IMP  2.2.1
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 
8 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_atom', [dirname(__file__)])
19  except ImportError:
20  import _IMP_atom
21  return _IMP_atom
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_atom', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_atom = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_atom
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 try:
73  import weakref
74  weakref_proxy = weakref.proxy
75 except:
76  weakref_proxy = lambda x: x
77 
78 
79 class IMP_ATOM_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_ATOM_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_ATOM_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
91  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
96  incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
97  """
98  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
103  decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
104  """
105  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
113  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
117  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
121  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
125  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
129  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
133  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
137  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
141  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
145  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
149  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
153  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
158  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
164 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_atom.IMP_DEBUG
172 IMP_RELEASE = _IMP_atom.IMP_RELEASE
173 IMP_SILENT = _IMP_atom.IMP_SILENT
174 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
175 IMP_TERSE = _IMP_atom.IMP_TERSE
176 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
177 IMP_MEMORY = _IMP_atom.IMP_MEMORY
178 IMP_NONE = _IMP_atom.IMP_NONE
179 IMP_USAGE = _IMP_atom.IMP_USAGE
180 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_atom.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_atom.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_atom.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_atom.IMPBASE_SHOW_WARNINGS
189 import sys
190 class _DirectorObjects(object):
191  """@internal Simple class to keep references to director objects
192  to prevent premature deletion."""
193  def __init__(self):
194  self._objects = []
195  def register(self, obj):
196  """Take a reference to a director object; will only work for
197  refcounted C++ classes"""
198  if hasattr(obj, 'get_ref_count'):
199  self._objects.append(obj)
200  def cleanup(self):
201  """Only drop our reference and allow cleanup by Python if no other
202  Python references exist (we hold 3 references: one in self._objects,
203  one in x, and one in the argument list for getrefcount) *and* no
204  other C++ references exist (the Python object always holds one)"""
205  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
206  or x.get_ref_count() > 1]
207 
208 
209  self._objects = objs
210  def get_object_count(self):
211  """Get number of director objects (useful for testing only)"""
212  return len(self._objects)
213 _director_objects = _DirectorObjects()
214 
215 DEFAULT_CHECK = _IMP_atom.DEFAULT_CHECK
216 NONE = _IMP_atom.NONE
217 USAGE = _IMP_atom.USAGE
218 USAGE_AND_INTERNAL = _IMP_atom.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_atom.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_atom.get_check_level()
227 class _ostream(_object):
228  """Proxy of C++ std::ostream class"""
229  __swig_setmethods__ = {}
230  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
231  __swig_getmethods__ = {}
232  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
233  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
234  __repr__ = _swig_repr
235  def write(self, *args):
236  """write(_ostream self, char const * osa_buf)"""
237  return _IMP_atom._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_atom._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_atom.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_atom.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_atom.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
278 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
279 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
280 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
281 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
282 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
283 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
284 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
285 import IMP.score_functor
286 IMP_CORE_HAS_IMP_BASE = _IMP_atom.IMP_CORE_HAS_IMP_BASE
287 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
288 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
289 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
290 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
292 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
293 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
294 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
295 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
296 import IMP.core
297 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
298 IMP_CONTAINER_HAS_IMP_BASE = _IMP_atom.IMP_CONTAINER_HAS_IMP_BASE
299 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
300 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
301 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
302 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
303 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
304 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
305 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
306 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
307 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
308 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
309 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
310 import IMP.container
311 IMP_ATOM_HAS_IMP_BASE = _IMP_atom.IMP_ATOM_HAS_IMP_BASE
312 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
313 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
314 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
315 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
316 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
317 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
318 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
319 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
320 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
321 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
322 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
323 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
324 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
326  """Proxy of C++ IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class"""
327  __swig_setmethods__ = {}
328  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
329  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyTree, name, value)
330  __swig_getmethods__ = {}
331  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
332  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyTree, name)
333  __repr__ = _swig_repr
334  def __init__(self):
335  """__init__(IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
336  this = _IMP_atom.new_HierarchyTree()
337  try: self.this.append(this)
338  except: self.this = this
339  def get_graph(self):
340  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
341  return _IMP_atom.HierarchyTree_get_graph(self)
342 
343  def get_vertices(self):
344  """get_vertices(HierarchyTree self) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
345  return _IMP_atom.HierarchyTree_get_vertices(self)
346 
347  def get_vertex_name(self, *args):
348  """get_vertex_name(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
349  return _IMP_atom.HierarchyTree_get_vertex_name(self, *args)
350 
351  def get_in_neighbors(self, *args):
352  """get_in_neighbors(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
353  return _IMP_atom.HierarchyTree_get_in_neighbors(self, *args)
354 
355  def get_out_neighbors(self, *args):
356  """get_out_neighbors(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
357  return _IMP_atom.HierarchyTree_get_out_neighbors(self, *args)
358 
359  def show_graphviz(self, *args):
360  """
361  show_graphviz(HierarchyTree self, _ostream out=std::cout)
362  show_graphviz(HierarchyTree self)
363  """
364  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
365 
366  def get_graphviz_string(self):
367  """get_graphviz_string(HierarchyTree self) -> std::string"""
368  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
369 
370  def add_edge(self, *args):
371  """
372  add_edge(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0,
373  IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)
374  """
375  return _IMP_atom.HierarchyTree_add_edge(self, *args)
376 
377  def add_vertex(self, *args):
378  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
379  return _IMP_atom.HierarchyTree_add_vertex(self, *args)
380 
381  def remove_vertex(self, *args):
382  """remove_vertex(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
383  return _IMP_atom.HierarchyTree_remove_vertex(self, *args)
384 
385  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
386  __del__ = lambda self : None;
387 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
388 HierarchyTree_swigregister(HierarchyTree)
389 
390 _value_types.append("HierarchyTree")
391 
392 _object_types.append("PDBSelector")
393 
394 
395 def _object_cast_to_PDBSelector(*args):
396  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
397  return _IMP_atom._object_cast_to_PDBSelector(*args)
398 def Angles(l=[]):
399  return [Angle(x) for x in l]
400 _plural_types.append("Angles")
401 
402 _value_types.append("Angle")
403 
404 def Atoms(l=[]):
405  return [Atom(x) for x in l]
406 _plural_types.append("Atoms")
407 
408 _value_types.append("Atom")
409 
410 def Bonds(l=[]):
411  return [Bond(x) for x in l]
412 _plural_types.append("Bonds")
413 
414 _value_types.append("Bond")
415 
416 def Bondeds(l=[]):
417  return [Bonded(x) for x in l]
418 _plural_types.append("Bondeds")
419 
420 _value_types.append("Bonded")
421 
422 def CHARMMAtomList(l=[]):
423  return [CHARMMAtom(x) for x in l]
424 _plural_types.append("CHARMMAtomList")
425 
426 _value_types.append("CHARMMAtom")
427 
428 def Chains(l=[]):
429  return [Chain(x) for x in l]
430 _plural_types.append("Chains")
431 
432 _value_types.append("Chain")
433 
434 def Chargeds(l=[]):
435  return [Charged(x) for x in l]
436 _plural_types.append("Chargeds")
437 
438 _value_types.append("Charged")
439 
440 def Diffusions(l=[]):
441  return [Diffusion(x) for x in l]
442 _plural_types.append("Diffusions")
443 
444 _value_types.append("Diffusion")
445 
446 def RigidBodyDiffusions(l=[]):
447  return [RigidBodyDiffusion(x) for x in l]
448 _plural_types.append("RigidBodyDiffusions")
449 
450 _value_types.append("RigidBodyDiffusion")
451 
452 def Dihedrals(l=[]):
453  return [Dihedral(x) for x in l]
454 _plural_types.append("Dihedrals")
455 
456 _value_types.append("Dihedral")
457 
458 def Domains(l=[]):
459  return [Domain(x) for x in l]
460 _plural_types.append("Domains")
461 
462 _value_types.append("Domain")
463 
464 def Fragments(l=[]):
465  return [Fragment(x) for x in l]
466 _plural_types.append("Fragments")
467 
468 _value_types.append("Fragment")
469 
470 def Hierarchies(l=[]):
471  return [Hierarchy(x) for x in l]
472 _plural_types.append("Hierarchies")
473 
474 _value_types.append("Hierarchy")
475 
476 def LennardJonesList(l=[]):
477  return [LennardJones(x) for x in l]
478 _plural_types.append("LennardJonesList")
479 
480 _value_types.append("LennardJones")
481 
482 def Masses(l=[]):
483  return [Mass(x) for x in l]
484 _plural_types.append("Masses")
485 
486 _value_types.append("Mass")
487 
488 def Molecules(l=[]):
489  return [Molecule(x) for x in l]
490 _plural_types.append("Molecules")
491 
492 _value_types.append("Molecule")
493 
494 def Residues(l=[]):
495  return [Residue(x) for x in l]
496 _plural_types.append("Residues")
497 
498 _value_types.append("Residue")
499 
500 def Representations(l=[]):
501  return [Representation(x) for x in l]
502 _plural_types.append("Representations")
503 
504 _value_types.append("Representation")
505 
506 def States(l=[]):
507  return [State(x) for x in l]
508 _plural_types.append("States")
509 
510 _value_types.append("State")
511 
512 def Copies(l=[]):
513  return [Copy(x) for x in l]
514 _plural_types.append("Copies")
515 
516 _value_types.append("Copy")
517 
518 def SecondaryStructureResidues(l=[]):
519  return [SecondaryStructureResidue(x) for x in l]
520 _plural_types.append("SecondaryStructureResidues")
521 
522 _value_types.append("SecondaryStructureResidue")
523 
524 _object_types.append("Simulator")
525 
526 
527 def _object_cast_to_Simulator(*args):
528  """_object_cast_to_Simulator(Object o) -> Simulator"""
529  return _IMP_atom._object_cast_to_Simulator(*args)
530 _object_types.append("ATOMPDBSelector")
531 
532 
533 def _object_cast_to_ATOMPDBSelector(*args):
534  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
535  return _IMP_atom._object_cast_to_ATOMPDBSelector(*args)
536 _object_types.append("AllMol2Selector")
537 
538 
539 def _object_cast_to_AllMol2Selector(*args):
540  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
541  return _IMP_atom._object_cast_to_AllMol2Selector(*args)
542 _object_types.append("AllPDBSelector")
543 
544 
545 def _object_cast_to_AllPDBSelector(*args):
546  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
547  return _IMP_atom._object_cast_to_AllPDBSelector(*args)
548 _object_types.append("AndPDBSelector")
549 
550 
551 def _object_cast_to_AndPDBSelector(*args):
552  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
553  return _IMP_atom._object_cast_to_AndPDBSelector(*args)
554 _object_types.append("AngleSingletonScore")
555 
556 
557 def _object_cast_to_AngleSingletonScore(*args):
558  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
559  return _IMP_atom._object_cast_to_AngleSingletonScore(*args)
560 _object_types.append("BondEndpointsRefiner")
561 
562 
563 def _object_cast_to_BondEndpointsRefiner(*args):
564  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
565  return _IMP_atom._object_cast_to_BondEndpointsRefiner(*args)
566 _object_types.append("BondPairContainer")
567 
568 
569 def _object_cast_to_BondPairContainer(*args):
570  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
571  return _IMP_atom._object_cast_to_BondPairContainer(*args)
572 _object_types.append("BondSingletonScore")
573 
574 
575 def _object_cast_to_BondSingletonScore(*args):
576  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
577  return _IMP_atom._object_cast_to_BondSingletonScore(*args)
578 _object_types.append("BondedPairFilter")
579 
580 
581 def _object_cast_to_BondedPairFilter(*args):
582  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
583  return _IMP_atom._object_cast_to_BondedPairFilter(*args)
584 _object_types.append("BrownianDynamics")
585 
586 
587 def _object_cast_to_BrownianDynamics(*args):
588  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
589  return _IMP_atom._object_cast_to_BrownianDynamics(*args)
590 _object_types.append("CAlphaPDBSelector")
591 
592 
593 def _object_cast_to_CAlphaPDBSelector(*args):
594  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
595  return _IMP_atom._object_cast_to_CAlphaPDBSelector(*args)
596 _object_types.append("CBetaPDBSelector")
597 
598 
599 def _object_cast_to_CBetaPDBSelector(*args):
600  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
601  return _IMP_atom._object_cast_to_CBetaPDBSelector(*args)
602 _object_types.append("BackbonePDBSelector")
603 
604 
605 def _object_cast_to_BackbonePDBSelector(*args):
606  """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
607  return _IMP_atom._object_cast_to_BackbonePDBSelector(*args)
608 _object_types.append("CHARMMParameters")
609 
610 
611 def _object_cast_to_CHARMMParameters(*args):
612  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
613  return _IMP_atom._object_cast_to_CHARMMParameters(*args)
614 _object_types.append("CHARMMResidueTopology")
615 
616 
617 def _object_cast_to_CHARMMResidueTopology(*args):
618  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
619  return _IMP_atom._object_cast_to_CHARMMResidueTopology(*args)
620 _object_types.append("CHARMMSegmentTopology")
621 
622 
623 def _object_cast_to_CHARMMSegmentTopology(*args):
624  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
625  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(*args)
626 _object_types.append("CHARMMStereochemistryRestraint")
627 
628 
629 def _object_cast_to_CHARMMStereochemistryRestraint(*args):
630  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
631  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(*args)
632 _object_types.append("CHARMMTopology")
633 
634 
635 def _object_cast_to_CHARMMTopology(*args):
636  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
637  return _IMP_atom._object_cast_to_CHARMMTopology(*args)
638 _object_types.append("CPDBSelector")
639 
640 
641 def _object_cast_to_CPDBSelector(*args):
642  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
643  return _IMP_atom._object_cast_to_CPDBSelector(*args)
644 _object_types.append("ChainPDBSelector")
645 
646 
647 def _object_cast_to_ChainPDBSelector(*args):
648  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
649  return _IMP_atom._object_cast_to_ChainPDBSelector(*args)
650 _object_types.append("CoulombPairScore")
651 
652 
653 def _object_cast_to_CoulombPairScore(*args):
654  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
655  return _IMP_atom._object_cast_to_CoulombPairScore(*args)
656 _object_types.append("CoverBond")
657 
658 
659 def _object_cast_to_CoverBond(*args):
660  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
661  return _IMP_atom._object_cast_to_CoverBond(*args)
662 _object_types.append("DihedralSingletonScore")
663 
664 
665 def _object_cast_to_DihedralSingletonScore(*args):
666  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
667  return _IMP_atom._object_cast_to_DihedralSingletonScore(*args)
668 _object_types.append("DopePairScore")
669 
670 
671 def _object_cast_to_DopePairScore(*args):
672  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
673  return _IMP_atom._object_cast_to_DopePairScore(*args)
674 _object_types.append("OrientedSoapPairScore")
675 
676 
677 def _object_cast_to_OrientedSoapPairScore(*args):
678  """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
679  return _IMP_atom._object_cast_to_OrientedSoapPairScore(*args)
680 _object_types.append("EzRestraint")
681 
682 
683 def _object_cast_to_EzRestraint(*args):
684  """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
685  return _IMP_atom._object_cast_to_EzRestraint(*args)
686 _object_types.append("ForceFieldParameters")
687 
688 
689 def _object_cast_to_ForceFieldParameters(*args):
690  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
691  return _IMP_atom._object_cast_to_ForceFieldParameters(*args)
692 _object_types.append("ForceSwitch")
693 
694 
695 def _object_cast_to_ForceSwitch(*args):
696  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
697  return _IMP_atom._object_cast_to_ForceSwitch(*args)
698 _object_types.append("HydrogenPDBSelector")
699 
700 
701 def _object_cast_to_HydrogenPDBSelector(*args):
702  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
703  return _IMP_atom._object_cast_to_HydrogenPDBSelector(*args)
704 _object_types.append("ImproperSingletonScore")
705 
706 
707 def _object_cast_to_ImproperSingletonScore(*args):
708  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
709  return _IMP_atom._object_cast_to_ImproperSingletonScore(*args)
710 _object_types.append("LennardJonesPairScore")
711 
712 
713 def _object_cast_to_LennardJonesPairScore(*args):
714  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
715  return _IMP_atom._object_cast_to_LennardJonesPairScore(*args)
716 _object_types.append("Mol2Selector")
717 
718 
719 def _object_cast_to_Mol2Selector(*args):
720  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
721  return _IMP_atom._object_cast_to_Mol2Selector(*args)
722 _object_types.append("MolecularDynamics")
723 
724 
725 def _object_cast_to_MolecularDynamics(*args):
726  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
727  return _IMP_atom._object_cast_to_MolecularDynamics(*args)
728 _object_types.append("NPDBSelector")
729 
730 
731 def _object_cast_to_NPDBSelector(*args):
732  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
733  return _IMP_atom._object_cast_to_NPDBSelector(*args)
734 _object_types.append("NonAlternativePDBSelector")
735 
736 
737 def _object_cast_to_NonAlternativePDBSelector(*args):
738  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
739  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(*args)
740 _object_types.append("NonHydrogenMol2Selector")
741 
742 
743 def _object_cast_to_NonHydrogenMol2Selector(*args):
744  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
745  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(*args)
746 _object_types.append("NonWaterNonHydrogenPDBSelector")
747 
748 
749 def _object_cast_to_NonWaterNonHydrogenPDBSelector(*args):
750  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
751  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(*args)
752 _object_types.append("NonWaterPDBSelector")
753 
754 
755 def _object_cast_to_NonWaterPDBSelector(*args):
756  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
757  return _IMP_atom._object_cast_to_NonWaterPDBSelector(*args)
758 _object_types.append("NotPDBSelector")
759 
760 
761 def _object_cast_to_NotPDBSelector(*args):
762  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
763  return _IMP_atom._object_cast_to_NotPDBSelector(*args)
764 _object_types.append("OrPDBSelector")
765 
766 
767 def _object_cast_to_OrPDBSelector(*args):
768  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
769  return _IMP_atom._object_cast_to_OrPDBSelector(*args)
770 _object_types.append("PPDBSelector")
771 
772 
773 def _object_cast_to_PPDBSelector(*args):
774  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
775  return _IMP_atom._object_cast_to_PPDBSelector(*args)
776 _object_types.append("ProteinLigandAtomPairScore")
777 
778 
779 def _object_cast_to_ProteinLigandAtomPairScore(*args):
780  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
781  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(*args)
782 _object_types.append("ProteinLigandRestraint")
783 
784 
785 def _object_cast_to_ProteinLigandRestraint(*args):
786  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
787  return _IMP_atom._object_cast_to_ProteinLigandRestraint(*args)
788 _object_types.append("SameResiduePairFilter")
789 
790 
791 def _object_cast_to_SameResiduePairFilter(*args):
792  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
793  return _IMP_atom._object_cast_to_SameResiduePairFilter(*args)
794 _object_types.append("SoapPairFilter")
795 
796 
797 def _object_cast_to_SoapPairFilter(*args):
798  """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
799  return _IMP_atom._object_cast_to_SoapPairFilter(*args)
800 _object_types.append("SmoothingFunction")
801 
802 
803 def _object_cast_to_SmoothingFunction(*args):
804  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
805  return _IMP_atom._object_cast_to_SmoothingFunction(*args)
806 _object_types.append("StereochemistryPairFilter")
807 
808 
809 def _object_cast_to_StereochemistryPairFilter(*args):
810  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
811  return _IMP_atom._object_cast_to_StereochemistryPairFilter(*args)
812 _object_types.append("VelocityScalingOptimizerState")
813 
814 
815 def _object_cast_to_VelocityScalingOptimizerState(*args):
816  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
817  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(*args)
818 _object_types.append("WaterPDBSelector")
819 
820 
821 def _object_cast_to_WaterPDBSelector(*args):
822  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
823  return _IMP_atom._object_cast_to_WaterPDBSelector(*args)
824 _object_types.append("WritePDBOptimizerState")
825 
826 
827 def _object_cast_to_WritePDBOptimizerState(*args):
828  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
829  return _IMP_atom._object_cast_to_WritePDBOptimizerState(*args)
830 AtomTypes=list
831 _plural_types.append("AtomTypes")
832 _value_types.append("AtomType")
833 
834 CHARMMAtomTopologies=list
835 _plural_types.append("CHARMMAtomTopologies")
836 _value_types.append("CHARMMAtomTopology")
837 
838 CHARMMBondEndpoints=list
839 _plural_types.append("CHARMMBondEndpoints")
840 _value_types.append("CHARMMBondEndpoint")
841 
842 CHARMMBondParametersList=list
843 _plural_types.append("CHARMMBondParametersList")
844 _value_types.append("CHARMMBondParameters")
845 
846 CHARMMDihedralParametersList=list
847 _plural_types.append("CHARMMDihedralParametersList")
848 _value_types.append("CHARMMDihedralParameters")
849 
850 _object_types.append("CHARMMIdealResidueTopology")
851 
852 
853 def _object_cast_to_CHARMMIdealResidueTopology(*args):
854  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
855  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(*args)
856 CHARMMInternalCoordinates=list
857 _plural_types.append("CHARMMInternalCoordinates")
858 _value_types.append("CHARMMInternalCoordinate")
859 
860 _object_types.append("CHARMMPatch")
861 
862 
863 def _object_cast_to_CHARMMPatch(*args):
864  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
865  return _IMP_atom._object_cast_to_CHARMMPatch(*args)
866 _object_types.append("CHARMMResidueTopologyBase")
867 
868 
869 def _object_cast_to_CHARMMResidueTopologyBase(*args):
870  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
871  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(*args)
872 ResidueTypes=list
873 _plural_types.append("ResidueTypes")
874 _value_types.append("ResidueType")
875 
876 Selections=list
877 _plural_types.append("Selections")
878 _value_types.append("Selection")
879 
880 _object_types.append("RemoveRigidMotionOptimizerState")
881 
882 
883 def _object_cast_to_RemoveRigidMotionOptimizerState(*args):
884  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
885  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(*args)
886 _object_types.append("BerendsenThermostatOptimizerState")
887 
888 
889 def _object_cast_to_BerendsenThermostatOptimizerState(*args):
890  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
891  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(*args)
892 _object_types.append("LangevinThermostatOptimizerState")
893 
894 
895 def _object_cast_to_LangevinThermostatOptimizerState(*args):
896  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
897  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(*args)
898 _object_types.append("SelectionGeometry")
899 
900 
901 def _object_cast_to_SelectionGeometry(*args):
902  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
903  return _IMP_atom._object_cast_to_SelectionGeometry(*args)
904 _object_types.append("HierarchyGeometry")
905 
906 
907 def _object_cast_to_HierarchyGeometry(*args):
908  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
909  return _IMP_atom._object_cast_to_HierarchyGeometry(*args)
910 _object_types.append("HierarchiesGeometry")
911 
912 
913 def _object_cast_to_HierarchiesGeometry(*args):
914  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
915  return _IMP_atom._object_cast_to_HierarchiesGeometry(*args)
916 _object_types.append("BondGeometry")
917 
918 
919 def _object_cast_to_BondGeometry(*args):
920  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
921  return _IMP_atom._object_cast_to_BondGeometry(*args)
922 _object_types.append("BondsGeometry")
923 
924 
925 def _object_cast_to_BondsGeometry(*args):
926  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
927  return _IMP_atom._object_cast_to_BondsGeometry(*args)
928 CHARMMDihedrals=list
929 _plural_types.append("CHARMMDihedrals")
930 _value_types.append("CHARMMDihedral")
931 
932 CHARMMBonds=list
933 _plural_types.append("CHARMMBonds")
934 _value_types.append("CHARMMBond")
935 
936 CHARMMAngles=list
937 _plural_types.append("CHARMMAngles")
938 _value_types.append("CHARMMAngle")
939 
940 class Bond(IMP.kernel.Decorator):
941  """Proxy of C++ IMP::atom::Bond class"""
942  __swig_setmethods__ = {}
943  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
944  __setattr__ = lambda self, name, value: _swig_setattr(self, Bond, name, value)
945  __swig_getmethods__ = {}
946  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
947  __getattr__ = lambda self, name: _swig_getattr(self, Bond, name)
948  def __init__(self, *args):
949  """
950  __init__(IMP::atom::Bond self) -> Bond
951  __init__(IMP::atom::Bond self, Model m, ::IMP::kernel::ParticleIndex id) -> Bond
952  __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
953  """
954  this = _IMP_atom.new_Bond(*args)
955  try: self.this.append(this)
956  except: self.this = this
957  def decorate_particle(*args):
958  """decorate_particle(Particle p) -> Bond"""
959  return _IMP_atom.Bond_decorate_particle(*args)
960 
961  if _newclass:decorate_particle = staticmethod(decorate_particle)
962  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
963  def show(self, *args):
964  """
965  show(Bond self, _ostream out=std::cout)
966  show(Bond self)
967  """
968  return _IMP_atom.Bond_show(self, *args)
969 
970  def get_is_setup(*args):
971  """
972  get_is_setup(_ParticleAdaptor p) -> bool
973  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
974  """
975  return _IMP_atom.Bond_get_is_setup(*args)
976 
977  if _newclass:get_is_setup = staticmethod(get_is_setup)
978  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
979  UNKNOWN = _IMP_atom.Bond_UNKNOWN
980  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
981  SINGLE = _IMP_atom.Bond_SINGLE
982  DOUBLE = _IMP_atom.Bond_DOUBLE
983  TRIPLE = _IMP_atom.Bond_TRIPLE
984  HYDROGEN = _IMP_atom.Bond_HYDROGEN
985  SALT = _IMP_atom.Bond_SALT
986  PEPTIDE = _IMP_atom.Bond_PEPTIDE
987  AMIDE = _IMP_atom.Bond_AMIDE
988  AROMATIC = _IMP_atom.Bond_AROMATIC
989  def get_bonded(self, *args):
990  """get_bonded(Bond self, unsigned int i) -> Bonded"""
991  return _IMP_atom.Bond_get_bonded(self, *args)
992 
993  def get_type(self):
994  """get_type(Bond self) -> IMP::Int"""
995  return _IMP_atom.Bond_get_type(self)
996 
997  def set_type(self, *args):
998  """set_type(Bond self, IMP::Int t)"""
999  return _IMP_atom.Bond_set_type(self, *args)
1000 
1001  def get_order(self):
1002  """get_order(Bond self) -> IMP::Int"""
1003  return _IMP_atom.Bond_get_order(self)
1004 
1005  def set_order(self, *args):
1006  """set_order(Bond self, IMP::Int t)"""
1007  return _IMP_atom.Bond_set_order(self, *args)
1008 
1009  def get_length(self):
1010  """get_length(Bond self) -> IMP::Float"""
1011  return _IMP_atom.Bond_get_length(self)
1012 
1013  def set_length(self, *args):
1014  """set_length(Bond self, IMP::Float t)"""
1015  return _IMP_atom.Bond_set_length(self, *args)
1016 
1017  def get_stiffness(self):
1018  """get_stiffness(Bond self) -> IMP::Float"""
1019  return _IMP_atom.Bond_get_stiffness(self)
1020 
1021  def set_stiffness(self, *args):
1022  """set_stiffness(Bond self, IMP::Float t)"""
1023  return _IMP_atom.Bond_set_stiffness(self, *args)
1024 
1025  def get_length_key():
1026  """get_length_key() -> FloatKey"""
1027  return _IMP_atom.Bond_get_length_key()
1028 
1029  if _newclass:get_length_key = staticmethod(get_length_key)
1030  __swig_getmethods__["get_length_key"] = lambda x: get_length_key
1031  def add_attribute(self, *args):
1032  """
1033  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1034  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1035  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1036  add_attribute(Bond self, StringKey a0, IMP::String a1)
1037  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1038  add_attribute(Bond self, ObjectKey a0, Object a1)
1039  """
1040  return _IMP_atom.Bond_add_attribute(self, *args)
1041 
1042  def get_value(self, *args):
1043  """
1044  get_value(Bond self, FloatKey a0) -> IMP::Float
1045  get_value(Bond self, IntKey a0) -> IMP::Int
1046  get_value(Bond self, StringKey a0) -> IMP::String
1047  get_value(Bond self, ParticleIndexKey a0) -> Particle
1048  get_value(Bond self, ObjectKey a0) -> Object
1049  """
1050  return _IMP_atom.Bond_get_value(self, *args)
1051 
1052  def set_value(self, *args):
1053  """
1054  set_value(Bond self, FloatKey a0, IMP::Float a1)
1055  set_value(Bond self, IntKey a0, IMP::Int a1)
1056  set_value(Bond self, StringKey a0, IMP::String a1)
1057  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1058  set_value(Bond self, ObjectKey a0, Object a1)
1059  """
1060  return _IMP_atom.Bond_set_value(self, *args)
1061 
1062  def remove_attribute(self, *args):
1063  """
1064  remove_attribute(Bond self, FloatKey a0)
1065  remove_attribute(Bond self, IntKey a0)
1066  remove_attribute(Bond self, StringKey a0)
1067  remove_attribute(Bond self, ParticleIndexKey a0)
1068  remove_attribute(Bond self, ObjectKey a0)
1069  """
1070  return _IMP_atom.Bond_remove_attribute(self, *args)
1071 
1072  def has_attribute(self, *args):
1073  """
1074  has_attribute(Bond self, FloatKey a0) -> bool
1075  has_attribute(Bond self, IntKey a0) -> bool
1076  has_attribute(Bond self, StringKey a0) -> bool
1077  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1078  has_attribute(Bond self, ObjectKey a0) -> bool
1079  """
1080  return _IMP_atom.Bond_has_attribute(self, *args)
1081 
1082  def get_derivative(self, *args):
1083  """get_derivative(Bond self, FloatKey a0) -> double"""
1084  return _IMP_atom.Bond_get_derivative(self, *args)
1085 
1086  def get_name(self):
1087  """get_name(Bond self) -> std::string"""
1088  return _IMP_atom.Bond_get_name(self)
1089 
1090  def clear_caches(self):
1091  """clear_caches(Bond self)"""
1092  return _IMP_atom.Bond_clear_caches(self)
1093 
1094  def set_name(self, *args):
1095  """set_name(Bond self, std::string a0)"""
1096  return _IMP_atom.Bond_set_name(self, *args)
1097 
1098  def set_check_level(self, *args):
1099  """set_check_level(Bond self, IMP::base::CheckLevel a0)"""
1100  return _IMP_atom.Bond_set_check_level(self, *args)
1101 
1102  def add_to_derivative(self, *args):
1103  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1104  return _IMP_atom.Bond_add_to_derivative(self, *args)
1105 
1106  def set_is_optimized(self, *args):
1107  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1108  return _IMP_atom.Bond_set_is_optimized(self, *args)
1109 
1110  def get_is_optimized(self, *args):
1111  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1112  return _IMP_atom.Bond_get_is_optimized(self, *args)
1113 
1114  def get_check_level(self):
1115  """get_check_level(Bond self) -> IMP::base::CheckLevel"""
1116  return _IMP_atom.Bond_get_check_level(self)
1117 
1118  def __eq__(self, *args):
1119  """
1120  __eq__(Bond self, Bond o) -> bool
1121  __eq__(Bond self, Particle d) -> bool
1122  """
1123  return _IMP_atom.Bond___eq__(self, *args)
1124 
1125  def __ne__(self, *args):
1126  """
1127  __ne__(Bond self, Bond o) -> bool
1128  __ne__(Bond self, Particle d) -> bool
1129  """
1130  return _IMP_atom.Bond___ne__(self, *args)
1131 
1132  def __le__(self, *args):
1133  """
1134  __le__(Bond self, Bond o) -> bool
1135  __le__(Bond self, Particle d) -> bool
1136  """
1137  return _IMP_atom.Bond___le__(self, *args)
1138 
1139  def __lt__(self, *args):
1140  """
1141  __lt__(Bond self, Bond o) -> bool
1142  __lt__(Bond self, Particle d) -> bool
1143  """
1144  return _IMP_atom.Bond___lt__(self, *args)
1145 
1146  def __ge__(self, *args):
1147  """
1148  __ge__(Bond self, Bond o) -> bool
1149  __ge__(Bond self, Particle d) -> bool
1150  """
1151  return _IMP_atom.Bond___ge__(self, *args)
1152 
1153  def __gt__(self, *args):
1154  """
1155  __gt__(Bond self, Bond o) -> bool
1156  __gt__(Bond self, Particle d) -> bool
1157  """
1158  return _IMP_atom.Bond___gt__(self, *args)
1159 
1160  def __str__(self):
1161  """__str__(Bond self) -> std::string"""
1162  return _IMP_atom.Bond___str__(self)
1163 
1164  def __repr__(self):
1165  """__repr__(Bond self) -> std::string"""
1166  return _IMP_atom.Bond___repr__(self)
1167 
1168  __swig_destroy__ = _IMP_atom.delete_Bond
1169  __del__ = lambda self : None;
1170 Bond_swigregister = _IMP_atom.Bond_swigregister
1171 Bond_swigregister(Bond)
1172 
1173 def Bond_decorate_particle(*args):
1174  """Bond_decorate_particle(Particle p) -> Bond"""
1175  return _IMP_atom.Bond_decorate_particle(*args)
1176 
1177 def Bond_get_is_setup(*args):
1178  """
1179  get_is_setup(_ParticleAdaptor p) -> bool
1180  Bond_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1181  """
1182  return _IMP_atom.Bond_get_is_setup(*args)
1183 
1184 def Bond_get_length_key():
1185  """Bond_get_length_key() -> FloatKey"""
1186  return _IMP_atom.Bond_get_length_key()
1187 
1188 class Bonded(IMP.kernel.Decorator):
1189  """Proxy of C++ IMP::atom::Bonded class"""
1190  __swig_setmethods__ = {}
1191  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1192  __setattr__ = lambda self, name, value: _swig_setattr(self, Bonded, name, value)
1193  __swig_getmethods__ = {}
1194  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1195  __getattr__ = lambda self, name: _swig_getattr(self, Bonded, name)
1196  def __init__(self, *args):
1197  """
1198  __init__(IMP::atom::Bonded self) -> Bonded
1199  __init__(IMP::atom::Bonded self, Model m, ::IMP::kernel::ParticleIndex id) -> Bonded
1200  __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1201  """
1202  this = _IMP_atom.new_Bonded(*args)
1203  try: self.this.append(this)
1204  except: self.this = this
1205  def decorate_particle(*args):
1206  """decorate_particle(Particle p) -> Bonded"""
1207  return _IMP_atom.Bonded_decorate_particle(*args)
1208 
1209  if _newclass:decorate_particle = staticmethod(decorate_particle)
1210  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1211  def show(self, *args):
1212  """
1213  show(Bonded self, _ostream out=std::cout)
1214  show(Bonded self)
1215  """
1216  return _IMP_atom.Bonded_show(self, *args)
1217 
1218  def setup_particle(*args):
1219  """
1220  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Bonded
1221  setup_particle(_ParticleAdaptor decorator) -> Bonded
1222  """
1223  return _IMP_atom.Bonded_setup_particle(*args)
1224 
1225  if _newclass:setup_particle = staticmethod(setup_particle)
1226  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1227  def get_is_setup(*args):
1228  """
1229  get_is_setup(_ParticleAdaptor p) -> bool
1230  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1231  """
1232  return _IMP_atom.Bonded_get_is_setup(*args)
1233 
1234  if _newclass:get_is_setup = staticmethod(get_is_setup)
1235  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1236  def get_number_of_bonds(self):
1237  """get_number_of_bonds(Bonded self) -> unsigned int"""
1238  return _IMP_atom.Bonded_get_number_of_bonds(self)
1239 
1240  def get_bond_indexes(self):
1241  """get_bond_indexes(Bonded self) -> IMP::kernel::ParticleIndexes"""
1242  return _IMP_atom.Bonded_get_bond_indexes(self)
1243 
1244  def get_bond(self, *args):
1245  """get_bond(Bonded self, unsigned int i) -> Bond"""
1246  return _IMP_atom.Bonded_get_bond(self, *args)
1247 
1248  def get_bonded(self, *args):
1249  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1250  return _IMP_atom.Bonded_get_bonded(self, *args)
1251 
1252  def add_attribute(self, *args):
1253  """
1254  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1255  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1256  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1257  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1258  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1259  add_attribute(Bonded self, ObjectKey a0, Object a1)
1260  """
1261  return _IMP_atom.Bonded_add_attribute(self, *args)
1262 
1263  def get_value(self, *args):
1264  """
1265  get_value(Bonded self, FloatKey a0) -> IMP::Float
1266  get_value(Bonded self, IntKey a0) -> IMP::Int
1267  get_value(Bonded self, StringKey a0) -> IMP::String
1268  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1269  get_value(Bonded self, ObjectKey a0) -> Object
1270  """
1271  return _IMP_atom.Bonded_get_value(self, *args)
1272 
1273  def set_value(self, *args):
1274  """
1275  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1276  set_value(Bonded self, IntKey a0, IMP::Int a1)
1277  set_value(Bonded self, StringKey a0, IMP::String a1)
1278  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1279  set_value(Bonded self, ObjectKey a0, Object a1)
1280  """
1281  return _IMP_atom.Bonded_set_value(self, *args)
1282 
1283  def remove_attribute(self, *args):
1284  """
1285  remove_attribute(Bonded self, FloatKey a0)
1286  remove_attribute(Bonded self, IntKey a0)
1287  remove_attribute(Bonded self, StringKey a0)
1288  remove_attribute(Bonded self, ParticleIndexKey a0)
1289  remove_attribute(Bonded self, ObjectKey a0)
1290  """
1291  return _IMP_atom.Bonded_remove_attribute(self, *args)
1292 
1293  def has_attribute(self, *args):
1294  """
1295  has_attribute(Bonded self, FloatKey a0) -> bool
1296  has_attribute(Bonded self, IntKey a0) -> bool
1297  has_attribute(Bonded self, StringKey a0) -> bool
1298  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1299  has_attribute(Bonded self, ObjectKey a0) -> bool
1300  """
1301  return _IMP_atom.Bonded_has_attribute(self, *args)
1302 
1303  def get_derivative(self, *args):
1304  """get_derivative(Bonded self, FloatKey a0) -> double"""
1305  return _IMP_atom.Bonded_get_derivative(self, *args)
1306 
1307  def get_name(self):
1308  """get_name(Bonded self) -> std::string"""
1309  return _IMP_atom.Bonded_get_name(self)
1310 
1311  def clear_caches(self):
1312  """clear_caches(Bonded self)"""
1313  return _IMP_atom.Bonded_clear_caches(self)
1314 
1315  def set_name(self, *args):
1316  """set_name(Bonded self, std::string a0)"""
1317  return _IMP_atom.Bonded_set_name(self, *args)
1318 
1319  def set_check_level(self, *args):
1320  """set_check_level(Bonded self, IMP::base::CheckLevel a0)"""
1321  return _IMP_atom.Bonded_set_check_level(self, *args)
1322 
1323  def add_to_derivative(self, *args):
1324  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1325  return _IMP_atom.Bonded_add_to_derivative(self, *args)
1326 
1327  def set_is_optimized(self, *args):
1328  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1329  return _IMP_atom.Bonded_set_is_optimized(self, *args)
1330 
1331  def get_is_optimized(self, *args):
1332  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1333  return _IMP_atom.Bonded_get_is_optimized(self, *args)
1334 
1335  def get_check_level(self):
1336  """get_check_level(Bonded self) -> IMP::base::CheckLevel"""
1337  return _IMP_atom.Bonded_get_check_level(self)
1338 
1339  def __eq__(self, *args):
1340  """
1341  __eq__(Bonded self, Bonded o) -> bool
1342  __eq__(Bonded self, Particle d) -> bool
1343  """
1344  return _IMP_atom.Bonded___eq__(self, *args)
1345 
1346  def __ne__(self, *args):
1347  """
1348  __ne__(Bonded self, Bonded o) -> bool
1349  __ne__(Bonded self, Particle d) -> bool
1350  """
1351  return _IMP_atom.Bonded___ne__(self, *args)
1352 
1353  def __le__(self, *args):
1354  """
1355  __le__(Bonded self, Bonded o) -> bool
1356  __le__(Bonded self, Particle d) -> bool
1357  """
1358  return _IMP_atom.Bonded___le__(self, *args)
1359 
1360  def __lt__(self, *args):
1361  """
1362  __lt__(Bonded self, Bonded o) -> bool
1363  __lt__(Bonded self, Particle d) -> bool
1364  """
1365  return _IMP_atom.Bonded___lt__(self, *args)
1366 
1367  def __ge__(self, *args):
1368  """
1369  __ge__(Bonded self, Bonded o) -> bool
1370  __ge__(Bonded self, Particle d) -> bool
1371  """
1372  return _IMP_atom.Bonded___ge__(self, *args)
1373 
1374  def __gt__(self, *args):
1375  """
1376  __gt__(Bonded self, Bonded o) -> bool
1377  __gt__(Bonded self, Particle d) -> bool
1378  """
1379  return _IMP_atom.Bonded___gt__(self, *args)
1380 
1381  def __str__(self):
1382  """__str__(Bonded self) -> std::string"""
1383  return _IMP_atom.Bonded___str__(self)
1384 
1385  def __repr__(self):
1386  """__repr__(Bonded self) -> std::string"""
1387  return _IMP_atom.Bonded___repr__(self)
1388 
1389  __swig_destroy__ = _IMP_atom.delete_Bonded
1390  __del__ = lambda self : None;
1391 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1392 Bonded_swigregister(Bonded)
1393 
1394 def Bonded_decorate_particle(*args):
1395  """Bonded_decorate_particle(Particle p) -> Bonded"""
1396  return _IMP_atom.Bonded_decorate_particle(*args)
1397 
1398 def Bonded_setup_particle(*args):
1399  """
1400  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Bonded
1401  Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1402  """
1403  return _IMP_atom.Bonded_setup_particle(*args)
1404 
1405 def Bonded_get_is_setup(*args):
1406  """
1407  get_is_setup(_ParticleAdaptor p) -> bool
1408  Bonded_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1409  """
1410  return _IMP_atom.Bonded_get_is_setup(*args)
1411 
1412 
1413 def create_custom_bond(*args):
1414  """
1415  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1416  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1417  """
1418  return _IMP_atom.create_custom_bond(*args)
1419 
1420 def create_bond(*args):
1421  """
1422  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1423  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1424  """
1425  return _IMP_atom.create_bond(*args)
1426 
1427 def destroy_bond(*args):
1428  """destroy_bond(Bond b)"""
1429  return _IMP_atom.destroy_bond(*args)
1430 
1431 def get_bond(*args):
1432  """get_bond(Bonded a, Bonded b) -> Bond"""
1433  return _IMP_atom.get_bond(*args)
1434 class BondGeometry(IMP.display.SingletonGeometry):
1435  """Proxy of C++ IMP::atom::BondGeometry class"""
1436  __swig_setmethods__ = {}
1437  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1438  __setattr__ = lambda self, name, value: _swig_setattr(self, BondGeometry, name, value)
1439  __swig_getmethods__ = {}
1440  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1441  __getattr__ = lambda self, name: _swig_getattr(self, BondGeometry, name)
1442  def __init__(self, *args):
1443  """
1444  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1445  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1446  """
1447  this = _IMP_atom.new_BondGeometry(*args)
1448  try: self.this.append(this)
1449  except: self.this = this
1450  def get_version_info(self):
1451  """get_version_info(BondGeometry self) -> VersionInfo"""
1452  return _IMP_atom.BondGeometry_get_version_info(self)
1453 
1454  def __str__(self):
1455  """__str__(BondGeometry self) -> std::string"""
1456  return _IMP_atom.BondGeometry___str__(self)
1457 
1458  def __repr__(self):
1459  """__repr__(BondGeometry self) -> std::string"""
1460  return _IMP_atom.BondGeometry___repr__(self)
1461 
1462  def get_from(o):
1463  return _object_cast_to_BondGeometry(o)
1464  get_from = staticmethod(get_from)
1465 
1466 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1467 BondGeometry_swigregister(BondGeometry)
1468 
1469 class BondsGeometry(IMP.display.SingletonsGeometry):
1470  """Proxy of C++ IMP::atom::BondsGeometry class"""
1471  __swig_setmethods__ = {}
1472  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1473  __setattr__ = lambda self, name, value: _swig_setattr(self, BondsGeometry, name, value)
1474  __swig_getmethods__ = {}
1475  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1476  __getattr__ = lambda self, name: _swig_getattr(self, BondsGeometry, name)
1477  def __init__(self, *args):
1478  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1479  this = _IMP_atom.new_BondsGeometry(*args)
1480  try: self.this.append(this)
1481  except: self.this = this
1482  def get_version_info(self):
1483  """get_version_info(BondsGeometry self) -> VersionInfo"""
1484  return _IMP_atom.BondsGeometry_get_version_info(self)
1485 
1486  def __str__(self):
1487  """__str__(BondsGeometry self) -> std::string"""
1488  return _IMP_atom.BondsGeometry___str__(self)
1489 
1490  def __repr__(self):
1491  """__repr__(BondsGeometry self) -> std::string"""
1492  return _IMP_atom.BondsGeometry___repr__(self)
1493 
1494  def get_from(o):
1495  return _object_cast_to_BondsGeometry(o)
1496  get_from = staticmethod(get_from)
1497 
1498 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1499 BondsGeometry_swigregister(BondsGeometry)
1500 
1501 class Hierarchy(IMP.core.Hierarchy):
1502  """Proxy of C++ IMP::atom::Hierarchy class"""
1503  __swig_setmethods__ = {}
1504  for _s in [IMP.core.Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1505  __setattr__ = lambda self, name, value: _swig_setattr(self, Hierarchy, name, value)
1506  __swig_getmethods__ = {}
1507  for _s in [IMP.core.Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1508  __getattr__ = lambda self, name: _swig_getattr(self, Hierarchy, name)
1509  def decorate_particle(*args):
1510  """decorate_particle(Particle p) -> Hierarchy"""
1511  return _IMP_atom.Hierarchy_decorate_particle(*args)
1512 
1513  if _newclass:decorate_particle = staticmethod(decorate_particle)
1514  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1515  def particle_is_instance(*args):
1516  """
1517  particle_is_instance(Particle p) -> bool
1518  particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1519  """
1520  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1521 
1522  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1523  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1524  def __init__(self, *args):
1525  """
1526  __init__(IMP::atom::Hierarchy self, Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1527  __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1528  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1529  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1530  """
1531  this = _IMP_atom.new_Hierarchy(*args)
1532  try: self.this.append(this)
1533  except: self.this = this
1534  def setup_particle(*args):
1535  """
1536  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1537  setup_particle(Particle p) -> Hierarchy
1538  setup_particle(Model m, IMP::kernel::ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::kernel::ParticleIndexesAdaptor()) -> Hierarchy
1539  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1540  """
1541  return _IMP_atom.Hierarchy_setup_particle(*args)
1542 
1543  if _newclass:setup_particle = staticmethod(setup_particle)
1544  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1545  def get_is_setup(*args):
1546  """
1547  get_is_setup(Particle p) -> bool
1548  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
1549  """
1550  return _IMP_atom.Hierarchy_get_is_setup(*args)
1551 
1552  if _newclass:get_is_setup = staticmethod(get_is_setup)
1553  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1554  def get_is_valid(self, *args):
1555  """get_is_valid(Hierarchy self, bool print_info) -> bool"""
1556  return _IMP_atom.Hierarchy_get_is_valid(self, *args)
1557 
1558  def add_child(self, *args):
1559  """add_child(Hierarchy self, Hierarchy o)"""
1560  return _IMP_atom.Hierarchy_add_child(self, *args)
1561 
1562  def get_child(self, *args):
1563  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1564  return _IMP_atom.Hierarchy_get_child(self, *args)
1565 
1566  def get_children(self):
1567  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1568  return _IMP_atom.Hierarchy_get_children(self)
1569 
1570  def get_parent(self):
1571  """get_parent(Hierarchy self) -> Hierarchy"""
1572  return _IMP_atom.Hierarchy_get_parent(self)
1573 
1574  def get_as_atom(self):
1575  """get_as_atom(Hierarchy self) -> Atom"""
1576  return _IMP_atom.Hierarchy_get_as_atom(self)
1577 
1578  def get_as_residue(self):
1579  """get_as_residue(Hierarchy self) -> Residue"""
1580  return _IMP_atom.Hierarchy_get_as_residue(self)
1581 
1582  def get_as_chain(self):
1583  """get_as_chain(Hierarchy self) -> Chain"""
1584  return _IMP_atom.Hierarchy_get_as_chain(self)
1585 
1586  def get_as_molecule(self):
1587  """get_as_molecule(Hierarchy self) -> Molecule"""
1588  return _IMP_atom.Hierarchy_get_as_molecule(self)
1589 
1590  def get_as_domain(self):
1591  """get_as_domain(Hierarchy self) -> Domain"""
1592  return _IMP_atom.Hierarchy_get_as_domain(self)
1593 
1594  def get_as_fragment(self):
1595  """get_as_fragment(Hierarchy self) -> Fragment"""
1596  return _IMP_atom.Hierarchy_get_as_fragment(self)
1597 
1598  def get_as_xyz(self):
1599  """get_as_xyz(Hierarchy self) -> XYZ"""
1600  return _IMP_atom.Hierarchy_get_as_xyz(self)
1601 
1602  def get_as_xyzr(self):
1603  """get_as_xyzr(Hierarchy self) -> XYZR"""
1604  return _IMP_atom.Hierarchy_get_as_xyzr(self)
1605 
1606  def get_as_mass(self):
1607  """get_as_mass(Hierarchy self) -> Mass"""
1608  return _IMP_atom.Hierarchy_get_as_mass(self)
1609 
1610  def get_traits():
1611  """get_traits() -> HierarchyTraits"""
1612  return _IMP_atom.Hierarchy_get_traits()
1613 
1614  if _newclass:get_traits = staticmethod(get_traits)
1615  __swig_getmethods__["get_traits"] = lambda x: get_traits
1616  def show(self, *args):
1617  """
1618  show(Hierarchy self, _ostream out, std::string delimiter)
1619  show(Hierarchy self, _ostream out=std::cout)
1620  show(Hierarchy self)
1621  """
1622  return _IMP_atom.Hierarchy_show(self, *args)
1623 
1624  def add_attribute(self, *args):
1625  """
1626  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1627  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1628  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1629  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1630  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1631  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1632  """
1633  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1634 
1635  def get_value(self, *args):
1636  """
1637  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1638  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1639  get_value(Hierarchy self, StringKey a0) -> IMP::String
1640  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1641  get_value(Hierarchy self, ObjectKey a0) -> Object
1642  """
1643  return _IMP_atom.Hierarchy_get_value(self, *args)
1644 
1645  def set_value(self, *args):
1646  """
1647  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1648  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1649  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1650  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1651  set_value(Hierarchy self, ObjectKey a0, Object a1)
1652  """
1653  return _IMP_atom.Hierarchy_set_value(self, *args)
1654 
1655  def remove_attribute(self, *args):
1656  """
1657  remove_attribute(Hierarchy self, FloatKey a0)
1658  remove_attribute(Hierarchy self, IntKey a0)
1659  remove_attribute(Hierarchy self, StringKey a0)
1660  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1661  remove_attribute(Hierarchy self, ObjectKey a0)
1662  """
1663  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1664 
1665  def has_attribute(self, *args):
1666  """
1667  has_attribute(Hierarchy self, FloatKey a0) -> bool
1668  has_attribute(Hierarchy self, IntKey a0) -> bool
1669  has_attribute(Hierarchy self, StringKey a0) -> bool
1670  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1671  has_attribute(Hierarchy self, ObjectKey a0) -> bool
1672  """
1673  return _IMP_atom.Hierarchy_has_attribute(self, *args)
1674 
1675  def get_derivative(self, *args):
1676  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
1677  return _IMP_atom.Hierarchy_get_derivative(self, *args)
1678 
1679  def get_name(self):
1680  """get_name(Hierarchy self) -> std::string"""
1681  return _IMP_atom.Hierarchy_get_name(self)
1682 
1683  def clear_caches(self):
1684  """clear_caches(Hierarchy self)"""
1685  return _IMP_atom.Hierarchy_clear_caches(self)
1686 
1687  def set_name(self, *args):
1688  """set_name(Hierarchy self, std::string a0)"""
1689  return _IMP_atom.Hierarchy_set_name(self, *args)
1690 
1691  def set_check_level(self, *args):
1692  """set_check_level(Hierarchy self, IMP::base::CheckLevel a0)"""
1693  return _IMP_atom.Hierarchy_set_check_level(self, *args)
1694 
1695  def add_to_derivative(self, *args):
1696  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1697  return _IMP_atom.Hierarchy_add_to_derivative(self, *args)
1698 
1699  def set_is_optimized(self, *args):
1700  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1701  return _IMP_atom.Hierarchy_set_is_optimized(self, *args)
1702 
1703  def get_is_optimized(self, *args):
1704  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1705  return _IMP_atom.Hierarchy_get_is_optimized(self, *args)
1706 
1707  def get_check_level(self):
1708  """get_check_level(Hierarchy self) -> IMP::base::CheckLevel"""
1709  return _IMP_atom.Hierarchy_get_check_level(self)
1710 
1711  def __eq__(self, *args):
1712  """
1713  __eq__(Hierarchy self, Hierarchy o) -> bool
1714  __eq__(Hierarchy self, Particle d) -> bool
1715  """
1716  return _IMP_atom.Hierarchy___eq__(self, *args)
1717 
1718  def __ne__(self, *args):
1719  """
1720  __ne__(Hierarchy self, Hierarchy o) -> bool
1721  __ne__(Hierarchy self, Particle d) -> bool
1722  """
1723  return _IMP_atom.Hierarchy___ne__(self, *args)
1724 
1725  def __le__(self, *args):
1726  """
1727  __le__(Hierarchy self, Hierarchy o) -> bool
1728  __le__(Hierarchy self, Particle d) -> bool
1729  """
1730  return _IMP_atom.Hierarchy___le__(self, *args)
1731 
1732  def __lt__(self, *args):
1733  """
1734  __lt__(Hierarchy self, Hierarchy o) -> bool
1735  __lt__(Hierarchy self, Particle d) -> bool
1736  """
1737  return _IMP_atom.Hierarchy___lt__(self, *args)
1738 
1739  def __ge__(self, *args):
1740  """
1741  __ge__(Hierarchy self, Hierarchy o) -> bool
1742  __ge__(Hierarchy self, Particle d) -> bool
1743  """
1744  return _IMP_atom.Hierarchy___ge__(self, *args)
1745 
1746  def __gt__(self, *args):
1747  """
1748  __gt__(Hierarchy self, Hierarchy o) -> bool
1749  __gt__(Hierarchy self, Particle d) -> bool
1750  """
1751  return _IMP_atom.Hierarchy___gt__(self, *args)
1752 
1753  def __str__(self):
1754  """__str__(Hierarchy self) -> std::string"""
1755  return _IMP_atom.Hierarchy___str__(self)
1756 
1757  def __repr__(self):
1758  """__repr__(Hierarchy self) -> std::string"""
1759  return _IMP_atom.Hierarchy___repr__(self)
1760 
1761  __swig_destroy__ = _IMP_atom.delete_Hierarchy
1762  __del__ = lambda self : None;
1763 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
1764 Hierarchy_swigregister(Hierarchy)
1765 
1766 def Hierarchy_decorate_particle(*args):
1767  """Hierarchy_decorate_particle(Particle p) -> Hierarchy"""
1768  return _IMP_atom.Hierarchy_decorate_particle(*args)
1769 
1770 def Hierarchy_particle_is_instance(*args):
1771  """
1772  particle_is_instance(Particle p) -> bool
1773  Hierarchy_particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1774  """
1775  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1776 
1777 def Hierarchy_setup_particle(*args):
1778  """
1779  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1780  setup_particle(Particle p) -> Hierarchy
1781  setup_particle(Model m, IMP::kernel::ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::kernel::ParticleIndexesAdaptor()) -> Hierarchy
1782  Hierarchy_setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1783  """
1784  return _IMP_atom.Hierarchy_setup_particle(*args)
1785 
1786 def Hierarchy_get_is_setup(*args):
1787  """
1788  get_is_setup(Particle p) -> bool
1789  Hierarchy_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
1790  """
1791  return _IMP_atom.Hierarchy_get_is_setup(*args)
1792 
1793 def Hierarchy_get_traits():
1794  """Hierarchy_get_traits() -> HierarchyTraits"""
1795  return _IMP_atom.Hierarchy_get_traits()
1796 
1797 ATOM_TYPE = _IMP_atom.ATOM_TYPE
1798 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
1799 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
1800 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
1801 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
1802 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
1803 XYZ_TYPE = _IMP_atom.XYZ_TYPE
1804 XYZR_TYPE = _IMP_atom.XYZR_TYPE
1805 MASS_TYPE = _IMP_atom.MASS_TYPE
1806 
1807 def get_by_type(*args):
1808  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
1809  return _IMP_atom.get_by_type(*args)
1810 
1811 def create_fragment(*args):
1812  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
1813  return _IMP_atom.create_fragment(*args)
1814 
1815 def get_internal_bonds(*args):
1816  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
1817  return _IMP_atom.get_internal_bonds(*args)
1818 
1819 def get_root(*args):
1820  """get_root(Hierarchy h) -> Hierarchy"""
1821  return _IMP_atom.get_root(*args)
1822 
1823 def show(*args):
1824  """
1825  show(Hierarchy h, _ostream out=std::cout)
1826  show(Hierarchy h)
1827  """
1828  return _IMP_atom.show(*args)
1829 
1830 def create_rigid_body(*args):
1831  """
1832  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
1833  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
1834  create_rigid_body(Hierarchy h) -> RigidBody
1835  """
1836  return _IMP_atom.create_rigid_body(*args)
1837 
1838 def create_compatible_rigid_body(*args):
1839  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
1840  return _IMP_atom.create_compatible_rigid_body(*args)
1841 
1842 def setup_as_rigid_body(*args):
1843  """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
1844  return _IMP_atom.setup_as_rigid_body(*args)
1845 
1846 def get_is_heterogen(*args):
1847  """get_is_heterogen(Hierarchy h) -> bool"""
1848  return _IMP_atom.get_is_heterogen(*args)
1849 
1850 def create_clone(*args):
1851  """create_clone(Hierarchy d) -> Hierarchy"""
1852  return _IMP_atom.create_clone(*args)
1853 
1854 def create_clone_one(*args):
1855  """create_clone_one(Hierarchy d) -> Hierarchy"""
1856  return _IMP_atom.create_clone_one(*args)
1857 
1858 def destroy(*args):
1859  """destroy(Hierarchy d)"""
1860  return _IMP_atom.destroy(*args)
1861 
1862 def get_bounding_box(*args):
1863  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
1864  return _IMP_atom.get_bounding_box(*args)
1865 
1866 def get_bounding_sphere(*args):
1867  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
1868  return _IMP_atom.get_bounding_sphere(*args)
1869 class Angle(IMP.kernel.Decorator):
1870  """Proxy of C++ IMP::atom::Angle class"""
1871  __swig_setmethods__ = {}
1872  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1873  __setattr__ = lambda self, name, value: _swig_setattr(self, Angle, name, value)
1874  __swig_getmethods__ = {}
1875  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1876  __getattr__ = lambda self, name: _swig_getattr(self, Angle, name)
1877  def __init__(self, *args):
1878  """
1879  __init__(IMP::atom::Angle self) -> Angle
1880  __init__(IMP::atom::Angle self, Model m, ::IMP::kernel::ParticleIndex id) -> Angle
1881  __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
1882  """
1883  this = _IMP_atom.new_Angle(*args)
1884  try: self.this.append(this)
1885  except: self.this = this
1886  def decorate_particle(*args):
1887  """decorate_particle(Particle p) -> Angle"""
1888  return _IMP_atom.Angle_decorate_particle(*args)
1889 
1890  if _newclass:decorate_particle = staticmethod(decorate_particle)
1891  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1892  def show(self, *args):
1893  """
1894  show(Angle self, _ostream out=std::cout)
1895  show(Angle self)
1896  """
1897  return _IMP_atom.Angle_show(self, *args)
1898 
1899  def setup_particle(*args):
1900  """
1901  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
1902  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
1903  """
1904  return _IMP_atom.Angle_setup_particle(*args)
1905 
1906  if _newclass:setup_particle = staticmethod(setup_particle)
1907  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1908  def get_is_setup(*args):
1909  """
1910  get_is_setup(_ParticleAdaptor p) -> bool
1911  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1912  """
1913  return _IMP_atom.Angle_get_is_setup(*args)
1914 
1915  if _newclass:get_is_setup = staticmethod(get_is_setup)
1916  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1917  def get_particle(self, *args):
1918  """
1919  get_particle(Angle self) -> Particle
1920  get_particle(Angle self, unsigned int i) -> Particle
1921  """
1922  return _IMP_atom.Angle_get_particle(self, *args)
1923 
1924  def get_ideal(self):
1925  """get_ideal(Angle self) -> IMP::Float"""
1926  return _IMP_atom.Angle_get_ideal(self)
1927 
1928  def set_ideal(self, *args):
1929  """set_ideal(Angle self, IMP::Float t)"""
1930  return _IMP_atom.Angle_set_ideal(self, *args)
1931 
1932  def get_stiffness(self):
1933  """get_stiffness(Angle self) -> IMP::Float"""
1934  return _IMP_atom.Angle_get_stiffness(self)
1935 
1936  def set_stiffness(self, *args):
1937  """set_stiffness(Angle self, IMP::Float t)"""
1938  return _IMP_atom.Angle_set_stiffness(self, *args)
1939 
1940  def get_particle_key(*args):
1941  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
1942  return _IMP_atom.Angle_get_particle_key(*args)
1943 
1944  if _newclass:get_particle_key = staticmethod(get_particle_key)
1945  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
1946  def get_ideal_key():
1947  """get_ideal_key() -> FloatKey"""
1948  return _IMP_atom.Angle_get_ideal_key()
1949 
1950  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
1951  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
1952  def get_stiffness_key():
1953  """get_stiffness_key() -> FloatKey"""
1954  return _IMP_atom.Angle_get_stiffness_key()
1955 
1956  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
1957  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
1958  def add_attribute(self, *args):
1959  """
1960  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
1961  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
1962  add_attribute(Angle self, IntKey a0, IMP::Int a1)
1963  add_attribute(Angle self, StringKey a0, IMP::String a1)
1964  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
1965  add_attribute(Angle self, ObjectKey a0, Object a1)
1966  """
1967  return _IMP_atom.Angle_add_attribute(self, *args)
1968 
1969  def get_value(self, *args):
1970  """
1971  get_value(Angle self, FloatKey a0) -> IMP::Float
1972  get_value(Angle self, IntKey a0) -> IMP::Int
1973  get_value(Angle self, StringKey a0) -> IMP::String
1974  get_value(Angle self, ParticleIndexKey a0) -> Particle
1975  get_value(Angle self, ObjectKey a0) -> Object
1976  """
1977  return _IMP_atom.Angle_get_value(self, *args)
1978 
1979  def set_value(self, *args):
1980  """
1981  set_value(Angle self, FloatKey a0, IMP::Float a1)
1982  set_value(Angle self, IntKey a0, IMP::Int a1)
1983  set_value(Angle self, StringKey a0, IMP::String a1)
1984  set_value(Angle self, ParticleIndexKey a0, Particle a1)
1985  set_value(Angle self, ObjectKey a0, Object a1)
1986  """
1987  return _IMP_atom.Angle_set_value(self, *args)
1988 
1989  def remove_attribute(self, *args):
1990  """
1991  remove_attribute(Angle self, FloatKey a0)
1992  remove_attribute(Angle self, IntKey a0)
1993  remove_attribute(Angle self, StringKey a0)
1994  remove_attribute(Angle self, ParticleIndexKey a0)
1995  remove_attribute(Angle self, ObjectKey a0)
1996  """
1997  return _IMP_atom.Angle_remove_attribute(self, *args)
1998 
1999  def has_attribute(self, *args):
2000  """
2001  has_attribute(Angle self, FloatKey a0) -> bool
2002  has_attribute(Angle self, IntKey a0) -> bool
2003  has_attribute(Angle self, StringKey a0) -> bool
2004  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2005  has_attribute(Angle self, ObjectKey a0) -> bool
2006  """
2007  return _IMP_atom.Angle_has_attribute(self, *args)
2008 
2009  def get_derivative(self, *args):
2010  """get_derivative(Angle self, FloatKey a0) -> double"""
2011  return _IMP_atom.Angle_get_derivative(self, *args)
2012 
2013  def get_name(self):
2014  """get_name(Angle self) -> std::string"""
2015  return _IMP_atom.Angle_get_name(self)
2016 
2017  def clear_caches(self):
2018  """clear_caches(Angle self)"""
2019  return _IMP_atom.Angle_clear_caches(self)
2020 
2021  def set_name(self, *args):
2022  """set_name(Angle self, std::string a0)"""
2023  return _IMP_atom.Angle_set_name(self, *args)
2024 
2025  def set_check_level(self, *args):
2026  """set_check_level(Angle self, IMP::base::CheckLevel a0)"""
2027  return _IMP_atom.Angle_set_check_level(self, *args)
2028 
2029  def add_to_derivative(self, *args):
2030  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2031  return _IMP_atom.Angle_add_to_derivative(self, *args)
2032 
2033  def set_is_optimized(self, *args):
2034  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2035  return _IMP_atom.Angle_set_is_optimized(self, *args)
2036 
2037  def get_is_optimized(self, *args):
2038  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2039  return _IMP_atom.Angle_get_is_optimized(self, *args)
2040 
2041  def get_check_level(self):
2042  """get_check_level(Angle self) -> IMP::base::CheckLevel"""
2043  return _IMP_atom.Angle_get_check_level(self)
2044 
2045  def __eq__(self, *args):
2046  """
2047  __eq__(Angle self, Angle o) -> bool
2048  __eq__(Angle self, Particle d) -> bool
2049  """
2050  return _IMP_atom.Angle___eq__(self, *args)
2051 
2052  def __ne__(self, *args):
2053  """
2054  __ne__(Angle self, Angle o) -> bool
2055  __ne__(Angle self, Particle d) -> bool
2056  """
2057  return _IMP_atom.Angle___ne__(self, *args)
2058 
2059  def __le__(self, *args):
2060  """
2061  __le__(Angle self, Angle o) -> bool
2062  __le__(Angle self, Particle d) -> bool
2063  """
2064  return _IMP_atom.Angle___le__(self, *args)
2065 
2066  def __lt__(self, *args):
2067  """
2068  __lt__(Angle self, Angle o) -> bool
2069  __lt__(Angle self, Particle d) -> bool
2070  """
2071  return _IMP_atom.Angle___lt__(self, *args)
2072 
2073  def __ge__(self, *args):
2074  """
2075  __ge__(Angle self, Angle o) -> bool
2076  __ge__(Angle self, Particle d) -> bool
2077  """
2078  return _IMP_atom.Angle___ge__(self, *args)
2079 
2080  def __gt__(self, *args):
2081  """
2082  __gt__(Angle self, Angle o) -> bool
2083  __gt__(Angle self, Particle d) -> bool
2084  """
2085  return _IMP_atom.Angle___gt__(self, *args)
2086 
2087  def __str__(self):
2088  """__str__(Angle self) -> std::string"""
2089  return _IMP_atom.Angle___str__(self)
2090 
2091  def __repr__(self):
2092  """__repr__(Angle self) -> std::string"""
2093  return _IMP_atom.Angle___repr__(self)
2094 
2095  __swig_destroy__ = _IMP_atom.delete_Angle
2096  __del__ = lambda self : None;
2097 Angle_swigregister = _IMP_atom.Angle_swigregister
2098 Angle_swigregister(Angle)
2099 
2100 def Angle_decorate_particle(*args):
2101  """Angle_decorate_particle(Particle p) -> Angle"""
2102  return _IMP_atom.Angle_decorate_particle(*args)
2103 
2104 def Angle_setup_particle(*args):
2105  """
2106  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2107  Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2108  """
2109  return _IMP_atom.Angle_setup_particle(*args)
2110 
2111 def Angle_get_is_setup(*args):
2112  """
2113  get_is_setup(_ParticleAdaptor p) -> bool
2114  Angle_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2115  """
2116  return _IMP_atom.Angle_get_is_setup(*args)
2117 
2118 def Angle_get_particle_key(*args):
2119  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2120  return _IMP_atom.Angle_get_particle_key(*args)
2121 
2122 def Angle_get_ideal_key():
2123  """Angle_get_ideal_key() -> FloatKey"""
2124  return _IMP_atom.Angle_get_ideal_key()
2125 
2126 def Angle_get_stiffness_key():
2127  """Angle_get_stiffness_key() -> FloatKey"""
2128  return _IMP_atom.Angle_get_stiffness_key()
2129 
2130 class Dihedral(IMP.kernel.Decorator):
2131  """Proxy of C++ IMP::atom::Dihedral class"""
2132  __swig_setmethods__ = {}
2133  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2134  __setattr__ = lambda self, name, value: _swig_setattr(self, Dihedral, name, value)
2135  __swig_getmethods__ = {}
2136  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2137  __getattr__ = lambda self, name: _swig_getattr(self, Dihedral, name)
2138  def __init__(self, *args):
2139  """
2140  __init__(IMP::atom::Dihedral self) -> Dihedral
2141  __init__(IMP::atom::Dihedral self, Model m, ::IMP::kernel::ParticleIndex id) -> Dihedral
2142  __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2143  """
2144  this = _IMP_atom.new_Dihedral(*args)
2145  try: self.this.append(this)
2146  except: self.this = this
2147  def decorate_particle(*args):
2148  """decorate_particle(Particle p) -> Dihedral"""
2149  return _IMP_atom.Dihedral_decorate_particle(*args)
2150 
2151  if _newclass:decorate_particle = staticmethod(decorate_particle)
2152  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
2153  def show(self, *args):
2154  """
2155  show(Dihedral self, _ostream out=std::cout)
2156  show(Dihedral self)
2157  """
2158  return _IMP_atom.Dihedral_show(self, *args)
2159 
2160  def setup_particle(*args):
2161  """
2162  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2163  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2164  """
2165  return _IMP_atom.Dihedral_setup_particle(*args)
2166 
2167  if _newclass:setup_particle = staticmethod(setup_particle)
2168  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
2169  def get_is_setup(*args):
2170  """
2171  get_is_setup(_ParticleAdaptor p) -> bool
2172  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2173  """
2174  return _IMP_atom.Dihedral_get_is_setup(*args)
2175 
2176  if _newclass:get_is_setup = staticmethod(get_is_setup)
2177  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
2178  def get_particle(self, *args):
2179  """
2180  get_particle(Dihedral self) -> Particle
2181  get_particle(Dihedral self, unsigned int i) -> Particle
2182  """
2183  return _IMP_atom.Dihedral_get_particle(self, *args)
2184 
2185  def get_ideal(self):
2186  """get_ideal(Dihedral self) -> IMP::Float"""
2187  return _IMP_atom.Dihedral_get_ideal(self)
2188 
2189  def set_ideal(self, *args):
2190  """set_ideal(Dihedral self, IMP::Float t)"""
2191  return _IMP_atom.Dihedral_set_ideal(self, *args)
2192 
2193  def get_multiplicity(self):
2194  """get_multiplicity(Dihedral self) -> IMP::Int"""
2195  return _IMP_atom.Dihedral_get_multiplicity(self)
2196 
2197  def set_multiplicity(self, *args):
2198  """set_multiplicity(Dihedral self, IMP::Int t)"""
2199  return _IMP_atom.Dihedral_set_multiplicity(self, *args)
2200 
2201  def get_stiffness(self):
2202  """get_stiffness(Dihedral self) -> IMP::Float"""
2203  return _IMP_atom.Dihedral_get_stiffness(self)
2204 
2205  def set_stiffness(self, *args):
2206  """set_stiffness(Dihedral self, IMP::Float t)"""
2207  return _IMP_atom.Dihedral_set_stiffness(self, *args)
2208 
2209  def get_particle_key(*args):
2210  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2211  return _IMP_atom.Dihedral_get_particle_key(*args)
2212 
2213  if _newclass:get_particle_key = staticmethod(get_particle_key)
2214  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
2215  def get_ideal_key():
2216  """get_ideal_key() -> FloatKey"""
2217  return _IMP_atom.Dihedral_get_ideal_key()
2218 
2219  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
2220  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
2221  def get_multiplicity_key():
2222  """get_multiplicity_key() -> IntKey"""
2223  return _IMP_atom.Dihedral_get_multiplicity_key()
2224 
2225  if _newclass:get_multiplicity_key = staticmethod(get_multiplicity_key)
2226  __swig_getmethods__["get_multiplicity_key"] = lambda x: get_multiplicity_key
2227  def get_stiffness_key():
2228  """get_stiffness_key() -> FloatKey"""
2229  return _IMP_atom.Dihedral_get_stiffness_key()
2230 
2231  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
2232  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
2233  def add_attribute(self, *args):
2234  """
2235  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2236  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2237  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2238  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2239  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2240  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2241  """
2242  return _IMP_atom.Dihedral_add_attribute(self, *args)
2243 
2244  def get_value(self, *args):
2245  """
2246  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2247  get_value(Dihedral self, IntKey a0) -> IMP::Int
2248  get_value(Dihedral self, StringKey a0) -> IMP::String
2249  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2250  get_value(Dihedral self, ObjectKey a0) -> Object
2251  """
2252  return _IMP_atom.Dihedral_get_value(self, *args)
2253 
2254  def set_value(self, *args):
2255  """
2256  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2257  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2258  set_value(Dihedral self, StringKey a0, IMP::String a1)
2259  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2260  set_value(Dihedral self, ObjectKey a0, Object a1)
2261  """
2262  return _IMP_atom.Dihedral_set_value(self, *args)
2263 
2264  def remove_attribute(self, *args):
2265  """
2266  remove_attribute(Dihedral self, FloatKey a0)
2267  remove_attribute(Dihedral self, IntKey a0)
2268  remove_attribute(Dihedral self, StringKey a0)
2269  remove_attribute(Dihedral self, ParticleIndexKey a0)
2270  remove_attribute(Dihedral self, ObjectKey a0)
2271  """
2272  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2273 
2274  def has_attribute(self, *args):
2275  """
2276  has_attribute(Dihedral self, FloatKey a0) -> bool
2277  has_attribute(Dihedral self, IntKey a0) -> bool
2278  has_attribute(Dihedral self, StringKey a0) -> bool
2279  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2280  has_attribute(Dihedral self, ObjectKey a0) -> bool
2281  """
2282  return _IMP_atom.Dihedral_has_attribute(self, *args)
2283 
2284  def get_derivative(self, *args):
2285  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2286  return _IMP_atom.Dihedral_get_derivative(self, *args)
2287 
2288  def get_name(self):
2289  """get_name(Dihedral self) -> std::string"""
2290  return _IMP_atom.Dihedral_get_name(self)
2291 
2292  def clear_caches(self):
2293  """clear_caches(Dihedral self)"""
2294  return _IMP_atom.Dihedral_clear_caches(self)
2295 
2296  def set_name(self, *args):
2297  """set_name(Dihedral self, std::string a0)"""
2298  return _IMP_atom.Dihedral_set_name(self, *args)
2299 
2300  def set_check_level(self, *args):
2301  """set_check_level(Dihedral self, IMP::base::CheckLevel a0)"""
2302  return _IMP_atom.Dihedral_set_check_level(self, *args)
2303 
2304  def add_to_derivative(self, *args):
2305  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2306  return _IMP_atom.Dihedral_add_to_derivative(self, *args)
2307 
2308  def set_is_optimized(self, *args):
2309  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2310  return _IMP_atom.Dihedral_set_is_optimized(self, *args)
2311 
2312  def get_is_optimized(self, *args):
2313  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2314  return _IMP_atom.Dihedral_get_is_optimized(self, *args)
2315 
2316  def get_check_level(self):
2317  """get_check_level(Dihedral self) -> IMP::base::CheckLevel"""
2318  return _IMP_atom.Dihedral_get_check_level(self)
2319 
2320  def __eq__(self, *args):
2321  """
2322  __eq__(Dihedral self, Dihedral o) -> bool
2323  __eq__(Dihedral self, Particle d) -> bool
2324  """
2325  return _IMP_atom.Dihedral___eq__(self, *args)
2326 
2327  def __ne__(self, *args):
2328  """
2329  __ne__(Dihedral self, Dihedral o) -> bool
2330  __ne__(Dihedral self, Particle d) -> bool
2331  """
2332  return _IMP_atom.Dihedral___ne__(self, *args)
2333 
2334  def __le__(self, *args):
2335  """
2336  __le__(Dihedral self, Dihedral o) -> bool
2337  __le__(Dihedral self, Particle d) -> bool
2338  """
2339  return _IMP_atom.Dihedral___le__(self, *args)
2340 
2341  def __lt__(self, *args):
2342  """
2343  __lt__(Dihedral self, Dihedral o) -> bool
2344  __lt__(Dihedral self, Particle d) -> bool
2345  """
2346  return _IMP_atom.Dihedral___lt__(self, *args)
2347 
2348  def __ge__(self, *args):
2349  """
2350  __ge__(Dihedral self, Dihedral o) -> bool
2351  __ge__(Dihedral self, Particle d) -> bool
2352  """
2353  return _IMP_atom.Dihedral___ge__(self, *args)
2354 
2355  def __gt__(self, *args):
2356  """
2357  __gt__(Dihedral self, Dihedral o) -> bool
2358  __gt__(Dihedral self, Particle d) -> bool
2359  """
2360  return _IMP_atom.Dihedral___gt__(self, *args)
2361 
2362  def __str__(self):
2363  """__str__(Dihedral self) -> std::string"""
2364  return _IMP_atom.Dihedral___str__(self)
2365 
2366  def __repr__(self):
2367  """__repr__(Dihedral self) -> std::string"""
2368  return _IMP_atom.Dihedral___repr__(self)
2369 
2370  __swig_destroy__ = _IMP_atom.delete_Dihedral
2371  __del__ = lambda self : None;
2372 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2373 Dihedral_swigregister(Dihedral)
2374 
2375 def Dihedral_decorate_particle(*args):
2376  """Dihedral_decorate_particle(Particle p) -> Dihedral"""
2377  return _IMP_atom.Dihedral_decorate_particle(*args)
2378 
2379 def Dihedral_setup_particle(*args):
2380  """
2381  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2382  Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2383  """
2384  return _IMP_atom.Dihedral_setup_particle(*args)
2385 
2386 def Dihedral_get_is_setup(*args):
2387  """
2388  get_is_setup(_ParticleAdaptor p) -> bool
2389  Dihedral_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2390  """
2391  return _IMP_atom.Dihedral_get_is_setup(*args)
2392 
2393 def Dihedral_get_particle_key(*args):
2394  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2395  return _IMP_atom.Dihedral_get_particle_key(*args)
2396 
2397 def Dihedral_get_ideal_key():
2398  """Dihedral_get_ideal_key() -> FloatKey"""
2399  return _IMP_atom.Dihedral_get_ideal_key()
2400 
2401 def Dihedral_get_multiplicity_key():
2402  """Dihedral_get_multiplicity_key() -> IntKey"""
2403  return _IMP_atom.Dihedral_get_multiplicity_key()
2404 
2405 def Dihedral_get_stiffness_key():
2406  """Dihedral_get_stiffness_key() -> FloatKey"""
2407  return _IMP_atom.Dihedral_get_stiffness_key()
2408 
2409 class SmoothingFunction(IMP.base.Object):
2410  """Proxy of C++ IMP::atom::SmoothingFunction class"""
2411  __swig_setmethods__ = {}
2412  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2413  __setattr__ = lambda self, name, value: _swig_setattr(self, SmoothingFunction, name, value)
2414  __swig_getmethods__ = {}
2415  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2416  __getattr__ = lambda self, name: _swig_getattr(self, SmoothingFunction, name)
2417  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
2418  def __call__(self, *args):
2419  """
2420  __call__(SmoothingFunction self, double score, double distance) -> double
2421  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2422  """
2423  return _IMP_atom.SmoothingFunction___call__(self, *args)
2424 
2425  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2426  __del__ = lambda self : None;
2427  def __str__(self):
2428  """__str__(SmoothingFunction self) -> std::string"""
2429  return _IMP_atom.SmoothingFunction___str__(self)
2430 
2431  def __repr__(self):
2432  """__repr__(SmoothingFunction self) -> std::string"""
2433  return _IMP_atom.SmoothingFunction___repr__(self)
2434 
2435  def get_from(o):
2436  return _object_cast_to_SmoothingFunction(o)
2437  get_from = staticmethod(get_from)
2438 
2439 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2440 SmoothingFunction_swigregister(SmoothingFunction)
2441 
2442 class ForceSwitch(SmoothingFunction):
2443  """Proxy of C++ IMP::atom::ForceSwitch class"""
2444  __swig_setmethods__ = {}
2445  for _s in [SmoothingFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2446  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceSwitch, name, value)
2447  __swig_getmethods__ = {}
2448  for _s in [SmoothingFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2449  __getattr__ = lambda self, name: _swig_getattr(self, ForceSwitch, name)
2450  def __init__(self, *args):
2451  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2452  this = _IMP_atom.new_ForceSwitch(*args)
2453  try: self.this.append(this)
2454  except: self.this = this
2455  def __call__(self, *args):
2456  """
2457  __call__(ForceSwitch self, double score, double distance) -> double
2458  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2459  """
2460  return _IMP_atom.ForceSwitch___call__(self, *args)
2461 
2462  def get_version_info(self):
2463  """get_version_info(ForceSwitch self) -> VersionInfo"""
2464  return _IMP_atom.ForceSwitch_get_version_info(self)
2465 
2466  def __str__(self):
2467  """__str__(ForceSwitch self) -> std::string"""
2468  return _IMP_atom.ForceSwitch___str__(self)
2469 
2470  def __repr__(self):
2471  """__repr__(ForceSwitch self) -> std::string"""
2472  return _IMP_atom.ForceSwitch___repr__(self)
2473 
2474  def get_from(o):
2475  return _object_cast_to_ForceSwitch(o)
2476  get_from = staticmethod(get_from)
2477 
2478 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2479 ForceSwitch_swigregister(ForceSwitch)
2480 
2481 class AngleSingletonScore(IMP.kernel.SingletonScore):
2482  """Proxy of C++ IMP::atom::AngleSingletonScore class"""
2483  __swig_setmethods__ = {}
2484  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2485  __setattr__ = lambda self, name, value: _swig_setattr(self, AngleSingletonScore, name, value)
2486  __swig_getmethods__ = {}
2487  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2488  __getattr__ = lambda self, name: _swig_getattr(self, AngleSingletonScore, name)
2489  def __init__(self, *args):
2490  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2491  this = _IMP_atom.new_AngleSingletonScore(*args)
2492  try: self.this.append(this)
2493  except: self.this = this
2494  def do_get_inputs(self, *args):
2495  """do_get_inputs(AngleSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2496  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, *args)
2497 
2498  def get_version_info(self):
2499  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2500  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2501 
2502  def __str__(self):
2503  """__str__(AngleSingletonScore self) -> std::string"""
2504  return _IMP_atom.AngleSingletonScore___str__(self)
2505 
2506  def __repr__(self):
2507  """__repr__(AngleSingletonScore self) -> std::string"""
2508  return _IMP_atom.AngleSingletonScore___repr__(self)
2509 
2510  def get_from(o):
2511  return _object_cast_to_AngleSingletonScore(o)
2512  get_from = staticmethod(get_from)
2513 
2514 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2515 AngleSingletonScore_swigregister(AngleSingletonScore)
2516 
2517 class BondEndpointsRefiner(IMP.kernel.Refiner):
2518  """Proxy of C++ IMP::atom::BondEndpointsRefiner class"""
2519  __swig_setmethods__ = {}
2520  for _s in [IMP.kernel.Refiner]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2521  __setattr__ = lambda self, name, value: _swig_setattr(self, BondEndpointsRefiner, name, value)
2522  __swig_getmethods__ = {}
2523  for _s in [IMP.kernel.Refiner]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2524  __getattr__ = lambda self, name: _swig_getattr(self, BondEndpointsRefiner, name)
2525  def __init__(self):
2526  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2527  this = _IMP_atom.new_BondEndpointsRefiner()
2528  try: self.this.append(this)
2529  except: self.this = this
2530  def do_get_inputs(self, *args):
2531  """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2532  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, *args)
2533 
2534  def get_version_info(self):
2535  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2536  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2537 
2538  def __str__(self):
2539  """__str__(BondEndpointsRefiner self) -> std::string"""
2540  return _IMP_atom.BondEndpointsRefiner___str__(self)
2541 
2542  def __repr__(self):
2543  """__repr__(BondEndpointsRefiner self) -> std::string"""
2544  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2545 
2546  def get_from(o):
2547  return _object_cast_to_BondEndpointsRefiner(o)
2548  get_from = staticmethod(get_from)
2549 
2550 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2551 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2552 
2553 class BondPairContainer(IMP.kernel.PairContainer):
2554  """Proxy of C++ IMP::atom::BondPairContainer class"""
2555  __swig_setmethods__ = {}
2556  for _s in [IMP.kernel.PairContainer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2557  __setattr__ = lambda self, name, value: _swig_setattr(self, BondPairContainer, name, value)
2558  __swig_getmethods__ = {}
2559  for _s in [IMP.kernel.PairContainer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2560  __getattr__ = lambda self, name: _swig_getattr(self, BondPairContainer, name)
2561  def __init__(self, *args):
2562  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2563  this = _IMP_atom.new_BondPairContainer(*args)
2564  try: self.this.append(this)
2565  except: self.this = this
2566  def do_get_inputs(self):
2567  """do_get_inputs(BondPairContainer self) -> IMP::kernel::ModelObjectsTemp"""
2568  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2569 
2570  def do_apply(self, *args):
2571  """do_apply(BondPairContainer self, PairModifier sm)"""
2572  return _IMP_atom.BondPairContainer_do_apply(self, *args)
2573 
2574  def get_version_info(self):
2575  """get_version_info(BondPairContainer self) -> VersionInfo"""
2576  return _IMP_atom.BondPairContainer_get_version_info(self)
2577 
2578  def __str__(self):
2579  """__str__(BondPairContainer self) -> std::string"""
2580  return _IMP_atom.BondPairContainer___str__(self)
2581 
2582  def __repr__(self):
2583  """__repr__(BondPairContainer self) -> std::string"""
2584  return _IMP_atom.BondPairContainer___repr__(self)
2585 
2586  def get_from(o):
2587  return _object_cast_to_BondPairContainer(o)
2588  get_from = staticmethod(get_from)
2589 
2590 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
2591 BondPairContainer_swigregister(BondPairContainer)
2592 
2593 class BondSingletonScore(IMP.kernel.SingletonScore):
2594  """Proxy of C++ IMP::atom::BondSingletonScore class"""
2595  __swig_setmethods__ = {}
2596  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2597  __setattr__ = lambda self, name, value: _swig_setattr(self, BondSingletonScore, name, value)
2598  __swig_getmethods__ = {}
2599  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2600  __getattr__ = lambda self, name: _swig_getattr(self, BondSingletonScore, name)
2601  def __init__(self, *args):
2602  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2603  this = _IMP_atom.new_BondSingletonScore(*args)
2604  try: self.this.append(this)
2605  except: self.this = this
2606  def get_unary_function(self):
2607  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2608  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2609 
2610  def do_get_inputs(self, *args):
2611  """do_get_inputs(BondSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2612  return _IMP_atom.BondSingletonScore_do_get_inputs(self, *args)
2613 
2614  def get_version_info(self):
2615  """get_version_info(BondSingletonScore self) -> VersionInfo"""
2616  return _IMP_atom.BondSingletonScore_get_version_info(self)
2617 
2618  def __str__(self):
2619  """__str__(BondSingletonScore self) -> std::string"""
2620  return _IMP_atom.BondSingletonScore___str__(self)
2621 
2622  def __repr__(self):
2623  """__repr__(BondSingletonScore self) -> std::string"""
2624  return _IMP_atom.BondSingletonScore___repr__(self)
2625 
2626  def get_from(o):
2627  return _object_cast_to_BondSingletonScore(o)
2628  get_from = staticmethod(get_from)
2629 
2630 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
2631 BondSingletonScore_swigregister(BondSingletonScore)
2632 
2633 class DihedralSingletonScore(IMP.kernel.SingletonScore):
2634  """Proxy of C++ IMP::atom::DihedralSingletonScore class"""
2635  __swig_setmethods__ = {}
2636  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2637  __setattr__ = lambda self, name, value: _swig_setattr(self, DihedralSingletonScore, name, value)
2638  __swig_getmethods__ = {}
2639  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2640  __getattr__ = lambda self, name: _swig_getattr(self, DihedralSingletonScore, name)
2641  def __init__(self):
2642  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
2643  this = _IMP_atom.new_DihedralSingletonScore()
2644  try: self.this.append(this)
2645  except: self.this = this
2646  def do_get_inputs(self, *args):
2647  """do_get_inputs(DihedralSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2648  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, *args)
2649 
2650  def get_version_info(self):
2651  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2652  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2653 
2654  def __str__(self):
2655  """__str__(DihedralSingletonScore self) -> std::string"""
2656  return _IMP_atom.DihedralSingletonScore___str__(self)
2657 
2658  def __repr__(self):
2659  """__repr__(DihedralSingletonScore self) -> std::string"""
2660  return _IMP_atom.DihedralSingletonScore___repr__(self)
2661 
2662  def get_from(o):
2663  return _object_cast_to_DihedralSingletonScore(o)
2664  get_from = staticmethod(get_from)
2665 
2666 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
2667 DihedralSingletonScore_swigregister(DihedralSingletonScore)
2668 
2669 class ImproperSingletonScore(IMP.kernel.SingletonScore):
2670  """Proxy of C++ IMP::atom::ImproperSingletonScore class"""
2671  __swig_setmethods__ = {}
2672  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2673  __setattr__ = lambda self, name, value: _swig_setattr(self, ImproperSingletonScore, name, value)
2674  __swig_getmethods__ = {}
2675  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2676  __getattr__ = lambda self, name: _swig_getattr(self, ImproperSingletonScore, name)
2677  def __init__(self, *args):
2678  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
2679  this = _IMP_atom.new_ImproperSingletonScore(*args)
2680  try: self.this.append(this)
2681  except: self.this = this
2682  def do_get_inputs(self, *args):
2683  """do_get_inputs(ImproperSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2684  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, *args)
2685 
2686  def get_version_info(self):
2687  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
2688  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
2689 
2690  def __str__(self):
2691  """__str__(ImproperSingletonScore self) -> std::string"""
2692  return _IMP_atom.ImproperSingletonScore___str__(self)
2693 
2694  def __repr__(self):
2695  """__repr__(ImproperSingletonScore self) -> std::string"""
2696  return _IMP_atom.ImproperSingletonScore___repr__(self)
2697 
2698  def get_from(o):
2699  return _object_cast_to_ImproperSingletonScore(o)
2700  get_from = staticmethod(get_from)
2701 
2702 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
2703 ImproperSingletonScore_swigregister(ImproperSingletonScore)
2704 
2705 class CoverBond(IMP.kernel.SingletonModifier):
2706  """Proxy of C++ IMP::atom::CoverBond class"""
2707  __swig_setmethods__ = {}
2708  for _s in [IMP.kernel.SingletonModifier]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2709  __setattr__ = lambda self, name, value: _swig_setattr(self, CoverBond, name, value)
2710  __swig_getmethods__ = {}
2711  for _s in [IMP.kernel.SingletonModifier]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2712  __getattr__ = lambda self, name: _swig_getattr(self, CoverBond, name)
2713  def __init__(self):
2714  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
2715  this = _IMP_atom.new_CoverBond()
2716  try: self.this.append(this)
2717  except: self.this = this
2718  def do_get_inputs(self, *args):
2719  """do_get_inputs(CoverBond self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2720  return _IMP_atom.CoverBond_do_get_inputs(self, *args)
2721 
2722  def do_get_outputs(self, *args):
2723  """do_get_outputs(CoverBond self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2724  return _IMP_atom.CoverBond_do_get_outputs(self, *args)
2725 
2726  def get_version_info(self):
2727  """get_version_info(CoverBond self) -> VersionInfo"""
2728  return _IMP_atom.CoverBond_get_version_info(self)
2729 
2730  def __str__(self):
2731  """__str__(CoverBond self) -> std::string"""
2732  return _IMP_atom.CoverBond___str__(self)
2733 
2734  def __repr__(self):
2735  """__repr__(CoverBond self) -> std::string"""
2736  return _IMP_atom.CoverBond___repr__(self)
2737 
2738  def get_from(o):
2739  return _object_cast_to_CoverBond(o)
2740  get_from = staticmethod(get_from)
2741 
2742 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
2743 CoverBond_swigregister(CoverBond)
2744 
2745 class Simulator(IMP.kernel.Optimizer):
2746  """Proxy of C++ IMP::atom::Simulator class"""
2747  __swig_setmethods__ = {}
2748  for _s in [IMP.kernel.Optimizer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2749  __setattr__ = lambda self, name, value: _swig_setattr(self, Simulator, name, value)
2750  __swig_getmethods__ = {}
2751  for _s in [IMP.kernel.Optimizer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2752  __getattr__ = lambda self, name: _swig_getattr(self, Simulator, name)
2753  def __init__(self, *args):
2754  """
2755  __init__(IMP::atom::Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator
2756  __init__(IMP::atom::Simulator self, Model m, std::string name="Simulator %1%") -> Simulator
2757  __init__(IMP::atom::Simulator self, Model m) -> Simulator
2758  """
2759  if self.__class__ == Simulator:
2760  _self = None
2761  else:
2762  _self = self
2763  this = _IMP_atom.new_Simulator(_self, *args)
2764  try: self.this.append(this)
2765  except: self.this = this
2766  if self.__class__ != Simulator:
2767  import IMP.base
2768  IMP.base._director_objects.register(self)
2769 
2770 
2771 
2772  def simulate(self, *args):
2773  """simulate(Simulator self, double time_in_fs) -> double"""
2774  return _IMP_atom.Simulator_simulate(self, *args)
2775 
2776  def simulate_wave(self, *args):
2777  """
2778  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
2779  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
2780  simulate_wave(Simulator self, double time_in_fs) -> double
2781  """
2782  return _IMP_atom.Simulator_simulate_wave(self, *args)
2783 
2784  def get_temperature(self):
2785  """get_temperature(Simulator self) -> double"""
2786  return _IMP_atom.Simulator_get_temperature(self)
2787 
2788  def set_temperature(self, *args):
2789  """set_temperature(Simulator self, double d)"""
2790  return _IMP_atom.Simulator_set_temperature(self, *args)
2791 
2792  def set_maximum_time_step(self, *args):
2793  """set_maximum_time_step(Simulator self, double ts)"""
2794  return _IMP_atom.Simulator_set_maximum_time_step(self, *args)
2795 
2796  def get_maximum_time_step(self):
2797  """get_maximum_time_step(Simulator self) -> double"""
2798  return _IMP_atom.Simulator_get_maximum_time_step(self)
2799 
2800  def get_last_time_step(self):
2801  """get_last_time_step(Simulator self) -> double"""
2802  return _IMP_atom.Simulator_get_last_time_step(self)
2803 
2804  def set_time_step(self, *args):
2805  """set_time_step(Simulator self, double ts)"""
2806  return _IMP_atom.Simulator_set_time_step(self, *args)
2807 
2808  def get_kt(self):
2809  """get_kt(Simulator self) -> double"""
2810  return _IMP_atom.Simulator_get_kt(self)
2811 
2812  def get_current_time(self):
2813  """get_current_time(Simulator self) -> double"""
2814  return _IMP_atom.Simulator_get_current_time(self)
2815 
2816  def set_current_time(self, *args):
2817  """set_current_time(Simulator self, double ct)"""
2818  return _IMP_atom.Simulator_set_current_time(self, *args)
2819 
2820  def get_simulation_particles(self):
2821  """get_simulation_particles(Simulator self) -> IMP::kernel::ParticlesTemp"""
2822  return _IMP_atom.Simulator_get_simulation_particles(self)
2823 
2824  def get_simulation_particle_indexes(self):
2825  """get_simulation_particle_indexes(Simulator self) -> IMP::kernel::ParticleIndexes"""
2826  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
2827 
2828  def remove_particle(self, *args):
2829  """remove_particle(Simulator self, Particle d)"""
2830  return _IMP_atom.Simulator_remove_particle(self, *args)
2831 
2832  def remove_particles(self, *args):
2833  """remove_particles(Simulator self, IMP::kernel::Particles const & d)"""
2834  return _IMP_atom.Simulator_remove_particles(self, *args)
2835 
2836  def set_particles(self, *args):
2837  """set_particles(Simulator self, IMP::kernel::Particles const & ps)"""
2838  return _IMP_atom.Simulator_set_particles(self, *args)
2839 
2840  def set_particles_order(self, *args):
2841  """set_particles_order(Simulator self, IMP::kernel::Particles const & objs)"""
2842  return _IMP_atom.Simulator_set_particles_order(self, *args)
2843 
2844  def add_particle(self, *args):
2845  """add_particle(Simulator self, Particle obj) -> unsigned int"""
2846  return _IMP_atom.Simulator_add_particle(self, *args)
2847 
2848  def add_particles(self, *args):
2849  """add_particles(Simulator self, IMP::kernel::Particles const & objs)"""
2850  return _IMP_atom.Simulator_add_particles(self, *args)
2851 
2852  def clear_particles(self):
2853  """clear_particles(Simulator self)"""
2854  return _IMP_atom.Simulator_clear_particles(self)
2855 
2856  def get_number_of_particles(self):
2857  """get_number_of_particles(Simulator self) -> unsigned int"""
2858  return _IMP_atom.Simulator_get_number_of_particles(self)
2859 
2860  def get_has_particles(self):
2861  """get_has_particles(Simulator self) -> bool"""
2862  return _IMP_atom.Simulator_get_has_particles(self)
2863 
2864  def get_particle(self, *args):
2865  """get_particle(Simulator self, unsigned int i) -> Particle"""
2866  return _IMP_atom.Simulator_get_particle(self, *args)
2867 
2868  def get_particles(self):
2869  """get_particles(Simulator self) -> IMP::kernel::Particles"""
2870  return _IMP_atom.Simulator_get_particles(self)
2871 
2872  def reserve_particles(self, *args):
2873  """reserve_particles(Simulator self, unsigned int sz)"""
2874  return _IMP_atom.Simulator_reserve_particles(self, *args)
2875 
2876  def do_optimize(self, *args):
2877  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
2878  return _IMP_atom.Simulator_do_optimize(self, *args)
2879 
2880  def setup(self, *args):
2881  """setup(Simulator self, IMP::kernel::ParticleIndexes const & arg0)"""
2882  return _IMP_atom.Simulator_setup(self, *args)
2883 
2884  def do_step(self, *args):
2885  """do_step(Simulator self, IMP::kernel::ParticleIndexes const & sc, double dt) -> double"""
2886  return _IMP_atom.Simulator_do_step(self, *args)
2887 
2888  def get_is_simulation_particle(self, *args):
2889  """get_is_simulation_particle(Simulator self, IMP::kernel::ParticleIndex p) -> bool"""
2890  return _IMP_atom.Simulator_get_is_simulation_particle(self, *args)
2891 
2892  def __str__(self):
2893  """__str__(Simulator self) -> std::string"""
2894  return _IMP_atom.Simulator___str__(self)
2895 
2896  def __repr__(self):
2897  """__repr__(Simulator self) -> std::string"""
2898  return _IMP_atom.Simulator___repr__(self)
2899 
2900  def get_from(o):
2901  return _object_cast_to_Simulator(o)
2902  get_from = staticmethod(get_from)
2903 
2904  def get_type_name(self):
2905  return self.__class__.__name__
2906  def do_show(self, out):
2907  pass
2908  def get_version_info(self):
2909  if"IMP::atom" == "IMP":
2910  return VersionInfo("python", "0")
2911  else:
2912  return IMP.VersionInfo("python", "0")
2913  def get_from(o):
2914  return _object_cast_to_Simulator(o)
2915  get_from = staticmethod(get_from)
2916 
2917  __swig_destroy__ = _IMP_atom.delete_Simulator
2918  __del__ = lambda self : None;
2919  def __disown__(self):
2920  self.this.disown()
2921  _IMP_atom.disown_Simulator(self)
2922  return weakref_proxy(self)
2923  def handle_set_has_required_score_states(self, *args):
2924  """handle_set_has_required_score_states(Simulator self, bool arg0)"""
2925  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, *args)
2926 
2927  def do_get_inputs(self):
2928  """do_get_inputs(Simulator self) -> IMP::kernel::ModelObjectsTemp"""
2929  return _IMP_atom.Simulator_do_get_inputs(self)
2930 
2931  def do_get_outputs(self):
2932  """do_get_outputs(Simulator self) -> IMP::kernel::ModelObjectsTemp"""
2933  return _IMP_atom.Simulator_do_get_outputs(self)
2934 
2935  def do_get_interactions(self):
2936  """do_get_interactions(Simulator self) -> IMP::kernel::ModelObjectsTemps"""
2937  return _IMP_atom.Simulator_do_get_interactions(self)
2938 
2939 Simulator_swigregister = _IMP_atom.Simulator_swigregister
2940 Simulator_swigregister(Simulator)
2941 
2942 
2943 def get_energy_in_femto_joules(*args):
2944  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
2945  return _IMP_atom.get_energy_in_femto_joules(*args)
2946 
2947 def get_force_in_femto_newtons(*args):
2948  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
2949  return _IMP_atom.get_force_in_femto_newtons(*args)
2950 
2951 def get_spring_constant_in_femto_newtons_per_angstrom(*args):
2952  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
2953  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(*args)
2954 class BrownianDynamics(Simulator):
2955  """Proxy of C++ IMP::atom::BrownianDynamics class"""
2956  __swig_setmethods__ = {}
2957  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2958  __setattr__ = lambda self, name, value: _swig_setattr(self, BrownianDynamics, name, value)
2959  __swig_getmethods__ = {}
2960  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2961  __getattr__ = lambda self, name: _swig_getattr(self, BrownianDynamics, name)
2962  def __init__(self, *args):
2963  """
2964  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0) -> BrownianDynamics
2965  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%") -> BrownianDynamics
2966  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
2967  """
2968  this = _IMP_atom.new_BrownianDynamics(*args)
2969  try: self.this.append(this)
2970  except: self.this = this
2971  def set_maximum_move(self, *args):
2972  """set_maximum_move(BrownianDynamics self, double ms)"""
2973  return _IMP_atom.BrownianDynamics_set_maximum_move(self, *args)
2974 
2975  def set_use_stochastic_runge_kutta(self, *args):
2976  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
2977  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, *args)
2978 
2979  def get_version_info(self):
2980  """get_version_info(BrownianDynamics self) -> VersionInfo"""
2981  return _IMP_atom.BrownianDynamics_get_version_info(self)
2982 
2983  def __str__(self):
2984  """__str__(BrownianDynamics self) -> std::string"""
2985  return _IMP_atom.BrownianDynamics___str__(self)
2986 
2987  def __repr__(self):
2988  """__repr__(BrownianDynamics self) -> std::string"""
2989  return _IMP_atom.BrownianDynamics___repr__(self)
2990 
2991  def get_from(o):
2992  return _object_cast_to_BrownianDynamics(o)
2993  get_from = staticmethod(get_from)
2994 
2995 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
2996 BrownianDynamics_swigregister(BrownianDynamics)
2997 
2998 
3000  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3001  return _IMP_atom.get_maximum_time_step_estimate(*args)
3002 
3003 def get_harmonic_sigma(*args):
3004  """get_harmonic_sigma(double D, double f) -> double"""
3005  return _IMP_atom.get_harmonic_sigma(*args)
3006 class Diffusion(IMP.core.XYZ):
3007  """Proxy of C++ IMP::atom::Diffusion class"""
3008  __swig_setmethods__ = {}
3009  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3010  __setattr__ = lambda self, name, value: _swig_setattr(self, Diffusion, name, value)
3011  __swig_getmethods__ = {}
3012  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3013  __getattr__ = lambda self, name: _swig_getattr(self, Diffusion, name)
3014  def __init__(self, *args):
3015  """
3016  __init__(IMP::atom::Diffusion self) -> Diffusion
3017  __init__(IMP::atom::Diffusion self, Model m, ::IMP::kernel::ParticleIndex id) -> Diffusion
3018  __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3019  """
3020  this = _IMP_atom.new_Diffusion(*args)
3021  try: self.this.append(this)
3022  except: self.this = this
3023  def decorate_particle(*args):
3024  """decorate_particle(Particle p) -> Diffusion"""
3025  return _IMP_atom.Diffusion_decorate_particle(*args)
3026 
3027  if _newclass:decorate_particle = staticmethod(decorate_particle)
3028  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3029  def show(self, *args):
3030  """
3031  show(Diffusion self, _ostream out=std::cout)
3032  show(Diffusion self)
3033  """
3034  return _IMP_atom.Diffusion_show(self, *args)
3035 
3036  def setup_particle(*args):
3037  """
3038  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float D) -> Diffusion
3039  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3040  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3041  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3042  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Diffusion
3043  setup_particle(_ParticleAdaptor decorator) -> Diffusion
3044  """
3045  return _IMP_atom.Diffusion_setup_particle(*args)
3046 
3047  if _newclass:setup_particle = staticmethod(setup_particle)
3048  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3049  def get_is_setup(*args):
3050  """
3051  get_is_setup(_ParticleAdaptor p) -> bool
3052  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3053  """
3054  return _IMP_atom.Diffusion_get_is_setup(*args)
3055 
3056  if _newclass:get_is_setup = staticmethod(get_is_setup)
3057  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3058  def set_diffusion_coefficient(self, *args):
3059  """set_diffusion_coefficient(Diffusion self, double d)"""
3060  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, *args)
3061 
3062  def get_diffusion_coefficient(self):
3063  """get_diffusion_coefficient(Diffusion self) -> double"""
3064  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3065 
3066  def get_diffusion_coefficient_key():
3067  """get_diffusion_coefficient_key() -> FloatKey"""
3068  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3069 
3070  if _newclass:get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3071  __swig_getmethods__["get_diffusion_coefficient_key"] = lambda x: get_diffusion_coefficient_key
3072  def add_attribute(self, *args):
3073  """
3074  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3075  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3076  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3077  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3078  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3079  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3080  """
3081  return _IMP_atom.Diffusion_add_attribute(self, *args)
3082 
3083  def get_value(self, *args):
3084  """
3085  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3086  get_value(Diffusion self, IntKey a0) -> IMP::Int
3087  get_value(Diffusion self, StringKey a0) -> IMP::String
3088  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3089  get_value(Diffusion self, ObjectKey a0) -> Object
3090  """
3091  return _IMP_atom.Diffusion_get_value(self, *args)
3092 
3093  def set_value(self, *args):
3094  """
3095  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3096  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3097  set_value(Diffusion self, StringKey a0, IMP::String a1)
3098  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3099  set_value(Diffusion self, ObjectKey a0, Object a1)
3100  """
3101  return _IMP_atom.Diffusion_set_value(self, *args)
3102 
3103  def remove_attribute(self, *args):
3104  """
3105  remove_attribute(Diffusion self, FloatKey a0)
3106  remove_attribute(Diffusion self, IntKey a0)
3107  remove_attribute(Diffusion self, StringKey a0)
3108  remove_attribute(Diffusion self, ParticleIndexKey a0)
3109  remove_attribute(Diffusion self, ObjectKey a0)
3110  """
3111  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3112 
3113  def has_attribute(self, *args):
3114  """
3115  has_attribute(Diffusion self, FloatKey a0) -> bool
3116  has_attribute(Diffusion self, IntKey a0) -> bool
3117  has_attribute(Diffusion self, StringKey a0) -> bool
3118  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3119  has_attribute(Diffusion self, ObjectKey a0) -> bool
3120  """
3121  return _IMP_atom.Diffusion_has_attribute(self, *args)
3122 
3123  def get_derivative(self, *args):
3124  """get_derivative(Diffusion self, FloatKey a0) -> double"""
3125  return _IMP_atom.Diffusion_get_derivative(self, *args)
3126 
3127  def get_name(self):
3128  """get_name(Diffusion self) -> std::string"""
3129  return _IMP_atom.Diffusion_get_name(self)
3130 
3131  def clear_caches(self):
3132  """clear_caches(Diffusion self)"""
3133  return _IMP_atom.Diffusion_clear_caches(self)
3134 
3135  def set_name(self, *args):
3136  """set_name(Diffusion self, std::string a0)"""
3137  return _IMP_atom.Diffusion_set_name(self, *args)
3138 
3139  def set_check_level(self, *args):
3140  """set_check_level(Diffusion self, IMP::base::CheckLevel a0)"""
3141  return _IMP_atom.Diffusion_set_check_level(self, *args)
3142 
3143  def add_to_derivative(self, *args):
3144  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3145  return _IMP_atom.Diffusion_add_to_derivative(self, *args)
3146 
3147  def set_is_optimized(self, *args):
3148  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3149  return _IMP_atom.Diffusion_set_is_optimized(self, *args)
3150 
3151  def get_is_optimized(self, *args):
3152  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3153  return _IMP_atom.Diffusion_get_is_optimized(self, *args)
3154 
3155  def get_check_level(self):
3156  """get_check_level(Diffusion self) -> IMP::base::CheckLevel"""
3157  return _IMP_atom.Diffusion_get_check_level(self)
3158 
3159  def __eq__(self, *args):
3160  """
3161  __eq__(Diffusion self, Diffusion o) -> bool
3162  __eq__(Diffusion self, Particle d) -> bool
3163  """
3164  return _IMP_atom.Diffusion___eq__(self, *args)
3165 
3166  def __ne__(self, *args):
3167  """
3168  __ne__(Diffusion self, Diffusion o) -> bool
3169  __ne__(Diffusion self, Particle d) -> bool
3170  """
3171  return _IMP_atom.Diffusion___ne__(self, *args)
3172 
3173  def __le__(self, *args):
3174  """
3175  __le__(Diffusion self, Diffusion o) -> bool
3176  __le__(Diffusion self, Particle d) -> bool
3177  """
3178  return _IMP_atom.Diffusion___le__(self, *args)
3179 
3180  def __lt__(self, *args):
3181  """
3182  __lt__(Diffusion self, Diffusion o) -> bool
3183  __lt__(Diffusion self, Particle d) -> bool
3184  """
3185  return _IMP_atom.Diffusion___lt__(self, *args)
3186 
3187  def __ge__(self, *args):
3188  """
3189  __ge__(Diffusion self, Diffusion o) -> bool
3190  __ge__(Diffusion self, Particle d) -> bool
3191  """
3192  return _IMP_atom.Diffusion___ge__(self, *args)
3193 
3194  def __gt__(self, *args):
3195  """
3196  __gt__(Diffusion self, Diffusion o) -> bool
3197  __gt__(Diffusion self, Particle d) -> bool
3198  """
3199  return _IMP_atom.Diffusion___gt__(self, *args)
3200 
3201  def __str__(self):
3202  """__str__(Diffusion self) -> std::string"""
3203  return _IMP_atom.Diffusion___str__(self)
3204 
3205  def __repr__(self):
3206  """__repr__(Diffusion self) -> std::string"""
3207  return _IMP_atom.Diffusion___repr__(self)
3208 
3209  __swig_destroy__ = _IMP_atom.delete_Diffusion
3210  __del__ = lambda self : None;
3211 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
3212 Diffusion_swigregister(Diffusion)
3213 
3214 def Diffusion_decorate_particle(*args):
3215  """Diffusion_decorate_particle(Particle p) -> Diffusion"""
3216  return _IMP_atom.Diffusion_decorate_particle(*args)
3217 
3218 def Diffusion_setup_particle(*args):
3219  """
3220  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float D) -> Diffusion
3221  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3222  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3223  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3224  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Diffusion
3225  Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
3226  """
3227  return _IMP_atom.Diffusion_setup_particle(*args)
3228 
3229 def Diffusion_get_is_setup(*args):
3230  """
3231  get_is_setup(_ParticleAdaptor p) -> bool
3232  Diffusion_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3233  """
3234  return _IMP_atom.Diffusion_get_is_setup(*args)
3235 
3236 def Diffusion_get_diffusion_coefficient_key():
3237  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
3238  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3239 
3240 
3241 def get_diffusion_coefficient_from_cm2_per_second(*args):
3242  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3243  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(*args)
3244 class RigidBodyDiffusion(Diffusion):
3245  """Proxy of C++ IMP::atom::RigidBodyDiffusion class"""
3246  __swig_setmethods__ = {}
3247  for _s in [Diffusion]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3248  __setattr__ = lambda self, name, value: _swig_setattr(self, RigidBodyDiffusion, name, value)
3249  __swig_getmethods__ = {}
3250  for _s in [Diffusion]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3251  __getattr__ = lambda self, name: _swig_getattr(self, RigidBodyDiffusion, name)
3252  def __init__(self, *args):
3253  """
3254  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
3255  __init__(IMP::atom::RigidBodyDiffusion self, Model m, ::IMP::kernel::ParticleIndex id) -> RigidBodyDiffusion
3256  __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3257  """
3258  this = _IMP_atom.new_RigidBodyDiffusion(*args)
3259  try: self.this.append(this)
3260  except: self.this = this
3261  def decorate_particle(*args):
3262  """decorate_particle(Particle p) -> RigidBodyDiffusion"""
3263  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3264 
3265  if _newclass:decorate_particle = staticmethod(decorate_particle)
3266  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3267  def show(self, *args):
3268  """
3269  show(RigidBodyDiffusion self, _ostream out=std::cout)
3270  show(RigidBodyDiffusion self)
3271  """
3272  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3273 
3274  def setup_particle(*args):
3275  """
3276  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> RigidBodyDiffusion
3277  setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3278  """
3279  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3280 
3281  if _newclass:setup_particle = staticmethod(setup_particle)
3282  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3284  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3285  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3286 
3287  def set_rotational_diffusion_coefficient(self, *args):
3288  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3289  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, *args)
3290 
3291  def get_is_setup(*args):
3292  """
3293  get_is_setup(_ParticleAdaptor p) -> bool
3294  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3295  """
3296  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3297 
3298  if _newclass:get_is_setup = staticmethod(get_is_setup)
3299  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3300  def get_rotational_diffusion_coefficient_key():
3301  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
3302  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3303 
3304  if _newclass:get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
3305  __swig_getmethods__["get_rotational_diffusion_coefficient_key"] = lambda x: get_rotational_diffusion_coefficient_key
3306  def add_attribute(self, *args):
3307  """
3308  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3309  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3310  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3311  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3312  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3313  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3314  """
3315  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3316 
3317  def get_value(self, *args):
3318  """
3319  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3320  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3321  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3322  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3323  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
3324  """
3325  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3326 
3327  def set_value(self, *args):
3328  """
3329  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3330  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3331  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3332  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3333  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3334  """
3335  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3336 
3337  def remove_attribute(self, *args):
3338  """
3339  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3340  remove_attribute(RigidBodyDiffusion self, IntKey a0)
3341  remove_attribute(RigidBodyDiffusion self, StringKey a0)
3342  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3343  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3344  """
3345  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3346 
3347  def has_attribute(self, *args):
3348  """
3349  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3350  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3351  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3352  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3353  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3354  """
3355  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3356 
3357  def get_derivative(self, *args):
3358  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3359  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, *args)
3360 
3361  def get_name(self):
3362  """get_name(RigidBodyDiffusion self) -> std::string"""
3363  return _IMP_atom.RigidBodyDiffusion_get_name(self)
3364 
3365  def clear_caches(self):
3366  """clear_caches(RigidBodyDiffusion self)"""
3367  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
3368 
3369  def set_name(self, *args):
3370  """set_name(RigidBodyDiffusion self, std::string a0)"""
3371  return _IMP_atom.RigidBodyDiffusion_set_name(self, *args)
3372 
3373  def set_check_level(self, *args):
3374  """set_check_level(RigidBodyDiffusion self, IMP::base::CheckLevel a0)"""
3375  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, *args)
3376 
3377  def add_to_derivative(self, *args):
3378  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3379  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, *args)
3380 
3381  def set_is_optimized(self, *args):
3382  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
3383  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, *args)
3384 
3385  def get_is_optimized(self, *args):
3386  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
3387  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, *args)
3388 
3389  def get_check_level(self):
3390  """get_check_level(RigidBodyDiffusion self) -> IMP::base::CheckLevel"""
3391  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
3392 
3393  def __eq__(self, *args):
3394  """
3395  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3396  __eq__(RigidBodyDiffusion self, Particle d) -> bool
3397  """
3398  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
3399 
3400  def __ne__(self, *args):
3401  """
3402  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3403  __ne__(RigidBodyDiffusion self, Particle d) -> bool
3404  """
3405  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
3406 
3407  def __le__(self, *args):
3408  """
3409  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3410  __le__(RigidBodyDiffusion self, Particle d) -> bool
3411  """
3412  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
3413 
3414  def __lt__(self, *args):
3415  """
3416  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3417  __lt__(RigidBodyDiffusion self, Particle d) -> bool
3418  """
3419  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
3420 
3421  def __ge__(self, *args):
3422  """
3423  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3424  __ge__(RigidBodyDiffusion self, Particle d) -> bool
3425  """
3426  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
3427 
3428  def __gt__(self, *args):
3429  """
3430  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3431  __gt__(RigidBodyDiffusion self, Particle d) -> bool
3432  """
3433  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
3434 
3435  def __str__(self):
3436  """__str__(RigidBodyDiffusion self) -> std::string"""
3437  return _IMP_atom.RigidBodyDiffusion___str__(self)
3438 
3439  def __repr__(self):
3440  """__repr__(RigidBodyDiffusion self) -> std::string"""
3441  return _IMP_atom.RigidBodyDiffusion___repr__(self)
3442 
3443  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
3444  __del__ = lambda self : None;
3445 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
3446 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
3447 
3448 def RigidBodyDiffusion_decorate_particle(*args):
3449  """RigidBodyDiffusion_decorate_particle(Particle p) -> RigidBodyDiffusion"""
3450  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3451 
3452 def RigidBodyDiffusion_setup_particle(*args):
3453  """
3454  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> RigidBodyDiffusion
3455  RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3456  """
3457  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3458 
3459 def RigidBodyDiffusion_get_is_setup(*args):
3460  """
3461  get_is_setup(_ParticleAdaptor p) -> bool
3462  RigidBodyDiffusion_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3463  """
3464  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3465 
3466 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
3467  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
3468  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3469 
3470 class Chain(Hierarchy):
3471  """Proxy of C++ IMP::atom::Chain class"""
3472  __swig_setmethods__ = {}
3473  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3474  __setattr__ = lambda self, name, value: _swig_setattr(self, Chain, name, value)
3475  __swig_getmethods__ = {}
3476  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3477  __getattr__ = lambda self, name: _swig_getattr(self, Chain, name)
3478  def __init__(self, *args):
3479  """
3480  __init__(IMP::atom::Chain self) -> Chain
3481  __init__(IMP::atom::Chain self, Model m, ::IMP::kernel::ParticleIndex id) -> Chain
3482  __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
3483  """
3484  this = _IMP_atom.new_Chain(*args)
3485  try: self.this.append(this)
3486  except: self.this = this
3487  def decorate_particle(*args):
3488  """decorate_particle(Particle p) -> Chain"""
3489  return _IMP_atom.Chain_decorate_particle(*args)
3490 
3491  if _newclass:decorate_particle = staticmethod(decorate_particle)
3492  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3493  def show(self, *args):
3494  """
3495  show(Chain self, _ostream out=std::cout)
3496  show(Chain self)
3497  """
3498  return _IMP_atom.Chain_show(self, *args)
3499 
3500  def setup_particle(*args):
3501  """
3502  setup_particle(Model m, IMP::kernel::ParticleIndex pi, std::string id) -> Chain
3503  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
3504  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3505  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
3506  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Chain other) -> Chain
3507  setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
3508  """
3509  return _IMP_atom.Chain_setup_particle(*args)
3510 
3511  if _newclass:setup_particle = staticmethod(setup_particle)
3512  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3513  def get_is_setup(*args):
3514  """
3515  get_is_setup(_ParticleAdaptor p) -> bool
3516  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3517  """
3518  return _IMP_atom.Chain_get_is_setup(*args)
3519 
3520  if _newclass:get_is_setup = staticmethod(get_is_setup)
3521  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3522  def get_id(self):
3523  """get_id(Chain self) -> std::string"""
3524  return _IMP_atom.Chain_get_id(self)
3525 
3526  def get_id_char(self):
3527  """get_id_char(Chain self) -> char"""
3528  return _IMP_atom.Chain_get_id_char(self)
3529 
3530  def set_id(self, *args):
3531  """set_id(Chain self, std::string c)"""
3532  return _IMP_atom.Chain_set_id(self, *args)
3533 
3534  def get_id_key():
3535  """get_id_key() -> StringKey"""
3536  return _IMP_atom.Chain_get_id_key()
3537 
3538  if _newclass:get_id_key = staticmethod(get_id_key)
3539  __swig_getmethods__["get_id_key"] = lambda x: get_id_key
3540  def add_attribute(self, *args):
3541  """
3542  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
3543  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
3544  add_attribute(Chain self, IntKey a0, IMP::Int a1)
3545  add_attribute(Chain self, StringKey a0, IMP::String a1)
3546  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
3547  add_attribute(Chain self, ObjectKey a0, Object a1)
3548  """
3549  return _IMP_atom.Chain_add_attribute(self, *args)
3550 
3551  def get_value(self, *args):
3552  """
3553  get_value(Chain self, FloatKey a0) -> IMP::Float
3554  get_value(Chain self, IntKey a0) -> IMP::Int
3555  get_value(Chain self, StringKey a0) -> IMP::String
3556  get_value(Chain self, ParticleIndexKey a0) -> Particle
3557  get_value(Chain self, ObjectKey a0) -> Object
3558  """
3559  return _IMP_atom.Chain_get_value(self, *args)
3560 
3561  def set_value(self, *args):
3562  """
3563  set_value(Chain self, FloatKey a0, IMP::Float a1)
3564  set_value(Chain self, IntKey a0, IMP::Int a1)
3565  set_value(Chain self, StringKey a0, IMP::String a1)
3566  set_value(Chain self, ParticleIndexKey a0, Particle a1)
3567  set_value(Chain self, ObjectKey a0, Object a1)
3568  """
3569  return _IMP_atom.Chain_set_value(self, *args)
3570 
3571  def remove_attribute(self, *args):
3572  """
3573  remove_attribute(Chain self, FloatKey a0)
3574  remove_attribute(Chain self, IntKey a0)
3575  remove_attribute(Chain self, StringKey a0)
3576  remove_attribute(Chain self, ParticleIndexKey a0)
3577  remove_attribute(Chain self, ObjectKey a0)
3578  """
3579  return _IMP_atom.Chain_remove_attribute(self, *args)
3580 
3581  def has_attribute(self, *args):
3582  """
3583  has_attribute(Chain self, FloatKey a0) -> bool
3584  has_attribute(Chain self, IntKey a0) -> bool
3585  has_attribute(Chain self, StringKey a0) -> bool
3586  has_attribute(Chain self, ParticleIndexKey a0) -> bool
3587  has_attribute(Chain self, ObjectKey a0) -> bool
3588  """
3589  return _IMP_atom.Chain_has_attribute(self, *args)
3590 
3591  def get_derivative(self, *args):
3592  """get_derivative(Chain self, FloatKey a0) -> double"""
3593  return _IMP_atom.Chain_get_derivative(self, *args)
3594 
3595  def get_name(self):
3596  """get_name(Chain self) -> std::string"""
3597  return _IMP_atom.Chain_get_name(self)
3598 
3599  def clear_caches(self):
3600  """clear_caches(Chain self)"""
3601  return _IMP_atom.Chain_clear_caches(self)
3602 
3603  def set_name(self, *args):
3604  """set_name(Chain self, std::string a0)"""
3605  return _IMP_atom.Chain_set_name(self, *args)
3606 
3607  def set_check_level(self, *args):
3608  """set_check_level(Chain self, IMP::base::CheckLevel a0)"""
3609  return _IMP_atom.Chain_set_check_level(self, *args)
3610 
3611  def add_to_derivative(self, *args):
3612  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3613  return _IMP_atom.Chain_add_to_derivative(self, *args)
3614 
3615  def set_is_optimized(self, *args):
3616  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
3617  return _IMP_atom.Chain_set_is_optimized(self, *args)
3618 
3619  def get_is_optimized(self, *args):
3620  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
3621  return _IMP_atom.Chain_get_is_optimized(self, *args)
3622 
3623  def get_check_level(self):
3624  """get_check_level(Chain self) -> IMP::base::CheckLevel"""
3625  return _IMP_atom.Chain_get_check_level(self)
3626 
3627  def __eq__(self, *args):
3628  """
3629  __eq__(Chain self, Chain o) -> bool
3630  __eq__(Chain self, Particle d) -> bool
3631  """
3632  return _IMP_atom.Chain___eq__(self, *args)
3633 
3634  def __ne__(self, *args):
3635  """
3636  __ne__(Chain self, Chain o) -> bool
3637  __ne__(Chain self, Particle d) -> bool
3638  """
3639  return _IMP_atom.Chain___ne__(self, *args)
3640 
3641  def __le__(self, *args):
3642  """
3643  __le__(Chain self, Chain o) -> bool
3644  __le__(Chain self, Particle d) -> bool
3645  """
3646  return _IMP_atom.Chain___le__(self, *args)
3647 
3648  def __lt__(self, *args):
3649  """
3650  __lt__(Chain self, Chain o) -> bool
3651  __lt__(Chain self, Particle d) -> bool
3652  """
3653  return _IMP_atom.Chain___lt__(self, *args)
3654 
3655  def __ge__(self, *args):
3656  """
3657  __ge__(Chain self, Chain o) -> bool
3658  __ge__(Chain self, Particle d) -> bool
3659  """
3660  return _IMP_atom.Chain___ge__(self, *args)
3661 
3662  def __gt__(self, *args):
3663  """
3664  __gt__(Chain self, Chain o) -> bool
3665  __gt__(Chain self, Particle d) -> bool
3666  """
3667  return _IMP_atom.Chain___gt__(self, *args)
3668 
3669  def __str__(self):
3670  """__str__(Chain self) -> std::string"""
3671  return _IMP_atom.Chain___str__(self)
3672 
3673  def __repr__(self):
3674  """__repr__(Chain self) -> std::string"""
3675  return _IMP_atom.Chain___repr__(self)
3676 
3677  __swig_destroy__ = _IMP_atom.delete_Chain
3678  __del__ = lambda self : None;
3679 Chain_swigregister = _IMP_atom.Chain_swigregister
3680 Chain_swigregister(Chain)
3681 
3682 def Chain_decorate_particle(*args):
3683  """Chain_decorate_particle(Particle p) -> Chain"""
3684  return _IMP_atom.Chain_decorate_particle(*args)
3685 
3686 def Chain_setup_particle(*args):
3687  """
3688  setup_particle(Model m, IMP::kernel::ParticleIndex pi, std::string id) -> Chain
3689  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
3690  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3691  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
3692  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Chain other) -> Chain
3693  Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
3694  """
3695  return _IMP_atom.Chain_setup_particle(*args)
3696 
3697 def Chain_get_is_setup(*args):
3698  """
3699  get_is_setup(_ParticleAdaptor p) -> bool
3700  Chain_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3701  """
3702  return _IMP_atom.Chain_get_is_setup(*args)
3703 
3704 def Chain_get_id_key():
3705  """Chain_get_id_key() -> StringKey"""
3706  return _IMP_atom.Chain_get_id_key()
3707 
3708 
3709 def get_chain(*args):
3710  """get_chain(Hierarchy h) -> Chain"""
3711  return _IMP_atom.get_chain(*args)
3712 
3713 def get_chain_id(*args):
3714  """get_chain_id(Hierarchy h) -> std::string"""
3715  return _IMP_atom.get_chain_id(*args)
3716 class Charged(IMP.core.XYZ):
3717  """Proxy of C++ IMP::atom::Charged class"""
3718  __swig_setmethods__ = {}
3719  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3720  __setattr__ = lambda self, name, value: _swig_setattr(self, Charged, name, value)
3721  __swig_getmethods__ = {}
3722  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3723  __getattr__ = lambda self, name: _swig_getattr(self, Charged, name)
3724  def __init__(self, *args):
3725  """
3726  __init__(IMP::atom::Charged self) -> Charged
3727  __init__(IMP::atom::Charged self, Model m, ::IMP::kernel::ParticleIndex id) -> Charged
3728  __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
3729  """
3730  this = _IMP_atom.new_Charged(*args)
3731  try: self.this.append(this)
3732  except: self.this = this
3733  def decorate_particle(*args):
3734  """decorate_particle(Particle p) -> Charged"""
3735  return _IMP_atom.Charged_decorate_particle(*args)
3736 
3737  if _newclass:decorate_particle = staticmethod(decorate_particle)
3738  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3739  def show(self, *args):
3740  """
3741  show(Charged self, _ostream out=std::cout)
3742  show(Charged self)
3743  """
3744  return _IMP_atom.Charged_show(self, *args)
3745 
3746  def setup_particle(*args):
3747  """
3748  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float charge) -> Charged
3749  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
3750  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
3751  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
3752  """
3753  return _IMP_atom.Charged_setup_particle(*args)
3754 
3755  if _newclass:setup_particle = staticmethod(setup_particle)
3756  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3757  def get_charge(self):
3758  """get_charge(Charged self) -> IMP::Float"""
3759  return _IMP_atom.Charged_get_charge(self)
3760 
3761  def set_charge(self, *args):
3762  """set_charge(Charged self, IMP::Float t)"""
3763  return _IMP_atom.Charged_set_charge(self, *args)
3764 
3765  def get_is_setup(*args):
3766  """
3767  get_is_setup(_ParticleAdaptor p) -> bool
3768  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3769  """
3770  return _IMP_atom.Charged_get_is_setup(*args)
3771 
3772  if _newclass:get_is_setup = staticmethod(get_is_setup)
3773  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3774  def get_charge_key():
3775  """get_charge_key() -> FloatKey"""
3776  return _IMP_atom.Charged_get_charge_key()
3777 
3778  if _newclass:get_charge_key = staticmethod(get_charge_key)
3779  __swig_getmethods__["get_charge_key"] = lambda x: get_charge_key
3780  def add_attribute(self, *args):
3781  """
3782  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
3783  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
3784  add_attribute(Charged self, IntKey a0, IMP::Int a1)
3785  add_attribute(Charged self, StringKey a0, IMP::String a1)
3786  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
3787  add_attribute(Charged self, ObjectKey a0, Object a1)
3788  """
3789  return _IMP_atom.Charged_add_attribute(self, *args)
3790 
3791  def get_value(self, *args):
3792  """
3793  get_value(Charged self, FloatKey a0) -> IMP::Float
3794  get_value(Charged self, IntKey a0) -> IMP::Int
3795  get_value(Charged self, StringKey a0) -> IMP::String
3796  get_value(Charged self, ParticleIndexKey a0) -> Particle
3797  get_value(Charged self, ObjectKey a0) -> Object
3798  """
3799  return _IMP_atom.Charged_get_value(self, *args)
3800 
3801  def set_value(self, *args):
3802  """
3803  set_value(Charged self, FloatKey a0, IMP::Float a1)
3804  set_value(Charged self, IntKey a0, IMP::Int a1)
3805  set_value(Charged self, StringKey a0, IMP::String a1)
3806  set_value(Charged self, ParticleIndexKey a0, Particle a1)
3807  set_value(Charged self, ObjectKey a0, Object a1)
3808  """
3809  return _IMP_atom.Charged_set_value(self, *args)
3810 
3811  def remove_attribute(self, *args):
3812  """
3813  remove_attribute(Charged self, FloatKey a0)
3814  remove_attribute(Charged self, IntKey a0)
3815  remove_attribute(Charged self, StringKey a0)
3816  remove_attribute(Charged self, ParticleIndexKey a0)
3817  remove_attribute(Charged self, ObjectKey a0)
3818  """
3819  return _IMP_atom.Charged_remove_attribute(self, *args)
3820 
3821  def has_attribute(self, *args):
3822  """
3823  has_attribute(Charged self, FloatKey a0) -> bool
3824  has_attribute(Charged self, IntKey a0) -> bool
3825  has_attribute(Charged self, StringKey a0) -> bool
3826  has_attribute(Charged self, ParticleIndexKey a0) -> bool
3827  has_attribute(Charged self, ObjectKey a0) -> bool
3828  """
3829  return _IMP_atom.Charged_has_attribute(self, *args)
3830 
3831  def get_derivative(self, *args):
3832  """get_derivative(Charged self, FloatKey a0) -> double"""
3833  return _IMP_atom.Charged_get_derivative(self, *args)
3834 
3835  def get_name(self):
3836  """get_name(Charged self) -> std::string"""
3837  return _IMP_atom.Charged_get_name(self)
3838 
3839  def clear_caches(self):
3840  """clear_caches(Charged self)"""
3841  return _IMP_atom.Charged_clear_caches(self)
3842 
3843  def set_name(self, *args):
3844  """set_name(Charged self, std::string a0)"""
3845  return _IMP_atom.Charged_set_name(self, *args)
3846 
3847  def set_check_level(self, *args):
3848  """set_check_level(Charged self, IMP::base::CheckLevel a0)"""
3849  return _IMP_atom.Charged_set_check_level(self, *args)
3850 
3851  def add_to_derivative(self, *args):
3852  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3853  return _IMP_atom.Charged_add_to_derivative(self, *args)
3854 
3855  def set_is_optimized(self, *args):
3856  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
3857  return _IMP_atom.Charged_set_is_optimized(self, *args)
3858 
3859  def get_is_optimized(self, *args):
3860  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
3861  return _IMP_atom.Charged_get_is_optimized(self, *args)
3862 
3863  def get_check_level(self):
3864  """get_check_level(Charged self) -> IMP::base::CheckLevel"""
3865  return _IMP_atom.Charged_get_check_level(self)
3866 
3867  def __eq__(self, *args):
3868  """
3869  __eq__(Charged self, Charged o) -> bool
3870  __eq__(Charged self, Particle d) -> bool
3871  """
3872  return _IMP_atom.Charged___eq__(self, *args)
3873 
3874  def __ne__(self, *args):
3875  """
3876  __ne__(Charged self, Charged o) -> bool
3877  __ne__(Charged self, Particle d) -> bool
3878  """
3879  return _IMP_atom.Charged___ne__(self, *args)
3880 
3881  def __le__(self, *args):
3882  """
3883  __le__(Charged self, Charged o) -> bool
3884  __le__(Charged self, Particle d) -> bool
3885  """
3886  return _IMP_atom.Charged___le__(self, *args)
3887 
3888  def __lt__(self, *args):
3889  """
3890  __lt__(Charged self, Charged o) -> bool
3891  __lt__(Charged self, Particle d) -> bool
3892  """
3893  return _IMP_atom.Charged___lt__(self, *args)
3894 
3895  def __ge__(self, *args):
3896  """
3897  __ge__(Charged self, Charged o) -> bool
3898  __ge__(Charged self, Particle d) -> bool
3899  """
3900  return _IMP_atom.Charged___ge__(self, *args)
3901 
3902  def __gt__(self, *args):
3903  """
3904  __gt__(Charged self, Charged o) -> bool
3905  __gt__(Charged self, Particle d) -> bool
3906  """
3907  return _IMP_atom.Charged___gt__(self, *args)
3908 
3909  def __str__(self):
3910  """__str__(Charged self) -> std::string"""
3911  return _IMP_atom.Charged___str__(self)
3912 
3913  def __repr__(self):
3914  """__repr__(Charged self) -> std::string"""
3915  return _IMP_atom.Charged___repr__(self)
3916 
3917  __swig_destroy__ = _IMP_atom.delete_Charged
3918  __del__ = lambda self : None;
3919 Charged_swigregister = _IMP_atom.Charged_swigregister
3920 Charged_swigregister(Charged)
3921 
3922 def Charged_decorate_particle(*args):
3923  """Charged_decorate_particle(Particle p) -> Charged"""
3924  return _IMP_atom.Charged_decorate_particle(*args)
3925 
3926 def Charged_setup_particle(*args):
3927  """
3928  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float charge) -> Charged
3929  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
3930  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
3931  Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
3932  """
3933  return _IMP_atom.Charged_setup_particle(*args)
3934 
3935 def Charged_get_is_setup(*args):
3936  """
3937  get_is_setup(_ParticleAdaptor p) -> bool
3938  Charged_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3939  """
3940  return _IMP_atom.Charged_get_is_setup(*args)
3941 
3942 def Charged_get_charge_key():
3943  """Charged_get_charge_key() -> FloatKey"""
3944  return _IMP_atom.Charged_get_charge_key()
3945 
3946 class CoulombPairScore(IMP.kernel.PairScore):
3947  """Proxy of C++ IMP::atom::CoulombPairScore class"""
3948  __swig_setmethods__ = {}
3949  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3950  __setattr__ = lambda self, name, value: _swig_setattr(self, CoulombPairScore, name, value)
3951  __swig_getmethods__ = {}
3952  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3953  __getattr__ = lambda self, name: _swig_getattr(self, CoulombPairScore, name)
3954  def __init__(self, *args):
3955  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
3956  this = _IMP_atom.new_CoulombPairScore(*args)
3957  try: self.this.append(this)
3958  except: self.this = this
3959  def set_relative_dielectric(self, *args):
3960  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
3961  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, *args)
3962 
3963  def get_relative_dielectric(self):
3964  """get_relative_dielectric(CoulombPairScore self) -> double"""
3965  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
3966 
3967  def do_get_inputs(self, *args):
3968  """do_get_inputs(CoulombPairScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
3969  return _IMP_atom.CoulombPairScore_do_get_inputs(self, *args)
3970 
3971  def get_version_info(self):
3972  """get_version_info(CoulombPairScore self) -> VersionInfo"""
3973  return _IMP_atom.CoulombPairScore_get_version_info(self)
3974 
3975  def __str__(self):
3976  """__str__(CoulombPairScore self) -> std::string"""
3977  return _IMP_atom.CoulombPairScore___str__(self)
3978 
3979  def __repr__(self):
3980  """__repr__(CoulombPairScore self) -> std::string"""
3981  return _IMP_atom.CoulombPairScore___repr__(self)
3982 
3983  def get_from(o):
3984  return _object_cast_to_CoulombPairScore(o)
3985  get_from = staticmethod(get_from)
3986 
3987 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
3988 CoulombPairScore_swigregister(CoulombPairScore)
3989 
3990 class Domain(Hierarchy):
3991  """Proxy of C++ IMP::atom::Domain class"""
3992  __swig_setmethods__ = {}
3993  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3994  __setattr__ = lambda self, name, value: _swig_setattr(self, Domain, name, value)
3995  __swig_getmethods__ = {}
3996  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3997  __getattr__ = lambda self, name: _swig_getattr(self, Domain, name)
3998  def set_index_range(self, *args):
3999  """set_index_range(Domain self, IMP::IntRange ir)"""
4000  return _IMP_atom.Domain_set_index_range(self, *args)
4001 
4002  def get_index_range(self):
4003  """get_index_range(Domain self) -> IMP::IntRange"""
4004  return _IMP_atom.Domain_get_index_range(self)
4005 
4006  def __init__(self, *args):
4007  """
4008  __init__(IMP::atom::Domain self) -> Domain
4009  __init__(IMP::atom::Domain self, Model m, ::IMP::kernel::ParticleIndex id) -> Domain
4010  __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
4011  """
4012  this = _IMP_atom.new_Domain(*args)
4013  try: self.this.append(this)
4014  except: self.this = this
4015  def decorate_particle(*args):
4016  """decorate_particle(Particle p) -> Domain"""
4017  return _IMP_atom.Domain_decorate_particle(*args)
4018 
4019  if _newclass:decorate_particle = staticmethod(decorate_particle)
4020  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4021  def get_is_setup(*args):
4022  """
4023  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4024  get_is_setup(_ParticleAdaptor p) -> bool
4025  """
4026  return _IMP_atom.Domain_get_is_setup(*args)
4027 
4028  if _newclass:get_is_setup = staticmethod(get_is_setup)
4029  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4030  def show(self, *args):
4031  """
4032  show(Domain self, _ostream out=std::cout)
4033  show(Domain self)
4034  """
4035  return _IMP_atom.Domain_show(self, *args)
4036 
4037  def setup_particle(*args):
4038  """
4039  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Domain other) -> Domain
4040  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
4041  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::IntRange residues) -> Domain
4042  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
4043  """
4044  return _IMP_atom.Domain_setup_particle(*args)
4045 
4046  if _newclass:setup_particle = staticmethod(setup_particle)
4047  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4048  def add_attribute(self, *args):
4049  """
4050  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4051  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4052  add_attribute(Domain self, IntKey a0, IMP::Int a1)
4053  add_attribute(Domain self, StringKey a0, IMP::String a1)
4054  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4055  add_attribute(Domain self, ObjectKey a0, Object a1)
4056  """
4057  return _IMP_atom.Domain_add_attribute(self, *args)
4058 
4059  def get_value(self, *args):
4060  """
4061  get_value(Domain self, FloatKey a0) -> IMP::Float
4062  get_value(Domain self, IntKey a0) -> IMP::Int
4063  get_value(Domain self, StringKey a0) -> IMP::String
4064  get_value(Domain self, ParticleIndexKey a0) -> Particle
4065  get_value(Domain self, ObjectKey a0) -> Object
4066  """
4067  return _IMP_atom.Domain_get_value(self, *args)
4068 
4069  def set_value(self, *args):
4070  """
4071  set_value(Domain self, FloatKey a0, IMP::Float a1)
4072  set_value(Domain self, IntKey a0, IMP::Int a1)
4073  set_value(Domain self, StringKey a0, IMP::String a1)
4074  set_value(Domain self, ParticleIndexKey a0, Particle a1)
4075  set_value(Domain self, ObjectKey a0, Object a1)
4076  """
4077  return _IMP_atom.Domain_set_value(self, *args)
4078 
4079  def remove_attribute(self, *args):
4080  """
4081  remove_attribute(Domain self, FloatKey a0)
4082  remove_attribute(Domain self, IntKey a0)
4083  remove_attribute(Domain self, StringKey a0)
4084  remove_attribute(Domain self, ParticleIndexKey a0)
4085  remove_attribute(Domain self, ObjectKey a0)
4086  """
4087  return _IMP_atom.Domain_remove_attribute(self, *args)
4088 
4089  def has_attribute(self, *args):
4090  """
4091  has_attribute(Domain self, FloatKey a0) -> bool
4092  has_attribute(Domain self, IntKey a0) -> bool
4093  has_attribute(Domain self, StringKey a0) -> bool
4094  has_attribute(Domain self, ParticleIndexKey a0) -> bool
4095  has_attribute(Domain self, ObjectKey a0) -> bool
4096  """
4097  return _IMP_atom.Domain_has_attribute(self, *args)
4098 
4099  def get_derivative(self, *args):
4100  """get_derivative(Domain self, FloatKey a0) -> double"""
4101  return _IMP_atom.Domain_get_derivative(self, *args)
4102 
4103  def get_name(self):
4104  """get_name(Domain self) -> std::string"""
4105  return _IMP_atom.Domain_get_name(self)
4106 
4107  def clear_caches(self):
4108  """clear_caches(Domain self)"""
4109  return _IMP_atom.Domain_clear_caches(self)
4110 
4111  def set_name(self, *args):
4112  """set_name(Domain self, std::string a0)"""
4113  return _IMP_atom.Domain_set_name(self, *args)
4114 
4115  def set_check_level(self, *args):
4116  """set_check_level(Domain self, IMP::base::CheckLevel a0)"""
4117  return _IMP_atom.Domain_set_check_level(self, *args)
4118 
4119  def add_to_derivative(self, *args):
4120  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4121  return _IMP_atom.Domain_add_to_derivative(self, *args)
4122 
4123  def set_is_optimized(self, *args):
4124  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4125  return _IMP_atom.Domain_set_is_optimized(self, *args)
4126 
4127  def get_is_optimized(self, *args):
4128  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
4129  return _IMP_atom.Domain_get_is_optimized(self, *args)
4130 
4131  def get_check_level(self):
4132  """get_check_level(Domain self) -> IMP::base::CheckLevel"""
4133  return _IMP_atom.Domain_get_check_level(self)
4134 
4135  def __eq__(self, *args):
4136  """
4137  __eq__(Domain self, Domain o) -> bool
4138  __eq__(Domain self, Particle d) -> bool
4139  """
4140  return _IMP_atom.Domain___eq__(self, *args)
4141 
4142  def __ne__(self, *args):
4143  """
4144  __ne__(Domain self, Domain o) -> bool
4145  __ne__(Domain self, Particle d) -> bool
4146  """
4147  return _IMP_atom.Domain___ne__(self, *args)
4148 
4149  def __le__(self, *args):
4150  """
4151  __le__(Domain self, Domain o) -> bool
4152  __le__(Domain self, Particle d) -> bool
4153  """
4154  return _IMP_atom.Domain___le__(self, *args)
4155 
4156  def __lt__(self, *args):
4157  """
4158  __lt__(Domain self, Domain o) -> bool
4159  __lt__(Domain self, Particle d) -> bool
4160  """
4161  return _IMP_atom.Domain___lt__(self, *args)
4162 
4163  def __ge__(self, *args):
4164  """
4165  __ge__(Domain self, Domain o) -> bool
4166  __ge__(Domain self, Particle d) -> bool
4167  """
4168  return _IMP_atom.Domain___ge__(self, *args)
4169 
4170  def __gt__(self, *args):
4171  """
4172  __gt__(Domain self, Domain o) -> bool
4173  __gt__(Domain self, Particle d) -> bool
4174  """
4175  return _IMP_atom.Domain___gt__(self, *args)
4176 
4177  def __str__(self):
4178  """__str__(Domain self) -> std::string"""
4179  return _IMP_atom.Domain___str__(self)
4180 
4181  def __repr__(self):
4182  """__repr__(Domain self) -> std::string"""
4183  return _IMP_atom.Domain___repr__(self)
4184 
4185  __swig_destroy__ = _IMP_atom.delete_Domain
4186  __del__ = lambda self : None;
4187 Domain_swigregister = _IMP_atom.Domain_swigregister
4188 Domain_swigregister(Domain)
4189 
4190 def Domain_decorate_particle(*args):
4191  """Domain_decorate_particle(Particle p) -> Domain"""
4192  return _IMP_atom.Domain_decorate_particle(*args)
4193 
4194 def Domain_get_is_setup(*args):
4195  """
4196  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4197  Domain_get_is_setup(_ParticleAdaptor p) -> bool
4198  """
4199  return _IMP_atom.Domain_get_is_setup(*args)
4200 
4201 def Domain_setup_particle(*args):
4202  """
4203  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Domain other) -> Domain
4204  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
4205  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::IntRange residues) -> Domain
4206  Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
4207  """
4208  return _IMP_atom.Domain_setup_particle(*args)
4209 
4210 class LennardJones(IMP.core.XYZR):
4211  """Proxy of C++ IMP::atom::LennardJones class"""
4212  __swig_setmethods__ = {}
4213  for _s in [IMP.core.XYZR]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4214  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJones, name, value)
4215  __swig_getmethods__ = {}
4216  for _s in [IMP.core.XYZR]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4217  __getattr__ = lambda self, name: _swig_getattr(self, LennardJones, name)
4218  def __init__(self, *args):
4219  """
4220  __init__(IMP::atom::LennardJones self) -> LennardJones
4221  __init__(IMP::atom::LennardJones self, Model m, ::IMP::kernel::ParticleIndex id) -> LennardJones
4222  __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
4223  """
4224  this = _IMP_atom.new_LennardJones(*args)
4225  try: self.this.append(this)
4226  except: self.this = this
4227  def decorate_particle(*args):
4228  """decorate_particle(Particle p) -> LennardJones"""
4229  return _IMP_atom.LennardJones_decorate_particle(*args)
4230 
4231  if _newclass:decorate_particle = staticmethod(decorate_particle)
4232  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4233  def show(self, *args):
4234  """
4235  show(LennardJones self, _ostream out=std::cout)
4236  show(LennardJones self)
4237  """
4238  return _IMP_atom.LennardJones_show(self, *args)
4239 
4240  def setup_particle(*args):
4241  """
4242  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> LennardJones
4243  setup_particle(_ParticleAdaptor decorator) -> LennardJones
4244  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4245  setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
4246  """
4247  return _IMP_atom.LennardJones_setup_particle(*args)
4248 
4249  if _newclass:setup_particle = staticmethod(setup_particle)
4250  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4251  def get_well_depth(self):
4252  """get_well_depth(LennardJones self) -> IMP::Float"""
4253  return _IMP_atom.LennardJones_get_well_depth(self)
4254 
4255  def set_well_depth(self, *args):
4256  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
4257  return _IMP_atom.LennardJones_set_well_depth(self, *args)
4258 
4259  def get_is_setup(*args):
4260  """
4261  get_is_setup(_ParticleAdaptor p) -> bool
4262  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4263  """
4264  return _IMP_atom.LennardJones_get_is_setup(*args)
4265 
4266  if _newclass:get_is_setup = staticmethod(get_is_setup)
4267  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4268  def get_well_depth_key():
4269  """get_well_depth_key() -> FloatKey"""
4270  return _IMP_atom.LennardJones_get_well_depth_key()
4271 
4272  if _newclass:get_well_depth_key = staticmethod(get_well_depth_key)
4273  __swig_getmethods__["get_well_depth_key"] = lambda x: get_well_depth_key
4274  def add_attribute(self, *args):
4275  """
4276  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
4277  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
4278  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
4279  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
4280  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
4281  add_attribute(LennardJones self, ObjectKey a0, Object a1)
4282  """
4283  return _IMP_atom.LennardJones_add_attribute(self, *args)
4284 
4285  def get_value(self, *args):
4286  """
4287  get_value(LennardJones self, FloatKey a0) -> IMP::Float
4288  get_value(LennardJones self, IntKey a0) -> IMP::Int
4289  get_value(LennardJones self, StringKey a0) -> IMP::String
4290  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
4291  get_value(LennardJones self, ObjectKey a0) -> Object
4292  """
4293  return _IMP_atom.LennardJones_get_value(self, *args)
4294 
4295  def set_value(self, *args):
4296  """
4297  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
4298  set_value(LennardJones self, IntKey a0, IMP::Int a1)
4299  set_value(LennardJones self, StringKey a0, IMP::String a1)
4300  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
4301  set_value(LennardJones self, ObjectKey a0, Object a1)
4302  """
4303  return _IMP_atom.LennardJones_set_value(self, *args)
4304 
4305  def remove_attribute(self, *args):
4306  """
4307  remove_attribute(LennardJones self, FloatKey a0)
4308  remove_attribute(LennardJones self, IntKey a0)
4309  remove_attribute(LennardJones self, StringKey a0)
4310  remove_attribute(LennardJones self, ParticleIndexKey a0)
4311  remove_attribute(LennardJones self, ObjectKey a0)
4312  """
4313  return _IMP_atom.LennardJones_remove_attribute(self, *args)
4314 
4315  def has_attribute(self, *args):
4316  """
4317  has_attribute(LennardJones self, FloatKey a0) -> bool
4318  has_attribute(LennardJones self, IntKey a0) -> bool
4319  has_attribute(LennardJones self, StringKey a0) -> bool
4320  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
4321  has_attribute(LennardJones self, ObjectKey a0) -> bool
4322  """
4323  return _IMP_atom.LennardJones_has_attribute(self, *args)
4324 
4325  def get_derivative(self, *args):
4326  """get_derivative(LennardJones self, FloatKey a0) -> double"""
4327  return _IMP_atom.LennardJones_get_derivative(self, *args)
4328 
4329  def get_name(self):
4330  """get_name(LennardJones self) -> std::string"""
4331  return _IMP_atom.LennardJones_get_name(self)
4332 
4333  def clear_caches(self):
4334  """clear_caches(LennardJones self)"""
4335  return _IMP_atom.LennardJones_clear_caches(self)
4336 
4337  def set_name(self, *args):
4338  """set_name(LennardJones self, std::string a0)"""
4339  return _IMP_atom.LennardJones_set_name(self, *args)
4340 
4341  def set_check_level(self, *args):
4342  """set_check_level(LennardJones self, IMP::base::CheckLevel a0)"""
4343  return _IMP_atom.LennardJones_set_check_level(self, *args)
4344 
4345  def add_to_derivative(self, *args):
4346  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4347  return _IMP_atom.LennardJones_add_to_derivative(self, *args)
4348 
4349  def set_is_optimized(self, *args):
4350  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
4351  return _IMP_atom.LennardJones_set_is_optimized(self, *args)
4352 
4353  def get_is_optimized(self, *args):
4354  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
4355  return _IMP_atom.LennardJones_get_is_optimized(self, *args)
4356 
4357  def get_check_level(self):
4358  """get_check_level(LennardJones self) -> IMP::base::CheckLevel"""
4359  return _IMP_atom.LennardJones_get_check_level(self)
4360 
4361  def __eq__(self, *args):
4362  """
4363  __eq__(LennardJones self, LennardJones o) -> bool
4364  __eq__(LennardJones self, Particle d) -> bool
4365  """
4366  return _IMP_atom.LennardJones___eq__(self, *args)
4367 
4368  def __ne__(self, *args):
4369  """
4370  __ne__(LennardJones self, LennardJones o) -> bool
4371  __ne__(LennardJones self, Particle d) -> bool
4372  """
4373  return _IMP_atom.LennardJones___ne__(self, *args)
4374 
4375  def __le__(self, *args):
4376  """
4377  __le__(LennardJones self, LennardJones o) -> bool
4378  __le__(LennardJones self, Particle d) -> bool
4379  """
4380  return _IMP_atom.LennardJones___le__(self, *args)
4381 
4382  def __lt__(self, *args):
4383  """
4384  __lt__(LennardJones self, LennardJones o) -> bool
4385  __lt__(LennardJones self, Particle d) -> bool
4386  """
4387  return _IMP_atom.LennardJones___lt__(self, *args)
4388 
4389  def __ge__(self, *args):
4390  """
4391  __ge__(LennardJones self, LennardJones o) -> bool
4392  __ge__(LennardJones self, Particle d) -> bool
4393  """
4394  return _IMP_atom.LennardJones___ge__(self, *args)
4395 
4396  def __gt__(self, *args):
4397  """
4398  __gt__(LennardJones self, LennardJones o) -> bool
4399  __gt__(LennardJones self, Particle d) -> bool
4400  """
4401  return _IMP_atom.LennardJones___gt__(self, *args)
4402 
4403  def __str__(self):
4404  """__str__(LennardJones self) -> std::string"""
4405  return _IMP_atom.LennardJones___str__(self)
4406 
4407  def __repr__(self):
4408  """__repr__(LennardJones self) -> std::string"""
4409  return _IMP_atom.LennardJones___repr__(self)
4410 
4411  __swig_destroy__ = _IMP_atom.delete_LennardJones
4412  __del__ = lambda self : None;
4413 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
4414 LennardJones_swigregister(LennardJones)
4415 
4416 def LennardJones_decorate_particle(*args):
4417  """LennardJones_decorate_particle(Particle p) -> LennardJones"""
4418  return _IMP_atom.LennardJones_decorate_particle(*args)
4419 
4420 def LennardJones_setup_particle(*args):
4421  """
4422  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> LennardJones
4423  setup_particle(_ParticleAdaptor decorator) -> LennardJones
4424  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4425  LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
4426  """
4427  return _IMP_atom.LennardJones_setup_particle(*args)
4428 
4429 def LennardJones_get_is_setup(*args):
4430  """
4431  get_is_setup(_ParticleAdaptor p) -> bool
4432  LennardJones_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4433  """
4434  return _IMP_atom.LennardJones_get_is_setup(*args)
4435 
4436 def LennardJones_get_well_depth_key():
4437  """LennardJones_get_well_depth_key() -> FloatKey"""
4438  return _IMP_atom.LennardJones_get_well_depth_key()
4439 
4440 class LennardJonesPairScore(IMP.kernel.PairScore):
4441  """Proxy of C++ IMP::atom::LennardJonesPairScore class"""
4442  __swig_setmethods__ = {}
4443  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4444  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJonesPairScore, name, value)
4445  __swig_getmethods__ = {}
4446  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4447  __getattr__ = lambda self, name: _swig_getattr(self, LennardJonesPairScore, name)
4448  def __init__(self, *args):
4449  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
4450  this = _IMP_atom.new_LennardJonesPairScore(*args)
4451  try: self.this.append(this)
4452  except: self.this = this
4453  def set_repulsive_weight(self, *args):
4454  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
4455  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, *args)
4456 
4457  def get_repulsive_weight(self):
4458  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
4459  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
4460 
4461  def set_attractive_weight(self, *args):
4462  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
4463  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, *args)
4464 
4465  def get_attractive_weight(self):
4466  """get_attractive_weight(LennardJonesPairScore self) -> double"""
4467  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
4468 
4469  def do_get_inputs(self, *args):
4470  """do_get_inputs(LennardJonesPairScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
4471  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, *args)
4472 
4473  def get_version_info(self):
4474  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
4475  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
4476 
4477  def __str__(self):
4478  """__str__(LennardJonesPairScore self) -> std::string"""
4479  return _IMP_atom.LennardJonesPairScore___str__(self)
4480 
4481  def __repr__(self):
4482  """__repr__(LennardJonesPairScore self) -> std::string"""
4483  return _IMP_atom.LennardJonesPairScore___repr__(self)
4484 
4485  def get_from(o):
4486  return _object_cast_to_LennardJonesPairScore(o)
4487  get_from = staticmethod(get_from)
4488 
4489 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
4490 LennardJonesPairScore_swigregister(LennardJonesPairScore)
4491 
4492 class MolecularDynamics(Simulator):
4493  """Proxy of C++ IMP::atom::MolecularDynamics class"""
4494  __swig_setmethods__ = {}
4495  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4496  __setattr__ = lambda self, name, value: _swig_setattr(self, MolecularDynamics, name, value)
4497  __swig_getmethods__ = {}
4498  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4499  __getattr__ = lambda self, name: _swig_getattr(self, MolecularDynamics, name)
4500  def __init__(self, *args):
4501  """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
4502  this = _IMP_atom.new_MolecularDynamics(*args)
4503  try: self.this.append(this)
4504  except: self.this = this
4505  def get_kinetic_energy(self):
4506  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
4507  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
4508 
4509  def get_kinetic_temperature(self, *args):
4510  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
4511  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, *args)
4512 
4513  def set_velocity_cap(self, *args):
4514  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
4515  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, *args)
4516 
4517  def assign_velocities(self, *args):
4518  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
4519  return _IMP_atom.MolecularDynamics_assign_velocities(self, *args)
4520 
4521  def setup(self, *args):
4522  """setup(MolecularDynamics self, IMP::kernel::ParticleIndexes const & ps)"""
4523  return _IMP_atom.MolecularDynamics_setup(self, *args)
4524 
4525  def do_step(self, *args):
4526  """do_step(MolecularDynamics self, IMP::kernel::ParticleIndexes const & sc, double dt) -> double"""
4527  return _IMP_atom.MolecularDynamics_do_step(self, *args)
4528 
4529  def get_is_simulation_particle(self, *args):
4530  """get_is_simulation_particle(MolecularDynamics self, IMP::kernel::ParticleIndex p) -> bool"""
4531  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, *args)
4532 
4533  def get_version_info(self):
4534  """get_version_info(MolecularDynamics self) -> VersionInfo"""
4535  return _IMP_atom.MolecularDynamics_get_version_info(self)
4536 
4537  def __str__(self):
4538  """__str__(MolecularDynamics self) -> std::string"""
4539  return _IMP_atom.MolecularDynamics___str__(self)
4540 
4541  def __repr__(self):
4542  """__repr__(MolecularDynamics self) -> std::string"""
4543  return _IMP_atom.MolecularDynamics___repr__(self)
4544 
4545  def get_from(o):
4546  return _object_cast_to_MolecularDynamics(o)
4547  get_from = staticmethod(get_from)
4548 
4549 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
4550 MolecularDynamics_swigregister(MolecularDynamics)
4551 
4552 class VelocityScalingOptimizerState(IMP.kernel.OptimizerState):
4553  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class"""
4554  __swig_setmethods__ = {}
4555  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4556  __setattr__ = lambda self, name, value: _swig_setattr(self, VelocityScalingOptimizerState, name, value)
4557  __swig_getmethods__ = {}
4558  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4559  __getattr__ = lambda self, name: _swig_getattr(self, VelocityScalingOptimizerState, name)
4560  def __init__(self, *args):
4561  """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
4562  this = _IMP_atom.new_VelocityScalingOptimizerState(*args)
4563  try: self.this.append(this)
4564  except: self.this = this
4565  def set_particles(self, *args):
4566  """set_particles(VelocityScalingOptimizerState self, IMP::kernel::Particles const & pis)"""
4567  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, *args)
4568 
4569  def set_temperature(self, *args):
4570  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
4571  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, *args)
4572 
4573  def rescale_velocities(self):
4574  """rescale_velocities(VelocityScalingOptimizerState self)"""
4575  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
4576 
4577  def get_version_info(self):
4578  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
4579  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
4580 
4581  def __str__(self):
4582  """__str__(VelocityScalingOptimizerState self) -> std::string"""
4583  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
4584 
4585  def __repr__(self):
4586  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
4587  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
4588 
4589  def get_from(o):
4590  return _object_cast_to_VelocityScalingOptimizerState(o)
4591  get_from = staticmethod(get_from)
4592 
4593 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
4594 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
4595 
4596 class Fragment(Hierarchy):
4597  """Proxy of C++ IMP::atom::Fragment class"""
4598  __swig_setmethods__ = {}
4599  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4600  __setattr__ = lambda self, name, value: _swig_setattr(self, Fragment, name, value)
4601  __swig_getmethods__ = {}
4602  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4603  __getattr__ = lambda self, name: _swig_getattr(self, Fragment, name)
4604  def set_residue_indexes(self, *args):
4605  """set_residue_indexes(Fragment self, IMP::Ints o)"""
4606  return _IMP_atom.Fragment_set_residue_indexes(self, *args)
4607 
4608  def get_residue_indexes(self):
4609  """get_residue_indexes(Fragment self) -> IMP::Ints"""
4610  return _IMP_atom.Fragment_get_residue_indexes(self)
4611 
4612  def get_contains_residue(self, *args):
4613  """get_contains_residue(Fragment self, int rindex) -> bool"""
4614  return _IMP_atom.Fragment_get_contains_residue(self, *args)
4615 
4616  def __init__(self, *args):
4617  """
4618  __init__(IMP::atom::Fragment self) -> Fragment
4619  __init__(IMP::atom::Fragment self, Model m, ::IMP::kernel::ParticleIndex id) -> Fragment
4620  __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
4621  """
4622  this = _IMP_atom.new_Fragment(*args)
4623  try: self.this.append(this)
4624  except: self.this = this
4625  def decorate_particle(*args):
4626  """decorate_particle(Particle p) -> Fragment"""
4627  return _IMP_atom.Fragment_decorate_particle(*args)
4628 
4629  if _newclass:decorate_particle = staticmethod(decorate_particle)
4630  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4631  def get_is_setup(*args):
4632  """
4633  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4634  get_is_setup(_ParticleAdaptor p) -> bool
4635  """
4636  return _IMP_atom.Fragment_get_is_setup(*args)
4637 
4638  if _newclass:get_is_setup = staticmethod(get_is_setup)
4639  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4640  def show(self, *args):
4641  """
4642  show(Fragment self, _ostream out=std::cout)
4643  show(Fragment self)
4644  """
4645  return _IMP_atom.Fragment_show(self, *args)
4646 
4647  def setup_particle(*args):
4648  """
4649  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Fragment
4650  setup_particle(_ParticleAdaptor decorator) -> Fragment
4651  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Fragment other) -> Fragment
4652  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
4653  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
4654  setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
4655  """
4656  return _IMP_atom.Fragment_setup_particle(*args)
4657 
4658  if _newclass:setup_particle = staticmethod(setup_particle)
4659  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4660  def add_attribute(self, *args):
4661  """
4662  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
4663  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
4664  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
4665  add_attribute(Fragment self, StringKey a0, IMP::String a1)
4666  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
4667  add_attribute(Fragment self, ObjectKey a0, Object a1)
4668  """
4669  return _IMP_atom.Fragment_add_attribute(self, *args)
4670 
4671  def get_value(self, *args):
4672  """
4673  get_value(Fragment self, FloatKey a0) -> IMP::Float
4674  get_value(Fragment self, IntKey a0) -> IMP::Int
4675  get_value(Fragment self, StringKey a0) -> IMP::String
4676  get_value(Fragment self, ParticleIndexKey a0) -> Particle
4677  get_value(Fragment self, ObjectKey a0) -> Object
4678  """
4679  return _IMP_atom.Fragment_get_value(self, *args)
4680 
4681  def set_value(self, *args):
4682  """
4683  set_value(Fragment self, FloatKey a0, IMP::Float a1)
4684  set_value(Fragment self, IntKey a0, IMP::Int a1)
4685  set_value(Fragment self, StringKey a0, IMP::String a1)
4686  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
4687  set_value(Fragment self, ObjectKey a0, Object a1)
4688  """
4689  return _IMP_atom.Fragment_set_value(self, *args)
4690 
4691  def remove_attribute(self, *args):
4692  """
4693  remove_attribute(Fragment self, FloatKey a0)
4694  remove_attribute(Fragment self, IntKey a0)
4695  remove_attribute(Fragment self, StringKey a0)
4696  remove_attribute(Fragment self, ParticleIndexKey a0)
4697  remove_attribute(Fragment self, ObjectKey a0)
4698  """
4699  return _IMP_atom.Fragment_remove_attribute(self, *args)
4700 
4701  def has_attribute(self, *args):
4702  """
4703  has_attribute(Fragment self, FloatKey a0) -> bool
4704  has_attribute(Fragment self, IntKey a0) -> bool
4705  has_attribute(Fragment self, StringKey a0) -> bool
4706  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
4707  has_attribute(Fragment self, ObjectKey a0) -> bool
4708  """
4709  return _IMP_atom.Fragment_has_attribute(self, *args)
4710 
4711  def get_derivative(self, *args):
4712  """get_derivative(Fragment self, FloatKey a0) -> double"""
4713  return _IMP_atom.Fragment_get_derivative(self, *args)
4714 
4715  def get_name(self):
4716  """get_name(Fragment self) -> std::string"""
4717  return _IMP_atom.Fragment_get_name(self)
4718 
4719  def clear_caches(self):
4720  """clear_caches(Fragment self)"""
4721  return _IMP_atom.Fragment_clear_caches(self)
4722 
4723  def set_name(self, *args):
4724  """set_name(Fragment self, std::string a0)"""
4725  return _IMP_atom.Fragment_set_name(self, *args)
4726 
4727  def set_check_level(self, *args):
4728  """set_check_level(Fragment self, IMP::base::CheckLevel a0)"""
4729  return _IMP_atom.Fragment_set_check_level(self, *args)
4730 
4731  def add_to_derivative(self, *args):
4732  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4733  return _IMP_atom.Fragment_add_to_derivative(self, *args)
4734 
4735  def set_is_optimized(self, *args):
4736  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
4737  return _IMP_atom.Fragment_set_is_optimized(self, *args)
4738 
4739  def get_is_optimized(self, *args):
4740  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
4741  return _IMP_atom.Fragment_get_is_optimized(self, *args)
4742 
4743  def get_check_level(self):
4744  """get_check_level(Fragment self) -> IMP::base::CheckLevel"""
4745  return _IMP_atom.Fragment_get_check_level(self)
4746 
4747  def __eq__(self, *args):
4748  """
4749  __eq__(Fragment self, Fragment o) -> bool
4750  __eq__(Fragment self, Particle d) -> bool
4751  """
4752  return _IMP_atom.Fragment___eq__(self, *args)
4753 
4754  def __ne__(self, *args):
4755  """
4756  __ne__(Fragment self, Fragment o) -> bool
4757  __ne__(Fragment self, Particle d) -> bool
4758  """
4759  return _IMP_atom.Fragment___ne__(self, *args)
4760 
4761  def __le__(self, *args):
4762  """
4763  __le__(Fragment self, Fragment o) -> bool
4764  __le__(Fragment self, Particle d) -> bool
4765  """
4766  return _IMP_atom.Fragment___le__(self, *args)
4767 
4768  def __lt__(self, *args):
4769  """
4770  __lt__(Fragment self, Fragment o) -> bool
4771  __lt__(Fragment self, Particle d) -> bool
4772  """
4773  return _IMP_atom.Fragment___lt__(self, *args)
4774 
4775  def __ge__(self, *args):
4776  """
4777  __ge__(Fragment self, Fragment o) -> bool
4778  __ge__(Fragment self, Particle d) -> bool
4779  """
4780  return _IMP_atom.Fragment___ge__(self, *args)
4781 
4782  def __gt__(self, *args):
4783  """
4784  __gt__(Fragment self, Fragment o) -> bool
4785  __gt__(Fragment self, Particle d) -> bool
4786  """
4787  return _IMP_atom.Fragment___gt__(self, *args)
4788 
4789  def __str__(self):
4790  """__str__(Fragment self) -> std::string"""
4791  return _IMP_atom.Fragment___str__(self)
4792 
4793  def __repr__(self):
4794  """__repr__(Fragment self) -> std::string"""
4795  return _IMP_atom.Fragment___repr__(self)
4796 
4797  __swig_destroy__ = _IMP_atom.delete_Fragment
4798  __del__ = lambda self : None;
4799 Fragment_swigregister = _IMP_atom.Fragment_swigregister
4800 Fragment_swigregister(Fragment)
4801 
4802 def Fragment_decorate_particle(*args):
4803  """Fragment_decorate_particle(Particle p) -> Fragment"""
4804  return _IMP_atom.Fragment_decorate_particle(*args)
4805 
4806 def Fragment_get_is_setup(*args):
4807  """
4808  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4809  Fragment_get_is_setup(_ParticleAdaptor p) -> bool
4810  """
4811  return _IMP_atom.Fragment_get_is_setup(*args)
4812 
4813 def Fragment_setup_particle(*args):
4814  """
4815  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Fragment
4816  setup_particle(_ParticleAdaptor decorator) -> Fragment
4817  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Fragment other) -> Fragment
4818  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
4819  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
4820  Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
4821  """
4822  return _IMP_atom.Fragment_setup_particle(*args)
4823 
4824 class StereochemistryPairFilter(IMP.kernel.PairPredicate):
4825  """Proxy of C++ IMP::atom::StereochemistryPairFilter class"""
4826  __swig_setmethods__ = {}
4827  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4828  __setattr__ = lambda self, name, value: _swig_setattr(self, StereochemistryPairFilter, name, value)
4829  __swig_getmethods__ = {}
4830  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4831  __getattr__ = lambda self, name: _swig_getattr(self, StereochemistryPairFilter, name)
4832  def __init__(self):
4833  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
4834  this = _IMP_atom.new_StereochemistryPairFilter()
4835  try: self.this.append(this)
4836  except: self.this = this
4837  def set_bonds(self, *args):
4838  """set_bonds(StereochemistryPairFilter self, IMP::kernel::Particles const & bonds)"""
4839  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, *args)
4840 
4841  def set_angles(self, *args):
4842  """set_angles(StereochemistryPairFilter self, IMP::kernel::Particles const & angles)"""
4843  return _IMP_atom.StereochemistryPairFilter_set_angles(self, *args)
4844 
4845  def set_dihedrals(self, *args):
4846  """set_dihedrals(StereochemistryPairFilter self, IMP::kernel::Particles const & dihedrals)"""
4847  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, *args)
4848 
4849  def do_get_inputs(self, *args):
4850  """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
4851  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, *args)
4852 
4853  def get_value(self, *args):
4854  """
4855  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePair const & a) -> int
4856  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
4857  """
4858  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
4859 
4860  def get_value_index(self, *args):
4861  """
4862  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
4863  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
4864  """
4865  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
4866 
4867  def get_version_info(self):
4868  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
4869  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
4870 
4871  def __str__(self):
4872  """__str__(StereochemistryPairFilter self) -> std::string"""
4873  return _IMP_atom.StereochemistryPairFilter___str__(self)
4874 
4875  def __repr__(self):
4876  """__repr__(StereochemistryPairFilter self) -> std::string"""
4877  return _IMP_atom.StereochemistryPairFilter___repr__(self)
4878 
4879  def get_from(o):
4880  return _object_cast_to_StereochemistryPairFilter(o)
4881  get_from = staticmethod(get_from)
4882 
4883 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
4884 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
4885 
4886 class SoapPairFilter(IMP.kernel.PairPredicate):
4887  """Proxy of C++ IMP::atom::SoapPairFilter class"""
4888  __swig_setmethods__ = {}
4889  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4890  __setattr__ = lambda self, name, value: _swig_setattr(self, SoapPairFilter, name, value)
4891  __swig_getmethods__ = {}
4892  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4893  __getattr__ = lambda self, name: _swig_getattr(self, SoapPairFilter, name)
4894  def __init__(self, *args):
4895  """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
4896  this = _IMP_atom.new_SoapPairFilter(*args)
4897  try: self.this.append(this)
4898  except: self.this = this
4899  def do_get_inputs(self, *args):
4900  """do_get_inputs(SoapPairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
4901  return _IMP_atom.SoapPairFilter_do_get_inputs(self, *args)
4902 
4903  def get_value(self, *args):
4904  """
4905  get_value(SoapPairFilter self, IMP::kernel::ParticlePair const & a) -> int
4906  get_value(SoapPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
4907  """
4908  return _IMP_atom.SoapPairFilter_get_value(self, *args)
4909 
4910  def get_value_index(self, *args):
4911  """
4912  get_value_index(SoapPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
4913  get_value_index(SoapPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
4914  """
4915  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
4916 
4917  def get_version_info(self):
4918  """get_version_info(SoapPairFilter self) -> VersionInfo"""
4919  return _IMP_atom.SoapPairFilter_get_version_info(self)
4920 
4921  def __str__(self):
4922  """__str__(SoapPairFilter self) -> std::string"""
4923  return _IMP_atom.SoapPairFilter___str__(self)
4924 
4925  def __repr__(self):
4926  """__repr__(SoapPairFilter self) -> std::string"""
4927  return _IMP_atom.SoapPairFilter___repr__(self)
4928 
4929  def get_from(o):
4930  return _object_cast_to_SoapPairFilter(o)
4931  get_from = staticmethod(get_from)
4932 
4933 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
4934 SoapPairFilter_swigregister(SoapPairFilter)
4935 
4936 class Mass(IMP.kernel.Decorator):
4937  """Proxy of C++ IMP::atom::Mass class"""
4938  __swig_setmethods__ = {}
4939  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4940  __setattr__ = lambda self, name, value: _swig_setattr(self, Mass, name, value)
4941  __swig_getmethods__ = {}
4942  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4943  __getattr__ = lambda self, name: _swig_getattr(self, Mass, name)
4944  def get_mass(self):
4945  """get_mass(Mass self) -> IMP::Float"""
4946  return _IMP_atom.Mass_get_mass(self)
4947 
4948  def set_mass(self, *args):
4949  """set_mass(Mass self, IMP::Float d)"""
4950  return _IMP_atom.Mass_set_mass(self, *args)
4951 
4952  def __init__(self, *args):
4953  """
4954  __init__(IMP::atom::Mass self) -> Mass
4955  __init__(IMP::atom::Mass self, Model m, ::IMP::kernel::ParticleIndex id) -> Mass
4956  __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
4957  """
4958  this = _IMP_atom.new_Mass(*args)
4959  try: self.this.append(this)
4960  except: self.this = this
4961  def decorate_particle(*args):
4962  """decorate_particle(Particle p) -> Mass"""
4963  return _IMP_atom.Mass_decorate_particle(*args)
4964 
4965  if _newclass:decorate_particle = staticmethod(decorate_particle)
4966  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4967  def get_is_setup(*args):
4968  """
4969  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4970  get_is_setup(_ParticleAdaptor p) -> bool
4971  """
4972  return _IMP_atom.Mass_get_is_setup(*args)
4973 
4974  if _newclass:get_is_setup = staticmethod(get_is_setup)
4975  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4976  def show(self, *args):
4977  """
4978  show(Mass self, _ostream out=std::cout)
4979  show(Mass self)
4980  """
4981  return _IMP_atom.Mass_show(self, *args)
4982 
4983  def setup_particle(*args):
4984  """
4985  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float mass) -> Mass
4986  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
4987  """
4988  return _IMP_atom.Mass_setup_particle(*args)
4989 
4990  if _newclass:setup_particle = staticmethod(setup_particle)
4991  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4992  def get_mass_key():
4993  """get_mass_key() -> FloatKey"""
4994  return _IMP_atom.Mass_get_mass_key()
4995 
4996  if _newclass:get_mass_key = staticmethod(get_mass_key)
4997  __swig_getmethods__["get_mass_key"] = lambda x: get_mass_key
4998  def add_attribute(self, *args):
4999  """
5000  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
5001  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
5002  add_attribute(Mass self, IntKey a0, IMP::Int a1)
5003  add_attribute(Mass self, StringKey a0, IMP::String a1)
5004  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
5005  add_attribute(Mass self, ObjectKey a0, Object a1)
5006  """
5007  return _IMP_atom.Mass_add_attribute(self, *args)
5008 
5009  def get_value(self, *args):
5010  """
5011  get_value(Mass self, FloatKey a0) -> IMP::Float
5012  get_value(Mass self, IntKey a0) -> IMP::Int
5013  get_value(Mass self, StringKey a0) -> IMP::String
5014  get_value(Mass self, ParticleIndexKey a0) -> Particle
5015  get_value(Mass self, ObjectKey a0) -> Object
5016  """
5017  return _IMP_atom.Mass_get_value(self, *args)
5018 
5019  def set_value(self, *args):
5020  """
5021  set_value(Mass self, FloatKey a0, IMP::Float a1)
5022  set_value(Mass self, IntKey a0, IMP::Int a1)
5023  set_value(Mass self, StringKey a0, IMP::String a1)
5024  set_value(Mass self, ParticleIndexKey a0, Particle a1)
5025  set_value(Mass self, ObjectKey a0, Object a1)
5026  """
5027  return _IMP_atom.Mass_set_value(self, *args)
5028 
5029  def remove_attribute(self, *args):
5030  """
5031  remove_attribute(Mass self, FloatKey a0)
5032  remove_attribute(Mass self, IntKey a0)
5033  remove_attribute(Mass self, StringKey a0)
5034  remove_attribute(Mass self, ParticleIndexKey a0)
5035  remove_attribute(Mass self, ObjectKey a0)
5036  """
5037  return _IMP_atom.Mass_remove_attribute(self, *args)
5038 
5039  def has_attribute(self, *args):
5040  """
5041  has_attribute(Mass self, FloatKey a0) -> bool
5042  has_attribute(Mass self, IntKey a0) -> bool
5043  has_attribute(Mass self, StringKey a0) -> bool
5044  has_attribute(Mass self, ParticleIndexKey a0) -> bool
5045  has_attribute(Mass self, ObjectKey a0) -> bool
5046  """
5047  return _IMP_atom.Mass_has_attribute(self, *args)
5048 
5049  def get_derivative(self, *args):
5050  """get_derivative(Mass self, FloatKey a0) -> double"""
5051  return _IMP_atom.Mass_get_derivative(self, *args)
5052 
5053  def get_name(self):
5054  """get_name(Mass self) -> std::string"""
5055  return _IMP_atom.Mass_get_name(self)
5056 
5057  def clear_caches(self):
5058  """clear_caches(Mass self)"""
5059  return _IMP_atom.Mass_clear_caches(self)
5060 
5061  def set_name(self, *args):
5062  """set_name(Mass self, std::string a0)"""
5063  return _IMP_atom.Mass_set_name(self, *args)
5064 
5065  def set_check_level(self, *args):
5066  """set_check_level(Mass self, IMP::base::CheckLevel a0)"""
5067  return _IMP_atom.Mass_set_check_level(self, *args)
5068 
5069  def add_to_derivative(self, *args):
5070  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5071  return _IMP_atom.Mass_add_to_derivative(self, *args)
5072 
5073  def set_is_optimized(self, *args):
5074  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
5075  return _IMP_atom.Mass_set_is_optimized(self, *args)
5076 
5077  def get_is_optimized(self, *args):
5078  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
5079  return _IMP_atom.Mass_get_is_optimized(self, *args)
5080 
5081  def get_check_level(self):
5082  """get_check_level(Mass self) -> IMP::base::CheckLevel"""
5083  return _IMP_atom.Mass_get_check_level(self)
5084 
5085  def __eq__(self, *args):
5086  """
5087  __eq__(Mass self, Mass o) -> bool
5088  __eq__(Mass self, Particle d) -> bool
5089  """
5090  return _IMP_atom.Mass___eq__(self, *args)
5091 
5092  def __ne__(self, *args):
5093  """
5094  __ne__(Mass self, Mass o) -> bool
5095  __ne__(Mass self, Particle d) -> bool
5096  """
5097  return _IMP_atom.Mass___ne__(self, *args)
5098 
5099  def __le__(self, *args):
5100  """
5101  __le__(Mass self, Mass o) -> bool
5102  __le__(Mass self, Particle d) -> bool
5103  """
5104  return _IMP_atom.Mass___le__(self, *args)
5105 
5106  def __lt__(self, *args):
5107  """
5108  __lt__(Mass self, Mass o) -> bool
5109  __lt__(Mass self, Particle d) -> bool
5110  """
5111  return _IMP_atom.Mass___lt__(self, *args)
5112 
5113  def __ge__(self, *args):
5114  """
5115  __ge__(Mass self, Mass o) -> bool
5116  __ge__(Mass self, Particle d) -> bool
5117  """
5118  return _IMP_atom.Mass___ge__(self, *args)
5119 
5120  def __gt__(self, *args):
5121  """
5122  __gt__(Mass self, Mass o) -> bool
5123  __gt__(Mass self, Particle d) -> bool
5124  """
5125  return _IMP_atom.Mass___gt__(self, *args)
5126 
5127  def __str__(self):
5128  """__str__(Mass self) -> std::string"""
5129  return _IMP_atom.Mass___str__(self)
5130 
5131  def __repr__(self):
5132  """__repr__(Mass self) -> std::string"""
5133  return _IMP_atom.Mass___repr__(self)
5134 
5135  __swig_destroy__ = _IMP_atom.delete_Mass
5136  __del__ = lambda self : None;
5137 Mass_swigregister = _IMP_atom.Mass_swigregister
5138 Mass_swigregister(Mass)
5139 
5140 def Mass_decorate_particle(*args):
5141  """Mass_decorate_particle(Particle p) -> Mass"""
5142  return _IMP_atom.Mass_decorate_particle(*args)
5143 
5144 def Mass_get_is_setup(*args):
5145  """
5146  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5147  Mass_get_is_setup(_ParticleAdaptor p) -> bool
5148  """
5149  return _IMP_atom.Mass_get_is_setup(*args)
5150 
5151 def Mass_setup_particle(*args):
5152  """
5153  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float mass) -> Mass
5154  Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
5155  """
5156  return _IMP_atom.Mass_setup_particle(*args)
5157 
5158 def Mass_get_mass_key():
5159  """Mass_get_mass_key() -> FloatKey"""
5160  return _IMP_atom.Mass_get_mass_key()
5161 
5162 class BondedPairFilter(IMP.kernel.PairPredicate):
5163  """Proxy of C++ IMP::atom::BondedPairFilter class"""
5164  __swig_setmethods__ = {}
5165  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5166  __setattr__ = lambda self, name, value: _swig_setattr(self, BondedPairFilter, name, value)
5167  __swig_getmethods__ = {}
5168  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5169  __getattr__ = lambda self, name: _swig_getattr(self, BondedPairFilter, name)
5170  def __init__(self):
5171  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
5172  this = _IMP_atom.new_BondedPairFilter()
5173  try: self.this.append(this)
5174  except: self.this = this
5175  def do_get_inputs(self, *args):
5176  """do_get_inputs(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5177  return _IMP_atom.BondedPairFilter_do_get_inputs(self, *args)
5178 
5179  def get_value(self, *args):
5180  """
5181  get_value(BondedPairFilter self, IMP::kernel::ParticlePair const & a) -> int
5182  get_value(BondedPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
5183  """
5184  return _IMP_atom.BondedPairFilter_get_value(self, *args)
5185 
5186  def get_value_index(self, *args):
5187  """
5188  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
5189  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
5190  """
5191  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
5192 
5193  def get_version_info(self):
5194  """get_version_info(BondedPairFilter self) -> VersionInfo"""
5195  return _IMP_atom.BondedPairFilter_get_version_info(self)
5196 
5197  def __str__(self):
5198  """__str__(BondedPairFilter self) -> std::string"""
5199  return _IMP_atom.BondedPairFilter___str__(self)
5200 
5201  def __repr__(self):
5202  """__repr__(BondedPairFilter self) -> std::string"""
5203  return _IMP_atom.BondedPairFilter___repr__(self)
5204 
5205  def get_from(o):
5206  return _object_cast_to_BondedPairFilter(o)
5207  get_from = staticmethod(get_from)
5208 
5209 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
5210 BondedPairFilter_swigregister(BondedPairFilter)
5211 
5212 class Mol2Selector(IMP.base.Object):
5213  """Proxy of C++ IMP::atom::Mol2Selector class"""
5214  __swig_setmethods__ = {}
5215  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5216  __setattr__ = lambda self, name, value: _swig_setattr(self, Mol2Selector, name, value)
5217  __swig_getmethods__ = {}
5218  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5219  __getattr__ = lambda self, name: _swig_getattr(self, Mol2Selector, name)
5220  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
5221  def get_is_selected(self, *args):
5222  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
5223  return _IMP_atom.Mol2Selector_get_is_selected(self, *args)
5224 
5225  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
5226  __del__ = lambda self : None;
5227  def __str__(self):
5228  """__str__(Mol2Selector self) -> std::string"""
5229  return _IMP_atom.Mol2Selector___str__(self)
5230 
5231  def __repr__(self):
5232  """__repr__(Mol2Selector self) -> std::string"""
5233  return _IMP_atom.Mol2Selector___repr__(self)
5234 
5235  def get_from(o):
5236  return _object_cast_to_Mol2Selector(o)
5237  get_from = staticmethod(get_from)
5238 
5239 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
5240 Mol2Selector_swigregister(Mol2Selector)
5241 
5242 class AllMol2Selector(Mol2Selector):
5243  """Proxy of C++ IMP::atom::AllMol2Selector class"""
5244  __swig_setmethods__ = {}
5245  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5246  __setattr__ = lambda self, name, value: _swig_setattr(self, AllMol2Selector, name, value)
5247  __swig_getmethods__ = {}
5248  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5249  __getattr__ = lambda self, name: _swig_getattr(self, AllMol2Selector, name)
5250  def get_version_info(self):
5251  """get_version_info(AllMol2Selector self) -> VersionInfo"""
5252  return _IMP_atom.AllMol2Selector_get_version_info(self)
5253 
5254  def __str__(self):
5255  """__str__(AllMol2Selector self) -> std::string"""
5256  return _IMP_atom.AllMol2Selector___str__(self)
5257 
5258  def __repr__(self):
5259  """__repr__(AllMol2Selector self) -> std::string"""
5260  return _IMP_atom.AllMol2Selector___repr__(self)
5261 
5262  def get_from(o):
5263  return _object_cast_to_AllMol2Selector(o)
5264  get_from = staticmethod(get_from)
5265 
5266  def __init__(self):
5267  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
5268  this = _IMP_atom.new_AllMol2Selector()
5269  try: self.this.append(this)
5270  except: self.this = this
5271 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
5272 AllMol2Selector_swigregister(AllMol2Selector)
5273 
5274 class NonHydrogenMol2Selector(Mol2Selector):
5275  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class"""
5276  __swig_setmethods__ = {}
5277  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5278  __setattr__ = lambda self, name, value: _swig_setattr(self, NonHydrogenMol2Selector, name, value)
5279  __swig_getmethods__ = {}
5280  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5281  __getattr__ = lambda self, name: _swig_getattr(self, NonHydrogenMol2Selector, name)
5282  def get_version_info(self):
5283  """get_version_info(NonHydrogenMol2Selector self) -> VersionInfo"""
5284  return _IMP_atom.NonHydrogenMol2Selector_get_version_info(self)
5285 
5286  def __str__(self):
5287  """__str__(NonHydrogenMol2Selector self) -> std::string"""
5288  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
5289 
5290  def __repr__(self):
5291  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
5292  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
5293 
5294  def get_from(o):
5295  return _object_cast_to_NonHydrogenMol2Selector(o)
5296  get_from = staticmethod(get_from)
5297 
5298  def __init__(self):
5299  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
5300  this = _IMP_atom.new_NonHydrogenMol2Selector()
5301  try: self.this.append(this)
5302  except: self.this = this
5303 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
5304 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
5305 
5306 
5307 def read_mol2(*args):
5308  """
5309  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
5310  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
5311  """
5312  return _IMP_atom.read_mol2(*args)
5313 
5314 def write_mol2(*args):
5315  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
5316  return _IMP_atom.write_mol2(*args)
5317 class SecondaryStructureResidue(IMP.kernel.Decorator):
5318  """Proxy of C++ IMP::atom::SecondaryStructureResidue class"""
5319  __swig_setmethods__ = {}
5320  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5321  __setattr__ = lambda self, name, value: _swig_setattr(self, SecondaryStructureResidue, name, value)
5322  __swig_getmethods__ = {}
5323  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5324  __getattr__ = lambda self, name: _swig_getattr(self, SecondaryStructureResidue, name)
5325  def __init__(self, *args):
5326  """
5327  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
5328  __init__(IMP::atom::SecondaryStructureResidue self, Model m, ::IMP::kernel::ParticleIndex id) -> SecondaryStructureResidue
5329  __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
5330  """
5331  this = _IMP_atom.new_SecondaryStructureResidue(*args)
5332  try: self.this.append(this)
5333  except: self.this = this
5334  def decorate_particle(*args):
5335  """decorate_particle(Particle p) -> SecondaryStructureResidue"""
5336  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5337 
5338  if _newclass:decorate_particle = staticmethod(decorate_particle)
5339  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
5340  def show(self, *args):
5341  """
5342  show(SecondaryStructureResidue self, _ostream out=std::cout)
5343  show(SecondaryStructureResidue self)
5344  """
5345  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
5346 
5347  def setup_particle(*args):
5348  """
5349  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand,
5350  IMP::Float prob_coil) -> SecondaryStructureResidue
5351  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5352  setup_particle(Particle res_p) -> SecondaryStructureResidue
5353  """
5354  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5355 
5356  if _newclass:setup_particle = staticmethod(setup_particle)
5357  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
5358  def get_is_setup(*args):
5359  """
5360  get_is_setup(_ParticleAdaptor p) -> bool
5361  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5362  """
5363  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
5364 
5365  if _newclass:get_is_setup = staticmethod(get_is_setup)
5366  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
5367  def get_particle(self):
5368  """get_particle(SecondaryStructureResidue self) -> Particle"""
5369  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
5370 
5371  def get_all_probabilities(self):
5372  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
5373  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
5374 
5375  def get_prob_helix(self):
5376  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
5377  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
5378 
5379  def set_prob_helix(self, *args):
5380  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
5381  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, *args)
5382 
5383  def get_prob_strand(self):
5384  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
5385  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
5386 
5387  def set_prob_strand(self, *args):
5388  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
5389  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, *args)
5390 
5391  def get_prob_coil(self):
5392  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
5393  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
5394 
5395  def set_prob_coil(self, *args):
5396  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
5397  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, *args)
5398 
5399  def get_prob_helix_key():
5400  """get_prob_helix_key() -> FloatKey"""
5401  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5402 
5403  if _newclass:get_prob_helix_key = staticmethod(get_prob_helix_key)
5404  __swig_getmethods__["get_prob_helix_key"] = lambda x: get_prob_helix_key
5405  def get_prob_strand_key():
5406  """get_prob_strand_key() -> FloatKey"""
5407  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5408 
5409  if _newclass:get_prob_strand_key = staticmethod(get_prob_strand_key)
5410  __swig_getmethods__["get_prob_strand_key"] = lambda x: get_prob_strand_key
5411  def get_prob_coil_key():
5412  """get_prob_coil_key() -> FloatKey"""
5413  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5414 
5415  if _newclass:get_prob_coil_key = staticmethod(get_prob_coil_key)
5416  __swig_getmethods__["get_prob_coil_key"] = lambda x: get_prob_coil_key
5417  def add_attribute(self, *args):
5418  """
5419  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
5420  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5421  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5422  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5423  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5424  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
5425  """
5426  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
5427 
5428  def get_value(self, *args):
5429  """
5430  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
5431  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
5432  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
5433  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
5434  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
5435  """
5436  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
5437 
5438  def set_value(self, *args):
5439  """
5440  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5441  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5442  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5443  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5444  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
5445  """
5446  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
5447 
5448  def remove_attribute(self, *args):
5449  """
5450  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
5451  remove_attribute(SecondaryStructureResidue self, IntKey a0)
5452  remove_attribute(SecondaryStructureResidue self, StringKey a0)
5453  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
5454  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
5455  """
5456  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
5457 
5458  def has_attribute(self, *args):
5459  """
5460  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
5461  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
5462  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
5463  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
5464  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
5465  """
5466  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
5467 
5468  def get_derivative(self, *args):
5469  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
5470  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, *args)
5471 
5472  def get_name(self):
5473  """get_name(SecondaryStructureResidue self) -> std::string"""
5474  return _IMP_atom.SecondaryStructureResidue_get_name(self)
5475 
5476  def clear_caches(self):
5477  """clear_caches(SecondaryStructureResidue self)"""
5478  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
5479 
5480  def set_name(self, *args):
5481  """set_name(SecondaryStructureResidue self, std::string a0)"""
5482  return _IMP_atom.SecondaryStructureResidue_set_name(self, *args)
5483 
5484  def set_check_level(self, *args):
5485  """set_check_level(SecondaryStructureResidue self, IMP::base::CheckLevel a0)"""
5486  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, *args)
5487 
5488  def add_to_derivative(self, *args):
5489  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5490  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, *args)
5491 
5492  def set_is_optimized(self, *args):
5493  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
5494  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, *args)
5495 
5496  def get_is_optimized(self, *args):
5497  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
5498  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, *args)
5499 
5500  def get_check_level(self):
5501  """get_check_level(SecondaryStructureResidue self) -> IMP::base::CheckLevel"""
5502  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
5503 
5504  def __eq__(self, *args):
5505  """
5506  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5507  __eq__(SecondaryStructureResidue self, Particle d) -> bool
5508  """
5509  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
5510 
5511  def __ne__(self, *args):
5512  """
5513  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5514  __ne__(SecondaryStructureResidue self, Particle d) -> bool
5515  """
5516  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
5517 
5518  def __le__(self, *args):
5519  """
5520  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5521  __le__(SecondaryStructureResidue self, Particle d) -> bool
5522  """
5523  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
5524 
5525  def __lt__(self, *args):
5526  """
5527  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5528  __lt__(SecondaryStructureResidue self, Particle d) -> bool
5529  """
5530  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
5531 
5532  def __ge__(self, *args):
5533  """
5534  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5535  __ge__(SecondaryStructureResidue self, Particle d) -> bool
5536  """
5537  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
5538 
5539  def __gt__(self, *args):
5540  """
5541  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5542  __gt__(SecondaryStructureResidue self, Particle d) -> bool
5543  """
5544  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
5545 
5546  def __str__(self):
5547  """__str__(SecondaryStructureResidue self) -> std::string"""
5548  return _IMP_atom.SecondaryStructureResidue___str__(self)
5549 
5550  def __repr__(self):
5551  """__repr__(SecondaryStructureResidue self) -> std::string"""
5552  return _IMP_atom.SecondaryStructureResidue___repr__(self)
5553 
5554  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
5555  __del__ = lambda self : None;
5556 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
5557 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
5558 
5559 def SecondaryStructureResidue_decorate_particle(*args):
5560  """SecondaryStructureResidue_decorate_particle(Particle p) -> SecondaryStructureResidue"""
5561  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5562 
5563 def SecondaryStructureResidue_setup_particle(*args):
5564  """
5565  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand,
5566  IMP::Float prob_coil) -> SecondaryStructureResidue
5567  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5568  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
5569  """
5570  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5571 
5572 def SecondaryStructureResidue_get_is_setup(*args):
5573  """
5574  get_is_setup(_ParticleAdaptor p) -> bool
5575  SecondaryStructureResidue_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5576  """
5577  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
5578 
5579 def SecondaryStructureResidue_get_prob_helix_key():
5580  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
5581  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5582 
5583 def SecondaryStructureResidue_get_prob_strand_key():
5584  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
5585  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5586 
5587 def SecondaryStructureResidue_get_prob_coil_key():
5588  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
5589  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5590 
5591 
5593  """
5594  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
5595  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
5596  """
5597  return _IMP_atom.setup_coarse_secondary_structure_residue(*args)
5598 
5600  """
5601  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num,
5602  bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues
5603  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
5604  """
5605  return _IMP_atom.setup_coarse_secondary_structure_residues(*args)
5606 
5608  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
5609  return _IMP_atom.get_secondary_structure_match_score(*args)
5610 
5611 def read_psipred(*args):
5612  """
5613  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
5614  read_psipred(TextInput inf, IMP::kernel::Particles ps) -> IMP::atom::SecondaryStructureResidues
5615  """
5616  return _IMP_atom.read_psipred(*args)
5617 class _ADopeBase(IMP.kernel.PairScore):
5618  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class"""
5619  __swig_setmethods__ = {}
5620  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5621  __setattr__ = lambda self, name, value: _swig_setattr(self, _ADopeBase, name, value)
5622  __swig_getmethods__ = {}
5623  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5624  __getattr__ = lambda self, name: _swig_getattr(self, _ADopeBase, name)
5625  __repr__ = _swig_repr
5626  def __init__(self, *args):
5627  """
5628  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
5629  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
5630  """
5631  this = _IMP_atom.new__ADopeBase(*args)
5632  try: self.this.append(this)
5633  except: self.this = this
5634  def do_get_inputs(self, *args):
5635  """do_get_inputs(_ADopeBase self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5636  return _IMP_atom._ADopeBase_do_get_inputs(self, *args)
5637 
5638  def get_version_info(self):
5639  """get_version_info(_ADopeBase self) -> VersionInfo"""
5640  return _IMP_atom._ADopeBase_get_version_info(self)
5641 
5642 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
5643 _ADopeBase_swigregister(_ADopeBase)
5644 
5645 class _BDopeBase(IMP.kernel.PairScore):
5646  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class"""
5647  __swig_setmethods__ = {}
5648  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5649  __setattr__ = lambda self, name, value: _swig_setattr(self, _BDopeBase, name, value)
5650  __swig_getmethods__ = {}
5651  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5652  __getattr__ = lambda self, name: _swig_getattr(self, _BDopeBase, name)
5653  __repr__ = _swig_repr
5654  def __init__(self, *args):
5655  """
5656  __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,
5657  std::string name="FunctorDistancePairScore %1%") -> _BDopeBase
5658  __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
5659  """
5660  this = _IMP_atom.new__BDopeBase(*args)
5661  try: self.this.append(this)
5662  except: self.this = this
5663  def do_get_inputs(self, *args):
5664  """do_get_inputs(_BDopeBase self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5665  return _IMP_atom._BDopeBase_do_get_inputs(self, *args)
5666 
5667  def get_version_info(self):
5668  """get_version_info(_BDopeBase self) -> VersionInfo"""
5669  return _IMP_atom._BDopeBase_get_version_info(self)
5670 
5671 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
5672 _BDopeBase_swigregister(_BDopeBase)
5673 
5674 class _OrientedSoapBase(IMP.kernel.PairScore):
5675  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class"""
5676  __swig_setmethods__ = {}
5677  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5678  __setattr__ = lambda self, name, value: _swig_setattr(self, _OrientedSoapBase, name, value)
5679  __swig_getmethods__ = {}
5680  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5681  __getattr__ = lambda self, name: _swig_getattr(self, _OrientedSoapBase, name)
5682  __repr__ = _swig_repr
5683  def __init__(self, *args):
5684  """
5685  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0,
5686  std::string name="FunctorDistancePairScore %1%") -> _OrientedSoapBase
5687  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
5688  """
5689  this = _IMP_atom.new__OrientedSoapBase(*args)
5690  try: self.this.append(this)
5691  except: self.this = this
5692  def do_get_inputs(self, *args):
5693  """do_get_inputs(_OrientedSoapBase self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5694  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, *args)
5695 
5696  def get_version_info(self):
5697  """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
5698  return _IMP_atom._OrientedSoapBase_get_version_info(self)
5699 
5700 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
5701 _OrientedSoapBase_swigregister(_OrientedSoapBase)
5702 
5703 class _SPSFTB(IMP.kernel.PairScore):
5704  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class"""
5705  __swig_setmethods__ = {}
5706  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5707  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFTB, name, value)
5708  __swig_getmethods__ = {}
5709  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5710  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFTB, name)
5711  __repr__ = _swig_repr
5712  def __init__(self, *args):
5713  """
5714  __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,
5715  std::string name="FunctorDistancePairScore %1%") -> _SPSFTB
5716  __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
5717  """
5718  this = _IMP_atom.new__SPSFTB(*args)
5719  try: self.this.append(this)
5720  except: self.this = this
5721  def do_get_inputs(self, *args):
5722  """do_get_inputs(_SPSFTB self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5723  return _IMP_atom._SPSFTB_do_get_inputs(self, *args)
5724 
5725  def get_version_info(self):
5726  """get_version_info(_SPSFTB self) -> VersionInfo"""
5727  return _IMP_atom._SPSFTB_get_version_info(self)
5728 
5729 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
5730 _SPSFTB_swigregister(_SPSFTB)
5731 
5732 class _SPSTF(_SPSFTB):
5733  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class"""
5734  __swig_setmethods__ = {}
5735  for _s in [_SPSFTB]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5736  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSTF, name, value)
5737  __swig_getmethods__ = {}
5738  for _s in [_SPSFTB]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5739  __getattr__ = lambda self, name: _swig_getattr(self, _SPSTF, name)
5740  __repr__ = _swig_repr
5741  def __init__(self, *args):
5742  """
5743  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
5744  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
5745  """
5746  this = _IMP_atom.new__SPSTF(*args)
5747  try: self.this.append(this)
5748  except: self.this = this
5749  __swig_destroy__ = _IMP_atom.delete__SPSTF
5750  __del__ = lambda self : None;
5751 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
5752 _SPSTF_swigregister(_SPSTF)
5753 
5754 class _SPSFT(_BDopeBase):
5755  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class"""
5756  __swig_setmethods__ = {}
5757  for _s in [_BDopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5758  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFT, name, value)
5759  __swig_getmethods__ = {}
5760  for _s in [_BDopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5761  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFT, name)
5762  __repr__ = _swig_repr
5763  def __init__(self, *args):
5764  """
5765  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
5766  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
5767  """
5768  this = _IMP_atom.new__SPSFT(*args)
5769  try: self.this.append(this)
5770  except: self.this = this
5771  __swig_destroy__ = _IMP_atom.delete__SPSFT
5772  __del__ = lambda self : None;
5773 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
5774 _SPSFT_swigregister(_SPSFT)
5775 
5776 class ProteinLigandAtomPairScore(_SPSTF):
5777  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class"""
5778  __swig_setmethods__ = {}
5779  for _s in [_SPSTF]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5780  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandAtomPairScore, name, value)
5781  __swig_getmethods__ = {}
5782  for _s in [_SPSTF]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5783  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandAtomPairScore, name)
5784  def __init__(self, *args):
5785  """
5786  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
5787  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
5788  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
5789  """
5790  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
5791  try: self.this.append(this)
5792  except: self.this = this
5793  def get_maximum_distance(self):
5794  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
5795  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
5796 
5797  def __str__(self):
5798  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
5799  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
5800 
5801  def __repr__(self):
5802  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
5803  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
5804 
5805  def get_from(o):
5806  return _object_cast_to_ProteinLigandAtomPairScore(o)
5807  get_from = staticmethod(get_from)
5808 
5809  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
5810  __del__ = lambda self : None;
5811 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
5812 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
5813 
5814 class ProteinLigandRestraint(IMP.container.PairsRestraint):
5815  """Proxy of C++ IMP::atom::ProteinLigandRestraint class"""
5816  __swig_setmethods__ = {}
5817  for _s in [IMP.container.PairsRestraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5818  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandRestraint, name, value)
5819  __swig_getmethods__ = {}
5820  for _s in [IMP.container.PairsRestraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5821  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandRestraint, name)
5822  def __init__(self, *args):
5823  """
5824  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
5825  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
5826  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
5827  """
5828  this = _IMP_atom.new_ProteinLigandRestraint(*args)
5829  try: self.this.append(this)
5830  except: self.this = this
5831  def __str__(self):
5832  """__str__(ProteinLigandRestraint self) -> std::string"""
5833  return _IMP_atom.ProteinLigandRestraint___str__(self)
5834 
5835  def __repr__(self):
5836  """__repr__(ProteinLigandRestraint self) -> std::string"""
5837  return _IMP_atom.ProteinLigandRestraint___repr__(self)
5838 
5839  def get_from(o):
5840  return _object_cast_to_ProteinLigandRestraint(o)
5841  get_from = staticmethod(get_from)
5842 
5843  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
5844  __del__ = lambda self : None;
5845 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
5846 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
5847 
5848 
5850  """add_protein_ligand_score_data(Hierarchy h)"""
5851  return _IMP_atom.add_protein_ligand_score_data(*args)
5852 class AtomType(IMP.base._Value):
5853  """Proxy of C++ IMP::Key<(8974343,false)> class"""
5854  __swig_setmethods__ = {}
5855  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5856  __setattr__ = lambda self, name, value: _swig_setattr(self, AtomType, name, value)
5857  __swig_getmethods__ = {}
5858  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5859  __getattr__ = lambda self, name: _swig_getattr(self, AtomType, name)
5860  def __init__(self, *args):
5861  """
5862  __init__(IMP::Key<(8974343,false)> self) -> AtomType
5863  __init__(IMP::Key<(8974343,false)> self, std::string c) -> AtomType
5864  __init__(IMP::Key<(8974343,false)> self, unsigned int i) -> AtomType
5865  """
5866  this = _IMP_atom.new_AtomType(*args)
5867  try: self.this.append(this)
5868  except: self.this = this
5869  def add_key(*args):
5870  """add_key(std::string sc) -> unsigned int"""
5871  return _IMP_atom.AtomType_add_key(*args)
5872 
5873  if _newclass:add_key = staticmethod(add_key)
5874  __swig_getmethods__["add_key"] = lambda x: add_key
5875  def get_key_exists(*args):
5876  """get_key_exists(std::string sc) -> bool"""
5877  return _IMP_atom.AtomType_get_key_exists(*args)
5878 
5879  if _newclass:get_key_exists = staticmethod(get_key_exists)
5880  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
5881  def get_string(self):
5882  """get_string(AtomType self) -> std::string const"""
5883  return _IMP_atom.AtomType_get_string(self)
5884 
5885  def __eq__(self, *args):
5886  """__eq__(AtomType self, AtomType o) -> bool"""
5887  return _IMP_atom.AtomType___eq__(self, *args)
5888 
5889  def __ne__(self, *args):
5890  """__ne__(AtomType self, AtomType o) -> bool"""
5891  return _IMP_atom.AtomType___ne__(self, *args)
5892 
5893  def __lt__(self, *args):
5894  """__lt__(AtomType self, AtomType o) -> bool"""
5895  return _IMP_atom.AtomType___lt__(self, *args)
5896 
5897  def __gt__(self, *args):
5898  """__gt__(AtomType self, AtomType o) -> bool"""
5899  return _IMP_atom.AtomType___gt__(self, *args)
5900 
5901  def __ge__(self, *args):
5902  """__ge__(AtomType self, AtomType o) -> bool"""
5903  return _IMP_atom.AtomType___ge__(self, *args)
5904 
5905  def __le__(self, *args):
5906  """__le__(AtomType self, AtomType o) -> bool"""
5907  return _IMP_atom.AtomType___le__(self, *args)
5908 
5909  def __hash__(self):
5910  """__hash__(AtomType self) -> std::size_t"""
5911  return _IMP_atom.AtomType___hash__(self)
5912 
5913  def show(self, *args):
5914  """
5915  show(AtomType self, _ostream out=std::cout)
5916  show(AtomType self)
5917  """
5918  return _IMP_atom.AtomType_show(self, *args)
5919 
5920  def add_alias(*args):
5921  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
5922  return _IMP_atom.AtomType_add_alias(*args)
5923 
5924  if _newclass:add_alias = staticmethod(add_alias)
5925  __swig_getmethods__["add_alias"] = lambda x: add_alias
5926  def get_index(self):
5927  """get_index(AtomType self) -> unsigned int"""
5928  return _IMP_atom.AtomType_get_index(self)
5929 
5930  def show_all(*args):
5931  """show_all(_ostream out)"""
5932  return _IMP_atom.AtomType_show_all(*args)
5933 
5934  if _newclass:show_all = staticmethod(show_all)
5935  __swig_getmethods__["show_all"] = lambda x: show_all
5936  def get_all_strings():
5937  """get_all_strings() -> IMP::base::Vector< std::string >"""
5938  return _IMP_atom.AtomType_get_all_strings()
5939 
5940  if _newclass:get_all_strings = staticmethod(get_all_strings)
5941  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
5942  def get_number_unique():
5943  """get_number_unique() -> unsigned int"""
5944  return _IMP_atom.AtomType_get_number_unique()
5945 
5946  if _newclass:get_number_unique = staticmethod(get_number_unique)
5947  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
5948  def __str__(self):
5949  """__str__(AtomType self) -> std::string"""
5950  return _IMP_atom.AtomType___str__(self)
5951 
5952  def __repr__(self):
5953  """__repr__(AtomType self) -> std::string"""
5954  return _IMP_atom.AtomType___repr__(self)
5955 
5956  __swig_destroy__ = _IMP_atom.delete_AtomType
5957  __del__ = lambda self : None;
5958 AtomType_swigregister = _IMP_atom.AtomType_swigregister
5959 AtomType_swigregister(AtomType)
5960 
5961 def AtomType_add_key(*args):
5962  """AtomType_add_key(std::string sc) -> unsigned int"""
5963  return _IMP_atom.AtomType_add_key(*args)
5964 
5965 def AtomType_get_key_exists(*args):
5966  """AtomType_get_key_exists(std::string sc) -> bool"""
5967  return _IMP_atom.AtomType_get_key_exists(*args)
5968 
5969 def AtomType_add_alias(*args):
5970  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
5971  return _IMP_atom.AtomType_add_alias(*args)
5972 
5973 def AtomType_show_all(*args):
5974  """AtomType_show_all(_ostream out)"""
5975  return _IMP_atom.AtomType_show_all(*args)
5976 
5977 def AtomType_get_all_strings():
5978  """AtomType_get_all_strings() -> IMP::base::Vector< std::string >"""
5979  return _IMP_atom.AtomType_get_all_strings()
5980 
5981 def AtomType_get_number_unique():
5982  """AtomType_get_number_unique() -> unsigned int"""
5983  return _IMP_atom.AtomType_get_number_unique()
5984 
5985 class ResidueType(IMP.base._Value):
5986  """Proxy of C++ IMP::Key<(90784334,true)> class"""
5987  __swig_setmethods__ = {}
5988  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5989  __setattr__ = lambda self, name, value: _swig_setattr(self, ResidueType, name, value)
5990  __swig_getmethods__ = {}
5991  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5992  __getattr__ = lambda self, name: _swig_getattr(self, ResidueType, name)
5993  def __init__(self, *args):
5994  """
5995  __init__(IMP::Key<(90784334,true)> self) -> ResidueType
5996  __init__(IMP::Key<(90784334,true)> self, std::string c) -> ResidueType
5997  __init__(IMP::Key<(90784334,true)> self, unsigned int i) -> ResidueType
5998  """
5999  this = _IMP_atom.new_ResidueType(*args)
6000  try: self.this.append(this)
6001  except: self.this = this
6002  def add_key(*args):
6003  """add_key(std::string sc) -> unsigned int"""
6004  return _IMP_atom.ResidueType_add_key(*args)
6005 
6006  if _newclass:add_key = staticmethod(add_key)
6007  __swig_getmethods__["add_key"] = lambda x: add_key
6008  def get_key_exists(*args):
6009  """get_key_exists(std::string sc) -> bool"""
6010  return _IMP_atom.ResidueType_get_key_exists(*args)
6011 
6012  if _newclass:get_key_exists = staticmethod(get_key_exists)
6013  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
6014  def get_string(self):
6015  """get_string(ResidueType self) -> std::string const"""
6016  return _IMP_atom.ResidueType_get_string(self)
6017 
6018  def __eq__(self, *args):
6019  """__eq__(ResidueType self, ResidueType o) -> bool"""
6020  return _IMP_atom.ResidueType___eq__(self, *args)
6021 
6022  def __ne__(self, *args):
6023  """__ne__(ResidueType self, ResidueType o) -> bool"""
6024  return _IMP_atom.ResidueType___ne__(self, *args)
6025 
6026  def __lt__(self, *args):
6027  """__lt__(ResidueType self, ResidueType o) -> bool"""
6028  return _IMP_atom.ResidueType___lt__(self, *args)
6029 
6030  def __gt__(self, *args):
6031  """__gt__(ResidueType self, ResidueType o) -> bool"""
6032  return _IMP_atom.ResidueType___gt__(self, *args)
6033 
6034  def __ge__(self, *args):
6035  """__ge__(ResidueType self, ResidueType o) -> bool"""
6036  return _IMP_atom.ResidueType___ge__(self, *args)
6037 
6038  def __le__(self, *args):
6039  """__le__(ResidueType self, ResidueType o) -> bool"""
6040  return _IMP_atom.ResidueType___le__(self, *args)
6041 
6042  def __hash__(self):
6043  """__hash__(ResidueType self) -> std::size_t"""
6044  return _IMP_atom.ResidueType___hash__(self)
6045 
6046  def show(self, *args):
6047  """
6048  show(ResidueType self, _ostream out=std::cout)
6049  show(ResidueType self)
6050  """
6051  return _IMP_atom.ResidueType_show(self, *args)
6052 
6053  def add_alias(*args):
6054  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
6055  return _IMP_atom.ResidueType_add_alias(*args)
6056 
6057  if _newclass:add_alias = staticmethod(add_alias)
6058  __swig_getmethods__["add_alias"] = lambda x: add_alias
6059  def get_index(self):
6060  """get_index(ResidueType self) -> unsigned int"""
6061  return _IMP_atom.ResidueType_get_index(self)
6062 
6063  def show_all(*args):
6064  """show_all(_ostream out)"""
6065  return _IMP_atom.ResidueType_show_all(*args)
6066 
6067  if _newclass:show_all = staticmethod(show_all)
6068  __swig_getmethods__["show_all"] = lambda x: show_all
6069  def get_all_strings():
6070  """get_all_strings() -> IMP::base::Vector< std::string >"""
6071  return _IMP_atom.ResidueType_get_all_strings()
6072 
6073  if _newclass:get_all_strings = staticmethod(get_all_strings)
6074  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
6075  def get_number_unique():
6076  """get_number_unique() -> unsigned int"""
6077  return _IMP_atom.ResidueType_get_number_unique()
6078 
6079  if _newclass:get_number_unique = staticmethod(get_number_unique)
6080  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
6081  def __str__(self):
6082  """__str__(ResidueType self) -> std::string"""
6083  return _IMP_atom.ResidueType___str__(self)
6084 
6085  def __repr__(self):
6086  """__repr__(ResidueType self) -> std::string"""
6087  return _IMP_atom.ResidueType___repr__(self)
6088 
6089  __swig_destroy__ = _IMP_atom.delete_ResidueType
6090  __del__ = lambda self : None;
6091 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
6092 ResidueType_swigregister(ResidueType)
6093 
6094 def ResidueType_add_key(*args):
6095  """ResidueType_add_key(std::string sc) -> unsigned int"""
6096  return _IMP_atom.ResidueType_add_key(*args)
6097 
6098 def ResidueType_get_key_exists(*args):
6099  """ResidueType_get_key_exists(std::string sc) -> bool"""
6100  return _IMP_atom.ResidueType_get_key_exists(*args)
6101 
6102 def ResidueType_add_alias(*args):
6103  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
6104  return _IMP_atom.ResidueType_add_alias(*args)
6105 
6106 def ResidueType_show_all(*args):
6107  """ResidueType_show_all(_ostream out)"""
6108  return _IMP_atom.ResidueType_show_all(*args)
6109 
6110 def ResidueType_get_all_strings():
6111  """ResidueType_get_all_strings() -> IMP::base::Vector< std::string >"""
6112  return _IMP_atom.ResidueType_get_all_strings()
6113 
6114 def ResidueType_get_number_unique():
6115  """ResidueType_get_number_unique() -> unsigned int"""
6116  return _IMP_atom.ResidueType_get_number_unique()
6117 
6118 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
6119 OH = _IMP_atom.OH
6120 H2O = _IMP_atom.H2O
6121 H = _IMP_atom.H
6122 He = _IMP_atom.He
6123 Li = _IMP_atom.Li
6124 Be = _IMP_atom.Be
6125 B = _IMP_atom.B
6126 C = _IMP_atom.C
6127 N = _IMP_atom.N
6128 O = _IMP_atom.O
6129 F = _IMP_atom.F
6130 Ne = _IMP_atom.Ne
6131 Na = _IMP_atom.Na
6132 Mg = _IMP_atom.Mg
6133 Al = _IMP_atom.Al
6134 Si = _IMP_atom.Si
6135 P = _IMP_atom.P
6136 S = _IMP_atom.S
6137 Cl = _IMP_atom.Cl
6138 Ar = _IMP_atom.Ar
6139 K = _IMP_atom.K
6140 Ca = _IMP_atom.Ca
6141 Sc = _IMP_atom.Sc
6142 Ti = _IMP_atom.Ti
6143 V = _IMP_atom.V
6144 Cr = _IMP_atom.Cr
6145 Mn = _IMP_atom.Mn
6146 Fe = _IMP_atom.Fe
6147 Co = _IMP_atom.Co
6148 Ni = _IMP_atom.Ni
6149 Cu = _IMP_atom.Cu
6150 Zn = _IMP_atom.Zn
6151 Ga = _IMP_atom.Ga
6152 Ge = _IMP_atom.Ge
6153 As = _IMP_atom.As
6154 Se = _IMP_atom.Se
6155 Br = _IMP_atom.Br
6156 Kr = _IMP_atom.Kr
6157 Rb = _IMP_atom.Rb
6158 Sr = _IMP_atom.Sr
6159 Y = _IMP_atom.Y
6160 Zr = _IMP_atom.Zr
6161 Nb = _IMP_atom.Nb
6162 Mo = _IMP_atom.Mo
6163 Tc = _IMP_atom.Tc
6164 Ru = _IMP_atom.Ru
6165 Rh = _IMP_atom.Rh
6166 Pd = _IMP_atom.Pd
6167 Ag = _IMP_atom.Ag
6168 Cd = _IMP_atom.Cd
6169 In = _IMP_atom.In
6170 Sn = _IMP_atom.Sn
6171 Sb = _IMP_atom.Sb
6172 Te = _IMP_atom.Te
6173 I = _IMP_atom.I
6174 Xe = _IMP_atom.Xe
6175 Cs = _IMP_atom.Cs
6176 Ba = _IMP_atom.Ba
6177 La = _IMP_atom.La
6178 Ce = _IMP_atom.Ce
6179 Pr = _IMP_atom.Pr
6180 Nd = _IMP_atom.Nd
6181 Pm = _IMP_atom.Pm
6182 Sm = _IMP_atom.Sm
6183 Eu = _IMP_atom.Eu
6184 Gd = _IMP_atom.Gd
6185 Tb = _IMP_atom.Tb
6186 Dy = _IMP_atom.Dy
6187 Ho = _IMP_atom.Ho
6188 Er = _IMP_atom.Er
6189 Tm = _IMP_atom.Tm
6190 Yb = _IMP_atom.Yb
6191 Lu = _IMP_atom.Lu
6192 Hf = _IMP_atom.Hf
6193 Ta = _IMP_atom.Ta
6194 W = _IMP_atom.W
6195 Re = _IMP_atom.Re
6196 Os = _IMP_atom.Os
6197 Ir = _IMP_atom.Ir
6198 Pt = _IMP_atom.Pt
6199 Au = _IMP_atom.Au
6200 Hg = _IMP_atom.Hg
6201 Tl = _IMP_atom.Tl
6202 Pb = _IMP_atom.Pb
6203 Bi = _IMP_atom.Bi
6204 Po = _IMP_atom.Po
6205 At = _IMP_atom.At
6206 Rn = _IMP_atom.Rn
6207 Fr = _IMP_atom.Fr
6208 Ra = _IMP_atom.Ra
6209 Ac = _IMP_atom.Ac
6210 Th = _IMP_atom.Th
6211 Pa = _IMP_atom.Pa
6212 U = _IMP_atom.U
6213 Np = _IMP_atom.Np
6214 Pu = _IMP_atom.Pu
6215 Am = _IMP_atom.Am
6216 Cm = _IMP_atom.Cm
6217 Bk = _IMP_atom.Bk
6218 Cf = _IMP_atom.Cf
6219 Es = _IMP_atom.Es
6220 Fm = _IMP_atom.Fm
6221 Md = _IMP_atom.Md
6222 No = _IMP_atom.No
6223 Lr = _IMP_atom.Lr
6224 Db = _IMP_atom.Db
6225 Jl = _IMP_atom.Jl
6226 Rf = _IMP_atom.Rf
6227 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
6228 
6229 def hash_value(*args):
6230  """hash_value(IMP::atom::Element e) -> size_t"""
6231  return _IMP_atom.hash_value(*args)
6232 class ElementTable(_object):
6233  """Proxy of C++ IMP::atom::ElementTable class"""
6234  __swig_setmethods__ = {}
6235  __setattr__ = lambda self, name, value: _swig_setattr(self, ElementTable, name, value)
6236  __swig_getmethods__ = {}
6237  __getattr__ = lambda self, name: _swig_getattr(self, ElementTable, name)
6238  __repr__ = _swig_repr
6239  def __init__(self):
6240  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
6241  this = _IMP_atom.new_ElementTable()
6242  try: self.this.append(this)
6243  except: self.this = this
6244  def get_element(self, *args):
6245  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
6246  return _IMP_atom.ElementTable_get_element(self, *args)
6247 
6248  def get_name(self, *args):
6249  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
6250  return _IMP_atom.ElementTable_get_name(self, *args)
6251 
6252  def get_mass(self, *args):
6253  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
6254  return _IMP_atom.ElementTable_get_mass(self, *args)
6255 
6256  __swig_destroy__ = _IMP_atom.delete_ElementTable
6257  __del__ = lambda self : None;
6258 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
6259 ElementTable_swigregister(ElementTable)
6260 
6261 
6262 def get_element_table():
6263  """get_element_table() -> ElementTable"""
6264  return _IMP_atom.get_element_table()
6265 class Atom(Hierarchy):
6266  """Proxy of C++ IMP::atom::Atom class"""
6267  __swig_setmethods__ = {}
6268  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6269  __setattr__ = lambda self, name, value: _swig_setattr(self, Atom, name, value)
6270  __swig_getmethods__ = {}
6271  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6272  __getattr__ = lambda self, name: _swig_getattr(self, Atom, name)
6273  def __init__(self, *args):
6274  """
6275  __init__(IMP::atom::Atom self) -> Atom
6276  __init__(IMP::atom::Atom self, Model m, ::IMP::kernel::ParticleIndex id) -> Atom
6277  __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
6278  """
6279  this = _IMP_atom.new_Atom(*args)
6280  try: self.this.append(this)
6281  except: self.this = this
6282  def decorate_particle(*args):
6283  """decorate_particle(Particle p) -> Atom"""
6284  return _IMP_atom.Atom_decorate_particle(*args)
6285 
6286  if _newclass:decorate_particle = staticmethod(decorate_particle)
6287  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6288  def show(self, *args):
6289  """
6290  show(Atom self, _ostream out=std::cout)
6291  show(Atom self)
6292  """
6293  return _IMP_atom.Atom_show(self, *args)
6294 
6295  def setup_particle(*args):
6296  """
6297  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Atom other) -> Atom
6298  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
6299  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType atom_type) -> Atom
6300  setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
6301  """
6302  return _IMP_atom.Atom_setup_particle(*args)
6303 
6304  if _newclass:setup_particle = staticmethod(setup_particle)
6305  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6306  def get_is_setup(*args):
6307  """
6308  get_is_setup(_ParticleAdaptor p) -> bool
6309  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6310  """
6311  return _IMP_atom.Atom_get_is_setup(*args)
6312 
6313  if _newclass:get_is_setup = staticmethod(get_is_setup)
6314  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
6315  def get_atom_type(self):
6316  """get_atom_type(Atom self) -> AtomType"""
6317  return _IMP_atom.Atom_get_atom_type(self)
6318 
6319  def set_atom_type(self, *args):
6320  """set_atom_type(Atom self, AtomType t)"""
6321  return _IMP_atom.Atom_set_atom_type(self, *args)
6322 
6323  def get_element(self):
6324  """get_element(Atom self) -> IMP::atom::Element"""
6325  return _IMP_atom.Atom_get_element(self)
6326 
6327  def set_element(self, *args):
6328  """set_element(Atom self, IMP::atom::Element e)"""
6329  return _IMP_atom.Atom_set_element(self, *args)
6330 
6331  def get_occupancy(self):
6332  """get_occupancy(Atom self) -> double"""
6333  return _IMP_atom.Atom_get_occupancy(self)
6334 
6335  def set_occupancy(self, *args):
6336  """set_occupancy(Atom self, double occupancy)"""
6337  return _IMP_atom.Atom_set_occupancy(self, *args)
6338 
6339  def get_temperature_factor(self):
6340  """get_temperature_factor(Atom self) -> double"""
6341  return _IMP_atom.Atom_get_temperature_factor(self)
6342 
6343  def set_temperature_factor(self, *args):
6344  """set_temperature_factor(Atom self, double tempFactor)"""
6345  return _IMP_atom.Atom_set_temperature_factor(self, *args)
6346 
6347  def get_input_index(self):
6348  """get_input_index(Atom self) -> IMP::Int"""
6349  return _IMP_atom.Atom_get_input_index(self)
6350 
6351  def set_input_index(self, *args):
6352  """set_input_index(Atom self, IMP::Int t)"""
6353  return _IMP_atom.Atom_set_input_index(self, *args)
6354 
6355  def get_atom_type_key():
6356  """get_atom_type_key() -> IntKey"""
6357  return _IMP_atom.Atom_get_atom_type_key()
6358 
6359  if _newclass:get_atom_type_key = staticmethod(get_atom_type_key)
6360  __swig_getmethods__["get_atom_type_key"] = lambda x: get_atom_type_key
6361  def get_element_key():
6362  """get_element_key() -> IntKey"""
6363  return _IMP_atom.Atom_get_element_key()
6364 
6365  if _newclass:get_element_key = staticmethod(get_element_key)
6366  __swig_getmethods__["get_element_key"] = lambda x: get_element_key
6367  def get_input_index_key():
6368  """get_input_index_key() -> IntKey"""
6369  return _IMP_atom.Atom_get_input_index_key()
6370 
6371  if _newclass:get_input_index_key = staticmethod(get_input_index_key)
6372  __swig_getmethods__["get_input_index_key"] = lambda x: get_input_index_key
6373  def get_occupancy_key():
6374  """get_occupancy_key() -> FloatKey"""
6375  return _IMP_atom.Atom_get_occupancy_key()
6376 
6377  if _newclass:get_occupancy_key = staticmethod(get_occupancy_key)
6378  __swig_getmethods__["get_occupancy_key"] = lambda x: get_occupancy_key
6379  def get_temperature_factor_key():
6380  """get_temperature_factor_key() -> FloatKey"""
6381  return _IMP_atom.Atom_get_temperature_factor_key()
6382 
6383  if _newclass:get_temperature_factor_key = staticmethod(get_temperature_factor_key)
6384  __swig_getmethods__["get_temperature_factor_key"] = lambda x: get_temperature_factor_key
6385  def add_attribute(self, *args):
6386  """
6387  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
6388  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
6389  add_attribute(Atom self, IntKey a0, IMP::Int a1)
6390  add_attribute(Atom self, StringKey a0, IMP::String a1)
6391  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
6392  add_attribute(Atom self, ObjectKey a0, Object a1)
6393  """
6394  return _IMP_atom.Atom_add_attribute(self, *args)
6395 
6396  def get_value(self, *args):
6397  """
6398  get_value(Atom self, FloatKey a0) -> IMP::Float
6399  get_value(Atom self, IntKey a0) -> IMP::Int
6400  get_value(Atom self, StringKey a0) -> IMP::String
6401  get_value(Atom self, ParticleIndexKey a0) -> Particle
6402  get_value(Atom self, ObjectKey a0) -> Object
6403  """
6404  return _IMP_atom.Atom_get_value(self, *args)
6405 
6406  def set_value(self, *args):
6407  """
6408  set_value(Atom self, FloatKey a0, IMP::Float a1)
6409  set_value(Atom self, IntKey a0, IMP::Int a1)
6410  set_value(Atom self, StringKey a0, IMP::String a1)
6411  set_value(Atom self, ParticleIndexKey a0, Particle a1)
6412  set_value(Atom self, ObjectKey a0, Object a1)
6413  """
6414  return _IMP_atom.Atom_set_value(self, *args)
6415 
6416  def remove_attribute(self, *args):
6417  """
6418  remove_attribute(Atom self, FloatKey a0)
6419  remove_attribute(Atom self, IntKey a0)
6420  remove_attribute(Atom self, StringKey a0)
6421  remove_attribute(Atom self, ParticleIndexKey a0)
6422  remove_attribute(Atom self, ObjectKey a0)
6423  """
6424  return _IMP_atom.Atom_remove_attribute(self, *args)
6425 
6426  def has_attribute(self, *args):
6427  """
6428  has_attribute(Atom self, FloatKey a0) -> bool
6429  has_attribute(Atom self, IntKey a0) -> bool
6430  has_attribute(Atom self, StringKey a0) -> bool
6431  has_attribute(Atom self, ParticleIndexKey a0) -> bool
6432  has_attribute(Atom self, ObjectKey a0) -> bool
6433  """
6434  return _IMP_atom.Atom_has_attribute(self, *args)
6435 
6436  def get_derivative(self, *args):
6437  """get_derivative(Atom self, FloatKey a0) -> double"""
6438  return _IMP_atom.Atom_get_derivative(self, *args)
6439 
6440  def get_name(self):
6441  """get_name(Atom self) -> std::string"""
6442  return _IMP_atom.Atom_get_name(self)
6443 
6444  def clear_caches(self):
6445  """clear_caches(Atom self)"""
6446  return _IMP_atom.Atom_clear_caches(self)
6447 
6448  def set_name(self, *args):
6449  """set_name(Atom self, std::string a0)"""
6450  return _IMP_atom.Atom_set_name(self, *args)
6451 
6452  def set_check_level(self, *args):
6453  """set_check_level(Atom self, IMP::base::CheckLevel a0)"""
6454  return _IMP_atom.Atom_set_check_level(self, *args)
6455 
6456  def add_to_derivative(self, *args):
6457  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6458  return _IMP_atom.Atom_add_to_derivative(self, *args)
6459 
6460  def set_is_optimized(self, *args):
6461  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
6462  return _IMP_atom.Atom_set_is_optimized(self, *args)
6463 
6464  def get_is_optimized(self, *args):
6465  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
6466  return _IMP_atom.Atom_get_is_optimized(self, *args)
6467 
6468  def get_check_level(self):
6469  """get_check_level(Atom self) -> IMP::base::CheckLevel"""
6470  return _IMP_atom.Atom_get_check_level(self)
6471 
6472  def __eq__(self, *args):
6473  """
6474  __eq__(Atom self, Atom o) -> bool
6475  __eq__(Atom self, Particle d) -> bool
6476  """
6477  return _IMP_atom.Atom___eq__(self, *args)
6478 
6479  def __ne__(self, *args):
6480  """
6481  __ne__(Atom self, Atom o) -> bool
6482  __ne__(Atom self, Particle d) -> bool
6483  """
6484  return _IMP_atom.Atom___ne__(self, *args)
6485 
6486  def __le__(self, *args):
6487  """
6488  __le__(Atom self, Atom o) -> bool
6489  __le__(Atom self, Particle d) -> bool
6490  """
6491  return _IMP_atom.Atom___le__(self, *args)
6492 
6493  def __lt__(self, *args):
6494  """
6495  __lt__(Atom self, Atom o) -> bool
6496  __lt__(Atom self, Particle d) -> bool
6497  """
6498  return _IMP_atom.Atom___lt__(self, *args)
6499 
6500  def __ge__(self, *args):
6501  """
6502  __ge__(Atom self, Atom o) -> bool
6503  __ge__(Atom self, Particle d) -> bool
6504  """
6505  return _IMP_atom.Atom___ge__(self, *args)
6506 
6507  def __gt__(self, *args):
6508  """
6509  __gt__(Atom self, Atom o) -> bool
6510  __gt__(Atom self, Particle d) -> bool
6511  """
6512  return _IMP_atom.Atom___gt__(self, *args)
6513 
6514  def __str__(self):
6515  """__str__(Atom self) -> std::string"""
6516  return _IMP_atom.Atom___str__(self)
6517 
6518  def __repr__(self):
6519  """__repr__(Atom self) -> std::string"""
6520  return _IMP_atom.Atom___repr__(self)
6521 
6522  __swig_destroy__ = _IMP_atom.delete_Atom
6523  __del__ = lambda self : None;
6524 Atom_swigregister = _IMP_atom.Atom_swigregister
6525 Atom_swigregister(Atom)
6526 cvar = _IMP_atom.cvar
6527 AT_UNKNOWN = cvar.AT_UNKNOWN
6528 AT_N = cvar.AT_N
6529 AT_CA = cvar.AT_CA
6530 AT_C = cvar.AT_C
6531 AT_O = cvar.AT_O
6532 AT_H = cvar.AT_H
6533 AT_H1 = cvar.AT_H1
6534 AT_H2 = cvar.AT_H2
6535 AT_H3 = cvar.AT_H3
6536 AT_HA = cvar.AT_HA
6537 AT_HA1 = cvar.AT_HA1
6538 AT_HA2 = cvar.AT_HA2
6539 AT_HA3 = cvar.AT_HA3
6540 AT_CB = cvar.AT_CB
6541 AT_HB = cvar.AT_HB
6542 AT_HB1 = cvar.AT_HB1
6543 AT_HB2 = cvar.AT_HB2
6544 AT_HB3 = cvar.AT_HB3
6545 AT_OXT = cvar.AT_OXT
6546 AT_CH3 = cvar.AT_CH3
6547 AT_CH = cvar.AT_CH
6548 AT_CG = cvar.AT_CG
6549 AT_CG1 = cvar.AT_CG1
6550 AT_CG2 = cvar.AT_CG2
6551 AT_HG = cvar.AT_HG
6552 AT_HG1 = cvar.AT_HG1
6553 AT_HG2 = cvar.AT_HG2
6554 AT_HG3 = cvar.AT_HG3
6555 AT_HG11 = cvar.AT_HG11
6556 AT_HG21 = cvar.AT_HG21
6557 AT_HG31 = cvar.AT_HG31
6558 AT_HG12 = cvar.AT_HG12
6559 AT_HG13 = cvar.AT_HG13
6560 AT_HG22 = cvar.AT_HG22
6561 AT_HG23 = cvar.AT_HG23
6562 AT_HG32 = cvar.AT_HG32
6563 AT_OG = cvar.AT_OG
6564 AT_OG1 = cvar.AT_OG1
6565 AT_SG = cvar.AT_SG
6566 AT_CD = cvar.AT_CD
6567 AT_CD1 = cvar.AT_CD1
6568 AT_CD2 = cvar.AT_CD2
6569 AT_HD = cvar.AT_HD
6570 AT_HD1 = cvar.AT_HD1
6571 AT_HD2 = cvar.AT_HD2
6572 AT_HD3 = cvar.AT_HD3
6573 AT_HD11 = cvar.AT_HD11
6574 AT_HD21 = cvar.AT_HD21
6575 AT_HD31 = cvar.AT_HD31
6576 AT_HD12 = cvar.AT_HD12
6577 AT_HD13 = cvar.AT_HD13
6578 AT_HD22 = cvar.AT_HD22
6579 AT_HD23 = cvar.AT_HD23
6580 AT_HD32 = cvar.AT_HD32
6581 AT_SD = cvar.AT_SD
6582 AT_OD1 = cvar.AT_OD1
6583 AT_OD2 = cvar.AT_OD2
6584 AT_ND1 = cvar.AT_ND1
6585 AT_ND2 = cvar.AT_ND2
6586 AT_CE = cvar.AT_CE
6587 AT_CE1 = cvar.AT_CE1
6588 AT_CE2 = cvar.AT_CE2
6589 AT_CE3 = cvar.AT_CE3
6590 AT_HE = cvar.AT_HE
6591 AT_HE1 = cvar.AT_HE1
6592 AT_HE2 = cvar.AT_HE2
6593 AT_HE3 = cvar.AT_HE3
6594 AT_HE21 = cvar.AT_HE21
6595 AT_HE22 = cvar.AT_HE22
6596 AT_OE1 = cvar.AT_OE1
6597 AT_OE2 = cvar.AT_OE2
6598 AT_NE = cvar.AT_NE
6599 AT_NE1 = cvar.AT_NE1
6600 AT_NE2 = cvar.AT_NE2
6601 AT_CZ = cvar.AT_CZ
6602 AT_CZ2 = cvar.AT_CZ2
6603 AT_CZ3 = cvar.AT_CZ3
6604 AT_NZ = cvar.AT_NZ
6605 AT_HZ = cvar.AT_HZ
6606 AT_HZ1 = cvar.AT_HZ1
6607 AT_HZ2 = cvar.AT_HZ2
6608 AT_HZ3 = cvar.AT_HZ3
6609 AT_CH2 = cvar.AT_CH2
6610 AT_NH1 = cvar.AT_NH1
6611 AT_NH2 = cvar.AT_NH2
6612 AT_OH = cvar.AT_OH
6613 AT_HH = cvar.AT_HH
6614 AT_HH11 = cvar.AT_HH11
6615 AT_HH21 = cvar.AT_HH21
6616 AT_HH2 = cvar.AT_HH2
6617 AT_HH12 = cvar.AT_HH12
6618 AT_HH22 = cvar.AT_HH22
6619 AT_HH13 = cvar.AT_HH13
6620 AT_HH23 = cvar.AT_HH23
6621 AT_HH33 = cvar.AT_HH33
6622 AT_P = cvar.AT_P
6623 AT_OP1 = cvar.AT_OP1
6624 AT_OP2 = cvar.AT_OP2
6625 AT_OP3 = cvar.AT_OP3
6626 AT_O5p = cvar.AT_O5p
6627 AT_C5p = cvar.AT_C5p
6628 AT_H5p = cvar.AT_H5p
6629 AT_H5pp = cvar.AT_H5pp
6630 AT_C4p = cvar.AT_C4p
6631 AT_H4p = cvar.AT_H4p
6632 AT_O4p = cvar.AT_O4p
6633 AT_C1p = cvar.AT_C1p
6634 AT_H1p = cvar.AT_H1p
6635 AT_C3p = cvar.AT_C3p
6636 AT_H3p = cvar.AT_H3p
6637 AT_O3p = cvar.AT_O3p
6638 AT_C2p = cvar.AT_C2p
6639 AT_H2p = cvar.AT_H2p
6640 AT_H2pp = cvar.AT_H2pp
6641 AT_O2p = cvar.AT_O2p
6642 AT_HO2p = cvar.AT_HO2p
6643 AT_N9 = cvar.AT_N9
6644 AT_C8 = cvar.AT_C8
6645 AT_H8 = cvar.AT_H8
6646 AT_N7 = cvar.AT_N7
6647 AT_C5 = cvar.AT_C5
6648 AT_C4 = cvar.AT_C4
6649 AT_N3 = cvar.AT_N3
6650 AT_C2 = cvar.AT_C2
6651 AT_N1 = cvar.AT_N1
6652 AT_C6 = cvar.AT_C6
6653 AT_N6 = cvar.AT_N6
6654 AT_H61 = cvar.AT_H61
6655 AT_H62 = cvar.AT_H62
6656 AT_O6 = cvar.AT_O6
6657 AT_N2 = cvar.AT_N2
6658 AT_NT = cvar.AT_NT
6659 AT_H21 = cvar.AT_H21
6660 AT_H22 = cvar.AT_H22
6661 AT_H6 = cvar.AT_H6
6662 AT_H5 = cvar.AT_H5
6663 AT_O2 = cvar.AT_O2
6664 AT_N4 = cvar.AT_N4
6665 AT_H41 = cvar.AT_H41
6666 AT_H42 = cvar.AT_H42
6667 AT_O4 = cvar.AT_O4
6668 AT_C7 = cvar.AT_C7
6669 AT_H71 = cvar.AT_H71
6670 AT_H72 = cvar.AT_H72
6671 AT_H73 = cvar.AT_H73
6672 AT_O1A = cvar.AT_O1A
6673 AT_O2A = cvar.AT_O2A
6674 AT_O3A = cvar.AT_O3A
6675 AT_O1B = cvar.AT_O1B
6676 AT_O2B = cvar.AT_O2B
6677 AT_O3B = cvar.AT_O3B
6678 
6679 def Atom_decorate_particle(*args):
6680  """Atom_decorate_particle(Particle p) -> Atom"""
6681  return _IMP_atom.Atom_decorate_particle(*args)
6682 
6683 def Atom_setup_particle(*args):
6684  """
6685  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Atom other) -> Atom
6686  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
6687  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType atom_type) -> Atom
6688  Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
6689  """
6690  return _IMP_atom.Atom_setup_particle(*args)
6691 
6692 def Atom_get_is_setup(*args):
6693  """
6694  get_is_setup(_ParticleAdaptor p) -> bool
6695  Atom_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6696  """
6697  return _IMP_atom.Atom_get_is_setup(*args)
6698 
6699 def Atom_get_atom_type_key():
6700  """Atom_get_atom_type_key() -> IntKey"""
6701  return _IMP_atom.Atom_get_atom_type_key()
6702 
6703 def Atom_get_element_key():
6704  """Atom_get_element_key() -> IntKey"""
6705  return _IMP_atom.Atom_get_element_key()
6706 
6707 def Atom_get_input_index_key():
6708  """Atom_get_input_index_key() -> IntKey"""
6709  return _IMP_atom.Atom_get_input_index_key()
6710 
6711 def Atom_get_occupancy_key():
6712  """Atom_get_occupancy_key() -> FloatKey"""
6713  return _IMP_atom.Atom_get_occupancy_key()
6714 
6715 def Atom_get_temperature_factor_key():
6716  """Atom_get_temperature_factor_key() -> FloatKey"""
6717  return _IMP_atom.Atom_get_temperature_factor_key()
6718 
6719 
6720 def get_residue(*args):
6721  """
6722  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
6723  get_residue(Atom d, bool nothrow=False) -> Residue
6724  get_residue(Atom d) -> Residue
6725  """
6726  return _IMP_atom.get_residue(*args)
6727 
6728 def get_atom(*args):
6729  """get_atom(Residue rd, AtomType at) -> Atom"""
6730  return _IMP_atom.get_atom(*args)
6731 
6732 def add_atom_type(*args):
6733  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
6734  return _IMP_atom.add_atom_type(*args)
6735 
6736 def get_element_for_atom_type(*args):
6737  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
6738  return _IMP_atom.get_element_for_atom_type(*args)
6739 
6740 def get_atom_type_exists(*args):
6741  """get_atom_type_exists(std::string name) -> bool"""
6742  return _IMP_atom.get_atom_type_exists(*args)
6743 class Residue(Hierarchy):
6744  """Proxy of C++ IMP::atom::Residue class"""
6745  __swig_setmethods__ = {}
6746  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6747  __setattr__ = lambda self, name, value: _swig_setattr(self, Residue, name, value)
6748  __swig_getmethods__ = {}
6749  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6750  __getattr__ = lambda self, name: _swig_getattr(self, Residue, name)
6751  def __init__(self, *args):
6752  """
6753  __init__(IMP::atom::Residue self) -> Residue
6754  __init__(IMP::atom::Residue self, Model m, ::IMP::kernel::ParticleIndex id) -> Residue
6755  __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
6756  """
6757  this = _IMP_atom.new_Residue(*args)
6758  try: self.this.append(this)
6759  except: self.this = this
6760  def decorate_particle(*args):
6761  """decorate_particle(Particle p) -> Residue"""
6762  return _IMP_atom.Residue_decorate_particle(*args)
6763 
6764  if _newclass:decorate_particle = staticmethod(decorate_particle)
6765  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6766  def show(self, *args):
6767  """
6768  show(Residue self, _ostream out=std::cout)
6769  show(Residue self)
6770  """
6771  return _IMP_atom.Residue_show(self, *args)
6772 
6773  def setup_particle(*args):
6774  """
6775  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
6776  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
6777  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index) -> Residue
6778  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
6779  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t) -> Residue
6780  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
6781  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Residue other) -> Residue
6782  setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
6783  """
6784  return _IMP_atom.Residue_setup_particle(*args)
6785 
6786  if _newclass:setup_particle = staticmethod(setup_particle)
6787  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6788  def get_is_setup(*args):
6789  """
6790  get_is_setup(_ParticleAdaptor p) -> bool
6791  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6792  """
6793  return _IMP_atom.Residue_get_is_setup(*args)
6794 
6795  if _newclass:get_is_setup = staticmethod(get_is_setup)
6796  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
6797  def get_residue_type(self):
6798  """get_residue_type(Residue self) -> ResidueType"""
6799  return _IMP_atom.Residue_get_residue_type(self)
6800 
6801  def set_residue_type(self, *args):
6802  """set_residue_type(Residue self, ResidueType t)"""
6803  return _IMP_atom.Residue_set_residue_type(self, *args)
6804 
6805  def get_is_protein(self):
6806  """get_is_protein(Residue self) -> bool"""
6807  return _IMP_atom.Residue_get_is_protein(self)
6808 
6809  def get_is_dna(self):
6810  """get_is_dna(Residue self) -> bool"""
6811  return _IMP_atom.Residue_get_is_dna(self)
6812 
6813  def get_is_rna(self):
6814  """get_is_rna(Residue self) -> bool"""
6815  return _IMP_atom.Residue_get_is_rna(self)
6816 
6817  def get_index(self):
6818  """get_index(Residue self) -> IMP::Int"""
6819  return _IMP_atom.Residue_get_index(self)
6820 
6821  def set_index(self, *args):
6822  """set_index(Residue self, IMP::Int t)"""
6823  return _IMP_atom.Residue_set_index(self, *args)
6824 
6825  def get_insertion_code(self):
6826  """get_insertion_code(Residue self) -> char"""
6827  return _IMP_atom.Residue_get_insertion_code(self)
6828 
6829  def set_insertion_code(self, *args):
6830  """set_insertion_code(Residue self, char insertion_code)"""
6831  return _IMP_atom.Residue_set_insertion_code(self, *args)
6832 
6833  def get_index_key():
6834  """get_index_key() -> IntKey"""
6835  return _IMP_atom.Residue_get_index_key()
6836 
6837  if _newclass:get_index_key = staticmethod(get_index_key)
6838  __swig_getmethods__["get_index_key"] = lambda x: get_index_key
6839  def get_residue_type_key():
6840  """get_residue_type_key() -> IntKey"""
6841  return _IMP_atom.Residue_get_residue_type_key()
6842 
6843  if _newclass:get_residue_type_key = staticmethod(get_residue_type_key)
6844  __swig_getmethods__["get_residue_type_key"] = lambda x: get_residue_type_key
6845  def get_insertion_code_key():
6846  """get_insertion_code_key() -> IntKey"""
6847  return _IMP_atom.Residue_get_insertion_code_key()
6848 
6849  if _newclass:get_insertion_code_key = staticmethod(get_insertion_code_key)
6850  __swig_getmethods__["get_insertion_code_key"] = lambda x: get_insertion_code_key
6851  def add_attribute(self, *args):
6852  """
6853  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
6854  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
6855  add_attribute(Residue self, IntKey a0, IMP::Int a1)
6856  add_attribute(Residue self, StringKey a0, IMP::String a1)
6857  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
6858  add_attribute(Residue self, ObjectKey a0, Object a1)
6859  """
6860  return _IMP_atom.Residue_add_attribute(self, *args)
6861 
6862  def get_value(self, *args):
6863  """
6864  get_value(Residue self, FloatKey a0) -> IMP::Float
6865  get_value(Residue self, IntKey a0) -> IMP::Int
6866  get_value(Residue self, StringKey a0) -> IMP::String
6867  get_value(Residue self, ParticleIndexKey a0) -> Particle
6868  get_value(Residue self, ObjectKey a0) -> Object
6869  """
6870  return _IMP_atom.Residue_get_value(self, *args)
6871 
6872  def set_value(self, *args):
6873  """
6874  set_value(Residue self, FloatKey a0, IMP::Float a1)
6875  set_value(Residue self, IntKey a0, IMP::Int a1)
6876  set_value(Residue self, StringKey a0, IMP::String a1)
6877  set_value(Residue self, ParticleIndexKey a0, Particle a1)
6878  set_value(Residue self, ObjectKey a0, Object a1)
6879  """
6880  return _IMP_atom.Residue_set_value(self, *args)
6881 
6882  def remove_attribute(self, *args):
6883  """
6884  remove_attribute(Residue self, FloatKey a0)
6885  remove_attribute(Residue self, IntKey a0)
6886  remove_attribute(Residue self, StringKey a0)
6887  remove_attribute(Residue self, ParticleIndexKey a0)
6888  remove_attribute(Residue self, ObjectKey a0)
6889  """
6890  return _IMP_atom.Residue_remove_attribute(self, *args)
6891 
6892  def has_attribute(self, *args):
6893  """
6894  has_attribute(Residue self, FloatKey a0) -> bool
6895  has_attribute(Residue self, IntKey a0) -> bool
6896  has_attribute(Residue self, StringKey a0) -> bool
6897  has_attribute(Residue self, ParticleIndexKey a0) -> bool
6898  has_attribute(Residue self, ObjectKey a0) -> bool
6899  """
6900  return _IMP_atom.Residue_has_attribute(self, *args)
6901 
6902  def get_derivative(self, *args):
6903  """get_derivative(Residue self, FloatKey a0) -> double"""
6904  return _IMP_atom.Residue_get_derivative(self, *args)
6905 
6906  def get_name(self):
6907  """get_name(Residue self) -> std::string"""
6908  return _IMP_atom.Residue_get_name(self)
6909 
6910  def clear_caches(self):
6911  """clear_caches(Residue self)"""
6912  return _IMP_atom.Residue_clear_caches(self)
6913 
6914  def set_name(self, *args):
6915  """set_name(Residue self, std::string a0)"""
6916  return _IMP_atom.Residue_set_name(self, *args)
6917 
6918  def set_check_level(self, *args):
6919  """set_check_level(Residue self, IMP::base::CheckLevel a0)"""
6920  return _IMP_atom.Residue_set_check_level(self, *args)
6921 
6922  def add_to_derivative(self, *args):
6923  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6924  return _IMP_atom.Residue_add_to_derivative(self, *args)
6925 
6926  def set_is_optimized(self, *args):
6927  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
6928  return _IMP_atom.Residue_set_is_optimized(self, *args)
6929 
6930  def get_is_optimized(self, *args):
6931  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
6932  return _IMP_atom.Residue_get_is_optimized(self, *args)
6933 
6934  def get_check_level(self):
6935  """get_check_level(Residue self) -> IMP::base::CheckLevel"""
6936  return _IMP_atom.Residue_get_check_level(self)
6937 
6938  def __eq__(self, *args):
6939  """
6940  __eq__(Residue self, Residue o) -> bool
6941  __eq__(Residue self, Particle d) -> bool
6942  """
6943  return _IMP_atom.Residue___eq__(self, *args)
6944 
6945  def __ne__(self, *args):
6946  """
6947  __ne__(Residue self, Residue o) -> bool
6948  __ne__(Residue self, Particle d) -> bool
6949  """
6950  return _IMP_atom.Residue___ne__(self, *args)
6951 
6952  def __le__(self, *args):
6953  """
6954  __le__(Residue self, Residue o) -> bool
6955  __le__(Residue self, Particle d) -> bool
6956  """
6957  return _IMP_atom.Residue___le__(self, *args)
6958 
6959  def __lt__(self, *args):
6960  """
6961  __lt__(Residue self, Residue o) -> bool
6962  __lt__(Residue self, Particle d) -> bool
6963  """
6964  return _IMP_atom.Residue___lt__(self, *args)
6965 
6966  def __ge__(self, *args):
6967  """
6968  __ge__(Residue self, Residue o) -> bool
6969  __ge__(Residue self, Particle d) -> bool
6970  """
6971  return _IMP_atom.Residue___ge__(self, *args)
6972 
6973  def __gt__(self, *args):
6974  """
6975  __gt__(Residue self, Residue o) -> bool
6976  __gt__(Residue self, Particle d) -> bool
6977  """
6978  return _IMP_atom.Residue___gt__(self, *args)
6979 
6980  def __str__(self):
6981  """__str__(Residue self) -> std::string"""
6982  return _IMP_atom.Residue___str__(self)
6983 
6984  def __repr__(self):
6985  """__repr__(Residue self) -> std::string"""
6986  return _IMP_atom.Residue___repr__(self)
6987 
6988  __swig_destroy__ = _IMP_atom.delete_Residue
6989  __del__ = lambda self : None;
6990 Residue_swigregister = _IMP_atom.Residue_swigregister
6991 Residue_swigregister(Residue)
6992 UNK = cvar.UNK
6993 GLY = cvar.GLY
6994 ALA = cvar.ALA
6995 VAL = cvar.VAL
6996 LEU = cvar.LEU
6997 ILE = cvar.ILE
6998 SER = cvar.SER
6999 THR = cvar.THR
7000 CYS = cvar.CYS
7001 MET = cvar.MET
7002 PRO = cvar.PRO
7003 ASP = cvar.ASP
7004 ASN = cvar.ASN
7005 GLU = cvar.GLU
7006 GLN = cvar.GLN
7007 LYS = cvar.LYS
7008 ARG = cvar.ARG
7009 HIS = cvar.HIS
7010 PHE = cvar.PHE
7011 TYR = cvar.TYR
7012 TRP = cvar.TRP
7013 ACE = cvar.ACE
7014 NH2 = cvar.NH2
7015 ADE = cvar.ADE
7016 URA = cvar.URA
7017 CYT = cvar.CYT
7018 GUA = cvar.GUA
7019 THY = cvar.THY
7020 DADE = cvar.DADE
7021 DURA = cvar.DURA
7022 DCYT = cvar.DCYT
7023 DGUA = cvar.DGUA
7024 DTHY = cvar.DTHY
7025 HOH = cvar.HOH
7026 HEME = cvar.HEME
7027 
7028 def Residue_decorate_particle(*args):
7029  """Residue_decorate_particle(Particle p) -> Residue"""
7030  return _IMP_atom.Residue_decorate_particle(*args)
7031 
7032 def Residue_setup_particle(*args):
7033  """
7034  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
7035  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
7036  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index) -> Residue
7037  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
7038  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t) -> Residue
7039  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
7040  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Residue other) -> Residue
7041  Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
7042  """
7043  return _IMP_atom.Residue_setup_particle(*args)
7044 
7045 def Residue_get_is_setup(*args):
7046  """
7047  get_is_setup(_ParticleAdaptor p) -> bool
7048  Residue_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7049  """
7050  return _IMP_atom.Residue_get_is_setup(*args)
7051 
7052 def Residue_get_index_key():
7053  """Residue_get_index_key() -> IntKey"""
7054  return _IMP_atom.Residue_get_index_key()
7055 
7056 def Residue_get_residue_type_key():
7057  """Residue_get_residue_type_key() -> IntKey"""
7058  return _IMP_atom.Residue_get_residue_type_key()
7059 
7060 def Residue_get_insertion_code_key():
7061  """Residue_get_insertion_code_key() -> IntKey"""
7062  return _IMP_atom.Residue_get_insertion_code_key()
7063 
7064 
7065 def get_next_residue(*args):
7066  """get_next_residue(Residue rd) -> Hierarchy"""
7067  return _IMP_atom.get_next_residue(*args)
7068 
7069 def get_previous_residue(*args):
7070  """get_previous_residue(Residue rd) -> Hierarchy"""
7071  return _IMP_atom.get_previous_residue(*args)
7072 
7073 def get_one_letter_code(*args):
7074  """get_one_letter_code(ResidueType c) -> char"""
7075  return _IMP_atom.get_one_letter_code(*args)
7076 BALLS = _IMP_atom.BALLS
7077 GAUSSIANS = _IMP_atom.GAUSSIANS
7078 class Representation(Hierarchy):
7079  """Proxy of C++ IMP::atom::Representation class"""
7080  __swig_setmethods__ = {}
7081  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7082  __setattr__ = lambda self, name, value: _swig_setattr(self, Representation, name, value)
7083  __swig_getmethods__ = {}
7084  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7085  __getattr__ = lambda self, name: _swig_getattr(self, Representation, name)
7086  def setup_particle(*args):
7087  """
7088  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Representation
7089  setup_particle(_ParticleAdaptor decorator) -> Representation
7090  setup_particle(Model m, IMP::kernel::ParticleIndex pi, double resolution) -> Representation
7091  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
7092  """
7093  return _IMP_atom.Representation_setup_particle(*args)
7094 
7095  if _newclass:setup_particle = staticmethod(setup_particle)
7096  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7097  def __init__(self, *args):
7098  """
7099  __init__(IMP::atom::Representation self) -> Representation
7100  __init__(IMP::atom::Representation self, Model m, ::IMP::kernel::ParticleIndex id) -> Representation
7101  __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
7102  """
7103  this = _IMP_atom.new_Representation(*args)
7104  try: self.this.append(this)
7105  except: self.this = this
7106  def decorate_particle(*args):
7107  """decorate_particle(Particle p) -> Representation"""
7108  return _IMP_atom.Representation_decorate_particle(*args)
7109 
7110  if _newclass:decorate_particle = staticmethod(decorate_particle)
7111  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7112  def show(self, *args):
7113  """
7114  show(Representation self, _ostream out=std::cout)
7115  show(Representation self)
7116  """
7117  return _IMP_atom.Representation_show(self, *args)
7118 
7119  def get_is_setup(*args):
7120  """
7121  get_is_setup(_ParticleAdaptor p) -> bool
7122  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7123  """
7124  return _IMP_atom.Representation_get_is_setup(*args)
7125 
7126  if _newclass:get_is_setup = staticmethod(get_is_setup)
7127  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7128  def get_representation(self, *args):
7129  """
7130  get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy
7131  get_representation(Representation self, double resolution) -> Hierarchy
7132  """
7133  return _IMP_atom.Representation_get_representation(self, *args)
7134 
7135  def get_representations(self, *args):
7136  """
7137  get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies
7138  get_representations(Representation self) -> IMP::atom::Hierarchies
7139  """
7140  return _IMP_atom.Representation_get_representations(self, *args)
7141 
7142  def add_representation(self, *args):
7143  """
7144  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)
7145  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS)
7146  add_representation(Representation self, _ParticleIndexAdaptor rep)
7147  """
7148  return _IMP_atom.Representation_add_representation(self, *args)
7149 
7150  def get_resolutions(self, *args):
7151  """
7152  get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats
7153  get_resolutions(Representation self) -> IMP::Floats
7154  """
7155  return _IMP_atom.Representation_get_resolutions(self, *args)
7156 
7157  def add_attribute(self, *args):
7158  """
7159  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
7160  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
7161  add_attribute(Representation self, IntKey a0, IMP::Int a1)
7162  add_attribute(Representation self, StringKey a0, IMP::String a1)
7163  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
7164  add_attribute(Representation self, ObjectKey a0, Object a1)
7165  """
7166  return _IMP_atom.Representation_add_attribute(self, *args)
7167 
7168  def get_value(self, *args):
7169  """
7170  get_value(Representation self, FloatKey a0) -> IMP::Float
7171  get_value(Representation self, IntKey a0) -> IMP::Int
7172  get_value(Representation self, StringKey a0) -> IMP::String
7173  get_value(Representation self, ParticleIndexKey a0) -> Particle
7174  get_value(Representation self, ObjectKey a0) -> Object
7175  """
7176  return _IMP_atom.Representation_get_value(self, *args)
7177 
7178  def set_value(self, *args):
7179  """
7180  set_value(Representation self, FloatKey a0, IMP::Float a1)
7181  set_value(Representation self, IntKey a0, IMP::Int a1)
7182  set_value(Representation self, StringKey a0, IMP::String a1)
7183  set_value(Representation self, ParticleIndexKey a0, Particle a1)
7184  set_value(Representation self, ObjectKey a0, Object a1)
7185  """
7186  return _IMP_atom.Representation_set_value(self, *args)
7187 
7188  def remove_attribute(self, *args):
7189  """
7190  remove_attribute(Representation self, FloatKey a0)
7191  remove_attribute(Representation self, IntKey a0)
7192  remove_attribute(Representation self, StringKey a0)
7193  remove_attribute(Representation self, ParticleIndexKey a0)
7194  remove_attribute(Representation self, ObjectKey a0)
7195  """
7196  return _IMP_atom.Representation_remove_attribute(self, *args)
7197 
7198  def has_attribute(self, *args):
7199  """
7200  has_attribute(Representation self, FloatKey a0) -> bool
7201  has_attribute(Representation self, IntKey a0) -> bool
7202  has_attribute(Representation self, StringKey a0) -> bool
7203  has_attribute(Representation self, ParticleIndexKey a0) -> bool
7204  has_attribute(Representation self, ObjectKey a0) -> bool
7205  """
7206  return _IMP_atom.Representation_has_attribute(self, *args)
7207 
7208  def get_derivative(self, *args):
7209  """get_derivative(Representation self, FloatKey a0) -> double"""
7210  return _IMP_atom.Representation_get_derivative(self, *args)
7211 
7212  def get_name(self):
7213  """get_name(Representation self) -> std::string"""
7214  return _IMP_atom.Representation_get_name(self)
7215 
7216  def clear_caches(self):
7217  """clear_caches(Representation self)"""
7218  return _IMP_atom.Representation_clear_caches(self)
7219 
7220  def set_name(self, *args):
7221  """set_name(Representation self, std::string a0)"""
7222  return _IMP_atom.Representation_set_name(self, *args)
7223 
7224  def set_check_level(self, *args):
7225  """set_check_level(Representation self, IMP::base::CheckLevel a0)"""
7226  return _IMP_atom.Representation_set_check_level(self, *args)
7227 
7228  def add_to_derivative(self, *args):
7229  """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7230  return _IMP_atom.Representation_add_to_derivative(self, *args)
7231 
7232  def set_is_optimized(self, *args):
7233  """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
7234  return _IMP_atom.Representation_set_is_optimized(self, *args)
7235 
7236  def get_is_optimized(self, *args):
7237  """get_is_optimized(Representation self, FloatKey a0) -> bool"""
7238  return _IMP_atom.Representation_get_is_optimized(self, *args)
7239 
7240  def get_check_level(self):
7241  """get_check_level(Representation self) -> IMP::base::CheckLevel"""
7242  return _IMP_atom.Representation_get_check_level(self)
7243 
7244  def __eq__(self, *args):
7245  """
7246  __eq__(Representation self, Representation o) -> bool
7247  __eq__(Representation self, Particle d) -> bool
7248  """
7249  return _IMP_atom.Representation___eq__(self, *args)
7250 
7251  def __ne__(self, *args):
7252  """
7253  __ne__(Representation self, Representation o) -> bool
7254  __ne__(Representation self, Particle d) -> bool
7255  """
7256  return _IMP_atom.Representation___ne__(self, *args)
7257 
7258  def __le__(self, *args):
7259  """
7260  __le__(Representation self, Representation o) -> bool
7261  __le__(Representation self, Particle d) -> bool
7262  """
7263  return _IMP_atom.Representation___le__(self, *args)
7264 
7265  def __lt__(self, *args):
7266  """
7267  __lt__(Representation self, Representation o) -> bool
7268  __lt__(Representation self, Particle d) -> bool
7269  """
7270  return _IMP_atom.Representation___lt__(self, *args)
7271 
7272  def __ge__(self, *args):
7273  """
7274  __ge__(Representation self, Representation o) -> bool
7275  __ge__(Representation self, Particle d) -> bool
7276  """
7277  return _IMP_atom.Representation___ge__(self, *args)
7278 
7279  def __gt__(self, *args):
7280  """
7281  __gt__(Representation self, Representation o) -> bool
7282  __gt__(Representation self, Particle d) -> bool
7283  """
7284  return _IMP_atom.Representation___gt__(self, *args)
7285 
7286  def __str__(self):
7287  """__str__(Representation self) -> std::string"""
7288  return _IMP_atom.Representation___str__(self)
7289 
7290  def __repr__(self):
7291  """__repr__(Representation self) -> std::string"""
7292  return _IMP_atom.Representation___repr__(self)
7293 
7294  __swig_destroy__ = _IMP_atom.delete_Representation
7295  __del__ = lambda self : None;
7296 Representation_swigregister = _IMP_atom.Representation_swigregister
7297 Representation_swigregister(Representation)
7298 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
7299 
7300 def Representation_setup_particle(*args):
7301  """
7302  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Representation
7303  setup_particle(_ParticleAdaptor decorator) -> Representation
7304  setup_particle(Model m, IMP::kernel::ParticleIndex pi, double resolution) -> Representation
7305  Representation_setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
7306  """
7307  return _IMP_atom.Representation_setup_particle(*args)
7308 
7309 def Representation_decorate_particle(*args):
7310  """Representation_decorate_particle(Particle p) -> Representation"""
7311  return _IMP_atom.Representation_decorate_particle(*args)
7312 
7313 def Representation_get_is_setup(*args):
7314  """
7315  get_is_setup(_ParticleAdaptor p) -> bool
7316  Representation_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7317  """
7318  return _IMP_atom.Representation_get_is_setup(*args)
7319 
7320 
7321 def get_resolution(*args):
7322  """
7323  get_resolution(Model m, IMP::kernel::ParticleIndex pi) -> double
7324  get_resolution(Hierarchy h) -> double
7325  """
7326  return _IMP_atom.get_resolution(*args)
7327 class State(Hierarchy):
7328  """Proxy of C++ IMP::atom::State class"""
7329  __swig_setmethods__ = {}
7330  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7331  __setattr__ = lambda self, name, value: _swig_setattr(self, State, name, value)
7332  __swig_getmethods__ = {}
7333  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7334  __getattr__ = lambda self, name: _swig_getattr(self, State, name)
7335  def setup_particle(*args):
7336  """
7337  setup_particle(Model m, IMP::kernel::ParticleIndex pi, unsigned int index) -> State
7338  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
7339  """
7340  return _IMP_atom.State_setup_particle(*args)
7341 
7342  if _newclass:setup_particle = staticmethod(setup_particle)
7343  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7344  def __init__(self, *args):
7345  """
7346  __init__(IMP::atom::State self) -> State
7347  __init__(IMP::atom::State self, Model m, ::IMP::kernel::ParticleIndex id) -> State
7348  __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
7349  """
7350  this = _IMP_atom.new_State(*args)
7351  try: self.this.append(this)
7352  except: self.this = this
7353  def decorate_particle(*args):
7354  """decorate_particle(Particle p) -> State"""
7355  return _IMP_atom.State_decorate_particle(*args)
7356 
7357  if _newclass:decorate_particle = staticmethod(decorate_particle)
7358  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7359  def show(self, *args):
7360  """
7361  show(State self, _ostream out=std::cout)
7362  show(State self)
7363  """
7364  return _IMP_atom.State_show(self, *args)
7365 
7366  def get_is_setup(*args):
7367  """
7368  get_is_setup(_ParticleAdaptor p) -> bool
7369  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7370  """
7371  return _IMP_atom.State_get_is_setup(*args)
7372 
7373  if _newclass:get_is_setup = staticmethod(get_is_setup)
7374  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7375  def get_state_index(self):
7376  """get_state_index(State self) -> unsigned int"""
7377  return _IMP_atom.State_get_state_index(self)
7378 
7379  def add_attribute(self, *args):
7380  """
7381  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
7382  add_attribute(State self, FloatKey a0, IMP::Float a1)
7383  add_attribute(State self, IntKey a0, IMP::Int a1)
7384  add_attribute(State self, StringKey a0, IMP::String a1)
7385  add_attribute(State self, ParticleIndexKey a0, Particle a1)
7386  add_attribute(State self, ObjectKey a0, Object a1)
7387  """
7388  return _IMP_atom.State_add_attribute(self, *args)
7389 
7390  def get_value(self, *args):
7391  """
7392  get_value(State self, FloatKey a0) -> IMP::Float
7393  get_value(State self, IntKey a0) -> IMP::Int
7394  get_value(State self, StringKey a0) -> IMP::String
7395  get_value(State self, ParticleIndexKey a0) -> Particle
7396  get_value(State self, ObjectKey a0) -> Object
7397  """
7398  return _IMP_atom.State_get_value(self, *args)
7399 
7400  def set_value(self, *args):
7401  """
7402  set_value(State self, FloatKey a0, IMP::Float a1)
7403  set_value(State self, IntKey a0, IMP::Int a1)
7404  set_value(State self, StringKey a0, IMP::String a1)
7405  set_value(State self, ParticleIndexKey a0, Particle a1)
7406  set_value(State self, ObjectKey a0, Object a1)
7407  """
7408  return _IMP_atom.State_set_value(self, *args)
7409 
7410  def remove_attribute(self, *args):
7411  """
7412  remove_attribute(State self, FloatKey a0)
7413  remove_attribute(State self, IntKey a0)
7414  remove_attribute(State self, StringKey a0)
7415  remove_attribute(State self, ParticleIndexKey a0)
7416  remove_attribute(State self, ObjectKey a0)
7417  """
7418  return _IMP_atom.State_remove_attribute(self, *args)
7419 
7420  def has_attribute(self, *args):
7421  """
7422  has_attribute(State self, FloatKey a0) -> bool
7423  has_attribute(State self, IntKey a0) -> bool
7424  has_attribute(State self, StringKey a0) -> bool
7425  has_attribute(State self, ParticleIndexKey a0) -> bool
7426  has_attribute(State self, ObjectKey a0) -> bool
7427  """
7428  return _IMP_atom.State_has_attribute(self, *args)
7429 
7430  def get_derivative(self, *args):
7431  """get_derivative(State self, FloatKey a0) -> double"""
7432  return _IMP_atom.State_get_derivative(self, *args)
7433 
7434  def get_name(self):
7435  """get_name(State self) -> std::string"""
7436  return _IMP_atom.State_get_name(self)
7437 
7438  def clear_caches(self):
7439  """clear_caches(State self)"""
7440  return _IMP_atom.State_clear_caches(self)
7441 
7442  def set_name(self, *args):
7443  """set_name(State self, std::string a0)"""
7444  return _IMP_atom.State_set_name(self, *args)
7445 
7446  def set_check_level(self, *args):
7447  """set_check_level(State self, IMP::base::CheckLevel a0)"""
7448  return _IMP_atom.State_set_check_level(self, *args)
7449 
7450  def add_to_derivative(self, *args):
7451  """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7452  return _IMP_atom.State_add_to_derivative(self, *args)
7453 
7454  def set_is_optimized(self, *args):
7455  """set_is_optimized(State self, FloatKey a0, bool a1)"""
7456  return _IMP_atom.State_set_is_optimized(self, *args)
7457 
7458  def get_is_optimized(self, *args):
7459  """get_is_optimized(State self, FloatKey a0) -> bool"""
7460  return _IMP_atom.State_get_is_optimized(self, *args)
7461 
7462  def get_check_level(self):
7463  """get_check_level(State self) -> IMP::base::CheckLevel"""
7464  return _IMP_atom.State_get_check_level(self)
7465 
7466  def __eq__(self, *args):
7467  """
7468  __eq__(State self, State o) -> bool
7469  __eq__(State self, Particle d) -> bool
7470  """
7471  return _IMP_atom.State___eq__(self, *args)
7472 
7473  def __ne__(self, *args):
7474  """
7475  __ne__(State self, State o) -> bool
7476  __ne__(State self, Particle d) -> bool
7477  """
7478  return _IMP_atom.State___ne__(self, *args)
7479 
7480  def __le__(self, *args):
7481  """
7482  __le__(State self, State o) -> bool
7483  __le__(State self, Particle d) -> bool
7484  """
7485  return _IMP_atom.State___le__(self, *args)
7486 
7487  def __lt__(self, *args):
7488  """
7489  __lt__(State self, State o) -> bool
7490  __lt__(State self, Particle d) -> bool
7491  """
7492  return _IMP_atom.State___lt__(self, *args)
7493 
7494  def __ge__(self, *args):
7495  """
7496  __ge__(State self, State o) -> bool
7497  __ge__(State self, Particle d) -> bool
7498  """
7499  return _IMP_atom.State___ge__(self, *args)
7500 
7501  def __gt__(self, *args):
7502  """
7503  __gt__(State self, State o) -> bool
7504  __gt__(State self, Particle d) -> bool
7505  """
7506  return _IMP_atom.State___gt__(self, *args)
7507 
7508  def __str__(self):
7509  """__str__(State self) -> std::string"""
7510  return _IMP_atom.State___str__(self)
7511 
7512  def __repr__(self):
7513  """__repr__(State self) -> std::string"""
7514  return _IMP_atom.State___repr__(self)
7515 
7516  __swig_destroy__ = _IMP_atom.delete_State
7517  __del__ = lambda self : None;
7518 State_swigregister = _IMP_atom.State_swigregister
7519 State_swigregister(State)
7520 
7521 def State_setup_particle(*args):
7522  """
7523  setup_particle(Model m, IMP::kernel::ParticleIndex pi, unsigned int index) -> State
7524  State_setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
7525  """
7526  return _IMP_atom.State_setup_particle(*args)
7527 
7528 def State_decorate_particle(*args):
7529  """State_decorate_particle(Particle p) -> State"""
7530  return _IMP_atom.State_decorate_particle(*args)
7531 
7532 def State_get_is_setup(*args):
7533  """
7534  get_is_setup(_ParticleAdaptor p) -> bool
7535  State_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7536  """
7537  return _IMP_atom.State_get_is_setup(*args)
7538 
7539 
7540 def get_state_index(*args):
7541  """get_state_index(Hierarchy h) -> int"""
7542  return _IMP_atom.get_state_index(*args)
7543 
7544 def get_phi_dihedral_atoms(*args):
7545  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
7546  return _IMP_atom.get_phi_dihedral_atoms(*args)
7547 
7548 def get_psi_dihedral_atoms(*args):
7549  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
7550  return _IMP_atom.get_psi_dihedral_atoms(*args)
7551 class Molecule(Hierarchy):
7552  """Proxy of C++ IMP::atom::Molecule class"""
7553  __swig_setmethods__ = {}
7554  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7555  __setattr__ = lambda self, name, value: _swig_setattr(self, Molecule, name, value)
7556  __swig_getmethods__ = {}
7557  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7558  __getattr__ = lambda self, name: _swig_getattr(self, Molecule, name)
7559  def __init__(self, *args):
7560  """
7561  __init__(IMP::atom::Molecule self) -> Molecule
7562  __init__(IMP::atom::Molecule self, Model m, ::IMP::kernel::ParticleIndex id) -> Molecule
7563  __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
7564  """
7565  this = _IMP_atom.new_Molecule(*args)
7566  try: self.this.append(this)
7567  except: self.this = this
7568  def decorate_particle(*args):
7569  """decorate_particle(Particle p) -> Molecule"""
7570  return _IMP_atom.Molecule_decorate_particle(*args)
7571 
7572  if _newclass:decorate_particle = staticmethod(decorate_particle)
7573  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7574  def show(self, *args):
7575  """
7576  show(Molecule self, _ostream out=std::cout)
7577  show(Molecule self)
7578  """
7579  return _IMP_atom.Molecule_show(self, *args)
7580 
7581  def setup_particle(*args):
7582  """
7583  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Molecule
7584  setup_particle(_ParticleAdaptor decorator) -> Molecule
7585  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Molecule other) -> Molecule
7586  setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
7587  """
7588  return _IMP_atom.Molecule_setup_particle(*args)
7589 
7590  if _newclass:setup_particle = staticmethod(setup_particle)
7591  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7592  def get_is_setup(*args):
7593  """
7594  get_is_setup(_ParticleAdaptor p) -> bool
7595  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7596  """
7597  return _IMP_atom.Molecule_get_is_setup(*args)
7598 
7599  if _newclass:get_is_setup = staticmethod(get_is_setup)
7600  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7601  def add_attribute(self, *args):
7602  """
7603  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
7604  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
7605  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
7606  add_attribute(Molecule self, StringKey a0, IMP::String a1)
7607  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
7608  add_attribute(Molecule self, ObjectKey a0, Object a1)
7609  """
7610  return _IMP_atom.Molecule_add_attribute(self, *args)
7611 
7612  def get_value(self, *args):
7613  """
7614  get_value(Molecule self, FloatKey a0) -> IMP::Float
7615  get_value(Molecule self, IntKey a0) -> IMP::Int
7616  get_value(Molecule self, StringKey a0) -> IMP::String
7617  get_value(Molecule self, ParticleIndexKey a0) -> Particle
7618  get_value(Molecule self, ObjectKey a0) -> Object
7619  """
7620  return _IMP_atom.Molecule_get_value(self, *args)
7621 
7622  def set_value(self, *args):
7623  """
7624  set_value(Molecule self, FloatKey a0, IMP::Float a1)
7625  set_value(Molecule self, IntKey a0, IMP::Int a1)
7626  set_value(Molecule self, StringKey a0, IMP::String a1)
7627  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
7628  set_value(Molecule self, ObjectKey a0, Object a1)
7629  """
7630  return _IMP_atom.Molecule_set_value(self, *args)
7631 
7632  def remove_attribute(self, *args):
7633  """
7634  remove_attribute(Molecule self, FloatKey a0)
7635  remove_attribute(Molecule self, IntKey a0)
7636  remove_attribute(Molecule self, StringKey a0)
7637  remove_attribute(Molecule self, ParticleIndexKey a0)
7638  remove_attribute(Molecule self, ObjectKey a0)
7639  """
7640  return _IMP_atom.Molecule_remove_attribute(self, *args)
7641 
7642  def has_attribute(self, *args):
7643  """
7644  has_attribute(Molecule self, FloatKey a0) -> bool
7645  has_attribute(Molecule self, IntKey a0) -> bool
7646  has_attribute(Molecule self, StringKey a0) -> bool
7647  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
7648  has_attribute(Molecule self, ObjectKey a0) -> bool
7649  """
7650  return _IMP_atom.Molecule_has_attribute(self, *args)
7651 
7652  def get_derivative(self, *args):
7653  """get_derivative(Molecule self, FloatKey a0) -> double"""
7654  return _IMP_atom.Molecule_get_derivative(self, *args)
7655 
7656  def get_name(self):
7657  """get_name(Molecule self) -> std::string"""
7658  return _IMP_atom.Molecule_get_name(self)
7659 
7660  def clear_caches(self):
7661  """clear_caches(Molecule self)"""
7662  return _IMP_atom.Molecule_clear_caches(self)
7663 
7664  def set_name(self, *args):
7665  """set_name(Molecule self, std::string a0)"""
7666  return _IMP_atom.Molecule_set_name(self, *args)
7667 
7668  def set_check_level(self, *args):
7669  """set_check_level(Molecule self, IMP::base::CheckLevel a0)"""
7670  return _IMP_atom.Molecule_set_check_level(self, *args)
7671 
7672  def add_to_derivative(self, *args):
7673  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7674  return _IMP_atom.Molecule_add_to_derivative(self, *args)
7675 
7676  def set_is_optimized(self, *args):
7677  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
7678  return _IMP_atom.Molecule_set_is_optimized(self, *args)
7679 
7680  def get_is_optimized(self, *args):
7681  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
7682  return _IMP_atom.Molecule_get_is_optimized(self, *args)
7683 
7684  def get_check_level(self):
7685  """get_check_level(Molecule self) -> IMP::base::CheckLevel"""
7686  return _IMP_atom.Molecule_get_check_level(self)
7687 
7688  def __eq__(self, *args):
7689  """
7690  __eq__(Molecule self, Molecule o) -> bool
7691  __eq__(Molecule self, Particle d) -> bool
7692  """
7693  return _IMP_atom.Molecule___eq__(self, *args)
7694 
7695  def __ne__(self, *args):
7696  """
7697  __ne__(Molecule self, Molecule o) -> bool
7698  __ne__(Molecule self, Particle d) -> bool
7699  """
7700  return _IMP_atom.Molecule___ne__(self, *args)
7701 
7702  def __le__(self, *args):
7703  """
7704  __le__(Molecule self, Molecule o) -> bool
7705  __le__(Molecule self, Particle d) -> bool
7706  """
7707  return _IMP_atom.Molecule___le__(self, *args)
7708 
7709  def __lt__(self, *args):
7710  """
7711  __lt__(Molecule self, Molecule o) -> bool
7712  __lt__(Molecule self, Particle d) -> bool
7713  """
7714  return _IMP_atom.Molecule___lt__(self, *args)
7715 
7716  def __ge__(self, *args):
7717  """
7718  __ge__(Molecule self, Molecule o) -> bool
7719  __ge__(Molecule self, Particle d) -> bool
7720  """
7721  return _IMP_atom.Molecule___ge__(self, *args)
7722 
7723  def __gt__(self, *args):
7724  """
7725  __gt__(Molecule self, Molecule o) -> bool
7726  __gt__(Molecule self, Particle d) -> bool
7727  """
7728  return _IMP_atom.Molecule___gt__(self, *args)
7729 
7730  def __str__(self):
7731  """__str__(Molecule self) -> std::string"""
7732  return _IMP_atom.Molecule___str__(self)
7733 
7734  def __repr__(self):
7735  """__repr__(Molecule self) -> std::string"""
7736  return _IMP_atom.Molecule___repr__(self)
7737 
7738  __swig_destroy__ = _IMP_atom.delete_Molecule
7739  __del__ = lambda self : None;
7740 Molecule_swigregister = _IMP_atom.Molecule_swigregister
7741 Molecule_swigregister(Molecule)
7742 
7743 def Molecule_decorate_particle(*args):
7744  """Molecule_decorate_particle(Particle p) -> Molecule"""
7745  return _IMP_atom.Molecule_decorate_particle(*args)
7746 
7747 def Molecule_setup_particle(*args):
7748  """
7749  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Molecule
7750  setup_particle(_ParticleAdaptor decorator) -> Molecule
7751  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Molecule other) -> Molecule
7752  Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
7753  """
7754  return _IMP_atom.Molecule_setup_particle(*args)
7755 
7756 def Molecule_get_is_setup(*args):
7757  """
7758  get_is_setup(_ParticleAdaptor p) -> bool
7759  Molecule_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7760  """
7761  return _IMP_atom.Molecule_get_is_setup(*args)
7762 
7763 
7764 def get_molecule_name(*args):
7765  """get_molecule_name(Hierarchy h) -> std::string"""
7766  return _IMP_atom.get_molecule_name(*args)
7767 class Copy(Molecule):
7768  """Proxy of C++ IMP::atom::Copy class"""
7769  __swig_setmethods__ = {}
7770  for _s in [Molecule]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7771  __setattr__ = lambda self, name, value: _swig_setattr(self, Copy, name, value)
7772  __swig_getmethods__ = {}
7773  for _s in [Molecule]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7774  __getattr__ = lambda self, name: _swig_getattr(self, Copy, name)
7775  def get_copy_index_key():
7776  """get_copy_index_key() -> IntKey"""
7777  return _IMP_atom.Copy_get_copy_index_key()
7778 
7779  if _newclass:get_copy_index_key = staticmethod(get_copy_index_key)
7780  __swig_getmethods__["get_copy_index_key"] = lambda x: get_copy_index_key
7781  def __init__(self, *args):
7782  """
7783  __init__(IMP::atom::Copy self) -> Copy
7784  __init__(IMP::atom::Copy self, Model m, ::IMP::kernel::ParticleIndex id) -> Copy
7785  __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
7786  """
7787  this = _IMP_atom.new_Copy(*args)
7788  try: self.this.append(this)
7789  except: self.this = this
7790  def decorate_particle(*args):
7791  """decorate_particle(Particle p) -> Copy"""
7792  return _IMP_atom.Copy_decorate_particle(*args)
7793 
7794  if _newclass:decorate_particle = staticmethod(decorate_particle)
7795  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7796  def show(self, *args):
7797  """
7798  show(Copy self, _ostream out=std::cout)
7799  show(Copy self)
7800  """
7801  return _IMP_atom.Copy_show(self, *args)
7802 
7803  def setup_particle(*args):
7804  """
7805  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int number) -> Copy
7806  setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
7807  """
7808  return _IMP_atom.Copy_setup_particle(*args)
7809 
7810  if _newclass:setup_particle = staticmethod(setup_particle)
7811  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7812  def get_is_setup(*args):
7813  """
7814  get_is_setup(_ParticleAdaptor p) -> bool
7815  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7816  """
7817  return _IMP_atom.Copy_get_is_setup(*args)
7818 
7819  if _newclass:get_is_setup = staticmethod(get_is_setup)
7820  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7821  def get_copy_index(self):
7822  """get_copy_index(Copy self) -> int"""
7823  return _IMP_atom.Copy_get_copy_index(self)
7824 
7825  def add_attribute(self, *args):
7826  """
7827  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
7828  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
7829  add_attribute(Copy self, IntKey a0, IMP::Int a1)
7830  add_attribute(Copy self, StringKey a0, IMP::String a1)
7831  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
7832  add_attribute(Copy self, ObjectKey a0, Object a1)
7833  """
7834  return _IMP_atom.Copy_add_attribute(self, *args)
7835 
7836  def get_value(self, *args):
7837  """
7838  get_value(Copy self, FloatKey a0) -> IMP::Float
7839  get_value(Copy self, IntKey a0) -> IMP::Int
7840  get_value(Copy self, StringKey a0) -> IMP::String
7841  get_value(Copy self, ParticleIndexKey a0) -> Particle
7842  get_value(Copy self, ObjectKey a0) -> Object
7843  """
7844  return _IMP_atom.Copy_get_value(self, *args)
7845 
7846  def set_value(self, *args):
7847  """
7848  set_value(Copy self, FloatKey a0, IMP::Float a1)
7849  set_value(Copy self, IntKey a0, IMP::Int a1)
7850  set_value(Copy self, StringKey a0, IMP::String a1)
7851  set_value(Copy self, ParticleIndexKey a0, Particle a1)
7852  set_value(Copy self, ObjectKey a0, Object a1)
7853  """
7854  return _IMP_atom.Copy_set_value(self, *args)
7855 
7856  def remove_attribute(self, *args):
7857  """
7858  remove_attribute(Copy self, FloatKey a0)
7859  remove_attribute(Copy self, IntKey a0)
7860  remove_attribute(Copy self, StringKey a0)
7861  remove_attribute(Copy self, ParticleIndexKey a0)
7862  remove_attribute(Copy self, ObjectKey a0)
7863  """
7864  return _IMP_atom.Copy_remove_attribute(self, *args)
7865 
7866  def has_attribute(self, *args):
7867  """
7868  has_attribute(Copy self, FloatKey a0) -> bool
7869  has_attribute(Copy self, IntKey a0) -> bool
7870  has_attribute(Copy self, StringKey a0) -> bool
7871  has_attribute(Copy self, ParticleIndexKey a0) -> bool
7872  has_attribute(Copy self, ObjectKey a0) -> bool
7873  """
7874  return _IMP_atom.Copy_has_attribute(self, *args)
7875 
7876  def get_derivative(self, *args):
7877  """get_derivative(Copy self, FloatKey a0) -> double"""
7878  return _IMP_atom.Copy_get_derivative(self, *args)
7879 
7880  def get_name(self):
7881  """get_name(Copy self) -> std::string"""
7882  return _IMP_atom.Copy_get_name(self)
7883 
7884  def clear_caches(self):
7885  """clear_caches(Copy self)"""
7886  return _IMP_atom.Copy_clear_caches(self)
7887 
7888  def set_name(self, *args):
7889  """set_name(Copy self, std::string a0)"""
7890  return _IMP_atom.Copy_set_name(self, *args)
7891 
7892  def set_check_level(self, *args):
7893  """set_check_level(Copy self, IMP::base::CheckLevel a0)"""
7894  return _IMP_atom.Copy_set_check_level(self, *args)
7895 
7896  def add_to_derivative(self, *args):
7897  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7898  return _IMP_atom.Copy_add_to_derivative(self, *args)
7899 
7900  def set_is_optimized(self, *args):
7901  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
7902  return _IMP_atom.Copy_set_is_optimized(self, *args)
7903 
7904  def get_is_optimized(self, *args):
7905  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
7906  return _IMP_atom.Copy_get_is_optimized(self, *args)
7907 
7908  def get_check_level(self):
7909  """get_check_level(Copy self) -> IMP::base::CheckLevel"""
7910  return _IMP_atom.Copy_get_check_level(self)
7911 
7912  def __eq__(self, *args):
7913  """
7914  __eq__(Copy self, Copy o) -> bool
7915  __eq__(Copy self, Particle d) -> bool
7916  """
7917  return _IMP_atom.Copy___eq__(self, *args)
7918 
7919  def __ne__(self, *args):
7920  """
7921  __ne__(Copy self, Copy o) -> bool
7922  __ne__(Copy self, Particle d) -> bool
7923  """
7924  return _IMP_atom.Copy___ne__(self, *args)
7925 
7926  def __le__(self, *args):
7927  """
7928  __le__(Copy self, Copy o) -> bool
7929  __le__(Copy self, Particle d) -> bool
7930  """
7931  return _IMP_atom.Copy___le__(self, *args)
7932 
7933  def __lt__(self, *args):
7934  """
7935  __lt__(Copy self, Copy o) -> bool
7936  __lt__(Copy self, Particle d) -> bool
7937  """
7938  return _IMP_atom.Copy___lt__(self, *args)
7939 
7940  def __ge__(self, *args):
7941  """
7942  __ge__(Copy self, Copy o) -> bool
7943  __ge__(Copy self, Particle d) -> bool
7944  """
7945  return _IMP_atom.Copy___ge__(self, *args)
7946 
7947  def __gt__(self, *args):
7948  """
7949  __gt__(Copy self, Copy o) -> bool
7950  __gt__(Copy self, Particle d) -> bool
7951  """
7952  return _IMP_atom.Copy___gt__(self, *args)
7953 
7954  def __str__(self):
7955  """__str__(Copy self) -> std::string"""
7956  return _IMP_atom.Copy___str__(self)
7957 
7958  def __repr__(self):
7959  """__repr__(Copy self) -> std::string"""
7960  return _IMP_atom.Copy___repr__(self)
7961 
7962  __swig_destroy__ = _IMP_atom.delete_Copy
7963  __del__ = lambda self : None;
7964 Copy_swigregister = _IMP_atom.Copy_swigregister
7965 Copy_swigregister(Copy)
7966 
7967 def Copy_get_copy_index_key():
7968  """Copy_get_copy_index_key() -> IntKey"""
7969  return _IMP_atom.Copy_get_copy_index_key()
7970 
7971 def Copy_decorate_particle(*args):
7972  """Copy_decorate_particle(Particle p) -> Copy"""
7973  return _IMP_atom.Copy_decorate_particle(*args)
7974 
7975 def Copy_setup_particle(*args):
7976  """
7977  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int number) -> Copy
7978  Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
7979  """
7980  return _IMP_atom.Copy_setup_particle(*args)
7981 
7982 def Copy_get_is_setup(*args):
7983  """
7984  get_is_setup(_ParticleAdaptor p) -> bool
7985  Copy_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7986  """
7987  return _IMP_atom.Copy_get_is_setup(*args)
7988 
7989 
7990 def __lshift__(*args):
7991  """
7992  __lshift__(_ostream out, Bonded n) -> _ostream
7993  __lshift__(_ostream out, Bond n) -> _ostream
7994  __lshift__(_ostream out, Hierarchy n) -> _ostream
7995  __lshift__(_ostream out, Angle n) -> _ostream
7996  __lshift__(_ostream out, Dihedral n) -> _ostream
7997  __lshift__(_ostream out, Diffusion n) -> _ostream
7998  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
7999  __lshift__(_ostream out, Chain n) -> _ostream
8000  __lshift__(_ostream out, Charged n) -> _ostream
8001  __lshift__(_ostream out, Domain n) -> _ostream
8002  __lshift__(_ostream out, LennardJones n) -> _ostream
8003  __lshift__(_ostream out, Fragment n) -> _ostream
8004  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
8005  __lshift__(_ostream out, Atom n) -> _ostream
8006  __lshift__(_ostream out, Residue n) -> _ostream
8007  __lshift__(_ostream out, Representation n) -> _ostream
8008  __lshift__(_ostream out, State n) -> _ostream
8009  __lshift__(_ostream out, Molecule n) -> _ostream
8010  __lshift__(_ostream out, Copy n) -> _ostream
8011  """
8012  return _IMP_atom.__lshift__(*args)
8013 
8014 def get_copy_index(*args):
8015  """get_copy_index(Hierarchy h) -> int"""
8016  return _IMP_atom.get_copy_index(*args)
8017 class Selection(IMP.kernel._ParticleIndexesAdaptor):
8018  """Proxy of C++ IMP::atom::Selection class"""
8019  __swig_setmethods__ = {}
8020  for _s in [IMP.kernel._ParticleIndexesAdaptor]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8021  __setattr__ = lambda self, name, value: _swig_setattr(self, Selection, name, value)
8022  __swig_getmethods__ = {}
8023  for _s in [IMP.kernel._ParticleIndexesAdaptor]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8024  __getattr__ = lambda self, name: _swig_getattr(self, Selection, name)
8025  NONE = _IMP_atom.Selection_NONE
8026  C = _IMP_atom.Selection_C
8027  N = _IMP_atom.Selection_N
8028  def __init__(self, *args):
8029  """
8030  __init__(IMP::atom::Selection self) -> Selection
8031  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
8032  __init__(IMP::atom::Selection self, Particle h) -> Selection
8033  __init__(IMP::atom::Selection self, Model m, IMP::kernel::ParticleIndexes const & pis) -> Selection
8034  __init__(IMP::atom::Selection self, IMP::kernel::ParticlesTemp const & h) -> Selection
8035  """
8036  this = _IMP_atom.new_Selection(*args)
8037  try: self.this.append(this)
8038  except: self.this = this
8039  def get_hierarchies(self):
8040  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
8041  return _IMP_atom.Selection_get_hierarchies(self)
8042 
8043  def set_molecules(self, *args):
8044  """set_molecules(Selection self, IMP::Strings mols)"""
8045  return _IMP_atom.Selection_set_molecules(self, *args)
8046 
8047  def set_resolution(self, *args):
8048  """set_resolution(Selection self, double r)"""
8049  return _IMP_atom.Selection_set_resolution(self, *args)
8050 
8051  def set_state_index(self, *args):
8052  """set_state_index(Selection self, int state)"""
8053  return _IMP_atom.Selection_set_state_index(self, *args)
8054 
8055  def set_state_indexes(self, *args):
8056  """set_state_indexes(Selection self, IMP::Ints states)"""
8057  return _IMP_atom.Selection_set_state_indexes(self, *args)
8058 
8059  def set_terminus(self, *args):
8060  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
8061  return _IMP_atom.Selection_set_terminus(self, *args)
8062 
8063  def set_chain_ids(self, *args):
8064  """set_chain_ids(Selection self, IMP::Strings chains)"""
8065  return _IMP_atom.Selection_set_chain_ids(self, *args)
8066 
8067  def set_chains(self, *args):
8068  """set_chains(Selection self, IMP::Strings chains)"""
8069  return _IMP_atom.Selection_set_chains(self, *args)
8070 
8071  def set_residue_indexes(self, *args):
8072  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
8073  return _IMP_atom.Selection_set_residue_indexes(self, *args)
8074 
8075  def set_atom_types(self, *args):
8076  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
8077  return _IMP_atom.Selection_set_atom_types(self, *args)
8078 
8079  def set_residue_types(self, *args):
8080  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
8081  return _IMP_atom.Selection_set_residue_types(self, *args)
8082 
8083  def set_domains(self, *args):
8084  """set_domains(Selection self, IMP::Strings names)"""
8085  return _IMP_atom.Selection_set_domains(self, *args)
8086 
8087  def set_molecule(self, *args):
8088  """set_molecule(Selection self, std::string mol)"""
8089  return _IMP_atom.Selection_set_molecule(self, *args)
8090 
8091  def set_chain_id(self, *args):
8092  """set_chain_id(Selection self, std::string c)"""
8093  return _IMP_atom.Selection_set_chain_id(self, *args)
8094 
8095  def set_chain(self, *args):
8096  """set_chain(Selection self, std::string c)"""
8097  return _IMP_atom.Selection_set_chain(self, *args)
8098 
8099  def set_residue_index(self, *args):
8100  """set_residue_index(Selection self, int i)"""
8101  return _IMP_atom.Selection_set_residue_index(self, *args)
8102 
8103  def set_atom_type(self, *args):
8104  """set_atom_type(Selection self, AtomType types)"""
8105  return _IMP_atom.Selection_set_atom_type(self, *args)
8106 
8107  def set_residue_type(self, *args):
8108  """set_residue_type(Selection self, ResidueType type)"""
8109  return _IMP_atom.Selection_set_residue_type(self, *args)
8110 
8111  def set_domain(self, *args):
8112  """set_domain(Selection self, std::string name)"""
8113  return _IMP_atom.Selection_set_domain(self, *args)
8114 
8115  def set_copy_index(self, *args):
8116  """set_copy_index(Selection self, unsigned int copy)"""
8117  return _IMP_atom.Selection_set_copy_index(self, *args)
8118 
8119  def set_copy_indexes(self, *args):
8120  """set_copy_indexes(Selection self, IMP::Ints copies)"""
8121  return _IMP_atom.Selection_set_copy_indexes(self, *args)
8122 
8123  def set_particle_type(self, *args):
8124  """set_particle_type(Selection self, ParticleType t)"""
8125  return _IMP_atom.Selection_set_particle_type(self, *args)
8126 
8127  def set_particle_types(self, *args):
8128  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
8129  return _IMP_atom.Selection_set_particle_types(self, *args)
8130 
8131  def set_hierarchy_types(self, *args):
8132  """set_hierarchy_types(Selection self, IMP::Ints types)"""
8133  return _IMP_atom.Selection_set_hierarchy_types(self, *args)
8134 
8135  def get_selected_particles(self):
8136  """get_selected_particles(Selection self) -> IMP::kernel::ParticlesTemp"""
8137  return _IMP_atom.Selection_get_selected_particles(self)
8138 
8139  def get_selected_particle_indexes(self):
8140  """get_selected_particle_indexes(Selection self) -> IMP::kernel::ParticleIndexes"""
8141  return _IMP_atom.Selection_get_selected_particle_indexes(self)
8142 
8143  def show(self, *args):
8144  """
8145  show(Selection self, _ostream out=std::cout)
8146  show(Selection self)
8147  """
8148  return _IMP_atom.Selection_show(self, *args)
8149 
8150  def __str__(self):
8151  """__str__(Selection self) -> std::string"""
8152  return _IMP_atom.Selection___str__(self)
8153 
8154  def __repr__(self):
8155  """__repr__(Selection self) -> std::string"""
8156  return _IMP_atom.Selection___repr__(self)
8157 
8158  def __init__(self, hierarchy=None,
8159  hierarchies=None, **params):
8160  if hierarchy and hierarchies:
8161  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
8162  if hierarchy:
8163  this = _IMP_atom.new_Selection(hierarchy)
8164  try: self.this.append(this)
8165  except: self.this = this
8166  else:
8167  this = _IMP_atom.new_Selection(hierarchies)
8168  try: self.this.append(this)
8169  except: self.this = this
8170  for k in params.keys():
8171  eval("self.set_%s(params[k])"%k)
8172 
8173  __swig_destroy__ = _IMP_atom.delete_Selection
8174  __del__ = lambda self : None;
8175 Selection_swigregister = _IMP_atom.Selection_swigregister
8176 Selection_swigregister(Selection)
8177 
8178 
8179 def create_distance_restraint(*args):
8180  """
8181  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint
8182  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
8183  """
8184  return _IMP_atom.create_distance_restraint(*args)
8185 
8187  """
8188  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
8189  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
8190  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
8191  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
8192  """
8193  return _IMP_atom.create_connectivity_restraint(*args)
8194 
8196  """
8197  create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
8198  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
8199  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
8200  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
8201  """
8202  return _IMP_atom.create_internal_connectivity_restraint(*args)
8203 
8204 def create_cover(*args):
8205  """
8206  create_cover(Selection s, std::string name=std::string()) -> XYZR
8207  create_cover(Selection s) -> XYZR
8208  """
8209  return _IMP_atom.create_cover(*args)
8210 
8211 def get_mass(*args):
8212  """get_mass(Selection s) -> double"""
8213  return _IMP_atom.get_mass(*args)
8214 
8215 def get_volume(*args):
8216  """get_volume(Selection s) -> double"""
8217  return _IMP_atom.get_volume(*args)
8218 
8219 def get_surface_area(*args):
8220  """get_surface_area(Selection s) -> double"""
8221  return _IMP_atom.get_surface_area(*args)
8222 
8223 def get_leaves(*args):
8224  """
8225  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
8226  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
8227  get_leaves(Selection h) -> IMP::atom::Hierarchies
8228  """
8229  return _IMP_atom.get_leaves(*args)
8230 class SelectionGeometry(IMP.display.Geometry):
8231  """Proxy of C++ IMP::atom::SelectionGeometry class"""
8232  __swig_setmethods__ = {}
8233  for _s in [IMP.display.Geometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8234  __setattr__ = lambda self, name, value: _swig_setattr(self, SelectionGeometry, name, value)
8235  __swig_getmethods__ = {}
8236  for _s in [IMP.display.Geometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8237  __getattr__ = lambda self, name: _swig_getattr(self, SelectionGeometry, name)
8238  def __init__(self, *args):
8239  """
8240  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry
8241  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
8242  """
8243  this = _IMP_atom.new_SelectionGeometry(*args)
8244  try: self.this.append(this)
8245  except: self.this = this
8246  def get_version_info(self):
8247  """get_version_info(SelectionGeometry self) -> VersionInfo"""
8248  return _IMP_atom.SelectionGeometry_get_version_info(self)
8249 
8250  def __str__(self):
8251  """__str__(SelectionGeometry self) -> std::string"""
8252  return _IMP_atom.SelectionGeometry___str__(self)
8253 
8254  def __repr__(self):
8255  """__repr__(SelectionGeometry self) -> std::string"""
8256  return _IMP_atom.SelectionGeometry___repr__(self)
8257 
8258  def get_from(o):
8259  return _object_cast_to_SelectionGeometry(o)
8260  get_from = staticmethod(get_from)
8261 
8262 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
8263 SelectionGeometry_swigregister(SelectionGeometry)
8264 
8265 
8266 def get_rmsd_transforming_first(*args):
8267  """
8268  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
8269  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
8270  """
8271  return _IMP_atom.get_rmsd_transforming_first(*args)
8272 
8273 def get_rmsd(*args):
8274  """
8275  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
8276  get_rmsd(Selection s0, Selection s1) -> double
8277  get_rmsd(Selection s0, Selection s1, Transformation3D tr_for_second) -> double
8278  get_rmsd(IMP::algebra::Vector3Ds const & s0, IMP::algebra::Vector3Ds const & s1, Transformation3D tr_for_second) -> double
8279  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1, Transformation3D tr_for_second) -> double
8280  """
8281  return _IMP_atom.get_rmsd(*args)
8282 
8283 def get_placement_score(*args):
8284  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
8285  return _IMP_atom.get_placement_score(*args)
8286 
8288  """
8289  get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
8290  IMP::core::XYZs const & mdl2) -> IMP::FloatPair
8291  """
8292  return _IMP_atom.get_component_placement_score(*args)
8293 
8294 def get_pairwise_rmsd_score(*args):
8295  """
8296  get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
8297  IMP::core::XYZs const & mdl2) -> double
8298  """
8299  return _IMP_atom.get_pairwise_rmsd_score(*args)
8300 
8301 def get_radius_of_gyration(*args):
8302  """
8303  get_radius_of_gyration(Selection s) -> double
8304  get_radius_of_gyration(IMP::kernel::ParticlesTemp const & ps) -> double
8305  """
8306  return _IMP_atom.get_radius_of_gyration(*args)
8307 class ForceFieldParameters(IMP.base.Object):
8308  """Proxy of C++ IMP::atom::ForceFieldParameters class"""
8309  __swig_setmethods__ = {}
8310  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8311  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceFieldParameters, name, value)
8312  __swig_getmethods__ = {}
8313  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8314  __getattr__ = lambda self, name: _swig_getattr(self, ForceFieldParameters, name)
8315  def __init__(self):
8316  """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
8317  this = _IMP_atom.new_ForceFieldParameters()
8318  try: self.this.append(this)
8319  except: self.this = this
8320  def get_radius(self, *args):
8321  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
8322  return _IMP_atom.ForceFieldParameters_get_radius(self, *args)
8323 
8324  def get_epsilon(self, *args):
8325  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
8326  return _IMP_atom.ForceFieldParameters_get_epsilon(self, *args)
8327 
8328  def add_radii(self, *args):
8329  """
8330  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius"))
8331  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
8332  add_radii(ForceFieldParameters self, Hierarchy mhd)
8333  """
8334  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
8335 
8336  def add_well_depths(self, *args):
8337  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
8338  return _IMP_atom.ForceFieldParameters_add_well_depths(self, *args)
8339 
8340  def add_bonds(self, *args):
8341  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
8342  return _IMP_atom.ForceFieldParameters_add_bonds(self, *args)
8343 
8344  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
8345  __del__ = lambda self : None;
8346  def __str__(self):
8347  """__str__(ForceFieldParameters self) -> std::string"""
8348  return _IMP_atom.ForceFieldParameters___str__(self)
8349 
8350  def __repr__(self):
8351  """__repr__(ForceFieldParameters self) -> std::string"""
8352  return _IMP_atom.ForceFieldParameters___repr__(self)
8353 
8354  def get_from(o):
8355  return _object_cast_to_ForceFieldParameters(o)
8356  get_from = staticmethod(get_from)
8357 
8358 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
8359 ForceFieldParameters_swigregister(ForceFieldParameters)
8360 
8361 class CHARMMAtomTopology(_object):
8362  """Proxy of C++ IMP::atom::CHARMMAtomTopology class"""
8363  __swig_setmethods__ = {}
8364  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtomTopology, name, value)
8365  __swig_getmethods__ = {}
8366  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtomTopology, name)
8367  def __init__(self, *args):
8368  """
8369  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
8370  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
8371  """
8372  this = _IMP_atom.new_CHARMMAtomTopology(*args)
8373  try: self.this.append(this)
8374  except: self.this = this
8375  def get_name(self):
8376  """get_name(CHARMMAtomTopology self) -> std::string"""
8377  return _IMP_atom.CHARMMAtomTopology_get_name(self)
8378 
8379  def get_charmm_type(self):
8380  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
8381  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
8382 
8383  def get_charge(self):
8384  """get_charge(CHARMMAtomTopology self) -> double"""
8385  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
8386 
8387  def set_charmm_type(self, *args):
8388  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
8389  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, *args)
8390 
8391  def set_charge(self, *args):
8392  """set_charge(CHARMMAtomTopology self, double charge)"""
8393  return _IMP_atom.CHARMMAtomTopology_set_charge(self, *args)
8394 
8395  def show(self, *args):
8396  """
8397  show(CHARMMAtomTopology self, _ostream out=std::cout)
8398  show(CHARMMAtomTopology self)
8399  """
8400  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
8401 
8402  def __str__(self):
8403  """__str__(CHARMMAtomTopology self) -> std::string"""
8404  return _IMP_atom.CHARMMAtomTopology___str__(self)
8405 
8406  def __repr__(self):
8407  """__repr__(CHARMMAtomTopology self) -> std::string"""
8408  return _IMP_atom.CHARMMAtomTopology___repr__(self)
8409 
8410  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
8411  __del__ = lambda self : None;
8412 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
8413 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
8414 
8415 class CHARMMBondEndpoint(_object):
8416  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class"""
8417  __swig_setmethods__ = {}
8418  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondEndpoint, name, value)
8419  __swig_getmethods__ = {}
8420  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondEndpoint, name)
8421  def __init__(self, *args):
8422  """
8423  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
8424  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
8425  """
8426  this = _IMP_atom.new_CHARMMBondEndpoint(*args)
8427  try: self.this.append(this)
8428  except: self.this = this
8429  def get_atom_name(self):
8430  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
8431  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
8432 
8433  def get_atom(self, *args):
8434  """
8435  get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue,
8436  std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom
8437  """
8438  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, *args)
8439 
8440  def show(self, *args):
8441  """
8442  show(CHARMMBondEndpoint self, _ostream out=std::cout)
8443  show(CHARMMBondEndpoint self)
8444  """
8445  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
8446 
8447  def __str__(self):
8448  """__str__(CHARMMBondEndpoint self) -> std::string"""
8449  return _IMP_atom.CHARMMBondEndpoint___str__(self)
8450 
8451  def __repr__(self):
8452  """__repr__(CHARMMBondEndpoint self) -> std::string"""
8453  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
8454 
8455  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
8456  __del__ = lambda self : None;
8457 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
8458 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
8459 
8460 class CHARMMDihedral(_object):
8461  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class"""
8462  __swig_setmethods__ = {}
8463  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedral, name, value)
8464  __swig_getmethods__ = {}
8465  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedral, name)
8466  __repr__ = _swig_repr
8467  def __init__(self, *args):
8468  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
8469  this = _IMP_atom.new_CHARMMDihedral(*args)
8470  try: self.this.append(this)
8471  except: self.this = this
8472  def get_endpoint(self, *args):
8473  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
8474  return _IMP_atom.CHARMMDihedral_get_endpoint(self, *args)
8475 
8476  def get_contains_atom(self, *args):
8477  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
8478  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, *args)
8479 
8480  def show(self, *args):
8481  """
8482  show(CHARMMDihedral self, _ostream out=std::cout)
8483  show(CHARMMDihedral self)
8484  """
8485  return _IMP_atom.CHARMMDihedral_show(self, *args)
8486 
8487  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
8488  __del__ = lambda self : None;
8489 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
8490 CHARMMDihedral_swigregister(CHARMMDihedral)
8491 
8492 class CHARMMInternalCoordinate(CHARMMDihedral):
8493  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class"""
8494  __swig_setmethods__ = {}
8495  for _s in [CHARMMDihedral]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8496  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMInternalCoordinate, name, value)
8497  __swig_getmethods__ = {}
8498  for _s in [CHARMMDihedral]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8499  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMInternalCoordinate, name)
8500  def __init__(self, *args):
8501  """
8502  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral,
8503  float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
8504  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::base::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance,
8505  float first_angle, float dihedral, float second_angle, float second_distance,
8506  bool improper) -> CHARMMInternalCoordinate
8507  """
8508  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
8509  try: self.this.append(this)
8510  except: self.this = this
8511  def get_first_distance(self):
8512  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
8513  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
8514 
8515  def get_second_distance(self):
8516  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
8517  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
8518 
8519  def get_first_angle(self):
8520  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
8521  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
8522 
8523  def get_second_angle(self):
8524  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
8525  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
8526 
8527  def get_dihedral(self):
8528  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
8529  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
8530 
8531  def get_improper(self):
8532  """get_improper(CHARMMInternalCoordinate self) -> bool"""
8533  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
8534 
8535  def show(self, *args):
8536  """
8537  show(CHARMMInternalCoordinate self, _ostream out=std::cout)
8538  show(CHARMMInternalCoordinate self)
8539  """
8540  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
8541 
8542  def __str__(self):
8543  """__str__(CHARMMInternalCoordinate self) -> std::string"""
8544  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
8545 
8546  def __repr__(self):
8547  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
8548  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
8549 
8550  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
8551  __del__ = lambda self : None;
8552 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
8553 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
8554 
8555 class CHARMMResidueTopologyBase(IMP.base.Object):
8556  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class"""
8557  __swig_setmethods__ = {}
8558  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8559  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopologyBase, name, value)
8560  __swig_getmethods__ = {}
8561  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8562  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopologyBase, name)
8563  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
8564  def get_type(self):
8565  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
8566  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
8567 
8568  def get_number_of_atoms(self):
8569  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
8570  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
8571 
8572  def add_atom(self, *args):
8573  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
8574  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, *args)
8575 
8576  def get_atom(self, *args):
8577  """
8578  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
8579  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
8580  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
8581  """
8582  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
8583 
8584  def get_number_of_bonds(self):
8585  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
8586  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
8587 
8588  def add_bond(self, *args):
8589  """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
8590  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, *args)
8591 
8592  def get_number_of_angles(self):
8593  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
8594  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
8595 
8596  def add_angle(self, *args):
8597  """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
8598  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, *args)
8599 
8600  def get_number_of_dihedrals(self):
8601  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
8602  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
8603 
8604  def add_dihedral(self, *args):
8605  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8606  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, *args)
8607 
8608  def get_number_of_impropers(self):
8609  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
8610  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
8611 
8612  def add_improper(self, *args):
8613  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8614  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, *args)
8615 
8616  def get_number_of_internal_coordinates(self):
8617  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
8618  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
8619 
8620  def add_internal_coordinate(self, *args):
8621  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
8622  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, *args)
8623 
8624  def get_internal_coordinate(self, *args):
8625  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
8626  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, *args)
8627 
8628  def get_bond(self, *args):
8629  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
8630  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, *args)
8631 
8632  def get_angle(self, *args):
8633  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
8634  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, *args)
8635 
8636  def get_dihedral(self, *args):
8637  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8638  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, *args)
8639 
8640  def get_improper(self, *args):
8641  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8642  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, *args)
8643 
8644  def get_version_info(self):
8645  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
8646  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
8647 
8648  def __str__(self):
8649  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
8650  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
8651 
8652  def __repr__(self):
8653  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
8654  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
8655 
8656  def get_from(o):
8657  return _object_cast_to_CHARMMResidueTopologyBase(o)
8658  get_from = staticmethod(get_from)
8659 
8660 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
8661 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
8662 
8663 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
8664  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class"""
8665  __swig_setmethods__ = {}
8666  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8667  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMIdealResidueTopology, name, value)
8668  __swig_getmethods__ = {}
8669  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8670  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMIdealResidueTopology, name)
8671  def __init__(self, *args):
8672  """
8673  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
8674  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
8675  """
8676  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
8677  try: self.this.append(this)
8678  except: self.this = this
8679  def remove_atom(self, *args):
8680  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
8681  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, *args)
8682 
8683  def set_default_first_patch(self, *args):
8684  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8685  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, *args)
8686 
8687  def set_default_last_patch(self, *args):
8688  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8689  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, *args)
8690 
8691  def get_default_first_patch(self):
8692  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
8693  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
8694 
8695  def get_default_last_patch(self):
8696  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
8697  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
8698 
8699  def __str__(self):
8700  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
8701  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
8702 
8703  def __repr__(self):
8704  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
8705  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
8706 
8707  def get_from(o):
8708  return _object_cast_to_CHARMMIdealResidueTopology(o)
8709  get_from = staticmethod(get_from)
8710 
8711 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
8712 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
8713 
8714 class CHARMMPatch(CHARMMResidueTopologyBase):
8715  """Proxy of C++ IMP::atom::CHARMMPatch class"""
8716  __swig_setmethods__ = {}
8717  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8718  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMPatch, name, value)
8719  __swig_getmethods__ = {}
8720  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8721  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMPatch, name)
8722  def __init__(self, *args):
8723  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
8724  this = _IMP_atom.new_CHARMMPatch(*args)
8725  try: self.this.append(this)
8726  except: self.this = this
8727  def add_removed_atom(self, *args):
8728  """add_removed_atom(CHARMMPatch self, std::string name)"""
8729  return _IMP_atom.CHARMMPatch_add_removed_atom(self, *args)
8730 
8731  def get_number_of_removed_atoms(self):
8732  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
8733  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
8734 
8735  def get_removed_atom(self, *args):
8736  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
8737  return _IMP_atom.CHARMMPatch_get_removed_atom(self, *args)
8738 
8739  def apply(self, *args):
8740  """
8741  apply(CHARMMPatch self, CHARMMResidueTopology res)
8742  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
8743  """
8744  return _IMP_atom.CHARMMPatch_apply(self, *args)
8745 
8746  def __str__(self):
8747  """__str__(CHARMMPatch self) -> std::string"""
8748  return _IMP_atom.CHARMMPatch___str__(self)
8749 
8750  def __repr__(self):
8751  """__repr__(CHARMMPatch self) -> std::string"""
8752  return _IMP_atom.CHARMMPatch___repr__(self)
8753 
8754  def get_from(o):
8755  return _object_cast_to_CHARMMPatch(o)
8756  get_from = staticmethod(get_from)
8757 
8758 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
8759 CHARMMPatch_swigregister(CHARMMPatch)
8760 
8761 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
8762  """Proxy of C++ IMP::atom::CHARMMResidueTopology class"""
8763  __swig_setmethods__ = {}
8764  for _s in [CHARMMIdealResidueTopology]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8765  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopology, name, value)
8766  __swig_getmethods__ = {}
8767  for _s in [CHARMMIdealResidueTopology]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8768  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopology, name)
8769  def __init__(self, *args):
8770  """
8771  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
8772  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
8773  """
8774  this = _IMP_atom.new_CHARMMResidueTopology(*args)
8775  try: self.this.append(this)
8776  except: self.this = this
8777  def get_patched(self):
8778  """get_patched(CHARMMResidueTopology self) -> bool"""
8779  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
8780 
8781  def set_patched(self, *args):
8782  """set_patched(CHARMMResidueTopology self, bool patched)"""
8783  return _IMP_atom.CHARMMResidueTopology_set_patched(self, *args)
8784 
8785  def __str__(self):
8786  """__str__(CHARMMResidueTopology self) -> std::string"""
8787  return _IMP_atom.CHARMMResidueTopology___str__(self)
8788 
8789  def __repr__(self):
8790  """__repr__(CHARMMResidueTopology self) -> std::string"""
8791  return _IMP_atom.CHARMMResidueTopology___repr__(self)
8792 
8793  def get_from(o):
8794  return _object_cast_to_CHARMMResidueTopology(o)
8795  get_from = staticmethod(get_from)
8796 
8797 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
8798 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
8799 
8800 class CHARMMAtom(Atom):
8801  """Proxy of C++ IMP::atom::CHARMMAtom class"""
8802  __swig_setmethods__ = {}
8803  for _s in [Atom]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8804  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtom, name, value)
8805  __swig_getmethods__ = {}
8806  for _s in [Atom]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8807  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtom, name)
8808  def __init__(self, *args):
8809  """
8810  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
8811  __init__(IMP::atom::CHARMMAtom self, Model m, ::IMP::kernel::ParticleIndex id) -> CHARMMAtom
8812  __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
8813  """
8814  this = _IMP_atom.new_CHARMMAtom(*args)
8815  try: self.this.append(this)
8816  except: self.this = this
8817  def decorate_particle(*args):
8818  """decorate_particle(Particle p) -> CHARMMAtom"""
8819  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
8820 
8821  if _newclass:decorate_particle = staticmethod(decorate_particle)
8822  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
8823  def show(self, *args):
8824  """
8825  show(CHARMMAtom self, _ostream out=std::cout)
8826  show(CHARMMAtom self)
8827  """
8828  return _IMP_atom.CHARMMAtom_show(self, *args)
8829 
8830  def setup_particle(*args):
8831  """
8832  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
8833  setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
8834  """
8835  return _IMP_atom.CHARMMAtom_setup_particle(*args)
8836 
8837  if _newclass:setup_particle = staticmethod(setup_particle)
8838  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
8839  def get_charmm_type(self):
8840  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
8841  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
8842 
8843  def set_charmm_type(self, *args):
8844  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
8845  return _IMP_atom.CHARMMAtom_set_charmm_type(self, *args)
8846 
8847  def get_is_setup(*args):
8848  """
8849  get_is_setup(_ParticleAdaptor p) -> bool
8850  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
8851  """
8852  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
8853 
8854  if _newclass:get_is_setup = staticmethod(get_is_setup)
8855  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
8856  def get_charmm_type_key():
8857  """get_charmm_type_key() -> StringKey"""
8858  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
8859 
8860  if _newclass:get_charmm_type_key = staticmethod(get_charmm_type_key)
8861  __swig_getmethods__["get_charmm_type_key"] = lambda x: get_charmm_type_key
8862  def add_attribute(self, *args):
8863  """
8864  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
8865  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8866  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
8867  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
8868  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8869  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
8870  """
8871  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
8872 
8873  def get_value(self, *args):
8874  """
8875  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
8876  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
8877  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
8878  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
8879  get_value(CHARMMAtom self, ObjectKey a0) -> Object
8880  """
8881  return _IMP_atom.CHARMMAtom_get_value(self, *args)
8882 
8883  def set_value(self, *args):
8884  """
8885  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8886  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
8887  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
8888  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8889  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
8890  """
8891  return _IMP_atom.CHARMMAtom_set_value(self, *args)
8892 
8893  def remove_attribute(self, *args):
8894  """
8895  remove_attribute(CHARMMAtom self, FloatKey a0)
8896  remove_attribute(CHARMMAtom self, IntKey a0)
8897  remove_attribute(CHARMMAtom self, StringKey a0)
8898  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
8899  remove_attribute(CHARMMAtom self, ObjectKey a0)
8900  """
8901  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
8902 
8903  def has_attribute(self, *args):
8904  """
8905  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
8906  has_attribute(CHARMMAtom self, IntKey a0) -> bool
8907  has_attribute(CHARMMAtom self, StringKey a0) -> bool
8908  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
8909  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
8910  """
8911  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
8912 
8913  def get_derivative(self, *args):
8914  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
8915  return _IMP_atom.CHARMMAtom_get_derivative(self, *args)
8916 
8917  def get_name(self):
8918  """get_name(CHARMMAtom self) -> std::string"""
8919  return _IMP_atom.CHARMMAtom_get_name(self)
8920 
8921  def clear_caches(self):
8922  """clear_caches(CHARMMAtom self)"""
8923  return _IMP_atom.CHARMMAtom_clear_caches(self)
8924 
8925  def set_name(self, *args):
8926  """set_name(CHARMMAtom self, std::string a0)"""
8927  return _IMP_atom.CHARMMAtom_set_name(self, *args)
8928 
8929  def set_check_level(self, *args):
8930  """set_check_level(CHARMMAtom self, IMP::base::CheckLevel a0)"""
8931  return _IMP_atom.CHARMMAtom_set_check_level(self, *args)
8932 
8933  def add_to_derivative(self, *args):
8934  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8935  return _IMP_atom.CHARMMAtom_add_to_derivative(self, *args)
8936 
8937  def set_is_optimized(self, *args):
8938  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
8939  return _IMP_atom.CHARMMAtom_set_is_optimized(self, *args)
8940 
8941  def get_is_optimized(self, *args):
8942  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
8943  return _IMP_atom.CHARMMAtom_get_is_optimized(self, *args)
8944 
8945  def get_check_level(self):
8946  """get_check_level(CHARMMAtom self) -> IMP::base::CheckLevel"""
8947  return _IMP_atom.CHARMMAtom_get_check_level(self)
8948 
8949  def __eq__(self, *args):
8950  """
8951  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
8952  __eq__(CHARMMAtom self, Particle d) -> bool
8953  """
8954  return _IMP_atom.CHARMMAtom___eq__(self, *args)
8955 
8956  def __ne__(self, *args):
8957  """
8958  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
8959  __ne__(CHARMMAtom self, Particle d) -> bool
8960  """
8961  return _IMP_atom.CHARMMAtom___ne__(self, *args)
8962 
8963  def __le__(self, *args):
8964  """
8965  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
8966  __le__(CHARMMAtom self, Particle d) -> bool
8967  """
8968  return _IMP_atom.CHARMMAtom___le__(self, *args)
8969 
8970  def __lt__(self, *args):
8971  """
8972  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
8973  __lt__(CHARMMAtom self, Particle d) -> bool
8974  """
8975  return _IMP_atom.CHARMMAtom___lt__(self, *args)
8976 
8977  def __ge__(self, *args):
8978  """
8979  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
8980  __ge__(CHARMMAtom self, Particle d) -> bool
8981  """
8982  return _IMP_atom.CHARMMAtom___ge__(self, *args)
8983 
8984  def __gt__(self, *args):
8985  """
8986  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
8987  __gt__(CHARMMAtom self, Particle d) -> bool
8988  """
8989  return _IMP_atom.CHARMMAtom___gt__(self, *args)
8990 
8991  def __str__(self):
8992  """__str__(CHARMMAtom self) -> std::string"""
8993  return _IMP_atom.CHARMMAtom___str__(self)
8994 
8995  def __repr__(self):
8996  """__repr__(CHARMMAtom self) -> std::string"""
8997  return _IMP_atom.CHARMMAtom___repr__(self)
8998 
8999  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
9000  __del__ = lambda self : None;
9001 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
9002 CHARMMAtom_swigregister(CHARMMAtom)
9003 
9004 def CHARMMAtom_decorate_particle(*args):
9005  """CHARMMAtom_decorate_particle(Particle p) -> CHARMMAtom"""
9006  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
9007 
9008 def CHARMMAtom_setup_particle(*args):
9009  """
9010  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
9011  CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
9012  """
9013  return _IMP_atom.CHARMMAtom_setup_particle(*args)
9014 
9015 def CHARMMAtom_get_is_setup(*args):
9016  """
9017  get_is_setup(_ParticleAdaptor p) -> bool
9018  CHARMMAtom_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
9019  """
9020  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
9021 
9022 def CHARMMAtom_get_charmm_type_key():
9023  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
9024  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
9025 
9026 
9027 def get_charmm_untyped_atoms(*args):
9028  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
9029  return _IMP_atom.get_charmm_untyped_atoms(*args)
9030 
9031 def remove_charmm_untyped_atoms(*args):
9032  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
9033  return _IMP_atom.remove_charmm_untyped_atoms(*args)
9034 class CHARMMBondParameters(_object):
9035  """Proxy of C++ IMP::atom::CHARMMBondParameters class"""
9036  __swig_setmethods__ = {}
9037  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondParameters, name, value)
9038  __swig_getmethods__ = {}
9039  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondParameters, name)
9040  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_set
9041  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_get
9042  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
9043  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_set
9044  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_get
9045  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
9046  def __init__(self):
9047  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
9048  this = _IMP_atom.new_CHARMMBondParameters()
9049  try: self.this.append(this)
9050  except: self.this = this
9051  def show(self, *args):
9052  """
9053  show(CHARMMBondParameters self, _ostream out=std::cout)
9054  show(CHARMMBondParameters self)
9055  """
9056  return _IMP_atom.CHARMMBondParameters_show(self, *args)
9057 
9058  def __str__(self):
9059  """__str__(CHARMMBondParameters self) -> std::string"""
9060  return _IMP_atom.CHARMMBondParameters___str__(self)
9061 
9062  def __repr__(self):
9063  """__repr__(CHARMMBondParameters self) -> std::string"""
9064  return _IMP_atom.CHARMMBondParameters___repr__(self)
9065 
9066  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
9067  __del__ = lambda self : None;
9068 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
9069 CHARMMBondParameters_swigregister(CHARMMBondParameters)
9070 
9071 class CHARMMDihedralParameters(_object):
9072  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class"""
9073  __swig_setmethods__ = {}
9074  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedralParameters, name, value)
9075  __swig_getmethods__ = {}
9076  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedralParameters, name)
9077  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_set
9078  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_get
9079  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
9080  __swig_setmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_set
9081  __swig_getmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_get
9082  if _newclass:multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
9083  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_set
9084  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_get
9085  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
9086  def __init__(self):
9087  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
9088  this = _IMP_atom.new_CHARMMDihedralParameters()
9089  try: self.this.append(this)
9090  except: self.this = this
9091  def show(self, *args):
9092  """
9093  show(CHARMMDihedralParameters self, _ostream out=std::cout)
9094  show(CHARMMDihedralParameters self)
9095  """
9096  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
9097 
9098  def __str__(self):
9099  """__str__(CHARMMDihedralParameters self) -> std::string"""
9100  return _IMP_atom.CHARMMDihedralParameters___str__(self)
9101 
9102  def __repr__(self):
9103  """__repr__(CHARMMDihedralParameters self) -> std::string"""
9104  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
9105 
9106  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
9107  __del__ = lambda self : None;
9108 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
9109 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
9110 
9111 class CHARMMParameters(ForceFieldParameters):
9112  """Proxy of C++ IMP::atom::CHARMMParameters class"""
9113  __swig_setmethods__ = {}
9114  for _s in [ForceFieldParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9115  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMParameters, name, value)
9116  __swig_getmethods__ = {}
9117  for _s in [ForceFieldParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9118  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMParameters, name)
9119  def __init__(self, *args):
9120  """
9121  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters
9122  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput()) -> CHARMMParameters
9123  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
9124  """
9125  this = _IMP_atom.new_CHARMMParameters(*args)
9126  try: self.this.append(this)
9127  except: self.this = this
9128  def add_residue_topology(self, *args):
9129  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
9130  return _IMP_atom.CHARMMParameters_add_residue_topology(self, *args)
9131 
9132  def get_residue_topology(self, *args):
9133  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
9134  return _IMP_atom.CHARMMParameters_get_residue_topology(self, *args)
9135 
9136  def add_patch(self, *args):
9137  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
9138  return _IMP_atom.CHARMMParameters_add_patch(self, *args)
9139 
9140  def get_patch(self, *args):
9141  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
9142  return _IMP_atom.CHARMMParameters_get_patch(self, *args)
9143 
9144  def create_topology(self, *args):
9145  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
9146  return _IMP_atom.CHARMMParameters_create_topology(self, *args)
9147 
9148  def get_bond_parameters(self, *args):
9149  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
9150  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, *args)
9151 
9152  def get_angle_parameters(self, *args):
9153  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
9154  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, *args)
9155 
9156  def get_dihedral_parameters(self, *args):
9157  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
9158  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, *args)
9159 
9160  def get_improper_parameters(self, *args):
9161  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
9162  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, *args)
9163 
9164  def create_angles(self, *args):
9165  """create_angles(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
9166  return _IMP_atom.CHARMMParameters_create_angles(self, *args)
9167 
9168  def create_dihedrals(self, *args):
9169  """create_dihedrals(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
9170  return _IMP_atom.CHARMMParameters_create_dihedrals(self, *args)
9171 
9172  def get_version_info(self):
9173  """get_version_info(CHARMMParameters self) -> VersionInfo"""
9174  return _IMP_atom.CHARMMParameters_get_version_info(self)
9175 
9176  def do_show(self, *args):
9177  """do_show(CHARMMParameters self, _ostream out)"""
9178  return _IMP_atom.CHARMMParameters_do_show(self, *args)
9179 
9180  __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
9181  __del__ = lambda self : None;
9182  def __str__(self):
9183  """__str__(CHARMMParameters self) -> std::string"""
9184  return _IMP_atom.CHARMMParameters___str__(self)
9185 
9186  def __repr__(self):
9187  """__repr__(CHARMMParameters self) -> std::string"""
9188  return _IMP_atom.CHARMMParameters___repr__(self)
9189 
9190  def get_from(o):
9191  return _object_cast_to_CHARMMParameters(o)
9192  get_from = staticmethod(get_from)
9193 
9194 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
9195 CHARMMParameters_swigregister(CHARMMParameters)
9196 
9197 
9199  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
9200  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
9201 
9203  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
9204  return _IMP_atom.get_all_atom_CHARMM_parameters()
9205 class CHARMMSegmentTopology(IMP.base.Object):
9206  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class"""
9207  __swig_setmethods__ = {}
9208  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9209  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMSegmentTopology, name, value)
9210  __swig_getmethods__ = {}
9211  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9212  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMSegmentTopology, name)
9213  def remove_residue(self, *args):
9214  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
9215  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, *args)
9216 
9217  def remove_residues(self, *args):
9218  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
9219  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, *args)
9220 
9221  def set_residues(self, *args):
9222  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
9223  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, *args)
9224 
9225  def set_residues_order(self, *args):
9226  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
9227  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, *args)
9228 
9229  def add_residue(self, *args):
9230  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
9231  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, *args)
9232 
9233  def add_residues(self, *args):
9234  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
9235  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, *args)
9236 
9237  def clear_residues(self):
9238  """clear_residues(CHARMMSegmentTopology self)"""
9239  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
9240 
9241  def get_number_of_residues(self):
9242  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
9243  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
9244 
9245  def get_has_residues(self):
9246  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
9247  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
9248 
9249  def get_residue(self, *args):
9250  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
9251  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, *args)
9252 
9253  def get_residues(self):
9254  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
9255  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
9256 
9257  def reserve_residues(self, *args):
9258  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
9259  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, *args)
9260 
9261  def get_version_info(self):
9262  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
9263  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
9264 
9265  def __init__(self, name="CHARMM segment topology %1%"):
9266  """
9267  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology
9268  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
9269  """
9270  this = _IMP_atom.new_CHARMMSegmentTopology(name)
9271  try: self.this.append(this)
9272  except: self.this = this
9273  def apply_default_patches(self, *args):
9274  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
9275  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, *args)
9276 
9277  def __str__(self):
9278  """__str__(CHARMMSegmentTopology self) -> std::string"""
9279  return _IMP_atom.CHARMMSegmentTopology___str__(self)
9280 
9281  def __repr__(self):
9282  """__repr__(CHARMMSegmentTopology self) -> std::string"""
9283  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
9284 
9285  def get_from(o):
9286  return _object_cast_to_CHARMMSegmentTopology(o)
9287  get_from = staticmethod(get_from)
9288 
9289 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
9290 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
9291 
9292 class CHARMMTopology(IMP.base.Object):
9293  """Proxy of C++ IMP::atom::CHARMMTopology class"""
9294  __swig_setmethods__ = {}
9295  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9296  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMTopology, name, value)
9297  __swig_getmethods__ = {}
9298  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9299  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMTopology, name)
9300  def __init__(self, *args):
9301  """
9302  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology
9303  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
9304  """
9305  this = _IMP_atom.new_CHARMMTopology(*args)
9306  try: self.this.append(this)
9307  except: self.this = this
9308  def get_parameters(self):
9309  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
9310  return _IMP_atom.CHARMMTopology_get_parameters(self)
9311 
9312  def add_sequence(self, *args):
9313  """add_sequence(CHARMMTopology self, std::string sequence)"""
9314  return _IMP_atom.CHARMMTopology_add_sequence(self, *args)
9315 
9316  def apply_default_patches(self):
9317  """apply_default_patches(CHARMMTopology self)"""
9318  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
9319 
9320  def create_hierarchy(self, *args):
9321  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
9322  return _IMP_atom.CHARMMTopology_create_hierarchy(self, *args)
9323 
9324  def add_atom_types(self, *args):
9325  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
9326  return _IMP_atom.CHARMMTopology_add_atom_types(self, *args)
9327 
9328  def add_coordinates(self, *args):
9329  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
9330  return _IMP_atom.CHARMMTopology_add_coordinates(self, *args)
9331 
9332  def add_missing_atoms(self, *args):
9333  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
9334  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, *args)
9335 
9336  def setup_hierarchy(self, *args):
9337  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
9338  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, *args)
9339 
9340  def add_charges(self, *args):
9341  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
9342  return _IMP_atom.CHARMMTopology_add_charges(self, *args)
9343 
9344  def add_bonds(self, *args):
9345  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9346  return _IMP_atom.CHARMMTopology_add_bonds(self, *args)
9347 
9348  def add_dihedrals(self, *args):
9349  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9350  return _IMP_atom.CHARMMTopology_add_dihedrals(self, *args)
9351 
9352  def add_impropers(self, *args):
9353  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9354  return _IMP_atom.CHARMMTopology_add_impropers(self, *args)
9355 
9356  def remove_segment(self, *args):
9357  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
9358  return _IMP_atom.CHARMMTopology_remove_segment(self, *args)
9359 
9360  def remove_segments(self, *args):
9361  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
9362  return _IMP_atom.CHARMMTopology_remove_segments(self, *args)
9363 
9364  def set_segments(self, *args):
9365  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
9366  return _IMP_atom.CHARMMTopology_set_segments(self, *args)
9367 
9368  def set_segments_order(self, *args):
9369  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
9370  return _IMP_atom.CHARMMTopology_set_segments_order(self, *args)
9371 
9372  def add_segment(self, *args):
9373  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
9374  return _IMP_atom.CHARMMTopology_add_segment(self, *args)
9375 
9376  def add_segments(self, *args):
9377  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
9378  return _IMP_atom.CHARMMTopology_add_segments(self, *args)
9379 
9380  def clear_segments(self):
9381  """clear_segments(CHARMMTopology self)"""
9382  return _IMP_atom.CHARMMTopology_clear_segments(self)
9383 
9384  def get_number_of_segments(self):
9385  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
9386  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
9387 
9388  def get_has_segments(self):
9389  """get_has_segments(CHARMMTopology self) -> bool"""
9390  return _IMP_atom.CHARMMTopology_get_has_segments(self)
9391 
9392  def get_segment(self, *args):
9393  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
9394  return _IMP_atom.CHARMMTopology_get_segment(self, *args)
9395 
9396  def get_segments(self):
9397  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
9398  return _IMP_atom.CHARMMTopology_get_segments(self)
9399 
9400  def reserve_segments(self, *args):
9401  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
9402  return _IMP_atom.CHARMMTopology_reserve_segments(self, *args)
9403 
9404  def get_version_info(self):
9405  """get_version_info(CHARMMTopology self) -> VersionInfo"""
9406  return _IMP_atom.CHARMMTopology_get_version_info(self)
9407 
9408  def __str__(self):
9409  """__str__(CHARMMTopology self) -> std::string"""
9410  return _IMP_atom.CHARMMTopology___str__(self)
9411 
9412  def __repr__(self):
9413  """__repr__(CHARMMTopology self) -> std::string"""
9414  return _IMP_atom.CHARMMTopology___repr__(self)
9415 
9416  def get_from(o):
9417  return _object_cast_to_CHARMMTopology(o)
9418  get_from = staticmethod(get_from)
9419 
9420 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
9421 CHARMMTopology_swigregister(CHARMMTopology)
9422 
9423 class CHARMMStereochemistryRestraint(IMP.kernel.Restraint):
9424  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class"""
9425  __swig_setmethods__ = {}
9426  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9427  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMStereochemistryRestraint, name, value)
9428  __swig_getmethods__ = {}
9429  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9430  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMStereochemistryRestraint, name)
9431  def __init__(self, *args):
9432  """__init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint"""
9433  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
9434  try: self.this.append(this)
9435  except: self.this = this
9436  def get_pair_filter(self):
9437  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
9438  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
9439 
9440  def do_get_inputs(self):
9441  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::kernel::ModelObjectsTemp"""
9442  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
9443 
9444  def get_version_info(self):
9445  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
9446  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
9447 
9448  def __str__(self):
9449  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
9450  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
9451 
9452  def __repr__(self):
9453  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
9454  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
9455 
9456  def get_from(o):
9457  return _object_cast_to_CHARMMStereochemistryRestraint(o)
9458  get_from = staticmethod(get_from)
9459 
9460 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
9461 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
9462 
9463 
9464 def add_bonds(*args):
9465  """
9466  add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
9467  add_bonds(Hierarchy d)
9468  """
9469  return _IMP_atom.add_bonds(*args)
9470 
9471 def add_radii(*args):
9472  """
9473  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(),
9474  FloatKey radius_key=FloatKey("radius"))
9475  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
9476  add_radii(Hierarchy d)
9477  """
9478  return _IMP_atom.add_radii(*args)
9479 ALBER = _IMP_atom.ALBER
9480 HARPAZ = _IMP_atom.HARPAZ
9481 ANDERSSON = _IMP_atom.ANDERSSON
9482 TSAI = _IMP_atom.TSAI
9483 QUILLIN = _IMP_atom.QUILLIN
9484 SQUIRE = _IMP_atom.SQUIRE
9485 
9487  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
9488  return _IMP_atom.get_protein_density_from_reference(*args)
9489 
9490 def get_volume_from_mass(*args):
9491  """
9492  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double
9493  get_volume_from_mass(double m) -> double
9494  """
9495  return _IMP_atom.get_volume_from_mass(*args)
9496 
9497 def get_mass_from_volume(*args):
9498  """
9499  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double
9500  get_mass_from_volume(double v) -> double
9501  """
9502  return _IMP_atom.get_mass_from_volume(*args)
9503 
9505  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
9506  return _IMP_atom.get_mass_from_number_of_residues(*args)
9507 
9508 def get_volume_from_residue_type(*args):
9509  """get_volume_from_residue_type(ResidueType rt) -> double"""
9510  return _IMP_atom.get_volume_from_residue_type(*args)
9511 
9512 def get_molarity(*args):
9513  """get_molarity(double n, double volume) -> double"""
9514  return _IMP_atom.get_molarity(*args)
9515 
9516 def get_kd(*args):
9517  """get_kd(double na, double nb, double nab, double volume) -> double"""
9518  return _IMP_atom.get_kd(*args)
9519 
9521  """get_einstein_diffusion_coefficient(double r) -> double"""
9522  return _IMP_atom.get_einstein_diffusion_coefficient(*args)
9523 
9525  """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
9526  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(*args)
9527 
9528 def get_diffusion_length(*args):
9529  """
9530  get_diffusion_length(double D, double t) -> double
9531  get_diffusion_length(double D, double force, double t, double temp=273) -> double
9532  get_diffusion_length(double D, double force, double t) -> double
9533  """
9534  return _IMP_atom.get_diffusion_length(*args)
9535 
9536 def get_diffusion_angle(*args):
9537  """get_diffusion_angle(double D, double dtfs) -> double"""
9538  return _IMP_atom.get_diffusion_angle(*args)
9539 
9540 def get_diffusion_coefficient(*args):
9541  """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
9542  return _IMP_atom.get_diffusion_coefficient(*args)
9543 
9545  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
9546  return _IMP_atom.get_rotational_diffusion_coefficient(*args)
9547 class EzRestraint(IMP.kernel.Restraint):
9548  """Proxy of C++ IMP::atom::EzRestraint class"""
9549  __swig_setmethods__ = {}
9550  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9551  __setattr__ = lambda self, name, value: _swig_setattr(self, EzRestraint, name, value)
9552  __swig_getmethods__ = {}
9553  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9554  __getattr__ = lambda self, name: _swig_getattr(self, EzRestraint, name)
9555  def __init__(self, *args):
9556  """__init__(IMP::atom::EzRestraint self, IMP::kernel::Particles ps) -> EzRestraint"""
9557  this = _IMP_atom.new_EzRestraint(*args)
9558  try: self.this.append(this)
9559  except: self.this = this
9560  def get_version_info(self):
9561  """get_version_info(EzRestraint self) -> VersionInfo"""
9562  return _IMP_atom.EzRestraint_get_version_info(self)
9563 
9564  def __str__(self):
9565  """__str__(EzRestraint self) -> std::string"""
9566  return _IMP_atom.EzRestraint___str__(self)
9567 
9568  def __repr__(self):
9569  """__repr__(EzRestraint self) -> std::string"""
9570  return _IMP_atom.EzRestraint___repr__(self)
9571 
9572  def get_from(o):
9573  return _object_cast_to_EzRestraint(o)
9574  get_from = staticmethod(get_from)
9575 
9576 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
9577 EzRestraint_swigregister(EzRestraint)
9578 
9579 
9580 def create_protein(*args):
9581  """
9582  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0,
9583  double volume=-1, bool ismol=True) -> Hierarchy
9584  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0,
9585  double volume=-1) -> Hierarchy
9586  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
9587  create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
9588  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
9589  """
9590  return _IMP_atom.create_protein(*args)
9591 
9593  """
9594  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
9595  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
9596  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
9597  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
9598  """
9599  return _IMP_atom.create_simplified_along_backbone(*args)
9600 
9602  """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
9603  return _IMP_atom.create_simplified_from_volume(*args)
9604 
9606  """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
9607  return _IMP_atom.create_simplified_assembly_from_volume(*args)
9608 
9609 def get_residue_indexes(*args):
9610  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
9611  return _IMP_atom.get_residue_indexes(*args)
9612 
9613 def get_residue_type(*args):
9614  """
9615  get_residue_type(char c) -> ResidueType
9616  get_residue_type(Hierarchy h) -> ResidueType
9617  """
9618  return _IMP_atom.get_residue_type(*args)
9619 
9620 def get_chain_id_char(*args):
9621  """get_chain_id_char(Hierarchy h) -> char"""
9622  return _IMP_atom.get_chain_id_char(*args)
9623 
9624 def get_atom_type(*args):
9625  """get_atom_type(Hierarchy h) -> AtomType"""
9626  return _IMP_atom.get_atom_type(*args)
9627 
9628 def get_domain_name(*args):
9629  """get_domain_name(Hierarchy h) -> std::string"""
9630  return _IMP_atom.get_domain_name(*args)
9631 
9633  """
9634  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
9635  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
9636  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
9637  """
9638  return _IMP_atom.create_excluded_volume_restraint(*args)
9639 
9640 def setup_as_approximation(*args):
9641  """
9642  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other, double resolution=-1)
9643  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other)
9644  setup_as_approximation(Hierarchy h, double resolution=-1)
9645  setup_as_approximation(Hierarchy h)
9646  """
9647  return _IMP_atom.setup_as_approximation(*args)
9648 class _HierarchyTreeVertexIndex(_object):
9649  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class"""
9650  __swig_setmethods__ = {}
9651  __setattr__ = lambda self, name, value: _swig_setattr(self, _HierarchyTreeVertexIndex, name, value)
9652  __swig_getmethods__ = {}
9653  __getattr__ = lambda self, name: _swig_getattr(self, _HierarchyTreeVertexIndex, name)
9654  __repr__ = _swig_repr
9655  def __init__(self):
9656  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
9657  this = _IMP_atom.new__HierarchyTreeVertexIndex()
9658  try: self.this.append(this)
9659  except: self.this = this
9660  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
9661  __del__ = lambda self : None;
9662 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
9663 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
9664 
9665 
9666 def show_as_graphviz(*args):
9667  """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
9668  return _IMP_atom.show_as_graphviz(*args)
9669 
9670 def get_vertex_index(*args):
9671  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
9672  return _IMP_atom.get_vertex_index(*args)
9673 
9674 def get_hierarchy_tree(*args):
9675  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
9676  return _IMP_atom.get_hierarchy_tree(*args)
9677 class HierarchyGeometry(IMP.display.SingletonGeometry):
9678  """Proxy of C++ IMP::atom::HierarchyGeometry class"""
9679  __swig_setmethods__ = {}
9680  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9681  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyGeometry, name, value)
9682  __swig_getmethods__ = {}
9683  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9684  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyGeometry, name)
9685  def __init__(self, *args):
9686  """
9687  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
9688  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
9689  """
9690  this = _IMP_atom.new_HierarchyGeometry(*args)
9691  try: self.this.append(this)
9692  except: self.this = this
9693  def get_version_info(self):
9694  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
9695  return _IMP_atom.HierarchyGeometry_get_version_info(self)
9696 
9697  def __str__(self):
9698  """__str__(HierarchyGeometry self) -> std::string"""
9699  return _IMP_atom.HierarchyGeometry___str__(self)
9700 
9701  def __repr__(self):
9702  """__repr__(HierarchyGeometry self) -> std::string"""
9703  return _IMP_atom.HierarchyGeometry___repr__(self)
9704 
9705  def get_from(o):
9706  return _object_cast_to_HierarchyGeometry(o)
9707  get_from = staticmethod(get_from)
9708 
9709 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
9710 HierarchyGeometry_swigregister(HierarchyGeometry)
9711 
9712 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
9713  """Proxy of C++ IMP::atom::HierarchiesGeometry class"""
9714  __swig_setmethods__ = {}
9715  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9716  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchiesGeometry, name, value)
9717  __swig_getmethods__ = {}
9718  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9719  __getattr__ = lambda self, name: _swig_getattr(self, HierarchiesGeometry, name)
9720  def __init__(self, *args):
9721  """
9722  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
9723  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
9724  """
9725  this = _IMP_atom.new_HierarchiesGeometry(*args)
9726  try: self.this.append(this)
9727  except: self.this = this
9728  def get_version_info(self):
9729  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
9730  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
9731 
9732  def __str__(self):
9733  """__str__(HierarchiesGeometry self) -> std::string"""
9734  return _IMP_atom.HierarchiesGeometry___str__(self)
9735 
9736  def __repr__(self):
9737  """__repr__(HierarchiesGeometry self) -> std::string"""
9738  return _IMP_atom.HierarchiesGeometry___repr__(self)
9739 
9740  def get_from(o):
9741  return _object_cast_to_HierarchiesGeometry(o)
9742  get_from = staticmethod(get_from)
9743 
9744 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
9745 HierarchiesGeometry_swigregister(HierarchiesGeometry)
9746 
9747 
9748 def transform(*args):
9749  """
9750  transform(Hierarchy h, Transformation3D tr)
9751  transform(Hierarchy h, Transformation3D tr)
9752  """
9753  return _IMP_atom.transform(*args)
9754 class DopePairScore(_ADopeBase):
9755  """Proxy of C++ IMP::atom::DopePairScore class"""
9756  __swig_setmethods__ = {}
9757  for _s in [_ADopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9758  __setattr__ = lambda self, name, value: _swig_setattr(self, DopePairScore, name, value)
9759  __swig_getmethods__ = {}
9760  for _s in [_ADopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9761  __getattr__ = lambda self, name: _swig_getattr(self, DopePairScore, name)
9762  def __init__(self, *args):
9763  """
9764  __init__(IMP::atom::DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
9765  __init__(IMP::atom::DopePairScore self) -> DopePairScore
9766  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
9767  """
9768  this = _IMP_atom.new_DopePairScore(*args)
9769  try: self.this.append(this)
9770  except: self.this = this
9771  def __str__(self):
9772  """__str__(DopePairScore self) -> std::string"""
9773  return _IMP_atom.DopePairScore___str__(self)
9774 
9775  def __repr__(self):
9776  """__repr__(DopePairScore self) -> std::string"""
9777  return _IMP_atom.DopePairScore___repr__(self)
9778 
9779  def get_from(o):
9780  return _object_cast_to_DopePairScore(o)
9781  get_from = staticmethod(get_from)
9782 
9783  __swig_destroy__ = _IMP_atom.delete_DopePairScore
9784  __del__ = lambda self : None;
9785 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
9786 DopePairScore_swigregister(DopePairScore)
9787 
9788 
9789 def add_dope_score_data(*args):
9790  """add_dope_score_data(Hierarchy h)"""
9791  return _IMP_atom.add_dope_score_data(*args)
9792 class OrientedSoapPairScore(_OrientedSoapBase):
9793  """Proxy of C++ IMP::atom::OrientedSoapPairScore class"""
9794  __swig_setmethods__ = {}
9795  for _s in [_OrientedSoapBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9796  __setattr__ = lambda self, name, value: _swig_setattr(self, OrientedSoapPairScore, name, value)
9797  __swig_getmethods__ = {}
9798  for _s in [_OrientedSoapBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9799  __getattr__ = lambda self, name: _swig_getattr(self, OrientedSoapPairScore, name)
9800  def __init__(self, *args):
9801  """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
9802  this = _IMP_atom.new_OrientedSoapPairScore(*args)
9803  try: self.this.append(this)
9804  except: self.this = this
9805  def get_pair_filter(self):
9806  """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
9807  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
9808 
9809  def __str__(self):
9810  """__str__(OrientedSoapPairScore self) -> std::string"""
9811  return _IMP_atom.OrientedSoapPairScore___str__(self)
9812 
9813  def __repr__(self):
9814  """__repr__(OrientedSoapPairScore self) -> std::string"""
9815  return _IMP_atom.OrientedSoapPairScore___repr__(self)
9816 
9817  def get_from(o):
9818  return _object_cast_to_OrientedSoapPairScore(o)
9819  get_from = staticmethod(get_from)
9820 
9821  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
9822  __del__ = lambda self : None;
9823 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
9824 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
9825 
9826 class SameResiduePairFilter(IMP.kernel.PairPredicate):
9827  """Proxy of C++ IMP::atom::SameResiduePairFilter class"""
9828  __swig_setmethods__ = {}
9829  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9830  __setattr__ = lambda self, name, value: _swig_setattr(self, SameResiduePairFilter, name, value)
9831  __swig_getmethods__ = {}
9832  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9833  __getattr__ = lambda self, name: _swig_getattr(self, SameResiduePairFilter, name)
9834  def __init__(self):
9835  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
9836  this = _IMP_atom.new_SameResiduePairFilter()
9837  try: self.this.append(this)
9838  except: self.this = this
9839  def do_get_inputs(self, *args):
9840  """do_get_inputs(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
9841  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, *args)
9842 
9843  def get_value(self, *args):
9844  """
9845  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePair const & a) -> int
9846  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
9847  """
9848  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
9849 
9850  def get_value_index(self, *args):
9851  """
9852  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
9853  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
9854  """
9855  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
9856 
9857  def get_version_info(self):
9858  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
9859  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
9860 
9861  def __str__(self):
9862  """__str__(SameResiduePairFilter self) -> std::string"""
9863  return _IMP_atom.SameResiduePairFilter___str__(self)
9864 
9865  def __repr__(self):
9866  """__repr__(SameResiduePairFilter self) -> std::string"""
9867  return _IMP_atom.SameResiduePairFilter___repr__(self)
9868 
9869  def get_from(o):
9870  return _object_cast_to_SameResiduePairFilter(o)
9871  get_from = staticmethod(get_from)
9872 
9873 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
9874 SameResiduePairFilter_swigregister(SameResiduePairFilter)
9875 
9876 class RemoveRigidMotionOptimizerState(IMP.kernel.OptimizerState):
9877  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class"""
9878  __swig_setmethods__ = {}
9879  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9880  __setattr__ = lambda self, name, value: _swig_setattr(self, RemoveRigidMotionOptimizerState, name, value)
9881  __swig_getmethods__ = {}
9882  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9883  __getattr__ = lambda self, name: _swig_getattr(self, RemoveRigidMotionOptimizerState, name)
9884  def __init__(self, *args):
9885  """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
9886  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(*args)
9887  try: self.this.append(this)
9888  except: self.this = this
9889  def set_particles(self, *args):
9890  """set_particles(RemoveRigidMotionOptimizerState self, IMP::kernel::Particles const & pis)"""
9891  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, *args)
9892 
9893  def remove_rigid_motion(self):
9894  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
9895  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
9896 
9897  def get_version_info(self):
9898  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
9899  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
9900 
9901  def __str__(self):
9902  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
9903  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
9904 
9905  def __repr__(self):
9906  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
9907  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
9908 
9909  def get_from(o):
9910  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
9911  get_from = staticmethod(get_from)
9912 
9913 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
9914 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
9915 
9916 class BerendsenThermostatOptimizerState(IMP.kernel.OptimizerState):
9917  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class"""
9918  __swig_setmethods__ = {}
9919  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9920  __setattr__ = lambda self, name, value: _swig_setattr(self, BerendsenThermostatOptimizerState, name, value)
9921  __swig_getmethods__ = {}
9922  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9923  __getattr__ = lambda self, name: _swig_getattr(self, BerendsenThermostatOptimizerState, name)
9924  def __init__(self, *args):
9925  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
9926  this = _IMP_atom.new_BerendsenThermostatOptimizerState(*args)
9927  try: self.this.append(this)
9928  except: self.this = this
9929  def set_particles(self, *args):
9930  """set_particles(BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9931  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, *args)
9932 
9933  def get_temperature(self):
9934  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
9935  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
9936 
9937  def get_tau(self):
9938  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
9939  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
9940 
9941  def set_temperature(self, *args):
9942  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
9943  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, *args)
9944 
9945  def set_tau(self, *args):
9946  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
9947  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, *args)
9948 
9949  def rescale_velocities(self):
9950  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
9951  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
9952 
9953  def get_version_info(self):
9954  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
9955  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
9956 
9957  def __str__(self):
9958  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
9959  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
9960 
9961  def __repr__(self):
9962  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
9963  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
9964 
9965  def get_from(o):
9966  return _object_cast_to_BerendsenThermostatOptimizerState(o)
9967  get_from = staticmethod(get_from)
9968 
9969 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
9970 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
9971 
9972 class LangevinThermostatOptimizerState(IMP.kernel.OptimizerState):
9973  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class"""
9974  __swig_setmethods__ = {}
9975  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9976  __setattr__ = lambda self, name, value: _swig_setattr(self, LangevinThermostatOptimizerState, name, value)
9977  __swig_getmethods__ = {}
9978  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9979  __getattr__ = lambda self, name: _swig_getattr(self, LangevinThermostatOptimizerState, name)
9980  def __init__(self, *args):
9981  """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
9982  this = _IMP_atom.new_LangevinThermostatOptimizerState(*args)
9983  try: self.this.append(this)
9984  except: self.this = this
9985  def set_particles(self, *args):
9986  """set_particles(LangevinThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9987  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, *args)
9988 
9989  def get_temperature(self):
9990  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
9991  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
9992 
9993  def get_gamma(self):
9994  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
9995  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
9996 
9997  def set_temperature(self, *args):
9998  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
9999  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, *args)
10000 
10001  def set_gamma(self, *args):
10002  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
10003  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, *args)
10004 
10005  def rescale_velocities(self):
10006  """rescale_velocities(LangevinThermostatOptimizerState self)"""
10007  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
10008 
10009  def get_version_info(self):
10010  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
10011  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
10012 
10013  def __str__(self):
10014  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
10015  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
10016 
10017  def __repr__(self):
10018  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
10019  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
10020 
10021  def get_from(o):
10022  return _object_cast_to_LangevinThermostatOptimizerState(o)
10023  get_from = staticmethod(get_from)
10024 
10025 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
10026 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
10027 
10028 class PDBSelector(IMP.base.Object):
10029  """Proxy of C++ IMP::atom::PDBSelector class"""
10030  __swig_setmethods__ = {}
10031  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10032  __setattr__ = lambda self, name, value: _swig_setattr(self, PDBSelector, name, value)
10033  __swig_getmethods__ = {}
10034  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10035  __getattr__ = lambda self, name: _swig_getattr(self, PDBSelector, name)
10036  def __init__(self, *args):
10037  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
10038  if self.__class__ == PDBSelector:
10039  _self = None
10040  else:
10041  _self = self
10042  this = _IMP_atom.new_PDBSelector(_self, *args)
10043  try: self.this.append(this)
10044  except: self.this = this
10045  if self.__class__ != PDBSelector:
10046  import IMP.base
10047  IMP.base._director_objects.register(self)
10048 
10049 
10050 
10051  def get_is_selected(self, *args):
10052  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
10053  return _IMP_atom.PDBSelector_get_is_selected(self, *args)
10054 
10055  __swig_destroy__ = _IMP_atom.delete_PDBSelector
10056  __del__ = lambda self : None;
10057  def __str__(self):
10058  """__str__(PDBSelector self) -> std::string"""
10059  return _IMP_atom.PDBSelector___str__(self)
10060 
10061  def __repr__(self):
10062  """__repr__(PDBSelector self) -> std::string"""
10063  return _IMP_atom.PDBSelector___repr__(self)
10064 
10065  def get_from(o):
10066  return _object_cast_to_PDBSelector(o)
10067  get_from = staticmethod(get_from)
10068 
10069  def get_type_name(self):
10070  return self.__class__.__name__
10071  def do_show(self, out):
10072  pass
10073  def get_version_info(self):
10074  if"IMP::atom" == "IMP":
10075  return VersionInfo("python", "0")
10076  else:
10077  return IMP.VersionInfo("python", "0")
10078  def get_from(o):
10079  return _object_cast_to_PDBSelector(o)
10080  get_from = staticmethod(get_from)
10081 
10082  def __disown__(self):
10083  self.this.disown()
10084  _IMP_atom.disown_PDBSelector(self)
10085  return weakref_proxy(self)
10086 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
10087 PDBSelector_swigregister(PDBSelector)
10088 
10089 class NonAlternativePDBSelector(PDBSelector):
10090  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class"""
10091  __swig_setmethods__ = {}
10092  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10093  __setattr__ = lambda self, name, value: _swig_setattr(self, NonAlternativePDBSelector, name, value)
10094  __swig_getmethods__ = {}
10095  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10096  __getattr__ = lambda self, name: _swig_getattr(self, NonAlternativePDBSelector, name)
10097  def __init__(self, name="NonAlternativePDBSelector%1%"):
10098  """
10099  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector
10100  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
10101  """
10102  this = _IMP_atom.new_NonAlternativePDBSelector(name)
10103  try: self.this.append(this)
10104  except: self.this = this
10105  def get_version_info(self):
10106  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
10107  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
10108 
10109  def __str__(self):
10110  """__str__(NonAlternativePDBSelector self) -> std::string"""
10111  return _IMP_atom.NonAlternativePDBSelector___str__(self)
10112 
10113  def __repr__(self):
10114  """__repr__(NonAlternativePDBSelector self) -> std::string"""
10115  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
10116 
10117  def get_from(o):
10118  return _object_cast_to_NonAlternativePDBSelector(o)
10119  get_from = staticmethod(get_from)
10120 
10121 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
10122 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
10123 
10124 class ATOMPDBSelector(NonAlternativePDBSelector):
10125  """Proxy of C++ IMP::atom::ATOMPDBSelector class"""
10126  __swig_setmethods__ = {}
10127  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10128  __setattr__ = lambda self, name, value: _swig_setattr(self, ATOMPDBSelector, name, value)
10129  __swig_getmethods__ = {}
10130  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10131  __getattr__ = lambda self, name: _swig_getattr(self, ATOMPDBSelector, name)
10132  def __init__(self, name="ATOMPDBSelector%1%"):
10133  """
10134  __init__(IMP::atom::ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector
10135  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
10136  """
10137  this = _IMP_atom.new_ATOMPDBSelector(name)
10138  try: self.this.append(this)
10139  except: self.this = this
10140  def __str__(self):
10141  """__str__(ATOMPDBSelector self) -> std::string"""
10142  return _IMP_atom.ATOMPDBSelector___str__(self)
10143 
10144  def __repr__(self):
10145  """__repr__(ATOMPDBSelector self) -> std::string"""
10146  return _IMP_atom.ATOMPDBSelector___repr__(self)
10147 
10148  def get_from(o):
10149  return _object_cast_to_ATOMPDBSelector(o)
10150  get_from = staticmethod(get_from)
10151 
10152 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
10153 ATOMPDBSelector_swigregister(ATOMPDBSelector)
10154 
10155 class CAlphaPDBSelector(NonAlternativePDBSelector):
10156  """Proxy of C++ IMP::atom::CAlphaPDBSelector class"""
10157  __swig_setmethods__ = {}
10158  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10159  __setattr__ = lambda self, name, value: _swig_setattr(self, CAlphaPDBSelector, name, value)
10160  __swig_getmethods__ = {}
10161  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10162  __getattr__ = lambda self, name: _swig_getattr(self, CAlphaPDBSelector, name)
10163  def __init__(self, name="CAlphaPDBSelector%1%"):
10164  """
10165  __init__(IMP::atom::CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector
10166  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
10167  """
10168  this = _IMP_atom.new_CAlphaPDBSelector(name)
10169  try: self.this.append(this)
10170  except: self.this = this
10171  def __str__(self):
10172  """__str__(CAlphaPDBSelector self) -> std::string"""
10173  return _IMP_atom.CAlphaPDBSelector___str__(self)
10174 
10175  def __repr__(self):
10176  """__repr__(CAlphaPDBSelector self) -> std::string"""
10177  return _IMP_atom.CAlphaPDBSelector___repr__(self)
10178 
10179  def get_from(o):
10180  return _object_cast_to_CAlphaPDBSelector(o)
10181  get_from = staticmethod(get_from)
10182 
10183 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
10184 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
10185 
10186 class CBetaPDBSelector(NonAlternativePDBSelector):
10187  """Proxy of C++ IMP::atom::CBetaPDBSelector class"""
10188  __swig_setmethods__ = {}
10189  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10190  __setattr__ = lambda self, name, value: _swig_setattr(self, CBetaPDBSelector, name, value)
10191  __swig_getmethods__ = {}
10192  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10193  __getattr__ = lambda self, name: _swig_getattr(self, CBetaPDBSelector, name)
10194  def __init__(self, name="CBetaPDBSelector%1%"):
10195  """
10196  __init__(IMP::atom::CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector
10197  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
10198  """
10199  this = _IMP_atom.new_CBetaPDBSelector(name)
10200  try: self.this.append(this)
10201  except: self.this = this
10202  def __str__(self):
10203  """__str__(CBetaPDBSelector self) -> std::string"""
10204  return _IMP_atom.CBetaPDBSelector___str__(self)
10205 
10206  def __repr__(self):
10207  """__repr__(CBetaPDBSelector self) -> std::string"""
10208  return _IMP_atom.CBetaPDBSelector___repr__(self)
10209 
10210  def get_from(o):
10211  return _object_cast_to_CBetaPDBSelector(o)
10212  get_from = staticmethod(get_from)
10213 
10214 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
10215 CBetaPDBSelector_swigregister(CBetaPDBSelector)
10216 
10217 class CPDBSelector(NonAlternativePDBSelector):
10218  """Proxy of C++ IMP::atom::CPDBSelector class"""
10219  __swig_setmethods__ = {}
10220  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10221  __setattr__ = lambda self, name, value: _swig_setattr(self, CPDBSelector, name, value)
10222  __swig_getmethods__ = {}
10223  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10224  __getattr__ = lambda self, name: _swig_getattr(self, CPDBSelector, name)
10225  def __init__(self, name="CPDBSelector%1%"):
10226  """
10227  __init__(IMP::atom::CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector
10228  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
10229  """
10230  this = _IMP_atom.new_CPDBSelector(name)
10231  try: self.this.append(this)
10232  except: self.this = this
10233  def __str__(self):
10234  """__str__(CPDBSelector self) -> std::string"""
10235  return _IMP_atom.CPDBSelector___str__(self)
10236 
10237  def __repr__(self):
10238  """__repr__(CPDBSelector self) -> std::string"""
10239  return _IMP_atom.CPDBSelector___repr__(self)
10240 
10241  def get_from(o):
10242  return _object_cast_to_CPDBSelector(o)
10243  get_from = staticmethod(get_from)
10244 
10245 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
10246 CPDBSelector_swigregister(CPDBSelector)
10247 
10248 class NPDBSelector(NonAlternativePDBSelector):
10249  """Proxy of C++ IMP::atom::NPDBSelector class"""
10250  __swig_setmethods__ = {}
10251  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10252  __setattr__ = lambda self, name, value: _swig_setattr(self, NPDBSelector, name, value)
10253  __swig_getmethods__ = {}
10254  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10255  __getattr__ = lambda self, name: _swig_getattr(self, NPDBSelector, name)
10256  def __init__(self, name="NPDBSelector%1%"):
10257  """
10258  __init__(IMP::atom::NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector
10259  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
10260  """
10261  this = _IMP_atom.new_NPDBSelector(name)
10262  try: self.this.append(this)
10263  except: self.this = this
10264  def __str__(self):
10265  """__str__(NPDBSelector self) -> std::string"""
10266  return _IMP_atom.NPDBSelector___str__(self)
10267 
10268  def __repr__(self):
10269  """__repr__(NPDBSelector self) -> std::string"""
10270  return _IMP_atom.NPDBSelector___repr__(self)
10271 
10272  def get_from(o):
10273  return _object_cast_to_NPDBSelector(o)
10274  get_from = staticmethod(get_from)
10275 
10276 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
10277 NPDBSelector_swigregister(NPDBSelector)
10278 
10279 class AllPDBSelector(PDBSelector):
10280  """Proxy of C++ IMP::atom::AllPDBSelector class"""
10281  __swig_setmethods__ = {}
10282  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10283  __setattr__ = lambda self, name, value: _swig_setattr(self, AllPDBSelector, name, value)
10284  __swig_getmethods__ = {}
10285  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10286  __getattr__ = lambda self, name: _swig_getattr(self, AllPDBSelector, name)
10287  def __init__(self, name="AllPDBSelector%1%"):
10288  """
10289  __init__(IMP::atom::AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector
10290  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
10291  """
10292  this = _IMP_atom.new_AllPDBSelector(name)
10293  try: self.this.append(this)
10294  except: self.this = this
10295  def get_version_info(self):
10296  """get_version_info(AllPDBSelector self) -> VersionInfo"""
10297  return _IMP_atom.AllPDBSelector_get_version_info(self)
10298 
10299  def __str__(self):
10300  """__str__(AllPDBSelector self) -> std::string"""
10301  return _IMP_atom.AllPDBSelector___str__(self)
10302 
10303  def __repr__(self):
10304  """__repr__(AllPDBSelector self) -> std::string"""
10305  return _IMP_atom.AllPDBSelector___repr__(self)
10306 
10307  def get_from(o):
10308  return _object_cast_to_AllPDBSelector(o)
10309  get_from = staticmethod(get_from)
10310 
10311 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
10312 AllPDBSelector_swigregister(AllPDBSelector)
10313 
10314 class ChainPDBSelector(NonAlternativePDBSelector):
10315  """Proxy of C++ IMP::atom::ChainPDBSelector class"""
10316  __swig_setmethods__ = {}
10317  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10318  __setattr__ = lambda self, name, value: _swig_setattr(self, ChainPDBSelector, name, value)
10319  __swig_getmethods__ = {}
10320  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10321  __getattr__ = lambda self, name: _swig_getattr(self, ChainPDBSelector, name)
10322  def __init__(self, *args):
10323  """
10324  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
10325  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
10326  """
10327  this = _IMP_atom.new_ChainPDBSelector(*args)
10328  try: self.this.append(this)
10329  except: self.this = this
10330  def __str__(self):
10331  """__str__(ChainPDBSelector self) -> std::string"""
10332  return _IMP_atom.ChainPDBSelector___str__(self)
10333 
10334  def __repr__(self):
10335  """__repr__(ChainPDBSelector self) -> std::string"""
10336  return _IMP_atom.ChainPDBSelector___repr__(self)
10337 
10338  def get_from(o):
10339  return _object_cast_to_ChainPDBSelector(o)
10340  get_from = staticmethod(get_from)
10341 
10342 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
10343 ChainPDBSelector_swigregister(ChainPDBSelector)
10344 
10345 class WaterPDBSelector(NonAlternativePDBSelector):
10346  """Proxy of C++ IMP::atom::WaterPDBSelector class"""
10347  __swig_setmethods__ = {}
10348  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10349  __setattr__ = lambda self, name, value: _swig_setattr(self, WaterPDBSelector, name, value)
10350  __swig_getmethods__ = {}
10351  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10352  __getattr__ = lambda self, name: _swig_getattr(self, WaterPDBSelector, name)
10353  def __init__(self, name="WaterPDBSelector%1%"):
10354  """
10355  __init__(IMP::atom::WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector
10356  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
10357  """
10358  this = _IMP_atom.new_WaterPDBSelector(name)
10359  try: self.this.append(this)
10360  except: self.this = this
10361  def __str__(self):
10362  """__str__(WaterPDBSelector self) -> std::string"""
10363  return _IMP_atom.WaterPDBSelector___str__(self)
10364 
10365  def __repr__(self):
10366  """__repr__(WaterPDBSelector self) -> std::string"""
10367  return _IMP_atom.WaterPDBSelector___repr__(self)
10368 
10369  def get_from(o):
10370  return _object_cast_to_WaterPDBSelector(o)
10371  get_from = staticmethod(get_from)
10372 
10373 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
10374 WaterPDBSelector_swigregister(WaterPDBSelector)
10375 
10376 class HydrogenPDBSelector(NonAlternativePDBSelector):
10377  """Proxy of C++ IMP::atom::HydrogenPDBSelector class"""
10378  __swig_setmethods__ = {}
10379  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10380  __setattr__ = lambda self, name, value: _swig_setattr(self, HydrogenPDBSelector, name, value)
10381  __swig_getmethods__ = {}
10382  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10383  __getattr__ = lambda self, name: _swig_getattr(self, HydrogenPDBSelector, name)
10384  def __init__(self, name="HydrogenPDBSelector%1%"):
10385  """
10386  __init__(IMP::atom::HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector
10387  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
10388  """
10389  this = _IMP_atom.new_HydrogenPDBSelector(name)
10390  try: self.this.append(this)
10391  except: self.this = this
10392  def __str__(self):
10393  """__str__(HydrogenPDBSelector self) -> std::string"""
10394  return _IMP_atom.HydrogenPDBSelector___str__(self)
10395 
10396  def __repr__(self):
10397  """__repr__(HydrogenPDBSelector self) -> std::string"""
10398  return _IMP_atom.HydrogenPDBSelector___repr__(self)
10399 
10400  def get_from(o):
10401  return _object_cast_to_HydrogenPDBSelector(o)
10402  get_from = staticmethod(get_from)
10403 
10404 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
10405 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
10406 
10407 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
10408  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class"""
10409  __swig_setmethods__ = {}
10410  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10411  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterNonHydrogenPDBSelector, name, value)
10412  __swig_getmethods__ = {}
10413  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10414  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterNonHydrogenPDBSelector, name)
10415  def __init__(self, *args):
10416  """
10417  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
10418  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
10419  """
10420  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
10421  try: self.this.append(this)
10422  except: self.this = this
10423  def __str__(self):
10424  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
10425  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
10426 
10427  def __repr__(self):
10428  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
10429  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
10430 
10431  def get_from(o):
10432  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
10433  get_from = staticmethod(get_from)
10434 
10435 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
10436 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
10437 
10438 class NonWaterPDBSelector(NonAlternativePDBSelector):
10439  """Proxy of C++ IMP::atom::NonWaterPDBSelector class"""
10440  __swig_setmethods__ = {}
10441  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10442  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterPDBSelector, name, value)
10443  __swig_getmethods__ = {}
10444  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10445  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterPDBSelector, name)
10446  def __init__(self, *args):
10447  """
10448  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
10449  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
10450  """
10451  this = _IMP_atom.new_NonWaterPDBSelector(*args)
10452  try: self.this.append(this)
10453  except: self.this = this
10454  def __str__(self):
10455  """__str__(NonWaterPDBSelector self) -> std::string"""
10456  return _IMP_atom.NonWaterPDBSelector___str__(self)
10457 
10458  def __repr__(self):
10459  """__repr__(NonWaterPDBSelector self) -> std::string"""
10460  return _IMP_atom.NonWaterPDBSelector___repr__(self)
10461 
10462  def get_from(o):
10463  return _object_cast_to_NonWaterPDBSelector(o)
10464  get_from = staticmethod(get_from)
10465 
10466 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
10467 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
10468 
10469 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
10470  """Proxy of C++ IMP::atom::BackbonePDBSelector class"""
10471  __swig_setmethods__ = {}
10472  for _s in [NonWaterNonHydrogenPDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10473  __setattr__ = lambda self, name, value: _swig_setattr(self, BackbonePDBSelector, name, value)
10474  __swig_getmethods__ = {}
10475  for _s in [NonWaterNonHydrogenPDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10476  __getattr__ = lambda self, name: _swig_getattr(self, BackbonePDBSelector, name)
10477  def __init__(self, name="BackbonePDBSelector%1%"):
10478  """
10479  __init__(IMP::atom::BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector
10480  __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
10481  """
10482  this = _IMP_atom.new_BackbonePDBSelector(name)
10483  try: self.this.append(this)
10484  except: self.this = this
10485  def __str__(self):
10486  """__str__(BackbonePDBSelector self) -> std::string"""
10487  return _IMP_atom.BackbonePDBSelector___str__(self)
10488 
10489  def __repr__(self):
10490  """__repr__(BackbonePDBSelector self) -> std::string"""
10491  return _IMP_atom.BackbonePDBSelector___repr__(self)
10492 
10493  def get_from(o):
10494  return _object_cast_to_BackbonePDBSelector(o)
10495  get_from = staticmethod(get_from)
10496 
10497 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
10498 BackbonePDBSelector_swigregister(BackbonePDBSelector)
10499 
10500 class PPDBSelector(NonAlternativePDBSelector):
10501  """Proxy of C++ IMP::atom::PPDBSelector class"""
10502  __swig_setmethods__ = {}
10503  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10504  __setattr__ = lambda self, name, value: _swig_setattr(self, PPDBSelector, name, value)
10505  __swig_getmethods__ = {}
10506  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10507  __getattr__ = lambda self, name: _swig_getattr(self, PPDBSelector, name)
10508  def __init__(self, name="PPDBSelector%1%"):
10509  """
10510  __init__(IMP::atom::PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector
10511  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
10512  """
10513  this = _IMP_atom.new_PPDBSelector(name)
10514  try: self.this.append(this)
10515  except: self.this = this
10516  def __str__(self):
10517  """__str__(PPDBSelector self) -> std::string"""
10518  return _IMP_atom.PPDBSelector___str__(self)
10519 
10520  def __repr__(self):
10521  """__repr__(PPDBSelector self) -> std::string"""
10522  return _IMP_atom.PPDBSelector___repr__(self)
10523 
10524  def get_from(o):
10525  return _object_cast_to_PPDBSelector(o)
10526  get_from = staticmethod(get_from)
10527 
10528 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
10529 PPDBSelector_swigregister(PPDBSelector)
10530 
10531 class AndPDBSelector(PDBSelector):
10532  """Proxy of C++ IMP::atom::AndPDBSelector class"""
10533  __swig_setmethods__ = {}
10534  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10535  __setattr__ = lambda self, name, value: _swig_setattr(self, AndPDBSelector, name, value)
10536  __swig_getmethods__ = {}
10537  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10538  __getattr__ = lambda self, name: _swig_getattr(self, AndPDBSelector, name)
10539  def get_version_info(self):
10540  """get_version_info(AndPDBSelector self) -> VersionInfo"""
10541  return _IMP_atom.AndPDBSelector_get_version_info(self)
10542 
10543  def __init__(self, *args):
10544  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
10545  this = _IMP_atom.new_AndPDBSelector(*args)
10546  try: self.this.append(this)
10547  except: self.this = this
10548  def __str__(self):
10549  """__str__(AndPDBSelector self) -> std::string"""
10550  return _IMP_atom.AndPDBSelector___str__(self)
10551 
10552  def __repr__(self):
10553  """__repr__(AndPDBSelector self) -> std::string"""
10554  return _IMP_atom.AndPDBSelector___repr__(self)
10555 
10556  def get_from(o):
10557  return _object_cast_to_AndPDBSelector(o)
10558  get_from = staticmethod(get_from)
10559 
10560 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
10561 AndPDBSelector_swigregister(AndPDBSelector)
10562 
10563 class OrPDBSelector(PDBSelector):
10564  """Proxy of C++ IMP::atom::OrPDBSelector class"""
10565  __swig_setmethods__ = {}
10566  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10567  __setattr__ = lambda self, name, value: _swig_setattr(self, OrPDBSelector, name, value)
10568  __swig_getmethods__ = {}
10569  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10570  __getattr__ = lambda self, name: _swig_getattr(self, OrPDBSelector, name)
10571  def get_version_info(self):
10572  """get_version_info(OrPDBSelector self) -> VersionInfo"""
10573  return _IMP_atom.OrPDBSelector_get_version_info(self)
10574 
10575  def __init__(self, *args):
10576  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
10577  this = _IMP_atom.new_OrPDBSelector(*args)
10578  try: self.this.append(this)
10579  except: self.this = this
10580  def __str__(self):
10581  """__str__(OrPDBSelector self) -> std::string"""
10582  return _IMP_atom.OrPDBSelector___str__(self)
10583 
10584  def __repr__(self):
10585  """__repr__(OrPDBSelector self) -> std::string"""
10586  return _IMP_atom.OrPDBSelector___repr__(self)
10587 
10588  def get_from(o):
10589  return _object_cast_to_OrPDBSelector(o)
10590  get_from = staticmethod(get_from)
10591 
10592 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
10593 OrPDBSelector_swigregister(OrPDBSelector)
10594 
10595 class NotPDBSelector(PDBSelector):
10596  """Proxy of C++ IMP::atom::NotPDBSelector class"""
10597  __swig_setmethods__ = {}
10598  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10599  __setattr__ = lambda self, name, value: _swig_setattr(self, NotPDBSelector, name, value)
10600  __swig_getmethods__ = {}
10601  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10602  __getattr__ = lambda self, name: _swig_getattr(self, NotPDBSelector, name)
10603  def get_version_info(self):
10604  """get_version_info(NotPDBSelector self) -> VersionInfo"""
10605  return _IMP_atom.NotPDBSelector_get_version_info(self)
10606 
10607  def __init__(self, *args):
10608  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
10609  this = _IMP_atom.new_NotPDBSelector(*args)
10610  try: self.this.append(this)
10611  except: self.this = this
10612  def __str__(self):
10613  """__str__(NotPDBSelector self) -> std::string"""
10614  return _IMP_atom.NotPDBSelector___str__(self)
10615 
10616  def __repr__(self):
10617  """__repr__(NotPDBSelector self) -> std::string"""
10618  return _IMP_atom.NotPDBSelector___repr__(self)
10619 
10620  def get_from(o):
10621  return _object_cast_to_NotPDBSelector(o)
10622  get_from = staticmethod(get_from)
10623 
10624 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
10625 NotPDBSelector_swigregister(NotPDBSelector)
10626 
10627 
10628 def get_default_pdb_selector():
10629  """get_default_pdb_selector() -> PDBSelector"""
10630  return _IMP_atom.get_default_pdb_selector()
10631 
10632 def read_pdb(*args):
10633  """
10634  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10635  bool select_first_model=True, bool no_radii=False) -> Hierarchy
10636  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10637  bool select_first_model=True) -> Hierarchy
10638  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector()) -> Hierarchy
10639  read_pdb(TextInput input, Model model) -> Hierarchy
10640  read_pdb(TextInput input, int model, Hierarchy h)
10641  """
10642  return _IMP_atom.read_pdb(*args)
10643 
10644 def read_multimodel_pdb(*args):
10645  """
10646  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10647  bool noradii=False) -> IMP::atom::Hierarchies
10648  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector()) -> IMP::atom::Hierarchies
10649  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
10650  """
10651  return _IMP_atom.read_multimodel_pdb(*args)
10652 
10653 def write_pdb(*args):
10654  """
10655  write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
10656  write_pdb(Selection mhd, TextOutput out)
10657  """
10658  return _IMP_atom.write_pdb(*args)
10659 
10660 def write_pdb_of_c_alphas(*args):
10661  """
10662  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
10663  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
10664  """
10665  return _IMP_atom.write_pdb_of_c_alphas(*args)
10666 
10667 def write_multimodel_pdb(*args):
10668  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
10669  return _IMP_atom.write_multimodel_pdb(*args)
10670 
10671 def get_pdb_string(*args):
10672  """
10673  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ',
10674  int res_index=1, char res_icode=' ', double occpancy=1.00, double tempFactor=0.00,
10675  IMP::atom::Element e=C) -> std::string
10676  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ',
10677  int res_index=1, char res_icode=' ', double occpancy=1.00, double tempFactor=0.00) -> std::string
10678  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ',
10679  int res_index=1, char res_icode=' ', double occpancy=1.00) -> std::string
10680  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ',
10681  int res_index=1, char res_icode=' ') -> std::string
10682  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ',
10683  int res_index=1) -> std::string
10684  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ') -> std::string
10685  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA) -> std::string
10686  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA) -> std::string
10687  get_pdb_string(Vector3D v, int index=-1) -> std::string
10688  get_pdb_string(Vector3D v) -> std::string
10689  """
10690  return _IMP_atom.get_pdb_string(*args)
10691 
10692 def get_pdb_conect_record_string(*args):
10693  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
10694  return _IMP_atom.get_pdb_conect_record_string(*args)
10695 class WritePDBOptimizerState(IMP.kernel.OptimizerState):
10696  """Proxy of C++ IMP::atom::WritePDBOptimizerState class"""
10697  __swig_setmethods__ = {}
10698  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10699  __setattr__ = lambda self, name, value: _swig_setattr(self, WritePDBOptimizerState, name, value)
10700  __swig_getmethods__ = {}
10701  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10702  __getattr__ = lambda self, name: _swig_getattr(self, WritePDBOptimizerState, name)
10703  def __init__(self, *args):
10704  """
10705  __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
10706  __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
10707  """
10708  this = _IMP_atom.new_WritePDBOptimizerState(*args)
10709  try: self.this.append(this)
10710  except: self.this = this
10711  def get_version_info(self):
10712  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
10713  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
10714 
10715  def __str__(self):
10716  """__str__(WritePDBOptimizerState self) -> std::string"""
10717  return _IMP_atom.WritePDBOptimizerState___str__(self)
10718 
10719  def __repr__(self):
10720  """__repr__(WritePDBOptimizerState self) -> std::string"""
10721  return _IMP_atom.WritePDBOptimizerState___repr__(self)
10722 
10723  def get_from(o):
10724  return _object_cast_to_WritePDBOptimizerState(o)
10725  get_from = staticmethod(get_from)
10726 
10727 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
10728 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
10729 
10730 
10731 def get_kt(*args):
10732  """get_kt(double T) -> double"""
10733  return _IMP_atom.get_kt(*args)
10734 
10735 def show_molecular_hierarchy(*args):
10736  """
10737  show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream
10738  show_molecular_hierarchy(Hierarchy h) -> _ostream
10739  """
10740  return _IMP_atom.show_molecular_hierarchy(*args)
10741 class CHARMMBond(_object):
10742  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class"""
10743  __swig_setmethods__ = {}
10744  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBond, name, value)
10745  __swig_getmethods__ = {}
10746  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBond, name)
10747  __repr__ = _swig_repr
10748  def __init__(self, *args):
10749  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
10750  this = _IMP_atom.new_CHARMMBond(*args)
10751  try: self.this.append(this)
10752  except: self.this = this
10753  def get_endpoint(self, *args):
10754  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
10755  return _IMP_atom.CHARMMBond_get_endpoint(self, *args)
10756 
10757  def get_contains_atom(self, *args):
10758  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
10759  return _IMP_atom.CHARMMBond_get_contains_atom(self, *args)
10760 
10761  def show(self, *args):
10762  """
10763  show(CHARMMBond self, _ostream out=std::cout)
10764  show(CHARMMBond self)
10765  """
10766  return _IMP_atom.CHARMMBond_show(self, *args)
10767 
10768  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
10769  __del__ = lambda self : None;
10770 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
10771 CHARMMBond_swigregister(CHARMMBond)
10772 
10773 class CHARMMAngle(_object):
10774  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class"""
10775  __swig_setmethods__ = {}
10776  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAngle, name, value)
10777  __swig_getmethods__ = {}
10778  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAngle, name)
10779  __repr__ = _swig_repr
10780  def __init__(self, *args):
10781  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
10782  this = _IMP_atom.new_CHARMMAngle(*args)
10783  try: self.this.append(this)
10784  except: self.this = this
10785  def get_endpoint(self, *args):
10786  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
10787  return _IMP_atom.CHARMMAngle_get_endpoint(self, *args)
10788 
10789  def get_contains_atom(self, *args):
10790  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
10791  return _IMP_atom.CHARMMAngle_get_contains_atom(self, *args)
10792 
10793  def show(self, *args):
10794  """
10795  show(CHARMMAngle self, _ostream out=std::cout)
10796  show(CHARMMAngle self)
10797  """
10798  return _IMP_atom.CHARMMAngle_show(self, *args)
10799 
10800  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
10801  __del__ = lambda self : None;
10802 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
10803 CHARMMAngle_swigregister(CHARMMAngle)
10804 
10805 
10806 def _get_native_overlap_cpp(*args):
10807  """
10808  _get_native_overlap_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10809  double threshold) -> double
10810  """
10811  return _IMP_atom._get_native_overlap_cpp(*args)
10812 
10813 def _get_drmsd_cpp(*args):
10814  """_get_drmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
10815  return _IMP_atom._get_drmsd_cpp(*args)
10816 
10817 def _get_drms_cpp(*args):
10818  """_get_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
10819  return _IMP_atom._get_drms_cpp(*args)
10820 
10821 def _get_rigid_bodies_drms_cpp(*args):
10822  """
10823  _get_rigid_bodies_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10824  IMP::IntRanges const & ranges) -> double
10825  """
10826  return _IMP_atom._get_rigid_bodies_drms_cpp(*args)
10827 def get_native_overlap(a, b, d):
10828  va= [IMP.algebra.get_vector(x) for x in a]
10829  vb= [IMP.algebra.get_vector(x) for x in b]
10830  return _get_native_overlap_cpp(va, vb, d)
10831 
10832 def get_drmsd(a, b):
10833  va= [IMP.algebra.get_vector(x) for x in a]
10834  vb= [IMP.algebra.get_vector(x) for x in b]
10835  return _get_drmsd_cpp(va, vb)
10836 
10837 def get_drms(a, b):
10838  va= [IMP.algebra.get_vector(x) for x in a]
10839  vb= [IMP.algebra.get_vector(x) for x in b]
10840  return _get_drms_cpp(va, vb)
10841 
10842 def get_rigid_bodies_drms(a, b, ranges):
10843  va= [IMP.algebra.get_vector(x) for x in a]
10844  vb= [IMP.algebra.get_vector(x) for x in b]
10845  #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
10846  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
10847 
10848 
10849 
10850 def get_module_version():
10851  """get_module_version() -> std::string const"""
10852  return _IMP_atom.get_module_version()
10853 
10854 def get_example_path(*args):
10855  """get_example_path(std::string fname) -> std::string"""
10856  return _IMP_atom.get_example_path(*args)
10857 
10858 def get_data_path(*args):
10859  """get_data_path(std::string fname) -> std::string"""
10860  return _IMP_atom.get_data_path(*args)
10861 import _version_check
10862 _version_check.check_version(get_module_version())
10863 
10864 # This file is compatible with both classic and new-style classes.
10865 
10866 
A base class for geometry contained in particles.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
Hierarchies get_leaves(Hierarchy h)
double get_kt(double T)
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
Hierarchies read_multimodel_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector())
Chain get_chain(Hierarchy h)
setup
Definition: setup.py:1
Atoms get_phi_dihedral_atoms(Residue rd)
void write_pdb(const Selection &mhd, base::TextOutput out, unsigned int model=1)
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_einstein_rotational_diffusion_coefficient(double r)
algebra::Sphere3D get_bounding_sphere(const Hierarchy &h)
kernel::ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
Ints get_index(const kernel::ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
double get_protein_density_from_reference(ProteinDensityReference densityReference)
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void setup_as_approximation(kernel::Particle *h, const kernel::ParticlesTemp &other)
double get_surface_area(const BoundingBoxD< 3 > &g)
Definition: BoundingBoxD.h:160
double get_mass(const Selection &s)
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
See IMP.container for more information.
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)
Hierarchy create_clone(Hierarchy d)
Clone the Hierarchy.
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate the root mean square deviation between two sets of 3D points.
Definition: atom/distance.h:88
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const kernel::Particles &ssr_ps, kernel::Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
Shared optimizer state that is invoked upon commitment of new coordinates.
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.
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
See IMP.cgal for more information.
Definition: cgal_config.h:107
double get_resolution(kernel::Model *m, kernel::ParticleIndex pi)
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Bonds get_internal_bonds(Hierarchy mhd)
Get the bonds internal to this tree.
See IMP.base for more information.
Definition: base/Array.h:20
A shared container for Pairs.
void write_multimodel_pdb(const Hierarchies &mhd, base::TextOutput out)
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 to particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
kernel::Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
bool get_is_heterogen(Hierarchy h)
Return true if the piece of hierarchy should be classified as a heterogen.
char get_one_letter_code(ResidueType c)
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
See IMP.score_functor for more information.
Definition: AddScores.h:14
A base class for modifiers of kernel::ParticlesTemp.
kernel::Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
double get_kd(double na, double nb, double nab, double volume)
Definition: estimates.h:94
Hierarchy read_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Abstract score function.
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)
Definition: BoundingBoxD.h:147
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &displacements, double dt)
Hierarchy create_fragment(const Hierarchies &ps)
Create a fragment containing the specified nodes.
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)
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.
Atoms get_psi_dihedral_atoms(Residue rd)
void write_pdb_of_c_alphas(const Selection &mhd, base::TextOutput out, unsigned int model=1)
Write a hierarchy to a pdb as C_alpha atoms.
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
void add_particles(RMF::FileHandle fh, const kernel::ParticlesTemp &hs)
See IMP.kernel for more information.
std::string show_graphviz(Graph g)
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
A restraint is a term in an IMP ScoringFunction.
double get_molarity(double n, double volume)
Definition: estimates.h:87
boost::graph HierarchyTree
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Definition: Vector3D.h:65
Hierarchy read_mol2(base::TextInput mol2_file, kernel::Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Hierarchy create_clone_one(Hierarchy d)
Clone the node in the Hierarchy.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void write_mol2(Hierarchy rhd, base::TextOutput file_name)
Write a lignand hierarchy as a mol2 file.
Abstract predicate function.
int get_state_index(Hierarchy h)
Common base class for heavy weight IMP objects.
Definition: base/Object.h:106
Base class for all optimizers.
kernel::Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
void destroy(Hierarchy d)
Delete the Hierarchy.
void add_protein_ligand_score_data(Hierarchy h)
std::string get_molecule_name(Hierarchy h)
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const kernel::Particles &ssr_ps, kernel::Model *mdl, bool winner_takes_all_per_res=false)
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.
See IMP.core for more information.
See IMP.algebra for more information.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
Abstract score function.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
kernel::Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Hierarchy create_protein(kernel::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.
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
base::Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 8 bounding points for the bounding box.
Definition: BoundingBoxD.h:256
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
int get_copy_index(Hierarchy h)
A decorator for helping deal with a hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
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.
char get_chain_id_char(Hierarchy h)
void add_particle(RMF::FileHandle fh, kernel::Particle *hs)
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
See IMP.display for more information.
Definition: ChimeraWriter.h:17
CheckLevel get_check_level()
Get the current audit mode.
std::string get_chain_id(Hierarchy h)
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
Abstract class to implement hierarchical methods.
CHARMMParameters * get_all_atom_CHARMM_parameters()
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)
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
double get_diffusion_length(double D, double t)
double get_einstein_diffusion_coefficient(double r)
BoundingBoxD< D > get_bounding_box(const BoundingBoxD< D > &g)
Definition: BoundingBoxD.h:160
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27