fragment self, ObjectKey a0) -> Object
6310  """
6311  return _IMP_atom.Fragment_get_value(self, *args)
6312 
6313 
6314  def set_value(self, *args):
6315  """
6316  set_value(Fragment self, FloatKey a0, IMP::Float a1)
6317  set_value(Fragment self, IntKey a0, IMP::Int a1)
6318  set_value(Fragment self, StringKey a0, IMP::String a1)
6319  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6320  set_value(Fragment self, ObjectKey a0, Object a1)
6321  """
6322  return _IMP_atom.Fragment_set_value(self, *args)
6323 
6324 
6325  def remove_attribute(self, *args):
6326  """
6327  remove_attribute(Fragment self, FloatKey a0)
6328  remove_attribute(Fragment self, IntKey a0)
6329  remove_attribute(Fragment self, StringKey a0)
6330  remove_attribute(Fragment self, ParticleIndexKey a0)
6331  remove_attribute(Fragment self, ObjectKey a0)
6332  """
6333  return _IMP_atom.Fragment_remove_attribute(self, *args)
6334 
6335 
6336  def has_attribute(self, *args):
6337  """
6338  has_attribute(Fragment self, FloatKey a0) -> bool
6339  has_attribute(Fragment self, IntKey a0) -> bool
6340  has_attribute(Fragment self, StringKey a0) -> bool
6341  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6342  has_attribute(Fragment self, ObjectKey a0) -> bool
6343  """
6344  return _IMP_atom.Fragment_has_attribute(self, *args)
6345 
6346 
6347  def get_derivative(self, a0):
6348  """get_derivative(Fragment self, FloatKey a0) -> double"""
6349  return _IMP_atom.Fragment_get_derivative(self, a0)
6350 
6351 
6352  def get_name(self):
6353  """get_name(Fragment self) -> std::string"""
6354  return _IMP_atom.Fragment_get_name(self)
6355 
6356 
6357  def clear_caches(self):
6358  """clear_caches(Fragment self)"""
6359  return _IMP_atom.Fragment_clear_caches(self)
6360 
6361 
6362  def set_name(self, a0):
6363  """set_name(Fragment self, std::string a0)"""
6364  return _IMP_atom.Fragment_set_name(self, a0)
6365 
6366 
6367  def set_check_level(self, a0):
6368  """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6369  return _IMP_atom.Fragment_set_check_level(self, a0)
6370 
6371 
6372  def add_to_derivative(self, a0, a1, a2):
6373  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6374  return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6375 
6376 
6377  def set_is_optimized(self, a0, a1):
6378  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6379  return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6380 
6381 
6382  def get_is_optimized(self, a0):
6383  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6384  return _IMP_atom.Fragment_get_is_optimized(self, a0)
6385 
6386 
6387  def get_check_level(self):
6388  """get_check_level(Fragment self) -> IMP::CheckLevel"""
6389  return _IMP_atom.Fragment_get_check_level(self)
6390 
6391 
6392  def __eq__(self, *args):
6393  """
6394  __eq__(Fragment self, Fragment o) -> bool
6395  __eq__(Fragment self, Particle d) -> bool
6396  """
6397  return _IMP_atom.Fragment___eq__(self, *args)
6398 
6399 
6400  def __ne__(self, *args):
6401  """
6402  __ne__(Fragment self, Fragment o) -> bool
6403  __ne__(Fragment self, Particle d) -> bool
6404  """
6405  return _IMP_atom.Fragment___ne__(self, *args)
6406 
6407 
6408  def __le__(self, *args):
6409  """
6410  __le__(Fragment self, Fragment o) -> bool
6411  __le__(Fragment self, Particle d) -> bool
6412  """
6413  return _IMP_atom.Fragment___le__(self, *args)
6414 
6415 
6416  def __lt__(self, *args):
6417  """
6418  __lt__(Fragment self, Fragment o) -> bool
6419  __lt__(Fragment self, Particle d) -> bool
6420  """
6421  return _IMP_atom.Fragment___lt__(self, *args)
6422 
6423 
6424  def __ge__(self, *args):
6425  """
6426  __ge__(Fragment self, Fragment o) -> bool
6427  __ge__(Fragment self, Particle d) -> bool
6428  """
6429  return _IMP_atom.Fragment___ge__(self, *args)
6430 
6431 
6432  def __gt__(self, *args):
6433  """
6434  __gt__(Fragment self, Fragment o) -> bool
6435  __gt__(Fragment self, Particle d) -> bool
6436  """
6437  return _IMP_atom.Fragment___gt__(self, *args)
6438 
6439 
6440  def __hash__(self):
6441  """__hash__(Fragment self) -> std::size_t"""
6442  return _IMP_atom.Fragment___hash__(self)
6443 
6444 
6445  def __str__(self):
6446  """__str__(Fragment self) -> std::string"""
6447  return _IMP_atom.Fragment___str__(self)
6448 
6449 
6450  def __repr__(self):
6451  """__repr__(Fragment self) -> std::string"""
6452  return _IMP_atom.Fragment___repr__(self)
6453 
6454  __swig_destroy__ = _IMP_atom.delete_Fragment
6455  __del__ = lambda self: None
6456 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6457 Fragment_swigregister(Fragment)
6458 
6459 def Fragment_get_is_setup(*args):
6460  """
6461  get_is_setup(Model m, ParticleIndex pi) -> bool
6462  Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6463  """
6464  return _IMP_atom.Fragment_get_is_setup(*args)
6465 
6466 def Fragment_setup_particle(*args):
6467  """
6468  setup_particle(Model m, ParticleIndex pi) -> Fragment
6469  setup_particle(_ParticleAdaptor decorator) -> Fragment
6470  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6471  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6472  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6473  Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6474  """
6475  return _IMP_atom.Fragment_setup_particle(*args)
6476 
6477 class StereochemistryPairFilter(IMP.PairPredicate):
6478  """Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6479 
6480  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6481 
6482  def __init__(self):
6483  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6484  this = _IMP_atom.new_StereochemistryPairFilter()
6485  try:
6486  self.this.append(this)
6487  except __builtin__.Exception:
6488  self.this = this
6489 
6490  def set_bonds(self, bonds):
6491  """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6492  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6493 
6494 
6495  def set_angles(self, angles):
6496  """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6497  return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6498 
6499 
6500  def set_dihedrals(self, dihedrals):
6501  """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6502  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6503 
6504 
6505  def do_get_inputs(self, m, pis):
6506  """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6507  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6508 
6509 
6510  def get_value(self, *args):
6511  """
6512  get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6513  get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6514  """
6515  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6516 
6517 
6518  def get_value_index(self, *args):
6519  """
6520  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6521  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6522  """
6523  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6524 
6525 
6526  def get_version_info(self):
6527  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6528  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6529 
6530 
6531  def __str__(self):
6532  """__str__(StereochemistryPairFilter self) -> std::string"""
6533  return _IMP_atom.StereochemistryPairFilter___str__(self)
6534 
6535 
6536  def __repr__(self):
6537  """__repr__(StereochemistryPairFilter self) -> std::string"""
6538  return _IMP_atom.StereochemistryPairFilter___repr__(self)
6539 
6540 
6541  @staticmethod
6542  def get_from(o):
6543  return _object_cast_to_StereochemistryPairFilter(o)
6544 
6545 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6546 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6547 
6548 class SoapPairFilter(IMP.PairPredicate):
6549  """Proxy of C++ IMP::atom::SoapPairFilter class."""
6550 
6551  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6552 
6553  def __init__(self, library):
6554  """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6555  this = _IMP_atom.new_SoapPairFilter(library)
6556  try:
6557  self.this.append(this)
6558  except __builtin__.Exception:
6559  self.this = this
6560 
6561  def do_get_inputs(self, m, pis):
6562  """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6563  return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6564 
6565 
6566  def get_value(self, *args):
6567  """
6568  get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6569  get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6570  """
6571  return _IMP_atom.SoapPairFilter_get_value(self, *args)
6572 
6573 
6574  def get_value_index(self, *args):
6575  """
6576  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6577  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6578  """
6579  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6580 
6581 
6582  def get_version_info(self):
6583  """get_version_info(SoapPairFilter self) -> VersionInfo"""
6584  return _IMP_atom.SoapPairFilter_get_version_info(self)
6585 
6586 
6587  def __str__(self):
6588  """__str__(SoapPairFilter self) -> std::string"""
6589  return _IMP_atom.SoapPairFilter___str__(self)
6590 
6591 
6592  def __repr__(self):
6593  """__repr__(SoapPairFilter self) -> std::string"""
6594  return _IMP_atom.SoapPairFilter___repr__(self)
6595 
6596 
6597  @staticmethod
6598  def get_from(o):
6599  return _object_cast_to_SoapPairFilter(o)
6600 
6601 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6602 SoapPairFilter_swigregister(SoapPairFilter)
6603 
6604 class Mass(IMP.Decorator):
6605  """Proxy of C++ IMP::atom::Mass class."""
6606 
6607  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6608 
6609  def get_mass(self):
6610  """get_mass(Mass self) -> IMP::Float"""
6611  return _IMP_atom.Mass_get_mass(self)
6612 
6613 
6614  def set_mass(self, d):
6615  """set_mass(Mass self, IMP::Float d)"""
6616  return _IMP_atom.Mass_set_mass(self, d)
6617 
6618 
6619  def __init__(self, *args):
6620  """
6621  __init__(IMP::atom::Mass self) -> Mass
6622  __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6623  __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6624  """
6625  this = _IMP_atom.new_Mass(*args)
6626  try:
6627  self.this.append(this)
6628  except __builtin__.Exception:
6629  self.this = this
6630 
6631  def get_is_setup(*args):
6632  """
6633  get_is_setup(Model m, ParticleIndex pi) -> bool
6634  get_is_setup(_ParticleAdaptor p) -> bool
6635  """
6636  return _IMP_atom.Mass_get_is_setup(*args)
6637 
6638  get_is_setup = staticmethod(get_is_setup)
6639 
6640  def show(self, *args):
6641  """
6642  show(Mass self, _ostream out)
6643  show(Mass self)
6644  """
6645  return _IMP_atom.Mass_show(self, *args)
6646 
6647 
6648  def setup_particle(*args):
6649  """
6650  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6651  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6652  """
6653  return _IMP_atom.Mass_setup_particle(*args)
6654 
6655  setup_particle = staticmethod(setup_particle)
6656 
6657  def get_mass_key():
6658  """get_mass_key() -> FloatKey"""
6659  return _IMP_atom.Mass_get_mass_key()
6660 
6661  get_mass_key = staticmethod(get_mass_key)
6662 
6663  def add_attribute(self, *args):
6664  """
6665  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6666  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6667  add_attribute(Mass self, IntKey a0, IMP::Int a1)
6668  add_attribute(Mass self, StringKey a0, IMP::String a1)
6669  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6670  add_attribute(Mass self, ObjectKey a0, Object a1)
6671  """
6672  return _IMP_atom.Mass_add_attribute(self, *args)
6673 
6674 
6675  def get_value(self, *args):
6676  """
6677  get_value(Mass self, FloatKey a0) -> IMP::Float
6678  get_value(Mass self, IntKey a0) -> IMP::Int
6679  get_value(Mass self, StringKey a0) -> IMP::String
6680  get_value(Mass self, ParticleIndexKey a0) -> Particle
6681  get_value(Mass self, ObjectKey a0) -> Object
6682  """
6683  return _IMP_atom.Mass_get_value(self, *args)
6684 
6685 
6686  def set_value(self, *args):
6687  """
6688  set_value(Mass self, FloatKey a0, IMP::Float a1)
6689  set_value(Mass self, IntKey a0, IMP::Int a1)
6690  set_value(Mass self, StringKey a0, IMP::String a1)
6691  set_value(Mass self, ParticleIndexKey a0, Particle a1)
6692  set_value(Mass self, ObjectKey a0, Object a1)
6693  """
6694  return _IMP_atom.Mass_set_value(self, *args)
6695 
6696 
6697  def remove_attribute(self, *args):
6698  """
6699  remove_attribute(Mass self, FloatKey a0)
6700  remove_attribute(Mass self, IntKey a0)
6701  remove_attribute(Mass self, StringKey a0)
6702  remove_attribute(Mass self, ParticleIndexKey a0)
6703  remove_attribute(Mass self, ObjectKey a0)
6704  """
6705  return _IMP_atom.Mass_remove_attribute(self, *args)
6706 
6707 
6708  def has_attribute(self, *args):
6709  """
6710  has_attribute(Mass self, FloatKey a0) -> bool
6711  has_attribute(Mass self, IntKey a0) -> bool
6712  has_attribute(Mass self, StringKey a0) -> bool
6713  has_attribute(Mass self, ParticleIndexKey a0) -> bool
6714  has_attribute(Mass self, ObjectKey a0) -> bool
6715  """
6716  return _IMP_atom.Mass_has_attribute(self, *args)
6717 
6718 
6719  def get_derivative(self, a0):
6720  """get_derivative(Mass self, FloatKey a0) -> double"""
6721  return _IMP_atom.Mass_get_derivative(self, a0)
6722 
6723 
6724  def get_name(self):
6725  """get_name(Mass self) -> std::string"""
6726  return _IMP_atom.Mass_get_name(self)
6727 
6728 
6729  def clear_caches(self):
6730  """clear_caches(Mass self)"""
6731  return _IMP_atom.Mass_clear_caches(self)
6732 
6733 
6734  def set_name(self, a0):
6735  """set_name(Mass self, std::string a0)"""
6736  return _IMP_atom.Mass_set_name(self, a0)
6737 
6738 
6739  def set_check_level(self, a0):
6740  """set_check_level(Mass self, IMP::CheckLevel a0)"""
6741  return _IMP_atom.Mass_set_check_level(self, a0)
6742 
6743 
6744  def add_to_derivative(self, a0, a1, a2):
6745  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6746  return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6747 
6748 
6749  def set_is_optimized(self, a0, a1):
6750  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6751  return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6752 
6753 
6754  def get_is_optimized(self, a0):
6755  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6756  return _IMP_atom.Mass_get_is_optimized(self, a0)
6757 
6758 
6759  def get_check_level(self):
6760  """get_check_level(Mass self) -> IMP::CheckLevel"""
6761  return _IMP_atom.Mass_get_check_level(self)
6762 
6763 
6764  def __eq__(self, *args):
6765  """
6766  __eq__(Mass self, Mass o) -> bool
6767  __eq__(Mass self, Particle d) -> bool
6768  """
6769  return _IMP_atom.Mass___eq__(self, *args)
6770 
6771 
6772  def __ne__(self, *args):
6773  """
6774  __ne__(Mass self, Mass o) -> bool
6775  __ne__(Mass self, Particle d) -> bool
6776  """
6777  return _IMP_atom.Mass___ne__(self, *args)
6778 
6779 
6780  def __le__(self, *args):
6781  """
6782  __le__(Mass self, Mass o) -> bool
6783  __le__(Mass self, Particle d) -> bool
6784  """
6785  return _IMP_atom.Mass___le__(self, *args)
6786 
6787 
6788  def __lt__(self, *args):
6789  """
6790  __lt__(Mass self, Mass o) -> bool
6791  __lt__(Mass self, Particle d) -> bool
6792  """
6793  return _IMP_atom.Mass___lt__(self, *args)
6794 
6795 
6796  def __ge__(self, *args):
6797  """
6798  __ge__(Mass self, Mass o) -> bool
6799  __ge__(Mass self, Particle d) -> bool
6800  """
6801  return _IMP_atom.Mass___ge__(self, *args)
6802 
6803 
6804  def __gt__(self, *args):
6805  """
6806  __gt__(Mass self, Mass o) -> bool
6807  __gt__(Mass self, Particle d) -> bool
6808  """
6809  return _IMP_atom.Mass___gt__(self, *args)
6810 
6811 
6812  def __hash__(self):
6813  """__hash__(Mass self) -> std::size_t"""
6814  return _IMP_atom.Mass___hash__(self)
6815 
6816 
6817  def __str__(self):
6818  """__str__(Mass self) -> std::string"""
6819  return _IMP_atom.Mass___str__(self)
6820 
6821 
6822  def __repr__(self):
6823  """__repr__(Mass self) -> std::string"""
6824  return _IMP_atom.Mass___repr__(self)
6825 
6826  __swig_destroy__ = _IMP_atom.delete_Mass
6827  __del__ = lambda self: None
6828 Mass_swigregister = _IMP_atom.Mass_swigregister
6829 Mass_swigregister(Mass)
6830 
6831 def Mass_get_is_setup(*args):
6832  """
6833  get_is_setup(Model m, ParticleIndex pi) -> bool
6834  Mass_get_is_setup(_ParticleAdaptor p) -> bool
6835  """
6836  return _IMP_atom.Mass_get_is_setup(*args)
6837 
6838 def Mass_setup_particle(*args):
6839  """
6840  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6841  Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6842  """
6843  return _IMP_atom.Mass_setup_particle(*args)
6844 
6845 def Mass_get_mass_key():
6846  """Mass_get_mass_key() -> FloatKey"""
6847  return _IMP_atom.Mass_get_mass_key()
6848 
6849 class BondedPairFilter(IMP.PairPredicate):
6850  """Proxy of C++ IMP::atom::BondedPairFilter class."""
6851 
6852  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6853 
6854  def __init__(self):
6855  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
6856  this = _IMP_atom.new_BondedPairFilter()
6857  try:
6858  self.this.append(this)
6859  except __builtin__.Exception:
6860  self.this = this
6861 
6862  def do_get_inputs(self, m, pis):
6863  """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6864  return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6865 
6866 
6867  def get_value(self, *args):
6868  """
6869  get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6870  get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6871  """
6872  return _IMP_atom.BondedPairFilter_get_value(self, *args)
6873 
6874 
6875  def get_value_index(self, *args):
6876  """
6877  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6878  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6879  """
6880  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6881 
6882 
6883  def get_version_info(self):
6884  """get_version_info(BondedPairFilter self) -> VersionInfo"""
6885  return _IMP_atom.BondedPairFilter_get_version_info(self)
6886 
6887 
6888  def __str__(self):
6889  """__str__(BondedPairFilter self) -> std::string"""
6890  return _IMP_atom.BondedPairFilter___str__(self)
6891 
6892 
6893  def __repr__(self):
6894  """__repr__(BondedPairFilter self) -> std::string"""
6895  return _IMP_atom.BondedPairFilter___repr__(self)
6896 
6897 
6898  @staticmethod
6899  def get_from(o):
6900  return _object_cast_to_BondedPairFilter(o)
6901 
6902 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
6903 BondedPairFilter_swigregister(BondedPairFilter)
6904 
6905 class Mol2Selector(IMP.Object):
6906  """Proxy of C++ IMP::atom::Mol2Selector class."""
6907 
6908  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6909 
6910  def __init__(self, *args, **kwargs):
6911  raise AttributeError("No constructor defined - class is abstract")
6912 
6913  def get_is_selected(self, atom_line):
6914  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6915  return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6916 
6917  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6918  __del__ = lambda self: None
6919 
6920  def __str__(self):
6921  """__str__(Mol2Selector self) -> std::string"""
6922  return _IMP_atom.Mol2Selector___str__(self)
6923 
6924 
6925  def __repr__(self):
6926  """__repr__(Mol2Selector self) -> std::string"""
6927  return _IMP_atom.Mol2Selector___repr__(self)
6928 
6929 
6930  @staticmethod
6931  def get_from(o):
6932  return _object_cast_to_Mol2Selector(o)
6933 
6934 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
6935 Mol2Selector_swigregister(Mol2Selector)
6936 
6937 class AllMol2Selector(Mol2Selector):
6938  """Proxy of C++ IMP::atom::AllMol2Selector class."""
6939 
6940  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6941 
6942  def __str__(self):
6943  """__str__(AllMol2Selector self) -> std::string"""
6944  return _IMP_atom.AllMol2Selector___str__(self)
6945 
6946 
6947  def __repr__(self):
6948  """__repr__(AllMol2Selector self) -> std::string"""
6949  return _IMP_atom.AllMol2Selector___repr__(self)
6950 
6951 
6952  @staticmethod
6953  def get_from(o):
6954  return _object_cast_to_AllMol2Selector(o)
6955 
6956 
6957  def __init__(self):
6958  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
6959  this = _IMP_atom.new_AllMol2Selector()
6960  try:
6961  self.this.append(this)
6962  except __builtin__.Exception:
6963  self.this = this
6964  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6965  __del__ = lambda self: None
6966 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
6967 AllMol2Selector_swigregister(AllMol2Selector)
6968 
6969 class NonHydrogenMol2Selector(Mol2Selector):
6970  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6971 
6972  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6973 
6974  def __str__(self):
6975  """__str__(NonHydrogenMol2Selector self) -> std::string"""
6976  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6977 
6978 
6979  def __repr__(self):
6980  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
6981  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6982 
6983 
6984  @staticmethod
6985  def get_from(o):
6986  return _object_cast_to_NonHydrogenMol2Selector(o)
6987 
6988 
6989  def __init__(self):
6990  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6991  this = _IMP_atom.new_NonHydrogenMol2Selector()
6992  try:
6993  self.this.append(this)
6994  except __builtin__.Exception:
6995  self.this = this
6996  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6997  __del__ = lambda self: None
6998 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
6999 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7000 
7001 
7002 def read_mol2(mol2_file, model, mol2sel=None):
7003  """
7004  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7005  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7006  """
7007  return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7008 
7009 def write_mol2(rhd, file_name):
7010  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7011  return _IMP_atom.write_mol2(rhd, file_name)
7012 class SecondaryStructureResidue(IMP.Decorator):
7013  """Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
7014 
7015  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7016 
7017  def __init__(self, *args):
7018  """
7019  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7020  __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7021  __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7022  """
7023  this = _IMP_atom.new_SecondaryStructureResidue(*args)
7024  try:
7025  self.this.append(this)
7026  except __builtin__.Exception:
7027  self.this = this
7028 
7029  def show(self, *args):
7030  """
7031  show(SecondaryStructureResidue self, _ostream out)
7032  show(SecondaryStructureResidue self)
7033  """
7034  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7035 
7036 
7037  def setup_particle(*args):
7038  """
7039  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7040  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7041  setup_particle(Particle res_p) -> SecondaryStructureResidue
7042  """
7043  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7044 
7045  setup_particle = staticmethod(setup_particle)
7046 
7047  def get_is_setup(*args):
7048  """
7049  get_is_setup(_ParticleAdaptor p) -> bool
7050  get_is_setup(Model m, ParticleIndex pi) -> bool
7051  """
7052  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7053 
7054  get_is_setup = staticmethod(get_is_setup)
7055 
7056  def get_particle(self):
7057  """get_particle(SecondaryStructureResidue self) -> Particle"""
7058  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7059 
7060 
7061  def get_all_probabilities(self):
7062  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7063  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7064 
7065 
7066  def get_prob_helix(self):
7067  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7068  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7069 
7070 
7071  def set_prob_helix(self, t):
7072  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7073  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7074 
7075 
7076  def get_prob_strand(self):
7077  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7078  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7079 
7080 
7081  def set_prob_strand(self, t):
7082  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7083  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7084 
7085 
7086  def get_prob_coil(self):
7087  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7088  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7089 
7090 
7091  def set_prob_coil(self, t):
7092  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7093  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7094 
7095 
7096  def get_prob_helix_key():
7097  """get_prob_helix_key() -> FloatKey"""
7098  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7099 
7100  get_prob_helix_key = staticmethod(get_prob_helix_key)
7101 
7102  def get_prob_strand_key():
7103  """get_prob_strand_key() -> FloatKey"""
7104  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7105 
7106  get_prob_strand_key = staticmethod(get_prob_strand_key)
7107 
7108  def get_prob_coil_key():
7109  """get_prob_coil_key() -> FloatKey"""
7110  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7111 
7112  get_prob_coil_key = staticmethod(get_prob_coil_key)
7113 
7114  def add_attribute(self, *args):
7115  """
7116  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7117  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7118  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7119  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7120  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7121  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7122  """
7123  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7124 
7125 
7126  def get_value(self, *args):
7127  """
7128  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7129  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7130  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7131  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7132  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7133  """
7134  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7135 
7136 
7137  def set_value(self, *args):
7138  """
7139  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7140  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7141  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7142  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7143  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7144  """
7145  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7146 
7147 
7148  def remove_attribute(self, *args):
7149  """
7150  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7151  remove_attribute(SecondaryStructureResidue self, IntKey a0)
7152  remove_attribute(SecondaryStructureResidue self, StringKey a0)
7153  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7154  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7155  """
7156  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7157 
7158 
7159  def has_attribute(self, *args):
7160  """
7161  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7162  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7163  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7164  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7165  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7166  """
7167  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7168 
7169 
7170  def get_derivative(self, a0):
7171  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7172  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7173 
7174 
7175  def get_name(self):
7176  """get_name(SecondaryStructureResidue self) -> std::string"""
7177  return _IMP_atom.SecondaryStructureResidue_get_name(self)
7178 
7179 
7180  def clear_caches(self):
7181  """clear_caches(SecondaryStructureResidue self)"""
7182  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7183 
7184 
7185  def set_name(self, a0):
7186  """set_name(SecondaryStructureResidue self, std::string a0)"""
7187  return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7188 
7189 
7190  def set_check_level(self, a0):
7191  """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7192  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7193 
7194 
7195  def add_to_derivative(self, a0, a1, a2):
7196  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7197  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7198 
7199 
7200  def set_is_optimized(self, a0, a1):
7201  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7202  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7203 
7204 
7205  def get_is_optimized(self, a0):
7206  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7207  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7208 
7209 
7210  def get_check_level(self):
7211  """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7212  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7213 
7214 
7215  def __eq__(self, *args):
7216  """
7217  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7218  __eq__(SecondaryStructureResidue self, Particle d) -> bool
7219  """
7220  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7221 
7222 
7223  def __ne__(self, *args):
7224  """
7225  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7226  __ne__(SecondaryStructureResidue self, Particle d) -> bool
7227  """
7228  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7229 
7230 
7231  def __le__(self, *args):
7232  """
7233  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7234  __le__(SecondaryStructureResidue self, Particle d) -> bool
7235  """
7236  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7237 
7238 
7239  def __lt__(self, *args):
7240  """
7241  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7242  __lt__(SecondaryStructureResidue self, Particle d) -> bool
7243  """
7244  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7245 
7246 
7247  def __ge__(self, *args):
7248  """
7249  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7250  __ge__(SecondaryStructureResidue self, Particle d) -> bool
7251  """
7252  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7253 
7254 
7255  def __gt__(self, *args):
7256  """
7257  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7258  __gt__(SecondaryStructureResidue self, Particle d) -> bool
7259  """
7260  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7261 
7262 
7263  def __hash__(self):
7264  """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7265  return _IMP_atom.SecondaryStructureResidue___hash__(self)
7266 
7267 
7268  def __str__(self):
7269  """__str__(SecondaryStructureResidue self) -> std::string"""
7270  return _IMP_atom.SecondaryStructureResidue___str__(self)
7271 
7272 
7273  def __repr__(self):
7274  """__repr__(SecondaryStructureResidue self) -> std::string"""
7275  return _IMP_atom.SecondaryStructureResidue___repr__(self)
7276 
7277  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7278  __del__ = lambda self: None
7279 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7280 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7281 
7282 def SecondaryStructureResidue_setup_particle(*args):
7283  """
7284  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7285  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7286  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7287  """
7288  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7289 
7290 def SecondaryStructureResidue_get_is_setup(*args):
7291  """
7292  get_is_setup(_ParticleAdaptor p) -> bool
7293  SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7294  """
7295  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7296 
7297 def SecondaryStructureResidue_get_prob_helix_key():
7298  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7299  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7300 
7301 def SecondaryStructureResidue_get_prob_strand_key():
7302  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7303  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7304 
7305 def SecondaryStructureResidue_get_prob_coil_key():
7306  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7307  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7308 
7309 
7310 def setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res=False):
7311  """
7312  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7313  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7314  """
7315  return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7316 
7317 def setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res=False):
7318  """
7319  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
7320  setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7321  """
7322  return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7323 
7324 def get_secondary_structure_match_score(ssr1, ssr2):
7325  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7326  return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7327 
7328 def read_psipred(*args):
7329  """
7330  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7331  read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7332  """
7333  return _IMP_atom.read_psipred(*args)
7334 class _ADopeBase(IMP.PairScore):
7335  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class."""
7336 
7337  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7338  __repr__ = _swig_repr
7339 
7340  def __init__(self, *args):
7341  """
7342  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7343  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7344  """
7345  this = _IMP_atom.new__ADopeBase(*args)
7346  try:
7347  self.this.append(this)
7348  except __builtin__.Exception:
7349  self.this = this
7350 
7351  def do_get_inputs(self, m, pis):
7352  """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7353  return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7354 
7355 
7356  def get_score_functor(self):
7357  """get_score_functor(_ADopeBase self) -> Dope"""
7358  return _IMP_atom._ADopeBase_get_score_functor(self)
7359 
7360 
7361  def get_version_info(self):
7362  """get_version_info(_ADopeBase self) -> VersionInfo"""
7363  return _IMP_atom._ADopeBase_get_version_info(self)
7364 
7365 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7366 _ADopeBase_swigregister(_ADopeBase)
7367 
7368 class _BDopeBase(IMP.PairScore):
7369  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class."""
7370 
7371  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7372  __repr__ = _swig_repr
7373 
7374  def __init__(self, *args):
7375  """
7376  __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
7377  __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
7378  """
7379  this = _IMP_atom.new__BDopeBase(*args)
7380  try:
7381  self.this.append(this)
7382  except __builtin__.Exception:
7383  self.this = this
7384 
7385  def do_get_inputs(self, m, pis):
7386  """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7387  return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7388 
7389 
7390  def get_score_functor(self):
7391  """get_score_functor(_BDopeBase self) -> _DopeBase"""
7392  return _IMP_atom._BDopeBase_get_score_functor(self)
7393 
7394 
7395  def get_version_info(self):
7396  """get_version_info(_BDopeBase self) -> VersionInfo"""
7397  return _IMP_atom._BDopeBase_get_version_info(self)
7398 
7399 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7400 _BDopeBase_swigregister(_BDopeBase)
7401 
7402 class _OrientedSoapBase(IMP.PairScore):
7403  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class."""
7404 
7405  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7406  __repr__ = _swig_repr
7407 
7408  def __init__(self, *args):
7409  """
7410  __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
7411  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7412  """
7413  this = _IMP_atom.new__OrientedSoapBase(*args)
7414  try:
7415  self.this.append(this)
7416  except __builtin__.Exception:
7417  self.this = this
7418 
7419  def do_get_inputs(self, m, pis):
7420  """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7421  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7422 
7423 
7424  def get_score_functor(self):
7425  """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7426  return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7427 
7428 
7429  def get_version_info(self):
7430  """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7431  return _IMP_atom._OrientedSoapBase_get_version_info(self)
7432 
7433 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7434 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7435 
7436 class _SPSFTB(IMP.PairScore):
7437  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class."""
7438 
7439  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7440  __repr__ = _swig_repr
7441 
7442  def __init__(self, *args):
7443  """
7444  __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
7445  __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
7446  """
7447  this = _IMP_atom.new__SPSFTB(*args)
7448  try:
7449  self.this.append(this)
7450  except __builtin__.Exception:
7451  self.this = this
7452 
7453  def do_get_inputs(self, m, pis):
7454  """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7455  return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7456 
7457 
7458  def get_score_functor(self):
7459  """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7460  return _IMP_atom._SPSFTB_get_score_functor(self)
7461 
7462 
7463  def get_version_info(self):
7464  """get_version_info(_SPSFTB self) -> VersionInfo"""
7465  return _IMP_atom._SPSFTB_get_version_info(self)
7466 
7467 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7468 _SPSFTB_swigregister(_SPSFTB)
7469 
7470 class _SPSTF(_SPSFTB):
7471  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class."""
7472 
7473  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7474  __repr__ = _swig_repr
7475 
7476  def __init__(self, *args):
7477  """
7478  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7479  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7480  """
7481  this = _IMP_atom.new__SPSTF(*args)
7482  try:
7483  self.this.append(this)
7484  except __builtin__.Exception:
7485  self.this = this
7486  __swig_destroy__ = _IMP_atom.delete__SPSTF
7487  __del__ = lambda self: None
7488 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7489 _SPSTF_swigregister(_SPSTF)
7490 
7491 class _SPSFT(_BDopeBase):
7492  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class."""
7493 
7494  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7495  __repr__ = _swig_repr
7496 
7497  def __init__(self, *args):
7498  """
7499  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7500  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7501  """
7502  this = _IMP_atom.new__SPSFT(*args)
7503  try:
7504  self.this.append(this)
7505  except __builtin__.Exception:
7506  self.this = this
7507  __swig_destroy__ = _IMP_atom.delete__SPSFT
7508  __del__ = lambda self: None
7509 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7510 _SPSFT_swigregister(_SPSFT)
7511 
7512 class ProteinLigandAtomPairScore(_SPSTF):
7513  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7514 
7515  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7516 
7517  def __init__(self, *args):
7518  """
7519  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7520  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7521  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7522  """
7523  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7524  try:
7525  self.this.append(this)
7526  except __builtin__.Exception:
7527  self.this = this
7528 
7529  def get_maximum_distance(self):
7530  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7531  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7532 
7533 
7534  def __str__(self):
7535  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7536  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7537 
7538 
7539  def __repr__(self):
7540  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7541  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7542 
7543 
7544  @staticmethod
7545  def get_from(o):
7546  return _object_cast_to_ProteinLigandAtomPairScore(o)
7547 
7548  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7549  __del__ = lambda self: None
7550 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7551 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7552 
7553 class ProteinLigandRestraint(IMP.container.PairsRestraint):
7554  """Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7555 
7556  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7557 
7558  def __init__(self, *args):
7559  """
7560  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7561  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7562  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7563  """
7564  this = _IMP_atom.new_ProteinLigandRestraint(*args)
7565  try:
7566  self.this.append(this)
7567  except __builtin__.Exception:
7568  self.this = this
7569 
7570  def __str__(self):
7571  """__str__(ProteinLigandRestraint self) -> std::string"""
7572  return _IMP_atom.ProteinLigandRestraint___str__(self)
7573 
7574 
7575  def __repr__(self):
7576  """__repr__(ProteinLigandRestraint self) -> std::string"""
7577  return _IMP_atom.ProteinLigandRestraint___repr__(self)
7578 
7579 
7580  @staticmethod
7581  def get_from(o):
7582  return _object_cast_to_ProteinLigandRestraint(o)
7583 
7584  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7585  __del__ = lambda self: None
7586 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7587 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7588 
7589 
7591  """add_protein_ligand_score_data(Hierarchy h)"""
7592  return _IMP_atom.add_protein_ligand_score_data(h)
7593 class AtomType(IMP._Value):
7594  """Proxy of C++ IMP::Key<(8974343)> class."""
7595 
7596  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7597 
7598  def __init__(self, *args):
7599  """
7600  __init__(IMP::Key<(8974343)> self) -> AtomType
7601  __init__(IMP::Key<(8974343)> self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7602  __init__(IMP::Key<(8974343)> self, std::string const & c) -> AtomType
7603  __init__(IMP::Key<(8974343)> self, unsigned int i) -> AtomType
7604  """
7605  this = _IMP_atom.new_AtomType(*args)
7606  try:
7607  self.this.append(this)
7608  except __builtin__.Exception:
7609  self.this = this
7610 
7611  def add_key(sc):
7612  """add_key(std::string sc) -> unsigned int"""
7613  return _IMP_atom.AtomType_add_key(sc)
7614 
7615  add_key = staticmethod(add_key)
7616 
7617  def get_key_exists(sc):
7618  """get_key_exists(std::string sc) -> bool"""
7619  return _IMP_atom.AtomType_get_key_exists(sc)
7620 
7621  get_key_exists = staticmethod(get_key_exists)
7622 
7623  def get_string(self):
7624  """get_string(AtomType self) -> std::string const"""
7625  return _IMP_atom.AtomType_get_string(self)
7626 
7627 
7628  def __cmp__(self, o):
7629  """__cmp__(AtomType self, AtomType o) -> int"""
7630  return _IMP_atom.AtomType___cmp__(self, o)
7631 
7632 
7633  def __eq__(self, o):
7634  """__eq__(AtomType self, AtomType o) -> bool"""
7635  return _IMP_atom.AtomType___eq__(self, o)
7636 
7637 
7638  def __ne__(self, o):
7639  """__ne__(AtomType self, AtomType o) -> bool"""
7640  return _IMP_atom.AtomType___ne__(self, o)
7641 
7642 
7643  def __lt__(self, o):
7644  """__lt__(AtomType self, AtomType o) -> bool"""
7645  return _IMP_atom.AtomType___lt__(self, o)
7646 
7647 
7648  def __gt__(self, o):
7649  """__gt__(AtomType self, AtomType o) -> bool"""
7650  return _IMP_atom.AtomType___gt__(self, o)
7651 
7652 
7653  def __ge__(self, o):
7654  """__ge__(AtomType self, AtomType o) -> bool"""
7655  return _IMP_atom.AtomType___ge__(self, o)
7656 
7657 
7658  def __le__(self, o):
7659  """__le__(AtomType self, AtomType o) -> bool"""
7660  return _IMP_atom.AtomType___le__(self, o)
7661 
7662 
7663  def __hash__(self):
7664  """__hash__(AtomType self) -> std::size_t"""
7665  return _IMP_atom.AtomType___hash__(self)
7666 
7667 
7668  def show(self, *args):
7669  """
7670  show(AtomType self, _ostream out)
7671  show(AtomType self)
7672  """
7673  return _IMP_atom.AtomType_show(self, *args)
7674 
7675 
7676  def add_alias(old_key, new_name):
7677  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7678  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7679 
7680  add_alias = staticmethod(add_alias)
7681 
7682  def get_number_of_keys():
7683  """get_number_of_keys() -> unsigned int"""
7684  return _IMP_atom.AtomType_get_number_of_keys()
7685 
7686  get_number_of_keys = staticmethod(get_number_of_keys)
7687 
7688  def get_index(self):
7689  """get_index(AtomType self) -> unsigned int"""
7690  return _IMP_atom.AtomType_get_index(self)
7691 
7692 
7693  def show_all(out):
7694  """show_all(_ostream out)"""
7695  return _IMP_atom.AtomType_show_all(out)
7696 
7697  show_all = staticmethod(show_all)
7698 
7699  def get_all_strings():
7700  """get_all_strings() -> IMP::Vector< std::string >"""
7701  return _IMP_atom.AtomType_get_all_strings()
7702 
7703  get_all_strings = staticmethod(get_all_strings)
7704 
7705  def get_number_unique():
7706  """get_number_unique() -> unsigned int"""
7707  return _IMP_atom.AtomType_get_number_unique()
7708 
7709  get_number_unique = staticmethod(get_number_unique)
7710 
7711  def __str__(self):
7712  """__str__(AtomType self) -> std::string"""
7713  return _IMP_atom.AtomType___str__(self)
7714 
7715 
7716  def __repr__(self):
7717  """__repr__(AtomType self) -> std::string"""
7718  return _IMP_atom.AtomType___repr__(self)
7719 
7720  __swig_destroy__ = _IMP_atom.delete_AtomType
7721  __del__ = lambda self: None
7722 AtomType_swigregister = _IMP_atom.AtomType_swigregister
7723 AtomType_swigregister(AtomType)
7724 
7725 def AtomType_add_key(sc):
7726  """AtomType_add_key(std::string sc) -> unsigned int"""
7727  return _IMP_atom.AtomType_add_key(sc)
7728 
7729 def AtomType_get_key_exists(sc):
7730  """AtomType_get_key_exists(std::string sc) -> bool"""
7731  return _IMP_atom.AtomType_get_key_exists(sc)
7732 
7733 def AtomType_add_alias(old_key, new_name):
7734  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7735  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7736 
7737 def AtomType_get_number_of_keys():
7738  """AtomType_get_number_of_keys() -> unsigned int"""
7739  return _IMP_atom.AtomType_get_number_of_keys()
7740 
7741 def AtomType_show_all(out):
7742  """AtomType_show_all(_ostream out)"""
7743  return _IMP_atom.AtomType_show_all(out)
7744 
7745 def AtomType_get_all_strings():
7746  """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
7747  return _IMP_atom.AtomType_get_all_strings()
7748 
7749 def AtomType_get_number_unique():
7750  """AtomType_get_number_unique() -> unsigned int"""
7751  return _IMP_atom.AtomType_get_number_unique()
7752 
7753 class ResidueType(IMP._Value):
7754  """Proxy of C++ IMP::Key<(90784334)> class."""
7755 
7756  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7757 
7758  def __init__(self, *args):
7759  """
7760  __init__(IMP::Key<(90784334)> self) -> ResidueType
7761  __init__(IMP::Key<(90784334)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7762  __init__(IMP::Key<(90784334)> self, std::string const & c) -> ResidueType
7763  __init__(IMP::Key<(90784334)> self, unsigned int i) -> ResidueType
7764  """
7765  this = _IMP_atom.new_ResidueType(*args)
7766  try:
7767  self.this.append(this)
7768  except __builtin__.Exception:
7769  self.this = this
7770 
7771  def add_key(sc):
7772  """add_key(std::string sc) -> unsigned int"""
7773  return _IMP_atom.ResidueType_add_key(sc)
7774 
7775  add_key = staticmethod(add_key)
7776 
7777  def get_key_exists(sc):
7778  """get_key_exists(std::string sc) -> bool"""
7779  return _IMP_atom.ResidueType_get_key_exists(sc)
7780 
7781  get_key_exists = staticmethod(get_key_exists)
7782 
7783  def get_string(self):
7784  """get_string(ResidueType self) -> std::string const"""
7785  return _IMP_atom.ResidueType_get_string(self)
7786 
7787 
7788  def __cmp__(self, o):
7789  """__cmp__(ResidueType self, ResidueType o) -> int"""
7790  return _IMP_atom.ResidueType___cmp__(self, o)
7791 
7792 
7793  def __eq__(self, o):
7794  """__eq__(ResidueType self, ResidueType o) -> bool"""
7795  return _IMP_atom.ResidueType___eq__(self, o)
7796 
7797 
7798  def __ne__(self, o):
7799  """__ne__(ResidueType self, ResidueType o) -> bool"""
7800  return _IMP_atom.ResidueType___ne__(self, o)
7801 
7802 
7803  def __lt__(self, o):
7804  """__lt__(ResidueType self, ResidueType o) -> bool"""
7805  return _IMP_atom.ResidueType___lt__(self, o)
7806 
7807 
7808  def __gt__(self, o):
7809  """__gt__(ResidueType self, ResidueType o) -> bool"""
7810  return _IMP_atom.ResidueType___gt__(self, o)
7811 
7812 
7813  def __ge__(self, o):
7814  """__ge__(ResidueType self, ResidueType o) -> bool"""
7815  return _IMP_atom.ResidueType___ge__(self, o)
7816 
7817 
7818  def __le__(self, o):
7819  """__le__(ResidueType self, ResidueType o) -> bool"""
7820  return _IMP_atom.ResidueType___le__(self, o)
7821 
7822 
7823  def __hash__(self):
7824  """__hash__(ResidueType self) -> std::size_t"""
7825  return _IMP_atom.ResidueType___hash__(self)
7826 
7827 
7828  def show(self, *args):
7829  """
7830  show(ResidueType self, _ostream out)
7831  show(ResidueType self)
7832  """
7833  return _IMP_atom.ResidueType_show(self, *args)
7834 
7835 
7836  def add_alias(old_key, new_name):
7837  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7838  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7839 
7840  add_alias = staticmethod(add_alias)
7841 
7842  def get_number_of_keys():
7843  """get_number_of_keys() -> unsigned int"""
7844  return _IMP_atom.ResidueType_get_number_of_keys()
7845 
7846  get_number_of_keys = staticmethod(get_number_of_keys)
7847 
7848  def get_index(self):
7849  """get_index(ResidueType self) -> unsigned int"""
7850  return _IMP_atom.ResidueType_get_index(self)
7851 
7852 
7853  def show_all(out):
7854  """show_all(_ostream out)"""
7855  return _IMP_atom.ResidueType_show_all(out)
7856 
7857  show_all = staticmethod(show_all)
7858 
7859  def get_all_strings():
7860  """get_all_strings() -> IMP::Vector< std::string >"""
7861  return _IMP_atom.ResidueType_get_all_strings()
7862 
7863  get_all_strings = staticmethod(get_all_strings)
7864 
7865  def get_number_unique():
7866  """get_number_unique() -> unsigned int"""
7867  return _IMP_atom.ResidueType_get_number_unique()
7868 
7869  get_number_unique = staticmethod(get_number_unique)
7870 
7871  def __str__(self):
7872  """__str__(ResidueType self) -> std::string"""
7873  return _IMP_atom.ResidueType___str__(self)
7874 
7875 
7876  def __repr__(self):
7877  """__repr__(ResidueType self) -> std::string"""
7878  return _IMP_atom.ResidueType___repr__(self)
7879 
7880  __swig_destroy__ = _IMP_atom.delete_ResidueType
7881  __del__ = lambda self: None
7882 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
7883 ResidueType_swigregister(ResidueType)
7884 
7885 def ResidueType_add_key(sc):
7886  """ResidueType_add_key(std::string sc) -> unsigned int"""
7887  return _IMP_atom.ResidueType_add_key(sc)
7888 
7889 def ResidueType_get_key_exists(sc):
7890  """ResidueType_get_key_exists(std::string sc) -> bool"""
7891  return _IMP_atom.ResidueType_get_key_exists(sc)
7892 
7893 def ResidueType_add_alias(old_key, new_name):
7894  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7895  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7896 
7897 def ResidueType_get_number_of_keys():
7898  """ResidueType_get_number_of_keys() -> unsigned int"""
7899  return _IMP_atom.ResidueType_get_number_of_keys()
7900 
7901 def ResidueType_show_all(out):
7902  """ResidueType_show_all(_ostream out)"""
7903  return _IMP_atom.ResidueType_show_all(out)
7904 
7905 def ResidueType_get_all_strings():
7906  """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
7907  return _IMP_atom.ResidueType_get_all_strings()
7908 
7909 def ResidueType_get_number_unique():
7910  """ResidueType_get_number_unique() -> unsigned int"""
7911  return _IMP_atom.ResidueType_get_number_unique()
7912 
7913 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
7914 OH = _IMP_atom.OH
7915 H2O = _IMP_atom.H2O
7916 H = _IMP_atom.H
7917 He = _IMP_atom.He
7918 Li = _IMP_atom.Li
7919 Be = _IMP_atom.Be
7920 B = _IMP_atom.B
7921 C = _IMP_atom.C
7922 N = _IMP_atom.N
7923 O = _IMP_atom.O
7924 F = _IMP_atom.F
7925 Ne = _IMP_atom.Ne
7926 Na = _IMP_atom.Na
7927 Mg = _IMP_atom.Mg
7928 Al = _IMP_atom.Al
7929 Si = _IMP_atom.Si
7930 P = _IMP_atom.P
7931 S = _IMP_atom.S
7932 Cl = _IMP_atom.Cl
7933 Ar = _IMP_atom.Ar
7934 K = _IMP_atom.K
7935 Ca = _IMP_atom.Ca
7936 Sc = _IMP_atom.Sc
7937 Ti = _IMP_atom.Ti
7938 V = _IMP_atom.V
7939 Cr = _IMP_atom.Cr
7940 Mn = _IMP_atom.Mn
7941 Fe = _IMP_atom.Fe
7942 Co = _IMP_atom.Co
7943 Ni = _IMP_atom.Ni
7944 Cu = _IMP_atom.Cu
7945 Zn = _IMP_atom.Zn
7946 Ga = _IMP_atom.Ga
7947 Ge = _IMP_atom.Ge
7948 As = _IMP_atom.As
7949 Se = _IMP_atom.Se
7950 Br = _IMP_atom.Br
7951 Kr = _IMP_atom.Kr
7952 Rb = _IMP_atom.Rb
7953 Sr = _IMP_atom.Sr
7954 Y = _IMP_atom.Y
7955 Zr = _IMP_atom.Zr
7956 Nb = _IMP_atom.Nb
7957 Mo = _IMP_atom.Mo
7958 Tc = _IMP_atom.Tc
7959 Ru = _IMP_atom.Ru
7960 Rh = _IMP_atom.Rh
7961 Pd = _IMP_atom.Pd
7962 Ag = _IMP_atom.Ag
7963 Cd = _IMP_atom.Cd
7964 In = _IMP_atom.In
7965 Sn = _IMP_atom.Sn
7966 Sb = _IMP_atom.Sb
7967 Te = _IMP_atom.Te
7968 I = _IMP_atom.I
7969 Xe = _IMP_atom.Xe
7970 Cs = _IMP_atom.Cs
7971 Ba = _IMP_atom.Ba
7972 La = _IMP_atom.La
7973 Ce = _IMP_atom.Ce
7974 Pr = _IMP_atom.Pr
7975 Nd = _IMP_atom.Nd
7976 Pm = _IMP_atom.Pm
7977 Sm = _IMP_atom.Sm
7978 Eu = _IMP_atom.Eu
7979 Gd = _IMP_atom.Gd
7980 Tb = _IMP_atom.Tb
7981 Dy = _IMP_atom.Dy
7982 Ho = _IMP_atom.Ho
7983 Er = _IMP_atom.Er
7984 Tm = _IMP_atom.Tm
7985 Yb = _IMP_atom.Yb
7986 Lu = _IMP_atom.Lu
7987 Hf = _IMP_atom.Hf
7988 Ta = _IMP_atom.Ta
7989 W = _IMP_atom.W
7990 Re = _IMP_atom.Re
7991 Os = _IMP_atom.Os
7992 Ir = _IMP_atom.Ir
7993 Pt = _IMP_atom.Pt
7994 Au = _IMP_atom.Au
7995 Hg = _IMP_atom.Hg
7996 Tl = _IMP_atom.Tl
7997 Pb = _IMP_atom.Pb
7998 Bi = _IMP_atom.Bi
7999 Po = _IMP_atom.Po
8000 At = _IMP_atom.At
8001 Rn = _IMP_atom.Rn
8002 Fr = _IMP_atom.Fr
8003 Ra = _IMP_atom.Ra
8004 Ac = _IMP_atom.Ac
8005 Th = _IMP_atom.Th
8006 Pa = _IMP_atom.Pa
8007 U = _IMP_atom.U
8008 Np = _IMP_atom.Np
8009 Pu = _IMP_atom.Pu
8010 Am = _IMP_atom.Am
8011 Cm = _IMP_atom.Cm
8012 Bk = _IMP_atom.Bk
8013 Cf = _IMP_atom.Cf
8014 Es = _IMP_atom.Es
8015 Fm = _IMP_atom.Fm
8016 Md = _IMP_atom.Md
8017 No = _IMP_atom.No
8018 Lr = _IMP_atom.Lr
8019 Db = _IMP_atom.Db
8020 Jl = _IMP_atom.Jl
8021 Rf = _IMP_atom.Rf
8022 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8023 
8024 def hash_value(e):
8025  """hash_value(IMP::atom::Element e) -> size_t"""
8026  return _IMP_atom.hash_value(e)
8027 class ElementTable(object):
8028  """Proxy of C++ IMP::atom::ElementTable class."""
8029 
8030  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8031  __repr__ = _swig_repr
8032 
8033  def __init__(self):
8034  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8035  this = _IMP_atom.new_ElementTable()
8036  try:
8037  self.this.append(this)
8038  except __builtin__.Exception:
8039  self.this = this
8040 
8041  def get_element(self, s):
8042  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8043  return _IMP_atom.ElementTable_get_element(self, s)
8044 
8045 
8046  def get_name(self, e):
8047  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8048  return _IMP_atom.ElementTable_get_name(self, e)
8049 
8050 
8051  def get_mass(self, e):
8052  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8053  return _IMP_atom.ElementTable_get_mass(self, e)
8054 
8055  __swig_destroy__ = _IMP_atom.delete_ElementTable
8056  __del__ = lambda self: None
8057 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8058 ElementTable_swigregister(ElementTable)
8059 
8060 
8061 def get_element_table():
8062  """get_element_table() -> ElementTable"""
8063  return _IMP_atom.get_element_table()
8064 class Atom(Hierarchy):
8065  """Proxy of C++ IMP::atom::Atom class."""
8066 
8067  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8068 
8069  def __init__(self, *args):
8070  """
8071  __init__(IMP::atom::Atom self) -> Atom
8072  __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8073  __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8074  """
8075  this = _IMP_atom.new_Atom(*args)
8076  try:
8077  self.this.append(this)
8078  except __builtin__.Exception:
8079  self.this = this
8080 
8081  def show(self, *args):
8082  """
8083  show(Atom self, _ostream out)
8084  show(Atom self)
8085  """
8086  return _IMP_atom.Atom_show(self, *args)
8087 
8088 
8089  def setup_particle(*args):
8090  """
8091  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8092  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8093  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8094  setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8095  """
8096  return _IMP_atom.Atom_setup_particle(*args)
8097 
8098  setup_particle = staticmethod(setup_particle)
8099 
8100  def get_is_setup(*args):
8101  """
8102  get_is_setup(_ParticleAdaptor p) -> bool
8103  get_is_setup(Model m, ParticleIndex pi) -> bool
8104  """
8105  return _IMP_atom.Atom_get_is_setup(*args)
8106 
8107  get_is_setup = staticmethod(get_is_setup)
8108 
8109  def get_atom_type(self):
8110  """get_atom_type(Atom self) -> AtomType"""
8111  return _IMP_atom.Atom_get_atom_type(self)
8112 
8113 
8114  def set_atom_type(self, t):
8115  """set_atom_type(Atom self, AtomType t)"""
8116  return _IMP_atom.Atom_set_atom_type(self, t)
8117 
8118 
8119  def get_element(self):
8120  """get_element(Atom self) -> IMP::atom::Element"""
8121  return _IMP_atom.Atom_get_element(self)
8122 
8123 
8124  def set_element(self, e):
8125  """set_element(Atom self, IMP::atom::Element e)"""
8126  return _IMP_atom.Atom_set_element(self, e)
8127 
8128 
8129  def get_occupancy(self):
8130  """get_occupancy(Atom self) -> double"""
8131  return _IMP_atom.Atom_get_occupancy(self)
8132 
8133 
8134  def set_occupancy(self, occupancy):
8135  """set_occupancy(Atom self, double occupancy)"""
8136  return _IMP_atom.Atom_set_occupancy(self, occupancy)
8137 
8138 
8139  def get_temperature_factor(self):
8140  """get_temperature_factor(Atom self) -> double"""
8141  return _IMP_atom.Atom_get_temperature_factor(self)
8142 
8143 
8144  def set_temperature_factor(self, tempFactor):
8145  """set_temperature_factor(Atom self, double tempFactor)"""
8146  return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8147 
8148 
8149  def get_input_index(self):
8150  """get_input_index(Atom self) -> IMP::Int"""
8151  return _IMP_atom.Atom_get_input_index(self)
8152 
8153 
8154  def set_input_index(self, t):
8155  """set_input_index(Atom self, IMP::Int t)"""
8156  return _IMP_atom.Atom_set_input_index(self, t)
8157 
8158 
8159  def get_atom_type_key():
8160  """get_atom_type_key() -> IntKey"""
8161  return _IMP_atom.Atom_get_atom_type_key()
8162 
8163  get_atom_type_key = staticmethod(get_atom_type_key)
8164 
8165  def get_element_key():
8166  """get_element_key() -> IntKey"""
8167  return _IMP_atom.Atom_get_element_key()
8168 
8169  get_element_key = staticmethod(get_element_key)
8170 
8171  def get_input_index_key():
8172  """get_input_index_key() -> IntKey"""
8173  return _IMP_atom.Atom_get_input_index_key()
8174 
8175  get_input_index_key = staticmethod(get_input_index_key)
8176 
8177  def get_occupancy_key():
8178  """get_occupancy_key() -> FloatKey"""
8179  return _IMP_atom.Atom_get_occupancy_key()
8180 
8181  get_occupancy_key = staticmethod(get_occupancy_key)
8182 
8183  def get_temperature_factor_key():
8184  """get_temperature_factor_key() -> FloatKey"""
8185  return _IMP_atom.Atom_get_temperature_factor_key()
8186 
8187  get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8188 
8189  def add_attribute(self, *args):
8190  """
8191  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8192  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8193  add_attribute(Atom self, IntKey a0, IMP::Int a1)
8194  add_attribute(Atom self, StringKey a0, IMP::String a1)
8195  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8196  add_attribute(Atom self, ObjectKey a0, Object a1)
8197  """
8198  return _IMP_atom.Atom_add_attribute(self, *args)
8199 
8200 
8201  def get_value(self, *args):
8202  """
8203  get_value(Atom self, FloatKey a0) -> IMP::Float
8204  get_value(Atom self, IntKey a0) -> IMP::Int
8205  get_value(Atom self, StringKey a0) -> IMP::String
8206  get_value(Atom self, ParticleIndexKey a0) -> Particle
8207  get_value(Atom self, ObjectKey a0) -> Object
8208  """
8209  return _IMP_atom.Atom_get_value(self, *args)
8210 
8211 
8212  def set_value(self, *args):
8213  """
8214  set_value(Atom self, FloatKey a0, IMP::Float a1)
8215  set_value(Atom self, IntKey a0, IMP::Int a1)
8216  set_value(Atom self, StringKey a0, IMP::String a1)
8217  set_value(Atom self, ParticleIndexKey a0, Particle a1)
8218  set_value(Atom self, ObjectKey a0, Object a1)
8219  """
8220  return _IMP_atom.Atom_set_value(self, *args)
8221 
8222 
8223  def remove_attribute(self, *args):
8224  """
8225  remove_attribute(Atom self, FloatKey a0)
8226  remove_attribute(Atom self, IntKey a0)
8227  remove_attribute(Atom self, StringKey a0)
8228  remove_attribute(Atom self, ParticleIndexKey a0)
8229  remove_attribute(Atom self, ObjectKey a0)
8230  """
8231  return _IMP_atom.Atom_remove_attribute(self, *args)
8232 
8233 
8234  def has_attribute(self, *args):
8235  """
8236  has_attribute(Atom self, FloatKey a0) -> bool
8237  has_attribute(Atom self, IntKey a0) -> bool
8238  has_attribute(Atom self, StringKey a0) -> bool
8239  has_attribute(Atom self, ParticleIndexKey a0) -> bool
8240  has_attribute(Atom self, ObjectKey a0) -> bool
8241  """
8242  return _IMP_atom.Atom_has_attribute(self, *args)
8243 
8244 
8245  def get_derivative(self, a0):
8246  """get_derivative(Atom self, FloatKey a0) -> double"""
8247  return _IMP_atom.Atom_get_derivative(self, a0)
8248 
8249 
8250  def get_name(self):
8251  """get_name(Atom self) -> std::string"""
8252  return _IMP_atom.Atom_get_name(self)
8253 
8254 
8255  def clear_caches(self):
8256  """clear_caches(Atom self)"""
8257  return _IMP_atom.Atom_clear_caches(self)
8258 
8259 
8260  def set_name(self, a0):
8261  """set_name(Atom self, std::string a0)"""
8262  return _IMP_atom.Atom_set_name(self, a0)
8263 
8264 
8265  def set_check_level(self, a0):
8266  """set_check_level(Atom self, IMP::CheckLevel a0)"""
8267  return _IMP_atom.Atom_set_check_level(self, a0)
8268 
8269 
8270  def add_to_derivative(self, a0, a1, a2):
8271  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8272  return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8273 
8274 
8275  def set_is_optimized(self, a0, a1):
8276  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8277  return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8278 
8279 
8280  def get_is_optimized(self, a0):
8281  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8282  return _IMP_atom.Atom_get_is_optimized(self, a0)
8283 
8284 
8285  def get_check_level(self):
8286  """get_check_level(Atom self) -> IMP::CheckLevel"""
8287  return _IMP_atom.Atom_get_check_level(self)
8288 
8289 
8290  def __eq__(self, *args):
8291  """
8292  __eq__(Atom self, Atom o) -> bool
8293  __eq__(Atom self, Particle d) -> bool
8294  """
8295  return _IMP_atom.Atom___eq__(self, *args)
8296 
8297 
8298  def __ne__(self, *args):
8299  """
8300  __ne__(Atom self, Atom o) -> bool
8301  __ne__(Atom self, Particle d) -> bool
8302  """
8303  return _IMP_atom.Atom___ne__(self, *args)
8304 
8305 
8306  def __le__(self, *args):
8307  """
8308  __le__(Atom self, Atom o) -> bool
8309  __le__(Atom self, Particle d) -> bool
8310  """
8311  return _IMP_atom.Atom___le__(self, *args)
8312 
8313 
8314  def __lt__(self, *args):
8315  """
8316  __lt__(Atom self, Atom o) -> bool
8317  __lt__(Atom self, Particle d) -> bool
8318  """
8319  return _IMP_atom.Atom___lt__(self, *args)
8320 
8321 
8322  def __ge__(self, *args):
8323  """
8324  __ge__(Atom self, Atom o) -> bool
8325  __ge__(Atom self, Particle d) -> bool
8326  """
8327  return _IMP_atom.Atom___ge__(self, *args)
8328 
8329 
8330  def __gt__(self, *args):
8331  """
8332  __gt__(Atom self, Atom o) -> bool
8333  __gt__(Atom self, Particle d) -> bool
8334  """
8335  return _IMP_atom.Atom___gt__(self, *args)
8336 
8337 
8338  def __hash__(self):
8339  """__hash__(Atom self) -> std::size_t"""
8340  return _IMP_atom.Atom___hash__(self)
8341 
8342 
8343  def __str__(self):
8344  """__str__(Atom self) -> std::string"""
8345  return _IMP_atom.Atom___str__(self)
8346 
8347 
8348  def __repr__(self):
8349  """__repr__(Atom self) -> std::string"""
8350  return _IMP_atom.Atom___repr__(self)
8351 
8352  __swig_destroy__ = _IMP_atom.delete_Atom
8353  __del__ = lambda self: None
8354 Atom_swigregister = _IMP_atom.Atom_swigregister
8355 Atom_swigregister(Atom)
8356 cvar = _IMP_atom.cvar
8357 AT_UNKNOWN = cvar.AT_UNKNOWN
8358 AT_N = cvar.AT_N
8359 AT_CA = cvar.AT_CA
8360 AT_C = cvar.AT_C
8361 AT_O = cvar.AT_O
8362 AT_H = cvar.AT_H
8363 AT_H1 = cvar.AT_H1
8364 AT_H2 = cvar.AT_H2
8365 AT_H3 = cvar.AT_H3
8366 AT_HA = cvar.AT_HA
8367 AT_HA1 = cvar.AT_HA1
8368 AT_HA2 = cvar.AT_HA2
8369 AT_HA3 = cvar.AT_HA3
8370 AT_CB = cvar.AT_CB
8371 AT_HB = cvar.AT_HB
8372 AT_HB1 = cvar.AT_HB1
8373 AT_HB2 = cvar.AT_HB2
8374 AT_HB3 = cvar.AT_HB3
8375 AT_OXT = cvar.AT_OXT
8376 AT_CH3 = cvar.AT_CH3
8377 AT_CH = cvar.AT_CH
8378 AT_CG = cvar.AT_CG
8379 AT_CG1 = cvar.AT_CG1
8380 AT_CG2 = cvar.AT_CG2
8381 AT_HG = cvar.AT_HG
8382 AT_HG1 = cvar.AT_HG1
8383 AT_HG2 = cvar.AT_HG2
8384 AT_HG3 = cvar.AT_HG3
8385 AT_HG11 = cvar.AT_HG11
8386 AT_HG21 = cvar.AT_HG21
8387 AT_HG31 = cvar.AT_HG31
8388 AT_HG12 = cvar.AT_HG12
8389 AT_HG13 = cvar.AT_HG13
8390 AT_HG22 = cvar.AT_HG22
8391 AT_HG23 = cvar.AT_HG23
8392 AT_HG32 = cvar.AT_HG32
8393 AT_OG = cvar.AT_OG
8394 AT_OG1 = cvar.AT_OG1
8395 AT_SG = cvar.AT_SG
8396 AT_CD = cvar.AT_CD
8397 AT_CD1 = cvar.AT_CD1
8398 AT_CD2 = cvar.AT_CD2
8399 AT_HD = cvar.AT_HD
8400 AT_HD1 = cvar.AT_HD1
8401 AT_HD2 = cvar.AT_HD2
8402 AT_HD3 = cvar.AT_HD3
8403 AT_HD11 = cvar.AT_HD11
8404 AT_HD21 = cvar.AT_HD21
8405 AT_HD31 = cvar.AT_HD31
8406 AT_HD12 = cvar.AT_HD12
8407 AT_HD13 = cvar.AT_HD13
8408 AT_HD22 = cvar.AT_HD22
8409 AT_HD23 = cvar.AT_HD23
8410 AT_HD32 = cvar.AT_HD32
8411 AT_SD = cvar.AT_SD
8412 AT_OD1 = cvar.AT_OD1
8413 AT_OD2 = cvar.AT_OD2
8414 AT_ND1 = cvar.AT_ND1
8415 AT_ND2 = cvar.AT_ND2
8416 AT_CE = cvar.AT_CE
8417 AT_CE1 = cvar.AT_CE1
8418 AT_CE2 = cvar.AT_CE2
8419 AT_CE3 = cvar.AT_CE3
8420 AT_HE = cvar.AT_HE
8421 AT_HE1 = cvar.AT_HE1
8422 AT_HE2 = cvar.AT_HE2
8423 AT_HE3 = cvar.AT_HE3
8424 AT_HE21 = cvar.AT_HE21
8425 AT_HE22 = cvar.AT_HE22
8426 AT_OE1 = cvar.AT_OE1
8427 AT_OE2 = cvar.AT_OE2
8428 AT_NE = cvar.AT_NE
8429 AT_NE1 = cvar.AT_NE1
8430 AT_NE2 = cvar.AT_NE2
8431 AT_CZ = cvar.AT_CZ
8432 AT_CZ2 = cvar.AT_CZ2
8433 AT_CZ3 = cvar.AT_CZ3
8434 AT_NZ = cvar.AT_NZ
8435 AT_HZ = cvar.AT_HZ
8436 AT_HZ1 = cvar.AT_HZ1
8437 AT_HZ2 = cvar.AT_HZ2
8438 AT_HZ3 = cvar.AT_HZ3
8439 AT_CH2 = cvar.AT_CH2
8440 AT_NH1 = cvar.AT_NH1
8441 AT_NH2 = cvar.AT_NH2
8442 AT_OH = cvar.AT_OH
8443 AT_HH = cvar.AT_HH
8444 AT_HH11 = cvar.AT_HH11
8445 AT_HH21 = cvar.AT_HH21
8446 AT_HH2 = cvar.AT_HH2
8447 AT_HH12 = cvar.AT_HH12
8448 AT_HH22 = cvar.AT_HH22
8449 AT_HH13 = cvar.AT_HH13
8450 AT_HH23 = cvar.AT_HH23
8451 AT_HH33 = cvar.AT_HH33
8452 AT_P = cvar.AT_P
8453 AT_OP1 = cvar.AT_OP1
8454 AT_OP2 = cvar.AT_OP2
8455 AT_OP3 = cvar.AT_OP3
8456 AT_O5p = cvar.AT_O5p
8457 AT_C5p = cvar.AT_C5p
8458 AT_H5p = cvar.AT_H5p
8459 AT_H5pp = cvar.AT_H5pp
8460 AT_C4p = cvar.AT_C4p
8461 AT_H4p = cvar.AT_H4p
8462 AT_O4p = cvar.AT_O4p
8463 AT_C1p = cvar.AT_C1p
8464 AT_H1p = cvar.AT_H1p
8465 AT_C3p = cvar.AT_C3p
8466 AT_H3p = cvar.AT_H3p
8467 AT_O3p = cvar.AT_O3p
8468 AT_C2p = cvar.AT_C2p
8469 AT_H2p = cvar.AT_H2p
8470 AT_H2pp = cvar.AT_H2pp
8471 AT_O2p = cvar.AT_O2p
8472 AT_HO2p = cvar.AT_HO2p
8473 AT_N9 = cvar.AT_N9
8474 AT_C8 = cvar.AT_C8
8475 AT_H8 = cvar.AT_H8
8476 AT_N7 = cvar.AT_N7
8477 AT_C5 = cvar.AT_C5
8478 AT_C4 = cvar.AT_C4
8479 AT_N3 = cvar.AT_N3
8480 AT_C2 = cvar.AT_C2
8481 AT_N1 = cvar.AT_N1
8482 AT_C6 = cvar.AT_C6
8483 AT_N6 = cvar.AT_N6
8484 AT_H61 = cvar.AT_H61
8485 AT_H62 = cvar.AT_H62
8486 AT_O6 = cvar.AT_O6
8487 AT_N2 = cvar.AT_N2
8488 AT_NT = cvar.AT_NT
8489 AT_H21 = cvar.AT_H21
8490 AT_H22 = cvar.AT_H22
8491 AT_H6 = cvar.AT_H6
8492 AT_H5 = cvar.AT_H5
8493 AT_O2 = cvar.AT_O2
8494 AT_N4 = cvar.AT_N4
8495 AT_H41 = cvar.AT_H41
8496 AT_H42 = cvar.AT_H42
8497 AT_O4 = cvar.AT_O4
8498 AT_C7 = cvar.AT_C7
8499 AT_H71 = cvar.AT_H71
8500 AT_H72 = cvar.AT_H72
8501 AT_H73 = cvar.AT_H73
8502 AT_O1A = cvar.AT_O1A
8503 AT_O2A = cvar.AT_O2A
8504 AT_O3A = cvar.AT_O3A
8505 AT_O1B = cvar.AT_O1B
8506 AT_O2B = cvar.AT_O2B
8507 AT_O3B = cvar.AT_O3B
8508 
8509 def Atom_setup_particle(*args):
8510  """
8511  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8512  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8513  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8514  Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8515  """
8516  return _IMP_atom.Atom_setup_particle(*args)
8517 
8518 def Atom_get_is_setup(*args):
8519  """
8520  get_is_setup(_ParticleAdaptor p) -> bool
8521  Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
8522  """
8523  return _IMP_atom.Atom_get_is_setup(*args)
8524 
8525 def Atom_get_atom_type_key():
8526  """Atom_get_atom_type_key() -> IntKey"""
8527  return _IMP_atom.Atom_get_atom_type_key()
8528 
8529 def Atom_get_element_key():
8530  """Atom_get_element_key() -> IntKey"""
8531  return _IMP_atom.Atom_get_element_key()
8532 
8533 def Atom_get_input_index_key():
8534  """Atom_get_input_index_key() -> IntKey"""
8535  return _IMP_atom.Atom_get_input_index_key()
8536 
8537 def Atom_get_occupancy_key():
8538  """Atom_get_occupancy_key() -> FloatKey"""
8539  return _IMP_atom.Atom_get_occupancy_key()
8540 
8541 def Atom_get_temperature_factor_key():
8542  """Atom_get_temperature_factor_key() -> FloatKey"""
8543  return _IMP_atom.Atom_get_temperature_factor_key()
8544 
8545 
8546 def get_residue(*args):
8547  """
8548  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8549  get_residue(Atom d, bool nothrow=False) -> Residue
8550  get_residue(Atom d) -> Residue
8551  """
8552  return _IMP_atom.get_residue(*args)
8553 
8554 def get_atom(rd, at):
8555  """get_atom(Residue rd, AtomType at) -> Atom"""
8556  return _IMP_atom.get_atom(rd, at)
8557 
8558 def add_atom_type(name, e):
8559  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8560  return _IMP_atom.add_atom_type(name, e)
8561 
8562 def get_element_for_atom_type(at):
8563  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8564  return _IMP_atom.get_element_for_atom_type(at)
8565 
8566 def get_atom_type_exists(name):
8567  """get_atom_type_exists(std::string name) -> bool"""
8568  return _IMP_atom.get_atom_type_exists(name)
8569 class Residue(Hierarchy):
8570  """Proxy of C++ IMP::atom::Residue class."""
8571 
8572  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8573 
8574  def __init__(self, *args):
8575  """
8576  __init__(IMP::atom::Residue self) -> Residue
8577  __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
8578  __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
8579  """
8580  this = _IMP_atom.new_Residue(*args)
8581  try:
8582  self.this.append(this)
8583  except __builtin__.Exception:
8584  self.this = this
8585 
8586  def show(self, *args):
8587  """
8588  show(Residue self, _ostream out)
8589  show(Residue self)
8590  """
8591  return _IMP_atom.Residue_show(self, *args)
8592 
8593 
8594  def setup_particle(*args):
8595  """
8596  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8597  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8598  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8599  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8600  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8601  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8602  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8603  setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8604  """
8605  return _IMP_atom.Residue_setup_particle(*args)
8606 
8607  setup_particle = staticmethod(setup_particle)
8608 
8609  def get_is_setup(*args):
8610  """
8611  get_is_setup(_ParticleAdaptor p) -> bool
8612  get_is_setup(Model m, ParticleIndex pi) -> bool
8613  """
8614  return _IMP_atom.Residue_get_is_setup(*args)
8615 
8616  get_is_setup = staticmethod(get_is_setup)
8617 
8618  def get_residue_type(self):
8619  """get_residue_type(Residue self) -> ResidueType"""
8620  return _IMP_atom.Residue_get_residue_type(self)
8621 
8622 
8623  def set_residue_type(self, t):
8624  """set_residue_type(Residue self, ResidueType t)"""
8625  return _IMP_atom.Residue_set_residue_type(self, t)
8626 
8627 
8628  def get_is_protein(self):
8629  """get_is_protein(Residue self) -> bool"""
8630  return _IMP_atom.Residue_get_is_protein(self)
8631 
8632 
8633  def get_is_dna(self):
8634  """get_is_dna(Residue self) -> bool"""
8635  return _IMP_atom.Residue_get_is_dna(self)
8636 
8637 
8638  def get_is_rna(self):
8639  """get_is_rna(Residue self) -> bool"""
8640  return _IMP_atom.Residue_get_is_rna(self)
8641 
8642 
8643  def get_index(self):
8644  """get_index(Residue self) -> IMP::Int"""
8645  return _IMP_atom.Residue_get_index(self)
8646 
8647 
8648  def set_index(self, t):
8649  """set_index(Residue self, IMP::Int t)"""
8650  return _IMP_atom.Residue_set_index(self, t)
8651 
8652 
8653  def get_insertion_code(self):
8654  """get_insertion_code(Residue self) -> char"""
8655  return _IMP_atom.Residue_get_insertion_code(self)
8656 
8657 
8658  def set_insertion_code(self, insertion_code):
8659  """set_insertion_code(Residue self, char insertion_code)"""
8660  return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8661 
8662 
8663  def get_index_key():
8664  """get_index_key() -> IntKey"""
8665  return _IMP_atom.Residue_get_index_key()
8666 
8667  get_index_key = staticmethod(get_index_key)
8668 
8669  def get_residue_type_key():
8670  """get_residue_type_key() -> IntKey"""
8671  return _IMP_atom.Residue_get_residue_type_key()
8672 
8673  get_residue_type_key = staticmethod(get_residue_type_key)
8674 
8675  def get_insertion_code_key():
8676  """get_insertion_code_key() -> IntKey"""
8677  return _IMP_atom.Residue_get_insertion_code_key()
8678 
8679  get_insertion_code_key = staticmethod(get_insertion_code_key)
8680 
8681  def add_attribute(self, *args):
8682  """
8683  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8684  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8685  add_attribute(Residue self, IntKey a0, IMP::Int a1)
8686  add_attribute(Residue self, StringKey a0, IMP::String a1)
8687  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8688  add_attribute(Residue self, ObjectKey a0, Object a1)
8689  """
8690  return _IMP_atom.Residue_add_attribute(self, *args)
8691 
8692 
8693  def get_value(self, *args):
8694  """
8695  get_value(Residue self, FloatKey a0) -> IMP::Float
8696  get_value(Residue self, IntKey a0) -> IMP::Int
8697  get_value(Residue self, StringKey a0) -> IMP::String
8698  get_value(Residue self, ParticleIndexKey a0) -> Particle
8699  get_value(Residue self, ObjectKey a0) -> Object
8700  """
8701  return _IMP_atom.Residue_get_value(self, *args)
8702 
8703 
8704  def set_value(self, *args):
8705  """
8706  set_value(Residue self, FloatKey a0, IMP::Float a1)
8707  set_value(Residue self, IntKey a0, IMP::Int a1)
8708  set_value(Residue self, StringKey a0, IMP::String a1)
8709  set_value(Residue self, ParticleIndexKey a0, Particle a1)
8710  set_value(Residue self, ObjectKey a0, Object a1)
8711  """
8712  return _IMP_atom.Residue_set_value(self, *args)
8713 
8714 
8715  def remove_attribute(self, *args):
8716  """
8717  remove_attribute(Residue self, FloatKey a0)
8718  remove_attribute(Residue self, IntKey a0)
8719  remove_attribute(Residue self, StringKey a0)
8720  remove_attribute(Residue self, ParticleIndexKey a0)
8721  remove_attribute(Residue self, ObjectKey a0)
8722  """
8723  return _IMP_atom.Residue_remove_attribute(self, *args)
8724 
8725 
8726  def has_attribute(self, *args):
8727  """
8728  has_attribute(Residue self, FloatKey a0) -> bool
8729  has_attribute(Residue self, IntKey a0) -> bool
8730  has_attribute(Residue self, StringKey a0) -> bool
8731  has_attribute(Residue self, ParticleIndexKey a0) -> bool
8732  has_attribute(Residue self, ObjectKey a0) -> bool
8733  """
8734  return _IMP_atom.Residue_has_attribute(self, *args)
8735 
8736 
8737  def get_derivative(self, a0):
8738  """get_derivative(Residue self, FloatKey a0) -> double"""
8739  return _IMP_atom.Residue_get_derivative(self, a0)
8740 
8741 
8742  def get_name(self):
8743  """get_name(Residue self) -> std::string"""
8744  return _IMP_atom.Residue_get_name(self)
8745 
8746 
8747  def clear_caches(self):
8748  """clear_caches(Residue self)"""
8749  return _IMP_atom.Residue_clear_caches(self)
8750 
8751 
8752  def set_name(self, a0):
8753  """set_name(Residue self, std::string a0)"""
8754  return _IMP_atom.Residue_set_name(self, a0)
8755 
8756 
8757  def set_check_level(self, a0):
8758  """set_check_level(Residue self, IMP::CheckLevel a0)"""
8759  return _IMP_atom.Residue_set_check_level(self, a0)
8760 
8761 
8762  def add_to_derivative(self, a0, a1, a2):
8763  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8764  return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8765 
8766 
8767  def set_is_optimized(self, a0, a1):
8768  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8769  return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8770 
8771 
8772  def get_is_optimized(self, a0):
8773  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
8774  return _IMP_atom.Residue_get_is_optimized(self, a0)
8775 
8776 
8777  def get_check_level(self):
8778  """get_check_level(Residue self) -> IMP::CheckLevel"""
8779  return _IMP_atom.Residue_get_check_level(self)
8780 
8781 
8782  def __eq__(self, *args):
8783  """
8784  __eq__(Residue self, Residue o) -> bool
8785  __eq__(Residue self, Particle d) -> bool
8786  """
8787  return _IMP_atom.Residue___eq__(self, *args)
8788 
8789 
8790  def __ne__(self, *args):
8791  """
8792  __ne__(Residue self, Residue o) -> bool
8793  __ne__(Residue self, Particle d) -> bool
8794  """
8795  return _IMP_atom.Residue___ne__(self, *args)
8796 
8797 
8798  def __le__(self, *args):
8799  """
8800  __le__(Residue self, Residue o) -> bool
8801  __le__(Residue self, Particle d) -> bool
8802  """
8803  return _IMP_atom.Residue___le__(self, *args)
8804 
8805 
8806  def __lt__(self, *args):
8807  """
8808  __lt__(Residue self, Residue o) -> bool
8809  __lt__(Residue self, Particle d) -> bool
8810  """
8811  return _IMP_atom.Residue___lt__(self, *args)
8812 
8813 
8814  def __ge__(self, *args):
8815  """
8816  __ge__(Residue self, Residue o) -> bool
8817  __ge__(Residue self, Particle d) -> bool
8818  """
8819  return _IMP_atom.Residue___ge__(self, *args)
8820 
8821 
8822  def __gt__(self, *args):
8823  """
8824  __gt__(Residue self, Residue o) -> bool
8825  __gt__(Residue self, Particle d) -> bool
8826  """
8827  return _IMP_atom.Residue___gt__(self, *args)
8828 
8829 
8830  def __hash__(self):
8831  """__hash__(Residue self) -> std::size_t"""
8832  return _IMP_atom.Residue___hash__(self)
8833 
8834 
8835  def __str__(self):
8836  """__str__(Residue self) -> std::string"""
8837  return _IMP_atom.Residue___str__(self)
8838 
8839 
8840  def __repr__(self):
8841  """__repr__(Residue self) -> std::string"""
8842  return _IMP_atom.Residue___repr__(self)
8843 
8844  __swig_destroy__ = _IMP_atom.delete_Residue
8845  __del__ = lambda self: None
8846 Residue_swigregister = _IMP_atom.Residue_swigregister
8847 Residue_swigregister(Residue)
8848 UNK = cvar.UNK
8849 GLY = cvar.GLY
8850 ALA = cvar.ALA
8851 VAL = cvar.VAL
8852 LEU = cvar.LEU
8853 ILE = cvar.ILE
8854 SER = cvar.SER
8855 THR = cvar.THR
8856 CYS = cvar.CYS
8857 MET = cvar.MET
8858 PRO = cvar.PRO
8859 ASP = cvar.ASP
8860 ASN = cvar.ASN
8861 GLU = cvar.GLU
8862 GLN = cvar.GLN
8863 LYS = cvar.LYS
8864 ARG = cvar.ARG
8865 HIS = cvar.HIS
8866 PHE = cvar.PHE
8867 TYR = cvar.TYR
8868 TRP = cvar.TRP
8869 ACE = cvar.ACE
8870 NH2 = cvar.NH2
8871 ADE = cvar.ADE
8872 URA = cvar.URA
8873 CYT = cvar.CYT
8874 GUA = cvar.GUA
8875 THY = cvar.THY
8876 DADE = cvar.DADE
8877 DURA = cvar.DURA
8878 DCYT = cvar.DCYT
8879 DGUA = cvar.DGUA
8880 DTHY = cvar.DTHY
8881 HOH = cvar.HOH
8882 HEME = cvar.HEME
8883 
8884 def Residue_setup_particle(*args):
8885  """
8886  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8887  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8888  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8889  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8890  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8891  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8892  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8893  Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8894  """
8895  return _IMP_atom.Residue_setup_particle(*args)
8896 
8897 def Residue_get_is_setup(*args):
8898  """
8899  get_is_setup(_ParticleAdaptor p) -> bool
8900  Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
8901  """
8902  return _IMP_atom.Residue_get_is_setup(*args)
8903 
8904 def Residue_get_index_key():
8905  """Residue_get_index_key() -> IntKey"""
8906  return _IMP_atom.Residue_get_index_key()
8907 
8908 def Residue_get_residue_type_key():
8909  """Residue_get_residue_type_key() -> IntKey"""
8910  return _IMP_atom.Residue_get_residue_type_key()
8911 
8912 def Residue_get_insertion_code_key():
8913  """Residue_get_insertion_code_key() -> IntKey"""
8914  return _IMP_atom.Residue_get_insertion_code_key()
8915 
8916 
8917 def get_next_residue(rd):
8918  """get_next_residue(Residue rd) -> Hierarchy"""
8919  return _IMP_atom.get_next_residue(rd)
8920 
8921 def get_previous_residue(rd):
8922  """get_previous_residue(Residue rd) -> Hierarchy"""
8923  return _IMP_atom.get_previous_residue(rd)
8924 
8925 def get_one_letter_code(c):
8926  """get_one_letter_code(ResidueType c) -> char"""
8927  return _IMP_atom.get_one_letter_code(c)
8928 BALLS = _IMP_atom.BALLS
8929 DENSITIES = _IMP_atom.DENSITIES
8930 class Representation(Hierarchy):
8931  """Proxy of C++ IMP::atom::Representation class."""
8932 
8933  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8934 
8935  def setup_particle(*args):
8936  """
8937  setup_particle(Model m, ParticleIndex pi) -> Representation
8938  setup_particle(_ParticleAdaptor decorator) -> Representation
8939  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
8940  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
8941  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
8942  setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
8943  """
8944  return _IMP_atom.Representation_setup_particle(*args)
8945 
8946  setup_particle = staticmethod(setup_particle)
8947 
8948  def __init__(self, *args):
8949  """
8950  __init__(IMP::atom::Representation self) -> Representation
8951  __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
8952  __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
8953  """
8954  this = _IMP_atom.new_Representation(*args)
8955  try:
8956  self.this.append(this)
8957  except __builtin__.Exception:
8958  self.this = this
8959 
8960  def show(self, *args):
8961  """
8962  show(Representation self, _ostream out)
8963  show(Representation self)
8964  """
8965  return _IMP_atom.Representation_show(self, *args)
8966 
8967 
8968  def get_is_setup(*args):
8969  """
8970  get_is_setup(_ParticleAdaptor p) -> bool
8971  get_is_setup(Model m, ParticleIndex pi) -> bool
8972  """
8973  return _IMP_atom.Representation_get_is_setup(*args)
8974 
8975  get_is_setup = staticmethod(get_is_setup)
8976 
8977  def get_representation(self, *args):
8978  """
8979  get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
8980  get_representation(Representation self, double resolution) -> Hierarchy
8981  """
8982  return _IMP_atom.Representation_get_representation(self, *args)
8983 
8984 
8985  def get_representations(self, *args):
8986  """
8987  get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
8988  get_representations(Representation self) -> IMP::atom::Hierarchies
8989  """
8990  return _IMP_atom.Representation_get_representations(self, *args)
8991 
8992 
8993  def add_representation(self, *args):
8994  """
8995  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
8996  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
8997  add_representation(Representation self, _ParticleIndexAdaptor rep)
8998  """
8999  return _IMP_atom.Representation_add_representation(self, *args)
9000 
9001 
9002  def get_resolutions(self, *args):
9003  """
9004  get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9005  get_resolutions(Representation self) -> IMP::Floats
9006  """
9007  return _IMP_atom.Representation_get_resolutions(self, *args)
9008 
9009 
9010  def update_parents(self):
9011  """update_parents(Representation self)"""
9012  return _IMP_atom.Representation_update_parents(self)
9013 
9014 
9015  def add_attribute(self, *args):
9016  """
9017  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9018  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9019  add_attribute(Representation self, IntKey a0, IMP::Int a1)
9020  add_attribute(Representation self, StringKey a0, IMP::String a1)
9021  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9022  add_attribute(Representation self, ObjectKey a0, Object a1)
9023  """
9024  return _IMP_atom.Representation_add_attribute(self, *args)
9025 
9026 
9027  def get_value(self, *args):
9028  """
9029  get_value(Representation self, FloatKey a0) -> IMP::Float
9030  get_value(Representation self, IntKey a0) -> IMP::Int
9031  get_value(Representation self, StringKey a0) -> IMP::String
9032  get_value(Representation self, ParticleIndexKey a0) -> Particle
9033  get_value(Representation self, ObjectKey a0) -> Object
9034  """
9035  return _IMP_atom.Representation_get_value(self, *args)
9036 
9037 
9038  def set_value(self, *args):
9039  """
9040  set_value(Representation self, FloatKey a0, IMP::Float a1)
9041  set_value(Representation self, IntKey a0, IMP::Int a1)
9042  set_value(Representation self, StringKey a0, IMP::String a1)
9043  set_value(Representation self, ParticleIndexKey a0, Particle a1)
9044  set_value(Representation self, ObjectKey a0, Object a1)
9045  """
9046  return _IMP_atom.Representation_set_value(self, *args)
9047 
9048 
9049  def remove_attribute(self, *args):
9050  """
9051  remove_attribute(Representation self, FloatKey a0)
9052  remove_attribute(Representation self, IntKey a0)
9053  remove_attribute(Representation self, StringKey a0)
9054  remove_attribute(Representation self, ParticleIndexKey a0)
9055  remove_attribute(Representation self, ObjectKey a0)
9056  """
9057  return _IMP_atom.Representation_remove_attribute(self, *args)
9058 
9059 
9060  def has_attribute(self, *args):
9061  """
9062  has_attribute(Representation self, FloatKey a0) -> bool
9063  has_attribute(Representation self, IntKey a0) -> bool
9064  has_attribute(Representation self, StringKey a0) -> bool
9065  has_attribute(Representation self, ParticleIndexKey a0) -> bool
9066  has_attribute(Representation self, ObjectKey a0) -> bool
9067  """
9068  return _IMP_atom.Representation_has_attribute(self, *args)
9069 
9070 
9071  def get_derivative(self, a0):
9072  """get_derivative(Representation self, FloatKey a0) -> double"""
9073  return _IMP_atom.Representation_get_derivative(self, a0)
9074 
9075 
9076  def get_name(self):
9077  """get_name(Representation self) -> std::string"""
9078  return _IMP_atom.Representation_get_name(self)
9079 
9080 
9081  def clear_caches(self):
9082  """clear_caches(Representation self)"""
9083  return _IMP_atom.Representation_clear_caches(self)
9084 
9085 
9086  def set_name(self, a0):
9087  """set_name(Representation self, std::string a0)"""
9088  return _IMP_atom.Representation_set_name(self, a0)
9089 
9090 
9091  def set_check_level(self, a0):
9092  """set_check_level(Representation self, IMP::CheckLevel a0)"""
9093  return _IMP_atom.Representation_set_check_level(self, a0)
9094 
9095 
9096  def add_to_derivative(self, a0, a1, a2):
9097  """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9098  return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9099 
9100 
9101  def set_is_optimized(self, a0, a1):
9102  """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9103  return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9104 
9105 
9106  def get_is_optimized(self, a0):
9107  """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9108  return _IMP_atom.Representation_get_is_optimized(self, a0)
9109 
9110 
9111  def get_check_level(self):
9112  """get_check_level(Representation self) -> IMP::CheckLevel"""
9113  return _IMP_atom.Representation_get_check_level(self)
9114 
9115 
9116  def __eq__(self, *args):
9117  """
9118  __eq__(Representation self, Representation o) -> bool
9119  __eq__(Representation self, Particle d) -> bool
9120  """
9121  return _IMP_atom.Representation___eq__(self, *args)
9122 
9123 
9124  def __ne__(self, *args):
9125  """
9126  __ne__(Representation self, Representation o) -> bool
9127  __ne__(Representation self, Particle d) -> bool
9128  """
9129  return _IMP_atom.Representation___ne__(self, *args)
9130 
9131 
9132  def __le__(self, *args):
9133  """
9134  __le__(Representation self, Representation o) -> bool
9135  __le__(Representation self, Particle d) -> bool
9136  """
9137  return _IMP_atom.Representation___le__(self, *args)
9138 
9139 
9140  def __lt__(self, *args):
9141  """
9142  __lt__(Representation self, Representation o) -> bool
9143  __lt__(Representation self, Particle d) -> bool
9144  """
9145  return _IMP_atom.Representation___lt__(self, *args)
9146 
9147 
9148  def __ge__(self, *args):
9149  """
9150  __ge__(Representation self, Representation o) -> bool
9151  __ge__(Representation self, Particle d) -> bool
9152  """
9153  return _IMP_atom.Representation___ge__(self, *args)
9154 
9155 
9156  def __gt__(self, *args):
9157  """
9158  __gt__(Representation self, Representation o) -> bool
9159  __gt__(Representation self, Particle d) -> bool
9160  """
9161  return _IMP_atom.Representation___gt__(self, *args)
9162 
9163 
9164  def __hash__(self):
9165  """__hash__(Representation self) -> std::size_t"""
9166  return _IMP_atom.Representation___hash__(self)
9167 
9168 
9169  def __str__(self):
9170  """__str__(Representation self) -> std::string"""
9171  return _IMP_atom.Representation___str__(self)
9172 
9173 
9174  def __repr__(self):
9175  """__repr__(Representation self) -> std::string"""
9176  return _IMP_atom.Representation___repr__(self)
9177 
9178  __swig_destroy__ = _IMP_atom.delete_Representation
9179  __del__ = lambda self: None
9180 Representation_swigregister = _IMP_atom.Representation_swigregister
9181 Representation_swigregister(Representation)
9182 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9183 
9184 def Representation_setup_particle(*args):
9185  """
9186  setup_particle(Model m, ParticleIndex pi) -> Representation
9187  setup_particle(_ParticleAdaptor decorator) -> Representation
9188  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9189  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9190  setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9191  Representation_setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9192  """
9193  return _IMP_atom.Representation_setup_particle(*args)
9194 
9195 def Representation_get_is_setup(*args):
9196  """
9197  get_is_setup(_ParticleAdaptor p) -> bool
9198  Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9199  """
9200  return _IMP_atom.Representation_get_is_setup(*args)
9201 
9202 
9203 def get_resolution(*args):
9204  """
9205  get_resolution(Model m, ParticleIndex pi) -> double
9206  get_resolution(Hierarchy h) -> double
9207  """
9208  return _IMP_atom.get_resolution(*args)
9209 
9210 def get_representation(h, nothrow=False):
9211  """
9212  get_representation(Hierarchy h, bool nothrow=False) -> Representation
9213  get_representation(Hierarchy h) -> Representation
9214  """
9215  return _IMP_atom.get_representation(h, nothrow)
9216 
9217 def show_with_representations(*args):
9218  """
9219  show_with_representations(Hierarchy h, _ostream out)
9220  show_with_representations(Hierarchy h)
9221  """
9222  return _IMP_atom.show_with_representations(*args)
9223 class State(Hierarchy):
9224  """Proxy of C++ IMP::atom::State class."""
9225 
9226  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9227 
9228  def setup_particle(*args):
9229  """
9230  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9231  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9232  setup_particle(Model m, ParticleIndex pi, State other) -> State
9233  setup_particle(_ParticleAdaptor decorator, State other) -> State
9234  """
9235  return _IMP_atom.State_setup_particle(*args)
9236 
9237  setup_particle = staticmethod(setup_particle)
9238 
9239  def __init__(self, *args):
9240  """
9241  __init__(IMP::atom::State self) -> State
9242  __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9243  __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9244  """
9245  this = _IMP_atom.new_State(*args)
9246  try:
9247  self.this.append(this)
9248  except __builtin__.Exception:
9249  self.this = this
9250 
9251  def show(self, *args):
9252  """
9253  show(State self, _ostream out)
9254  show(State self)
9255  """
9256  return _IMP_atom.State_show(self, *args)
9257 
9258 
9259  def get_is_setup(*args):
9260  """
9261  get_is_setup(_ParticleAdaptor p) -> bool
9262  get_is_setup(Model m, ParticleIndex pi) -> bool
9263  """
9264  return _IMP_atom.State_get_is_setup(*args)
9265 
9266  get_is_setup = staticmethod(get_is_setup)
9267 
9268  def get_state_index(self):
9269  """get_state_index(State self) -> unsigned int"""
9270  return _IMP_atom.State_get_state_index(self)
9271 
9272 
9273  def add_attribute(self, *args):
9274  """
9275  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9276  add_attribute(State self, FloatKey a0, IMP::Float a1)
9277  add_attribute(State self, IntKey a0, IMP::Int a1)
9278  add_attribute(State self, StringKey a0, IMP::String a1)
9279  add_attribute(State self, ParticleIndexKey a0, Particle a1)
9280  add_attribute(State self, ObjectKey a0, Object a1)
9281  """
9282  return _IMP_atom.State_add_attribute(self, *args)
9283 
9284 
9285  def get_value(self, *args):
9286  """
9287  get_value(State self, FloatKey a0) -> IMP::Float
9288  get_value(State self, IntKey a0) -> IMP::Int
9289  get_value(State self, StringKey a0) -> IMP::String
9290  get_value(State self, ParticleIndexKey a0) -> Particle
9291  get_value(State self, ObjectKey a0) -> Object
9292  """
9293  return _IMP_atom.State_get_value(self, *args)
9294 
9295 
9296  def set_value(self, *args):
9297  """
9298  set_value(State self, FloatKey a0, IMP::Float a1)
9299  set_value(State self, IntKey a0, IMP::Int a1)
9300  set_value(State self, StringKey a0, IMP::String a1)
9301  set_value(State self, ParticleIndexKey a0, Particle a1)
9302  set_value(State self, ObjectKey a0, Object a1)
9303  """
9304  return _IMP_atom.State_set_value(self, *args)
9305 
9306 
9307  def remove_attribute(self, *args):
9308  """
9309  remove_attribute(State self, FloatKey a0)
9310  remove_attribute(State self, IntKey a0)
9311  remove_attribute(State self, StringKey a0)
9312  remove_attribute(State self, ParticleIndexKey a0)
9313  remove_attribute(State self, ObjectKey a0)
9314  """
9315  return _IMP_atom.State_remove_attribute(self, *args)
9316 
9317 
9318  def has_attribute(self, *args):
9319  """
9320  has_attribute(State self, FloatKey a0) -> bool
9321  has_attribute(State self, IntKey a0) -> bool
9322  has_attribute(State self, StringKey a0) -> bool
9323  has_attribute(State self, ParticleIndexKey a0) -> bool
9324  has_attribute(State self, ObjectKey a0) -> bool
9325  """
9326  return _IMP_atom.State_has_attribute(self, *args)
9327 
9328 
9329  def get_derivative(self, a0):
9330  """get_derivative(State self, FloatKey a0) -> double"""
9331  return _IMP_atom.State_get_derivative(self, a0)
9332 
9333 
9334  def get_name(self):
9335  """get_name(State self) -> std::string"""
9336  return _IMP_atom.State_get_name(self)
9337 
9338 
9339  def clear_caches(self):
9340  """clear_caches(State self)"""
9341  return _IMP_atom.State_clear_caches(self)
9342 
9343 
9344  def set_name(self, a0):
9345  """set_name(State self, std::string a0)"""
9346  return _IMP_atom.State_set_name(self, a0)
9347 
9348 
9349  def set_check_level(self, a0):
9350  """set_check_level(State self, IMP::CheckLevel a0)"""
9351  return _IMP_atom.State_set_check_level(self, a0)
9352 
9353 
9354  def add_to_derivative(self, a0, a1, a2):
9355  """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9356  return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9357 
9358 
9359  def set_is_optimized(self, a0, a1):
9360  """set_is_optimized(State self, FloatKey a0, bool a1)"""
9361  return _IMP_atom.State_set_is_optimized(self, a0, a1)
9362 
9363 
9364  def get_is_optimized(self, a0):
9365  """get_is_optimized(State self, FloatKey a0) -> bool"""
9366  return _IMP_atom.State_get_is_optimized(self, a0)
9367 
9368 
9369  def get_check_level(self):
9370  """get_check_level(State self) -> IMP::CheckLevel"""
9371  return _IMP_atom.State_get_check_level(self)
9372 
9373 
9374  def __eq__(self, *args):
9375  """
9376  __eq__(State self, State o) -> bool
9377  __eq__(State self, Particle d) -> bool
9378  """
9379  return _IMP_atom.State___eq__(self, *args)
9380 
9381 
9382  def __ne__(self, *args):
9383  """
9384  __ne__(State self, State o) -> bool
9385  __ne__(State self, Particle d) -> bool
9386  """
9387  return _IMP_atom.State___ne__(self, *args)
9388 
9389 
9390  def __le__(self, *args):
9391  """
9392  __le__(State self, State o) -> bool
9393  __le__(State self, Particle d) -> bool
9394  """
9395  return _IMP_atom.State___le__(self, *args)
9396 
9397 
9398  def __lt__(self, *args):
9399  """
9400  __lt__(State self, State o) -> bool
9401  __lt__(State self, Particle d) -> bool
9402  """
9403  return _IMP_atom.State___lt__(self, *args)
9404 
9405 
9406  def __ge__(self, *args):
9407  """
9408  __ge__(State self, State o) -> bool
9409  __ge__(State self, Particle d) -> bool
9410  """
9411  return _IMP_atom.State___ge__(self, *args)
9412 
9413 
9414  def __gt__(self, *args):
9415  """
9416  __gt__(State self, State o) -> bool
9417  __gt__(State self, Particle d) -> bool
9418  """
9419  return _IMP_atom.State___gt__(self, *args)
9420 
9421 
9422  def __hash__(self):
9423  """__hash__(State self) -> std::size_t"""
9424  return _IMP_atom.State___hash__(self)
9425 
9426 
9427  def __str__(self):
9428  """__str__(State self) -> std::string"""
9429  return _IMP_atom.State___str__(self)
9430 
9431 
9432  def __repr__(self):
9433  """__repr__(State self) -> std::string"""
9434  return _IMP_atom.State___repr__(self)
9435 
9436  __swig_destroy__ = _IMP_atom.delete_State
9437  __del__ = lambda self: None
9438 State_swigregister = _IMP_atom.State_swigregister
9439 State_swigregister(State)
9440 
9441 def State_setup_particle(*args):
9442  """
9443  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9444  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9445  setup_particle(Model m, ParticleIndex pi, State other) -> State
9446  State_setup_particle(_ParticleAdaptor decorator, State other) -> State
9447  """
9448  return _IMP_atom.State_setup_particle(*args)
9449 
9450 def State_get_is_setup(*args):
9451  """
9452  get_is_setup(_ParticleAdaptor p) -> bool
9453  State_get_is_setup(Model m, ParticleIndex pi) -> bool
9454  """
9455  return _IMP_atom.State_get_is_setup(*args)
9456 
9457 
9458 def get_state_index(h):
9459  """get_state_index(Hierarchy h) -> int"""
9460  return _IMP_atom.get_state_index(h)
9461 
9462 def get_phi_dihedral_atoms(rd):
9463  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9464  return _IMP_atom.get_phi_dihedral_atoms(rd)
9465 
9466 def get_psi_dihedral_atoms(rd):
9467  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9468  return _IMP_atom.get_psi_dihedral_atoms(rd)
9469 class Molecule(Hierarchy):
9470  """Proxy of C++ IMP::atom::Molecule class."""
9471 
9472  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9473 
9474  def __init__(self, *args):
9475  """
9476  __init__(IMP::atom::Molecule self) -> Molecule
9477  __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
9478  __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
9479  """
9480  this = _IMP_atom.new_Molecule(*args)
9481  try:
9482  self.this.append(this)
9483  except __builtin__.Exception:
9484  self.this = this
9485 
9486  def show(self, *args):
9487  """
9488  show(Molecule self, _ostream out)
9489  show(Molecule self)
9490  """
9491  return _IMP_atom.Molecule_show(self, *args)
9492 
9493 
9494  def setup_particle(*args):
9495  """
9496  setup_particle(Model m, ParticleIndex pi) -> Molecule
9497  setup_particle(_ParticleAdaptor decorator) -> Molecule
9498  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9499  setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9500  """
9501  return _IMP_atom.Molecule_setup_particle(*args)
9502 
9503  setup_particle = staticmethod(setup_particle)
9504 
9505  def get_is_setup(*args):
9506  """
9507  get_is_setup(_ParticleAdaptor p) -> bool
9508  get_is_setup(Model m, ParticleIndex pi) -> bool
9509  """
9510  return _IMP_atom.Molecule_get_is_setup(*args)
9511 
9512  get_is_setup = staticmethod(get_is_setup)
9513 
9514  def add_attribute(self, *args):
9515  """
9516  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9517  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9518  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9519  add_attribute(Molecule self, StringKey a0, IMP::String a1)
9520  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9521  add_attribute(Molecule self, ObjectKey a0, Object a1)
9522  """
9523  return _IMP_atom.Molecule_add_attribute(self, *args)
9524 
9525 
9526  def get_value(self, *args):
9527  """
9528  get_value(Molecule self, FloatKey a0) -> IMP::Float
9529  get_value(Molecule self, IntKey a0) -> IMP::Int
9530  get_value(Molecule self, StringKey a0) -> IMP::String
9531  get_value(Molecule self, ParticleIndexKey a0) -> Particle
9532  get_value(Molecule self, ObjectKey a0) -> Object
9533  """
9534  return _IMP_atom.Molecule_get_value(self, *args)
9535 
9536 
9537  def set_value(self, *args):
9538  """
9539  set_value(Molecule self, FloatKey a0, IMP::Float a1)
9540  set_value(Molecule self, IntKey a0, IMP::Int a1)
9541  set_value(Molecule self, StringKey a0, IMP::String a1)
9542  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9543  set_value(Molecule self, ObjectKey a0, Object a1)
9544  """
9545  return _IMP_atom.Molecule_set_value(self, *args)
9546 
9547 
9548  def remove_attribute(self, *args):
9549  """
9550  remove_attribute(Molecule self, FloatKey a0)
9551  remove_attribute(Molecule self, IntKey a0)
9552  remove_attribute(Molecule self, StringKey a0)
9553  remove_attribute(Molecule self, ParticleIndexKey a0)
9554  remove_attribute(Molecule self, ObjectKey a0)
9555  """
9556  return _IMP_atom.Molecule_remove_attribute(self, *args)
9557 
9558 
9559  def has_attribute(self, *args):
9560  """
9561  has_attribute(Molecule self, FloatKey a0) -> bool
9562  has_attribute(Molecule self, IntKey a0) -> bool
9563  has_attribute(Molecule self, StringKey a0) -> bool
9564  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9565  has_attribute(Molecule self, ObjectKey a0) -> bool
9566  """
9567  return _IMP_atom.Molecule_has_attribute(self, *args)
9568 
9569 
9570  def get_derivative(self, a0):
9571  """get_derivative(Molecule self, FloatKey a0) -> double"""
9572  return _IMP_atom.Molecule_get_derivative(self, a0)
9573 
9574 
9575  def get_name(self):
9576  """get_name(Molecule self) -> std::string"""
9577  return _IMP_atom.Molecule_get_name(self)
9578 
9579 
9580  def clear_caches(self):
9581  """clear_caches(Molecule self)"""
9582  return _IMP_atom.Molecule_clear_caches(self)
9583 
9584 
9585  def set_name(self, a0):
9586  """set_name(Molecule self, std::string a0)"""
9587  return _IMP_atom.Molecule_set_name(self, a0)
9588 
9589 
9590  def set_check_level(self, a0):
9591  """set_check_level(Molecule self, IMP::CheckLevel a0)"""
9592  return _IMP_atom.Molecule_set_check_level(self, a0)
9593 
9594 
9595  def add_to_derivative(self, a0, a1, a2):
9596  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9597  return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9598 
9599 
9600  def set_is_optimized(self, a0, a1):
9601  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9602  return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9603 
9604 
9605  def get_is_optimized(self, a0):
9606  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9607  return _IMP_atom.Molecule_get_is_optimized(self, a0)
9608 
9609 
9610  def get_check_level(self):
9611  """get_check_level(Molecule self) -> IMP::CheckLevel"""
9612  return _IMP_atom.Molecule_get_check_level(self)
9613 
9614 
9615  def __eq__(self, *args):
9616  """
9617  __eq__(Molecule self, Molecule o) -> bool
9618  __eq__(Molecule self, Particle d) -> bool
9619  """
9620  return _IMP_atom.Molecule___eq__(self, *args)
9621 
9622 
9623  def __ne__(self, *args):
9624  """
9625  __ne__(Molecule self, Molecule o) -> bool
9626  __ne__(Molecule self, Particle d) -> bool
9627  """
9628  return _IMP_atom.Molecule___ne__(self, *args)
9629 
9630 
9631  def __le__(self, *args):
9632  """
9633  __le__(Molecule self, Molecule o) -> bool
9634  __le__(Molecule self, Particle d) -> bool
9635  """
9636  return _IMP_atom.Molecule___le__(self, *args)
9637 
9638 
9639  def __lt__(self, *args):
9640  """
9641  __lt__(Molecule self, Molecule o) -> bool
9642  __lt__(Molecule self, Particle d) -> bool
9643  """
9644  return _IMP_atom.Molecule___lt__(self, *args)
9645 
9646 
9647  def __ge__(self, *args):
9648  """
9649  __ge__(Molecule self, Molecule o) -> bool
9650  __ge__(Molecule self, Particle d) -> bool
9651  """
9652  return _IMP_atom.Molecule___ge__(self, *args)
9653 
9654 
9655  def __gt__(self, *args):
9656  """
9657  __gt__(Molecule self, Molecule o) -> bool
9658  __gt__(Molecule self, Particle d) -> bool
9659  """
9660  return _IMP_atom.Molecule___gt__(self, *args)
9661 
9662 
9663  def __hash__(self):
9664  """__hash__(Molecule self) -> std::size_t"""
9665  return _IMP_atom.Molecule___hash__(self)
9666 
9667 
9668  def __str__(self):
9669  """__str__(Molecule self) -> std::string"""
9670  return _IMP_atom.Molecule___str__(self)
9671 
9672 
9673  def __repr__(self):
9674  """__repr__(Molecule self) -> std::string"""
9675  return _IMP_atom.Molecule___repr__(self)
9676 
9677  __swig_destroy__ = _IMP_atom.delete_Molecule
9678  __del__ = lambda self: None
9679 Molecule_swigregister = _IMP_atom.Molecule_swigregister
9680 Molecule_swigregister(Molecule)
9681 
9682 def Molecule_setup_particle(*args):
9683  """
9684  setup_particle(Model m, ParticleIndex pi) -> Molecule
9685  setup_particle(_ParticleAdaptor decorator) -> Molecule
9686  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9687  Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9688  """
9689  return _IMP_atom.Molecule_setup_particle(*args)
9690 
9691 def Molecule_get_is_setup(*args):
9692  """
9693  get_is_setup(_ParticleAdaptor p) -> bool
9694  Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
9695  """
9696  return _IMP_atom.Molecule_get_is_setup(*args)
9697 
9698 
9699 def get_molecule_name(h):
9700  """get_molecule_name(Hierarchy h) -> std::string"""
9701  return _IMP_atom.get_molecule_name(h)
9702 class Copy(Molecule):
9703  """Proxy of C++ IMP::atom::Copy class."""
9704 
9705  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9706 
9707  def get_copy_index_key():
9708  """get_copy_index_key() -> IntKey"""
9709  return _IMP_atom.Copy_get_copy_index_key()
9710 
9711  get_copy_index_key = staticmethod(get_copy_index_key)
9712 
9713  def __init__(self, *args):
9714  """
9715  __init__(IMP::atom::Copy self) -> Copy
9716  __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
9717  __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
9718  """
9719  this = _IMP_atom.new_Copy(*args)
9720  try:
9721  self.this.append(this)
9722  except __builtin__.Exception:
9723  self.this = this
9724 
9725  def show(self, *args):
9726  """
9727  show(Copy self, _ostream out)
9728  show(Copy self)
9729  """
9730  return _IMP_atom.Copy_show(self, *args)
9731 
9732 
9733  def setup_particle(*args):
9734  """
9735  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9736  setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
9737  """
9738  return _IMP_atom.Copy_setup_particle(*args)
9739 
9740  setup_particle = staticmethod(setup_particle)
9741 
9742  def get_is_setup(*args):
9743  """
9744  get_is_setup(_ParticleAdaptor p) -> bool
9745  get_is_setup(Model m, ParticleIndex pi) -> bool
9746  """
9747  return _IMP_atom.Copy_get_is_setup(*args)
9748 
9749  get_is_setup = staticmethod(get_is_setup)
9750 
9751  def get_copy_index(self):
9752  """get_copy_index(Copy self) -> int"""
9753  return _IMP_atom.Copy_get_copy_index(self)
9754 
9755 
9756  def add_attribute(self, *args):
9757  """
9758  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9759  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9760  add_attribute(Copy self, IntKey a0, IMP::Int a1)
9761  add_attribute(Copy self, StringKey a0, IMP::String a1)
9762  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9763  add_attribute(Copy self, ObjectKey a0, Object a1)
9764  """
9765  return _IMP_atom.Copy_add_attribute(self, *args)
9766 
9767 
9768  def get_value(self, *args):
9769  """
9770  get_value(Copy self, FloatKey a0) -> IMP::Float
9771  get_value(Copy self, IntKey a0) -> IMP::Int
9772  get_value(Copy self, StringKey a0) -> IMP::String
9773  get_value(Copy self, ParticleIndexKey a0) -> Particle
9774  get_value(Copy self, ObjectKey a0) -> Object
9775  """
9776  return _IMP_atom.Copy_get_value(self, *args)
9777 
9778 
9779  def set_value(self, *args):
9780  """
9781  set_value(Copy self, FloatKey a0, IMP::Float a1)
9782  set_value(Copy self, IntKey a0, IMP::Int a1)
9783  set_value(Copy self, StringKey a0, IMP::String a1)
9784  set_value(Copy self, ParticleIndexKey a0, Particle a1)
9785  set_value(Copy self, ObjectKey a0, Object a1)
9786  """
9787  return _IMP_atom.Copy_set_value(self, *args)
9788 
9789 
9790  def remove_attribute(self, *args):
9791  """
9792  remove_attribute(Copy self, FloatKey a0)
9793  remove_attribute(Copy self, IntKey a0)
9794  remove_attribute(Copy self, StringKey a0)
9795  remove_attribute(Copy self, ParticleIndexKey a0)
9796  remove_attribute(Copy self, ObjectKey a0)
9797  """
9798  return _IMP_atom.Copy_remove_attribute(self, *args)
9799 
9800 
9801  def has_attribute(self, *args):
9802  """
9803  has_attribute(Copy self, FloatKey a0) -> bool
9804  has_attribute(Copy self, IntKey a0) -> bool
9805  has_attribute(Copy self, StringKey a0) -> bool
9806  has_attribute(Copy self, ParticleIndexKey a0) -> bool
9807  has_attribute(Copy self, ObjectKey a0) -> bool
9808  """
9809  return _IMP_atom.Copy_has_attribute(self, *args)
9810 
9811 
9812  def get_derivative(self, a0):
9813  """get_derivative(Copy self, FloatKey a0) -> double"""
9814  return _IMP_atom.Copy_get_derivative(self, a0)
9815 
9816 
9817  def get_name(self):
9818  """get_name(Copy self) -> std::string"""
9819  return _IMP_atom.Copy_get_name(self)
9820 
9821 
9822  def clear_caches(self):
9823  """clear_caches(Copy self)"""
9824  return _IMP_atom.Copy_clear_caches(self)
9825 
9826 
9827  def set_name(self, a0):
9828  """set_name(Copy self, std::string a0)"""
9829  return _IMP_atom.Copy_set_name(self, a0)
9830 
9831 
9832  def set_check_level(self, a0):
9833  """set_check_level(Copy self, IMP::CheckLevel a0)"""
9834  return _IMP_atom.Copy_set_check_level(self, a0)
9835 
9836 
9837  def add_to_derivative(self, a0, a1, a2):
9838  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9839  return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9840 
9841 
9842  def set_is_optimized(self, a0, a1):
9843  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9844  return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9845 
9846 
9847  def get_is_optimized(self, a0):
9848  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
9849  return _IMP_atom.Copy_get_is_optimized(self, a0)
9850 
9851 
9852  def get_check_level(self):
9853  """get_check_level(Copy self) -> IMP::CheckLevel"""
9854  return _IMP_atom.Copy_get_check_level(self)
9855 
9856 
9857  def __eq__(self, *args):
9858  """
9859  __eq__(Copy self, Copy o) -> bool
9860  __eq__(Copy self, Particle d) -> bool
9861  """
9862  return _IMP_atom.Copy___eq__(self, *args)
9863 
9864 
9865  def __ne__(self, *args):
9866  """
9867  __ne__(Copy self, Copy o) -> bool
9868  __ne__(Copy self, Particle d) -> bool
9869  """
9870  return _IMP_atom.Copy___ne__(self, *args)
9871 
9872 
9873  def __le__(self, *args):
9874  """
9875  __le__(Copy self, Copy o) -> bool
9876  __le__(Copy self, Particle d) -> bool
9877  """
9878  return _IMP_atom.Copy___le__(self, *args)
9879 
9880 
9881  def __lt__(self, *args):
9882  """
9883  __lt__(Copy self, Copy o) -> bool
9884  __lt__(Copy self, Particle d) -> bool
9885  """
9886  return _IMP_atom.Copy___lt__(self, *args)
9887 
9888 
9889  def __ge__(self, *args):
9890  """
9891  __ge__(Copy self, Copy o) -> bool
9892  __ge__(Copy self, Particle d) -> bool
9893  """
9894  return _IMP_atom.Copy___ge__(self, *args)
9895 
9896 
9897  def __gt__(self, *args):
9898  """
9899  __gt__(Copy self, Copy o) -> bool
9900  __gt__(Copy self, Particle d) -> bool
9901  """
9902  return _IMP_atom.Copy___gt__(self, *args)
9903 
9904 
9905  def __hash__(self):
9906  """__hash__(Copy self) -> std::size_t"""
9907  return _IMP_atom.Copy___hash__(self)
9908 
9909 
9910  def __str__(self):
9911  """__str__(Copy self) -> std::string"""
9912  return _IMP_atom.Copy___str__(self)
9913 
9914 
9915  def __repr__(self):
9916  """__repr__(Copy self) -> std::string"""
9917  return _IMP_atom.Copy___repr__(self)
9918 
9919  __swig_destroy__ = _IMP_atom.delete_Copy
9920  __del__ = lambda self: None
9921 Copy_swigregister = _IMP_atom.Copy_swigregister
9922 Copy_swigregister(Copy)
9923 
9924 def Copy_get_copy_index_key():
9925  """Copy_get_copy_index_key() -> IntKey"""
9926  return _IMP_atom.Copy_get_copy_index_key()
9927 
9928 def Copy_setup_particle(*args):
9929  """
9930  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9931  Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
9932  """
9933  return _IMP_atom.Copy_setup_particle(*args)
9934 
9935 def Copy_get_is_setup(*args):
9936  """
9937  get_is_setup(_ParticleAdaptor p) -> bool
9938  Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
9939  """
9940  return _IMP_atom.Copy_get_is_setup(*args)
9941 
9942 
9943 def get_copy_index(h):
9944  """get_copy_index(Hierarchy h) -> int"""
9945  return _IMP_atom.get_copy_index(h)
9946 class Selection(IMP._ParticleIndexesAdaptor):
9947  """Proxy of C++ IMP::atom::Selection class."""
9948 
9949  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9950  NONE = _IMP_atom.Selection_NONE
9951  C = _IMP_atom.Selection_C
9952  N = _IMP_atom.Selection_N
9953 
9954  def __init__(self, *args):
9955  """
9956  __init__(IMP::atom::Selection self) -> Selection
9957  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
9958  __init__(IMP::atom::Selection self, Particle h) -> Selection
9959  __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
9960  __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
9961  """
9962  this = _IMP_atom.new_Selection(*args)
9963  try:
9964  self.this.append(this)
9965  except __builtin__.Exception:
9966  self.this = this
9967 
9968  def create_clone(self):
9969  """create_clone(Selection self) -> Selection"""
9970  return _IMP_atom.Selection_create_clone(self)
9971 
9972 
9973  def get_hierarchies(self):
9974  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
9975  return _IMP_atom.Selection_get_hierarchies(self)
9976 
9977 
9978  def set_molecules(self, mols):
9979  """set_molecules(Selection self, IMP::Strings mols)"""
9980  return _IMP_atom.Selection_set_molecules(self, mols)
9981 
9982 
9983  def set_resolution(self, r):
9984  """set_resolution(Selection self, double r)"""
9985  return _IMP_atom.Selection_set_resolution(self, r)
9986 
9987 
9988  def set_representation_type(self, t):
9989  """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
9990  return _IMP_atom.Selection_set_representation_type(self, t)
9991 
9992 
9993  def set_state_index(self, state):
9994  """set_state_index(Selection self, int state)"""
9995  return _IMP_atom.Selection_set_state_index(self, state)
9996 
9997 
9998  def set_state_indexes(self, states):
9999  """set_state_indexes(Selection self, IMP::Ints states)"""
10000  return _IMP_atom.Selection_set_state_indexes(self, states)
10001 
10002 
10003  def set_terminus(self, t):
10004  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10005  return _IMP_atom.Selection_set_terminus(self, t)
10006 
10007 
10008  def set_element(self, e):
10009  """set_element(Selection self, IMP::atom::Element e)"""
10010  return _IMP_atom.Selection_set_element(self, e)
10011 
10012 
10013  def set_chain_ids(self, chains):
10014  """set_chain_ids(Selection self, IMP::Strings chains)"""
10015  return _IMP_atom.Selection_set_chain_ids(self, chains)
10016 
10017 
10018  def set_chains(self, chains):
10019  """set_chains(Selection self, IMP::Strings chains)"""
10020  return _IMP_atom.Selection_set_chains(self, chains)
10021 
10022 
10023  def set_residue_indexes(self, indexes):
10024  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10025  return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10026 
10027 
10028  def set_atom_types(self, types):
10029  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10030  return _IMP_atom.Selection_set_atom_types(self, types)
10031 
10032 
10033  def set_residue_types(self, types):
10034  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10035  return _IMP_atom.Selection_set_residue_types(self, types)
10036 
10037 
10038  def set_domains(self, names):
10039  """set_domains(Selection self, IMP::Strings names)"""
10040  return _IMP_atom.Selection_set_domains(self, names)
10041 
10042 
10043  def set_molecule(self, mol):
10044  """set_molecule(Selection self, std::string mol)"""
10045  return _IMP_atom.Selection_set_molecule(self, mol)
10046 
10047 
10048  def set_chain_id(self, c):
10049  """set_chain_id(Selection self, std::string c)"""
10050  return _IMP_atom.Selection_set_chain_id(self, c)
10051 
10052 
10053  def set_chain(self, c):
10054  """set_chain(Selection self, std::string c)"""
10055  return _IMP_atom.Selection_set_chain(self, c)
10056 
10057 
10058  def set_residue_index(self, i):
10059  """set_residue_index(Selection self, int i)"""
10060  return _IMP_atom.Selection_set_residue_index(self, i)
10061 
10062 
10063  def set_atom_type(self, types):
10064  """set_atom_type(Selection self, AtomType types)"""
10065  return _IMP_atom.Selection_set_atom_type(self, types)
10066 
10067 
10068  def set_residue_type(self, type):
10069  """set_residue_type(Selection self, ResidueType type)"""
10070  return _IMP_atom.Selection_set_residue_type(self, type)
10071 
10072 
10073  def set_domain(self, name):
10074  """set_domain(Selection self, std::string name)"""
10075  return _IMP_atom.Selection_set_domain(self, name)
10076 
10077 
10078  def set_copy_index(self, copy):
10079  """set_copy_index(Selection self, unsigned int copy)"""
10080  return _IMP_atom.Selection_set_copy_index(self, copy)
10081 
10082 
10083  def set_copy_indexes(self, copies):
10084  """set_copy_indexes(Selection self, IMP::Ints copies)"""
10085  return _IMP_atom.Selection_set_copy_indexes(self, copies)
10086 
10087 
10088  def set_particle_type(self, t):
10089  """set_particle_type(Selection self, ParticleType t)"""
10090  return _IMP_atom.Selection_set_particle_type(self, t)
10091 
10092 
10093  def set_particle_types(self, t):
10094  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10095  return _IMP_atom.Selection_set_particle_types(self, t)
10096 
10097 
10098  def set_hierarchy_types(self, types):
10099  """set_hierarchy_types(Selection self, IMP::Ints types)"""
10100  return _IMP_atom.Selection_set_hierarchy_types(self, types)
10101 
10102 
10103  def set_intersection(self, s):
10104  """set_intersection(Selection self, Selection s)"""
10105  return _IMP_atom.Selection_set_intersection(self, s)
10106 
10107 
10108  def set_union(self, s):
10109  """set_union(Selection self, Selection s)"""
10110  return _IMP_atom.Selection_set_union(self, s)
10111 
10112 
10113  def set_symmetric_difference(self, s):
10114  """set_symmetric_difference(Selection self, Selection s)"""
10115  return _IMP_atom.Selection_set_symmetric_difference(self, s)
10116 
10117 
10118  def set_difference(self, s):
10119  """set_difference(Selection self, Selection s)"""
10120  return _IMP_atom.Selection_set_difference(self, s)
10121 
10122 
10123  def get_selected_particles(self, with_representation=True):
10124  """
10125  get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10126  get_selected_particles(Selection self) -> IMP::ParticlesTemp
10127  """
10128  return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10129 
10130 
10131  def get_selected_particle_indexes(self, with_representation=True):
10132  """
10133  get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10134  get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10135  """
10136  return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10137 
10138 
10139  def show(self, *args):
10140  """
10141  show(Selection self, _ostream out)
10142  show(Selection self)
10143  """
10144  return _IMP_atom.Selection_show(self, *args)
10145 
10146 
10147  def __str__(self):
10148  """__str__(Selection self) -> std::string"""
10149  return _IMP_atom.Selection___str__(self)
10150 
10151 
10152  def __repr__(self):
10153  """__repr__(Selection self) -> std::string"""
10154  return _IMP_atom.Selection___repr__(self)
10155 
10156 
10157  def __init__(self, hierarchy=None,
10158  hierarchies=None, **params):
10159  if hierarchy and hierarchies:
10160  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
10161  if hierarchy:
10162  this = _IMP_atom.new_Selection(hierarchy)
10163  try: self.this.append(this)
10164  except: self.this = this
10165  elif hierarchies:
10166  this = _IMP_atom.new_Selection(hierarchies)
10167  try: self.this.append(this)
10168  except: self.this = this
10169  else:
10170  raise ValueError("Either hierarchy or hierarchies must be provided.")
10171  for k in params.keys():
10172  eval("self.set_%s(params[k])"%k)
10173 
10174  def union(self, s):
10175  news = self.create_clone()
10176  news.union_update(s)
10177  return news
10178  def intersection(self, s):
10179  news = self.create_clone()
10180  news.intersection_update(s)
10181  return news
10182  def symmetric_difference(self, s):
10183  news = self.create_clone()
10184  news.symmetric_difference_update(s)
10185  return news
10186  def difference(self, s):
10187  news = self.create_clone()
10188  news.difference_update(s)
10189  return news
10190  def union_update(self, s):
10191  self.set_union(s)
10192  return self
10193  def intersection_update(self, s):
10194  self.set_intersection(s)
10195  return self
10196  def symmetric_difference_update(self, s):
10197  self.set_symmetric_difference(s)
10198  return self
10199  def difference_update(self, s):
10200  self.set_difference(s)
10201  return self
10202  __or__ = union
10203  __and__ = intersection
10204  __xor__ = symmetric_difference
10205  __sub__ = difference
10206  __ior__ = union_update
10207  __iand__ = intersection_update
10208  __ixor__ = symmetric_difference_update
10209  __isub__ = difference_update
10210 
10211  __swig_destroy__ = _IMP_atom.delete_Selection
10212  __del__ = lambda self: None
10213 Selection_swigregister = _IMP_atom.Selection_swigregister
10214 Selection_swigregister(Selection)
10215 
10216 
10217 def create_distance_restraint(*args):
10218  """
10219  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10220  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10221  """
10222  return _IMP_atom.create_distance_restraint(*args)
10223 
10225  """
10226  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10227  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10228  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10229  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10230  """
10231  return _IMP_atom.create_connectivity_restraint(*args)
10232 
10234  """
10235  create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10236  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10237  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10238  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10239  """
10240  return _IMP_atom.create_internal_connectivity_restraint(*args)
10241 
10242 def create_cover(*args):
10243  """
10244  create_cover(Selection s, std::string name) -> XYZR
10245  create_cover(Selection s) -> XYZR
10246  """
10247  return _IMP_atom.create_cover(*args)
10248 
10249 def get_mass(*args):
10250  """
10251  get_mass(ResidueType c) -> double
10252  get_mass(Selection s) -> double
10253  """
10254  return _IMP_atom.get_mass(*args)
10255 
10256 def get_volume(s):
10257  """get_volume(Selection s) -> double"""
10258  return _IMP_atom.get_volume(s)
10259 
10260 def get_surface_area(s):
10261  """get_surface_area(Selection s) -> double"""
10262  return _IMP_atom.get_surface_area(s)
10263 
10264 def get_leaves(*args):
10265  """
10266  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10267  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10268  get_leaves(Selection h) -> IMP::atom::Hierarchies
10269  """
10270  return _IMP_atom.get_leaves(*args)
10271 class SelectionGeometry(IMP.display.Geometry):
10272  """Proxy of C++ IMP::atom::SelectionGeometry class."""
10273 
10274  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10275 
10276  def __init__(self, *args):
10277  """
10278  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10279  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10280  """
10281  this = _IMP_atom.new_SelectionGeometry(*args)
10282  try:
10283  self.this.append(this)
10284  except __builtin__.Exception:
10285  self.this = this
10286 
10287  def get_version_info(self):
10288  """get_version_info(SelectionGeometry self) -> VersionInfo"""
10289  return _IMP_atom.SelectionGeometry_get_version_info(self)
10290 
10291 
10292  def __str__(self):
10293  """__str__(SelectionGeometry self) -> std::string"""
10294  return _IMP_atom.SelectionGeometry___str__(self)
10295 
10296 
10297  def __repr__(self):
10298  """__repr__(SelectionGeometry self) -> std::string"""
10299  return _IMP_atom.SelectionGeometry___repr__(self)
10300 
10301 
10302  @staticmethod
10303  def get_from(o):
10304  return _object_cast_to_SelectionGeometry(o)
10305 
10306 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10307 SelectionGeometry_swigregister(SelectionGeometry)
10308 
10309 
10310 def get_rmsd(*args):
10311  """
10312  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10313  get_rmsd(Selection s0, Selection s1) -> double
10314  """
10315  return _IMP_atom.get_rmsd(*args)
10316 
10317 def get_rmsd_transforming_first(*args):
10318  """
10319  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10320  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10321  """
10322  return _IMP_atom.get_rmsd_transforming_first(*args)
10323 
10324 def get_placement_score(source, target):
10325  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10326  return _IMP_atom.get_placement_score(source, target)
10327 
10328 def get_component_placement_score(ref1, ref2, mdl1, mdl2):
10329  """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"""
10330  return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10331 
10332 def get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2):
10333  """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"""
10334  return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10335 
10336 def get_radius_of_gyration(*args):
10337  """
10338  get_radius_of_gyration(Selection s) -> double
10339  get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10340  get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10341  """
10342  return _IMP_atom.get_radius_of_gyration(*args)
10343 class ForceFieldParameters(IMP.Object):
10344  """Proxy of C++ IMP::atom::ForceFieldParameters class."""
10345 
10346  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10347 
10348  def __init__(self):
10349  """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10350  this = _IMP_atom.new_ForceFieldParameters()
10351  try:
10352  self.this.append(this)
10353  except __builtin__.Exception:
10354  self.this = this
10355 
10356  def get_radius(self, atom):
10357  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10358  return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10359 
10360 
10361  def get_epsilon(self, atom):
10362  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10363  return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10364 
10365 
10366  def add_radii(self, *args):
10367  """
10368  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10369  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10370  add_radii(ForceFieldParameters self, Hierarchy mhd)
10371  """
10372  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10373 
10374 
10375  def add_well_depths(self, mhd):
10376  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10377  return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10378 
10379 
10380  def add_bonds(self, mhd):
10381  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10382  return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10383 
10384  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10385  __del__ = lambda self: None
10386 
10387  def __str__(self):
10388  """__str__(ForceFieldParameters self) -> std::string"""
10389  return _IMP_atom.ForceFieldParameters___str__(self)
10390 
10391 
10392  def __repr__(self):
10393  """__repr__(ForceFieldParameters self) -> std::string"""
10394  return _IMP_atom.ForceFieldParameters___repr__(self)
10395 
10396 
10397  @staticmethod
10398  def get_from(o):
10399  return _object_cast_to_ForceFieldParameters(o)
10400 
10401 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10402 ForceFieldParameters_swigregister(ForceFieldParameters)
10403 
10404 class CHARMMAtomTopology(object):
10405  """Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10406 
10407  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10408 
10409  def __init__(self, *args):
10410  """
10411  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10412  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10413  """
10414  this = _IMP_atom.new_CHARMMAtomTopology(*args)
10415  try:
10416  self.this.append(this)
10417  except __builtin__.Exception:
10418  self.this = this
10419 
10420  def get_name(self):
10421  """get_name(CHARMMAtomTopology self) -> std::string"""
10422  return _IMP_atom.CHARMMAtomTopology_get_name(self)
10423 
10424 
10425  def get_charmm_type(self):
10426  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10427  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10428 
10429 
10430  def get_charge(self):
10431  """get_charge(CHARMMAtomTopology self) -> double"""
10432  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10433 
10434 
10435  def set_charmm_type(self, charmm_type):
10436  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10437  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10438 
10439 
10440  def set_charge(self, charge):
10441  """set_charge(CHARMMAtomTopology self, double charge)"""
10442  return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10443 
10444 
10445  def show(self, *args):
10446  """
10447  show(CHARMMAtomTopology self, _ostream out)
10448  show(CHARMMAtomTopology self)
10449  """
10450  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10451 
10452 
10453  def __str__(self):
10454  """__str__(CHARMMAtomTopology self) -> std::string"""
10455  return _IMP_atom.CHARMMAtomTopology___str__(self)
10456 
10457 
10458  def __repr__(self):
10459  """__repr__(CHARMMAtomTopology self) -> std::string"""
10460  return _IMP_atom.CHARMMAtomTopology___repr__(self)
10461 
10462  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10463  __del__ = lambda self: None
10464 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
10465 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10466 
10467 class CHARMMBondEndpoint(object):
10468  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10469 
10470  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10471 
10472  def __init__(self, atom_name, residue=None):
10473  """
10474  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
10475  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
10476  """
10477  this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
10478  try:
10479  self.this.append(this)
10480  except __builtin__.Exception:
10481  self.this = this
10482 
10483  def get_atom_name(self):
10484  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10485  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10486 
10487 
10488  def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10489  """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"""
10490  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10491 
10492 
10493  def show(self, *args):
10494  """
10495  show(CHARMMBondEndpoint self, _ostream out)
10496  show(CHARMMBondEndpoint self)
10497  """
10498  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10499 
10500 
10501  def __str__(self):
10502  """__str__(CHARMMBondEndpoint self) -> std::string"""
10503  return _IMP_atom.CHARMMBondEndpoint___str__(self)
10504 
10505 
10506  def __repr__(self):
10507  """__repr__(CHARMMBondEndpoint self) -> std::string"""
10508  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10509 
10510  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10511  __del__ = lambda self: None
10512 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
10513 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10514 
10515 class CHARMMDihedral(object):
10516  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class."""
10517 
10518  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10519  __repr__ = _swig_repr
10520 
10521  def __init__(self, atoms):
10522  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10523  this = _IMP_atom.new_CHARMMDihedral(atoms)
10524  try:
10525  self.this.append(this)
10526  except __builtin__.Exception:
10527  self.this = this
10528 
10529  def get_endpoint(self, i):
10530  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10531  return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10532 
10533 
10534  def get_contains_atom(self, name):
10535  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10536  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10537 
10538 
10539  def show(self, *args):
10540  """
10541  show(CHARMMDihedral self, _ostream out)
10542  show(CHARMMDihedral self)
10543  """
10544  return _IMP_atom.CHARMMDihedral_show(self, *args)
10545 
10546  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10547  __del__ = lambda self: None
10548 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
10549 CHARMMDihedral_swigregister(CHARMMDihedral)
10550 
10551 class CHARMMInternalCoordinate(CHARMMDihedral):
10552  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10553 
10554  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10555 
10556  def __init__(self, *args):
10557  """
10558  __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
10559  __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
10560  """
10561  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
10562  try:
10563  self.this.append(this)
10564  except __builtin__.Exception:
10565  self.this = this
10566 
10567  def get_first_distance(self):
10568  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
10569  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10570 
10571 
10572  def get_second_distance(self):
10573  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
10574  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10575 
10576 
10577  def get_first_angle(self):
10578  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
10579  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10580 
10581 
10582  def get_second_angle(self):
10583  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
10584  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10585 
10586 
10587  def get_dihedral(self):
10588  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
10589  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10590 
10591 
10592  def get_improper(self):
10593  """get_improper(CHARMMInternalCoordinate self) -> bool"""
10594  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10595 
10596 
10597  def show(self, *args):
10598  """
10599  show(CHARMMInternalCoordinate self, _ostream out)
10600  show(CHARMMInternalCoordinate self)
10601  """
10602  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10603 
10604 
10605  def __str__(self):
10606  """__str__(CHARMMInternalCoordinate self) -> std::string"""
10607  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10608 
10609 
10610  def __repr__(self):
10611  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
10612  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10613 
10614  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10615  __del__ = lambda self: None
10616 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
10617 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10618 
10619 class CHARMMResidueTopologyBase(IMP.Object):
10620  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10621 
10622  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10623 
10624  def __init__(self, *args, **kwargs):
10625  raise AttributeError("No constructor defined")
10626 
10627  def get_type(self):
10628  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
10629  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10630 
10631 
10632  def get_number_of_atoms(self):
10633  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10634  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10635 
10636 
10637  def add_atom(self, atom):
10638  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10639  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10640 
10641 
10642  def get_atom(self, *args):
10643  """
10644  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10645  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10646  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10647  """
10648  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10649 
10650 
10651  def get_number_of_bonds(self):
10652  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10653  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10654 
10655 
10656  def add_bond(self, bond):
10657  """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
10658  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10659 
10660 
10661  def get_number_of_angles(self):
10662  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10663  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10664 
10665 
10666  def add_angle(self, bond):
10667  """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
10668  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10669 
10670 
10671  def get_number_of_dihedrals(self):
10672  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10673  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10674 
10675 
10676  def add_dihedral(self, bond):
10677  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10678  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10679 
10680 
10681  def get_number_of_impropers(self):
10682  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10683  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10684 
10685 
10686  def add_improper(self, bond):
10687  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10688  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10689 
10690 
10691  def get_number_of_internal_coordinates(self):
10692  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
10693  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
10694 
10695 
10696  def add_internal_coordinate(self, ic):
10697  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
10698  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
10699 
10700 
10701  def get_internal_coordinate(self, index):
10702  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
10703  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
10704 
10705 
10706  def get_bond(self, index):
10707  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
10708  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
10709 
10710 
10711  def get_angle(self, index):
10712  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
10713  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
10714 
10715 
10716  def get_dihedral(self, index):
10717  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10718  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
10719 
10720 
10721  def get_improper(self, index):
10722  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10723  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
10724 
10725 
10726  def get_version_info(self):
10727  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
10728  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
10729 
10730 
10731  def __str__(self):
10732  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
10733  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
10734 
10735 
10736  def __repr__(self):
10737  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
10738  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
10739 
10740 
10741  @staticmethod
10742  def get_from(o):
10743  return _object_cast_to_CHARMMResidueTopologyBase(o)
10744 
10745 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
10746 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
10747 
10748 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
10749  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
10750 
10751  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10752 
10753  def __init__(self, *args):
10754  """
10755  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
10756  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
10757  """
10758  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
10759  try:
10760  self.this.append(this)
10761  except __builtin__.Exception:
10762  self.this = this
10763 
10764  def remove_atom(self, name):
10765  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
10766  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
10767 
10768 
10769  def set_default_first_patch(self, patch):
10770  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10771  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
10772 
10773 
10774  def set_default_last_patch(self, patch):
10775  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10776  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
10777 
10778 
10779  def get_default_first_patch(self):
10780  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
10781  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
10782 
10783 
10784  def get_default_last_patch(self):
10785  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
10786  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
10787 
10788 
10789  def __str__(self):
10790  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
10791  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
10792 
10793 
10794  def __repr__(self):
10795  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
10796  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
10797 
10798 
10799  @staticmethod
10800  def get_from(o):
10801  return _object_cast_to_CHARMMIdealResidueTopology(o)
10802 
10803 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
10804 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
10805 
10806 class CHARMMPatch(CHARMMResidueTopologyBase):
10807  """Proxy of C++ IMP::atom::CHARMMPatch class."""
10808 
10809  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10810 
10811  def __init__(self, type):
10812  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
10813  this = _IMP_atom.new_CHARMMPatch(type)
10814  try:
10815  self.this.append(this)
10816  except __builtin__.Exception:
10817  self.this = this
10818 
10819  def add_removed_atom(self, name):
10820  """add_removed_atom(CHARMMPatch self, std::string name)"""
10821  return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
10822 
10823 
10824  def get_number_of_removed_atoms(self):
10825  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
10826  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
10827 
10828 
10829  def get_removed_atom(self, i):
10830  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
10831  return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
10832 
10833 
10834  def apply(self, *args):
10835  """
10836  apply(CHARMMPatch self, CHARMMResidueTopology res)
10837  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
10838  """
10839  return _IMP_atom.CHARMMPatch_apply(self, *args)
10840 
10841 
10842  def __str__(self):
10843  """__str__(CHARMMPatch self) -> std::string"""
10844  return _IMP_atom.CHARMMPatch___str__(self)
10845 
10846 
10847  def __repr__(self):
10848  """__repr__(CHARMMPatch self) -> std::string"""
10849  return _IMP_atom.CHARMMPatch___repr__(self)
10850 
10851 
10852  @staticmethod
10853  def get_from(o):
10854  return _object_cast_to_CHARMMPatch(o)
10855 
10856 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
10857 CHARMMPatch_swigregister(CHARMMPatch)
10858 
10859 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
10860  """Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
10861 
10862  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10863 
10864  def __init__(self, *args):
10865  """
10866  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
10867  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
10868  """
10869  this = _IMP_atom.new_CHARMMResidueTopology(*args)
10870  try:
10871  self.this.append(this)
10872  except __builtin__.Exception:
10873  self.this = this
10874 
10875  def get_patched(self):
10876  """get_patched(CHARMMResidueTopology self) -> bool"""
10877  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
10878 
10879 
10880  def set_patched(self, patched):
10881  """set_patched(CHARMMResidueTopology self, bool patched)"""
10882  return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
10883 
10884 
10885  def __str__(self):
10886  """__str__(CHARMMResidueTopology self) -> std::string"""
10887  return _IMP_atom.CHARMMResidueTopology___str__(self)
10888 
10889 
10890  def __repr__(self):
10891  """__repr__(CHARMMResidueTopology self) -> std::string"""
10892  return _IMP_atom.CHARMMResidueTopology___repr__(self)
10893 
10894 
10895  @staticmethod
10896  def get_from(o):
10897  return _object_cast_to_CHARMMResidueTopology(o)
10898 
10899 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
10900 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
10901 
10902 class CHARMMAtom(Atom):
10903  """Proxy of C++ IMP::atom::CHARMMAtom class."""
10904 
10905  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10906 
10907  def __init__(self, *args):
10908  """
10909  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
10910  __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
10911  __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
10912  """
10913  this = _IMP_atom.new_CHARMMAtom(*args)
10914  try:
10915  self.this.append(this)
10916  except __builtin__.Exception:
10917  self.this = this
10918 
10919  def show(self, *args):
10920  """
10921  show(CHARMMAtom self, _ostream out)
10922  show(CHARMMAtom self)
10923  """
10924  return _IMP_atom.CHARMMAtom_show(self, *args)
10925 
10926 
10927  def setup_particle(*args):
10928  """
10929  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
10930  setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
10931  """
10932  return _IMP_atom.CHARMMAtom_setup_particle(*args)
10933 
10934  setup_particle = staticmethod(setup_particle)
10935 
10936  def get_charmm_type(self):
10937  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
10938  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
10939 
10940 
10941  def set_charmm_type(self, t):
10942  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
10943  return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
10944 
10945 
10946  def get_is_setup(*args):
10947  """
10948  get_is_setup(_ParticleAdaptor p) -> bool
10949  get_is_setup(Model m, ParticleIndex pi) -> bool
10950  """
10951  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
10952 
10953  get_is_setup = staticmethod(get_is_setup)
10954 
10955  def get_charmm_type_key():
10956  """get_charmm_type_key() -> StringKey"""
10957  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
10958 
10959  get_charmm_type_key = staticmethod(get_charmm_type_key)
10960 
10961  def add_attribute(self, *args):
10962  """
10963  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
10964  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10965  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
10966  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
10967  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10968  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
10969  """
10970  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
10971 
10972 
10973  def get_value(self, *args):
10974  """
10975  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
10976  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
10977  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
10978  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
10979  get_value(CHARMMAtom self, ObjectKey a0) -> Object
10980  """
10981  return _IMP_atom.CHARMMAtom_get_value(self, *args)
10982 
10983 
10984  def set_value(self, *args):
10985  """
10986  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10987  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
10988  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
10989  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10990  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
10991  """
10992  return _IMP_atom.CHARMMAtom_set_value(self, *args)
10993 
10994 
10995  def remove_attribute(self, *args):
10996  """
10997  remove_attribute(CHARMMAtom self, FloatKey a0)
10998  remove_attribute(CHARMMAtom self, IntKey a0)
10999  remove_attribute(CHARMMAtom self, StringKey a0)
11000  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11001  remove_attribute(CHARMMAtom self, ObjectKey a0)
11002  """
11003  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11004 
11005 
11006  def has_attribute(self, *args):
11007  """
11008  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11009  has_attribute(CHARMMAtom self, IntKey a0) -> bool
11010  has_attribute(CHARMMAtom self, StringKey a0) -> bool
11011  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11012  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11013  """
11014  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11015 
11016 
11017  def get_derivative(self, a0):
11018  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11019  return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11020 
11021 
11022  def get_name(self):
11023  """get_name(CHARMMAtom self) -> std::string"""
11024  return _IMP_atom.CHARMMAtom_get_name(self)
11025 
11026 
11027  def clear_caches(self):
11028  """clear_caches(CHARMMAtom self)"""
11029  return _IMP_atom.CHARMMAtom_clear_caches(self)
11030 
11031 
11032  def set_name(self, a0):
11033  """set_name(CHARMMAtom self, std::string a0)"""
11034  return _IMP_atom.CHARMMAtom_set_name(self, a0)
11035 
11036 
11037  def set_check_level(self, a0):
11038  """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11039  return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11040 
11041 
11042  def add_to_derivative(self, a0, a1, a2):
11043  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11044  return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11045 
11046 
11047  def set_is_optimized(self, a0, a1):
11048  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11049  return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11050 
11051 
11052  def get_is_optimized(self, a0):
11053  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11054  return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11055 
11056 
11057  def get_check_level(self):
11058  """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11059  return _IMP_atom.CHARMMAtom_get_check_level(self)
11060 
11061 
11062  def __eq__(self, *args):
11063  """
11064  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11065  __eq__(CHARMMAtom self, Particle d) -> bool
11066  """
11067  return _IMP_atom.CHARMMAtom___eq__(self, *args)
11068 
11069 
11070  def __ne__(self, *args):
11071  """
11072  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11073  __ne__(CHARMMAtom self, Particle d) -> bool
11074  """
11075  return _IMP_atom.CHARMMAtom___ne__(self, *args)
11076 
11077 
11078  def __le__(self, *args):
11079  """
11080  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11081  __le__(CHARMMAtom self, Particle d) -> bool
11082  """
11083  return _IMP_atom.CHARMMAtom___le__(self, *args)
11084 
11085 
11086  def __lt__(self, *args):
11087  """
11088  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11089  __lt__(CHARMMAtom self, Particle d) -> bool
11090  """
11091  return _IMP_atom.CHARMMAtom___lt__(self, *args)
11092 
11093 
11094  def __ge__(self, *args):
11095  """
11096  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11097  __ge__(CHARMMAtom self, Particle d) -> bool
11098  """
11099  return _IMP_atom.CHARMMAtom___ge__(self, *args)
11100 
11101 
11102  def __gt__(self, *args):
11103  """
11104  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11105  __gt__(CHARMMAtom self, Particle d) -> bool
11106  """
11107  return _IMP_atom.CHARMMAtom___gt__(self, *args)
11108 
11109 
11110  def __hash__(self):
11111  """__hash__(CHARMMAtom self) -> std::size_t"""
11112  return _IMP_atom.CHARMMAtom___hash__(self)
11113 
11114 
11115  def __str__(self):
11116  """__str__(CHARMMAtom self) -> std::string"""
11117  return _IMP_atom.CHARMMAtom___str__(self)
11118 
11119 
11120  def __repr__(self):
11121  """__repr__(CHARMMAtom self) -> std::string"""
11122  return _IMP_atom.CHARMMAtom___repr__(self)
11123 
11124  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11125  __del__ = lambda self: None
11126 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11127 CHARMMAtom_swigregister(CHARMMAtom)
11128 
11129 def CHARMMAtom_setup_particle(*args):
11130  """
11131  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11132  CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11133  """
11134  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11135 
11136 def CHARMMAtom_get_is_setup(*args):
11137  """
11138  get_is_setup(_ParticleAdaptor p) -> bool
11139  CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11140  """
11141  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11142 
11143 def CHARMMAtom_get_charmm_type_key():
11144  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11145  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11146 
11147 
11148 def get_charmm_untyped_atoms(hierarchy):
11149  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11150  return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11151 
11152 def remove_charmm_untyped_atoms(hierarchy):
11153  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11154  return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11155 class CHARMMBondParameters(object):
11156  """Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11157 
11158  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11159  force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11160  ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11161 
11162  def __init__(self):
11163  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11164  this = _IMP_atom.new_CHARMMBondParameters()
11165  try:
11166  self.this.append(this)
11167  except __builtin__.Exception:
11168  self.this = this
11169 
11170  def show(self, *args):
11171  """
11172  show(CHARMMBondParameters self, _ostream out)
11173  show(CHARMMBondParameters self)
11174  """
11175  return _IMP_atom.CHARMMBondParameters_show(self, *args)
11176 
11177 
11178  def __str__(self):
11179  """__str__(CHARMMBondParameters self) -> std::string"""
11180  return _IMP_atom.CHARMMBondParameters___str__(self)
11181 
11182 
11183  def __repr__(self):
11184  """__repr__(CHARMMBondParameters self) -> std::string"""
11185  return _IMP_atom.CHARMMBondParameters___repr__(self)
11186 
11187  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11188  __del__ = lambda self: None
11189 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11190 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11191 
11192 class CHARMMDihedralParameters(object):
11193  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11194 
11195  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11196  force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11197  multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11198  ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11199 
11200  def __init__(self):
11201  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11202  this = _IMP_atom.new_CHARMMDihedralParameters()
11203  try:
11204  self.this.append(this)
11205  except __builtin__.Exception:
11206  self.this = this
11207 
11208  def show(self, *args):
11209  """
11210  show(CHARMMDihedralParameters self, _ostream out)
11211  show(CHARMMDihedralParameters self)
11212  """
11213  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11214 
11215 
11216  def __str__(self):
11217  """__str__(CHARMMDihedralParameters self) -> std::string"""
11218  return _IMP_atom.CHARMMDihedralParameters___str__(self)
11219 
11220 
11221  def __repr__(self):
11222  """__repr__(CHARMMDihedralParameters self) -> std::string"""
11223  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11224 
11225  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11226  __del__ = lambda self: None
11227 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11228 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11229 
11230 class CHARMMParameters(ForceFieldParameters):
11231  """Proxy of C++ IMP::atom::CHARMMParameters class."""
11232 
11233  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11234 
11235  def __init__(self, *args):
11236  """
11237  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11238  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11239  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11240  """
11241  this = _IMP_atom.new_CHARMMParameters(*args)
11242  try:
11243  self.this.append(this)
11244  except __builtin__.Exception:
11245  self.this = this
11246 
11247  def add_residue_topology(self, res):
11248  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11249  return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11250 
11251 
11252  def get_residue_topology(self, type):
11253  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11254  return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11255 
11256 
11257  def add_patch(self, patch):
11258  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11259  return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11260 
11261 
11262  def get_patch(self, name):
11263  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11264  return _IMP_atom.CHARMMParameters_get_patch(self, name)
11265 
11266 
11267  def create_topology(self, hierarchy):
11268  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11269  return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11270 
11271 
11272  def get_bond_parameters(self, type1, type2):
11273  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11274  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11275 
11276 
11277  def get_angle_parameters(self, type1, type2, type3):
11278  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11279  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11280 
11281 
11282  def get_dihedral_parameters(self, type1, type2, type3, type4):
11283  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11284  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11285 
11286 
11287  def get_improper_parameters(self, type1, type2, type3, type4):
11288  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11289  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11290 
11291 
11292  def create_angles(self, bonds):
11293  """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11294  return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11295 
11296 
11297  def create_dihedrals(self, bonds):
11298  """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11299  return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11300 
11301 
11302  def get_version_info(self):
11303  """get_version_info(CHARMMParameters self) -> VersionInfo"""
11304  return _IMP_atom.CHARMMParameters_get_version_info(self)
11305 
11306 
11307  def __str__(self):
11308  """__str__(CHARMMParameters self) -> std::string"""
11309  return _IMP_atom.CHARMMParameters___str__(self)
11310 
11311 
11312  def __repr__(self):
11313  """__repr__(CHARMMParameters self) -> std::string"""
11314  return _IMP_atom.CHARMMParameters___repr__(self)
11315 
11316 
11317  @staticmethod
11318  def get_from(o):
11319  return _object_cast_to_CHARMMParameters(o)
11320 
11321 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11322 CHARMMParameters_swigregister(CHARMMParameters)
11323 
11324 
11326  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11327  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11328 
11330  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11331  return _IMP_atom.get_all_atom_CHARMM_parameters()
11332 class CHARMMSegmentTopology(IMP.Object):
11333  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11334 
11335  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11336 
11337  def remove_residue(self, d):
11338  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11339  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11340 
11341 
11342  def remove_residues(self, d):
11343  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11344  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11345 
11346 
11347  def set_residues(self, ps):
11348  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11349  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11350 
11351 
11352  def set_residues_order(self, objs):
11353  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11354  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11355 
11356 
11357  def add_residue(self, obj):
11358  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11359  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11360 
11361 
11362  def add_residues(self, objs):
11363  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11364  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11365 
11366 
11367  def clear_residues(self):
11368  """clear_residues(CHARMMSegmentTopology self)"""
11369  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11370 
11371 
11372  def get_number_of_residues(self):
11373  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11374  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11375 
11376 
11377  def get_has_residues(self):
11378  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11379  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11380 
11381 
11382  def get_residue(self, i):
11383  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11384  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11385 
11386 
11387  def get_residues(self):
11388  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11389  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11390 
11391 
11392  def reserve_residues(self, sz):
11393  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11394  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11395 
11396 
11397  def get_version_info(self):
11398  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11399  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11400 
11401 
11402  def __init__(self, *args):
11403  """
11404  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11405  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11406  """
11407  this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11408  try:
11409  self.this.append(this)
11410  except __builtin__.Exception:
11411  self.this = this
11412 
11413  def apply_default_patches(self, ff):
11414  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11415  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11416 
11417 
11418  def __str__(self):
11419  """__str__(CHARMMSegmentTopology self) -> std::string"""
11420  return _IMP_atom.CHARMMSegmentTopology___str__(self)
11421 
11422 
11423  def __repr__(self):
11424  """__repr__(CHARMMSegmentTopology self) -> std::string"""
11425  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11426 
11427 
11428  @staticmethod
11429  def get_from(o):
11430  return _object_cast_to_CHARMMSegmentTopology(o)
11431 
11432 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
11433 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11434 
11435 class CHARMMTopology(IMP.Object):
11436  """Proxy of C++ IMP::atom::CHARMMTopology class."""
11437 
11438  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11439 
11440  def __init__(self, *args):
11441  """
11442  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
11443  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
11444  """
11445  this = _IMP_atom.new_CHARMMTopology(*args)
11446  try:
11447  self.this.append(this)
11448  except __builtin__.Exception:
11449  self.this = this
11450 
11451  def get_parameters(self):
11452  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11453  return _IMP_atom.CHARMMTopology_get_parameters(self)
11454 
11455 
11456  def add_sequence(self, sequence):
11457  """add_sequence(CHARMMTopology self, std::string sequence)"""
11458  return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11459 
11460 
11461  def apply_default_patches(self):
11462  """apply_default_patches(CHARMMTopology self)"""
11463  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11464 
11465 
11466  def create_hierarchy(self, model):
11467  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11468  return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11469 
11470 
11471  def add_atom_types(self, hierarchy):
11472  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11473  return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11474 
11475 
11476  def add_coordinates(self, hierarchy):
11477  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11478  return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11479 
11480 
11481  def add_missing_atoms(self, hierarchy):
11482  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11483  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11484 
11485 
11486  def setup_hierarchy(self, hierarchy):
11487  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11488  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11489 
11490 
11491  def add_charges(self, hierarchy):
11492  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11493  return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11494 
11495 
11496  def add_bonds(self, hierarchy):
11497  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11498  return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11499 
11500 
11501  def add_dihedrals(self, hierarchy):
11502  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11503  return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11504 
11505 
11506  def add_impropers(self, hierarchy):
11507  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11508  return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11509 
11510 
11511  def remove_segment(self, d):
11512  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11513  return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11514 
11515 
11516  def remove_segments(self, d):
11517  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11518  return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11519 
11520 
11521  def set_segments(self, ps):
11522  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11523  return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11524 
11525 
11526  def set_segments_order(self, objs):
11527  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11528  return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11529 
11530 
11531  def add_segment(self, obj):
11532  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11533  return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11534 
11535 
11536  def add_segments(self, objs):
11537  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11538  return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11539 
11540 
11541  def clear_segments(self):
11542  """clear_segments(CHARMMTopology self)"""
11543  return _IMP_atom.CHARMMTopology_clear_segments(self)
11544 
11545 
11546  def get_number_of_segments(self):
11547  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11548  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11549 
11550 
11551  def get_has_segments(self):
11552  """get_has_segments(CHARMMTopology self) -> bool"""
11553  return _IMP_atom.CHARMMTopology_get_has_segments(self)
11554 
11555 
11556  def get_segment(self, i):
11557  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11558  return _IMP_atom.CHARMMTopology_get_segment(self, i)
11559 
11560 
11561  def get_segments(self):
11562  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11563  return _IMP_atom.CHARMMTopology_get_segments(self)
11564 
11565 
11566  def reserve_segments(self, sz):
11567  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
11568  return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11569 
11570 
11571  def get_version_info(self):
11572  """get_version_info(CHARMMTopology self) -> VersionInfo"""
11573  return _IMP_atom.CHARMMTopology_get_version_info(self)
11574 
11575 
11576  def __str__(self):
11577  """__str__(CHARMMTopology self) -> std::string"""
11578  return _IMP_atom.CHARMMTopology___str__(self)
11579 
11580 
11581  def __repr__(self):
11582  """__repr__(CHARMMTopology self) -> std::string"""
11583  return _IMP_atom.CHARMMTopology___repr__(self)
11584 
11585 
11586  @staticmethod
11587  def get_from(o):
11588  return _object_cast_to_CHARMMTopology(o)
11589 
11590 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
11591 CHARMMTopology_swigregister(CHARMMTopology)
11592 
11593 class CHARMMStereochemistryRestraint(IMP.Restraint):
11594  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11595 
11596  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11597 
11598  def __init__(self, *args):
11599  """
11600  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11601  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11602  """
11603  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
11604  try:
11605  self.this.append(this)
11606  except __builtin__.Exception:
11607  self.this = this
11608 
11609  def get_pair_filter(self):
11610  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11611  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11612 
11613 
11614  def get_full_pair_filter(self):
11615  """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11616  return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11617 
11618 
11619  def do_get_inputs(self):
11620  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11621  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11622 
11623 
11624  def get_version_info(self):
11625  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11626  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11627 
11628 
11629  def __str__(self):
11630  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11631  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11632 
11633 
11634  def __repr__(self):
11635  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11636  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11637 
11638 
11639  @staticmethod
11640  def get_from(o):
11641  return _object_cast_to_CHARMMStereochemistryRestraint(o)
11642 
11643 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
11644 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11645 
11646 
11647 def add_bonds(*args):
11648  """
11649  add_bonds(Hierarchy d, ForceFieldParameters ffp)
11650  add_bonds(Hierarchy d)
11651  """
11652  return _IMP_atom.add_bonds(*args)
11653 
11654 def add_radii(*args):
11655  """
11656  add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
11657  add_radii(Hierarchy d, ForceFieldParameters ffp)
11658  add_radii(Hierarchy d)
11659  """
11660  return _IMP_atom.add_radii(*args)
11661 ALBER = _IMP_atom.ALBER
11662 HARPAZ = _IMP_atom.HARPAZ
11663 ANDERSSON = _IMP_atom.ANDERSSON
11664 TSAI = _IMP_atom.TSAI
11665 QUILLIN = _IMP_atom.QUILLIN
11666 SQUIRE = _IMP_atom.SQUIRE
11667 
11668 def get_protein_density_from_reference(densityReference):
11669  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11670  return _IMP_atom.get_protein_density_from_reference(densityReference)
11671 
11672 def get_volume_from_mass(*args):
11673  """
11674  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
11675  get_volume_from_mass(double m) -> double
11676  """
11677  return _IMP_atom.get_volume_from_mass(*args)
11678 
11679 def get_mass_from_volume(*args):
11680  """
11681  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
11682  get_mass_from_volume(double v) -> double
11683  """
11684  return _IMP_atom.get_mass_from_volume(*args)
11685 
11687  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11688  return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11689 
11691  """get_volume_from_residue_type(ResidueType rt) -> double"""
11692  return _IMP_atom.get_volume_from_residue_type(rt)
11693 
11694 def get_molarity(n, volume):
11695  """get_molarity(double n, double volume) -> double"""
11696  return _IMP_atom.get_molarity(n, volume)
11697 
11698 def get_kd(na, nb, nab, volume):
11699  """get_kd(double na, double nb, double nab, double volume) -> double"""
11700  return _IMP_atom.get_kd(na, nb, nab, volume)
11701 
11703  """get_einstein_diffusion_coefficient(double r) -> double"""
11704  return _IMP_atom.get_einstein_diffusion_coefficient(r)
11705 
11707  """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
11708  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r)
11709 
11710 def get_diffusion_length(*args):
11711  """
11712  get_diffusion_length(double D, double t) -> double
11713  get_diffusion_length(double D, double force, double t, double temp=273) -> double
11714  get_diffusion_length(double D, double force, double t) -> double
11715  """
11716  return _IMP_atom.get_diffusion_length(*args)
11717 
11718 def get_diffusion_angle(D, dtfs):
11719  """get_diffusion_angle(double D, double dtfs) -> double"""
11720  return _IMP_atom.get_diffusion_angle(D, dtfs)
11721 
11722 def get_diffusion_coefficient(displacements, dt):
11723  """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
11724  return _IMP_atom.get_diffusion_coefficient(displacements, dt)
11725 
11726 def get_rotational_diffusion_coefficient(displacements, dt):
11727  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
11728  return _IMP_atom.get_rotational_diffusion_coefficient(displacements, dt)
11729 
11730 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11731  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11732  return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11733 
11734 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
11735  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11736  return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11737 
11738 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
11739  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11740  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11741 class EzRestraint(IMP.Restraint):
11742  """Proxy of C++ IMP::atom::EzRestraint class."""
11743 
11744  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11745 
11746  def __init__(self, m, ps):
11747  """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11748  this = _IMP_atom.new_EzRestraint(m, ps)
11749  try:
11750  self.this.append(this)
11751  except __builtin__.Exception:
11752  self.this = this
11753 
11754  def get_version_info(self):
11755  """get_version_info(EzRestraint self) -> VersionInfo"""
11756  return _IMP_atom.EzRestraint_get_version_info(self)
11757 
11758 
11759  def __str__(self):
11760  """__str__(EzRestraint self) -> std::string"""
11761  return _IMP_atom.EzRestraint___str__(self)
11762 
11763 
11764  def __repr__(self):
11765  """__repr__(EzRestraint self) -> std::string"""
11766  return _IMP_atom.EzRestraint___repr__(self)
11767 
11768 
11769  @staticmethod
11770  def get_from(o):
11771  return _object_cast_to_EzRestraint(o)
11772 
11773 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
11774 EzRestraint_swigregister(EzRestraint)
11775 
11776 
11777 def create_protein(*args):
11778  """
11779  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
11780  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
11781  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
11782  create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
11783  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
11784  """
11785  return _IMP_atom.create_protein(*args)
11786 
11788  """
11789  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
11790  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
11791  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
11792  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
11793  """
11794  return _IMP_atom.create_simplified_along_backbone(*args)
11795 
11796 def create_simplified_from_volume(h, resolution):
11797  """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11798  return _IMP_atom.create_simplified_from_volume(h, resolution)
11799 
11800 def create_simplified_assembly_from_volume(h, resolution):
11801  """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11802  return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
11803 
11804 def get_residue_indexes(h):
11805  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
11806  return _IMP_atom.get_residue_indexes(h)
11807 
11808 def get_residue_type(*args):
11809  """
11810  get_residue_type(char c) -> ResidueType
11811  get_residue_type(Hierarchy h) -> ResidueType
11812  """
11813  return _IMP_atom.get_residue_type(*args)
11814 
11815 def get_atom_type(h):
11816  """get_atom_type(Hierarchy h) -> AtomType"""
11817  return _IMP_atom.get_atom_type(h)
11818 
11819 def get_domain_name(h):
11820  """get_domain_name(Hierarchy h) -> std::string"""
11821  return _IMP_atom.get_domain_name(h)
11822 
11824  """
11825  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
11826  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
11827  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
11828  """
11829  return _IMP_atom.create_excluded_volume_restraint(*args)
11830 
11831 def setup_as_approximation(*args):
11832  """
11833  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
11834  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
11835  setup_as_approximation(Hierarchy h, double resolution=-1)
11836  setup_as_approximation(Hierarchy h)
11837  """
11838  return _IMP_atom.setup_as_approximation(*args)
11839 class _HierarchyTreeVertexIndex(object):
11840  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
11841 
11842  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11843  __repr__ = _swig_repr
11844 
11845  def __init__(self):
11846  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
11847  this = _IMP_atom.new__HierarchyTreeVertexIndex()
11848  try:
11849  self.this.append(this)
11850  except __builtin__.Exception:
11851  self.this = this
11852  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
11853  __del__ = lambda self: None
11854 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
11855 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
11856 
11857 
11858 def show_as_graphviz(name, out):
11859  """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
11860  return _IMP_atom.show_as_graphviz(name, out)
11861 
11862 def get_vertex_index(g):
11863  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
11864  return _IMP_atom.get_vertex_index(g)
11865 
11866 def get_hierarchy_tree(h):
11867  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
11868  return _IMP_atom.get_hierarchy_tree(h)
11869 class HierarchyGeometry(IMP.display.SingletonGeometry):
11870  """Proxy of C++ IMP::atom::HierarchyGeometry class."""
11871 
11872  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11873 
11874  def __init__(self, d, resolution=0):
11875  """
11876  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
11877  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
11878  """
11879  this = _IMP_atom.new_HierarchyGeometry(d, resolution)
11880  try:
11881  self.this.append(this)
11882  except __builtin__.Exception:
11883  self.this = this
11884 
11885  def get_version_info(self):
11886  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
11887  return _IMP_atom.HierarchyGeometry_get_version_info(self)
11888 
11889 
11890  def __str__(self):
11891  """__str__(HierarchyGeometry self) -> std::string"""
11892  return _IMP_atom.HierarchyGeometry___str__(self)
11893 
11894 
11895  def __repr__(self):
11896  """__repr__(HierarchyGeometry self) -> std::string"""
11897  return _IMP_atom.HierarchyGeometry___repr__(self)
11898 
11899 
11900  @staticmethod
11901  def get_from(o):
11902  return _object_cast_to_HierarchyGeometry(o)
11903 
11904 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
11905 HierarchyGeometry_swigregister(HierarchyGeometry)
11906 
11907 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
11908  """Proxy of C++ IMP::atom::HierarchiesGeometry class."""
11909 
11910  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11911 
11912  def __init__(self, sc, resolution=-1):
11913  """
11914  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
11915  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
11916  """
11917  this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
11918  try:
11919  self.this.append(this)
11920  except __builtin__.Exception:
11921  self.this = this
11922 
11923  def get_version_info(self):
11924  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
11925  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
11926 
11927 
11928  def __str__(self):
11929  """__str__(HierarchiesGeometry self) -> std::string"""
11930  return _IMP_atom.HierarchiesGeometry___str__(self)
11931 
11932 
11933  def __repr__(self):
11934  """__repr__(HierarchiesGeometry self) -> std::string"""
11935  return _IMP_atom.HierarchiesGeometry___repr__(self)
11936 
11937 
11938  @staticmethod
11939  def get_from(o):
11940  return _object_cast_to_HierarchiesGeometry(o)
11941 
11942 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
11943 HierarchiesGeometry_swigregister(HierarchiesGeometry)
11944 
11945 
11946 def transform(*args):
11947  """
11948  transform(Hierarchy h, Transformation3D tr)
11949  transform(Hierarchy h, Transformation3D tr)
11950  """
11951  return _IMP_atom.transform(*args)
11952 class DopePairScore(_ADopeBase):
11953  """Proxy of C++ IMP::atom::DopePairScore class."""
11954 
11955  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11956 
11957  def __init__(self, *args):
11958  """
11959  __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
11960  __init__(IMP::atom::DopePairScore self) -> DopePairScore
11961  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
11962  """
11963  this = _IMP_atom.new_DopePairScore(*args)
11964  try:
11965  self.this.append(this)
11966  except __builtin__.Exception:
11967  self.this = this
11968 
11969  def __str__(self):
11970  """__str__(DopePairScore self) -> std::string"""
11971  return _IMP_atom.DopePairScore___str__(self)
11972 
11973 
11974  def __repr__(self):
11975  """__repr__(DopePairScore self) -> std::string"""
11976  return _IMP_atom.DopePairScore___repr__(self)
11977 
11978 
11979  @staticmethod
11980  def get_from(o):
11981  return _object_cast_to_DopePairScore(o)
11982 
11983  __swig_destroy__ = _IMP_atom.delete_DopePairScore
11984  __del__ = lambda self: None
11985 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
11986 DopePairScore_swigregister(DopePairScore)
11987 
11988 
11989 def add_dope_score_data(h):
11990  """add_dope_score_data(Hierarchy h)"""
11991  return _IMP_atom.add_dope_score_data(h)
11992 class OrientedSoapPairScore(_OrientedSoapBase):
11993  """Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
11994 
11995  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11996 
11997  def __init__(self, library):
11998  """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
11999  this = _IMP_atom.new_OrientedSoapPairScore(library)
12000  try:
12001  self.this.append(this)
12002  except __builtin__.Exception:
12003  self.this = this
12004 
12005  def get_pair_filter(self):
12006  """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12007  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12008 
12009 
12010  def __str__(self):
12011  """__str__(OrientedSoapPairScore self) -> std::string"""
12012  return _IMP_atom.OrientedSoapPairScore___str__(self)
12013 
12014 
12015  def __repr__(self):
12016  """__repr__(OrientedSoapPairScore self) -> std::string"""
12017  return _IMP_atom.OrientedSoapPairScore___repr__(self)
12018 
12019 
12020  @staticmethod
12021  def get_from(o):
12022  return _object_cast_to_OrientedSoapPairScore(o)
12023 
12024  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12025  __del__ = lambda self: None
12026 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12027 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12028 
12029 class SameResiduePairFilter(IMP.PairPredicate):
12030  """Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12031 
12032  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12033 
12034  def __init__(self):
12035  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12036  this = _IMP_atom.new_SameResiduePairFilter()
12037  try:
12038  self.this.append(this)
12039  except __builtin__.Exception:
12040  self.this = this
12041 
12042  def do_get_inputs(self, m, pis):
12043  """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12044  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12045 
12046 
12047  def get_value(self, *args):
12048  """
12049  get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12050  get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12051  """
12052  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12053 
12054 
12055  def get_value_index(self, *args):
12056  """
12057  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12058  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12059  """
12060  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12061 
12062 
12063  def get_version_info(self):
12064  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12065  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12066 
12067 
12068  def __str__(self):
12069  """__str__(SameResiduePairFilter self) -> std::string"""
12070  return _IMP_atom.SameResiduePairFilter___str__(self)
12071 
12072 
12073  def __repr__(self):
12074  """__repr__(SameResiduePairFilter self) -> std::string"""
12075  return _IMP_atom.SameResiduePairFilter___repr__(self)
12076 
12077 
12078  @staticmethod
12079  def get_from(o):
12080  return _object_cast_to_SameResiduePairFilter(o)
12081 
12082 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12083 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12084 
12085 class RemoveRigidMotionOptimizerState(IMP.OptimizerState):
12086  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12087 
12088  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12089 
12090  def __init__(self, m, pis):
12091  """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12092  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12093  try:
12094  self.this.append(this)
12095  except __builtin__.Exception:
12096  self.this = this
12097 
12098  def set_particles(self, pis):
12099  """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12100  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12101 
12102 
12103  def remove_rigid_motion(self):
12104  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12105  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12106 
12107 
12108  def get_version_info(self):
12109  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12110  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12111 
12112 
12113  def __str__(self):
12114  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12115  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12116 
12117 
12118  def __repr__(self):
12119  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12120  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12121 
12122 
12123  @staticmethod
12124  def get_from(o):
12125  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12126 
12127 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12128 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12129 
12130 class BerendsenThermostatOptimizerState(IMP.OptimizerState):
12131  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12132 
12133  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12134 
12135  def __init__(self, pis, temperature, tau):
12136  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12137  this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12138  try:
12139  self.this.append(this)
12140  except __builtin__.Exception:
12141  self.this = this
12142 
12143  def set_particles(self, pis):
12144  """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12145  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12146 
12147 
12148  def get_temperature(self):
12149  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12150  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12151 
12152 
12153  def get_tau(self):
12154  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12155  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12156 
12157 
12158  def set_temperature(self, temperature):
12159  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12160  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12161 
12162 
12163  def set_tau(self, tau):
12164  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12165  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12166 
12167 
12168  def rescale_velocities(self):
12169  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12170  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12171 
12172 
12173  def get_version_info(self):
12174  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12175  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12176 
12177 
12178  def __str__(self):
12179  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12180  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12181 
12182 
12183  def __repr__(self):
12184  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12185  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12186 
12187 
12188  @staticmethod
12189  def get_from(o):
12190  return _object_cast_to_BerendsenThermostatOptimizerState(o)
12191 
12192 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12193 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12194 
12195 class LangevinThermostatOptimizerState(IMP.OptimizerState):
12196  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12197 
12198  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12199 
12200  def __init__(self, m, pis, temperature, gamma):
12201  """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12202  this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12203  try:
12204  self.this.append(this)
12205  except __builtin__.Exception:
12206  self.this = this
12207 
12208  def set_particles(self, pis):
12209  """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12210  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12211 
12212 
12213  def get_temperature(self):
12214  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12215  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12216 
12217 
12218  def get_gamma(self):
12219  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12220  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12221 
12222 
12223  def set_temperature(self, temperature):
12224  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12225  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12226 
12227 
12228  def set_gamma(self, gamma):
12229  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12230  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12231 
12232 
12233  def rescale_velocities(self):
12234  """rescale_velocities(LangevinThermostatOptimizerState self)"""
12235  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12236 
12237 
12238  def get_version_info(self):
12239  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12240  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12241 
12242 
12243  def __str__(self):
12244  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12245  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12246 
12247 
12248  def __repr__(self):
12249  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12250  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12251 
12252 
12253  @staticmethod
12254  def get_from(o):
12255  return _object_cast_to_LangevinThermostatOptimizerState(o)
12256 
12257 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12258 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12259 
12260 class PDBSelector(IMP.Object):
12261  """Proxy of C++ IMP::atom::PDBSelector class."""
12262 
12263  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12264 
12265  def __init__(self, name):
12266  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12267  if self.__class__ == PDBSelector:
12268  _self = None
12269  else:
12270  _self = self
12271  this = _IMP_atom.new_PDBSelector(_self, name)
12272  try:
12273  self.this.append(this)
12274  except __builtin__.Exception:
12275  self.this = this
12276 
12277  if self.__class__ != PDBSelector:
12278  _director_objects.register(self)
12279 
12280 
12281 
12282 
12283  def get_is_selected(self, pdb_line):
12284  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12285  return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12286 
12287  __swig_destroy__ = _IMP_atom.delete_PDBSelector
12288  __del__ = lambda self: None
12289 
12290  def __str__(self):
12291  """__str__(PDBSelector self) -> std::string"""
12292  return _IMP_atom.PDBSelector___str__(self)
12293 
12294 
12295  def __repr__(self):
12296  """__repr__(PDBSelector self) -> std::string"""
12297  return _IMP_atom.PDBSelector___repr__(self)
12298 
12299 
12300  @staticmethod
12301  def get_from(o):
12302  return _object_cast_to_PDBSelector(o)
12303 
12304 
12305  def get_type_name(self):
12306  return self.__class__.__name__
12307  def do_show(self, out):
12308  pass
12309  def get_version_info(self):
12310  if"IMP::atom" == "IMP":
12311  return VersionInfo(self.__module__,
12312  __import__(self.__module__).get_module_version())
12313  else:
12314  return IMP.VersionInfo(self.__module__,
12315  __import__(self.__module__).get_module_version())
12316  @staticmethod
12317  def get_from(o):
12318  return _object_cast_to_PDBSelector(o)
12319 
12320 
12321  def __and__(self, s):
12322  return AndPDBSelector(self, s)
12323  def __or__(self, s):
12324  return OrPDBSelector(self, s)
12325  def __xor__(self, s):
12326  return XorPDBSelector(self, s)
12327  def __invert__(self):
12328  return NotPDBSelector(self)
12329  def __sub__(self, s):
12330  return AndPDBSelector(self, NotPDBSelector(s))
12331 
12332  def __disown__(self):
12333  self.this.disown()
12334  _IMP_atom.disown_PDBSelector(self)
12335  return weakref_proxy(self)
12336 
12337  def do_destroy(self):
12338  """do_destroy(PDBSelector self)"""
12339  return _IMP_atom.PDBSelector_do_destroy(self)
12340 
12341 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12342 PDBSelector_swigregister(PDBSelector)
12343 
12344 class NonAlternativePDBSelector(PDBSelector):
12345  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12346 
12347  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12348 
12349  def __init__(self, *args):
12350  """
12351  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12352  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12353  """
12354  this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12355  try:
12356  self.this.append(this)
12357  except __builtin__.Exception:
12358  self.this = this
12359 
12360  def get_version_info(self):
12361  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12362  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12363 
12364 
12365  def __str__(self):
12366  """__str__(NonAlternativePDBSelector self) -> std::string"""
12367  return _IMP_atom.NonAlternativePDBSelector___str__(self)
12368 
12369 
12370  def __repr__(self):
12371  """__repr__(NonAlternativePDBSelector self) -> std::string"""
12372  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12373 
12374 
12375  @staticmethod
12376  def get_from(o):
12377  return _object_cast_to_NonAlternativePDBSelector(o)
12378 
12379 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
12380 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12381 
12382 class ATOMPDBSelector(NonAlternativePDBSelector):
12383  """Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12384 
12385  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12386 
12387  def __init__(self, *args):
12388  """
12389  __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
12390  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
12391  """
12392  this = _IMP_atom.new_ATOMPDBSelector(*args)
12393  try:
12394  self.this.append(this)
12395  except __builtin__.Exception:
12396  self.this = this
12397 
12398  def __str__(self):
12399  """__str__(ATOMPDBSelector self) -> std::string"""
12400  return _IMP_atom.ATOMPDBSelector___str__(self)
12401 
12402 
12403  def __repr__(self):
12404  """__repr__(ATOMPDBSelector self) -> std::string"""
12405  return _IMP_atom.ATOMPDBSelector___repr__(self)
12406 
12407 
12408  @staticmethod
12409  def get_from(o):
12410  return _object_cast_to_ATOMPDBSelector(o)
12411 
12412 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
12413 ATOMPDBSelector_swigregister(ATOMPDBSelector)
12414 
12415 class CAlphaPDBSelector(NonAlternativePDBSelector):
12416  """Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12417 
12418  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12419 
12420  def __init__(self, *args):
12421  """
12422  __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
12423  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
12424  """
12425  this = _IMP_atom.new_CAlphaPDBSelector(*args)
12426  try:
12427  self.this.append(this)
12428  except __builtin__.Exception:
12429  self.this = this
12430 
12431  def __str__(self):
12432  """__str__(CAlphaPDBSelector self) -> std::string"""
12433  return _IMP_atom.CAlphaPDBSelector___str__(self)
12434 
12435 
12436  def __repr__(self):
12437  """__repr__(CAlphaPDBSelector self) -> std::string"""
12438  return _IMP_atom.CAlphaPDBSelector___repr__(self)
12439 
12440 
12441  @staticmethod
12442  def get_from(o):
12443  return _object_cast_to_CAlphaPDBSelector(o)
12444 
12445 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
12446 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12447 
12448 class CBetaPDBSelector(NonAlternativePDBSelector):
12449  """Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12450 
12451  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12452 
12453  def __init__(self, *args):
12454  """
12455  __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
12456  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
12457  """
12458  this = _IMP_atom.new_CBetaPDBSelector(*args)
12459  try:
12460  self.this.append(this)
12461  except __builtin__.Exception:
12462  self.this = this
12463 
12464  def __str__(self):
12465  """__str__(CBetaPDBSelector self) -> std::string"""
12466  return _IMP_atom.CBetaPDBSelector___str__(self)
12467 
12468 
12469  def __repr__(self):
12470  """__repr__(CBetaPDBSelector self) -> std::string"""
12471  return _IMP_atom.CBetaPDBSelector___repr__(self)
12472 
12473 
12474  @staticmethod
12475  def get_from(o):
12476  return _object_cast_to_CBetaPDBSelector(o)
12477 
12478 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
12479 CBetaPDBSelector_swigregister(CBetaPDBSelector)
12480 
12481 class AtomTypePDBSelector(PDBSelector):
12482  """Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12483 
12484  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12485 
12486  def __init__(self, *args):
12487  """
12488  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
12489  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
12490  """
12491  this = _IMP_atom.new_AtomTypePDBSelector(*args)
12492  try:
12493  self.this.append(this)
12494  except __builtin__.Exception:
12495  self.this = this
12496 
12497  def get_version_info(self):
12498  """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12499  return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12500 
12501 
12502  def __str__(self):
12503  """__str__(AtomTypePDBSelector self) -> std::string"""
12504  return _IMP_atom.AtomTypePDBSelector___str__(self)
12505 
12506 
12507  def __repr__(self):
12508  """__repr__(AtomTypePDBSelector self) -> std::string"""
12509  return _IMP_atom.AtomTypePDBSelector___repr__(self)
12510 
12511 
12512  @staticmethod
12513  def get_from(o):
12514  return _object_cast_to_AtomTypePDBSelector(o)
12515 
12516 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
12517 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12518 
12519 class ResidueTypePDBSelector(PDBSelector):
12520  """Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12521 
12522  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12523 
12524  def __init__(self, *args):
12525  """
12526  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
12527  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
12528  """
12529  this = _IMP_atom.new_ResidueTypePDBSelector(*args)
12530  try:
12531  self.this.append(this)
12532  except __builtin__.Exception:
12533  self.this = this
12534 
12535  def get_version_info(self):
12536  """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12537  return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12538 
12539 
12540  def __str__(self):
12541  """__str__(ResidueTypePDBSelector self) -> std::string"""
12542  return _IMP_atom.ResidueTypePDBSelector___str__(self)
12543 
12544 
12545  def __repr__(self):
12546  """__repr__(ResidueTypePDBSelector self) -> std::string"""
12547  return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12548 
12549 
12550  @staticmethod
12551  def get_from(o):
12552  return _object_cast_to_ResidueTypePDBSelector(o)
12553 
12554 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
12555 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12556 
12557 class CPDBSelector(NonAlternativePDBSelector):
12558  """Proxy of C++ IMP::atom::CPDBSelector class."""
12559 
12560  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12561 
12562  def __init__(self, *args):
12563  """
12564  __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
12565  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
12566  """
12567  this = _IMP_atom.new_CPDBSelector(*args)
12568  try:
12569  self.this.append(this)
12570  except __builtin__.Exception:
12571  self.this = this
12572 
12573  def __str__(self):
12574  """__str__(CPDBSelector self) -> std::string"""
12575  return _IMP_atom.CPDBSelector___str__(self)
12576 
12577 
12578  def __repr__(self):
12579  """__repr__(CPDBSelector self) -> std::string"""
12580  return _IMP_atom.CPDBSelector___repr__(self)
12581 
12582 
12583  @staticmethod
12584  def get_from(o):
12585  return _object_cast_to_CPDBSelector(o)
12586 
12587 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
12588 CPDBSelector_swigregister(CPDBSelector)
12589 
12590 class NPDBSelector(NonAlternativePDBSelector):
12591  """Proxy of C++ IMP::atom::NPDBSelector class."""
12592 
12593  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12594 
12595  def __init__(self, *args):
12596  """
12597  __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
12598  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
12599  """
12600  this = _IMP_atom.new_NPDBSelector(*args)
12601  try:
12602  self.this.append(this)
12603  except __builtin__.Exception:
12604  self.this = this
12605 
12606  def __str__(self):
12607  """__str__(NPDBSelector self) -> std::string"""
12608  return _IMP_atom.NPDBSelector___str__(self)
12609 
12610 
12611  def __repr__(self):
12612  """__repr__(NPDBSelector self) -> std::string"""
12613  return _IMP_atom.NPDBSelector___repr__(self)
12614 
12615 
12616  @staticmethod
12617  def get_from(o):
12618  return _object_cast_to_NPDBSelector(o)
12619 
12620 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
12621 NPDBSelector_swigregister(NPDBSelector)
12622 
12623 class AllPDBSelector(PDBSelector):
12624  """Proxy of C++ IMP::atom::AllPDBSelector class."""
12625 
12626  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12627 
12628  def __init__(self, *args):
12629  """
12630  __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
12631  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
12632  """
12633  this = _IMP_atom.new_AllPDBSelector(*args)
12634  try:
12635  self.this.append(this)
12636  except __builtin__.Exception:
12637  self.this = this
12638 
12639  def get_version_info(self):
12640  """get_version_info(AllPDBSelector self) -> VersionInfo"""
12641  return _IMP_atom.AllPDBSelector_get_version_info(self)
12642 
12643 
12644  def __str__(self):
12645  """__str__(AllPDBSelector self) -> std::string"""
12646  return _IMP_atom.AllPDBSelector___str__(self)
12647 
12648 
12649  def __repr__(self):
12650  """__repr__(AllPDBSelector self) -> std::string"""
12651  return _IMP_atom.AllPDBSelector___repr__(self)
12652 
12653 
12654  @staticmethod
12655  def get_from(o):
12656  return _object_cast_to_AllPDBSelector(o)
12657 
12658 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
12659 AllPDBSelector_swigregister(AllPDBSelector)
12660 
12661 class ChainPDBSelector(NonAlternativePDBSelector):
12662  """Proxy of C++ IMP::atom::ChainPDBSelector class."""
12663 
12664  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12665 
12666  def __init__(self, *args):
12667  """
12668  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
12669  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
12670  """
12671  this = _IMP_atom.new_ChainPDBSelector(*args)
12672  try:
12673  self.this.append(this)
12674  except __builtin__.Exception:
12675  self.this = this
12676 
12677  def __str__(self):
12678  """__str__(ChainPDBSelector self) -> std::string"""
12679  return _IMP_atom.ChainPDBSelector___str__(self)
12680 
12681 
12682  def __repr__(self):
12683  """__repr__(ChainPDBSelector self) -> std::string"""
12684  return _IMP_atom.ChainPDBSelector___repr__(self)
12685 
12686 
12687  @staticmethod
12688  def get_from(o):
12689  return _object_cast_to_ChainPDBSelector(o)
12690 
12691 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
12692 ChainPDBSelector_swigregister(ChainPDBSelector)
12693 
12694 class WaterPDBSelector(NonAlternativePDBSelector):
12695  """Proxy of C++ IMP::atom::WaterPDBSelector class."""
12696 
12697  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12698 
12699  def __init__(self, *args):
12700  """
12701  __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
12702  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
12703  """
12704  this = _IMP_atom.new_WaterPDBSelector(*args)
12705  try:
12706  self.this.append(this)
12707  except __builtin__.Exception:
12708  self.this = this
12709 
12710  def __str__(self):
12711  """__str__(WaterPDBSelector self) -> std::string"""
12712  return _IMP_atom.WaterPDBSelector___str__(self)
12713 
12714 
12715  def __repr__(self):
12716  """__repr__(WaterPDBSelector self) -> std::string"""
12717  return _IMP_atom.WaterPDBSelector___repr__(self)
12718 
12719 
12720  @staticmethod
12721  def get_from(o):
12722  return _object_cast_to_WaterPDBSelector(o)
12723 
12724 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
12725 WaterPDBSelector_swigregister(WaterPDBSelector)
12726 
12727 class HydrogenPDBSelector(NonAlternativePDBSelector):
12728  """Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12729 
12730  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12731 
12732  def __init__(self, *args):
12733  """
12734  __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
12735  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
12736  """
12737  this = _IMP_atom.new_HydrogenPDBSelector(*args)
12738  try:
12739  self.this.append(this)
12740  except __builtin__.Exception:
12741  self.this = this
12742 
12743  def __str__(self):
12744  """__str__(HydrogenPDBSelector self) -> std::string"""
12745  return _IMP_atom.HydrogenPDBSelector___str__(self)
12746 
12747 
12748  def __repr__(self):
12749  """__repr__(HydrogenPDBSelector self) -> std::string"""
12750  return _IMP_atom.HydrogenPDBSelector___repr__(self)
12751 
12752 
12753  @staticmethod
12754  def get_from(o):
12755  return _object_cast_to_HydrogenPDBSelector(o)
12756 
12757 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
12758 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12759 
12760 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12761  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12762 
12763  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12764 
12765  def __init__(self, *args):
12766  """
12767  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12768  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12769  """
12770  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
12771  try:
12772  self.this.append(this)
12773  except __builtin__.Exception:
12774  self.this = this
12775 
12776  def __str__(self):
12777  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12778  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12779 
12780 
12781  def __repr__(self):
12782  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12783  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12784 
12785 
12786  @staticmethod
12787  def get_from(o):
12788  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12789 
12790 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
12791 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12792 
12793 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12794  """Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12795 
12796  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12797 
12798  def __init__(self, *args):
12799  """
12800  __init__(IMP::atom::NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12801  __init__(IMP::atom::NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12802  """
12803  this = _IMP_atom.new_NonHydrogenPDBSelector(*args)
12804  try:
12805  self.this.append(this)
12806  except __builtin__.Exception:
12807  self.this = this
12808 
12809  def __str__(self):
12810  """__str__(NonHydrogenPDBSelector self) -> std::string"""
12811  return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12812 
12813 
12814  def __repr__(self):
12815  """__repr__(NonHydrogenPDBSelector self) -> std::string"""
12816  return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12817 
12818 
12819  @staticmethod
12820  def get_from(o):
12821  return _object_cast_to_NonHydrogenPDBSelector(o)
12822 
12823 NonHydrogenPDBSelector_swigregister = _IMP_atom.NonHydrogenPDBSelector_swigregister
12824 NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12825 
12826 class NonWaterPDBSelector(NonAlternativePDBSelector):
12827  """Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12828 
12829  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12830 
12831  def __init__(self, *args):
12832  """
12833  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12834  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
12835  """
12836  this = _IMP_atom.new_NonWaterPDBSelector(*args)
12837  try:
12838  self.this.append(this)
12839  except __builtin__.Exception:
12840  self.this = this
12841 
12842  def __str__(self):
12843  """__str__(NonWaterPDBSelector self) -> std::string"""
12844  return _IMP_atom.NonWaterPDBSelector___str__(self)
12845 
12846 
12847  def __repr__(self):
12848  """__repr__(NonWaterPDBSelector self) -> std::string"""
12849  return _IMP_atom.NonWaterPDBSelector___repr__(self)
12850 
12851 
12852  @staticmethod
12853  def get_from(o):
12854  return _object_cast_to_NonWaterPDBSelector(o)
12855 
12856 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
12857 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12858 
12859 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12860  """Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12861 
12862  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12863 
12864  def __init__(self, *args):
12865  """
12866  __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
12867  __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
12868  """
12869  this = _IMP_atom.new_BackbonePDBSelector(*args)
12870  try:
12871  self.this.append(this)
12872  except __builtin__.Exception:
12873  self.this = this
12874 
12875  def __str__(self):
12876  """__str__(BackbonePDBSelector self) -> std::string"""
12877  return _IMP_atom.BackbonePDBSelector___str__(self)
12878 
12879 
12880  def __repr__(self):
12881  """__repr__(BackbonePDBSelector self) -> std::string"""
12882  return _IMP_atom.BackbonePDBSelector___repr__(self)
12883 
12884 
12885  @staticmethod
12886  def get_from(o):
12887  return _object_cast_to_BackbonePDBSelector(o)
12888 
12889 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
12890 BackbonePDBSelector_swigregister(BackbonePDBSelector)
12891 
12892 class PPDBSelector(NonAlternativePDBSelector):
12893  """Proxy of C++ IMP::atom::PPDBSelector class."""
12894 
12895  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12896 
12897  def __init__(self, *args):
12898  """
12899  __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
12900  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
12901  """
12902  this = _IMP_atom.new_PPDBSelector(*args)
12903  try:
12904  self.this.append(this)
12905  except __builtin__.Exception:
12906  self.this = this
12907 
12908  def __str__(self):
12909  """__str__(PPDBSelector self) -> std::string"""
12910  return _IMP_atom.PPDBSelector___str__(self)
12911 
12912 
12913  def __repr__(self):
12914  """__repr__(PPDBSelector self) -> std::string"""
12915  return _IMP_atom.PPDBSelector___repr__(self)
12916 
12917 
12918  @staticmethod
12919  def get_from(o):
12920  return _object_cast_to_PPDBSelector(o)
12921 
12922 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
12923 PPDBSelector_swigregister(PPDBSelector)
12924 
12925 class AndPDBSelector(PDBSelector):
12926  """Proxy of C++ IMP::atom::AndPDBSelector class."""
12927 
12928  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12929 
12930  def get_version_info(self):
12931  """get_version_info(AndPDBSelector self) -> VersionInfo"""
12932  return _IMP_atom.AndPDBSelector_get_version_info(self)
12933 
12934 
12935  def __init__(self, a, b):
12936  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
12937  this = _IMP_atom.new_AndPDBSelector(a, b)
12938  try:
12939  self.this.append(this)
12940  except __builtin__.Exception:
12941  self.this = this
12942 
12943  def __str__(self):
12944  """__str__(AndPDBSelector self) -> std::string"""
12945  return _IMP_atom.AndPDBSelector___str__(self)
12946 
12947 
12948  def __repr__(self):
12949  """__repr__(AndPDBSelector self) -> std::string"""
12950  return _IMP_atom.AndPDBSelector___repr__(self)
12951 
12952 
12953  @staticmethod
12954  def get_from(o):
12955  return _object_cast_to_AndPDBSelector(o)
12956 
12957 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
12958 AndPDBSelector_swigregister(AndPDBSelector)
12959 
12960 class OrPDBSelector(PDBSelector):
12961  """Proxy of C++ IMP::atom::OrPDBSelector class."""
12962 
12963  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12964 
12965  def get_version_info(self):
12966  """get_version_info(OrPDBSelector self) -> VersionInfo"""
12967  return _IMP_atom.OrPDBSelector_get_version_info(self)
12968 
12969 
12970  def __init__(self, a, b):
12971  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
12972  this = _IMP_atom.new_OrPDBSelector(a, b)
12973  try:
12974  self.this.append(this)
12975  except __builtin__.Exception:
12976  self.this = this
12977 
12978  def __str__(self):
12979  """__str__(OrPDBSelector self) -> std::string"""
12980  return _IMP_atom.OrPDBSelector___str__(self)
12981 
12982 
12983  def __repr__(self):
12984  """__repr__(OrPDBSelector self) -> std::string"""
12985  return _IMP_atom.OrPDBSelector___repr__(self)
12986 
12987 
12988  @staticmethod
12989  def get_from(o):
12990  return _object_cast_to_OrPDBSelector(o)
12991 
12992 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
12993 OrPDBSelector_swigregister(OrPDBSelector)
12994 
12995 class XorPDBSelector(PDBSelector):
12996  """Proxy of C++ IMP::atom::XorPDBSelector class."""
12997 
12998  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12999 
13000  def get_version_info(self):
13001  """get_version_info(XorPDBSelector self) -> VersionInfo"""
13002  return _IMP_atom.XorPDBSelector_get_version_info(self)
13003 
13004 
13005  def __init__(self, a, b):
13006  """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13007  this = _IMP_atom.new_XorPDBSelector(a, b)
13008  try:
13009  self.this.append(this)
13010  except __builtin__.Exception:
13011  self.this = this
13012 
13013  def __str__(self):
13014  """__str__(XorPDBSelector self) -> std::string"""
13015  return _IMP_atom.XorPDBSelector___str__(self)
13016 
13017 
13018  def __repr__(self):
13019  """__repr__(XorPDBSelector self) -> std::string"""
13020  return _IMP_atom.XorPDBSelector___repr__(self)
13021 
13022 
13023  @staticmethod
13024  def get_from(o):
13025  return _object_cast_to_XorPDBSelector(o)
13026 
13027 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13028 XorPDBSelector_swigregister(XorPDBSelector)
13029 
13030 class NotPDBSelector(PDBSelector):
13031  """Proxy of C++ IMP::atom::NotPDBSelector class."""
13032 
13033  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13034 
13035  def get_version_info(self):
13036  """get_version_info(NotPDBSelector self) -> VersionInfo"""
13037  return _IMP_atom.NotPDBSelector_get_version_info(self)
13038 
13039 
13040  def __init__(self, a):
13041  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13042  this = _IMP_atom.new_NotPDBSelector(a)
13043  try:
13044  self.this.append(this)
13045  except __builtin__.Exception:
13046  self.this = this
13047 
13048  def __str__(self):
13049  """__str__(NotPDBSelector self) -> std::string"""
13050  return _IMP_atom.NotPDBSelector___str__(self)
13051 
13052 
13053  def __repr__(self):
13054  """__repr__(NotPDBSelector self) -> std::string"""
13055  return _IMP_atom.NotPDBSelector___repr__(self)
13056 
13057 
13058  @staticmethod
13059  def get_from(o):
13060  return _object_cast_to_NotPDBSelector(o)
13061 
13062 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13063 NotPDBSelector_swigregister(NotPDBSelector)
13064 
13065 
13066 def get_default_pdb_selector():
13067  """get_default_pdb_selector() -> PDBSelector"""
13068  return _IMP_atom.get_default_pdb_selector()
13069 
13070 def read_pdb(*args):
13071  """
13072  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13073  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13074  read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13075  read_pdb(TextInput input, Model model) -> Hierarchy
13076  read_pdb(TextInput input, int model, Hierarchy h)
13077  """
13078  return _IMP_atom.read_pdb(*args)
13079 
13080 def read_multimodel_pdb(*args):
13081  """
13082  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13083  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13084  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13085  """
13086  return _IMP_atom.read_multimodel_pdb(*args)
13087 
13088 def write_pdb(mhd, out, model=1):
13089  """
13090  write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13091  write_pdb(Selection mhd, TextOutput out)
13092  """
13093  return _IMP_atom.write_pdb(mhd, out, model)
13094 
13095 def write_pdb_of_c_alphas(mhd, out, model=1):
13096  """
13097  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13098  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13099  """
13100  return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13101 
13102 def write_multimodel_pdb(mhd, out):
13103  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13104  return _IMP_atom.write_multimodel_pdb(mhd, out)
13105 
13106 def get_pdb_string(*args):
13107  """
13108  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
13109  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
13110  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
13111  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13112  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13113  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13114  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13115  get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13116  get_pdb_string(Vector3D v, int index=-1) -> std::string
13117  get_pdb_string(Vector3D v) -> std::string
13118  """
13119  return _IMP_atom.get_pdb_string(*args)
13120 
13121 def get_pdb_conect_record_string(arg1, arg2):
13122  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13123  return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13124 class WritePDBOptimizerState(IMP.OptimizerState):
13125  """Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13126 
13127  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13128 
13129  def __init__(self, *args):
13130  """
13131  __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13132  __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13133  """
13134  this = _IMP_atom.new_WritePDBOptimizerState(*args)
13135  try:
13136  self.this.append(this)
13137  except __builtin__.Exception:
13138  self.this = this
13139 
13140  def get_version_info(self):
13141  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13142  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13143 
13144 
13145  def __str__(self):
13146  """__str__(WritePDBOptimizerState self) -> std::string"""
13147  return _IMP_atom.WritePDBOptimizerState___str__(self)
13148 
13149 
13150  def __repr__(self):
13151  """__repr__(WritePDBOptimizerState self) -> std::string"""
13152  return _IMP_atom.WritePDBOptimizerState___repr__(self)
13153 
13154 
13155  @staticmethod
13156  def get_from(o):
13157  return _object_cast_to_WritePDBOptimizerState(o)
13158 
13159 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13160 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13161 
13162 
13163 def get_kt(T):
13164  """get_kt(double T) -> double"""
13165  return _IMP_atom.get_kt(T)
13166 class CAAngleRestraint(IMP.Restraint):
13167  """Proxy of C++ IMP::atom::CAAngleRestraint class."""
13168 
13169  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13170 
13171  def __init__(self, m, p1, p2, p3, phi0, score):
13172  """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13173  this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13174  try:
13175  self.this.append(this)
13176  except __builtin__.Exception:
13177  self.this = this
13178 
13179  def do_get_inputs(self):
13180  """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13181  return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13182 
13183 
13184  def get_version_info(self):
13185  """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13186  return _IMP_atom.CAAngleRestraint_get_version_info(self)
13187 
13188 
13189  def __str__(self):
13190  """__str__(CAAngleRestraint self) -> std::string"""
13191  return _IMP_atom.CAAngleRestraint___str__(self)
13192 
13193 
13194  def __repr__(self):
13195  """__repr__(CAAngleRestraint self) -> std::string"""
13196  return _IMP_atom.CAAngleRestraint___repr__(self)
13197 
13198 
13199  @staticmethod
13200  def get_from(o):
13201  return _object_cast_to_CAAngleRestraint(o)
13202 
13203 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13204 CAAngleRestraint_swigregister(CAAngleRestraint)
13205 
13206 class CADihedralRestraint(IMP.Restraint):
13207  """Proxy of C++ IMP::atom::CADihedralRestraint class."""
13208 
13209  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13210 
13211  def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13212  """__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"""
13213  this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13214  try:
13215  self.this.append(this)
13216  except __builtin__.Exception:
13217  self.this = this
13218 
13219  def do_get_inputs(self):
13220  """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13221  return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13222 
13223 
13224  def get_version_info(self):
13225  """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13226  return _IMP_atom.CADihedralRestraint_get_version_info(self)
13227 
13228 
13229  def __str__(self):
13230  """__str__(CADihedralRestraint self) -> std::string"""
13231  return _IMP_atom.CADihedralRestraint___str__(self)
13232 
13233 
13234  def __repr__(self):
13235  """__repr__(CADihedralRestraint self) -> std::string"""
13236  return _IMP_atom.CADihedralRestraint___repr__(self)
13237 
13238 
13239  @staticmethod
13240  def get_from(o):
13241  return _object_cast_to_CADihedralRestraint(o)
13242 
13243 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13244 CADihedralRestraint_swigregister(CADihedralRestraint)
13245 
13246 class StructureSource(IMP.Decorator):
13247  """Proxy of C++ IMP::atom::StructureSource class."""
13248 
13249  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13250 
13251  def get_source_id(self):
13252  """get_source_id(StructureSource self) -> std::string"""
13253  return _IMP_atom.StructureSource_get_source_id(self)
13254 
13255 
13256  def get_source_chain_id(self):
13257  """get_source_chain_id(StructureSource self) -> std::string"""
13258  return _IMP_atom.StructureSource_get_source_chain_id(self)
13259 
13260 
13261  def set_source_id(self, source_id):
13262  """set_source_id(StructureSource self, std::string source_id)"""
13263  return _IMP_atom.StructureSource_set_source_id(self, source_id)
13264 
13265 
13266  def set_source_chain_id(self, source_chain_id):
13267  """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13268  return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13269 
13270 
13271  def __init__(self, *args):
13272  """
13273  __init__(IMP::atom::StructureSource self) -> StructureSource
13274  __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13275  __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13276  """
13277  this = _IMP_atom.new_StructureSource(*args)
13278  try:
13279  self.this.append(this)
13280  except __builtin__.Exception:
13281  self.this = this
13282 
13283  def get_is_setup(*args):
13284  """
13285  get_is_setup(Model m, ParticleIndex pi) -> bool
13286  get_is_setup(_ParticleAdaptor p) -> bool
13287  """
13288  return _IMP_atom.StructureSource_get_is_setup(*args)
13289 
13290  get_is_setup = staticmethod(get_is_setup)
13291 
13292  def show(self, *args):
13293  """
13294  show(StructureSource self, _ostream out)
13295  show(StructureSource self)
13296  """
13297  return _IMP_atom.StructureSource_show(self, *args)
13298 
13299 
13300  def setup_particle(*args):
13301  """
13302  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13303  setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13304  """
13305  return _IMP_atom.StructureSource_setup_particle(*args)
13306 
13307  setup_particle = staticmethod(setup_particle)
13308 
13309  def add_attribute(self, *args):
13310  """
13311  add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13312  add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13313  add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13314  add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13315  add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13316  add_attribute(StructureSource self, ObjectKey a0, Object a1)
13317  """
13318  return _IMP_atom.StructureSource_add_attribute(self, *args)
13319 
13320 
13321  def get_value(self, *args):
13322  """
13323  get_value(StructureSource self, FloatKey a0) -> IMP::Float
13324  get_value(StructureSource self, IntKey a0) -> IMP::Int
13325  get_value(StructureSource self, StringKey a0) -> IMP::String
13326  get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13327  get_value(StructureSource self, ObjectKey a0) -> Object
13328  """
13329  return _IMP_atom.StructureSource_get_value(self, *args)
13330 
13331 
13332  def set_value(self, *args):
13333  """
13334  set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13335  set_value(StructureSource self, IntKey a0, IMP::Int a1)
13336  set_value(StructureSource self, StringKey a0, IMP::String a1)
13337  set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13338  set_value(StructureSource self, ObjectKey a0, Object a1)
13339  """
13340  return _IMP_atom.StructureSource_set_value(self, *args)
13341 
13342 
13343  def remove_attribute(self, *args):
13344  """
13345  remove_attribute(StructureSource self, FloatKey a0)
13346  remove_attribute(StructureSource self, IntKey a0)
13347  remove_attribute(StructureSource self, StringKey a0)
13348  remove_attribute(StructureSource self, ParticleIndexKey a0)
13349  remove_attribute(StructureSource self, ObjectKey a0)
13350  """
13351  return _IMP_atom.StructureSource_remove_attribute(self, *args)
13352 
13353 
13354  def has_attribute(self, *args):
13355  """
13356  has_attribute(StructureSource self, FloatKey a0) -> bool
13357  has_attribute(StructureSource self, IntKey a0) -> bool
13358  has_attribute(StructureSource self, StringKey a0) -> bool
13359  has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13360  has_attribute(StructureSource self, ObjectKey a0) -> bool
13361  """
13362  return _IMP_atom.StructureSource_has_attribute(self, *args)
13363 
13364 
13365  def get_derivative(self, a0):
13366  """get_derivative(StructureSource self, FloatKey a0) -> double"""
13367  return _IMP_atom.StructureSource_get_derivative(self, a0)
13368 
13369 
13370  def get_name(self):
13371  """get_name(StructureSource self) -> std::string"""
13372  return _IMP_atom.StructureSource_get_name(self)
13373 
13374 
13375  def clear_caches(self):
13376  """clear_caches(StructureSource self)"""
13377  return _IMP_atom.StructureSource_clear_caches(self)
13378 
13379 
13380  def set_name(self, a0):
13381  """set_name(StructureSource self, std::string a0)"""
13382  return _IMP_atom.StructureSource_set_name(self, a0)
13383 
13384 
13385  def set_check_level(self, a0):
13386  """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13387  return _IMP_atom.StructureSource_set_check_level(self, a0)
13388 
13389 
13390  def add_to_derivative(self, a0, a1, a2):
13391  """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13392  return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13393 
13394 
13395  def set_is_optimized(self, a0, a1):
13396  """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13397  return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13398 
13399 
13400  def get_is_optimized(self, a0):
13401  """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13402  return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13403 
13404 
13405  def get_check_level(self):
13406  """get_check_level(StructureSource self) -> IMP::CheckLevel"""
13407  return _IMP_atom.StructureSource_get_check_level(self)
13408 
13409 
13410  def __eq__(self, *args):
13411  """
13412  __eq__(StructureSource self, StructureSource o) -> bool
13413  __eq__(StructureSource self, Particle d) -> bool
13414  """
13415  return _IMP_atom.StructureSource___eq__(self, *args)
13416 
13417 
13418  def __ne__(self, *args):
13419  """
13420  __ne__(StructureSource self, StructureSource o) -> bool
13421  __ne__(StructureSource self, Particle d) -> bool
13422  """
13423  return _IMP_atom.StructureSource___ne__(self, *args)
13424 
13425 
13426  def __le__(self, *args):
13427  """
13428  __le__(StructureSource self, StructureSource o) -> bool
13429  __le__(StructureSource self, Particle d) -> bool
13430  """
13431  return _IMP_atom.StructureSource___le__(self, *args)
13432 
13433 
13434  def __lt__(self, *args):
13435  """
13436  __lt__(StructureSource self, StructureSource o) -> bool
13437  __lt__(StructureSource self, Particle d) -> bool
13438  """
13439  return _IMP_atom.StructureSource___lt__(self, *args)
13440 
13441 
13442  def __ge__(self, *args):
13443  """
13444  __ge__(StructureSource self, StructureSource o) -> bool
13445  __ge__(StructureSource self, Particle d) -> bool
13446  """
13447  return _IMP_atom.StructureSource___ge__(self, *args)
13448 
13449 
13450  def __gt__(self, *args):
13451  """
13452  __gt__(StructureSource self, StructureSource o) -> bool
13453  __gt__(StructureSource self, Particle d) -> bool
13454  """
13455  return _IMP_atom.StructureSource___gt__(self, *args)
13456 
13457 
13458  def __hash__(self):
13459  """__hash__(StructureSource self) -> std::size_t"""
13460  return _IMP_atom.StructureSource___hash__(self)
13461 
13462 
13463  def __str__(self):
13464  """__str__(StructureSource self) -> std::string"""
13465  return _IMP_atom.StructureSource___str__(self)
13466 
13467 
13468  def __repr__(self):
13469  """__repr__(StructureSource self) -> std::string"""
13470  return _IMP_atom.StructureSource___repr__(self)
13471 
13472  __swig_destroy__ = _IMP_atom.delete_StructureSource
13473  __del__ = lambda self: None
13474 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
13475 StructureSource_swigregister(StructureSource)
13476 
13477 def StructureSource_get_is_setup(*args):
13478  """
13479  get_is_setup(Model m, ParticleIndex pi) -> bool
13480  StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
13481  """
13482  return _IMP_atom.StructureSource_get_is_setup(*args)
13483 
13484 def StructureSource_setup_particle(*args):
13485  """
13486  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13487  StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13488  """
13489  return _IMP_atom.StructureSource_setup_particle(*args)
13490 
13491 
13492 def __lshift__(*args):
13493  """
13494  __lshift__(_ostream out, Bonded n) -> _ostream
13495  __lshift__(_ostream out, Bond n) -> _ostream
13496  __lshift__(_ostream out, Hierarchy n) -> _ostream
13497  __lshift__(_ostream out, Angle n) -> _ostream
13498  __lshift__(_ostream out, Dihedral n) -> _ostream
13499  __lshift__(_ostream out, CenterOfMass n) -> _ostream
13500  __lshift__(_ostream out, Diffusion n) -> _ostream
13501  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13502  __lshift__(_ostream out, TAMDParticle n) -> _ostream
13503  __lshift__(_ostream out, Chain n) -> _ostream
13504  __lshift__(_ostream out, Charged n) -> _ostream
13505  __lshift__(_ostream out, Domain n) -> _ostream
13506  __lshift__(_ostream out, LennardJones n) -> _ostream
13507  __lshift__(_ostream out, Fragment n) -> _ostream
13508  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13509  __lshift__(_ostream out, Atom n) -> _ostream
13510  __lshift__(_ostream out, Residue n) -> _ostream
13511  __lshift__(_ostream out, Representation n) -> _ostream
13512  __lshift__(_ostream out, State n) -> _ostream
13513  __lshift__(_ostream out, Molecule n) -> _ostream
13514  __lshift__(_ostream out, Copy n) -> _ostream
13515  __lshift__(_ostream out, StructureSource n) -> _ostream
13516  """
13517  return _IMP_atom.__lshift__(*args)
13518 class HelixRestraint(IMP.Restraint):
13519  """Proxy of C++ IMP::atom::HelixRestraint 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, rs, ideal=True):
13524  """
13525  __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint
13526  __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs) -> HelixRestraint
13527  """
13528  this = _IMP_atom.new_HelixRestraint(rs, ideal)
13529  try:
13530  self.this.append(this)
13531  except __builtin__.Exception:
13532  self.this = this
13533 
13534  def get_number_of_bonds(self):
13535  """get_number_of_bonds(HelixRestraint self) -> int"""
13536  return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13537 
13538 
13539  def get_number_of_dihedrals(self):
13540  """get_number_of_dihedrals(HelixRestraint self) -> int"""
13541  return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13542 
13543 
13544  def do_get_inputs(self):
13545  """do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13546  return _IMP_atom.HelixRestraint_do_get_inputs(self)
13547 
13548 
13549  def get_version_info(self):
13550  """get_version_info(HelixRestraint self) -> VersionInfo"""
13551  return _IMP_atom.HelixRestraint_get_version_info(self)
13552 
13553 
13554  def __str__(self):
13555  """__str__(HelixRestraint self) -> std::string"""
13556  return _IMP_atom.HelixRestraint___str__(self)
13557 
13558 
13559  def __repr__(self):
13560  """__repr__(HelixRestraint self) -> std::string"""
13561  return _IMP_atom.HelixRestraint___repr__(self)
13562 
13563 
13564  @staticmethod
13565  def get_from(o):
13566  return _object_cast_to_HelixRestraint(o)
13567 
13568 HelixRestraint_swigregister = _IMP_atom.HelixRestraint_swigregister
13569 HelixRestraint_swigregister(HelixRestraint)
13570 
13571 
13572 def show_molecular_hierarchy(*args):
13573  """
13574  show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
13575  show_molecular_hierarchy(Hierarchy h) -> _ostream
13576  """
13577  return _IMP_atom.show_molecular_hierarchy(*args)
13578 class CHARMMBond(object):
13579  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class."""
13580 
13581  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13582  __repr__ = _swig_repr
13583 
13584  def __init__(self, atoms):
13585  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
13586  this = _IMP_atom.new_CHARMMBond(atoms)
13587  try:
13588  self.this.append(this)
13589  except __builtin__.Exception:
13590  self.this = this
13591 
13592  def get_endpoint(self, i):
13593  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13594  return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13595 
13596 
13597  def get_contains_atom(self, name):
13598  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13599  return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13600 
13601 
13602  def show(self, *args):
13603  """
13604  show(CHARMMBond self, _ostream out)
13605  show(CHARMMBond self)
13606  """
13607  return _IMP_atom.CHARMMBond_show(self, *args)
13608 
13609  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13610  __del__ = lambda self: None
13611 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
13612 CHARMMBond_swigregister(CHARMMBond)
13613 
13614 class CHARMMAngle(object):
13615  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class."""
13616 
13617  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13618  __repr__ = _swig_repr
13619 
13620  def __init__(self, atoms):
13621  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
13622  this = _IMP_atom.new_CHARMMAngle(atoms)
13623  try:
13624  self.this.append(this)
13625  except __builtin__.Exception:
13626  self.this = this
13627 
13628  def get_endpoint(self, i):
13629  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13630  return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13631 
13632 
13633  def get_contains_atom(self, name):
13634  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13635  return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13636 
13637 
13638  def show(self, *args):
13639  """
13640  show(CHARMMAngle self, _ostream out)
13641  show(CHARMMAngle self)
13642  """
13643  return _IMP_atom.CHARMMAngle_show(self, *args)
13644 
13645  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13646  __del__ = lambda self: None
13647 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
13648 CHARMMAngle_swigregister(CHARMMAngle)
13649 
13650 
13651 def _get_native_overlap_cpp(m1, m2, threshold):
13652  """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13653  return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13654 
13655 def _get_drmsd_cpp(m0, m1):
13656  """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13657  return _IMP_atom._get_drmsd_cpp(m0, m1)
13658 
13659 def _get_drmsd_Q_cpp(m0, m1, threshold):
13660  """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13661  return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13662 
13663 def _get_drms_cpp(m1, m2):
13664  """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13665  return _IMP_atom._get_drms_cpp(m1, m2)
13666 
13667 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13668  """_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"""
13669  return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13670 
13671 def get_native_overlap(a, b, d):
13672  va= [IMP.algebra.get_vector(x) for x in a]
13673  vb= [IMP.algebra.get_vector(x) for x in b]
13674  return _get_native_overlap_cpp(va, vb, d)
13675 
13676 def get_drmsd(a, b):
13677  va= [IMP.algebra.get_vector(x) for x in a]
13678  vb= [IMP.algebra.get_vector(x) for x in b]
13679  return _get_drmsd_cpp(va, vb)
13680 
13681 def get_drms(a, b):
13682  va= [IMP.algebra.get_vector(x) for x in a]
13683  vb= [IMP.algebra.get_vector(x) for x in b]
13684  return _get_drms_cpp(va, vb)
13685 
13686 def get_drmsd_Q(a, b, t):
13687  va= [IMP.algebra.get_vector(x) for x in a]
13688  vb= [IMP.algebra.get_vector(x) for x in b]
13689  return _get_drmsd_Q_cpp(va, vb, t)
13690 
13691 def get_rigid_bodies_drms(a, b, ranges):
13692  va= [IMP.algebra.get_vector(x) for x in a]
13693  vb= [IMP.algebra.get_vector(x) for x in b]
13694 #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
13695  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13696 
13697 
13698 
13699 def get_module_version():
13700  """get_module_version() -> std::string const"""
13701  return _IMP_atom.get_module_version()
13702 
13703 def get_example_path(fname):
13704  """get_example_path(std::string fname) -> std::string"""
13705  return _IMP_atom.get_example_path(fname)
13706 
13707 def get_data_path(fname):
13708  """get_data_path(std::string fname) -> std::string"""
13709  return _IMP_atom.get_data_path(fname)
13710 
13711 from . import _version_check
13712 _version_check.check_version(get_module_version())
13713 __version__ = get_module_version()
13714 
13715 
13716 
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()
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
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)
double get_einstein_rotational_diffusion_coefficient(double r)
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.
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.
double get_kd(double na, double nb, double nab, double volume)
Definition: estimates.h:94
double get_diffusion_angle(double D, double dtfs)
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
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &displacements, double dt)
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.
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:87
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
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)
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.
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_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)
double get_einstein_diffusion_coefficient(double r)
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27