IMP  2.1.0
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.11
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 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
284 import IMP.score_functor
285 IMP_CORE_HAS_IMP_BASE = _IMP_atom.IMP_CORE_HAS_IMP_BASE
286 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
287 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
288 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
289 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
290 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
291 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
292 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
293 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
294 import IMP.core
295 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
296 IMP_CONTAINER_HAS_IMP_BASE = _IMP_atom.IMP_CONTAINER_HAS_IMP_BASE
297 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
298 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
299 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
300 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
301 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
302 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
303 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
304 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
305 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
306 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
307 import IMP.container
308 IMP_ATOM_HAS_IMP_BASE = _IMP_atom.IMP_ATOM_HAS_IMP_BASE
309 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
310 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
311 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
312 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
313 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
314 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
315 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
316 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
317 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
318 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
319 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
320 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
322  """Proxy of C++ IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class"""
323  __swig_setmethods__ = {}
324  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
325  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyTree, name, value)
326  __swig_getmethods__ = {}
327  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
328  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyTree, name)
329  __repr__ = _swig_repr
330  def __init__(self):
331  """__init__(IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
332  this = _IMP_atom.new_HierarchyTree()
333  try: self.this.append(this)
334  except: self.this = this
335  def get_graph(self):
336  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
337  return _IMP_atom.HierarchyTree_get_graph(self)
338 
339  def get_vertices(self):
340  """get_vertices(HierarchyTree self) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
341  return _IMP_atom.HierarchyTree_get_vertices(self)
342 
343  def get_vertex_name(self, *args):
344  """get_vertex_name(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
345  return _IMP_atom.HierarchyTree_get_vertex_name(self, *args)
346 
347  def get_in_neighbors(self, *args):
348  """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"""
349  return _IMP_atom.HierarchyTree_get_in_neighbors(self, *args)
350 
351  def get_out_neighbors(self, *args):
352  """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"""
353  return _IMP_atom.HierarchyTree_get_out_neighbors(self, *args)
354 
355  def show_graphviz(self, *args):
356  """
357  show_graphviz(HierarchyTree self, _ostream out=std::cout)
358  show_graphviz(HierarchyTree self)
359  """
360  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
361 
362  def get_graphviz_string(self):
363  """get_graphviz_string(HierarchyTree self) -> std::string"""
364  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
365 
366  def add_edge(self, *args):
367  """
368  add_edge(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0,
369  IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)
370  """
371  return _IMP_atom.HierarchyTree_add_edge(self, *args)
372 
373  def add_vertex(self, *args):
374  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
375  return _IMP_atom.HierarchyTree_add_vertex(self, *args)
376 
377  def remove_vertex(self, *args):
378  """remove_vertex(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
379  return _IMP_atom.HierarchyTree_remove_vertex(self, *args)
380 
381  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
382  __del__ = lambda self : None;
383 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
384 HierarchyTree_swigregister(HierarchyTree)
385 
386 _value_types.append("HierarchyTree")
387 
388 _object_types.append("PDBSelector")
389 
390 
391 def _object_cast_to_PDBSelector(*args):
392  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
393  return _IMP_atom._object_cast_to_PDBSelector(*args)
394 def Angles(l=[]):
395  return [Angle(x) for x in l]
396 _plural_types.append("Angles")
397 
398 _value_types.append("Angle")
399 
400 def Atoms(l=[]):
401  return [Atom(x) for x in l]
402 _plural_types.append("Atoms")
403 
404 _value_types.append("Atom")
405 
406 def Bonds(l=[]):
407  return [Bond(x) for x in l]
408 _plural_types.append("Bonds")
409 
410 _value_types.append("Bond")
411 
412 def Bondeds(l=[]):
413  return [Bonded(x) for x in l]
414 _plural_types.append("Bondeds")
415 
416 _value_types.append("Bonded")
417 
418 def CHARMMAtomList(l=[]):
419  return [CHARMMAtom(x) for x in l]
420 _plural_types.append("CHARMMAtomList")
421 
422 _value_types.append("CHARMMAtom")
423 
424 def Chains(l=[]):
425  return [Chain(x) for x in l]
426 _plural_types.append("Chains")
427 
428 _value_types.append("Chain")
429 
430 def Chargeds(l=[]):
431  return [Charged(x) for x in l]
432 _plural_types.append("Chargeds")
433 
434 _value_types.append("Charged")
435 
436 def Diffusions(l=[]):
437  return [Diffusion(x) for x in l]
438 _plural_types.append("Diffusions")
439 
440 _value_types.append("Diffusion")
441 
442 def RigidBodyDiffusions(l=[]):
443  return [RigidBodyDiffusion(x) for x in l]
444 _plural_types.append("RigidBodyDiffusions")
445 
446 _value_types.append("RigidBodyDiffusion")
447 
448 def Dihedrals(l=[]):
449  return [Dihedral(x) for x in l]
450 _plural_types.append("Dihedrals")
451 
452 _value_types.append("Dihedral")
453 
454 def Domains(l=[]):
455  return [Domain(x) for x in l]
456 _plural_types.append("Domains")
457 
458 _value_types.append("Domain")
459 
460 def Fragments(l=[]):
461  return [Fragment(x) for x in l]
462 _plural_types.append("Fragments")
463 
464 _value_types.append("Fragment")
465 
466 def Hierarchies(l=[]):
467  return [Hierarchy(x) for x in l]
468 _plural_types.append("Hierarchies")
469 
470 _value_types.append("Hierarchy")
471 
472 def LennardJonesList(l=[]):
473  return [LennardJones(x) for x in l]
474 _plural_types.append("LennardJonesList")
475 
476 _value_types.append("LennardJones")
477 
478 def Masses(l=[]):
479  return [Mass(x) for x in l]
480 _plural_types.append("Masses")
481 
482 _value_types.append("Mass")
483 
484 def Molecules(l=[]):
485  return [Molecule(x) for x in l]
486 _plural_types.append("Molecules")
487 
488 _value_types.append("Molecule")
489 
490 def Residues(l=[]):
491  return [Residue(x) for x in l]
492 _plural_types.append("Residues")
493 
494 _value_types.append("Residue")
495 
496 def Copies(l=[]):
497  return [Copy(x) for x in l]
498 _plural_types.append("Copies")
499 
500 _value_types.append("Copy")
501 
502 def SecondaryStructureResidues(l=[]):
503  return [SecondaryStructureResidue(x) for x in l]
504 _plural_types.append("SecondaryStructureResidues")
505 
506 _value_types.append("SecondaryStructureResidue")
507 
508 _object_types.append("Simulator")
509 
510 
511 def _object_cast_to_Simulator(*args):
512  """_object_cast_to_Simulator(Object o) -> Simulator"""
513  return _IMP_atom._object_cast_to_Simulator(*args)
514 _object_types.append("ATOMPDBSelector")
515 
516 
517 def _object_cast_to_ATOMPDBSelector(*args):
518  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
519  return _IMP_atom._object_cast_to_ATOMPDBSelector(*args)
520 _object_types.append("AllMol2Selector")
521 
522 
523 def _object_cast_to_AllMol2Selector(*args):
524  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
525  return _IMP_atom._object_cast_to_AllMol2Selector(*args)
526 _object_types.append("AllPDBSelector")
527 
528 
529 def _object_cast_to_AllPDBSelector(*args):
530  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
531  return _IMP_atom._object_cast_to_AllPDBSelector(*args)
532 _object_types.append("AndPDBSelector")
533 
534 
535 def _object_cast_to_AndPDBSelector(*args):
536  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
537  return _IMP_atom._object_cast_to_AndPDBSelector(*args)
538 _object_types.append("AngleSingletonScore")
539 
540 
541 def _object_cast_to_AngleSingletonScore(*args):
542  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
543  return _IMP_atom._object_cast_to_AngleSingletonScore(*args)
544 _object_types.append("BondEndpointsRefiner")
545 
546 
547 def _object_cast_to_BondEndpointsRefiner(*args):
548  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
549  return _IMP_atom._object_cast_to_BondEndpointsRefiner(*args)
550 _object_types.append("BondPairContainer")
551 
552 
553 def _object_cast_to_BondPairContainer(*args):
554  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
555  return _IMP_atom._object_cast_to_BondPairContainer(*args)
556 _object_types.append("BondSingletonScore")
557 
558 
559 def _object_cast_to_BondSingletonScore(*args):
560  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
561  return _IMP_atom._object_cast_to_BondSingletonScore(*args)
562 _object_types.append("BondedPairFilter")
563 
564 
565 def _object_cast_to_BondedPairFilter(*args):
566  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
567  return _IMP_atom._object_cast_to_BondedPairFilter(*args)
568 _object_types.append("BrownianDynamics")
569 
570 
571 def _object_cast_to_BrownianDynamics(*args):
572  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
573  return _IMP_atom._object_cast_to_BrownianDynamics(*args)
574 _object_types.append("CAlphaPDBSelector")
575 
576 
577 def _object_cast_to_CAlphaPDBSelector(*args):
578  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
579  return _IMP_atom._object_cast_to_CAlphaPDBSelector(*args)
580 _object_types.append("CBetaPDBSelector")
581 
582 
583 def _object_cast_to_CBetaPDBSelector(*args):
584  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
585  return _IMP_atom._object_cast_to_CBetaPDBSelector(*args)
586 _object_types.append("BackbonePDBSelector")
587 
588 
589 def _object_cast_to_BackbonePDBSelector(*args):
590  """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
591  return _IMP_atom._object_cast_to_BackbonePDBSelector(*args)
592 _object_types.append("CHARMMParameters")
593 
594 
595 def _object_cast_to_CHARMMParameters(*args):
596  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
597  return _IMP_atom._object_cast_to_CHARMMParameters(*args)
598 _object_types.append("CHARMMResidueTopology")
599 
600 
601 def _object_cast_to_CHARMMResidueTopology(*args):
602  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
603  return _IMP_atom._object_cast_to_CHARMMResidueTopology(*args)
604 _object_types.append("CHARMMSegmentTopology")
605 
606 
607 def _object_cast_to_CHARMMSegmentTopology(*args):
608  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
609  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(*args)
610 _object_types.append("CHARMMStereochemistryRestraint")
611 
612 
613 def _object_cast_to_CHARMMStereochemistryRestraint(*args):
614  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
615  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(*args)
616 _object_types.append("CHARMMTopology")
617 
618 
619 def _object_cast_to_CHARMMTopology(*args):
620  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
621  return _IMP_atom._object_cast_to_CHARMMTopology(*args)
622 _object_types.append("CPDBSelector")
623 
624 
625 def _object_cast_to_CPDBSelector(*args):
626  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
627  return _IMP_atom._object_cast_to_CPDBSelector(*args)
628 _object_types.append("ChainPDBSelector")
629 
630 
631 def _object_cast_to_ChainPDBSelector(*args):
632  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
633  return _IMP_atom._object_cast_to_ChainPDBSelector(*args)
634 _object_types.append("CoulombPairScore")
635 
636 
637 def _object_cast_to_CoulombPairScore(*args):
638  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
639  return _IMP_atom._object_cast_to_CoulombPairScore(*args)
640 _object_types.append("CoverBond")
641 
642 
643 def _object_cast_to_CoverBond(*args):
644  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
645  return _IMP_atom._object_cast_to_CoverBond(*args)
646 _object_types.append("DihedralSingletonScore")
647 
648 
649 def _object_cast_to_DihedralSingletonScore(*args):
650  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
651  return _IMP_atom._object_cast_to_DihedralSingletonScore(*args)
652 _object_types.append("DopePairScore")
653 
654 
655 def _object_cast_to_DopePairScore(*args):
656  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
657  return _IMP_atom._object_cast_to_DopePairScore(*args)
658 _object_types.append("EzRestraint")
659 
660 
661 def _object_cast_to_EzRestraint(*args):
662  """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
663  return _IMP_atom._object_cast_to_EzRestraint(*args)
664 _object_types.append("ForceFieldParameters")
665 
666 
667 def _object_cast_to_ForceFieldParameters(*args):
668  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
669  return _IMP_atom._object_cast_to_ForceFieldParameters(*args)
670 _object_types.append("ForceSwitch")
671 
672 
673 def _object_cast_to_ForceSwitch(*args):
674  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
675  return _IMP_atom._object_cast_to_ForceSwitch(*args)
676 _object_types.append("HydrogenPDBSelector")
677 
678 
679 def _object_cast_to_HydrogenPDBSelector(*args):
680  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
681  return _IMP_atom._object_cast_to_HydrogenPDBSelector(*args)
682 _object_types.append("ImproperSingletonScore")
683 
684 
685 def _object_cast_to_ImproperSingletonScore(*args):
686  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
687  return _IMP_atom._object_cast_to_ImproperSingletonScore(*args)
688 _object_types.append("LennardJonesPairScore")
689 
690 
691 def _object_cast_to_LennardJonesPairScore(*args):
692  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
693  return _IMP_atom._object_cast_to_LennardJonesPairScore(*args)
694 _object_types.append("Mol2Selector")
695 
696 
697 def _object_cast_to_Mol2Selector(*args):
698  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
699  return _IMP_atom._object_cast_to_Mol2Selector(*args)
700 _object_types.append("MolecularDynamics")
701 
702 
703 def _object_cast_to_MolecularDynamics(*args):
704  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
705  return _IMP_atom._object_cast_to_MolecularDynamics(*args)
706 _object_types.append("NPDBSelector")
707 
708 
709 def _object_cast_to_NPDBSelector(*args):
710  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
711  return _IMP_atom._object_cast_to_NPDBSelector(*args)
712 _object_types.append("NonAlternativePDBSelector")
713 
714 
715 def _object_cast_to_NonAlternativePDBSelector(*args):
716  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
717  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(*args)
718 _object_types.append("NonHydrogenMol2Selector")
719 
720 
721 def _object_cast_to_NonHydrogenMol2Selector(*args):
722  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
723  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(*args)
724 _object_types.append("NonWaterNonHydrogenPDBSelector")
725 
726 
727 def _object_cast_to_NonWaterNonHydrogenPDBSelector(*args):
728  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
729  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(*args)
730 _object_types.append("NonWaterPDBSelector")
731 
732 
733 def _object_cast_to_NonWaterPDBSelector(*args):
734  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
735  return _IMP_atom._object_cast_to_NonWaterPDBSelector(*args)
736 _object_types.append("NotPDBSelector")
737 
738 
739 def _object_cast_to_NotPDBSelector(*args):
740  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
741  return _IMP_atom._object_cast_to_NotPDBSelector(*args)
742 _object_types.append("OrPDBSelector")
743 
744 
745 def _object_cast_to_OrPDBSelector(*args):
746  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
747  return _IMP_atom._object_cast_to_OrPDBSelector(*args)
748 _object_types.append("PPDBSelector")
749 
750 
751 def _object_cast_to_PPDBSelector(*args):
752  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
753  return _IMP_atom._object_cast_to_PPDBSelector(*args)
754 _object_types.append("ProteinLigandAtomPairScore")
755 
756 
757 def _object_cast_to_ProteinLigandAtomPairScore(*args):
758  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
759  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(*args)
760 _object_types.append("ProteinLigandRestraint")
761 
762 
763 def _object_cast_to_ProteinLigandRestraint(*args):
764  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
765  return _IMP_atom._object_cast_to_ProteinLigandRestraint(*args)
766 _object_types.append("SameResiduePairFilter")
767 
768 
769 def _object_cast_to_SameResiduePairFilter(*args):
770  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
771  return _IMP_atom._object_cast_to_SameResiduePairFilter(*args)
772 _object_types.append("SmoothingFunction")
773 
774 
775 def _object_cast_to_SmoothingFunction(*args):
776  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
777  return _IMP_atom._object_cast_to_SmoothingFunction(*args)
778 _object_types.append("StereochemistryPairFilter")
779 
780 
781 def _object_cast_to_StereochemistryPairFilter(*args):
782  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
783  return _IMP_atom._object_cast_to_StereochemistryPairFilter(*args)
784 _object_types.append("VelocityScalingOptimizerState")
785 
786 
787 def _object_cast_to_VelocityScalingOptimizerState(*args):
788  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
789  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(*args)
790 _object_types.append("WaterPDBSelector")
791 
792 
793 def _object_cast_to_WaterPDBSelector(*args):
794  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
795  return _IMP_atom._object_cast_to_WaterPDBSelector(*args)
796 _object_types.append("WritePDBOptimizerState")
797 
798 
799 def _object_cast_to_WritePDBOptimizerState(*args):
800  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
801  return _IMP_atom._object_cast_to_WritePDBOptimizerState(*args)
802 AtomTypes=list
803 _plural_types.append("AtomTypes")
804 _value_types.append("AtomType")
805 
806 CHARMMAtomTopologies=list
807 _plural_types.append("CHARMMAtomTopologies")
808 _value_types.append("CHARMMAtomTopology")
809 
810 CHARMMBondEndpoints=list
811 _plural_types.append("CHARMMBondEndpoints")
812 _value_types.append("CHARMMBondEndpoint")
813 
814 CHARMMBondParametersList=list
815 _plural_types.append("CHARMMBondParametersList")
816 _value_types.append("CHARMMBondParameters")
817 
818 CHARMMDihedralParametersList=list
819 _plural_types.append("CHARMMDihedralParametersList")
820 _value_types.append("CHARMMDihedralParameters")
821 
822 _object_types.append("CHARMMIdealResidueTopology")
823 
824 
825 def _object_cast_to_CHARMMIdealResidueTopology(*args):
826  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
827  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(*args)
828 CHARMMInternalCoordinates=list
829 _plural_types.append("CHARMMInternalCoordinates")
830 _value_types.append("CHARMMInternalCoordinate")
831 
832 _object_types.append("CHARMMPatch")
833 
834 
835 def _object_cast_to_CHARMMPatch(*args):
836  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
837  return _IMP_atom._object_cast_to_CHARMMPatch(*args)
838 _object_types.append("CHARMMResidueTopologyBase")
839 
840 
841 def _object_cast_to_CHARMMResidueTopologyBase(*args):
842  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
843  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(*args)
844 ResidueTypes=list
845 _plural_types.append("ResidueTypes")
846 _value_types.append("ResidueType")
847 
848 Selections=list
849 _plural_types.append("Selections")
850 _value_types.append("Selection")
851 
852 _object_types.append("RemoveRigidMotionOptimizerState")
853 
854 
855 def _object_cast_to_RemoveRigidMotionOptimizerState(*args):
856  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
857  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(*args)
858 _object_types.append("BerendsenThermostatOptimizerState")
859 
860 
861 def _object_cast_to_BerendsenThermostatOptimizerState(*args):
862  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
863  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(*args)
864 _object_types.append("LangevinThermostatOptimizerState")
865 
866 
867 def _object_cast_to_LangevinThermostatOptimizerState(*args):
868  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
869  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(*args)
870 _object_types.append("SelectionGeometry")
871 
872 
873 def _object_cast_to_SelectionGeometry(*args):
874  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
875  return _IMP_atom._object_cast_to_SelectionGeometry(*args)
876 _object_types.append("HierarchyGeometry")
877 
878 
879 def _object_cast_to_HierarchyGeometry(*args):
880  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
881  return _IMP_atom._object_cast_to_HierarchyGeometry(*args)
882 _object_types.append("HierarchiesGeometry")
883 
884 
885 def _object_cast_to_HierarchiesGeometry(*args):
886  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
887  return _IMP_atom._object_cast_to_HierarchiesGeometry(*args)
888 _object_types.append("BondGeometry")
889 
890 
891 def _object_cast_to_BondGeometry(*args):
892  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
893  return _IMP_atom._object_cast_to_BondGeometry(*args)
894 _object_types.append("BondsGeometry")
895 
896 
897 def _object_cast_to_BondsGeometry(*args):
898  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
899  return _IMP_atom._object_cast_to_BondsGeometry(*args)
900 CHARMMDihedrals=list
901 _plural_types.append("CHARMMDihedrals")
902 _value_types.append("CHARMMDihedral")
903 
904 CHARMMBonds=list
905 _plural_types.append("CHARMMBonds")
906 _value_types.append("CHARMMBond")
907 
908 CHARMMAngles=list
909 _plural_types.append("CHARMMAngles")
910 _value_types.append("CHARMMAngle")
911 
912 class Bond(IMP.kernel.Decorator):
913  """Proxy of C++ IMP::atom::Bond class"""
914  __swig_setmethods__ = {}
915  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
916  __setattr__ = lambda self, name, value: _swig_setattr(self, Bond, name, value)
917  __swig_getmethods__ = {}
918  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
919  __getattr__ = lambda self, name: _swig_getattr(self, Bond, name)
920  def __init__(self, *args):
921  """
922  __init__(IMP::atom::Bond self) -> Bond
923  __init__(IMP::atom::Bond self, Model m, ::IMP::kernel::ParticleIndex id) -> Bond
924  __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
925  """
926  this = _IMP_atom.new_Bond(*args)
927  try: self.this.append(this)
928  except: self.this = this
929  def decorate_particle(*args):
930  """decorate_particle(Particle p) -> Bond"""
931  return _IMP_atom.Bond_decorate_particle(*args)
932 
933  if _newclass:decorate_particle = staticmethod(decorate_particle)
934  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
935  def particle_is_instance(*args):
936  """
937  particle_is_instance(Particle p) -> bool
938  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
939  """
940  return _IMP_atom.Bond_particle_is_instance(*args)
941 
942  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
943  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
944  def show(self, *args):
945  """
946  show(Bond self, _ostream out=std::cout)
947  show(Bond self)
948  """
949  return _IMP_atom.Bond_show(self, *args)
950 
951  def get_is_setup(*args):
952  """
953  get_is_setup(_ParticleAdaptor p) -> bool
954  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
955  """
956  return _IMP_atom.Bond_get_is_setup(*args)
957 
958  if _newclass:get_is_setup = staticmethod(get_is_setup)
959  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
960  UNKNOWN = _IMP_atom.Bond_UNKNOWN
961  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
962  SINGLE = _IMP_atom.Bond_SINGLE
963  DOUBLE = _IMP_atom.Bond_DOUBLE
964  TRIPLE = _IMP_atom.Bond_TRIPLE
965  HYDROGEN = _IMP_atom.Bond_HYDROGEN
966  SALT = _IMP_atom.Bond_SALT
967  PEPTIDE = _IMP_atom.Bond_PEPTIDE
968  AMIDE = _IMP_atom.Bond_AMIDE
969  AROMATIC = _IMP_atom.Bond_AROMATIC
970  def get_bonded(self, *args):
971  """get_bonded(Bond self, unsigned int i) -> Bonded"""
972  return _IMP_atom.Bond_get_bonded(self, *args)
973 
974  def get_type(self):
975  """get_type(Bond self) -> IMP::Int"""
976  return _IMP_atom.Bond_get_type(self)
977 
978  def set_type(self, *args):
979  """set_type(Bond self, IMP::Int t)"""
980  return _IMP_atom.Bond_set_type(self, *args)
981 
982  def get_order(self):
983  """get_order(Bond self) -> IMP::Int"""
984  return _IMP_atom.Bond_get_order(self)
985 
986  def set_order(self, *args):
987  """set_order(Bond self, IMP::Int t)"""
988  return _IMP_atom.Bond_set_order(self, *args)
989 
990  def get_length(self):
991  """get_length(Bond self) -> IMP::Float"""
992  return _IMP_atom.Bond_get_length(self)
993 
994  def set_length(self, *args):
995  """set_length(Bond self, IMP::Float t)"""
996  return _IMP_atom.Bond_set_length(self, *args)
997 
998  def get_stiffness(self):
999  """get_stiffness(Bond self) -> IMP::Float"""
1000  return _IMP_atom.Bond_get_stiffness(self)
1001 
1002  def set_stiffness(self, *args):
1003  """set_stiffness(Bond self, IMP::Float t)"""
1004  return _IMP_atom.Bond_set_stiffness(self, *args)
1005 
1006  def get_length_key():
1007  """get_length_key() -> FloatKey"""
1008  return _IMP_atom.Bond_get_length_key()
1009 
1010  if _newclass:get_length_key = staticmethod(get_length_key)
1011  __swig_getmethods__["get_length_key"] = lambda x: get_length_key
1012  def add_attribute(self, *args):
1013  """
1014  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1015  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1016  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1017  add_attribute(Bond self, StringKey a0, IMP::String a1)
1018  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1019  add_attribute(Bond self, ObjectKey a0, IMP::Object * a1)
1020  """
1021  return _IMP_atom.Bond_add_attribute(self, *args)
1022 
1023  def get_value(self, *args):
1024  """
1025  get_value(Bond self, FloatKey a0) -> IMP::Float
1026  get_value(Bond self, IntKey a0) -> IMP::Int
1027  get_value(Bond self, StringKey a0) -> IMP::String
1028  get_value(Bond self, ParticleIndexKey a0) -> Particle
1029  get_value(Bond self, ObjectKey a0) -> IMP::Object *
1030  """
1031  return _IMP_atom.Bond_get_value(self, *args)
1032 
1033  def set_value(self, *args):
1034  """
1035  set_value(Bond self, FloatKey a0, IMP::Float a1)
1036  set_value(Bond self, IntKey a0, IMP::Int a1)
1037  set_value(Bond self, StringKey a0, IMP::String a1)
1038  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1039  set_value(Bond self, ObjectKey a0, IMP::Object * a1)
1040  """
1041  return _IMP_atom.Bond_set_value(self, *args)
1042 
1043  def remove_attribute(self, *args):
1044  """
1045  remove_attribute(Bond self, FloatKey a0)
1046  remove_attribute(Bond self, IntKey a0)
1047  remove_attribute(Bond self, StringKey a0)
1048  remove_attribute(Bond self, ParticleIndexKey a0)
1049  remove_attribute(Bond self, ObjectKey a0)
1050  """
1051  return _IMP_atom.Bond_remove_attribute(self, *args)
1052 
1053  def has_attribute(self, *args):
1054  """
1055  has_attribute(Bond self, FloatKey a0) -> bool
1056  has_attribute(Bond self, IntKey a0) -> bool
1057  has_attribute(Bond self, StringKey a0) -> bool
1058  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1059  has_attribute(Bond self, ObjectKey a0) -> bool
1060  """
1061  return _IMP_atom.Bond_has_attribute(self, *args)
1062 
1063  def get_derivative(self, *args):
1064  """get_derivative(Bond self, FloatKey a0) -> double"""
1065  return _IMP_atom.Bond_get_derivative(self, *args)
1066 
1067  def get_name(self):
1068  """get_name(Bond self) -> std::string"""
1069  return _IMP_atom.Bond_get_name(self)
1070 
1071  def clear_caches(self):
1072  """clear_caches(Bond self)"""
1073  return _IMP_atom.Bond_clear_caches(self)
1074 
1075  def set_name(self, *args):
1076  """set_name(Bond self, std::string a0)"""
1077  return _IMP_atom.Bond_set_name(self, *args)
1078 
1079  def set_check_level(self, *args):
1080  """set_check_level(Bond self, IMP::base::CheckLevel a0)"""
1081  return _IMP_atom.Bond_set_check_level(self, *args)
1082 
1083  def add_to_derivative(self, *args):
1084  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1085  return _IMP_atom.Bond_add_to_derivative(self, *args)
1086 
1087  def set_is_optimized(self, *args):
1088  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1089  return _IMP_atom.Bond_set_is_optimized(self, *args)
1090 
1091  def get_is_optimized(self, *args):
1092  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1093  return _IMP_atom.Bond_get_is_optimized(self, *args)
1094 
1095  def get_check_level(self):
1096  """get_check_level(Bond self) -> IMP::base::CheckLevel"""
1097  return _IMP_atom.Bond_get_check_level(self)
1098 
1099  def __eq__(self, *args):
1100  """
1101  __eq__(Bond self, Bond o) -> bool
1102  __eq__(Bond self, Particle d) -> bool
1103  """
1104  return _IMP_atom.Bond___eq__(self, *args)
1105 
1106  def __ne__(self, *args):
1107  """
1108  __ne__(Bond self, Bond o) -> bool
1109  __ne__(Bond self, Particle d) -> bool
1110  """
1111  return _IMP_atom.Bond___ne__(self, *args)
1112 
1113  def __le__(self, *args):
1114  """
1115  __le__(Bond self, Bond o) -> bool
1116  __le__(Bond self, Particle d) -> bool
1117  """
1118  return _IMP_atom.Bond___le__(self, *args)
1119 
1120  def __lt__(self, *args):
1121  """
1122  __lt__(Bond self, Bond o) -> bool
1123  __lt__(Bond self, Particle d) -> bool
1124  """
1125  return _IMP_atom.Bond___lt__(self, *args)
1126 
1127  def __ge__(self, *args):
1128  """
1129  __ge__(Bond self, Bond o) -> bool
1130  __ge__(Bond self, Particle d) -> bool
1131  """
1132  return _IMP_atom.Bond___ge__(self, *args)
1133 
1134  def __gt__(self, *args):
1135  """
1136  __gt__(Bond self, Bond o) -> bool
1137  __gt__(Bond self, Particle d) -> bool
1138  """
1139  return _IMP_atom.Bond___gt__(self, *args)
1140 
1141  def __str__(self):
1142  """__str__(Bond self) -> std::string"""
1143  return _IMP_atom.Bond___str__(self)
1144 
1145  def __repr__(self):
1146  """__repr__(Bond self) -> std::string"""
1147  return _IMP_atom.Bond___repr__(self)
1148 
1149  __swig_destroy__ = _IMP_atom.delete_Bond
1150  __del__ = lambda self : None;
1151 Bond_swigregister = _IMP_atom.Bond_swigregister
1152 Bond_swigregister(Bond)
1153 
1154 def Bond_decorate_particle(*args):
1155  """Bond_decorate_particle(Particle p) -> Bond"""
1156  return _IMP_atom.Bond_decorate_particle(*args)
1157 
1158 def Bond_particle_is_instance(*args):
1159  """
1160  particle_is_instance(Particle p) -> bool
1161  Bond_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
1162  """
1163  return _IMP_atom.Bond_particle_is_instance(*args)
1164 
1165 def Bond_get_is_setup(*args):
1166  """
1167  get_is_setup(_ParticleAdaptor p) -> bool
1168  Bond_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1169  """
1170  return _IMP_atom.Bond_get_is_setup(*args)
1171 
1172 def Bond_get_length_key():
1173  """Bond_get_length_key() -> FloatKey"""
1174  return _IMP_atom.Bond_get_length_key()
1175 
1176 class Bonded(IMP.kernel.Decorator):
1177  """Proxy of C++ IMP::atom::Bonded class"""
1178  __swig_setmethods__ = {}
1179  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1180  __setattr__ = lambda self, name, value: _swig_setattr(self, Bonded, name, value)
1181  __swig_getmethods__ = {}
1182  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1183  __getattr__ = lambda self, name: _swig_getattr(self, Bonded, name)
1184  def __init__(self, *args):
1185  """
1186  __init__(IMP::atom::Bonded self) -> Bonded
1187  __init__(IMP::atom::Bonded self, Model m, ::IMP::kernel::ParticleIndex id) -> Bonded
1188  __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1189  """
1190  this = _IMP_atom.new_Bonded(*args)
1191  try: self.this.append(this)
1192  except: self.this = this
1193  def decorate_particle(*args):
1194  """decorate_particle(Particle p) -> Bonded"""
1195  return _IMP_atom.Bonded_decorate_particle(*args)
1196 
1197  if _newclass:decorate_particle = staticmethod(decorate_particle)
1198  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1199  def particle_is_instance(*args):
1200  """
1201  particle_is_instance(Particle p) -> bool
1202  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
1203  """
1204  return _IMP_atom.Bonded_particle_is_instance(*args)
1205 
1206  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1207  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1208  def show(self, *args):
1209  """
1210  show(Bonded self, _ostream out=std::cout)
1211  show(Bonded self)
1212  """
1213  return _IMP_atom.Bonded_show(self, *args)
1214 
1215  def setup_particle(*args):
1216  """
1217  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Bonded
1218  setup_particle(_ParticleAdaptor decorator) -> Bonded
1219  """
1220  return _IMP_atom.Bonded_setup_particle(*args)
1221 
1222  if _newclass:setup_particle = staticmethod(setup_particle)
1223  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1224  def get_is_setup(*args):
1225  """
1226  get_is_setup(_ParticleAdaptor p) -> bool
1227  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1228  """
1229  return _IMP_atom.Bonded_get_is_setup(*args)
1230 
1231  if _newclass:get_is_setup = staticmethod(get_is_setup)
1232  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1233  def get_number_of_bonds(self):
1234  """get_number_of_bonds(Bonded self) -> unsigned int"""
1235  return _IMP_atom.Bonded_get_number_of_bonds(self)
1236 
1237  def get_bonds(self):
1238  """get_bonds(Bonded self) -> IMP::kernel::ParticleIndexes"""
1239  return _IMP_atom.Bonded_get_bonds(self)
1240 
1241  def get_bond_indexes(self):
1242  """get_bond_indexes(Bonded self) -> IMP::kernel::ParticleIndexes"""
1243  return _IMP_atom.Bonded_get_bond_indexes(self)
1244 
1245  def get_bond(self, *args):
1246  """get_bond(Bonded self, unsigned int i) -> Bond"""
1247  return _IMP_atom.Bonded_get_bond(self, *args)
1248 
1249  def get_bonded(self, *args):
1250  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1251  return _IMP_atom.Bonded_get_bonded(self, *args)
1252 
1253  def add_attribute(self, *args):
1254  """
1255  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1256  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1257  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1258  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1259  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1260  add_attribute(Bonded self, ObjectKey a0, IMP::Object * a1)
1261  """
1262  return _IMP_atom.Bonded_add_attribute(self, *args)
1263 
1264  def get_value(self, *args):
1265  """
1266  get_value(Bonded self, FloatKey a0) -> IMP::Float
1267  get_value(Bonded self, IntKey a0) -> IMP::Int
1268  get_value(Bonded self, StringKey a0) -> IMP::String
1269  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1270  get_value(Bonded self, ObjectKey a0) -> IMP::Object *
1271  """
1272  return _IMP_atom.Bonded_get_value(self, *args)
1273 
1274  def set_value(self, *args):
1275  """
1276  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1277  set_value(Bonded self, IntKey a0, IMP::Int a1)
1278  set_value(Bonded self, StringKey a0, IMP::String a1)
1279  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1280  set_value(Bonded self, ObjectKey a0, IMP::Object * a1)
1281  """
1282  return _IMP_atom.Bonded_set_value(self, *args)
1283 
1284  def remove_attribute(self, *args):
1285  """
1286  remove_attribute(Bonded self, FloatKey a0)
1287  remove_attribute(Bonded self, IntKey a0)
1288  remove_attribute(Bonded self, StringKey a0)
1289  remove_attribute(Bonded self, ParticleIndexKey a0)
1290  remove_attribute(Bonded self, ObjectKey a0)
1291  """
1292  return _IMP_atom.Bonded_remove_attribute(self, *args)
1293 
1294  def has_attribute(self, *args):
1295  """
1296  has_attribute(Bonded self, FloatKey a0) -> bool
1297  has_attribute(Bonded self, IntKey a0) -> bool
1298  has_attribute(Bonded self, StringKey a0) -> bool
1299  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1300  has_attribute(Bonded self, ObjectKey a0) -> bool
1301  """
1302  return _IMP_atom.Bonded_has_attribute(self, *args)
1303 
1304  def get_derivative(self, *args):
1305  """get_derivative(Bonded self, FloatKey a0) -> double"""
1306  return _IMP_atom.Bonded_get_derivative(self, *args)
1307 
1308  def get_name(self):
1309  """get_name(Bonded self) -> std::string"""
1310  return _IMP_atom.Bonded_get_name(self)
1311 
1312  def clear_caches(self):
1313  """clear_caches(Bonded self)"""
1314  return _IMP_atom.Bonded_clear_caches(self)
1315 
1316  def set_name(self, *args):
1317  """set_name(Bonded self, std::string a0)"""
1318  return _IMP_atom.Bonded_set_name(self, *args)
1319 
1320  def set_check_level(self, *args):
1321  """set_check_level(Bonded self, IMP::base::CheckLevel a0)"""
1322  return _IMP_atom.Bonded_set_check_level(self, *args)
1323 
1324  def add_to_derivative(self, *args):
1325  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1326  return _IMP_atom.Bonded_add_to_derivative(self, *args)
1327 
1328  def set_is_optimized(self, *args):
1329  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1330  return _IMP_atom.Bonded_set_is_optimized(self, *args)
1331 
1332  def get_is_optimized(self, *args):
1333  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1334  return _IMP_atom.Bonded_get_is_optimized(self, *args)
1335 
1336  def get_check_level(self):
1337  """get_check_level(Bonded self) -> IMP::base::CheckLevel"""
1338  return _IMP_atom.Bonded_get_check_level(self)
1339 
1340  def __eq__(self, *args):
1341  """
1342  __eq__(Bonded self, Bonded o) -> bool
1343  __eq__(Bonded self, Particle d) -> bool
1344  """
1345  return _IMP_atom.Bonded___eq__(self, *args)
1346 
1347  def __ne__(self, *args):
1348  """
1349  __ne__(Bonded self, Bonded o) -> bool
1350  __ne__(Bonded self, Particle d) -> bool
1351  """
1352  return _IMP_atom.Bonded___ne__(self, *args)
1353 
1354  def __le__(self, *args):
1355  """
1356  __le__(Bonded self, Bonded o) -> bool
1357  __le__(Bonded self, Particle d) -> bool
1358  """
1359  return _IMP_atom.Bonded___le__(self, *args)
1360 
1361  def __lt__(self, *args):
1362  """
1363  __lt__(Bonded self, Bonded o) -> bool
1364  __lt__(Bonded self, Particle d) -> bool
1365  """
1366  return _IMP_atom.Bonded___lt__(self, *args)
1367 
1368  def __ge__(self, *args):
1369  """
1370  __ge__(Bonded self, Bonded o) -> bool
1371  __ge__(Bonded self, Particle d) -> bool
1372  """
1373  return _IMP_atom.Bonded___ge__(self, *args)
1374 
1375  def __gt__(self, *args):
1376  """
1377  __gt__(Bonded self, Bonded o) -> bool
1378  __gt__(Bonded self, Particle d) -> bool
1379  """
1380  return _IMP_atom.Bonded___gt__(self, *args)
1381 
1382  def __str__(self):
1383  """__str__(Bonded self) -> std::string"""
1384  return _IMP_atom.Bonded___str__(self)
1385 
1386  def __repr__(self):
1387  """__repr__(Bonded self) -> std::string"""
1388  return _IMP_atom.Bonded___repr__(self)
1389 
1390  __swig_destroy__ = _IMP_atom.delete_Bonded
1391  __del__ = lambda self : None;
1392 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1393 Bonded_swigregister(Bonded)
1394 
1395 def Bonded_decorate_particle(*args):
1396  """Bonded_decorate_particle(Particle p) -> Bonded"""
1397  return _IMP_atom.Bonded_decorate_particle(*args)
1398 
1399 def Bonded_particle_is_instance(*args):
1400  """
1401  particle_is_instance(Particle p) -> bool
1402  Bonded_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
1403  """
1404  return _IMP_atom.Bonded_particle_is_instance(*args)
1405 
1406 def Bonded_setup_particle(*args):
1407  """
1408  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Bonded
1409  Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1410  """
1411  return _IMP_atom.Bonded_setup_particle(*args)
1412 
1413 def Bonded_get_is_setup(*args):
1414  """
1415  get_is_setup(_ParticleAdaptor p) -> bool
1416  Bonded_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1417  """
1418  return _IMP_atom.Bonded_get_is_setup(*args)
1419 
1420 
1421 def create_custom_bond(*args):
1422  """
1423  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1424  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1425  """
1426  return _IMP_atom.create_custom_bond(*args)
1427 
1428 def create_bond(*args):
1429  """
1430  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1431  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1432  """
1433  return _IMP_atom.create_bond(*args)
1434 
1435 def destroy_bond(*args):
1436  """destroy_bond(Bond b)"""
1437  return _IMP_atom.destroy_bond(*args)
1438 
1439 def get_bond(*args):
1440  """get_bond(Bonded a, Bonded b) -> Bond"""
1441  return _IMP_atom.get_bond(*args)
1442 class BondGeometry(IMP.display.SingletonGeometry):
1443  """Proxy of C++ IMP::atom::BondGeometry class"""
1444  __swig_setmethods__ = {}
1445  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1446  __setattr__ = lambda self, name, value: _swig_setattr(self, BondGeometry, name, value)
1447  __swig_getmethods__ = {}
1448  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1449  __getattr__ = lambda self, name: _swig_getattr(self, BondGeometry, name)
1450  def __init__(self, *args):
1451  """
1452  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1453  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1454  """
1455  this = _IMP_atom.new_BondGeometry(*args)
1456  try: self.this.append(this)
1457  except: self.this = this
1458  def get_version_info(self):
1459  """get_version_info(BondGeometry self) -> VersionInfo"""
1460  return _IMP_atom.BondGeometry_get_version_info(self)
1461 
1462  __swig_destroy__ = _IMP_atom.delete_BondGeometry
1463  __del__ = lambda self : None;
1464  def __str__(self):
1465  """__str__(BondGeometry self) -> std::string"""
1466  return _IMP_atom.BondGeometry___str__(self)
1467 
1468  def __repr__(self):
1469  """__repr__(BondGeometry self) -> std::string"""
1470  return _IMP_atom.BondGeometry___repr__(self)
1471 
1472  def get_from(o):
1473  return _object_cast_to_BondGeometry(o)
1474  get_from = staticmethod(get_from)
1475 
1476 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1477 BondGeometry_swigregister(BondGeometry)
1478 
1479 class BondsGeometry(IMP.display.SingletonsGeometry):
1480  """Proxy of C++ IMP::atom::BondsGeometry class"""
1481  __swig_setmethods__ = {}
1482  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1483  __setattr__ = lambda self, name, value: _swig_setattr(self, BondsGeometry, name, value)
1484  __swig_getmethods__ = {}
1485  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1486  __getattr__ = lambda self, name: _swig_getattr(self, BondsGeometry, name)
1487  def __init__(self, *args):
1488  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1489  this = _IMP_atom.new_BondsGeometry(*args)
1490  try: self.this.append(this)
1491  except: self.this = this
1492  def get_version_info(self):
1493  """get_version_info(BondsGeometry self) -> VersionInfo"""
1494  return _IMP_atom.BondsGeometry_get_version_info(self)
1495 
1496  __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1497  __del__ = lambda self : None;
1498  def __str__(self):
1499  """__str__(BondsGeometry self) -> std::string"""
1500  return _IMP_atom.BondsGeometry___str__(self)
1501 
1502  def __repr__(self):
1503  """__repr__(BondsGeometry self) -> std::string"""
1504  return _IMP_atom.BondsGeometry___repr__(self)
1505 
1506  def get_from(o):
1507  return _object_cast_to_BondsGeometry(o)
1508  get_from = staticmethod(get_from)
1509 
1510 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1511 BondsGeometry_swigregister(BondsGeometry)
1512 
1513 class Hierarchy(IMP.core.Hierarchy):
1514  """Proxy of C++ IMP::atom::Hierarchy class"""
1515  __swig_setmethods__ = {}
1516  for _s in [IMP.core.Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1517  __setattr__ = lambda self, name, value: _swig_setattr(self, Hierarchy, name, value)
1518  __swig_getmethods__ = {}
1519  for _s in [IMP.core.Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1520  __getattr__ = lambda self, name: _swig_getattr(self, Hierarchy, name)
1521  def decorate_particle(*args):
1522  """decorate_particle(Particle p) -> Hierarchy"""
1523  return _IMP_atom.Hierarchy_decorate_particle(*args)
1524 
1525  if _newclass:decorate_particle = staticmethod(decorate_particle)
1526  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1527  def particle_is_instance(*args):
1528  """
1529  particle_is_instance(Particle p) -> bool
1530  particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1531  """
1532  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1533 
1534  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1535  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1536  def __init__(self, *args):
1537  """
1538  __init__(IMP::atom::Hierarchy self, Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1539  __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1540  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1541  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1542  """
1543  this = _IMP_atom.new_Hierarchy(*args)
1544  try: self.this.append(this)
1545  except: self.this = this
1546  def setup_particle(*args):
1547  """
1548  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1549  setup_particle(Particle p) -> Hierarchy
1550  setup_particle(Model m, IMP::kernel::ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::kernel::ParticleIndexesAdaptor()) -> Hierarchy
1551  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1552  """
1553  return _IMP_atom.Hierarchy_setup_particle(*args)
1554 
1555  if _newclass:setup_particle = staticmethod(setup_particle)
1556  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1557  def get_is_setup(*args):
1558  """
1559  get_is_setup(Particle p) -> bool
1560  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
1561  """
1562  return _IMP_atom.Hierarchy_get_is_setup(*args)
1563 
1564  if _newclass:get_is_setup = staticmethod(get_is_setup)
1565  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1566  def get_is_valid(self, *args):
1567  """get_is_valid(Hierarchy self, bool print_info) -> bool"""
1568  return _IMP_atom.Hierarchy_get_is_valid(self, *args)
1569 
1570  def add_child(self, *args):
1571  """add_child(Hierarchy self, Hierarchy o)"""
1572  return _IMP_atom.Hierarchy_add_child(self, *args)
1573 
1574  def get_child(self, *args):
1575  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1576  return _IMP_atom.Hierarchy_get_child(self, *args)
1577 
1578  def get_children(self):
1579  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1580  return _IMP_atom.Hierarchy_get_children(self)
1581 
1582  def get_parent(self):
1583  """get_parent(Hierarchy self) -> Hierarchy"""
1584  return _IMP_atom.Hierarchy_get_parent(self)
1585 
1586  def get_as_atom(self):
1587  """get_as_atom(Hierarchy self) -> Atom"""
1588  return _IMP_atom.Hierarchy_get_as_atom(self)
1589 
1590  def get_as_residue(self):
1591  """get_as_residue(Hierarchy self) -> Residue"""
1592  return _IMP_atom.Hierarchy_get_as_residue(self)
1593 
1594  def get_as_chain(self):
1595  """get_as_chain(Hierarchy self) -> Chain"""
1596  return _IMP_atom.Hierarchy_get_as_chain(self)
1597 
1598  def get_as_molecule(self):
1599  """get_as_molecule(Hierarchy self) -> Molecule"""
1600  return _IMP_atom.Hierarchy_get_as_molecule(self)
1601 
1602  def get_as_domain(self):
1603  """get_as_domain(Hierarchy self) -> Domain"""
1604  return _IMP_atom.Hierarchy_get_as_domain(self)
1605 
1606  def get_as_fragment(self):
1607  """get_as_fragment(Hierarchy self) -> Fragment"""
1608  return _IMP_atom.Hierarchy_get_as_fragment(self)
1609 
1610  def get_as_xyz(self):
1611  """get_as_xyz(Hierarchy self) -> XYZ"""
1612  return _IMP_atom.Hierarchy_get_as_xyz(self)
1613 
1614  def get_as_xyzr(self):
1615  """get_as_xyzr(Hierarchy self) -> XYZR"""
1616  return _IMP_atom.Hierarchy_get_as_xyzr(self)
1617 
1618  def get_as_mass(self):
1619  """get_as_mass(Hierarchy self) -> Mass"""
1620  return _IMP_atom.Hierarchy_get_as_mass(self)
1621 
1622  def get_traits():
1623  """get_traits() -> HierarchyTraits"""
1624  return _IMP_atom.Hierarchy_get_traits()
1625 
1626  if _newclass:get_traits = staticmethod(get_traits)
1627  __swig_getmethods__["get_traits"] = lambda x: get_traits
1628  def show(self, *args):
1629  """
1630  show(Hierarchy self, _ostream out, std::string delimiter)
1631  show(Hierarchy self, _ostream out=std::cout)
1632  show(Hierarchy self)
1633  """
1634  return _IMP_atom.Hierarchy_show(self, *args)
1635 
1636  def add_attribute(self, *args):
1637  """
1638  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1639  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1640  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1641  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1642  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1643  add_attribute(Hierarchy self, ObjectKey a0, IMP::Object * a1)
1644  """
1645  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1646 
1647  def get_value(self, *args):
1648  """
1649  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1650  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1651  get_value(Hierarchy self, StringKey a0) -> IMP::String
1652  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1653  get_value(Hierarchy self, ObjectKey a0) -> IMP::Object *
1654  """
1655  return _IMP_atom.Hierarchy_get_value(self, *args)
1656 
1657  def set_value(self, *args):
1658  """
1659  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1660  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1661  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1662  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1663  set_value(Hierarchy self, ObjectKey a0, IMP::Object * a1)
1664  """
1665  return _IMP_atom.Hierarchy_set_value(self, *args)
1666 
1667  def remove_attribute(self, *args):
1668  """
1669  remove_attribute(Hierarchy self, FloatKey a0)
1670  remove_attribute(Hierarchy self, IntKey a0)
1671  remove_attribute(Hierarchy self, StringKey a0)
1672  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1673  remove_attribute(Hierarchy self, ObjectKey a0)
1674  """
1675  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1676 
1677  def has_attribute(self, *args):
1678  """
1679  has_attribute(Hierarchy self, FloatKey a0) -> bool
1680  has_attribute(Hierarchy self, IntKey a0) -> bool
1681  has_attribute(Hierarchy self, StringKey a0) -> bool
1682  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1683  has_attribute(Hierarchy self, ObjectKey a0) -> bool
1684  """
1685  return _IMP_atom.Hierarchy_has_attribute(self, *args)
1686 
1687  def get_derivative(self, *args):
1688  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
1689  return _IMP_atom.Hierarchy_get_derivative(self, *args)
1690 
1691  def get_name(self):
1692  """get_name(Hierarchy self) -> std::string"""
1693  return _IMP_atom.Hierarchy_get_name(self)
1694 
1695  def clear_caches(self):
1696  """clear_caches(Hierarchy self)"""
1697  return _IMP_atom.Hierarchy_clear_caches(self)
1698 
1699  def set_name(self, *args):
1700  """set_name(Hierarchy self, std::string a0)"""
1701  return _IMP_atom.Hierarchy_set_name(self, *args)
1702 
1703  def set_check_level(self, *args):
1704  """set_check_level(Hierarchy self, IMP::base::CheckLevel a0)"""
1705  return _IMP_atom.Hierarchy_set_check_level(self, *args)
1706 
1707  def add_to_derivative(self, *args):
1708  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1709  return _IMP_atom.Hierarchy_add_to_derivative(self, *args)
1710 
1711  def set_is_optimized(self, *args):
1712  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1713  return _IMP_atom.Hierarchy_set_is_optimized(self, *args)
1714 
1715  def get_is_optimized(self, *args):
1716  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1717  return _IMP_atom.Hierarchy_get_is_optimized(self, *args)
1718 
1719  def get_check_level(self):
1720  """get_check_level(Hierarchy self) -> IMP::base::CheckLevel"""
1721  return _IMP_atom.Hierarchy_get_check_level(self)
1722 
1723  def __eq__(self, *args):
1724  """
1725  __eq__(Hierarchy self, Hierarchy o) -> bool
1726  __eq__(Hierarchy self, Particle d) -> bool
1727  """
1728  return _IMP_atom.Hierarchy___eq__(self, *args)
1729 
1730  def __ne__(self, *args):
1731  """
1732  __ne__(Hierarchy self, Hierarchy o) -> bool
1733  __ne__(Hierarchy self, Particle d) -> bool
1734  """
1735  return _IMP_atom.Hierarchy___ne__(self, *args)
1736 
1737  def __le__(self, *args):
1738  """
1739  __le__(Hierarchy self, Hierarchy o) -> bool
1740  __le__(Hierarchy self, Particle d) -> bool
1741  """
1742  return _IMP_atom.Hierarchy___le__(self, *args)
1743 
1744  def __lt__(self, *args):
1745  """
1746  __lt__(Hierarchy self, Hierarchy o) -> bool
1747  __lt__(Hierarchy self, Particle d) -> bool
1748  """
1749  return _IMP_atom.Hierarchy___lt__(self, *args)
1750 
1751  def __ge__(self, *args):
1752  """
1753  __ge__(Hierarchy self, Hierarchy o) -> bool
1754  __ge__(Hierarchy self, Particle d) -> bool
1755  """
1756  return _IMP_atom.Hierarchy___ge__(self, *args)
1757 
1758  def __gt__(self, *args):
1759  """
1760  __gt__(Hierarchy self, Hierarchy o) -> bool
1761  __gt__(Hierarchy self, Particle d) -> bool
1762  """
1763  return _IMP_atom.Hierarchy___gt__(self, *args)
1764 
1765  def __str__(self):
1766  """__str__(Hierarchy self) -> std::string"""
1767  return _IMP_atom.Hierarchy___str__(self)
1768 
1769  def __repr__(self):
1770  """__repr__(Hierarchy self) -> std::string"""
1771  return _IMP_atom.Hierarchy___repr__(self)
1772 
1773  __swig_destroy__ = _IMP_atom.delete_Hierarchy
1774  __del__ = lambda self : None;
1775 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
1776 Hierarchy_swigregister(Hierarchy)
1777 
1778 def Hierarchy_decorate_particle(*args):
1779  """Hierarchy_decorate_particle(Particle p) -> Hierarchy"""
1780  return _IMP_atom.Hierarchy_decorate_particle(*args)
1781 
1782 def Hierarchy_particle_is_instance(*args):
1783  """
1784  particle_is_instance(Particle p) -> bool
1785  Hierarchy_particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1786  """
1787  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1788 
1789 def Hierarchy_setup_particle(*args):
1790  """
1791  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1792  setup_particle(Particle p) -> Hierarchy
1793  setup_particle(Model m, IMP::kernel::ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::kernel::ParticleIndexesAdaptor()) -> Hierarchy
1794  Hierarchy_setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1795  """
1796  return _IMP_atom.Hierarchy_setup_particle(*args)
1797 
1798 def Hierarchy_get_is_setup(*args):
1799  """
1800  get_is_setup(Particle p) -> bool
1801  Hierarchy_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
1802  """
1803  return _IMP_atom.Hierarchy_get_is_setup(*args)
1804 
1805 def Hierarchy_get_traits():
1806  """Hierarchy_get_traits() -> HierarchyTraits"""
1807  return _IMP_atom.Hierarchy_get_traits()
1808 
1809 ATOM_TYPE = _IMP_atom.ATOM_TYPE
1810 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
1811 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
1812 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
1813 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
1814 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
1815 XYZ_TYPE = _IMP_atom.XYZ_TYPE
1816 XYZR_TYPE = _IMP_atom.XYZR_TYPE
1817 MASS_TYPE = _IMP_atom.MASS_TYPE
1818 
1819 def get_by_type(*args):
1820  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
1821  return _IMP_atom.get_by_type(*args)
1822 
1823 def create_fragment(*args):
1824  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
1825  return _IMP_atom.create_fragment(*args)
1826 
1827 def get_internal_bonds(*args):
1828  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
1829  return _IMP_atom.get_internal_bonds(*args)
1830 
1831 def get_root(*args):
1832  """get_root(Hierarchy h) -> Hierarchy"""
1833  return _IMP_atom.get_root(*args)
1834 
1835 def show(*args):
1836  """
1837  show(Hierarchy h, _ostream out=std::cout)
1838  show(Hierarchy h)
1839  """
1840  return _IMP_atom.show(*args)
1841 
1842 def create_rigid_body(*args):
1843  """
1844  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
1845  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
1846  create_rigid_body(Hierarchy h) -> RigidBody
1847  """
1848  return _IMP_atom.create_rigid_body(*args)
1849 
1850 def create_compatible_rigid_body(*args):
1851  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
1852  return _IMP_atom.create_compatible_rigid_body(*args)
1853 
1854 def setup_as_rigid_body(*args):
1855  """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
1856  return _IMP_atom.setup_as_rigid_body(*args)
1857 
1858 def get_is_heterogen(*args):
1859  """get_is_heterogen(Hierarchy h) -> bool"""
1860  return _IMP_atom.get_is_heterogen(*args)
1861 
1862 def create_clone(*args):
1863  """create_clone(Hierarchy d) -> Hierarchy"""
1864  return _IMP_atom.create_clone(*args)
1865 
1866 def create_clone_one(*args):
1867  """create_clone_one(Hierarchy d) -> Hierarchy"""
1868  return _IMP_atom.create_clone_one(*args)
1869 
1870 def destroy(*args):
1871  """destroy(Hierarchy d)"""
1872  return _IMP_atom.destroy(*args)
1873 
1874 def get_bounding_box(*args):
1875  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
1876  return _IMP_atom.get_bounding_box(*args)
1877 
1878 def get_bounding_sphere(*args):
1879  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
1880  return _IMP_atom.get_bounding_sphere(*args)
1881 class Angle(IMP.kernel.Decorator):
1882  """Proxy of C++ IMP::atom::Angle class"""
1883  __swig_setmethods__ = {}
1884  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1885  __setattr__ = lambda self, name, value: _swig_setattr(self, Angle, name, value)
1886  __swig_getmethods__ = {}
1887  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1888  __getattr__ = lambda self, name: _swig_getattr(self, Angle, name)
1889  def __init__(self, *args):
1890  """
1891  __init__(IMP::atom::Angle self) -> Angle
1892  __init__(IMP::atom::Angle self, Model m, ::IMP::kernel::ParticleIndex id) -> Angle
1893  __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
1894  """
1895  this = _IMP_atom.new_Angle(*args)
1896  try: self.this.append(this)
1897  except: self.this = this
1898  def decorate_particle(*args):
1899  """decorate_particle(Particle p) -> Angle"""
1900  return _IMP_atom.Angle_decorate_particle(*args)
1901 
1902  if _newclass:decorate_particle = staticmethod(decorate_particle)
1903  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1904  def particle_is_instance(*args):
1905  """
1906  particle_is_instance(Particle p) -> bool
1907  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
1908  """
1909  return _IMP_atom.Angle_particle_is_instance(*args)
1910 
1911  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1912  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1913  def show(self, *args):
1914  """
1915  show(Angle self, _ostream out=std::cout)
1916  show(Angle self)
1917  """
1918  return _IMP_atom.Angle_show(self, *args)
1919 
1920  def setup_particle(*args):
1921  """
1922  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
1923  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
1924  """
1925  return _IMP_atom.Angle_setup_particle(*args)
1926 
1927  if _newclass:setup_particle = staticmethod(setup_particle)
1928  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1929  def get_is_setup(*args):
1930  """
1931  get_is_setup(_ParticleAdaptor p) -> bool
1932  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1933  """
1934  return _IMP_atom.Angle_get_is_setup(*args)
1935 
1936  if _newclass:get_is_setup = staticmethod(get_is_setup)
1937  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1938  def get_particle(self, *args):
1939  """
1940  get_particle(Angle self) -> Particle
1941  get_particle(Angle self, unsigned int i) -> Particle
1942  """
1943  return _IMP_atom.Angle_get_particle(self, *args)
1944 
1945  def get_ideal(self):
1946  """get_ideal(Angle self) -> IMP::Float"""
1947  return _IMP_atom.Angle_get_ideal(self)
1948 
1949  def set_ideal(self, *args):
1950  """set_ideal(Angle self, IMP::Float t)"""
1951  return _IMP_atom.Angle_set_ideal(self, *args)
1952 
1953  def get_stiffness(self):
1954  """get_stiffness(Angle self) -> IMP::Float"""
1955  return _IMP_atom.Angle_get_stiffness(self)
1956 
1957  def set_stiffness(self, *args):
1958  """set_stiffness(Angle self, IMP::Float t)"""
1959  return _IMP_atom.Angle_set_stiffness(self, *args)
1960 
1961  def get_particle_key(*args):
1962  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
1963  return _IMP_atom.Angle_get_particle_key(*args)
1964 
1965  if _newclass:get_particle_key = staticmethod(get_particle_key)
1966  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
1967  def get_ideal_key():
1968  """get_ideal_key() -> FloatKey"""
1969  return _IMP_atom.Angle_get_ideal_key()
1970 
1971  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
1972  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
1973  def get_stiffness_key():
1974  """get_stiffness_key() -> FloatKey"""
1975  return _IMP_atom.Angle_get_stiffness_key()
1976 
1977  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
1978  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
1979  def add_attribute(self, *args):
1980  """
1981  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
1982  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
1983  add_attribute(Angle self, IntKey a0, IMP::Int a1)
1984  add_attribute(Angle self, StringKey a0, IMP::String a1)
1985  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
1986  add_attribute(Angle self, ObjectKey a0, IMP::Object * a1)
1987  """
1988  return _IMP_atom.Angle_add_attribute(self, *args)
1989 
1990  def get_value(self, *args):
1991  """
1992  get_value(Angle self, FloatKey a0) -> IMP::Float
1993  get_value(Angle self, IntKey a0) -> IMP::Int
1994  get_value(Angle self, StringKey a0) -> IMP::String
1995  get_value(Angle self, ParticleIndexKey a0) -> Particle
1996  get_value(Angle self, ObjectKey a0) -> IMP::Object *
1997  """
1998  return _IMP_atom.Angle_get_value(self, *args)
1999 
2000  def set_value(self, *args):
2001  """
2002  set_value(Angle self, FloatKey a0, IMP::Float a1)
2003  set_value(Angle self, IntKey a0, IMP::Int a1)
2004  set_value(Angle self, StringKey a0, IMP::String a1)
2005  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2006  set_value(Angle self, ObjectKey a0, IMP::Object * a1)
2007  """
2008  return _IMP_atom.Angle_set_value(self, *args)
2009 
2010  def remove_attribute(self, *args):
2011  """
2012  remove_attribute(Angle self, FloatKey a0)
2013  remove_attribute(Angle self, IntKey a0)
2014  remove_attribute(Angle self, StringKey a0)
2015  remove_attribute(Angle self, ParticleIndexKey a0)
2016  remove_attribute(Angle self, ObjectKey a0)
2017  """
2018  return _IMP_atom.Angle_remove_attribute(self, *args)
2019 
2020  def has_attribute(self, *args):
2021  """
2022  has_attribute(Angle self, FloatKey a0) -> bool
2023  has_attribute(Angle self, IntKey a0) -> bool
2024  has_attribute(Angle self, StringKey a0) -> bool
2025  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2026  has_attribute(Angle self, ObjectKey a0) -> bool
2027  """
2028  return _IMP_atom.Angle_has_attribute(self, *args)
2029 
2030  def get_derivative(self, *args):
2031  """get_derivative(Angle self, FloatKey a0) -> double"""
2032  return _IMP_atom.Angle_get_derivative(self, *args)
2033 
2034  def get_name(self):
2035  """get_name(Angle self) -> std::string"""
2036  return _IMP_atom.Angle_get_name(self)
2037 
2038  def clear_caches(self):
2039  """clear_caches(Angle self)"""
2040  return _IMP_atom.Angle_clear_caches(self)
2041 
2042  def set_name(self, *args):
2043  """set_name(Angle self, std::string a0)"""
2044  return _IMP_atom.Angle_set_name(self, *args)
2045 
2046  def set_check_level(self, *args):
2047  """set_check_level(Angle self, IMP::base::CheckLevel a0)"""
2048  return _IMP_atom.Angle_set_check_level(self, *args)
2049 
2050  def add_to_derivative(self, *args):
2051  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2052  return _IMP_atom.Angle_add_to_derivative(self, *args)
2053 
2054  def set_is_optimized(self, *args):
2055  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2056  return _IMP_atom.Angle_set_is_optimized(self, *args)
2057 
2058  def get_is_optimized(self, *args):
2059  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2060  return _IMP_atom.Angle_get_is_optimized(self, *args)
2061 
2062  def get_check_level(self):
2063  """get_check_level(Angle self) -> IMP::base::CheckLevel"""
2064  return _IMP_atom.Angle_get_check_level(self)
2065 
2066  def __eq__(self, *args):
2067  """
2068  __eq__(Angle self, Angle o) -> bool
2069  __eq__(Angle self, Particle d) -> bool
2070  """
2071  return _IMP_atom.Angle___eq__(self, *args)
2072 
2073  def __ne__(self, *args):
2074  """
2075  __ne__(Angle self, Angle o) -> bool
2076  __ne__(Angle self, Particle d) -> bool
2077  """
2078  return _IMP_atom.Angle___ne__(self, *args)
2079 
2080  def __le__(self, *args):
2081  """
2082  __le__(Angle self, Angle o) -> bool
2083  __le__(Angle self, Particle d) -> bool
2084  """
2085  return _IMP_atom.Angle___le__(self, *args)
2086 
2087  def __lt__(self, *args):
2088  """
2089  __lt__(Angle self, Angle o) -> bool
2090  __lt__(Angle self, Particle d) -> bool
2091  """
2092  return _IMP_atom.Angle___lt__(self, *args)
2093 
2094  def __ge__(self, *args):
2095  """
2096  __ge__(Angle self, Angle o) -> bool
2097  __ge__(Angle self, Particle d) -> bool
2098  """
2099  return _IMP_atom.Angle___ge__(self, *args)
2100 
2101  def __gt__(self, *args):
2102  """
2103  __gt__(Angle self, Angle o) -> bool
2104  __gt__(Angle self, Particle d) -> bool
2105  """
2106  return _IMP_atom.Angle___gt__(self, *args)
2107 
2108  def __str__(self):
2109  """__str__(Angle self) -> std::string"""
2110  return _IMP_atom.Angle___str__(self)
2111 
2112  def __repr__(self):
2113  """__repr__(Angle self) -> std::string"""
2114  return _IMP_atom.Angle___repr__(self)
2115 
2116  __swig_destroy__ = _IMP_atom.delete_Angle
2117  __del__ = lambda self : None;
2118 Angle_swigregister = _IMP_atom.Angle_swigregister
2119 Angle_swigregister(Angle)
2120 
2121 def Angle_decorate_particle(*args):
2122  """Angle_decorate_particle(Particle p) -> Angle"""
2123  return _IMP_atom.Angle_decorate_particle(*args)
2124 
2125 def Angle_particle_is_instance(*args):
2126  """
2127  particle_is_instance(Particle p) -> bool
2128  Angle_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
2129  """
2130  return _IMP_atom.Angle_particle_is_instance(*args)
2131 
2132 def Angle_setup_particle(*args):
2133  """
2134  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2135  Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2136  """
2137  return _IMP_atom.Angle_setup_particle(*args)
2138 
2139 def Angle_get_is_setup(*args):
2140  """
2141  get_is_setup(_ParticleAdaptor p) -> bool
2142  Angle_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2143  """
2144  return _IMP_atom.Angle_get_is_setup(*args)
2145 
2146 def Angle_get_particle_key(*args):
2147  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2148  return _IMP_atom.Angle_get_particle_key(*args)
2149 
2150 def Angle_get_ideal_key():
2151  """Angle_get_ideal_key() -> FloatKey"""
2152  return _IMP_atom.Angle_get_ideal_key()
2153 
2154 def Angle_get_stiffness_key():
2155  """Angle_get_stiffness_key() -> FloatKey"""
2156  return _IMP_atom.Angle_get_stiffness_key()
2157 
2158 class Dihedral(IMP.kernel.Decorator):
2159  """Proxy of C++ IMP::atom::Dihedral class"""
2160  __swig_setmethods__ = {}
2161  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2162  __setattr__ = lambda self, name, value: _swig_setattr(self, Dihedral, name, value)
2163  __swig_getmethods__ = {}
2164  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2165  __getattr__ = lambda self, name: _swig_getattr(self, Dihedral, name)
2166  def __init__(self, *args):
2167  """
2168  __init__(IMP::atom::Dihedral self) -> Dihedral
2169  __init__(IMP::atom::Dihedral self, Model m, ::IMP::kernel::ParticleIndex id) -> Dihedral
2170  __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2171  """
2172  this = _IMP_atom.new_Dihedral(*args)
2173  try: self.this.append(this)
2174  except: self.this = this
2175  def decorate_particle(*args):
2176  """decorate_particle(Particle p) -> Dihedral"""
2177  return _IMP_atom.Dihedral_decorate_particle(*args)
2178 
2179  if _newclass:decorate_particle = staticmethod(decorate_particle)
2180  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
2181  def particle_is_instance(*args):
2182  """
2183  particle_is_instance(Particle p) -> bool
2184  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
2185  """
2186  return _IMP_atom.Dihedral_particle_is_instance(*args)
2187 
2188  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
2189  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
2190  def show(self, *args):
2191  """
2192  show(Dihedral self, _ostream out=std::cout)
2193  show(Dihedral self)
2194  """
2195  return _IMP_atom.Dihedral_show(self, *args)
2196 
2197  def setup_particle(*args):
2198  """
2199  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2200  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2201  """
2202  return _IMP_atom.Dihedral_setup_particle(*args)
2203 
2204  if _newclass:setup_particle = staticmethod(setup_particle)
2205  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
2206  def get_is_setup(*args):
2207  """
2208  get_is_setup(_ParticleAdaptor p) -> bool
2209  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2210  """
2211  return _IMP_atom.Dihedral_get_is_setup(*args)
2212 
2213  if _newclass:get_is_setup = staticmethod(get_is_setup)
2214  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
2215  def get_particle(self, *args):
2216  """
2217  get_particle(Dihedral self) -> Particle
2218  get_particle(Dihedral self, unsigned int i) -> Particle
2219  """
2220  return _IMP_atom.Dihedral_get_particle(self, *args)
2221 
2222  def get_ideal(self):
2223  """get_ideal(Dihedral self) -> IMP::Float"""
2224  return _IMP_atom.Dihedral_get_ideal(self)
2225 
2226  def set_ideal(self, *args):
2227  """set_ideal(Dihedral self, IMP::Float t)"""
2228  return _IMP_atom.Dihedral_set_ideal(self, *args)
2229 
2230  def get_multiplicity(self):
2231  """get_multiplicity(Dihedral self) -> IMP::Int"""
2232  return _IMP_atom.Dihedral_get_multiplicity(self)
2233 
2234  def set_multiplicity(self, *args):
2235  """set_multiplicity(Dihedral self, IMP::Int t)"""
2236  return _IMP_atom.Dihedral_set_multiplicity(self, *args)
2237 
2238  def get_stiffness(self):
2239  """get_stiffness(Dihedral self) -> IMP::Float"""
2240  return _IMP_atom.Dihedral_get_stiffness(self)
2241 
2242  def set_stiffness(self, *args):
2243  """set_stiffness(Dihedral self, IMP::Float t)"""
2244  return _IMP_atom.Dihedral_set_stiffness(self, *args)
2245 
2246  def get_particle_key(*args):
2247  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2248  return _IMP_atom.Dihedral_get_particle_key(*args)
2249 
2250  if _newclass:get_particle_key = staticmethod(get_particle_key)
2251  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
2252  def get_ideal_key():
2253  """get_ideal_key() -> FloatKey"""
2254  return _IMP_atom.Dihedral_get_ideal_key()
2255 
2256  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
2257  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
2258  def get_multiplicity_key():
2259  """get_multiplicity_key() -> IntKey"""
2260  return _IMP_atom.Dihedral_get_multiplicity_key()
2261 
2262  if _newclass:get_multiplicity_key = staticmethod(get_multiplicity_key)
2263  __swig_getmethods__["get_multiplicity_key"] = lambda x: get_multiplicity_key
2264  def get_stiffness_key():
2265  """get_stiffness_key() -> FloatKey"""
2266  return _IMP_atom.Dihedral_get_stiffness_key()
2267 
2268  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
2269  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
2270  def add_attribute(self, *args):
2271  """
2272  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2273  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2274  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2275  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2276  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2277  add_attribute(Dihedral self, ObjectKey a0, IMP::Object * a1)
2278  """
2279  return _IMP_atom.Dihedral_add_attribute(self, *args)
2280 
2281  def get_value(self, *args):
2282  """
2283  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2284  get_value(Dihedral self, IntKey a0) -> IMP::Int
2285  get_value(Dihedral self, StringKey a0) -> IMP::String
2286  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2287  get_value(Dihedral self, ObjectKey a0) -> IMP::Object *
2288  """
2289  return _IMP_atom.Dihedral_get_value(self, *args)
2290 
2291  def set_value(self, *args):
2292  """
2293  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2294  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2295  set_value(Dihedral self, StringKey a0, IMP::String a1)
2296  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2297  set_value(Dihedral self, ObjectKey a0, IMP::Object * a1)
2298  """
2299  return _IMP_atom.Dihedral_set_value(self, *args)
2300 
2301  def remove_attribute(self, *args):
2302  """
2303  remove_attribute(Dihedral self, FloatKey a0)
2304  remove_attribute(Dihedral self, IntKey a0)
2305  remove_attribute(Dihedral self, StringKey a0)
2306  remove_attribute(Dihedral self, ParticleIndexKey a0)
2307  remove_attribute(Dihedral self, ObjectKey a0)
2308  """
2309  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2310 
2311  def has_attribute(self, *args):
2312  """
2313  has_attribute(Dihedral self, FloatKey a0) -> bool
2314  has_attribute(Dihedral self, IntKey a0) -> bool
2315  has_attribute(Dihedral self, StringKey a0) -> bool
2316  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2317  has_attribute(Dihedral self, ObjectKey a0) -> bool
2318  """
2319  return _IMP_atom.Dihedral_has_attribute(self, *args)
2320 
2321  def get_derivative(self, *args):
2322  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2323  return _IMP_atom.Dihedral_get_derivative(self, *args)
2324 
2325  def get_name(self):
2326  """get_name(Dihedral self) -> std::string"""
2327  return _IMP_atom.Dihedral_get_name(self)
2328 
2329  def clear_caches(self):
2330  """clear_caches(Dihedral self)"""
2331  return _IMP_atom.Dihedral_clear_caches(self)
2332 
2333  def set_name(self, *args):
2334  """set_name(Dihedral self, std::string a0)"""
2335  return _IMP_atom.Dihedral_set_name(self, *args)
2336 
2337  def set_check_level(self, *args):
2338  """set_check_level(Dihedral self, IMP::base::CheckLevel a0)"""
2339  return _IMP_atom.Dihedral_set_check_level(self, *args)
2340 
2341  def add_to_derivative(self, *args):
2342  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2343  return _IMP_atom.Dihedral_add_to_derivative(self, *args)
2344 
2345  def set_is_optimized(self, *args):
2346  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2347  return _IMP_atom.Dihedral_set_is_optimized(self, *args)
2348 
2349  def get_is_optimized(self, *args):
2350  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2351  return _IMP_atom.Dihedral_get_is_optimized(self, *args)
2352 
2353  def get_check_level(self):
2354  """get_check_level(Dihedral self) -> IMP::base::CheckLevel"""
2355  return _IMP_atom.Dihedral_get_check_level(self)
2356 
2357  def __eq__(self, *args):
2358  """
2359  __eq__(Dihedral self, Dihedral o) -> bool
2360  __eq__(Dihedral self, Particle d) -> bool
2361  """
2362  return _IMP_atom.Dihedral___eq__(self, *args)
2363 
2364  def __ne__(self, *args):
2365  """
2366  __ne__(Dihedral self, Dihedral o) -> bool
2367  __ne__(Dihedral self, Particle d) -> bool
2368  """
2369  return _IMP_atom.Dihedral___ne__(self, *args)
2370 
2371  def __le__(self, *args):
2372  """
2373  __le__(Dihedral self, Dihedral o) -> bool
2374  __le__(Dihedral self, Particle d) -> bool
2375  """
2376  return _IMP_atom.Dihedral___le__(self, *args)
2377 
2378  def __lt__(self, *args):
2379  """
2380  __lt__(Dihedral self, Dihedral o) -> bool
2381  __lt__(Dihedral self, Particle d) -> bool
2382  """
2383  return _IMP_atom.Dihedral___lt__(self, *args)
2384 
2385  def __ge__(self, *args):
2386  """
2387  __ge__(Dihedral self, Dihedral o) -> bool
2388  __ge__(Dihedral self, Particle d) -> bool
2389  """
2390  return _IMP_atom.Dihedral___ge__(self, *args)
2391 
2392  def __gt__(self, *args):
2393  """
2394  __gt__(Dihedral self, Dihedral o) -> bool
2395  __gt__(Dihedral self, Particle d) -> bool
2396  """
2397  return _IMP_atom.Dihedral___gt__(self, *args)
2398 
2399  def __str__(self):
2400  """__str__(Dihedral self) -> std::string"""
2401  return _IMP_atom.Dihedral___str__(self)
2402 
2403  def __repr__(self):
2404  """__repr__(Dihedral self) -> std::string"""
2405  return _IMP_atom.Dihedral___repr__(self)
2406 
2407  __swig_destroy__ = _IMP_atom.delete_Dihedral
2408  __del__ = lambda self : None;
2409 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2410 Dihedral_swigregister(Dihedral)
2411 
2412 def Dihedral_decorate_particle(*args):
2413  """Dihedral_decorate_particle(Particle p) -> Dihedral"""
2414  return _IMP_atom.Dihedral_decorate_particle(*args)
2415 
2416 def Dihedral_particle_is_instance(*args):
2417  """
2418  particle_is_instance(Particle p) -> bool
2419  Dihedral_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
2420  """
2421  return _IMP_atom.Dihedral_particle_is_instance(*args)
2422 
2423 def Dihedral_setup_particle(*args):
2424  """
2425  setup_particle(Model m, IMP::kernel::ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2426  Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2427  """
2428  return _IMP_atom.Dihedral_setup_particle(*args)
2429 
2430 def Dihedral_get_is_setup(*args):
2431  """
2432  get_is_setup(_ParticleAdaptor p) -> bool
2433  Dihedral_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
2434  """
2435  return _IMP_atom.Dihedral_get_is_setup(*args)
2436 
2437 def Dihedral_get_particle_key(*args):
2438  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2439  return _IMP_atom.Dihedral_get_particle_key(*args)
2440 
2441 def Dihedral_get_ideal_key():
2442  """Dihedral_get_ideal_key() -> FloatKey"""
2443  return _IMP_atom.Dihedral_get_ideal_key()
2444 
2445 def Dihedral_get_multiplicity_key():
2446  """Dihedral_get_multiplicity_key() -> IntKey"""
2447  return _IMP_atom.Dihedral_get_multiplicity_key()
2448 
2449 def Dihedral_get_stiffness_key():
2450  """Dihedral_get_stiffness_key() -> FloatKey"""
2451  return _IMP_atom.Dihedral_get_stiffness_key()
2452 
2453 class SmoothingFunction(IMP.base.Object):
2454  """Proxy of C++ IMP::atom::SmoothingFunction class"""
2455  __swig_setmethods__ = {}
2456  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2457  __setattr__ = lambda self, name, value: _swig_setattr(self, SmoothingFunction, name, value)
2458  __swig_getmethods__ = {}
2459  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2460  __getattr__ = lambda self, name: _swig_getattr(self, SmoothingFunction, name)
2461  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
2462  def __call__(self, *args):
2463  """
2464  __call__(SmoothingFunction self, double score, double distance) -> double
2465  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2466  """
2467  return _IMP_atom.SmoothingFunction___call__(self, *args)
2468 
2469  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2470  __del__ = lambda self : None;
2471  def __str__(self):
2472  """__str__(SmoothingFunction self) -> std::string"""
2473  return _IMP_atom.SmoothingFunction___str__(self)
2474 
2475  def __repr__(self):
2476  """__repr__(SmoothingFunction self) -> std::string"""
2477  return _IMP_atom.SmoothingFunction___repr__(self)
2478 
2479  def get_from(o):
2480  return _object_cast_to_SmoothingFunction(o)
2481  get_from = staticmethod(get_from)
2482 
2483 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2484 SmoothingFunction_swigregister(SmoothingFunction)
2485 
2486 class ForceSwitch(SmoothingFunction):
2487  """Proxy of C++ IMP::atom::ForceSwitch class"""
2488  __swig_setmethods__ = {}
2489  for _s in [SmoothingFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2490  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceSwitch, name, value)
2491  __swig_getmethods__ = {}
2492  for _s in [SmoothingFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2493  __getattr__ = lambda self, name: _swig_getattr(self, ForceSwitch, name)
2494  def __init__(self, *args):
2495  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2496  this = _IMP_atom.new_ForceSwitch(*args)
2497  try: self.this.append(this)
2498  except: self.this = this
2499  def __call__(self, *args):
2500  """
2501  __call__(ForceSwitch self, double score, double distance) -> double
2502  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2503  """
2504  return _IMP_atom.ForceSwitch___call__(self, *args)
2505 
2506  def get_version_info(self):
2507  """get_version_info(ForceSwitch self) -> VersionInfo"""
2508  return _IMP_atom.ForceSwitch_get_version_info(self)
2509 
2510  __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2511  __del__ = lambda self : None;
2512  def __str__(self):
2513  """__str__(ForceSwitch self) -> std::string"""
2514  return _IMP_atom.ForceSwitch___str__(self)
2515 
2516  def __repr__(self):
2517  """__repr__(ForceSwitch self) -> std::string"""
2518  return _IMP_atom.ForceSwitch___repr__(self)
2519 
2520  def get_from(o):
2521  return _object_cast_to_ForceSwitch(o)
2522  get_from = staticmethod(get_from)
2523 
2524 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2525 ForceSwitch_swigregister(ForceSwitch)
2526 
2527 class AngleSingletonScore(IMP.kernel.SingletonScore):
2528  """Proxy of C++ IMP::atom::AngleSingletonScore class"""
2529  __swig_setmethods__ = {}
2530  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2531  __setattr__ = lambda self, name, value: _swig_setattr(self, AngleSingletonScore, name, value)
2532  __swig_getmethods__ = {}
2533  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2534  __getattr__ = lambda self, name: _swig_getattr(self, AngleSingletonScore, name)
2535  def __init__(self, *args):
2536  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2537  this = _IMP_atom.new_AngleSingletonScore(*args)
2538  try: self.this.append(this)
2539  except: self.this = this
2540  def do_get_inputs(self, *args):
2541  """do_get_inputs(AngleSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2542  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, *args)
2543 
2544  def get_version_info(self):
2545  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2546  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2547 
2548  __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2549  __del__ = lambda self : None;
2550  def __str__(self):
2551  """__str__(AngleSingletonScore self) -> std::string"""
2552  return _IMP_atom.AngleSingletonScore___str__(self)
2553 
2554  def __repr__(self):
2555  """__repr__(AngleSingletonScore self) -> std::string"""
2556  return _IMP_atom.AngleSingletonScore___repr__(self)
2557 
2558  def get_from(o):
2559  return _object_cast_to_AngleSingletonScore(o)
2560  get_from = staticmethod(get_from)
2561 
2562 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2563 AngleSingletonScore_swigregister(AngleSingletonScore)
2564 
2565 class BondEndpointsRefiner(IMP.kernel.Refiner):
2566  """Proxy of C++ IMP::atom::BondEndpointsRefiner class"""
2567  __swig_setmethods__ = {}
2568  for _s in [IMP.kernel.Refiner]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2569  __setattr__ = lambda self, name, value: _swig_setattr(self, BondEndpointsRefiner, name, value)
2570  __swig_getmethods__ = {}
2571  for _s in [IMP.kernel.Refiner]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2572  __getattr__ = lambda self, name: _swig_getattr(self, BondEndpointsRefiner, name)
2573  def __init__(self):
2574  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2575  this = _IMP_atom.new_BondEndpointsRefiner()
2576  try: self.this.append(this)
2577  except: self.this = this
2578  def do_get_inputs(self, *args):
2579  """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2580  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, *args)
2581 
2582  def get_version_info(self):
2583  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2584  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2585 
2586  __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2587  __del__ = lambda self : None;
2588  def __str__(self):
2589  """__str__(BondEndpointsRefiner self) -> std::string"""
2590  return _IMP_atom.BondEndpointsRefiner___str__(self)
2591 
2592  def __repr__(self):
2593  """__repr__(BondEndpointsRefiner self) -> std::string"""
2594  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2595 
2596  def get_from(o):
2597  return _object_cast_to_BondEndpointsRefiner(o)
2598  get_from = staticmethod(get_from)
2599 
2600 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2601 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2602 
2603 class BondPairContainer(IMP.kernel.PairContainer):
2604  """Proxy of C++ IMP::atom::BondPairContainer class"""
2605  __swig_setmethods__ = {}
2606  for _s in [IMP.kernel.PairContainer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2607  __setattr__ = lambda self, name, value: _swig_setattr(self, BondPairContainer, name, value)
2608  __swig_getmethods__ = {}
2609  for _s in [IMP.kernel.PairContainer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2610  __getattr__ = lambda self, name: _swig_getattr(self, BondPairContainer, name)
2611  def __init__(self, *args):
2612  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2613  this = _IMP_atom.new_BondPairContainer(*args)
2614  try: self.this.append(this)
2615  except: self.this = this
2616  def do_before_evaluate(self):
2617  """do_before_evaluate(BondPairContainer self)"""
2618  return _IMP_atom.BondPairContainer_do_before_evaluate(self)
2619 
2620  def do_get_inputs(self):
2621  """do_get_inputs(BondPairContainer self) -> IMP::kernel::ModelObjectsTemp"""
2622  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2623 
2624  def do_apply(self, *args):
2625  """do_apply(BondPairContainer self, PairModifier sm)"""
2626  return _IMP_atom.BondPairContainer_do_apply(self, *args)
2627 
2628  def get_version_info(self):
2629  """get_version_info(BondPairContainer self) -> VersionInfo"""
2630  return _IMP_atom.BondPairContainer_get_version_info(self)
2631 
2632  __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2633  __del__ = lambda self : None;
2634  def __str__(self):
2635  """__str__(BondPairContainer self) -> std::string"""
2636  return _IMP_atom.BondPairContainer___str__(self)
2637 
2638  def __repr__(self):
2639  """__repr__(BondPairContainer self) -> std::string"""
2640  return _IMP_atom.BondPairContainer___repr__(self)
2641 
2642  def get_from(o):
2643  return _object_cast_to_BondPairContainer(o)
2644  get_from = staticmethod(get_from)
2645 
2646 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
2647 BondPairContainer_swigregister(BondPairContainer)
2648 
2649 class BondSingletonScore(IMP.kernel.SingletonScore):
2650  """Proxy of C++ IMP::atom::BondSingletonScore class"""
2651  __swig_setmethods__ = {}
2652  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2653  __setattr__ = lambda self, name, value: _swig_setattr(self, BondSingletonScore, name, value)
2654  __swig_getmethods__ = {}
2655  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2656  __getattr__ = lambda self, name: _swig_getattr(self, BondSingletonScore, name)
2657  def __init__(self, *args):
2658  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2659  this = _IMP_atom.new_BondSingletonScore(*args)
2660  try: self.this.append(this)
2661  except: self.this = this
2662  def get_unary_function(self):
2663  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2664  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2665 
2666  def do_get_inputs(self, *args):
2667  """do_get_inputs(BondSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2668  return _IMP_atom.BondSingletonScore_do_get_inputs(self, *args)
2669 
2670  def get_version_info(self):
2671  """get_version_info(BondSingletonScore self) -> VersionInfo"""
2672  return _IMP_atom.BondSingletonScore_get_version_info(self)
2673 
2674  __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2675  __del__ = lambda self : None;
2676  def __str__(self):
2677  """__str__(BondSingletonScore self) -> std::string"""
2678  return _IMP_atom.BondSingletonScore___str__(self)
2679 
2680  def __repr__(self):
2681  """__repr__(BondSingletonScore self) -> std::string"""
2682  return _IMP_atom.BondSingletonScore___repr__(self)
2683 
2684  def get_from(o):
2685  return _object_cast_to_BondSingletonScore(o)
2686  get_from = staticmethod(get_from)
2687 
2688 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
2689 BondSingletonScore_swigregister(BondSingletonScore)
2690 
2691 class DihedralSingletonScore(IMP.kernel.SingletonScore):
2692  """Proxy of C++ IMP::atom::DihedralSingletonScore class"""
2693  __swig_setmethods__ = {}
2694  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2695  __setattr__ = lambda self, name, value: _swig_setattr(self, DihedralSingletonScore, name, value)
2696  __swig_getmethods__ = {}
2697  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2698  __getattr__ = lambda self, name: _swig_getattr(self, DihedralSingletonScore, name)
2699  def __init__(self):
2700  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
2701  this = _IMP_atom.new_DihedralSingletonScore()
2702  try: self.this.append(this)
2703  except: self.this = this
2704  def do_get_inputs(self, *args):
2705  """do_get_inputs(DihedralSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2706  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, *args)
2707 
2708  def get_version_info(self):
2709  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2710  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2711 
2712  __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
2713  __del__ = lambda self : None;
2714  def __str__(self):
2715  """__str__(DihedralSingletonScore self) -> std::string"""
2716  return _IMP_atom.DihedralSingletonScore___str__(self)
2717 
2718  def __repr__(self):
2719  """__repr__(DihedralSingletonScore self) -> std::string"""
2720  return _IMP_atom.DihedralSingletonScore___repr__(self)
2721 
2722  def get_from(o):
2723  return _object_cast_to_DihedralSingletonScore(o)
2724  get_from = staticmethod(get_from)
2725 
2726 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
2727 DihedralSingletonScore_swigregister(DihedralSingletonScore)
2728 
2729 class ImproperSingletonScore(IMP.kernel.SingletonScore):
2730  """Proxy of C++ IMP::atom::ImproperSingletonScore class"""
2731  __swig_setmethods__ = {}
2732  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2733  __setattr__ = lambda self, name, value: _swig_setattr(self, ImproperSingletonScore, name, value)
2734  __swig_getmethods__ = {}
2735  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2736  __getattr__ = lambda self, name: _swig_getattr(self, ImproperSingletonScore, name)
2737  def __init__(self, *args):
2738  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
2739  this = _IMP_atom.new_ImproperSingletonScore(*args)
2740  try: self.this.append(this)
2741  except: self.this = this
2742  def do_get_inputs(self, *args):
2743  """do_get_inputs(ImproperSingletonScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2744  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, *args)
2745 
2746  def get_version_info(self):
2747  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
2748  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
2749 
2750  __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
2751  __del__ = lambda self : None;
2752  def __str__(self):
2753  """__str__(ImproperSingletonScore self) -> std::string"""
2754  return _IMP_atom.ImproperSingletonScore___str__(self)
2755 
2756  def __repr__(self):
2757  """__repr__(ImproperSingletonScore self) -> std::string"""
2758  return _IMP_atom.ImproperSingletonScore___repr__(self)
2759 
2760  def get_from(o):
2761  return _object_cast_to_ImproperSingletonScore(o)
2762  get_from = staticmethod(get_from)
2763 
2764 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
2765 ImproperSingletonScore_swigregister(ImproperSingletonScore)
2766 
2767 class CoverBond(IMP.kernel.SingletonModifier):
2768  """Proxy of C++ IMP::atom::CoverBond class"""
2769  __swig_setmethods__ = {}
2770  for _s in [IMP.kernel.SingletonModifier]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2771  __setattr__ = lambda self, name, value: _swig_setattr(self, CoverBond, name, value)
2772  __swig_getmethods__ = {}
2773  for _s in [IMP.kernel.SingletonModifier]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2774  __getattr__ = lambda self, name: _swig_getattr(self, CoverBond, name)
2775  def __init__(self):
2776  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
2777  this = _IMP_atom.new_CoverBond()
2778  try: self.this.append(this)
2779  except: self.this = this
2780  def do_get_inputs(self, *args):
2781  """do_get_inputs(CoverBond self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2782  return _IMP_atom.CoverBond_do_get_inputs(self, *args)
2783 
2784  def do_get_outputs(self, *args):
2785  """do_get_outputs(CoverBond self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
2786  return _IMP_atom.CoverBond_do_get_outputs(self, *args)
2787 
2788  def get_version_info(self):
2789  """get_version_info(CoverBond self) -> VersionInfo"""
2790  return _IMP_atom.CoverBond_get_version_info(self)
2791 
2792  __swig_destroy__ = _IMP_atom.delete_CoverBond
2793  __del__ = lambda self : None;
2794  def __str__(self):
2795  """__str__(CoverBond self) -> std::string"""
2796  return _IMP_atom.CoverBond___str__(self)
2797 
2798  def __repr__(self):
2799  """__repr__(CoverBond self) -> std::string"""
2800  return _IMP_atom.CoverBond___repr__(self)
2801 
2802  def get_from(o):
2803  return _object_cast_to_CoverBond(o)
2804  get_from = staticmethod(get_from)
2805 
2806 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
2807 CoverBond_swigregister(CoverBond)
2808 
2809 class Simulator(IMP.kernel.Optimizer):
2810  """Proxy of C++ IMP::atom::Simulator class"""
2811  __swig_setmethods__ = {}
2812  for _s in [IMP.kernel.Optimizer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2813  __setattr__ = lambda self, name, value: _swig_setattr(self, Simulator, name, value)
2814  __swig_getmethods__ = {}
2815  for _s in [IMP.kernel.Optimizer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2816  __getattr__ = lambda self, name: _swig_getattr(self, Simulator, name)
2817  def __init__(self, *args):
2818  """
2819  __init__(IMP::atom::Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator
2820  __init__(IMP::atom::Simulator self, Model m, std::string name="Simulator %1%") -> Simulator
2821  __init__(IMP::atom::Simulator self, Model m) -> Simulator
2822  """
2823  if self.__class__ == Simulator:
2824  _self = None
2825  else:
2826  _self = self
2827  this = _IMP_atom.new_Simulator(_self, *args)
2828  try: self.this.append(this)
2829  except: self.this = this
2830  if self.__class__ != Simulator:
2831  import IMP.base
2832  IMP.base._director_objects.register(self)
2833 
2834 
2835 
2836  def simulate(self, *args):
2837  """simulate(Simulator self, double time_in_fs) -> double"""
2838  return _IMP_atom.Simulator_simulate(self, *args)
2839 
2840  def simulate_wave(self, *args):
2841  """
2842  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
2843  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
2844  simulate_wave(Simulator self, double time_in_fs) -> double
2845  """
2846  return _IMP_atom.Simulator_simulate_wave(self, *args)
2847 
2848  def get_temperature(self):
2849  """get_temperature(Simulator self) -> double"""
2850  return _IMP_atom.Simulator_get_temperature(self)
2851 
2852  def set_temperature(self, *args):
2853  """set_temperature(Simulator self, double d)"""
2854  return _IMP_atom.Simulator_set_temperature(self, *args)
2855 
2856  def set_maximum_time_step(self, *args):
2857  """set_maximum_time_step(Simulator self, double ts)"""
2858  return _IMP_atom.Simulator_set_maximum_time_step(self, *args)
2859 
2860  def get_maximum_time_step(self):
2861  """get_maximum_time_step(Simulator self) -> double"""
2862  return _IMP_atom.Simulator_get_maximum_time_step(self)
2863 
2864  def get_last_time_step(self):
2865  """get_last_time_step(Simulator self) -> double"""
2866  return _IMP_atom.Simulator_get_last_time_step(self)
2867 
2868  def set_time_step(self, *args):
2869  """set_time_step(Simulator self, double ts)"""
2870  return _IMP_atom.Simulator_set_time_step(self, *args)
2871 
2872  def get_kt(self):
2873  """get_kt(Simulator self) -> double"""
2874  return _IMP_atom.Simulator_get_kt(self)
2875 
2876  def get_current_time(self):
2877  """get_current_time(Simulator self) -> double"""
2878  return _IMP_atom.Simulator_get_current_time(self)
2879 
2880  def set_current_time(self, *args):
2881  """set_current_time(Simulator self, double ct)"""
2882  return _IMP_atom.Simulator_set_current_time(self, *args)
2883 
2884  def get_simulation_particles(self):
2885  """get_simulation_particles(Simulator self) -> IMP::kernel::ParticlesTemp"""
2886  return _IMP_atom.Simulator_get_simulation_particles(self)
2887 
2888  def get_simulation_particle_indexes(self):
2889  """get_simulation_particle_indexes(Simulator self) -> IMP::kernel::ParticleIndexes"""
2890  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
2891 
2892  def remove_particle(self, *args):
2893  """remove_particle(Simulator self, Particle d)"""
2894  return _IMP_atom.Simulator_remove_particle(self, *args)
2895 
2896  def remove_particles(self, *args):
2897  """remove_particles(Simulator self, IMP::kernel::Particles const & d)"""
2898  return _IMP_atom.Simulator_remove_particles(self, *args)
2899 
2900  def set_particles(self, *args):
2901  """set_particles(Simulator self, IMP::kernel::Particles const & ps)"""
2902  return _IMP_atom.Simulator_set_particles(self, *args)
2903 
2904  def set_particles_order(self, *args):
2905  """set_particles_order(Simulator self, IMP::kernel::Particles const & objs)"""
2906  return _IMP_atom.Simulator_set_particles_order(self, *args)
2907 
2908  def add_particle(self, *args):
2909  """add_particle(Simulator self, Particle obj) -> unsigned int"""
2910  return _IMP_atom.Simulator_add_particle(self, *args)
2911 
2912  def add_particles(self, *args):
2913  """add_particles(Simulator self, IMP::kernel::Particles const & objs)"""
2914  return _IMP_atom.Simulator_add_particles(self, *args)
2915 
2916  def clear_particles(self):
2917  """clear_particles(Simulator self)"""
2918  return _IMP_atom.Simulator_clear_particles(self)
2919 
2920  def get_number_of_particles(self):
2921  """get_number_of_particles(Simulator self) -> unsigned int"""
2922  return _IMP_atom.Simulator_get_number_of_particles(self)
2923 
2924  def get_has_particles(self):
2925  """get_has_particles(Simulator self) -> bool"""
2926  return _IMP_atom.Simulator_get_has_particles(self)
2927 
2928  def get_particle(self, *args):
2929  """get_particle(Simulator self, unsigned int i) -> Particle"""
2930  return _IMP_atom.Simulator_get_particle(self, *args)
2931 
2932  def get_particles(self):
2933  """get_particles(Simulator self) -> IMP::kernel::Particles"""
2934  return _IMP_atom.Simulator_get_particles(self)
2935 
2936  def reserve_particles(self, *args):
2937  """reserve_particles(Simulator self, unsigned int sz)"""
2938  return _IMP_atom.Simulator_reserve_particles(self, *args)
2939 
2940  def do_optimize(self, *args):
2941  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
2942  return _IMP_atom.Simulator_do_optimize(self, *args)
2943 
2944  def setup(self, *args):
2945  """setup(Simulator self, IMP::kernel::ParticleIndexes const & arg0)"""
2946  return _IMP_atom.Simulator_setup(self, *args)
2947 
2948  def do_step(self, *args):
2949  """do_step(Simulator self, IMP::kernel::ParticleIndexes const & sc, double dt) -> double"""
2950  return _IMP_atom.Simulator_do_step(self, *args)
2951 
2952  def get_is_simulation_particle(self, *args):
2953  """get_is_simulation_particle(Simulator self, IMP::kernel::ParticleIndex p) -> bool"""
2954  return _IMP_atom.Simulator_get_is_simulation_particle(self, *args)
2955 
2956  def __str__(self):
2957  """__str__(Simulator self) -> std::string"""
2958  return _IMP_atom.Simulator___str__(self)
2959 
2960  def __repr__(self):
2961  """__repr__(Simulator self) -> std::string"""
2962  return _IMP_atom.Simulator___repr__(self)
2963 
2964  def get_from(o):
2965  return _object_cast_to_Simulator(o)
2966  get_from = staticmethod(get_from)
2967 
2968  def get_type_name(self):
2969  return self.__class__.__name__
2970  def do_show(self, out):
2971  pass
2972  def get_version_info(self):
2973  if"IMP::atom" == "IMP":
2974  return VersionInfo("python", "0")
2975  else:
2976  return IMP.VersionInfo("python", "0")
2977  def get_from(o):
2978  return _object_cast_to_Simulator(o)
2979  get_from = staticmethod(get_from)
2980 
2981  __swig_destroy__ = _IMP_atom.delete_Simulator
2982  __del__ = lambda self : None;
2983  def __disown__(self):
2984  self.this.disown()
2985  _IMP_atom.disown_Simulator(self)
2986  return weakref_proxy(self)
2987  def handle_set_has_required_score_states(self, *args):
2988  """handle_set_has_required_score_states(Simulator self, bool arg0)"""
2989  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, *args)
2990 
2991  def do_get_inputs(self):
2992  """do_get_inputs(Simulator self) -> IMP::kernel::ModelObjectsTemp"""
2993  return _IMP_atom.Simulator_do_get_inputs(self)
2994 
2995  def do_get_outputs(self):
2996  """do_get_outputs(Simulator self) -> IMP::kernel::ModelObjectsTemp"""
2997  return _IMP_atom.Simulator_do_get_outputs(self)
2998 
2999  def do_get_interactions(self):
3000  """do_get_interactions(Simulator self) -> IMP::kernel::ModelObjectsTemps"""
3001  return _IMP_atom.Simulator_do_get_interactions(self)
3002 
3003 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3004 Simulator_swigregister(Simulator)
3005 
3006 
3007 def get_energy_in_femto_joules(*args):
3008  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
3009  return _IMP_atom.get_energy_in_femto_joules(*args)
3010 
3011 def get_force_in_femto_newtons(*args):
3012  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
3013  return _IMP_atom.get_force_in_femto_newtons(*args)
3014 
3015 def get_spring_constant_in_femto_newtons_per_angstrom(*args):
3016  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
3017  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(*args)
3018 class BrownianDynamics(Simulator):
3019  """Proxy of C++ IMP::atom::BrownianDynamics class"""
3020  __swig_setmethods__ = {}
3021  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3022  __setattr__ = lambda self, name, value: _swig_setattr(self, BrownianDynamics, name, value)
3023  __swig_getmethods__ = {}
3024  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3025  __getattr__ = lambda self, name: _swig_getattr(self, BrownianDynamics, name)
3026  def __init__(self, *args):
3027  """
3028  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0) -> BrownianDynamics
3029  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%") -> BrownianDynamics
3030  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3031  """
3032  this = _IMP_atom.new_BrownianDynamics(*args)
3033  try: self.this.append(this)
3034  except: self.this = this
3035  def set_maximum_move(self, *args):
3036  """set_maximum_move(BrownianDynamics self, double ms)"""
3037  return _IMP_atom.BrownianDynamics_set_maximum_move(self, *args)
3038 
3039  def set_use_stochastic_runge_kutta(self, *args):
3040  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3041  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, *args)
3042 
3043  def get_version_info(self):
3044  """get_version_info(BrownianDynamics self) -> VersionInfo"""
3045  return _IMP_atom.BrownianDynamics_get_version_info(self)
3046 
3047  __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3048  __del__ = lambda self : None;
3049  def __str__(self):
3050  """__str__(BrownianDynamics self) -> std::string"""
3051  return _IMP_atom.BrownianDynamics___str__(self)
3052 
3053  def __repr__(self):
3054  """__repr__(BrownianDynamics self) -> std::string"""
3055  return _IMP_atom.BrownianDynamics___repr__(self)
3056 
3057  def get_from(o):
3058  return _object_cast_to_BrownianDynamics(o)
3059  get_from = staticmethod(get_from)
3060 
3061 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3062 BrownianDynamics_swigregister(BrownianDynamics)
3063 
3064 
3066  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3067  return _IMP_atom.get_maximum_time_step_estimate(*args)
3068 
3069 def get_harmonic_sigma(*args):
3070  """get_harmonic_sigma(double D, double f) -> double"""
3071  return _IMP_atom.get_harmonic_sigma(*args)
3072 class Diffusion(IMP.core.XYZ):
3073  """Proxy of C++ IMP::atom::Diffusion class"""
3074  __swig_setmethods__ = {}
3075  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3076  __setattr__ = lambda self, name, value: _swig_setattr(self, Diffusion, name, value)
3077  __swig_getmethods__ = {}
3078  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3079  __getattr__ = lambda self, name: _swig_getattr(self, Diffusion, name)
3080  def __init__(self, *args):
3081  """
3082  __init__(IMP::atom::Diffusion self) -> Diffusion
3083  __init__(IMP::atom::Diffusion self, Model m, ::IMP::kernel::ParticleIndex id) -> Diffusion
3084  __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3085  """
3086  this = _IMP_atom.new_Diffusion(*args)
3087  try: self.this.append(this)
3088  except: self.this = this
3089  def decorate_particle(*args):
3090  """decorate_particle(Particle p) -> Diffusion"""
3091  return _IMP_atom.Diffusion_decorate_particle(*args)
3092 
3093  if _newclass:decorate_particle = staticmethod(decorate_particle)
3094  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3095  def particle_is_instance(*args):
3096  """
3097  particle_is_instance(Particle p) -> bool
3098  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3099  """
3100  return _IMP_atom.Diffusion_particle_is_instance(*args)
3101 
3102  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3103  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3104  def show(self, *args):
3105  """
3106  show(Diffusion self, _ostream out=std::cout)
3107  show(Diffusion self)
3108  """
3109  return _IMP_atom.Diffusion_show(self, *args)
3110 
3111  def setup_particle(*args):
3112  """
3113  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float D) -> Diffusion
3114  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3115  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3116  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3117  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Diffusion
3118  setup_particle(_ParticleAdaptor decorator) -> Diffusion
3119  """
3120  return _IMP_atom.Diffusion_setup_particle(*args)
3121 
3122  if _newclass:setup_particle = staticmethod(setup_particle)
3123  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3124  def get_is_setup(*args):
3125  """
3126  get_is_setup(_ParticleAdaptor p) -> bool
3127  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3128  """
3129  return _IMP_atom.Diffusion_get_is_setup(*args)
3130 
3131  if _newclass:get_is_setup = staticmethod(get_is_setup)
3132  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3133  def set_diffusion_coefficient(self, *args):
3134  """set_diffusion_coefficient(Diffusion self, double d)"""
3135  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, *args)
3136 
3137  def get_diffusion_coefficient(self):
3138  """get_diffusion_coefficient(Diffusion self) -> double"""
3139  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3140 
3141  def get_diffusion_coefficient_key():
3142  """get_diffusion_coefficient_key() -> FloatKey"""
3143  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3144 
3145  if _newclass:get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3146  __swig_getmethods__["get_diffusion_coefficient_key"] = lambda x: get_diffusion_coefficient_key
3147  def set_d(self, *args):
3148  """set_d(Diffusion self, double d)"""
3149  return _IMP_atom.Diffusion_set_d(self, *args)
3150 
3151  def get_d(self):
3152  """get_d(Diffusion self) -> double"""
3153  return _IMP_atom.Diffusion_get_d(self)
3154 
3155  def add_attribute(self, *args):
3156  """
3157  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3158  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3159  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3160  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3161  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3162  add_attribute(Diffusion self, ObjectKey a0, IMP::Object * a1)
3163  """
3164  return _IMP_atom.Diffusion_add_attribute(self, *args)
3165 
3166  def get_value(self, *args):
3167  """
3168  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3169  get_value(Diffusion self, IntKey a0) -> IMP::Int
3170  get_value(Diffusion self, StringKey a0) -> IMP::String
3171  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3172  get_value(Diffusion self, ObjectKey a0) -> IMP::Object *
3173  """
3174  return _IMP_atom.Diffusion_get_value(self, *args)
3175 
3176  def set_value(self, *args):
3177  """
3178  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3179  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3180  set_value(Diffusion self, StringKey a0, IMP::String a1)
3181  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3182  set_value(Diffusion self, ObjectKey a0, IMP::Object * a1)
3183  """
3184  return _IMP_atom.Diffusion_set_value(self, *args)
3185 
3186  def remove_attribute(self, *args):
3187  """
3188  remove_attribute(Diffusion self, FloatKey a0)
3189  remove_attribute(Diffusion self, IntKey a0)
3190  remove_attribute(Diffusion self, StringKey a0)
3191  remove_attribute(Diffusion self, ParticleIndexKey a0)
3192  remove_attribute(Diffusion self, ObjectKey a0)
3193  """
3194  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3195 
3196  def has_attribute(self, *args):
3197  """
3198  has_attribute(Diffusion self, FloatKey a0) -> bool
3199  has_attribute(Diffusion self, IntKey a0) -> bool
3200  has_attribute(Diffusion self, StringKey a0) -> bool
3201  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3202  has_attribute(Diffusion self, ObjectKey a0) -> bool
3203  """
3204  return _IMP_atom.Diffusion_has_attribute(self, *args)
3205 
3206  def get_derivative(self, *args):
3207  """get_derivative(Diffusion self, FloatKey a0) -> double"""
3208  return _IMP_atom.Diffusion_get_derivative(self, *args)
3209 
3210  def get_name(self):
3211  """get_name(Diffusion self) -> std::string"""
3212  return _IMP_atom.Diffusion_get_name(self)
3213 
3214  def clear_caches(self):
3215  """clear_caches(Diffusion self)"""
3216  return _IMP_atom.Diffusion_clear_caches(self)
3217 
3218  def set_name(self, *args):
3219  """set_name(Diffusion self, std::string a0)"""
3220  return _IMP_atom.Diffusion_set_name(self, *args)
3221 
3222  def set_check_level(self, *args):
3223  """set_check_level(Diffusion self, IMP::base::CheckLevel a0)"""
3224  return _IMP_atom.Diffusion_set_check_level(self, *args)
3225 
3226  def add_to_derivative(self, *args):
3227  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3228  return _IMP_atom.Diffusion_add_to_derivative(self, *args)
3229 
3230  def set_is_optimized(self, *args):
3231  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3232  return _IMP_atom.Diffusion_set_is_optimized(self, *args)
3233 
3234  def get_is_optimized(self, *args):
3235  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3236  return _IMP_atom.Diffusion_get_is_optimized(self, *args)
3237 
3238  def get_check_level(self):
3239  """get_check_level(Diffusion self) -> IMP::base::CheckLevel"""
3240  return _IMP_atom.Diffusion_get_check_level(self)
3241 
3242  def __eq__(self, *args):
3243  """
3244  __eq__(Diffusion self, Diffusion o) -> bool
3245  __eq__(Diffusion self, Particle d) -> bool
3246  """
3247  return _IMP_atom.Diffusion___eq__(self, *args)
3248 
3249  def __ne__(self, *args):
3250  """
3251  __ne__(Diffusion self, Diffusion o) -> bool
3252  __ne__(Diffusion self, Particle d) -> bool
3253  """
3254  return _IMP_atom.Diffusion___ne__(self, *args)
3255 
3256  def __le__(self, *args):
3257  """
3258  __le__(Diffusion self, Diffusion o) -> bool
3259  __le__(Diffusion self, Particle d) -> bool
3260  """
3261  return _IMP_atom.Diffusion___le__(self, *args)
3262 
3263  def __lt__(self, *args):
3264  """
3265  __lt__(Diffusion self, Diffusion o) -> bool
3266  __lt__(Diffusion self, Particle d) -> bool
3267  """
3268  return _IMP_atom.Diffusion___lt__(self, *args)
3269 
3270  def __ge__(self, *args):
3271  """
3272  __ge__(Diffusion self, Diffusion o) -> bool
3273  __ge__(Diffusion self, Particle d) -> bool
3274  """
3275  return _IMP_atom.Diffusion___ge__(self, *args)
3276 
3277  def __gt__(self, *args):
3278  """
3279  __gt__(Diffusion self, Diffusion o) -> bool
3280  __gt__(Diffusion self, Particle d) -> bool
3281  """
3282  return _IMP_atom.Diffusion___gt__(self, *args)
3283 
3284  def __str__(self):
3285  """__str__(Diffusion self) -> std::string"""
3286  return _IMP_atom.Diffusion___str__(self)
3287 
3288  def __repr__(self):
3289  """__repr__(Diffusion self) -> std::string"""
3290  return _IMP_atom.Diffusion___repr__(self)
3291 
3292  __swig_destroy__ = _IMP_atom.delete_Diffusion
3293  __del__ = lambda self : None;
3294 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
3295 Diffusion_swigregister(Diffusion)
3296 
3297 def Diffusion_decorate_particle(*args):
3298  """Diffusion_decorate_particle(Particle p) -> Diffusion"""
3299  return _IMP_atom.Diffusion_decorate_particle(*args)
3300 
3301 def Diffusion_particle_is_instance(*args):
3302  """
3303  particle_is_instance(Particle p) -> bool
3304  Diffusion_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3305  """
3306  return _IMP_atom.Diffusion_particle_is_instance(*args)
3307 
3308 def Diffusion_setup_particle(*args):
3309  """
3310  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float D) -> Diffusion
3311  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3312  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3313  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3314  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Diffusion
3315  Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
3316  """
3317  return _IMP_atom.Diffusion_setup_particle(*args)
3318 
3319 def Diffusion_get_is_setup(*args):
3320  """
3321  get_is_setup(_ParticleAdaptor p) -> bool
3322  Diffusion_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3323  """
3324  return _IMP_atom.Diffusion_get_is_setup(*args)
3325 
3326 def Diffusion_get_diffusion_coefficient_key():
3327  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
3328  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3329 
3330 
3331 def get_diffusion_coefficient_from_cm2_per_second(*args):
3332  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3333  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(*args)
3334 class RigidBodyDiffusion(Diffusion):
3335  """Proxy of C++ IMP::atom::RigidBodyDiffusion class"""
3336  __swig_setmethods__ = {}
3337  for _s in [Diffusion]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3338  __setattr__ = lambda self, name, value: _swig_setattr(self, RigidBodyDiffusion, name, value)
3339  __swig_getmethods__ = {}
3340  for _s in [Diffusion]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3341  __getattr__ = lambda self, name: _swig_getattr(self, RigidBodyDiffusion, name)
3342  def __init__(self, *args):
3343  """
3344  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
3345  __init__(IMP::atom::RigidBodyDiffusion self, Model m, ::IMP::kernel::ParticleIndex id) -> RigidBodyDiffusion
3346  __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3347  """
3348  this = _IMP_atom.new_RigidBodyDiffusion(*args)
3349  try: self.this.append(this)
3350  except: self.this = this
3351  def decorate_particle(*args):
3352  """decorate_particle(Particle p) -> RigidBodyDiffusion"""
3353  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3354 
3355  if _newclass:decorate_particle = staticmethod(decorate_particle)
3356  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3357  def particle_is_instance(*args):
3358  """
3359  particle_is_instance(Particle p) -> bool
3360  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3361  """
3362  return _IMP_atom.RigidBodyDiffusion_particle_is_instance(*args)
3363 
3364  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3365  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3366  def show(self, *args):
3367  """
3368  show(RigidBodyDiffusion self, _ostream out=std::cout)
3369  show(RigidBodyDiffusion self)
3370  """
3371  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3372 
3373  def setup_particle(*args):
3374  """
3375  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> RigidBodyDiffusion
3376  setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3377  """
3378  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3379 
3380  if _newclass:setup_particle = staticmethod(setup_particle)
3381  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3383  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3384  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3385 
3386  def set_rotational_diffusion_coefficient(self, *args):
3387  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3388  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, *args)
3389 
3390  def get_is_setup(*args):
3391  """
3392  get_is_setup(_ParticleAdaptor p) -> bool
3393  get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3394  """
3395  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3396 
3397  if _newclass:get_is_setup = staticmethod(get_is_setup)
3398  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3399  def get_rotational_diffusion_coefficient_key():
3400  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
3401  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3402 
3403  if _newclass:get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
3404  __swig_getmethods__["get_rotational_diffusion_coefficient_key"] = lambda x: get_rotational_diffusion_coefficient_key
3405  def add_attribute(self, *args):
3406  """
3407  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3408  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3409  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3410  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3411  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3412  add_attribute(RigidBodyDiffusion self, ObjectKey a0, IMP::Object * a1)
3413  """
3414  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3415 
3416  def get_value(self, *args):
3417  """
3418  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3419  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3420  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3421  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3422  get_value(RigidBodyDiffusion self, ObjectKey a0) -> IMP::Object *
3423  """
3424  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3425 
3426  def set_value(self, *args):
3427  """
3428  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3429  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3430  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3431  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3432  set_value(RigidBodyDiffusion self, ObjectKey a0, IMP::Object * a1)
3433  """
3434  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3435 
3436  def remove_attribute(self, *args):
3437  """
3438  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3439  remove_attribute(RigidBodyDiffusion self, IntKey a0)
3440  remove_attribute(RigidBodyDiffusion self, StringKey a0)
3441  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3442  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3443  """
3444  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3445 
3446  def has_attribute(self, *args):
3447  """
3448  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3449  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3450  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3451  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3452  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3453  """
3454  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3455 
3456  def get_derivative(self, *args):
3457  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3458  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, *args)
3459 
3460  def get_name(self):
3461  """get_name(RigidBodyDiffusion self) -> std::string"""
3462  return _IMP_atom.RigidBodyDiffusion_get_name(self)
3463 
3464  def clear_caches(self):
3465  """clear_caches(RigidBodyDiffusion self)"""
3466  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
3467 
3468  def set_name(self, *args):
3469  """set_name(RigidBodyDiffusion self, std::string a0)"""
3470  return _IMP_atom.RigidBodyDiffusion_set_name(self, *args)
3471 
3472  def set_check_level(self, *args):
3473  """set_check_level(RigidBodyDiffusion self, IMP::base::CheckLevel a0)"""
3474  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, *args)
3475 
3476  def add_to_derivative(self, *args):
3477  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3478  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, *args)
3479 
3480  def set_is_optimized(self, *args):
3481  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
3482  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, *args)
3483 
3484  def get_is_optimized(self, *args):
3485  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
3486  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, *args)
3487 
3488  def get_check_level(self):
3489  """get_check_level(RigidBodyDiffusion self) -> IMP::base::CheckLevel"""
3490  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
3491 
3492  def __eq__(self, *args):
3493  """
3494  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3495  __eq__(RigidBodyDiffusion self, Particle d) -> bool
3496  """
3497  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
3498 
3499  def __ne__(self, *args):
3500  """
3501  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3502  __ne__(RigidBodyDiffusion self, Particle d) -> bool
3503  """
3504  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
3505 
3506  def __le__(self, *args):
3507  """
3508  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3509  __le__(RigidBodyDiffusion self, Particle d) -> bool
3510  """
3511  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
3512 
3513  def __lt__(self, *args):
3514  """
3515  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3516  __lt__(RigidBodyDiffusion self, Particle d) -> bool
3517  """
3518  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
3519 
3520  def __ge__(self, *args):
3521  """
3522  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3523  __ge__(RigidBodyDiffusion self, Particle d) -> bool
3524  """
3525  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
3526 
3527  def __gt__(self, *args):
3528  """
3529  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3530  __gt__(RigidBodyDiffusion self, Particle d) -> bool
3531  """
3532  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
3533 
3534  def __str__(self):
3535  """__str__(RigidBodyDiffusion self) -> std::string"""
3536  return _IMP_atom.RigidBodyDiffusion___str__(self)
3537 
3538  def __repr__(self):
3539  """__repr__(RigidBodyDiffusion self) -> std::string"""
3540  return _IMP_atom.RigidBodyDiffusion___repr__(self)
3541 
3542  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
3543  __del__ = lambda self : None;
3544 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
3545 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
3546 
3547 def RigidBodyDiffusion_decorate_particle(*args):
3548  """RigidBodyDiffusion_decorate_particle(Particle p) -> RigidBodyDiffusion"""
3549  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3550 
3551 def RigidBodyDiffusion_particle_is_instance(*args):
3552  """
3553  particle_is_instance(Particle p) -> bool
3554  RigidBodyDiffusion_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3555  """
3556  return _IMP_atom.RigidBodyDiffusion_particle_is_instance(*args)
3557 
3558 def RigidBodyDiffusion_setup_particle(*args):
3559  """
3560  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> RigidBodyDiffusion
3561  RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3562  """
3563  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3564 
3565 def RigidBodyDiffusion_get_is_setup(*args):
3566  """
3567  get_is_setup(_ParticleAdaptor p) -> bool
3568  RigidBodyDiffusion_get_is_setup(Model m, IMP::kernel::ParticleIndex p) -> bool
3569  """
3570  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3571 
3572 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
3573  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
3574  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3575 
3576 class Chain(Hierarchy):
3577  """Proxy of C++ IMP::atom::Chain class"""
3578  __swig_setmethods__ = {}
3579  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3580  __setattr__ = lambda self, name, value: _swig_setattr(self, Chain, name, value)
3581  __swig_getmethods__ = {}
3582  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3583  __getattr__ = lambda self, name: _swig_getattr(self, Chain, name)
3584  def __init__(self, *args):
3585  """
3586  __init__(IMP::atom::Chain self) -> Chain
3587  __init__(IMP::atom::Chain self, Model m, ::IMP::kernel::ParticleIndex id) -> Chain
3588  __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
3589  """
3590  this = _IMP_atom.new_Chain(*args)
3591  try: self.this.append(this)
3592  except: self.this = this
3593  def decorate_particle(*args):
3594  """decorate_particle(Particle p) -> Chain"""
3595  return _IMP_atom.Chain_decorate_particle(*args)
3596 
3597  if _newclass:decorate_particle = staticmethod(decorate_particle)
3598  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3599  def particle_is_instance(*args):
3600  """
3601  particle_is_instance(Particle p) -> bool
3602  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3603  """
3604  return _IMP_atom.Chain_particle_is_instance(*args)
3605 
3606  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3607  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3608  def show(self, *args):
3609  """
3610  show(Chain self, _ostream out=std::cout)
3611  show(Chain self)
3612  """
3613  return _IMP_atom.Chain_show(self, *args)
3614 
3615  def setup_particle(*args):
3616  """
3617  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3618  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
3619  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Chain other) -> Chain
3620  setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
3621  """
3622  return _IMP_atom.Chain_setup_particle(*args)
3623 
3624  if _newclass:setup_particle = staticmethod(setup_particle)
3625  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3626  def get_is_setup(*args):
3627  """
3628  get_is_setup(_ParticleAdaptor p) -> bool
3629  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3630  """
3631  return _IMP_atom.Chain_get_is_setup(*args)
3632 
3633  if _newclass:get_is_setup = staticmethod(get_is_setup)
3634  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3635  def get_id(self):
3636  """get_id(Chain self) -> char"""
3637  return _IMP_atom.Chain_get_id(self)
3638 
3639  def set_id(self, *args):
3640  """set_id(Chain self, char c)"""
3641  return _IMP_atom.Chain_set_id(self, *args)
3642 
3643  def get_id_key():
3644  """get_id_key() -> IntKey"""
3645  return _IMP_atom.Chain_get_id_key()
3646 
3647  if _newclass:get_id_key = staticmethod(get_id_key)
3648  __swig_getmethods__["get_id_key"] = lambda x: get_id_key
3649  def add_attribute(self, *args):
3650  """
3651  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
3652  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
3653  add_attribute(Chain self, IntKey a0, IMP::Int a1)
3654  add_attribute(Chain self, StringKey a0, IMP::String a1)
3655  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
3656  add_attribute(Chain self, ObjectKey a0, IMP::Object * a1)
3657  """
3658  return _IMP_atom.Chain_add_attribute(self, *args)
3659 
3660  def get_value(self, *args):
3661  """
3662  get_value(Chain self, FloatKey a0) -> IMP::Float
3663  get_value(Chain self, IntKey a0) -> IMP::Int
3664  get_value(Chain self, StringKey a0) -> IMP::String
3665  get_value(Chain self, ParticleIndexKey a0) -> Particle
3666  get_value(Chain self, ObjectKey a0) -> IMP::Object *
3667  """
3668  return _IMP_atom.Chain_get_value(self, *args)
3669 
3670  def set_value(self, *args):
3671  """
3672  set_value(Chain self, FloatKey a0, IMP::Float a1)
3673  set_value(Chain self, IntKey a0, IMP::Int a1)
3674  set_value(Chain self, StringKey a0, IMP::String a1)
3675  set_value(Chain self, ParticleIndexKey a0, Particle a1)
3676  set_value(Chain self, ObjectKey a0, IMP::Object * a1)
3677  """
3678  return _IMP_atom.Chain_set_value(self, *args)
3679 
3680  def remove_attribute(self, *args):
3681  """
3682  remove_attribute(Chain self, FloatKey a0)
3683  remove_attribute(Chain self, IntKey a0)
3684  remove_attribute(Chain self, StringKey a0)
3685  remove_attribute(Chain self, ParticleIndexKey a0)
3686  remove_attribute(Chain self, ObjectKey a0)
3687  """
3688  return _IMP_atom.Chain_remove_attribute(self, *args)
3689 
3690  def has_attribute(self, *args):
3691  """
3692  has_attribute(Chain self, FloatKey a0) -> bool
3693  has_attribute(Chain self, IntKey a0) -> bool
3694  has_attribute(Chain self, StringKey a0) -> bool
3695  has_attribute(Chain self, ParticleIndexKey a0) -> bool
3696  has_attribute(Chain self, ObjectKey a0) -> bool
3697  """
3698  return _IMP_atom.Chain_has_attribute(self, *args)
3699 
3700  def get_derivative(self, *args):
3701  """get_derivative(Chain self, FloatKey a0) -> double"""
3702  return _IMP_atom.Chain_get_derivative(self, *args)
3703 
3704  def get_name(self):
3705  """get_name(Chain self) -> std::string"""
3706  return _IMP_atom.Chain_get_name(self)
3707 
3708  def clear_caches(self):
3709  """clear_caches(Chain self)"""
3710  return _IMP_atom.Chain_clear_caches(self)
3711 
3712  def set_name(self, *args):
3713  """set_name(Chain self, std::string a0)"""
3714  return _IMP_atom.Chain_set_name(self, *args)
3715 
3716  def set_check_level(self, *args):
3717  """set_check_level(Chain self, IMP::base::CheckLevel a0)"""
3718  return _IMP_atom.Chain_set_check_level(self, *args)
3719 
3720  def add_to_derivative(self, *args):
3721  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3722  return _IMP_atom.Chain_add_to_derivative(self, *args)
3723 
3724  def set_is_optimized(self, *args):
3725  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
3726  return _IMP_atom.Chain_set_is_optimized(self, *args)
3727 
3728  def get_is_optimized(self, *args):
3729  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
3730  return _IMP_atom.Chain_get_is_optimized(self, *args)
3731 
3732  def get_check_level(self):
3733  """get_check_level(Chain self) -> IMP::base::CheckLevel"""
3734  return _IMP_atom.Chain_get_check_level(self)
3735 
3736  def __eq__(self, *args):
3737  """
3738  __eq__(Chain self, Chain o) -> bool
3739  __eq__(Chain self, Particle d) -> bool
3740  """
3741  return _IMP_atom.Chain___eq__(self, *args)
3742 
3743  def __ne__(self, *args):
3744  """
3745  __ne__(Chain self, Chain o) -> bool
3746  __ne__(Chain self, Particle d) -> bool
3747  """
3748  return _IMP_atom.Chain___ne__(self, *args)
3749 
3750  def __le__(self, *args):
3751  """
3752  __le__(Chain self, Chain o) -> bool
3753  __le__(Chain self, Particle d) -> bool
3754  """
3755  return _IMP_atom.Chain___le__(self, *args)
3756 
3757  def __lt__(self, *args):
3758  """
3759  __lt__(Chain self, Chain o) -> bool
3760  __lt__(Chain self, Particle d) -> bool
3761  """
3762  return _IMP_atom.Chain___lt__(self, *args)
3763 
3764  def __ge__(self, *args):
3765  """
3766  __ge__(Chain self, Chain o) -> bool
3767  __ge__(Chain self, Particle d) -> bool
3768  """
3769  return _IMP_atom.Chain___ge__(self, *args)
3770 
3771  def __gt__(self, *args):
3772  """
3773  __gt__(Chain self, Chain o) -> bool
3774  __gt__(Chain self, Particle d) -> bool
3775  """
3776  return _IMP_atom.Chain___gt__(self, *args)
3777 
3778  def __str__(self):
3779  """__str__(Chain self) -> std::string"""
3780  return _IMP_atom.Chain___str__(self)
3781 
3782  def __repr__(self):
3783  """__repr__(Chain self) -> std::string"""
3784  return _IMP_atom.Chain___repr__(self)
3785 
3786  __swig_destroy__ = _IMP_atom.delete_Chain
3787  __del__ = lambda self : None;
3788 Chain_swigregister = _IMP_atom.Chain_swigregister
3789 Chain_swigregister(Chain)
3790 
3791 def Chain_decorate_particle(*args):
3792  """Chain_decorate_particle(Particle p) -> Chain"""
3793  return _IMP_atom.Chain_decorate_particle(*args)
3794 
3795 def Chain_particle_is_instance(*args):
3796  """
3797  particle_is_instance(Particle p) -> bool
3798  Chain_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3799  """
3800  return _IMP_atom.Chain_particle_is_instance(*args)
3801 
3802 def Chain_setup_particle(*args):
3803  """
3804  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3805  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
3806  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Chain other) -> Chain
3807  Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
3808  """
3809  return _IMP_atom.Chain_setup_particle(*args)
3810 
3811 def Chain_get_is_setup(*args):
3812  """
3813  get_is_setup(_ParticleAdaptor p) -> bool
3814  Chain_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3815  """
3816  return _IMP_atom.Chain_get_is_setup(*args)
3817 
3818 def Chain_get_id_key():
3819  """Chain_get_id_key() -> IntKey"""
3820  return _IMP_atom.Chain_get_id_key()
3821 
3822 
3823 def get_chain(*args):
3824  """get_chain(Hierarchy h) -> Chain"""
3825  return _IMP_atom.get_chain(*args)
3826 class Charged(IMP.core.XYZ):
3827  """Proxy of C++ IMP::atom::Charged class"""
3828  __swig_setmethods__ = {}
3829  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3830  __setattr__ = lambda self, name, value: _swig_setattr(self, Charged, name, value)
3831  __swig_getmethods__ = {}
3832  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3833  __getattr__ = lambda self, name: _swig_getattr(self, Charged, name)
3834  def __init__(self, *args):
3835  """
3836  __init__(IMP::atom::Charged self) -> Charged
3837  __init__(IMP::atom::Charged self, Model m, ::IMP::kernel::ParticleIndex id) -> Charged
3838  __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
3839  """
3840  this = _IMP_atom.new_Charged(*args)
3841  try: self.this.append(this)
3842  except: self.this = this
3843  def decorate_particle(*args):
3844  """decorate_particle(Particle p) -> Charged"""
3845  return _IMP_atom.Charged_decorate_particle(*args)
3846 
3847  if _newclass:decorate_particle = staticmethod(decorate_particle)
3848  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3849  def particle_is_instance(*args):
3850  """
3851  particle_is_instance(Particle p) -> bool
3852  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
3853  """
3854  return _IMP_atom.Charged_particle_is_instance(*args)
3855 
3856  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3857  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3858  def show(self, *args):
3859  """
3860  show(Charged self, _ostream out=std::cout)
3861  show(Charged self)
3862  """
3863  return _IMP_atom.Charged_show(self, *args)
3864 
3865  def setup_particle(*args):
3866  """
3867  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float charge) -> Charged
3868  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
3869  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
3870  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
3871  """
3872  return _IMP_atom.Charged_setup_particle(*args)
3873 
3874  if _newclass:setup_particle = staticmethod(setup_particle)
3875  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3876  def get_charge(self):
3877  """get_charge(Charged self) -> IMP::Float"""
3878  return _IMP_atom.Charged_get_charge(self)
3879 
3880  def set_charge(self, *args):
3881  """set_charge(Charged self, IMP::Float t)"""
3882  return _IMP_atom.Charged_set_charge(self, *args)
3883 
3884  def get_is_setup(*args):
3885  """
3886  get_is_setup(_ParticleAdaptor p) -> bool
3887  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
3888  """
3889  return _IMP_atom.Charged_get_is_setup(*args)
3890 
3891  if _newclass:get_is_setup = staticmethod(get_is_setup)
3892  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
3893  def get_charge_key():
3894  """get_charge_key() -> FloatKey"""
3895  return _IMP_atom.Charged_get_charge_key()
3896 
3897  if _newclass:get_charge_key = staticmethod(get_charge_key)
3898  __swig_getmethods__["get_charge_key"] = lambda x: get_charge_key
3899  def add_attribute(self, *args):
3900  """
3901  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
3902  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
3903  add_attribute(Charged self, IntKey a0, IMP::Int a1)
3904  add_attribute(Charged self, StringKey a0, IMP::String a1)
3905  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
3906  add_attribute(Charged self, ObjectKey a0, IMP::Object * a1)
3907  """
3908  return _IMP_atom.Charged_add_attribute(self, *args)
3909 
3910  def get_value(self, *args):
3911  """
3912  get_value(Charged self, FloatKey a0) -> IMP::Float
3913  get_value(Charged self, IntKey a0) -> IMP::Int
3914  get_value(Charged self, StringKey a0) -> IMP::String
3915  get_value(Charged self, ParticleIndexKey a0) -> Particle
3916  get_value(Charged self, ObjectKey a0) -> IMP::Object *
3917  """
3918  return _IMP_atom.Charged_get_value(self, *args)
3919 
3920  def set_value(self, *args):
3921  """
3922  set_value(Charged self, FloatKey a0, IMP::Float a1)
3923  set_value(Charged self, IntKey a0, IMP::Int a1)
3924  set_value(Charged self, StringKey a0, IMP::String a1)
3925  set_value(Charged self, ParticleIndexKey a0, Particle a1)
3926  set_value(Charged self, ObjectKey a0, IMP::Object * a1)
3927  """
3928  return _IMP_atom.Charged_set_value(self, *args)
3929 
3930  def remove_attribute(self, *args):
3931  """
3932  remove_attribute(Charged self, FloatKey a0)
3933  remove_attribute(Charged self, IntKey a0)
3934  remove_attribute(Charged self, StringKey a0)
3935  remove_attribute(Charged self, ParticleIndexKey a0)
3936  remove_attribute(Charged self, ObjectKey a0)
3937  """
3938  return _IMP_atom.Charged_remove_attribute(self, *args)
3939 
3940  def has_attribute(self, *args):
3941  """
3942  has_attribute(Charged self, FloatKey a0) -> bool
3943  has_attribute(Charged self, IntKey a0) -> bool
3944  has_attribute(Charged self, StringKey a0) -> bool
3945  has_attribute(Charged self, ParticleIndexKey a0) -> bool
3946  has_attribute(Charged self, ObjectKey a0) -> bool
3947  """
3948  return _IMP_atom.Charged_has_attribute(self, *args)
3949 
3950  def get_derivative(self, *args):
3951  """get_derivative(Charged self, FloatKey a0) -> double"""
3952  return _IMP_atom.Charged_get_derivative(self, *args)
3953 
3954  def get_name(self):
3955  """get_name(Charged self) -> std::string"""
3956  return _IMP_atom.Charged_get_name(self)
3957 
3958  def clear_caches(self):
3959  """clear_caches(Charged self)"""
3960  return _IMP_atom.Charged_clear_caches(self)
3961 
3962  def set_name(self, *args):
3963  """set_name(Charged self, std::string a0)"""
3964  return _IMP_atom.Charged_set_name(self, *args)
3965 
3966  def set_check_level(self, *args):
3967  """set_check_level(Charged self, IMP::base::CheckLevel a0)"""
3968  return _IMP_atom.Charged_set_check_level(self, *args)
3969 
3970  def add_to_derivative(self, *args):
3971  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3972  return _IMP_atom.Charged_add_to_derivative(self, *args)
3973 
3974  def set_is_optimized(self, *args):
3975  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
3976  return _IMP_atom.Charged_set_is_optimized(self, *args)
3977 
3978  def get_is_optimized(self, *args):
3979  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
3980  return _IMP_atom.Charged_get_is_optimized(self, *args)
3981 
3982  def get_check_level(self):
3983  """get_check_level(Charged self) -> IMP::base::CheckLevel"""
3984  return _IMP_atom.Charged_get_check_level(self)
3985 
3986  def __eq__(self, *args):
3987  """
3988  __eq__(Charged self, Charged o) -> bool
3989  __eq__(Charged self, Particle d) -> bool
3990  """
3991  return _IMP_atom.Charged___eq__(self, *args)
3992 
3993  def __ne__(self, *args):
3994  """
3995  __ne__(Charged self, Charged o) -> bool
3996  __ne__(Charged self, Particle d) -> bool
3997  """
3998  return _IMP_atom.Charged___ne__(self, *args)
3999 
4000  def __le__(self, *args):
4001  """
4002  __le__(Charged self, Charged o) -> bool
4003  __le__(Charged self, Particle d) -> bool
4004  """
4005  return _IMP_atom.Charged___le__(self, *args)
4006 
4007  def __lt__(self, *args):
4008  """
4009  __lt__(Charged self, Charged o) -> bool
4010  __lt__(Charged self, Particle d) -> bool
4011  """
4012  return _IMP_atom.Charged___lt__(self, *args)
4013 
4014  def __ge__(self, *args):
4015  """
4016  __ge__(Charged self, Charged o) -> bool
4017  __ge__(Charged self, Particle d) -> bool
4018  """
4019  return _IMP_atom.Charged___ge__(self, *args)
4020 
4021  def __gt__(self, *args):
4022  """
4023  __gt__(Charged self, Charged o) -> bool
4024  __gt__(Charged self, Particle d) -> bool
4025  """
4026  return _IMP_atom.Charged___gt__(self, *args)
4027 
4028  def __str__(self):
4029  """__str__(Charged self) -> std::string"""
4030  return _IMP_atom.Charged___str__(self)
4031 
4032  def __repr__(self):
4033  """__repr__(Charged self) -> std::string"""
4034  return _IMP_atom.Charged___repr__(self)
4035 
4036  __swig_destroy__ = _IMP_atom.delete_Charged
4037  __del__ = lambda self : None;
4038 Charged_swigregister = _IMP_atom.Charged_swigregister
4039 Charged_swigregister(Charged)
4040 
4041 def Charged_decorate_particle(*args):
4042  """Charged_decorate_particle(Particle p) -> Charged"""
4043  return _IMP_atom.Charged_decorate_particle(*args)
4044 
4045 def Charged_particle_is_instance(*args):
4046  """
4047  particle_is_instance(Particle p) -> bool
4048  Charged_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4049  """
4050  return _IMP_atom.Charged_particle_is_instance(*args)
4051 
4052 def Charged_setup_particle(*args):
4053  """
4054  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float charge) -> Charged
4055  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4056  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4057  Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4058  """
4059  return _IMP_atom.Charged_setup_particle(*args)
4060 
4061 def Charged_get_is_setup(*args):
4062  """
4063  get_is_setup(_ParticleAdaptor p) -> bool
4064  Charged_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4065  """
4066  return _IMP_atom.Charged_get_is_setup(*args)
4067 
4068 def Charged_get_charge_key():
4069  """Charged_get_charge_key() -> FloatKey"""
4070  return _IMP_atom.Charged_get_charge_key()
4071 
4072 class CoulombPairScore(IMP.kernel.PairScore):
4073  """Proxy of C++ IMP::atom::CoulombPairScore class"""
4074  __swig_setmethods__ = {}
4075  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4076  __setattr__ = lambda self, name, value: _swig_setattr(self, CoulombPairScore, name, value)
4077  __swig_getmethods__ = {}
4078  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4079  __getattr__ = lambda self, name: _swig_getattr(self, CoulombPairScore, name)
4080  def __init__(self, *args):
4081  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4082  this = _IMP_atom.new_CoulombPairScore(*args)
4083  try: self.this.append(this)
4084  except: self.this = this
4085  def set_relative_dielectric(self, *args):
4086  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4087  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, *args)
4088 
4089  def get_relative_dielectric(self):
4090  """get_relative_dielectric(CoulombPairScore self) -> double"""
4091  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4092 
4093  def do_get_inputs(self, *args):
4094  """do_get_inputs(CoulombPairScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
4095  return _IMP_atom.CoulombPairScore_do_get_inputs(self, *args)
4096 
4097  def get_version_info(self):
4098  """get_version_info(CoulombPairScore self) -> VersionInfo"""
4099  return _IMP_atom.CoulombPairScore_get_version_info(self)
4100 
4101  __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4102  __del__ = lambda self : None;
4103  def __str__(self):
4104  """__str__(CoulombPairScore self) -> std::string"""
4105  return _IMP_atom.CoulombPairScore___str__(self)
4106 
4107  def __repr__(self):
4108  """__repr__(CoulombPairScore self) -> std::string"""
4109  return _IMP_atom.CoulombPairScore___repr__(self)
4110 
4111  def get_from(o):
4112  return _object_cast_to_CoulombPairScore(o)
4113  get_from = staticmethod(get_from)
4114 
4115 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
4116 CoulombPairScore_swigregister(CoulombPairScore)
4117 
4118 class Domain(Hierarchy):
4119  """Proxy of C++ IMP::atom::Domain class"""
4120  __swig_setmethods__ = {}
4121  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4122  __setattr__ = lambda self, name, value: _swig_setattr(self, Domain, name, value)
4123  __swig_getmethods__ = {}
4124  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4125  __getattr__ = lambda self, name: _swig_getattr(self, Domain, name)
4126  def set_index_range(self, *args):
4127  """set_index_range(Domain self, IMP::IntRange ir)"""
4128  return _IMP_atom.Domain_set_index_range(self, *args)
4129 
4130  def get_index_range(self):
4131  """get_index_range(Domain self) -> IMP::IntRange"""
4132  return _IMP_atom.Domain_get_index_range(self)
4133 
4134  def __init__(self, *args):
4135  """
4136  __init__(IMP::atom::Domain self) -> Domain
4137  __init__(IMP::atom::Domain self, Model m, ::IMP::kernel::ParticleIndex id) -> Domain
4138  __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
4139  """
4140  this = _IMP_atom.new_Domain(*args)
4141  try: self.this.append(this)
4142  except: self.this = this
4143  def decorate_particle(*args):
4144  """decorate_particle(Particle p) -> Domain"""
4145  return _IMP_atom.Domain_decorate_particle(*args)
4146 
4147  if _newclass:decorate_particle = staticmethod(decorate_particle)
4148  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4149  def particle_is_instance(*args):
4150  """
4151  particle_is_instance(Particle p) -> bool
4152  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4153  """
4154  return _IMP_atom.Domain_particle_is_instance(*args)
4155 
4156  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4157  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4158  def get_is_setup(*args):
4159  """
4160  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4161  get_is_setup(_ParticleAdaptor p) -> bool
4162  """
4163  return _IMP_atom.Domain_get_is_setup(*args)
4164 
4165  if _newclass:get_is_setup = staticmethod(get_is_setup)
4166  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4167  def show(self, *args):
4168  """
4169  show(Domain self, _ostream out=std::cout)
4170  show(Domain self)
4171  """
4172  return _IMP_atom.Domain_show(self, *args)
4173 
4174  def get_begin_index(self):
4175  """get_begin_index(Domain self) -> IMP::Int"""
4176  return _IMP_atom.Domain_get_begin_index(self)
4177 
4178  def get_end_index(self):
4179  """get_end_index(Domain self) -> IMP::Int"""
4180  return _IMP_atom.Domain_get_end_index(self)
4181 
4182  def setup_particle(*args):
4183  """
4184  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Domain other) -> Domain
4185  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
4186  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::IntRange residues) -> Domain
4187  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
4188  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int residues_begin, IMP::Int residues_end) -> Domain
4189  setup_particle(_ParticleAdaptor decorator, IMP::Int residues_begin, IMP::Int residues_end) -> Domain
4190  """
4191  return _IMP_atom.Domain_setup_particle(*args)
4192 
4193  if _newclass:setup_particle = staticmethod(setup_particle)
4194  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4195  def add_attribute(self, *args):
4196  """
4197  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4198  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4199  add_attribute(Domain self, IntKey a0, IMP::Int a1)
4200  add_attribute(Domain self, StringKey a0, IMP::String a1)
4201  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4202  add_attribute(Domain self, ObjectKey a0, IMP::Object * a1)
4203  """
4204  return _IMP_atom.Domain_add_attribute(self, *args)
4205 
4206  def get_value(self, *args):
4207  """
4208  get_value(Domain self, FloatKey a0) -> IMP::Float
4209  get_value(Domain self, IntKey a0) -> IMP::Int
4210  get_value(Domain self, StringKey a0) -> IMP::String
4211  get_value(Domain self, ParticleIndexKey a0) -> Particle
4212  get_value(Domain self, ObjectKey a0) -> IMP::Object *
4213  """
4214  return _IMP_atom.Domain_get_value(self, *args)
4215 
4216  def set_value(self, *args):
4217  """
4218  set_value(Domain self, FloatKey a0, IMP::Float a1)
4219  set_value(Domain self, IntKey a0, IMP::Int a1)
4220  set_value(Domain self, StringKey a0, IMP::String a1)
4221  set_value(Domain self, ParticleIndexKey a0, Particle a1)
4222  set_value(Domain self, ObjectKey a0, IMP::Object * a1)
4223  """
4224  return _IMP_atom.Domain_set_value(self, *args)
4225 
4226  def remove_attribute(self, *args):
4227  """
4228  remove_attribute(Domain self, FloatKey a0)
4229  remove_attribute(Domain self, IntKey a0)
4230  remove_attribute(Domain self, StringKey a0)
4231  remove_attribute(Domain self, ParticleIndexKey a0)
4232  remove_attribute(Domain self, ObjectKey a0)
4233  """
4234  return _IMP_atom.Domain_remove_attribute(self, *args)
4235 
4236  def has_attribute(self, *args):
4237  """
4238  has_attribute(Domain self, FloatKey a0) -> bool
4239  has_attribute(Domain self, IntKey a0) -> bool
4240  has_attribute(Domain self, StringKey a0) -> bool
4241  has_attribute(Domain self, ParticleIndexKey a0) -> bool
4242  has_attribute(Domain self, ObjectKey a0) -> bool
4243  """
4244  return _IMP_atom.Domain_has_attribute(self, *args)
4245 
4246  def get_derivative(self, *args):
4247  """get_derivative(Domain self, FloatKey a0) -> double"""
4248  return _IMP_atom.Domain_get_derivative(self, *args)
4249 
4250  def get_name(self):
4251  """get_name(Domain self) -> std::string"""
4252  return _IMP_atom.Domain_get_name(self)
4253 
4254  def clear_caches(self):
4255  """clear_caches(Domain self)"""
4256  return _IMP_atom.Domain_clear_caches(self)
4257 
4258  def set_name(self, *args):
4259  """set_name(Domain self, std::string a0)"""
4260  return _IMP_atom.Domain_set_name(self, *args)
4261 
4262  def set_check_level(self, *args):
4263  """set_check_level(Domain self, IMP::base::CheckLevel a0)"""
4264  return _IMP_atom.Domain_set_check_level(self, *args)
4265 
4266  def add_to_derivative(self, *args):
4267  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4268  return _IMP_atom.Domain_add_to_derivative(self, *args)
4269 
4270  def set_is_optimized(self, *args):
4271  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4272  return _IMP_atom.Domain_set_is_optimized(self, *args)
4273 
4274  def get_is_optimized(self, *args):
4275  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
4276  return _IMP_atom.Domain_get_is_optimized(self, *args)
4277 
4278  def get_check_level(self):
4279  """get_check_level(Domain self) -> IMP::base::CheckLevel"""
4280  return _IMP_atom.Domain_get_check_level(self)
4281 
4282  def __eq__(self, *args):
4283  """
4284  __eq__(Domain self, Domain o) -> bool
4285  __eq__(Domain self, Particle d) -> bool
4286  """
4287  return _IMP_atom.Domain___eq__(self, *args)
4288 
4289  def __ne__(self, *args):
4290  """
4291  __ne__(Domain self, Domain o) -> bool
4292  __ne__(Domain self, Particle d) -> bool
4293  """
4294  return _IMP_atom.Domain___ne__(self, *args)
4295 
4296  def __le__(self, *args):
4297  """
4298  __le__(Domain self, Domain o) -> bool
4299  __le__(Domain self, Particle d) -> bool
4300  """
4301  return _IMP_atom.Domain___le__(self, *args)
4302 
4303  def __lt__(self, *args):
4304  """
4305  __lt__(Domain self, Domain o) -> bool
4306  __lt__(Domain self, Particle d) -> bool
4307  """
4308  return _IMP_atom.Domain___lt__(self, *args)
4309 
4310  def __ge__(self, *args):
4311  """
4312  __ge__(Domain self, Domain o) -> bool
4313  __ge__(Domain self, Particle d) -> bool
4314  """
4315  return _IMP_atom.Domain___ge__(self, *args)
4316 
4317  def __gt__(self, *args):
4318  """
4319  __gt__(Domain self, Domain o) -> bool
4320  __gt__(Domain self, Particle d) -> bool
4321  """
4322  return _IMP_atom.Domain___gt__(self, *args)
4323 
4324  def __str__(self):
4325  """__str__(Domain self) -> std::string"""
4326  return _IMP_atom.Domain___str__(self)
4327 
4328  def __repr__(self):
4329  """__repr__(Domain self) -> std::string"""
4330  return _IMP_atom.Domain___repr__(self)
4331 
4332  __swig_destroy__ = _IMP_atom.delete_Domain
4333  __del__ = lambda self : None;
4334 Domain_swigregister = _IMP_atom.Domain_swigregister
4335 Domain_swigregister(Domain)
4336 
4337 def Domain_decorate_particle(*args):
4338  """Domain_decorate_particle(Particle p) -> Domain"""
4339  return _IMP_atom.Domain_decorate_particle(*args)
4340 
4341 def Domain_particle_is_instance(*args):
4342  """
4343  particle_is_instance(Particle p) -> bool
4344  Domain_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4345  """
4346  return _IMP_atom.Domain_particle_is_instance(*args)
4347 
4348 def Domain_get_is_setup(*args):
4349  """
4350  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4351  Domain_get_is_setup(_ParticleAdaptor p) -> bool
4352  """
4353  return _IMP_atom.Domain_get_is_setup(*args)
4354 
4355 def Domain_setup_particle(*args):
4356  """
4357  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Domain other) -> Domain
4358  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
4359  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::IntRange residues) -> Domain
4360  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
4361  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int residues_begin, IMP::Int residues_end) -> Domain
4362  Domain_setup_particle(_ParticleAdaptor decorator, IMP::Int residues_begin, IMP::Int residues_end) -> Domain
4363  """
4364  return _IMP_atom.Domain_setup_particle(*args)
4365 
4366 class LennardJones(IMP.core.XYZR):
4367  """Proxy of C++ IMP::atom::LennardJones class"""
4368  __swig_setmethods__ = {}
4369  for _s in [IMP.core.XYZR]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4370  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJones, name, value)
4371  __swig_getmethods__ = {}
4372  for _s in [IMP.core.XYZR]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4373  __getattr__ = lambda self, name: _swig_getattr(self, LennardJones, name)
4374  def __init__(self, *args):
4375  """
4376  __init__(IMP::atom::LennardJones self) -> LennardJones
4377  __init__(IMP::atom::LennardJones self, Model m, ::IMP::kernel::ParticleIndex id) -> LennardJones
4378  __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
4379  """
4380  this = _IMP_atom.new_LennardJones(*args)
4381  try: self.this.append(this)
4382  except: self.this = this
4383  def decorate_particle(*args):
4384  """decorate_particle(Particle p) -> LennardJones"""
4385  return _IMP_atom.LennardJones_decorate_particle(*args)
4386 
4387  if _newclass:decorate_particle = staticmethod(decorate_particle)
4388  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4389  def particle_is_instance(*args):
4390  """
4391  particle_is_instance(Particle p) -> bool
4392  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4393  """
4394  return _IMP_atom.LennardJones_particle_is_instance(*args)
4395 
4396  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4397  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4398  def show(self, *args):
4399  """
4400  show(LennardJones self, _ostream out=std::cout)
4401  show(LennardJones self)
4402  """
4403  return _IMP_atom.LennardJones_show(self, *args)
4404 
4405  def setup_particle(*args):
4406  """
4407  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> LennardJones
4408  setup_particle(_ParticleAdaptor decorator) -> LennardJones
4409  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4410  setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
4411  """
4412  return _IMP_atom.LennardJones_setup_particle(*args)
4413 
4414  if _newclass:setup_particle = staticmethod(setup_particle)
4415  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4416  def get_well_depth(self):
4417  """get_well_depth(LennardJones self) -> IMP::Float"""
4418  return _IMP_atom.LennardJones_get_well_depth(self)
4419 
4420  def set_well_depth(self, *args):
4421  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
4422  return _IMP_atom.LennardJones_set_well_depth(self, *args)
4423 
4424  def get_is_setup(*args):
4425  """
4426  get_is_setup(_ParticleAdaptor p) -> bool
4427  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4428  """
4429  return _IMP_atom.LennardJones_get_is_setup(*args)
4430 
4431  if _newclass:get_is_setup = staticmethod(get_is_setup)
4432  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4433  def get_well_depth_key():
4434  """get_well_depth_key() -> FloatKey"""
4435  return _IMP_atom.LennardJones_get_well_depth_key()
4436 
4437  if _newclass:get_well_depth_key = staticmethod(get_well_depth_key)
4438  __swig_getmethods__["get_well_depth_key"] = lambda x: get_well_depth_key
4439  def add_attribute(self, *args):
4440  """
4441  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
4442  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
4443  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
4444  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
4445  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
4446  add_attribute(LennardJones self, ObjectKey a0, IMP::Object * a1)
4447  """
4448  return _IMP_atom.LennardJones_add_attribute(self, *args)
4449 
4450  def get_value(self, *args):
4451  """
4452  get_value(LennardJones self, FloatKey a0) -> IMP::Float
4453  get_value(LennardJones self, IntKey a0) -> IMP::Int
4454  get_value(LennardJones self, StringKey a0) -> IMP::String
4455  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
4456  get_value(LennardJones self, ObjectKey a0) -> IMP::Object *
4457  """
4458  return _IMP_atom.LennardJones_get_value(self, *args)
4459 
4460  def set_value(self, *args):
4461  """
4462  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
4463  set_value(LennardJones self, IntKey a0, IMP::Int a1)
4464  set_value(LennardJones self, StringKey a0, IMP::String a1)
4465  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
4466  set_value(LennardJones self, ObjectKey a0, IMP::Object * a1)
4467  """
4468  return _IMP_atom.LennardJones_set_value(self, *args)
4469 
4470  def remove_attribute(self, *args):
4471  """
4472  remove_attribute(LennardJones self, FloatKey a0)
4473  remove_attribute(LennardJones self, IntKey a0)
4474  remove_attribute(LennardJones self, StringKey a0)
4475  remove_attribute(LennardJones self, ParticleIndexKey a0)
4476  remove_attribute(LennardJones self, ObjectKey a0)
4477  """
4478  return _IMP_atom.LennardJones_remove_attribute(self, *args)
4479 
4480  def has_attribute(self, *args):
4481  """
4482  has_attribute(LennardJones self, FloatKey a0) -> bool
4483  has_attribute(LennardJones self, IntKey a0) -> bool
4484  has_attribute(LennardJones self, StringKey a0) -> bool
4485  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
4486  has_attribute(LennardJones self, ObjectKey a0) -> bool
4487  """
4488  return _IMP_atom.LennardJones_has_attribute(self, *args)
4489 
4490  def get_derivative(self, *args):
4491  """get_derivative(LennardJones self, FloatKey a0) -> double"""
4492  return _IMP_atom.LennardJones_get_derivative(self, *args)
4493 
4494  def get_name(self):
4495  """get_name(LennardJones self) -> std::string"""
4496  return _IMP_atom.LennardJones_get_name(self)
4497 
4498  def clear_caches(self):
4499  """clear_caches(LennardJones self)"""
4500  return _IMP_atom.LennardJones_clear_caches(self)
4501 
4502  def set_name(self, *args):
4503  """set_name(LennardJones self, std::string a0)"""
4504  return _IMP_atom.LennardJones_set_name(self, *args)
4505 
4506  def set_check_level(self, *args):
4507  """set_check_level(LennardJones self, IMP::base::CheckLevel a0)"""
4508  return _IMP_atom.LennardJones_set_check_level(self, *args)
4509 
4510  def add_to_derivative(self, *args):
4511  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4512  return _IMP_atom.LennardJones_add_to_derivative(self, *args)
4513 
4514  def set_is_optimized(self, *args):
4515  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
4516  return _IMP_atom.LennardJones_set_is_optimized(self, *args)
4517 
4518  def get_is_optimized(self, *args):
4519  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
4520  return _IMP_atom.LennardJones_get_is_optimized(self, *args)
4521 
4522  def get_check_level(self):
4523  """get_check_level(LennardJones self) -> IMP::base::CheckLevel"""
4524  return _IMP_atom.LennardJones_get_check_level(self)
4525 
4526  def __eq__(self, *args):
4527  """
4528  __eq__(LennardJones self, LennardJones o) -> bool
4529  __eq__(LennardJones self, Particle d) -> bool
4530  """
4531  return _IMP_atom.LennardJones___eq__(self, *args)
4532 
4533  def __ne__(self, *args):
4534  """
4535  __ne__(LennardJones self, LennardJones o) -> bool
4536  __ne__(LennardJones self, Particle d) -> bool
4537  """
4538  return _IMP_atom.LennardJones___ne__(self, *args)
4539 
4540  def __le__(self, *args):
4541  """
4542  __le__(LennardJones self, LennardJones o) -> bool
4543  __le__(LennardJones self, Particle d) -> bool
4544  """
4545  return _IMP_atom.LennardJones___le__(self, *args)
4546 
4547  def __lt__(self, *args):
4548  """
4549  __lt__(LennardJones self, LennardJones o) -> bool
4550  __lt__(LennardJones self, Particle d) -> bool
4551  """
4552  return _IMP_atom.LennardJones___lt__(self, *args)
4553 
4554  def __ge__(self, *args):
4555  """
4556  __ge__(LennardJones self, LennardJones o) -> bool
4557  __ge__(LennardJones self, Particle d) -> bool
4558  """
4559  return _IMP_atom.LennardJones___ge__(self, *args)
4560 
4561  def __gt__(self, *args):
4562  """
4563  __gt__(LennardJones self, LennardJones o) -> bool
4564  __gt__(LennardJones self, Particle d) -> bool
4565  """
4566  return _IMP_atom.LennardJones___gt__(self, *args)
4567 
4568  def __str__(self):
4569  """__str__(LennardJones self) -> std::string"""
4570  return _IMP_atom.LennardJones___str__(self)
4571 
4572  def __repr__(self):
4573  """__repr__(LennardJones self) -> std::string"""
4574  return _IMP_atom.LennardJones___repr__(self)
4575 
4576  __swig_destroy__ = _IMP_atom.delete_LennardJones
4577  __del__ = lambda self : None;
4578 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
4579 LennardJones_swigregister(LennardJones)
4580 
4581 def LennardJones_decorate_particle(*args):
4582  """LennardJones_decorate_particle(Particle p) -> LennardJones"""
4583  return _IMP_atom.LennardJones_decorate_particle(*args)
4584 
4585 def LennardJones_particle_is_instance(*args):
4586  """
4587  particle_is_instance(Particle p) -> bool
4588  LennardJones_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4589  """
4590  return _IMP_atom.LennardJones_particle_is_instance(*args)
4591 
4592 def LennardJones_setup_particle(*args):
4593  """
4594  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> LennardJones
4595  setup_particle(_ParticleAdaptor decorator) -> LennardJones
4596  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4597  LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
4598  """
4599  return _IMP_atom.LennardJones_setup_particle(*args)
4600 
4601 def LennardJones_get_is_setup(*args):
4602  """
4603  get_is_setup(_ParticleAdaptor p) -> bool
4604  LennardJones_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4605  """
4606  return _IMP_atom.LennardJones_get_is_setup(*args)
4607 
4608 def LennardJones_get_well_depth_key():
4609  """LennardJones_get_well_depth_key() -> FloatKey"""
4610  return _IMP_atom.LennardJones_get_well_depth_key()
4611 
4612 class LennardJonesPairScore(IMP.kernel.PairScore):
4613  """Proxy of C++ IMP::atom::LennardJonesPairScore class"""
4614  __swig_setmethods__ = {}
4615  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4616  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJonesPairScore, name, value)
4617  __swig_getmethods__ = {}
4618  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4619  __getattr__ = lambda self, name: _swig_getattr(self, LennardJonesPairScore, name)
4620  def __init__(self, *args):
4621  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
4622  this = _IMP_atom.new_LennardJonesPairScore(*args)
4623  try: self.this.append(this)
4624  except: self.this = this
4625  def set_repulsive_weight(self, *args):
4626  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
4627  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, *args)
4628 
4629  def get_repulsive_weight(self):
4630  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
4631  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
4632 
4633  def set_attractive_weight(self, *args):
4634  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
4635  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, *args)
4636 
4637  def get_attractive_weight(self):
4638  """get_attractive_weight(LennardJonesPairScore self) -> double"""
4639  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
4640 
4641  def do_get_inputs(self, *args):
4642  """do_get_inputs(LennardJonesPairScore self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
4643  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, *args)
4644 
4645  def get_version_info(self):
4646  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
4647  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
4648 
4649  __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
4650  __del__ = lambda self : None;
4651  def __str__(self):
4652  """__str__(LennardJonesPairScore self) -> std::string"""
4653  return _IMP_atom.LennardJonesPairScore___str__(self)
4654 
4655  def __repr__(self):
4656  """__repr__(LennardJonesPairScore self) -> std::string"""
4657  return _IMP_atom.LennardJonesPairScore___repr__(self)
4658 
4659  def get_from(o):
4660  return _object_cast_to_LennardJonesPairScore(o)
4661  get_from = staticmethod(get_from)
4662 
4663 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
4664 LennardJonesPairScore_swigregister(LennardJonesPairScore)
4665 
4666 class MolecularDynamics(Simulator):
4667  """Proxy of C++ IMP::atom::MolecularDynamics class"""
4668  __swig_setmethods__ = {}
4669  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4670  __setattr__ = lambda self, name, value: _swig_setattr(self, MolecularDynamics, name, value)
4671  __swig_getmethods__ = {}
4672  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4673  __getattr__ = lambda self, name: _swig_getattr(self, MolecularDynamics, name)
4674  def __init__(self, *args):
4675  """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
4676  this = _IMP_atom.new_MolecularDynamics(*args)
4677  try: self.this.append(this)
4678  except: self.this = this
4679  def get_kinetic_energy(self):
4680  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
4681  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
4682 
4683  def get_kinetic_temperature(self, *args):
4684  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
4685  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, *args)
4686 
4687  def set_velocity_cap(self, *args):
4688  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
4689  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, *args)
4690 
4691  def assign_velocities(self, *args):
4692  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
4693  return _IMP_atom.MolecularDynamics_assign_velocities(self, *args)
4694 
4695  def setup(self, *args):
4696  """setup(MolecularDynamics self, IMP::kernel::ParticleIndexes const & ps)"""
4697  return _IMP_atom.MolecularDynamics_setup(self, *args)
4698 
4699  def do_step(self, *args):
4700  """do_step(MolecularDynamics self, IMP::kernel::ParticleIndexes const & sc, double dt) -> double"""
4701  return _IMP_atom.MolecularDynamics_do_step(self, *args)
4702 
4703  def get_is_simulation_particle(self, *args):
4704  """get_is_simulation_particle(MolecularDynamics self, IMP::kernel::ParticleIndex p) -> bool"""
4705  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, *args)
4706 
4707  def get_version_info(self):
4708  """get_version_info(MolecularDynamics self) -> VersionInfo"""
4709  return _IMP_atom.MolecularDynamics_get_version_info(self)
4710 
4711  __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
4712  __del__ = lambda self : None;
4713  def __str__(self):
4714  """__str__(MolecularDynamics self) -> std::string"""
4715  return _IMP_atom.MolecularDynamics___str__(self)
4716 
4717  def __repr__(self):
4718  """__repr__(MolecularDynamics self) -> std::string"""
4719  return _IMP_atom.MolecularDynamics___repr__(self)
4720 
4721  def get_from(o):
4722  return _object_cast_to_MolecularDynamics(o)
4723  get_from = staticmethod(get_from)
4724 
4725 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
4726 MolecularDynamics_swigregister(MolecularDynamics)
4727 
4728 class VelocityScalingOptimizerState(IMP.kernel.OptimizerState):
4729  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class"""
4730  __swig_setmethods__ = {}
4731  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4732  __setattr__ = lambda self, name, value: _swig_setattr(self, VelocityScalingOptimizerState, name, value)
4733  __swig_getmethods__ = {}
4734  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4735  __getattr__ = lambda self, name: _swig_getattr(self, VelocityScalingOptimizerState, name)
4736  def __init__(self, *args):
4737  """
4738  __init__(IMP::atom::VelocityScalingOptimizerState self, IMP::kernel::Particles const & pis, IMP::Float temperature, unsigned int skip_steps) -> VelocityScalingOptimizerState
4739  __init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState
4740  """
4741  this = _IMP_atom.new_VelocityScalingOptimizerState(*args)
4742  try: self.this.append(this)
4743  except: self.this = this
4744  def set_particles(self, *args):
4745  """set_particles(VelocityScalingOptimizerState self, IMP::kernel::Particles const & pis)"""
4746  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, *args)
4747 
4748  def set_temperature(self, *args):
4749  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
4750  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, *args)
4751 
4752  def rescale_velocities(self):
4753  """rescale_velocities(VelocityScalingOptimizerState self)"""
4754  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
4755 
4756  def get_version_info(self):
4757  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
4758  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
4759 
4760  __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
4761  __del__ = lambda self : None;
4762  def __str__(self):
4763  """__str__(VelocityScalingOptimizerState self) -> std::string"""
4764  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
4765 
4766  def __repr__(self):
4767  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
4768  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
4769 
4770  def get_from(o):
4771  return _object_cast_to_VelocityScalingOptimizerState(o)
4772  get_from = staticmethod(get_from)
4773 
4774 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
4775 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
4776 
4777 class Fragment(Hierarchy):
4778  """Proxy of C++ IMP::atom::Fragment class"""
4779  __swig_setmethods__ = {}
4780  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4781  __setattr__ = lambda self, name, value: _swig_setattr(self, Fragment, name, value)
4782  __swig_getmethods__ = {}
4783  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4784  __getattr__ = lambda self, name: _swig_getattr(self, Fragment, name)
4785  def set_residue_indexes(self, *args):
4786  """set_residue_indexes(Fragment self, IMP::Ints o)"""
4787  return _IMP_atom.Fragment_set_residue_indexes(self, *args)
4788 
4789  def get_residue_indexes(self):
4790  """get_residue_indexes(Fragment self) -> IMP::Ints"""
4791  return _IMP_atom.Fragment_get_residue_indexes(self)
4792 
4793  def get_residue_index_ranges(self):
4794  """get_residue_index_ranges(Fragment self) -> IMP::IntPairs"""
4795  return _IMP_atom.Fragment_get_residue_index_ranges(self)
4796 
4797  def get_contains_residue(self, *args):
4798  """get_contains_residue(Fragment self, int rindex) -> bool"""
4799  return _IMP_atom.Fragment_get_contains_residue(self, *args)
4800 
4801  def __init__(self, *args):
4802  """
4803  __init__(IMP::atom::Fragment self) -> Fragment
4804  __init__(IMP::atom::Fragment self, Model m, ::IMP::kernel::ParticleIndex id) -> Fragment
4805  __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
4806  """
4807  this = _IMP_atom.new_Fragment(*args)
4808  try: self.this.append(this)
4809  except: self.this = this
4810  def decorate_particle(*args):
4811  """decorate_particle(Particle p) -> Fragment"""
4812  return _IMP_atom.Fragment_decorate_particle(*args)
4813 
4814  if _newclass:decorate_particle = staticmethod(decorate_particle)
4815  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4816  def particle_is_instance(*args):
4817  """
4818  particle_is_instance(Particle p) -> bool
4819  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
4820  """
4821  return _IMP_atom.Fragment_particle_is_instance(*args)
4822 
4823  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4824  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4825  def get_is_setup(*args):
4826  """
4827  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
4828  get_is_setup(_ParticleAdaptor p) -> bool
4829  """
4830  return _IMP_atom.Fragment_get_is_setup(*args)
4831 
4832  if _newclass:get_is_setup = staticmethod(get_is_setup)
4833  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
4834  def show(self, *args):
4835  """
4836  show(Fragment self, _ostream out=std::cout)
4837  show(Fragment self)
4838  """
4839  return _IMP_atom.Fragment_show(self, *args)
4840 
4841  def setup_particle(*args):
4842  """
4843  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Fragment
4844  setup_particle(_ParticleAdaptor decorator) -> Fragment
4845  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Fragment other) -> Fragment
4846  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
4847  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
4848  setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
4849  """
4850  return _IMP_atom.Fragment_setup_particle(*args)
4851 
4852  if _newclass:setup_particle = staticmethod(setup_particle)
4853  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4854  def add_attribute(self, *args):
4855  """
4856  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
4857  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
4858  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
4859  add_attribute(Fragment self, StringKey a0, IMP::String a1)
4860  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
4861  add_attribute(Fragment self, ObjectKey a0, IMP::Object * a1)
4862  """
4863  return _IMP_atom.Fragment_add_attribute(self, *args)
4864 
4865  def get_value(self, *args):
4866  """
4867  get_value(Fragment self, FloatKey a0) -> IMP::Float
4868  get_value(Fragment self, IntKey a0) -> IMP::Int
4869  get_value(Fragment self, StringKey a0) -> IMP::String
4870  get_value(Fragment self, ParticleIndexKey a0) -> Particle
4871  get_value(Fragment self, ObjectKey a0) -> IMP::Object *
4872  """
4873  return _IMP_atom.Fragment_get_value(self, *args)
4874 
4875  def set_value(self, *args):
4876  """
4877  set_value(Fragment self, FloatKey a0, IMP::Float a1)
4878  set_value(Fragment self, IntKey a0, IMP::Int a1)
4879  set_value(Fragment self, StringKey a0, IMP::String a1)
4880  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
4881  set_value(Fragment self, ObjectKey a0, IMP::Object * a1)
4882  """
4883  return _IMP_atom.Fragment_set_value(self, *args)
4884 
4885  def remove_attribute(self, *args):
4886  """
4887  remove_attribute(Fragment self, FloatKey a0)
4888  remove_attribute(Fragment self, IntKey a0)
4889  remove_attribute(Fragment self, StringKey a0)
4890  remove_attribute(Fragment self, ParticleIndexKey a0)
4891  remove_attribute(Fragment self, ObjectKey a0)
4892  """
4893  return _IMP_atom.Fragment_remove_attribute(self, *args)
4894 
4895  def has_attribute(self, *args):
4896  """
4897  has_attribute(Fragment self, FloatKey a0) -> bool
4898  has_attribute(Fragment self, IntKey a0) -> bool
4899  has_attribute(Fragment self, StringKey a0) -> bool
4900  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
4901  has_attribute(Fragment self, ObjectKey a0) -> bool
4902  """
4903  return _IMP_atom.Fragment_has_attribute(self, *args)
4904 
4905  def get_derivative(self, *args):
4906  """get_derivative(Fragment self, FloatKey a0) -> double"""
4907  return _IMP_atom.Fragment_get_derivative(self, *args)
4908 
4909  def get_name(self):
4910  """get_name(Fragment self) -> std::string"""
4911  return _IMP_atom.Fragment_get_name(self)
4912 
4913  def clear_caches(self):
4914  """clear_caches(Fragment self)"""
4915  return _IMP_atom.Fragment_clear_caches(self)
4916 
4917  def set_name(self, *args):
4918  """set_name(Fragment self, std::string a0)"""
4919  return _IMP_atom.Fragment_set_name(self, *args)
4920 
4921  def set_check_level(self, *args):
4922  """set_check_level(Fragment self, IMP::base::CheckLevel a0)"""
4923  return _IMP_atom.Fragment_set_check_level(self, *args)
4924 
4925  def add_to_derivative(self, *args):
4926  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4927  return _IMP_atom.Fragment_add_to_derivative(self, *args)
4928 
4929  def set_is_optimized(self, *args):
4930  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
4931  return _IMP_atom.Fragment_set_is_optimized(self, *args)
4932 
4933  def get_is_optimized(self, *args):
4934  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
4935  return _IMP_atom.Fragment_get_is_optimized(self, *args)
4936 
4937  def get_check_level(self):
4938  """get_check_level(Fragment self) -> IMP::base::CheckLevel"""
4939  return _IMP_atom.Fragment_get_check_level(self)
4940 
4941  def __eq__(self, *args):
4942  """
4943  __eq__(Fragment self, Fragment o) -> bool
4944  __eq__(Fragment self, Particle d) -> bool
4945  """
4946  return _IMP_atom.Fragment___eq__(self, *args)
4947 
4948  def __ne__(self, *args):
4949  """
4950  __ne__(Fragment self, Fragment o) -> bool
4951  __ne__(Fragment self, Particle d) -> bool
4952  """
4953  return _IMP_atom.Fragment___ne__(self, *args)
4954 
4955  def __le__(self, *args):
4956  """
4957  __le__(Fragment self, Fragment o) -> bool
4958  __le__(Fragment self, Particle d) -> bool
4959  """
4960  return _IMP_atom.Fragment___le__(self, *args)
4961 
4962  def __lt__(self, *args):
4963  """
4964  __lt__(Fragment self, Fragment o) -> bool
4965  __lt__(Fragment self, Particle d) -> bool
4966  """
4967  return _IMP_atom.Fragment___lt__(self, *args)
4968 
4969  def __ge__(self, *args):
4970  """
4971  __ge__(Fragment self, Fragment o) -> bool
4972  __ge__(Fragment self, Particle d) -> bool
4973  """
4974  return _IMP_atom.Fragment___ge__(self, *args)
4975 
4976  def __gt__(self, *args):
4977  """
4978  __gt__(Fragment self, Fragment o) -> bool
4979  __gt__(Fragment self, Particle d) -> bool
4980  """
4981  return _IMP_atom.Fragment___gt__(self, *args)
4982 
4983  def __str__(self):
4984  """__str__(Fragment self) -> std::string"""
4985  return _IMP_atom.Fragment___str__(self)
4986 
4987  def __repr__(self):
4988  """__repr__(Fragment self) -> std::string"""
4989  return _IMP_atom.Fragment___repr__(self)
4990 
4991  __swig_destroy__ = _IMP_atom.delete_Fragment
4992  __del__ = lambda self : None;
4993 Fragment_swigregister = _IMP_atom.Fragment_swigregister
4994 Fragment_swigregister(Fragment)
4995 
4996 def Fragment_decorate_particle(*args):
4997  """Fragment_decorate_particle(Particle p) -> Fragment"""
4998  return _IMP_atom.Fragment_decorate_particle(*args)
4999 
5000 def Fragment_particle_is_instance(*args):
5001  """
5002  particle_is_instance(Particle p) -> bool
5003  Fragment_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
5004  """
5005  return _IMP_atom.Fragment_particle_is_instance(*args)
5006 
5007 def Fragment_get_is_setup(*args):
5008  """
5009  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5010  Fragment_get_is_setup(_ParticleAdaptor p) -> bool
5011  """
5012  return _IMP_atom.Fragment_get_is_setup(*args)
5013 
5014 def Fragment_setup_particle(*args):
5015  """
5016  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Fragment
5017  setup_particle(_ParticleAdaptor decorator) -> Fragment
5018  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Fragment other) -> Fragment
5019  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
5020  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
5021  Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
5022  """
5023  return _IMP_atom.Fragment_setup_particle(*args)
5024 
5025 class StereochemistryPairFilter(IMP.kernel.PairPredicate):
5026  """Proxy of C++ IMP::atom::StereochemistryPairFilter class"""
5027  __swig_setmethods__ = {}
5028  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5029  __setattr__ = lambda self, name, value: _swig_setattr(self, StereochemistryPairFilter, name, value)
5030  __swig_getmethods__ = {}
5031  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5032  __getattr__ = lambda self, name: _swig_getattr(self, StereochemistryPairFilter, name)
5033  def __init__(self):
5034  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
5035  this = _IMP_atom.new_StereochemistryPairFilter()
5036  try: self.this.append(this)
5037  except: self.this = this
5038  def set_bonds(self, *args):
5039  """set_bonds(StereochemistryPairFilter self, IMP::kernel::Particles const & bonds)"""
5040  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, *args)
5041 
5042  def set_angles(self, *args):
5043  """set_angles(StereochemistryPairFilter self, IMP::kernel::Particles const & angles)"""
5044  return _IMP_atom.StereochemistryPairFilter_set_angles(self, *args)
5045 
5046  def set_dihedrals(self, *args):
5047  """set_dihedrals(StereochemistryPairFilter self, IMP::kernel::Particles const & dihedrals)"""
5048  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, *args)
5049 
5050  def do_get_inputs(self, *args):
5051  """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5052  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, *args)
5053 
5054  def get_value(self, *args):
5055  """
5056  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePair const & a) -> int
5057  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
5058  """
5059  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
5060 
5061  def get_value_index(self, *args):
5062  """
5063  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
5064  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
5065  """
5066  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
5067 
5068  def get_version_info(self):
5069  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
5070  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
5071 
5072  __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
5073  __del__ = lambda self : None;
5074  def __str__(self):
5075  """__str__(StereochemistryPairFilter self) -> std::string"""
5076  return _IMP_atom.StereochemistryPairFilter___str__(self)
5077 
5078  def __repr__(self):
5079  """__repr__(StereochemistryPairFilter self) -> std::string"""
5080  return _IMP_atom.StereochemistryPairFilter___repr__(self)
5081 
5082  def get_from(o):
5083  return _object_cast_to_StereochemistryPairFilter(o)
5084  get_from = staticmethod(get_from)
5085 
5086 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
5087 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
5088 
5089 class Mass(IMP.kernel.Decorator):
5090  """Proxy of C++ IMP::atom::Mass class"""
5091  __swig_setmethods__ = {}
5092  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5093  __setattr__ = lambda self, name, value: _swig_setattr(self, Mass, name, value)
5094  __swig_getmethods__ = {}
5095  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5096  __getattr__ = lambda self, name: _swig_getattr(self, Mass, name)
5097  def get_mass(self):
5098  """get_mass(Mass self) -> IMP::Float"""
5099  return _IMP_atom.Mass_get_mass(self)
5100 
5101  def set_mass(self, *args):
5102  """set_mass(Mass self, IMP::Float d)"""
5103  return _IMP_atom.Mass_set_mass(self, *args)
5104 
5105  def __init__(self, *args):
5106  """
5107  __init__(IMP::atom::Mass self) -> Mass
5108  __init__(IMP::atom::Mass self, Model m, ::IMP::kernel::ParticleIndex id) -> Mass
5109  __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
5110  """
5111  this = _IMP_atom.new_Mass(*args)
5112  try: self.this.append(this)
5113  except: self.this = this
5114  def decorate_particle(*args):
5115  """decorate_particle(Particle p) -> Mass"""
5116  return _IMP_atom.Mass_decorate_particle(*args)
5117 
5118  if _newclass:decorate_particle = staticmethod(decorate_particle)
5119  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
5120  def particle_is_instance(*args):
5121  """
5122  particle_is_instance(Particle p) -> bool
5123  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
5124  """
5125  return _IMP_atom.Mass_particle_is_instance(*args)
5126 
5127  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
5128  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
5129  def get_is_setup(*args):
5130  """
5131  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5132  get_is_setup(_ParticleAdaptor p) -> bool
5133  """
5134  return _IMP_atom.Mass_get_is_setup(*args)
5135 
5136  if _newclass:get_is_setup = staticmethod(get_is_setup)
5137  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
5138  def show(self, *args):
5139  """
5140  show(Mass self, _ostream out=std::cout)
5141  show(Mass self)
5142  """
5143  return _IMP_atom.Mass_show(self, *args)
5144 
5145  def setup_particle(*args):
5146  """
5147  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float mass) -> Mass
5148  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
5149  """
5150  return _IMP_atom.Mass_setup_particle(*args)
5151 
5152  if _newclass:setup_particle = staticmethod(setup_particle)
5153  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
5154  def get_mass_key():
5155  """get_mass_key() -> FloatKey"""
5156  return _IMP_atom.Mass_get_mass_key()
5157 
5158  if _newclass:get_mass_key = staticmethod(get_mass_key)
5159  __swig_getmethods__["get_mass_key"] = lambda x: get_mass_key
5160  def add_attribute(self, *args):
5161  """
5162  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
5163  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
5164  add_attribute(Mass self, IntKey a0, IMP::Int a1)
5165  add_attribute(Mass self, StringKey a0, IMP::String a1)
5166  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
5167  add_attribute(Mass self, ObjectKey a0, IMP::Object * a1)
5168  """
5169  return _IMP_atom.Mass_add_attribute(self, *args)
5170 
5171  def get_value(self, *args):
5172  """
5173  get_value(Mass self, FloatKey a0) -> IMP::Float
5174  get_value(Mass self, IntKey a0) -> IMP::Int
5175  get_value(Mass self, StringKey a0) -> IMP::String
5176  get_value(Mass self, ParticleIndexKey a0) -> Particle
5177  get_value(Mass self, ObjectKey a0) -> IMP::Object *
5178  """
5179  return _IMP_atom.Mass_get_value(self, *args)
5180 
5181  def set_value(self, *args):
5182  """
5183  set_value(Mass self, FloatKey a0, IMP::Float a1)
5184  set_value(Mass self, IntKey a0, IMP::Int a1)
5185  set_value(Mass self, StringKey a0, IMP::String a1)
5186  set_value(Mass self, ParticleIndexKey a0, Particle a1)
5187  set_value(Mass self, ObjectKey a0, IMP::Object * a1)
5188  """
5189  return _IMP_atom.Mass_set_value(self, *args)
5190 
5191  def remove_attribute(self, *args):
5192  """
5193  remove_attribute(Mass self, FloatKey a0)
5194  remove_attribute(Mass self, IntKey a0)
5195  remove_attribute(Mass self, StringKey a0)
5196  remove_attribute(Mass self, ParticleIndexKey a0)
5197  remove_attribute(Mass self, ObjectKey a0)
5198  """
5199  return _IMP_atom.Mass_remove_attribute(self, *args)
5200 
5201  def has_attribute(self, *args):
5202  """
5203  has_attribute(Mass self, FloatKey a0) -> bool
5204  has_attribute(Mass self, IntKey a0) -> bool
5205  has_attribute(Mass self, StringKey a0) -> bool
5206  has_attribute(Mass self, ParticleIndexKey a0) -> bool
5207  has_attribute(Mass self, ObjectKey a0) -> bool
5208  """
5209  return _IMP_atom.Mass_has_attribute(self, *args)
5210 
5211  def get_derivative(self, *args):
5212  """get_derivative(Mass self, FloatKey a0) -> double"""
5213  return _IMP_atom.Mass_get_derivative(self, *args)
5214 
5215  def get_name(self):
5216  """get_name(Mass self) -> std::string"""
5217  return _IMP_atom.Mass_get_name(self)
5218 
5219  def clear_caches(self):
5220  """clear_caches(Mass self)"""
5221  return _IMP_atom.Mass_clear_caches(self)
5222 
5223  def set_name(self, *args):
5224  """set_name(Mass self, std::string a0)"""
5225  return _IMP_atom.Mass_set_name(self, *args)
5226 
5227  def set_check_level(self, *args):
5228  """set_check_level(Mass self, IMP::base::CheckLevel a0)"""
5229  return _IMP_atom.Mass_set_check_level(self, *args)
5230 
5231  def add_to_derivative(self, *args):
5232  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5233  return _IMP_atom.Mass_add_to_derivative(self, *args)
5234 
5235  def set_is_optimized(self, *args):
5236  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
5237  return _IMP_atom.Mass_set_is_optimized(self, *args)
5238 
5239  def get_is_optimized(self, *args):
5240  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
5241  return _IMP_atom.Mass_get_is_optimized(self, *args)
5242 
5243  def get_check_level(self):
5244  """get_check_level(Mass self) -> IMP::base::CheckLevel"""
5245  return _IMP_atom.Mass_get_check_level(self)
5246 
5247  def __eq__(self, *args):
5248  """
5249  __eq__(Mass self, Mass o) -> bool
5250  __eq__(Mass self, Particle d) -> bool
5251  """
5252  return _IMP_atom.Mass___eq__(self, *args)
5253 
5254  def __ne__(self, *args):
5255  """
5256  __ne__(Mass self, Mass o) -> bool
5257  __ne__(Mass self, Particle d) -> bool
5258  """
5259  return _IMP_atom.Mass___ne__(self, *args)
5260 
5261  def __le__(self, *args):
5262  """
5263  __le__(Mass self, Mass o) -> bool
5264  __le__(Mass self, Particle d) -> bool
5265  """
5266  return _IMP_atom.Mass___le__(self, *args)
5267 
5268  def __lt__(self, *args):
5269  """
5270  __lt__(Mass self, Mass o) -> bool
5271  __lt__(Mass self, Particle d) -> bool
5272  """
5273  return _IMP_atom.Mass___lt__(self, *args)
5274 
5275  def __ge__(self, *args):
5276  """
5277  __ge__(Mass self, Mass o) -> bool
5278  __ge__(Mass self, Particle d) -> bool
5279  """
5280  return _IMP_atom.Mass___ge__(self, *args)
5281 
5282  def __gt__(self, *args):
5283  """
5284  __gt__(Mass self, Mass o) -> bool
5285  __gt__(Mass self, Particle d) -> bool
5286  """
5287  return _IMP_atom.Mass___gt__(self, *args)
5288 
5289  def __str__(self):
5290  """__str__(Mass self) -> std::string"""
5291  return _IMP_atom.Mass___str__(self)
5292 
5293  def __repr__(self):
5294  """__repr__(Mass self) -> std::string"""
5295  return _IMP_atom.Mass___repr__(self)
5296 
5297  __swig_destroy__ = _IMP_atom.delete_Mass
5298  __del__ = lambda self : None;
5299 Mass_swigregister = _IMP_atom.Mass_swigregister
5300 Mass_swigregister(Mass)
5301 
5302 def Mass_decorate_particle(*args):
5303  """Mass_decorate_particle(Particle p) -> Mass"""
5304  return _IMP_atom.Mass_decorate_particle(*args)
5305 
5306 def Mass_particle_is_instance(*args):
5307  """
5308  particle_is_instance(Particle p) -> bool
5309  Mass_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
5310  """
5311  return _IMP_atom.Mass_particle_is_instance(*args)
5312 
5313 def Mass_get_is_setup(*args):
5314  """
5315  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5316  Mass_get_is_setup(_ParticleAdaptor p) -> bool
5317  """
5318  return _IMP_atom.Mass_get_is_setup(*args)
5319 
5320 def Mass_setup_particle(*args):
5321  """
5322  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float mass) -> Mass
5323  Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
5324  """
5325  return _IMP_atom.Mass_setup_particle(*args)
5326 
5327 def Mass_get_mass_key():
5328  """Mass_get_mass_key() -> FloatKey"""
5329  return _IMP_atom.Mass_get_mass_key()
5330 
5331 class BondedPairFilter(IMP.kernel.PairPredicate):
5332  """Proxy of C++ IMP::atom::BondedPairFilter class"""
5333  __swig_setmethods__ = {}
5334  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5335  __setattr__ = lambda self, name, value: _swig_setattr(self, BondedPairFilter, name, value)
5336  __swig_getmethods__ = {}
5337  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5338  __getattr__ = lambda self, name: _swig_getattr(self, BondedPairFilter, name)
5339  def __init__(self):
5340  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
5341  this = _IMP_atom.new_BondedPairFilter()
5342  try: self.this.append(this)
5343  except: self.this = this
5344  def do_get_inputs(self, *args):
5345  """do_get_inputs(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5346  return _IMP_atom.BondedPairFilter_do_get_inputs(self, *args)
5347 
5348  def get_value(self, *args):
5349  """
5350  get_value(BondedPairFilter self, IMP::kernel::ParticlePair const & a) -> int
5351  get_value(BondedPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
5352  """
5353  return _IMP_atom.BondedPairFilter_get_value(self, *args)
5354 
5355  def get_value_index(self, *args):
5356  """
5357  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
5358  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
5359  """
5360  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
5361 
5362  def get_version_info(self):
5363  """get_version_info(BondedPairFilter self) -> VersionInfo"""
5364  return _IMP_atom.BondedPairFilter_get_version_info(self)
5365 
5366  __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
5367  __del__ = lambda self : None;
5368  def __str__(self):
5369  """__str__(BondedPairFilter self) -> std::string"""
5370  return _IMP_atom.BondedPairFilter___str__(self)
5371 
5372  def __repr__(self):
5373  """__repr__(BondedPairFilter self) -> std::string"""
5374  return _IMP_atom.BondedPairFilter___repr__(self)
5375 
5376  def get_from(o):
5377  return _object_cast_to_BondedPairFilter(o)
5378  get_from = staticmethod(get_from)
5379 
5380 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
5381 BondedPairFilter_swigregister(BondedPairFilter)
5382 
5383 class Mol2Selector(IMP.base.Object):
5384  """Proxy of C++ IMP::atom::Mol2Selector class"""
5385  __swig_setmethods__ = {}
5386  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5387  __setattr__ = lambda self, name, value: _swig_setattr(self, Mol2Selector, name, value)
5388  __swig_getmethods__ = {}
5389  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5390  __getattr__ = lambda self, name: _swig_getattr(self, Mol2Selector, name)
5391  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
5392  def get_is_selected(self, *args):
5393  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
5394  return _IMP_atom.Mol2Selector_get_is_selected(self, *args)
5395 
5396  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
5397  __del__ = lambda self : None;
5398  def __str__(self):
5399  """__str__(Mol2Selector self) -> std::string"""
5400  return _IMP_atom.Mol2Selector___str__(self)
5401 
5402  def __repr__(self):
5403  """__repr__(Mol2Selector self) -> std::string"""
5404  return _IMP_atom.Mol2Selector___repr__(self)
5405 
5406  def get_from(o):
5407  return _object_cast_to_Mol2Selector(o)
5408  get_from = staticmethod(get_from)
5409 
5410 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
5411 Mol2Selector_swigregister(Mol2Selector)
5412 
5413 class AllMol2Selector(Mol2Selector):
5414  """Proxy of C++ IMP::atom::AllMol2Selector class"""
5415  __swig_setmethods__ = {}
5416  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5417  __setattr__ = lambda self, name, value: _swig_setattr(self, AllMol2Selector, name, value)
5418  __swig_getmethods__ = {}
5419  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5420  __getattr__ = lambda self, name: _swig_getattr(self, AllMol2Selector, name)
5421  def get_version_info(self):
5422  """get_version_info(AllMol2Selector self) -> VersionInfo"""
5423  return _IMP_atom.AllMol2Selector_get_version_info(self)
5424 
5425  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
5426  __del__ = lambda self : None;
5427  def __str__(self):
5428  """__str__(AllMol2Selector self) -> std::string"""
5429  return _IMP_atom.AllMol2Selector___str__(self)
5430 
5431  def __repr__(self):
5432  """__repr__(AllMol2Selector self) -> std::string"""
5433  return _IMP_atom.AllMol2Selector___repr__(self)
5434 
5435  def get_from(o):
5436  return _object_cast_to_AllMol2Selector(o)
5437  get_from = staticmethod(get_from)
5438 
5439  def __init__(self):
5440  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
5441  this = _IMP_atom.new_AllMol2Selector()
5442  try: self.this.append(this)
5443  except: self.this = this
5444 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
5445 AllMol2Selector_swigregister(AllMol2Selector)
5446 
5447 class NonHydrogenMol2Selector(Mol2Selector):
5448  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class"""
5449  __swig_setmethods__ = {}
5450  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5451  __setattr__ = lambda self, name, value: _swig_setattr(self, NonHydrogenMol2Selector, name, value)
5452  __swig_getmethods__ = {}
5453  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5454  __getattr__ = lambda self, name: _swig_getattr(self, NonHydrogenMol2Selector, name)
5455  def get_version_info(self):
5456  """get_version_info(NonHydrogenMol2Selector self) -> VersionInfo"""
5457  return _IMP_atom.NonHydrogenMol2Selector_get_version_info(self)
5458 
5459  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
5460  __del__ = lambda self : None;
5461  def __str__(self):
5462  """__str__(NonHydrogenMol2Selector self) -> std::string"""
5463  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
5464 
5465  def __repr__(self):
5466  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
5467  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
5468 
5469  def get_from(o):
5470  return _object_cast_to_NonHydrogenMol2Selector(o)
5471  get_from = staticmethod(get_from)
5472 
5473  def __init__(self):
5474  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
5475  this = _IMP_atom.new_NonHydrogenMol2Selector()
5476  try: self.this.append(this)
5477  except: self.this = this
5478 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
5479 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
5480 
5481 
5482 def read_mol2(*args):
5483  """
5484  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=nullptr) -> Hierarchy
5485  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
5486  """
5487  return _IMP_atom.read_mol2(*args)
5488 
5489 def write_mol2(*args):
5490  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
5491  return _IMP_atom.write_mol2(*args)
5492 class SecondaryStructureResidue(IMP.kernel.Decorator):
5493  """Proxy of C++ IMP::atom::SecondaryStructureResidue class"""
5494  __swig_setmethods__ = {}
5495  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5496  __setattr__ = lambda self, name, value: _swig_setattr(self, SecondaryStructureResidue, name, value)
5497  __swig_getmethods__ = {}
5498  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5499  __getattr__ = lambda self, name: _swig_getattr(self, SecondaryStructureResidue, name)
5500  def __init__(self, *args):
5501  """
5502  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
5503  __init__(IMP::atom::SecondaryStructureResidue self, Model m, ::IMP::kernel::ParticleIndex id) -> SecondaryStructureResidue
5504  __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
5505  """
5506  this = _IMP_atom.new_SecondaryStructureResidue(*args)
5507  try: self.this.append(this)
5508  except: self.this = this
5509  def decorate_particle(*args):
5510  """decorate_particle(Particle p) -> SecondaryStructureResidue"""
5511  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5512 
5513  if _newclass:decorate_particle = staticmethod(decorate_particle)
5514  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
5515  def particle_is_instance(*args):
5516  """
5517  particle_is_instance(Particle p) -> bool
5518  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
5519  """
5520  return _IMP_atom.SecondaryStructureResidue_particle_is_instance(*args)
5521 
5522  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
5523  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
5524  def show(self, *args):
5525  """
5526  show(SecondaryStructureResidue self, _ostream out=std::cout)
5527  show(SecondaryStructureResidue self)
5528  """
5529  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
5530 
5531  def setup_particle(*args):
5532  """
5533  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand,
5534  IMP::Float prob_coil) -> SecondaryStructureResidue
5535  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5536  setup_particle(Particle res_p) -> SecondaryStructureResidue
5537  """
5538  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5539 
5540  if _newclass:setup_particle = staticmethod(setup_particle)
5541  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
5542  def get_is_setup(*args):
5543  """
5544  get_is_setup(_ParticleAdaptor p) -> bool
5545  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5546  """
5547  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
5548 
5549  if _newclass:get_is_setup = staticmethod(get_is_setup)
5550  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
5551  def get_particle(self):
5552  """get_particle(SecondaryStructureResidue self) -> Particle"""
5553  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
5554 
5555  def get_all_probabilities(self):
5556  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
5557  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
5558 
5559  def get_prob_helix(self):
5560  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
5561  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
5562 
5563  def set_prob_helix(self, *args):
5564  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
5565  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, *args)
5566 
5567  def get_prob_strand(self):
5568  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
5569  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
5570 
5571  def set_prob_strand(self, *args):
5572  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
5573  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, *args)
5574 
5575  def get_prob_coil(self):
5576  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
5577  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
5578 
5579  def set_prob_coil(self, *args):
5580  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
5581  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, *args)
5582 
5583  def get_prob_helix_key():
5584  """get_prob_helix_key() -> FloatKey"""
5585  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5586 
5587  if _newclass:get_prob_helix_key = staticmethod(get_prob_helix_key)
5588  __swig_getmethods__["get_prob_helix_key"] = lambda x: get_prob_helix_key
5589  def get_prob_strand_key():
5590  """get_prob_strand_key() -> FloatKey"""
5591  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5592 
5593  if _newclass:get_prob_strand_key = staticmethod(get_prob_strand_key)
5594  __swig_getmethods__["get_prob_strand_key"] = lambda x: get_prob_strand_key
5595  def get_prob_coil_key():
5596  """get_prob_coil_key() -> FloatKey"""
5597  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5598 
5599  if _newclass:get_prob_coil_key = staticmethod(get_prob_coil_key)
5600  __swig_getmethods__["get_prob_coil_key"] = lambda x: get_prob_coil_key
5601  def add_attribute(self, *args):
5602  """
5603  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
5604  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5605  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5606  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5607  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5608  add_attribute(SecondaryStructureResidue self, ObjectKey a0, IMP::Object * a1)
5609  """
5610  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
5611 
5612  def get_value(self, *args):
5613  """
5614  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
5615  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
5616  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
5617  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
5618  get_value(SecondaryStructureResidue self, ObjectKey a0) -> IMP::Object *
5619  """
5620  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
5621 
5622  def set_value(self, *args):
5623  """
5624  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5625  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5626  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5627  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5628  set_value(SecondaryStructureResidue self, ObjectKey a0, IMP::Object * a1)
5629  """
5630  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
5631 
5632  def remove_attribute(self, *args):
5633  """
5634  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
5635  remove_attribute(SecondaryStructureResidue self, IntKey a0)
5636  remove_attribute(SecondaryStructureResidue self, StringKey a0)
5637  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
5638  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
5639  """
5640  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
5641 
5642  def has_attribute(self, *args):
5643  """
5644  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
5645  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
5646  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
5647  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
5648  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
5649  """
5650  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
5651 
5652  def get_derivative(self, *args):
5653  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
5654  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, *args)
5655 
5656  def get_name(self):
5657  """get_name(SecondaryStructureResidue self) -> std::string"""
5658  return _IMP_atom.SecondaryStructureResidue_get_name(self)
5659 
5660  def clear_caches(self):
5661  """clear_caches(SecondaryStructureResidue self)"""
5662  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
5663 
5664  def set_name(self, *args):
5665  """set_name(SecondaryStructureResidue self, std::string a0)"""
5666  return _IMP_atom.SecondaryStructureResidue_set_name(self, *args)
5667 
5668  def set_check_level(self, *args):
5669  """set_check_level(SecondaryStructureResidue self, IMP::base::CheckLevel a0)"""
5670  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, *args)
5671 
5672  def add_to_derivative(self, *args):
5673  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5674  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, *args)
5675 
5676  def set_is_optimized(self, *args):
5677  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
5678  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, *args)
5679 
5680  def get_is_optimized(self, *args):
5681  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
5682  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, *args)
5683 
5684  def get_check_level(self):
5685  """get_check_level(SecondaryStructureResidue self) -> IMP::base::CheckLevel"""
5686  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
5687 
5688  def __eq__(self, *args):
5689  """
5690  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5691  __eq__(SecondaryStructureResidue self, Particle d) -> bool
5692  """
5693  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
5694 
5695  def __ne__(self, *args):
5696  """
5697  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5698  __ne__(SecondaryStructureResidue self, Particle d) -> bool
5699  """
5700  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
5701 
5702  def __le__(self, *args):
5703  """
5704  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5705  __le__(SecondaryStructureResidue self, Particle d) -> bool
5706  """
5707  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
5708 
5709  def __lt__(self, *args):
5710  """
5711  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5712  __lt__(SecondaryStructureResidue self, Particle d) -> bool
5713  """
5714  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
5715 
5716  def __ge__(self, *args):
5717  """
5718  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5719  __ge__(SecondaryStructureResidue self, Particle d) -> bool
5720  """
5721  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
5722 
5723  def __gt__(self, *args):
5724  """
5725  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5726  __gt__(SecondaryStructureResidue self, Particle d) -> bool
5727  """
5728  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
5729 
5730  def __str__(self):
5731  """__str__(SecondaryStructureResidue self) -> std::string"""
5732  return _IMP_atom.SecondaryStructureResidue___str__(self)
5733 
5734  def __repr__(self):
5735  """__repr__(SecondaryStructureResidue self) -> std::string"""
5736  return _IMP_atom.SecondaryStructureResidue___repr__(self)
5737 
5738  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
5739  __del__ = lambda self : None;
5740 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
5741 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
5742 
5743 def SecondaryStructureResidue_decorate_particle(*args):
5744  """SecondaryStructureResidue_decorate_particle(Particle p) -> SecondaryStructureResidue"""
5745  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5746 
5747 def SecondaryStructureResidue_particle_is_instance(*args):
5748  """
5749  particle_is_instance(Particle p) -> bool
5750  SecondaryStructureResidue_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
5751  """
5752  return _IMP_atom.SecondaryStructureResidue_particle_is_instance(*args)
5753 
5754 def SecondaryStructureResidue_setup_particle(*args):
5755  """
5756  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand,
5757  IMP::Float prob_coil) -> SecondaryStructureResidue
5758  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5759  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
5760  """
5761  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5762 
5763 def SecondaryStructureResidue_get_is_setup(*args):
5764  """
5765  get_is_setup(_ParticleAdaptor p) -> bool
5766  SecondaryStructureResidue_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
5767  """
5768  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
5769 
5770 def SecondaryStructureResidue_get_prob_helix_key():
5771  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
5772  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5773 
5774 def SecondaryStructureResidue_get_prob_strand_key():
5775  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
5776  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5777 
5778 def SecondaryStructureResidue_get_prob_coil_key():
5779  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
5780  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5781 
5782 
5784  """
5785  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
5786  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
5787  """
5788  return _IMP_atom.setup_coarse_secondary_structure_residue(*args)
5789 
5791  """
5792  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num,
5793  bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues
5794  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
5795  """
5796  return _IMP_atom.setup_coarse_secondary_structure_residues(*args)
5797 
5799  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
5800  return _IMP_atom.get_secondary_structure_match_score(*args)
5801 
5802 def read_psipred(*args):
5803  """
5804  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
5805  read_psipred(TextInput inf, IMP::kernel::Particles ps) -> IMP::atom::SecondaryStructureResidues
5806  """
5807  return _IMP_atom.read_psipred(*args)
5808 class _ADopeBase(IMP.kernel.PairScore):
5809  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class"""
5810  __swig_setmethods__ = {}
5811  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5812  __setattr__ = lambda self, name, value: _swig_setattr(self, _ADopeBase, name, value)
5813  __swig_getmethods__ = {}
5814  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5815  __getattr__ = lambda self, name: _swig_getattr(self, _ADopeBase, name)
5816  __repr__ = _swig_repr
5817  def __init__(self, *args):
5818  """
5819  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
5820  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
5821  """
5822  this = _IMP_atom.new__ADopeBase(*args)
5823  try: self.this.append(this)
5824  except: self.this = this
5825  def do_get_inputs(self, *args):
5826  """do_get_inputs(_ADopeBase self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5827  return _IMP_atom._ADopeBase_do_get_inputs(self, *args)
5828 
5829  def get_version_info(self):
5830  """get_version_info(_ADopeBase self) -> VersionInfo"""
5831  return _IMP_atom._ADopeBase_get_version_info(self)
5832 
5833  __swig_destroy__ = _IMP_atom.delete__ADopeBase
5834  __del__ = lambda self : None;
5835 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
5836 _ADopeBase_swigregister(_ADopeBase)
5837 
5838 class _BDopeBase(IMP.kernel.PairScore):
5839  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class"""
5840  __swig_setmethods__ = {}
5841  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5842  __setattr__ = lambda self, name, value: _swig_setattr(self, _BDopeBase, name, value)
5843  __swig_getmethods__ = {}
5844  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5845  __getattr__ = lambda self, name: _swig_getattr(self, _BDopeBase, name)
5846  __repr__ = _swig_repr
5847  def __init__(self, *args):
5848  """
5849  __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,
5850  std::string name="FunctorDistancePairScore %1%") -> _BDopeBase
5851  __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
5852  """
5853  this = _IMP_atom.new__BDopeBase(*args)
5854  try: self.this.append(this)
5855  except: self.this = this
5856  def do_get_inputs(self, *args):
5857  """do_get_inputs(_BDopeBase self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5858  return _IMP_atom._BDopeBase_do_get_inputs(self, *args)
5859 
5860  def get_version_info(self):
5861  """get_version_info(_BDopeBase self) -> VersionInfo"""
5862  return _IMP_atom._BDopeBase_get_version_info(self)
5863 
5864  __swig_destroy__ = _IMP_atom.delete__BDopeBase
5865  __del__ = lambda self : None;
5866 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
5867 _BDopeBase_swigregister(_BDopeBase)
5868 
5869 class _SPSFTB(IMP.kernel.PairScore):
5870  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class"""
5871  __swig_setmethods__ = {}
5872  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5873  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFTB, name, value)
5874  __swig_getmethods__ = {}
5875  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5876  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFTB, name)
5877  __repr__ = _swig_repr
5878  def __init__(self, *args):
5879  """
5880  __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,
5881  std::string name="FunctorDistancePairScore %1%") -> _SPSFTB
5882  __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
5883  """
5884  this = _IMP_atom.new__SPSFTB(*args)
5885  try: self.this.append(this)
5886  except: self.this = this
5887  def do_get_inputs(self, *args):
5888  """do_get_inputs(_SPSFTB self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
5889  return _IMP_atom._SPSFTB_do_get_inputs(self, *args)
5890 
5891  def get_version_info(self):
5892  """get_version_info(_SPSFTB self) -> VersionInfo"""
5893  return _IMP_atom._SPSFTB_get_version_info(self)
5894 
5895  __swig_destroy__ = _IMP_atom.delete__SPSFTB
5896  __del__ = lambda self : None;
5897 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
5898 _SPSFTB_swigregister(_SPSFTB)
5899 
5900 class _SPSTF(_SPSFTB):
5901  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class"""
5902  __swig_setmethods__ = {}
5903  for _s in [_SPSFTB]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5904  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSTF, name, value)
5905  __swig_getmethods__ = {}
5906  for _s in [_SPSFTB]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5907  __getattr__ = lambda self, name: _swig_getattr(self, _SPSTF, name)
5908  __repr__ = _swig_repr
5909  def __init__(self, *args):
5910  """
5911  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
5912  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
5913  """
5914  this = _IMP_atom.new__SPSTF(*args)
5915  try: self.this.append(this)
5916  except: self.this = this
5917  __swig_destroy__ = _IMP_atom.delete__SPSTF
5918  __del__ = lambda self : None;
5919 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
5920 _SPSTF_swigregister(_SPSTF)
5921 
5922 class _SPSFT(_BDopeBase):
5923  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class"""
5924  __swig_setmethods__ = {}
5925  for _s in [_BDopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5926  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFT, name, value)
5927  __swig_getmethods__ = {}
5928  for _s in [_BDopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5929  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFT, name)
5930  __repr__ = _swig_repr
5931  def __init__(self, *args):
5932  """
5933  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
5934  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
5935  """
5936  this = _IMP_atom.new__SPSFT(*args)
5937  try: self.this.append(this)
5938  except: self.this = this
5939  __swig_destroy__ = _IMP_atom.delete__SPSFT
5940  __del__ = lambda self : None;
5941 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
5942 _SPSFT_swigregister(_SPSFT)
5943 
5944 class ProteinLigandAtomPairScore(_SPSTF):
5945  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class"""
5946  __swig_setmethods__ = {}
5947  for _s in [_SPSTF]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5948  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandAtomPairScore, name, value)
5949  __swig_getmethods__ = {}
5950  for _s in [_SPSTF]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5951  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandAtomPairScore, name)
5952  def __init__(self, *args):
5953  """
5954  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
5955  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
5956  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
5957  """
5958  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
5959  try: self.this.append(this)
5960  except: self.this = this
5961  def get_maximum_distance(self):
5962  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
5963  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
5964 
5965  def __str__(self):
5966  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
5967  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
5968 
5969  def __repr__(self):
5970  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
5971  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
5972 
5973  def get_from(o):
5974  return _object_cast_to_ProteinLigandAtomPairScore(o)
5975  get_from = staticmethod(get_from)
5976 
5977  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
5978  __del__ = lambda self : None;
5979 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
5980 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
5981 
5982 class ProteinLigandRestraint(IMP.container.PairsRestraint):
5983  """Proxy of C++ IMP::atom::ProteinLigandRestraint class"""
5984  __swig_setmethods__ = {}
5985  for _s in [IMP.container.PairsRestraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5986  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandRestraint, name, value)
5987  __swig_getmethods__ = {}
5988  for _s in [IMP.container.PairsRestraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5989  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandRestraint, name)
5990  def __init__(self, *args):
5991  """
5992  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
5993  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
5994  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
5995  """
5996  this = _IMP_atom.new_ProteinLigandRestraint(*args)
5997  try: self.this.append(this)
5998  except: self.this = this
5999  def __str__(self):
6000  """__str__(ProteinLigandRestraint self) -> std::string"""
6001  return _IMP_atom.ProteinLigandRestraint___str__(self)
6002 
6003  def __repr__(self):
6004  """__repr__(ProteinLigandRestraint self) -> std::string"""
6005  return _IMP_atom.ProteinLigandRestraint___repr__(self)
6006 
6007  def get_from(o):
6008  return _object_cast_to_ProteinLigandRestraint(o)
6009  get_from = staticmethod(get_from)
6010 
6011  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
6012  __del__ = lambda self : None;
6013 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
6014 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
6015 
6016 
6018  """add_protein_ligand_score_data(Hierarchy h)"""
6019  return _IMP_atom.add_protein_ligand_score_data(*args)
6020 class AtomType(IMP.base._Value):
6021  """Proxy of C++ IMP::Key<(8974343,false)> class"""
6022  __swig_setmethods__ = {}
6023  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6024  __setattr__ = lambda self, name, value: _swig_setattr(self, AtomType, name, value)
6025  __swig_getmethods__ = {}
6026  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6027  __getattr__ = lambda self, name: _swig_getattr(self, AtomType, name)
6028  def __init__(self, *args):
6029  """
6030  __init__(IMP::Key<(8974343,false)> self) -> AtomType
6031  __init__(IMP::Key<(8974343,false)> self, std::string c) -> AtomType
6032  __init__(IMP::Key<(8974343,false)> self, unsigned int i) -> AtomType
6033  """
6034  this = _IMP_atom.new_AtomType(*args)
6035  try: self.this.append(this)
6036  except: self.this = this
6037  def add_key(*args):
6038  """add_key(std::string sc) -> unsigned int"""
6039  return _IMP_atom.AtomType_add_key(*args)
6040 
6041  if _newclass:add_key = staticmethod(add_key)
6042  __swig_getmethods__["add_key"] = lambda x: add_key
6043  def get_key_exists(*args):
6044  """get_key_exists(std::string sc) -> bool"""
6045  return _IMP_atom.AtomType_get_key_exists(*args)
6046 
6047  if _newclass:get_key_exists = staticmethod(get_key_exists)
6048  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
6049  def get_string(self):
6050  """get_string(AtomType self) -> std::string const"""
6051  return _IMP_atom.AtomType_get_string(self)
6052 
6053  def __eq__(self, *args):
6054  """__eq__(AtomType self, AtomType o) -> bool"""
6055  return _IMP_atom.AtomType___eq__(self, *args)
6056 
6057  def __ne__(self, *args):
6058  """__ne__(AtomType self, AtomType o) -> bool"""
6059  return _IMP_atom.AtomType___ne__(self, *args)
6060 
6061  def __lt__(self, *args):
6062  """__lt__(AtomType self, AtomType o) -> bool"""
6063  return _IMP_atom.AtomType___lt__(self, *args)
6064 
6065  def __gt__(self, *args):
6066  """__gt__(AtomType self, AtomType o) -> bool"""
6067  return _IMP_atom.AtomType___gt__(self, *args)
6068 
6069  def __ge__(self, *args):
6070  """__ge__(AtomType self, AtomType o) -> bool"""
6071  return _IMP_atom.AtomType___ge__(self, *args)
6072 
6073  def __le__(self, *args):
6074  """__le__(AtomType self, AtomType o) -> bool"""
6075  return _IMP_atom.AtomType___le__(self, *args)
6076 
6077  def __hash__(self):
6078  """__hash__(AtomType self) -> std::size_t"""
6079  return _IMP_atom.AtomType___hash__(self)
6080 
6081  def show(self, *args):
6082  """
6083  show(AtomType self, _ostream out=std::cout)
6084  show(AtomType self)
6085  """
6086  return _IMP_atom.AtomType_show(self, *args)
6087 
6088  def add_alias(*args):
6089  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
6090  return _IMP_atom.AtomType_add_alias(*args)
6091 
6092  if _newclass:add_alias = staticmethod(add_alias)
6093  __swig_getmethods__["add_alias"] = lambda x: add_alias
6094  def get_index(self):
6095  """get_index(AtomType self) -> unsigned int"""
6096  return _IMP_atom.AtomType_get_index(self)
6097 
6098  def show_all(*args):
6099  """show_all(_ostream out)"""
6100  return _IMP_atom.AtomType_show_all(*args)
6101 
6102  if _newclass:show_all = staticmethod(show_all)
6103  __swig_getmethods__["show_all"] = lambda x: show_all
6104  def get_all_strings():
6105  """get_all_strings() -> IMP::base::Vector< std::string >"""
6106  return _IMP_atom.AtomType_get_all_strings()
6107 
6108  if _newclass:get_all_strings = staticmethod(get_all_strings)
6109  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
6110  def get_number_unique():
6111  """get_number_unique() -> unsigned int"""
6112  return _IMP_atom.AtomType_get_number_unique()
6113 
6114  if _newclass:get_number_unique = staticmethod(get_number_unique)
6115  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
6116  def __str__(self):
6117  """__str__(AtomType self) -> std::string"""
6118  return _IMP_atom.AtomType___str__(self)
6119 
6120  def __repr__(self):
6121  """__repr__(AtomType self) -> std::string"""
6122  return _IMP_atom.AtomType___repr__(self)
6123 
6124  __swig_destroy__ = _IMP_atom.delete_AtomType
6125  __del__ = lambda self : None;
6126 AtomType_swigregister = _IMP_atom.AtomType_swigregister
6127 AtomType_swigregister(AtomType)
6128 
6129 def AtomType_add_key(*args):
6130  """AtomType_add_key(std::string sc) -> unsigned int"""
6131  return _IMP_atom.AtomType_add_key(*args)
6132 
6133 def AtomType_get_key_exists(*args):
6134  """AtomType_get_key_exists(std::string sc) -> bool"""
6135  return _IMP_atom.AtomType_get_key_exists(*args)
6136 
6137 def AtomType_add_alias(*args):
6138  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
6139  return _IMP_atom.AtomType_add_alias(*args)
6140 
6141 def AtomType_show_all(*args):
6142  """AtomType_show_all(_ostream out)"""
6143  return _IMP_atom.AtomType_show_all(*args)
6144 
6145 def AtomType_get_all_strings():
6146  """AtomType_get_all_strings() -> IMP::base::Vector< std::string >"""
6147  return _IMP_atom.AtomType_get_all_strings()
6148 
6149 def AtomType_get_number_unique():
6150  """AtomType_get_number_unique() -> unsigned int"""
6151  return _IMP_atom.AtomType_get_number_unique()
6152 
6153 class ResidueType(IMP.base._Value):
6154  """Proxy of C++ IMP::Key<(90784334,true)> class"""
6155  __swig_setmethods__ = {}
6156  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6157  __setattr__ = lambda self, name, value: _swig_setattr(self, ResidueType, name, value)
6158  __swig_getmethods__ = {}
6159  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6160  __getattr__ = lambda self, name: _swig_getattr(self, ResidueType, name)
6161  def __init__(self, *args):
6162  """
6163  __init__(IMP::Key<(90784334,true)> self) -> ResidueType
6164  __init__(IMP::Key<(90784334,true)> self, std::string c) -> ResidueType
6165  __init__(IMP::Key<(90784334,true)> self, unsigned int i) -> ResidueType
6166  """
6167  this = _IMP_atom.new_ResidueType(*args)
6168  try: self.this.append(this)
6169  except: self.this = this
6170  def add_key(*args):
6171  """add_key(std::string sc) -> unsigned int"""
6172  return _IMP_atom.ResidueType_add_key(*args)
6173 
6174  if _newclass:add_key = staticmethod(add_key)
6175  __swig_getmethods__["add_key"] = lambda x: add_key
6176  def get_key_exists(*args):
6177  """get_key_exists(std::string sc) -> bool"""
6178  return _IMP_atom.ResidueType_get_key_exists(*args)
6179 
6180  if _newclass:get_key_exists = staticmethod(get_key_exists)
6181  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
6182  def get_string(self):
6183  """get_string(ResidueType self) -> std::string const"""
6184  return _IMP_atom.ResidueType_get_string(self)
6185 
6186  def __eq__(self, *args):
6187  """__eq__(ResidueType self, ResidueType o) -> bool"""
6188  return _IMP_atom.ResidueType___eq__(self, *args)
6189 
6190  def __ne__(self, *args):
6191  """__ne__(ResidueType self, ResidueType o) -> bool"""
6192  return _IMP_atom.ResidueType___ne__(self, *args)
6193 
6194  def __lt__(self, *args):
6195  """__lt__(ResidueType self, ResidueType o) -> bool"""
6196  return _IMP_atom.ResidueType___lt__(self, *args)
6197 
6198  def __gt__(self, *args):
6199  """__gt__(ResidueType self, ResidueType o) -> bool"""
6200  return _IMP_atom.ResidueType___gt__(self, *args)
6201 
6202  def __ge__(self, *args):
6203  """__ge__(ResidueType self, ResidueType o) -> bool"""
6204  return _IMP_atom.ResidueType___ge__(self, *args)
6205 
6206  def __le__(self, *args):
6207  """__le__(ResidueType self, ResidueType o) -> bool"""
6208  return _IMP_atom.ResidueType___le__(self, *args)
6209 
6210  def __hash__(self):
6211  """__hash__(ResidueType self) -> std::size_t"""
6212  return _IMP_atom.ResidueType___hash__(self)
6213 
6214  def show(self, *args):
6215  """
6216  show(ResidueType self, _ostream out=std::cout)
6217  show(ResidueType self)
6218  """
6219  return _IMP_atom.ResidueType_show(self, *args)
6220 
6221  def add_alias(*args):
6222  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
6223  return _IMP_atom.ResidueType_add_alias(*args)
6224 
6225  if _newclass:add_alias = staticmethod(add_alias)
6226  __swig_getmethods__["add_alias"] = lambda x: add_alias
6227  def get_index(self):
6228  """get_index(ResidueType self) -> unsigned int"""
6229  return _IMP_atom.ResidueType_get_index(self)
6230 
6231  def show_all(*args):
6232  """show_all(_ostream out)"""
6233  return _IMP_atom.ResidueType_show_all(*args)
6234 
6235  if _newclass:show_all = staticmethod(show_all)
6236  __swig_getmethods__["show_all"] = lambda x: show_all
6237  def get_all_strings():
6238  """get_all_strings() -> IMP::base::Vector< std::string >"""
6239  return _IMP_atom.ResidueType_get_all_strings()
6240 
6241  if _newclass:get_all_strings = staticmethod(get_all_strings)
6242  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
6243  def get_number_unique():
6244  """get_number_unique() -> unsigned int"""
6245  return _IMP_atom.ResidueType_get_number_unique()
6246 
6247  if _newclass:get_number_unique = staticmethod(get_number_unique)
6248  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
6249  def __str__(self):
6250  """__str__(ResidueType self) -> std::string"""
6251  return _IMP_atom.ResidueType___str__(self)
6252 
6253  def __repr__(self):
6254  """__repr__(ResidueType self) -> std::string"""
6255  return _IMP_atom.ResidueType___repr__(self)
6256 
6257  __swig_destroy__ = _IMP_atom.delete_ResidueType
6258  __del__ = lambda self : None;
6259 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
6260 ResidueType_swigregister(ResidueType)
6261 
6262 def ResidueType_add_key(*args):
6263  """ResidueType_add_key(std::string sc) -> unsigned int"""
6264  return _IMP_atom.ResidueType_add_key(*args)
6265 
6266 def ResidueType_get_key_exists(*args):
6267  """ResidueType_get_key_exists(std::string sc) -> bool"""
6268  return _IMP_atom.ResidueType_get_key_exists(*args)
6269 
6270 def ResidueType_add_alias(*args):
6271  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
6272  return _IMP_atom.ResidueType_add_alias(*args)
6273 
6274 def ResidueType_show_all(*args):
6275  """ResidueType_show_all(_ostream out)"""
6276  return _IMP_atom.ResidueType_show_all(*args)
6277 
6278 def ResidueType_get_all_strings():
6279  """ResidueType_get_all_strings() -> IMP::base::Vector< std::string >"""
6280  return _IMP_atom.ResidueType_get_all_strings()
6281 
6282 def ResidueType_get_number_unique():
6283  """ResidueType_get_number_unique() -> unsigned int"""
6284  return _IMP_atom.ResidueType_get_number_unique()
6285 
6286 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
6287 OH = _IMP_atom.OH
6288 H2O = _IMP_atom.H2O
6289 H = _IMP_atom.H
6290 He = _IMP_atom.He
6291 Li = _IMP_atom.Li
6292 Be = _IMP_atom.Be
6293 B = _IMP_atom.B
6294 C = _IMP_atom.C
6295 N = _IMP_atom.N
6296 O = _IMP_atom.O
6297 F = _IMP_atom.F
6298 Ne = _IMP_atom.Ne
6299 Na = _IMP_atom.Na
6300 Mg = _IMP_atom.Mg
6301 Al = _IMP_atom.Al
6302 Si = _IMP_atom.Si
6303 P = _IMP_atom.P
6304 S = _IMP_atom.S
6305 Cl = _IMP_atom.Cl
6306 Ar = _IMP_atom.Ar
6307 K = _IMP_atom.K
6308 Ca = _IMP_atom.Ca
6309 Sc = _IMP_atom.Sc
6310 Ti = _IMP_atom.Ti
6311 V = _IMP_atom.V
6312 Cr = _IMP_atom.Cr
6313 Mn = _IMP_atom.Mn
6314 Fe = _IMP_atom.Fe
6315 Co = _IMP_atom.Co
6316 Ni = _IMP_atom.Ni
6317 Cu = _IMP_atom.Cu
6318 Zn = _IMP_atom.Zn
6319 Ga = _IMP_atom.Ga
6320 Ge = _IMP_atom.Ge
6321 As = _IMP_atom.As
6322 Se = _IMP_atom.Se
6323 Br = _IMP_atom.Br
6324 Kr = _IMP_atom.Kr
6325 Rb = _IMP_atom.Rb
6326 Sr = _IMP_atom.Sr
6327 Y = _IMP_atom.Y
6328 Zr = _IMP_atom.Zr
6329 Nb = _IMP_atom.Nb
6330 Mo = _IMP_atom.Mo
6331 Tc = _IMP_atom.Tc
6332 Ru = _IMP_atom.Ru
6333 Rh = _IMP_atom.Rh
6334 Pd = _IMP_atom.Pd
6335 Ag = _IMP_atom.Ag
6336 Cd = _IMP_atom.Cd
6337 In = _IMP_atom.In
6338 Sn = _IMP_atom.Sn
6339 Sb = _IMP_atom.Sb
6340 Te = _IMP_atom.Te
6341 I = _IMP_atom.I
6342 Xe = _IMP_atom.Xe
6343 Cs = _IMP_atom.Cs
6344 Ba = _IMP_atom.Ba
6345 La = _IMP_atom.La
6346 Ce = _IMP_atom.Ce
6347 Pr = _IMP_atom.Pr
6348 Nd = _IMP_atom.Nd
6349 Pm = _IMP_atom.Pm
6350 Sm = _IMP_atom.Sm
6351 Eu = _IMP_atom.Eu
6352 Gd = _IMP_atom.Gd
6353 Tb = _IMP_atom.Tb
6354 Dy = _IMP_atom.Dy
6355 Ho = _IMP_atom.Ho
6356 Er = _IMP_atom.Er
6357 Tm = _IMP_atom.Tm
6358 Yb = _IMP_atom.Yb
6359 Lu = _IMP_atom.Lu
6360 Hf = _IMP_atom.Hf
6361 Ta = _IMP_atom.Ta
6362 W = _IMP_atom.W
6363 Re = _IMP_atom.Re
6364 Os = _IMP_atom.Os
6365 Ir = _IMP_atom.Ir
6366 Pt = _IMP_atom.Pt
6367 Au = _IMP_atom.Au
6368 Hg = _IMP_atom.Hg
6369 Tl = _IMP_atom.Tl
6370 Pb = _IMP_atom.Pb
6371 Bi = _IMP_atom.Bi
6372 Po = _IMP_atom.Po
6373 At = _IMP_atom.At
6374 Rn = _IMP_atom.Rn
6375 Fr = _IMP_atom.Fr
6376 Ra = _IMP_atom.Ra
6377 Ac = _IMP_atom.Ac
6378 Th = _IMP_atom.Th
6379 Pa = _IMP_atom.Pa
6380 U = _IMP_atom.U
6381 Np = _IMP_atom.Np
6382 Pu = _IMP_atom.Pu
6383 Am = _IMP_atom.Am
6384 Cm = _IMP_atom.Cm
6385 Bk = _IMP_atom.Bk
6386 Cf = _IMP_atom.Cf
6387 Es = _IMP_atom.Es
6388 Fm = _IMP_atom.Fm
6389 Md = _IMP_atom.Md
6390 No = _IMP_atom.No
6391 Lr = _IMP_atom.Lr
6392 Db = _IMP_atom.Db
6393 Jl = _IMP_atom.Jl
6394 Rf = _IMP_atom.Rf
6395 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
6396 
6397 def hash_value(*args):
6398  """hash_value(IMP::atom::Element e) -> size_t"""
6399  return _IMP_atom.hash_value(*args)
6400 class ElementTable(_object):
6401  """Proxy of C++ IMP::atom::ElementTable class"""
6402  __swig_setmethods__ = {}
6403  __setattr__ = lambda self, name, value: _swig_setattr(self, ElementTable, name, value)
6404  __swig_getmethods__ = {}
6405  __getattr__ = lambda self, name: _swig_getattr(self, ElementTable, name)
6406  __repr__ = _swig_repr
6407  def __init__(self):
6408  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
6409  this = _IMP_atom.new_ElementTable()
6410  try: self.this.append(this)
6411  except: self.this = this
6412  def get_element(self, *args):
6413  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
6414  return _IMP_atom.ElementTable_get_element(self, *args)
6415 
6416  def get_name(self, *args):
6417  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
6418  return _IMP_atom.ElementTable_get_name(self, *args)
6419 
6420  def get_mass(self, *args):
6421  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
6422  return _IMP_atom.ElementTable_get_mass(self, *args)
6423 
6424  __swig_destroy__ = _IMP_atom.delete_ElementTable
6425  __del__ = lambda self : None;
6426 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
6427 ElementTable_swigregister(ElementTable)
6428 
6429 
6430 def get_element_table():
6431  """get_element_table() -> ElementTable"""
6432  return _IMP_atom.get_element_table()
6433 class Atom(Hierarchy):
6434  """Proxy of C++ IMP::atom::Atom class"""
6435  __swig_setmethods__ = {}
6436  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6437  __setattr__ = lambda self, name, value: _swig_setattr(self, Atom, name, value)
6438  __swig_getmethods__ = {}
6439  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6440  __getattr__ = lambda self, name: _swig_getattr(self, Atom, name)
6441  def __init__(self, *args):
6442  """
6443  __init__(IMP::atom::Atom self) -> Atom
6444  __init__(IMP::atom::Atom self, Model m, ::IMP::kernel::ParticleIndex id) -> Atom
6445  __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
6446  """
6447  this = _IMP_atom.new_Atom(*args)
6448  try: self.this.append(this)
6449  except: self.this = this
6450  def decorate_particle(*args):
6451  """decorate_particle(Particle p) -> Atom"""
6452  return _IMP_atom.Atom_decorate_particle(*args)
6453 
6454  if _newclass:decorate_particle = staticmethod(decorate_particle)
6455  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6456  def particle_is_instance(*args):
6457  """
6458  particle_is_instance(Particle p) -> bool
6459  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
6460  """
6461  return _IMP_atom.Atom_particle_is_instance(*args)
6462 
6463  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
6464  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
6465  def show(self, *args):
6466  """
6467  show(Atom self, _ostream out=std::cout)
6468  show(Atom self)
6469  """
6470  return _IMP_atom.Atom_show(self, *args)
6471 
6472  def setup_particle(*args):
6473  """
6474  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Atom other) -> Atom
6475  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
6476  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType atom_type) -> Atom
6477  setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
6478  """
6479  return _IMP_atom.Atom_setup_particle(*args)
6480 
6481  if _newclass:setup_particle = staticmethod(setup_particle)
6482  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6483  def get_is_setup(*args):
6484  """
6485  get_is_setup(_ParticleAdaptor p) -> bool
6486  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6487  """
6488  return _IMP_atom.Atom_get_is_setup(*args)
6489 
6490  if _newclass:get_is_setup = staticmethod(get_is_setup)
6491  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
6492  def get_atom_type(self):
6493  """get_atom_type(Atom self) -> AtomType"""
6494  return _IMP_atom.Atom_get_atom_type(self)
6495 
6496  def set_atom_type(self, *args):
6497  """set_atom_type(Atom self, AtomType t)"""
6498  return _IMP_atom.Atom_set_atom_type(self, *args)
6499 
6500  def get_element(self):
6501  """get_element(Atom self) -> IMP::atom::Element"""
6502  return _IMP_atom.Atom_get_element(self)
6503 
6504  def set_element(self, *args):
6505  """set_element(Atom self, IMP::atom::Element e)"""
6506  return _IMP_atom.Atom_set_element(self, *args)
6507 
6508  def get_occupancy(self):
6509  """get_occupancy(Atom self) -> double"""
6510  return _IMP_atom.Atom_get_occupancy(self)
6511 
6512  def set_occupancy(self, *args):
6513  """set_occupancy(Atom self, double occupancy)"""
6514  return _IMP_atom.Atom_set_occupancy(self, *args)
6515 
6516  def get_temperature_factor(self):
6517  """get_temperature_factor(Atom self) -> double"""
6518  return _IMP_atom.Atom_get_temperature_factor(self)
6519 
6520  def set_temperature_factor(self, *args):
6521  """set_temperature_factor(Atom self, double tempFactor)"""
6522  return _IMP_atom.Atom_set_temperature_factor(self, *args)
6523 
6524  def get_input_index(self):
6525  """get_input_index(Atom self) -> IMP::Int"""
6526  return _IMP_atom.Atom_get_input_index(self)
6527 
6528  def set_input_index(self, *args):
6529  """set_input_index(Atom self, IMP::Int t)"""
6530  return _IMP_atom.Atom_set_input_index(self, *args)
6531 
6532  def get_atom_type_key():
6533  """get_atom_type_key() -> IntKey"""
6534  return _IMP_atom.Atom_get_atom_type_key()
6535 
6536  if _newclass:get_atom_type_key = staticmethod(get_atom_type_key)
6537  __swig_getmethods__["get_atom_type_key"] = lambda x: get_atom_type_key
6538  def get_element_key():
6539  """get_element_key() -> IntKey"""
6540  return _IMP_atom.Atom_get_element_key()
6541 
6542  if _newclass:get_element_key = staticmethod(get_element_key)
6543  __swig_getmethods__["get_element_key"] = lambda x: get_element_key
6544  def get_input_index_key():
6545  """get_input_index_key() -> IntKey"""
6546  return _IMP_atom.Atom_get_input_index_key()
6547 
6548  if _newclass:get_input_index_key = staticmethod(get_input_index_key)
6549  __swig_getmethods__["get_input_index_key"] = lambda x: get_input_index_key
6550  def get_occupancy_key():
6551  """get_occupancy_key() -> FloatKey"""
6552  return _IMP_atom.Atom_get_occupancy_key()
6553 
6554  if _newclass:get_occupancy_key = staticmethod(get_occupancy_key)
6555  __swig_getmethods__["get_occupancy_key"] = lambda x: get_occupancy_key
6556  def get_temperature_factor_key():
6557  """get_temperature_factor_key() -> FloatKey"""
6558  return _IMP_atom.Atom_get_temperature_factor_key()
6559 
6560  if _newclass:get_temperature_factor_key = staticmethod(get_temperature_factor_key)
6561  __swig_getmethods__["get_temperature_factor_key"] = lambda x: get_temperature_factor_key
6562  def add_attribute(self, *args):
6563  """
6564  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
6565  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
6566  add_attribute(Atom self, IntKey a0, IMP::Int a1)
6567  add_attribute(Atom self, StringKey a0, IMP::String a1)
6568  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
6569  add_attribute(Atom self, ObjectKey a0, IMP::Object * a1)
6570  """
6571  return _IMP_atom.Atom_add_attribute(self, *args)
6572 
6573  def get_value(self, *args):
6574  """
6575  get_value(Atom self, FloatKey a0) -> IMP::Float
6576  get_value(Atom self, IntKey a0) -> IMP::Int
6577  get_value(Atom self, StringKey a0) -> IMP::String
6578  get_value(Atom self, ParticleIndexKey a0) -> Particle
6579  get_value(Atom self, ObjectKey a0) -> IMP::Object *
6580  """
6581  return _IMP_atom.Atom_get_value(self, *args)
6582 
6583  def set_value(self, *args):
6584  """
6585  set_value(Atom self, FloatKey a0, IMP::Float a1)
6586  set_value(Atom self, IntKey a0, IMP::Int a1)
6587  set_value(Atom self, StringKey a0, IMP::String a1)
6588  set_value(Atom self, ParticleIndexKey a0, Particle a1)
6589  set_value(Atom self, ObjectKey a0, IMP::Object * a1)
6590  """
6591  return _IMP_atom.Atom_set_value(self, *args)
6592 
6593  def remove_attribute(self, *args):
6594  """
6595  remove_attribute(Atom self, FloatKey a0)
6596  remove_attribute(Atom self, IntKey a0)
6597  remove_attribute(Atom self, StringKey a0)
6598  remove_attribute(Atom self, ParticleIndexKey a0)
6599  remove_attribute(Atom self, ObjectKey a0)
6600  """
6601  return _IMP_atom.Atom_remove_attribute(self, *args)
6602 
6603  def has_attribute(self, *args):
6604  """
6605  has_attribute(Atom self, FloatKey a0) -> bool
6606  has_attribute(Atom self, IntKey a0) -> bool
6607  has_attribute(Atom self, StringKey a0) -> bool
6608  has_attribute(Atom self, ParticleIndexKey a0) -> bool
6609  has_attribute(Atom self, ObjectKey a0) -> bool
6610  """
6611  return _IMP_atom.Atom_has_attribute(self, *args)
6612 
6613  def get_derivative(self, *args):
6614  """get_derivative(Atom self, FloatKey a0) -> double"""
6615  return _IMP_atom.Atom_get_derivative(self, *args)
6616 
6617  def get_name(self):
6618  """get_name(Atom self) -> std::string"""
6619  return _IMP_atom.Atom_get_name(self)
6620 
6621  def clear_caches(self):
6622  """clear_caches(Atom self)"""
6623  return _IMP_atom.Atom_clear_caches(self)
6624 
6625  def set_name(self, *args):
6626  """set_name(Atom self, std::string a0)"""
6627  return _IMP_atom.Atom_set_name(self, *args)
6628 
6629  def set_check_level(self, *args):
6630  """set_check_level(Atom self, IMP::base::CheckLevel a0)"""
6631  return _IMP_atom.Atom_set_check_level(self, *args)
6632 
6633  def add_to_derivative(self, *args):
6634  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6635  return _IMP_atom.Atom_add_to_derivative(self, *args)
6636 
6637  def set_is_optimized(self, *args):
6638  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
6639  return _IMP_atom.Atom_set_is_optimized(self, *args)
6640 
6641  def get_is_optimized(self, *args):
6642  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
6643  return _IMP_atom.Atom_get_is_optimized(self, *args)
6644 
6645  def get_check_level(self):
6646  """get_check_level(Atom self) -> IMP::base::CheckLevel"""
6647  return _IMP_atom.Atom_get_check_level(self)
6648 
6649  def __eq__(self, *args):
6650  """
6651  __eq__(Atom self, Atom o) -> bool
6652  __eq__(Atom self, Particle d) -> bool
6653  """
6654  return _IMP_atom.Atom___eq__(self, *args)
6655 
6656  def __ne__(self, *args):
6657  """
6658  __ne__(Atom self, Atom o) -> bool
6659  __ne__(Atom self, Particle d) -> bool
6660  """
6661  return _IMP_atom.Atom___ne__(self, *args)
6662 
6663  def __le__(self, *args):
6664  """
6665  __le__(Atom self, Atom o) -> bool
6666  __le__(Atom self, Particle d) -> bool
6667  """
6668  return _IMP_atom.Atom___le__(self, *args)
6669 
6670  def __lt__(self, *args):
6671  """
6672  __lt__(Atom self, Atom o) -> bool
6673  __lt__(Atom self, Particle d) -> bool
6674  """
6675  return _IMP_atom.Atom___lt__(self, *args)
6676 
6677  def __ge__(self, *args):
6678  """
6679  __ge__(Atom self, Atom o) -> bool
6680  __ge__(Atom self, Particle d) -> bool
6681  """
6682  return _IMP_atom.Atom___ge__(self, *args)
6683 
6684  def __gt__(self, *args):
6685  """
6686  __gt__(Atom self, Atom o) -> bool
6687  __gt__(Atom self, Particle d) -> bool
6688  """
6689  return _IMP_atom.Atom___gt__(self, *args)
6690 
6691  def __str__(self):
6692  """__str__(Atom self) -> std::string"""
6693  return _IMP_atom.Atom___str__(self)
6694 
6695  def __repr__(self):
6696  """__repr__(Atom self) -> std::string"""
6697  return _IMP_atom.Atom___repr__(self)
6698 
6699  __swig_destroy__ = _IMP_atom.delete_Atom
6700  __del__ = lambda self : None;
6701 Atom_swigregister = _IMP_atom.Atom_swigregister
6702 Atom_swigregister(Atom)
6703 cvar = _IMP_atom.cvar
6704 AT_UNKNOWN = cvar.AT_UNKNOWN
6705 AT_N = cvar.AT_N
6706 AT_CA = cvar.AT_CA
6707 AT_C = cvar.AT_C
6708 AT_O = cvar.AT_O
6709 AT_H = cvar.AT_H
6710 AT_H1 = cvar.AT_H1
6711 AT_H2 = cvar.AT_H2
6712 AT_H3 = cvar.AT_H3
6713 AT_HA = cvar.AT_HA
6714 AT_HA1 = cvar.AT_HA1
6715 AT_HA2 = cvar.AT_HA2
6716 AT_HA3 = cvar.AT_HA3
6717 AT_CB = cvar.AT_CB
6718 AT_HB = cvar.AT_HB
6719 AT_HB1 = cvar.AT_HB1
6720 AT_HB2 = cvar.AT_HB2
6721 AT_HB3 = cvar.AT_HB3
6722 AT_OXT = cvar.AT_OXT
6723 AT_CH3 = cvar.AT_CH3
6724 AT_CH = cvar.AT_CH
6725 AT_CG = cvar.AT_CG
6726 AT_CG1 = cvar.AT_CG1
6727 AT_CG2 = cvar.AT_CG2
6728 AT_HG = cvar.AT_HG
6729 AT_HG1 = cvar.AT_HG1
6730 AT_HG2 = cvar.AT_HG2
6731 AT_HG3 = cvar.AT_HG3
6732 AT_HG11 = cvar.AT_HG11
6733 AT_HG21 = cvar.AT_HG21
6734 AT_HG31 = cvar.AT_HG31
6735 AT_HG12 = cvar.AT_HG12
6736 AT_HG13 = cvar.AT_HG13
6737 AT_HG22 = cvar.AT_HG22
6738 AT_HG23 = cvar.AT_HG23
6739 AT_HG32 = cvar.AT_HG32
6740 AT_OG = cvar.AT_OG
6741 AT_OG1 = cvar.AT_OG1
6742 AT_SG = cvar.AT_SG
6743 AT_CD = cvar.AT_CD
6744 AT_CD1 = cvar.AT_CD1
6745 AT_CD2 = cvar.AT_CD2
6746 AT_HD = cvar.AT_HD
6747 AT_HD1 = cvar.AT_HD1
6748 AT_HD2 = cvar.AT_HD2
6749 AT_HD3 = cvar.AT_HD3
6750 AT_HD11 = cvar.AT_HD11
6751 AT_HD21 = cvar.AT_HD21
6752 AT_HD31 = cvar.AT_HD31
6753 AT_HD12 = cvar.AT_HD12
6754 AT_HD13 = cvar.AT_HD13
6755 AT_HD22 = cvar.AT_HD22
6756 AT_HD23 = cvar.AT_HD23
6757 AT_HD32 = cvar.AT_HD32
6758 AT_SD = cvar.AT_SD
6759 AT_OD1 = cvar.AT_OD1
6760 AT_OD2 = cvar.AT_OD2
6761 AT_ND1 = cvar.AT_ND1
6762 AT_ND2 = cvar.AT_ND2
6763 AT_CE = cvar.AT_CE
6764 AT_CE1 = cvar.AT_CE1
6765 AT_CE2 = cvar.AT_CE2
6766 AT_CE3 = cvar.AT_CE3
6767 AT_HE = cvar.AT_HE
6768 AT_HE1 = cvar.AT_HE1
6769 AT_HE2 = cvar.AT_HE2
6770 AT_HE3 = cvar.AT_HE3
6771 AT_HE21 = cvar.AT_HE21
6772 AT_HE22 = cvar.AT_HE22
6773 AT_OE1 = cvar.AT_OE1
6774 AT_OE2 = cvar.AT_OE2
6775 AT_NE = cvar.AT_NE
6776 AT_NE1 = cvar.AT_NE1
6777 AT_NE2 = cvar.AT_NE2
6778 AT_CZ = cvar.AT_CZ
6779 AT_CZ2 = cvar.AT_CZ2
6780 AT_CZ3 = cvar.AT_CZ3
6781 AT_NZ = cvar.AT_NZ
6782 AT_HZ = cvar.AT_HZ
6783 AT_HZ1 = cvar.AT_HZ1
6784 AT_HZ2 = cvar.AT_HZ2
6785 AT_HZ3 = cvar.AT_HZ3
6786 AT_CH2 = cvar.AT_CH2
6787 AT_NH1 = cvar.AT_NH1
6788 AT_NH2 = cvar.AT_NH2
6789 AT_OH = cvar.AT_OH
6790 AT_HH = cvar.AT_HH
6791 AT_HH11 = cvar.AT_HH11
6792 AT_HH21 = cvar.AT_HH21
6793 AT_HH2 = cvar.AT_HH2
6794 AT_HH12 = cvar.AT_HH12
6795 AT_HH22 = cvar.AT_HH22
6796 AT_HH13 = cvar.AT_HH13
6797 AT_HH23 = cvar.AT_HH23
6798 AT_HH33 = cvar.AT_HH33
6799 AT_P = cvar.AT_P
6800 AT_OP1 = cvar.AT_OP1
6801 AT_OP2 = cvar.AT_OP2
6802 AT_OP3 = cvar.AT_OP3
6803 AT_O5p = cvar.AT_O5p
6804 AT_C5p = cvar.AT_C5p
6805 AT_H5p = cvar.AT_H5p
6806 AT_H5pp = cvar.AT_H5pp
6807 AT_C4p = cvar.AT_C4p
6808 AT_H4p = cvar.AT_H4p
6809 AT_O4p = cvar.AT_O4p
6810 AT_C1p = cvar.AT_C1p
6811 AT_H1p = cvar.AT_H1p
6812 AT_C3p = cvar.AT_C3p
6813 AT_H3p = cvar.AT_H3p
6814 AT_O3p = cvar.AT_O3p
6815 AT_C2p = cvar.AT_C2p
6816 AT_H2p = cvar.AT_H2p
6817 AT_H2pp = cvar.AT_H2pp
6818 AT_O2p = cvar.AT_O2p
6819 AT_HO2p = cvar.AT_HO2p
6820 AT_N9 = cvar.AT_N9
6821 AT_C8 = cvar.AT_C8
6822 AT_H8 = cvar.AT_H8
6823 AT_N7 = cvar.AT_N7
6824 AT_C5 = cvar.AT_C5
6825 AT_C4 = cvar.AT_C4
6826 AT_N3 = cvar.AT_N3
6827 AT_C2 = cvar.AT_C2
6828 AT_N1 = cvar.AT_N1
6829 AT_C6 = cvar.AT_C6
6830 AT_N6 = cvar.AT_N6
6831 AT_H61 = cvar.AT_H61
6832 AT_H62 = cvar.AT_H62
6833 AT_O6 = cvar.AT_O6
6834 AT_N2 = cvar.AT_N2
6835 AT_NT = cvar.AT_NT
6836 AT_H21 = cvar.AT_H21
6837 AT_H22 = cvar.AT_H22
6838 AT_H6 = cvar.AT_H6
6839 AT_H5 = cvar.AT_H5
6840 AT_O2 = cvar.AT_O2
6841 AT_N4 = cvar.AT_N4
6842 AT_H41 = cvar.AT_H41
6843 AT_H42 = cvar.AT_H42
6844 AT_O4 = cvar.AT_O4
6845 AT_C7 = cvar.AT_C7
6846 AT_H71 = cvar.AT_H71
6847 AT_H72 = cvar.AT_H72
6848 AT_H73 = cvar.AT_H73
6849 AT_O1A = cvar.AT_O1A
6850 AT_O2A = cvar.AT_O2A
6851 AT_O3A = cvar.AT_O3A
6852 AT_O1B = cvar.AT_O1B
6853 AT_O2B = cvar.AT_O2B
6854 AT_O3B = cvar.AT_O3B
6855 
6856 def Atom_decorate_particle(*args):
6857  """Atom_decorate_particle(Particle p) -> Atom"""
6858  return _IMP_atom.Atom_decorate_particle(*args)
6859 
6860 def Atom_particle_is_instance(*args):
6861  """
6862  particle_is_instance(Particle p) -> bool
6863  Atom_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
6864  """
6865  return _IMP_atom.Atom_particle_is_instance(*args)
6866 
6867 def Atom_setup_particle(*args):
6868  """
6869  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Atom other) -> Atom
6870  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
6871  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType atom_type) -> Atom
6872  Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
6873  """
6874  return _IMP_atom.Atom_setup_particle(*args)
6875 
6876 def Atom_get_is_setup(*args):
6877  """
6878  get_is_setup(_ParticleAdaptor p) -> bool
6879  Atom_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6880  """
6881  return _IMP_atom.Atom_get_is_setup(*args)
6882 
6883 def Atom_get_atom_type_key():
6884  """Atom_get_atom_type_key() -> IntKey"""
6885  return _IMP_atom.Atom_get_atom_type_key()
6886 
6887 def Atom_get_element_key():
6888  """Atom_get_element_key() -> IntKey"""
6889  return _IMP_atom.Atom_get_element_key()
6890 
6891 def Atom_get_input_index_key():
6892  """Atom_get_input_index_key() -> IntKey"""
6893  return _IMP_atom.Atom_get_input_index_key()
6894 
6895 def Atom_get_occupancy_key():
6896  """Atom_get_occupancy_key() -> FloatKey"""
6897  return _IMP_atom.Atom_get_occupancy_key()
6898 
6899 def Atom_get_temperature_factor_key():
6900  """Atom_get_temperature_factor_key() -> FloatKey"""
6901  return _IMP_atom.Atom_get_temperature_factor_key()
6902 
6903 
6904 def get_residue(*args):
6905  """
6906  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
6907  get_residue(Atom d, bool nothrow=False) -> Residue
6908  get_residue(Atom d) -> Residue
6909  """
6910  return _IMP_atom.get_residue(*args)
6911 
6912 def get_atom(*args):
6913  """get_atom(Residue rd, AtomType at) -> Atom"""
6914  return _IMP_atom.get_atom(*args)
6915 
6916 def add_atom_type(*args):
6917  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
6918  return _IMP_atom.add_atom_type(*args)
6919 
6920 def get_element_for_atom_type(*args):
6921  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
6922  return _IMP_atom.get_element_for_atom_type(*args)
6923 
6924 def get_atom_type_exists(*args):
6925  """get_atom_type_exists(std::string name) -> bool"""
6926  return _IMP_atom.get_atom_type_exists(*args)
6927 class Residue(Hierarchy):
6928  """Proxy of C++ IMP::atom::Residue class"""
6929  __swig_setmethods__ = {}
6930  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6931  __setattr__ = lambda self, name, value: _swig_setattr(self, Residue, name, value)
6932  __swig_getmethods__ = {}
6933  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6934  __getattr__ = lambda self, name: _swig_getattr(self, Residue, name)
6935  def __init__(self, *args):
6936  """
6937  __init__(IMP::atom::Residue self) -> Residue
6938  __init__(IMP::atom::Residue self, Model m, ::IMP::kernel::ParticleIndex id) -> Residue
6939  __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
6940  """
6941  this = _IMP_atom.new_Residue(*args)
6942  try: self.this.append(this)
6943  except: self.this = this
6944  def decorate_particle(*args):
6945  """decorate_particle(Particle p) -> Residue"""
6946  return _IMP_atom.Residue_decorate_particle(*args)
6947 
6948  if _newclass:decorate_particle = staticmethod(decorate_particle)
6949  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6950  def particle_is_instance(*args):
6951  """
6952  particle_is_instance(Particle p) -> bool
6953  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
6954  """
6955  return _IMP_atom.Residue_particle_is_instance(*args)
6956 
6957  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
6958  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
6959  def show(self, *args):
6960  """
6961  show(Residue self, _ostream out=std::cout)
6962  show(Residue self)
6963  """
6964  return _IMP_atom.Residue_show(self, *args)
6965 
6966  def setup_particle(*args):
6967  """
6968  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
6969  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
6970  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index) -> Residue
6971  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
6972  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t) -> Residue
6973  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
6974  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Residue other) -> Residue
6975  setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
6976  """
6977  return _IMP_atom.Residue_setup_particle(*args)
6978 
6979  if _newclass:setup_particle = staticmethod(setup_particle)
6980  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6981  def get_is_setup(*args):
6982  """
6983  get_is_setup(_ParticleAdaptor p) -> bool
6984  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
6985  """
6986  return _IMP_atom.Residue_get_is_setup(*args)
6987 
6988  if _newclass:get_is_setup = staticmethod(get_is_setup)
6989  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
6990  def get_residue_type(self):
6991  """get_residue_type(Residue self) -> ResidueType"""
6992  return _IMP_atom.Residue_get_residue_type(self)
6993 
6994  def set_residue_type(self, *args):
6995  """set_residue_type(Residue self, ResidueType t)"""
6996  return _IMP_atom.Residue_set_residue_type(self, *args)
6997 
6998  def get_is_protein(self):
6999  """get_is_protein(Residue self) -> bool"""
7000  return _IMP_atom.Residue_get_is_protein(self)
7001 
7002  def get_is_dna(self):
7003  """get_is_dna(Residue self) -> bool"""
7004  return _IMP_atom.Residue_get_is_dna(self)
7005 
7006  def get_is_rna(self):
7007  """get_is_rna(Residue self) -> bool"""
7008  return _IMP_atom.Residue_get_is_rna(self)
7009 
7010  def get_index(self):
7011  """get_index(Residue self) -> IMP::Int"""
7012  return _IMP_atom.Residue_get_index(self)
7013 
7014  def set_index(self, *args):
7015  """set_index(Residue self, IMP::Int t)"""
7016  return _IMP_atom.Residue_set_index(self, *args)
7017 
7018  def get_insertion_code(self):
7019  """get_insertion_code(Residue self) -> char"""
7020  return _IMP_atom.Residue_get_insertion_code(self)
7021 
7022  def set_insertion_code(self, *args):
7023  """set_insertion_code(Residue self, char insertion_code)"""
7024  return _IMP_atom.Residue_set_insertion_code(self, *args)
7025 
7026  def get_index_key():
7027  """get_index_key() -> IntKey"""
7028  return _IMP_atom.Residue_get_index_key()
7029 
7030  if _newclass:get_index_key = staticmethod(get_index_key)
7031  __swig_getmethods__["get_index_key"] = lambda x: get_index_key
7032  def get_residue_type_key():
7033  """get_residue_type_key() -> IntKey"""
7034  return _IMP_atom.Residue_get_residue_type_key()
7035 
7036  if _newclass:get_residue_type_key = staticmethod(get_residue_type_key)
7037  __swig_getmethods__["get_residue_type_key"] = lambda x: get_residue_type_key
7038  def get_insertion_code_key():
7039  """get_insertion_code_key() -> IntKey"""
7040  return _IMP_atom.Residue_get_insertion_code_key()
7041 
7042  if _newclass:get_insertion_code_key = staticmethod(get_insertion_code_key)
7043  __swig_getmethods__["get_insertion_code_key"] = lambda x: get_insertion_code_key
7044  def add_attribute(self, *args):
7045  """
7046  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
7047  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
7048  add_attribute(Residue self, IntKey a0, IMP::Int a1)
7049  add_attribute(Residue self, StringKey a0, IMP::String a1)
7050  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
7051  add_attribute(Residue self, ObjectKey a0, IMP::Object * a1)
7052  """
7053  return _IMP_atom.Residue_add_attribute(self, *args)
7054 
7055  def get_value(self, *args):
7056  """
7057  get_value(Residue self, FloatKey a0) -> IMP::Float
7058  get_value(Residue self, IntKey a0) -> IMP::Int
7059  get_value(Residue self, StringKey a0) -> IMP::String
7060  get_value(Residue self, ParticleIndexKey a0) -> Particle
7061  get_value(Residue self, ObjectKey a0) -> IMP::Object *
7062  """
7063  return _IMP_atom.Residue_get_value(self, *args)
7064 
7065  def set_value(self, *args):
7066  """
7067  set_value(Residue self, FloatKey a0, IMP::Float a1)
7068  set_value(Residue self, IntKey a0, IMP::Int a1)
7069  set_value(Residue self, StringKey a0, IMP::String a1)
7070  set_value(Residue self, ParticleIndexKey a0, Particle a1)
7071  set_value(Residue self, ObjectKey a0, IMP::Object * a1)
7072  """
7073  return _IMP_atom.Residue_set_value(self, *args)
7074 
7075  def remove_attribute(self, *args):
7076  """
7077  remove_attribute(Residue self, FloatKey a0)
7078  remove_attribute(Residue self, IntKey a0)
7079  remove_attribute(Residue self, StringKey a0)
7080  remove_attribute(Residue self, ParticleIndexKey a0)
7081  remove_attribute(Residue self, ObjectKey a0)
7082  """
7083  return _IMP_atom.Residue_remove_attribute(self, *args)
7084 
7085  def has_attribute(self, *args):
7086  """
7087  has_attribute(Residue self, FloatKey a0) -> bool
7088  has_attribute(Residue self, IntKey a0) -> bool
7089  has_attribute(Residue self, StringKey a0) -> bool
7090  has_attribute(Residue self, ParticleIndexKey a0) -> bool
7091  has_attribute(Residue self, ObjectKey a0) -> bool
7092  """
7093  return _IMP_atom.Residue_has_attribute(self, *args)
7094 
7095  def get_derivative(self, *args):
7096  """get_derivative(Residue self, FloatKey a0) -> double"""
7097  return _IMP_atom.Residue_get_derivative(self, *args)
7098 
7099  def get_name(self):
7100  """get_name(Residue self) -> std::string"""
7101  return _IMP_atom.Residue_get_name(self)
7102 
7103  def clear_caches(self):
7104  """clear_caches(Residue self)"""
7105  return _IMP_atom.Residue_clear_caches(self)
7106 
7107  def set_name(self, *args):
7108  """set_name(Residue self, std::string a0)"""
7109  return _IMP_atom.Residue_set_name(self, *args)
7110 
7111  def set_check_level(self, *args):
7112  """set_check_level(Residue self, IMP::base::CheckLevel a0)"""
7113  return _IMP_atom.Residue_set_check_level(self, *args)
7114 
7115  def add_to_derivative(self, *args):
7116  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7117  return _IMP_atom.Residue_add_to_derivative(self, *args)
7118 
7119  def set_is_optimized(self, *args):
7120  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
7121  return _IMP_atom.Residue_set_is_optimized(self, *args)
7122 
7123  def get_is_optimized(self, *args):
7124  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
7125  return _IMP_atom.Residue_get_is_optimized(self, *args)
7126 
7127  def get_check_level(self):
7128  """get_check_level(Residue self) -> IMP::base::CheckLevel"""
7129  return _IMP_atom.Residue_get_check_level(self)
7130 
7131  def __eq__(self, *args):
7132  """
7133  __eq__(Residue self, Residue o) -> bool
7134  __eq__(Residue self, Particle d) -> bool
7135  """
7136  return _IMP_atom.Residue___eq__(self, *args)
7137 
7138  def __ne__(self, *args):
7139  """
7140  __ne__(Residue self, Residue o) -> bool
7141  __ne__(Residue self, Particle d) -> bool
7142  """
7143  return _IMP_atom.Residue___ne__(self, *args)
7144 
7145  def __le__(self, *args):
7146  """
7147  __le__(Residue self, Residue o) -> bool
7148  __le__(Residue self, Particle d) -> bool
7149  """
7150  return _IMP_atom.Residue___le__(self, *args)
7151 
7152  def __lt__(self, *args):
7153  """
7154  __lt__(Residue self, Residue o) -> bool
7155  __lt__(Residue self, Particle d) -> bool
7156  """
7157  return _IMP_atom.Residue___lt__(self, *args)
7158 
7159  def __ge__(self, *args):
7160  """
7161  __ge__(Residue self, Residue o) -> bool
7162  __ge__(Residue self, Particle d) -> bool
7163  """
7164  return _IMP_atom.Residue___ge__(self, *args)
7165 
7166  def __gt__(self, *args):
7167  """
7168  __gt__(Residue self, Residue o) -> bool
7169  __gt__(Residue self, Particle d) -> bool
7170  """
7171  return _IMP_atom.Residue___gt__(self, *args)
7172 
7173  def __str__(self):
7174  """__str__(Residue self) -> std::string"""
7175  return _IMP_atom.Residue___str__(self)
7176 
7177  def __repr__(self):
7178  """__repr__(Residue self) -> std::string"""
7179  return _IMP_atom.Residue___repr__(self)
7180 
7181  __swig_destroy__ = _IMP_atom.delete_Residue
7182  __del__ = lambda self : None;
7183 Residue_swigregister = _IMP_atom.Residue_swigregister
7184 Residue_swigregister(Residue)
7185 UNK = cvar.UNK
7186 GLY = cvar.GLY
7187 ALA = cvar.ALA
7188 VAL = cvar.VAL
7189 LEU = cvar.LEU
7190 ILE = cvar.ILE
7191 SER = cvar.SER
7192 THR = cvar.THR
7193 CYS = cvar.CYS
7194 MET = cvar.MET
7195 PRO = cvar.PRO
7196 ASP = cvar.ASP
7197 ASN = cvar.ASN
7198 GLU = cvar.GLU
7199 GLN = cvar.GLN
7200 LYS = cvar.LYS
7201 ARG = cvar.ARG
7202 HIS = cvar.HIS
7203 PHE = cvar.PHE
7204 TYR = cvar.TYR
7205 TRP = cvar.TRP
7206 ACE = cvar.ACE
7207 NH2 = cvar.NH2
7208 ADE = cvar.ADE
7209 URA = cvar.URA
7210 CYT = cvar.CYT
7211 GUA = cvar.GUA
7212 THY = cvar.THY
7213 DADE = cvar.DADE
7214 DURA = cvar.DURA
7215 DCYT = cvar.DCYT
7216 DGUA = cvar.DGUA
7217 DTHY = cvar.DTHY
7218 HOH = cvar.HOH
7219 HEME = cvar.HEME
7220 
7221 def Residue_decorate_particle(*args):
7222  """Residue_decorate_particle(Particle p) -> Residue"""
7223  return _IMP_atom.Residue_decorate_particle(*args)
7224 
7225 def Residue_particle_is_instance(*args):
7226  """
7227  particle_is_instance(Particle p) -> bool
7228  Residue_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
7229  """
7230  return _IMP_atom.Residue_particle_is_instance(*args)
7231 
7232 def Residue_setup_particle(*args):
7233  """
7234  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
7235  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
7236  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t, int index) -> Residue
7237  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
7238  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t) -> Residue
7239  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
7240  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Residue other) -> Residue
7241  Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
7242  """
7243  return _IMP_atom.Residue_setup_particle(*args)
7244 
7245 def Residue_get_is_setup(*args):
7246  """
7247  get_is_setup(_ParticleAdaptor p) -> bool
7248  Residue_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7249  """
7250  return _IMP_atom.Residue_get_is_setup(*args)
7251 
7252 def Residue_get_index_key():
7253  """Residue_get_index_key() -> IntKey"""
7254  return _IMP_atom.Residue_get_index_key()
7255 
7256 def Residue_get_residue_type_key():
7257  """Residue_get_residue_type_key() -> IntKey"""
7258  return _IMP_atom.Residue_get_residue_type_key()
7259 
7260 def Residue_get_insertion_code_key():
7261  """Residue_get_insertion_code_key() -> IntKey"""
7262  return _IMP_atom.Residue_get_insertion_code_key()
7263 
7264 
7265 def get_next_residue(*args):
7266  """get_next_residue(Residue rd) -> Hierarchy"""
7267  return _IMP_atom.get_next_residue(*args)
7268 
7269 def get_previous_residue(*args):
7270  """get_previous_residue(Residue rd) -> Hierarchy"""
7271  return _IMP_atom.get_previous_residue(*args)
7272 
7273 def get_one_letter_code(*args):
7274  """get_one_letter_code(ResidueType c) -> char"""
7275  return _IMP_atom.get_one_letter_code(*args)
7276 
7277 def get_phi_dihedral_atoms(*args):
7278  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
7279  return _IMP_atom.get_phi_dihedral_atoms(*args)
7280 
7281 def get_psi_dihedral_atoms(*args):
7282  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
7283  return _IMP_atom.get_psi_dihedral_atoms(*args)
7284 class Molecule(Hierarchy):
7285  """Proxy of C++ IMP::atom::Molecule class"""
7286  __swig_setmethods__ = {}
7287  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7288  __setattr__ = lambda self, name, value: _swig_setattr(self, Molecule, name, value)
7289  __swig_getmethods__ = {}
7290  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7291  __getattr__ = lambda self, name: _swig_getattr(self, Molecule, name)
7292  def __init__(self, *args):
7293  """
7294  __init__(IMP::atom::Molecule self) -> Molecule
7295  __init__(IMP::atom::Molecule self, Model m, ::IMP::kernel::ParticleIndex id) -> Molecule
7296  __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
7297  """
7298  this = _IMP_atom.new_Molecule(*args)
7299  try: self.this.append(this)
7300  except: self.this = this
7301  def decorate_particle(*args):
7302  """decorate_particle(Particle p) -> Molecule"""
7303  return _IMP_atom.Molecule_decorate_particle(*args)
7304 
7305  if _newclass:decorate_particle = staticmethod(decorate_particle)
7306  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7307  def particle_is_instance(*args):
7308  """
7309  particle_is_instance(Particle p) -> bool
7310  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
7311  """
7312  return _IMP_atom.Molecule_particle_is_instance(*args)
7313 
7314  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
7315  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
7316  def show(self, *args):
7317  """
7318  show(Molecule self, _ostream out=std::cout)
7319  show(Molecule self)
7320  """
7321  return _IMP_atom.Molecule_show(self, *args)
7322 
7323  def setup_particle(*args):
7324  """
7325  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Molecule
7326  setup_particle(_ParticleAdaptor decorator) -> Molecule
7327  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Molecule other) -> Molecule
7328  setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
7329  """
7330  return _IMP_atom.Molecule_setup_particle(*args)
7331 
7332  if _newclass:setup_particle = staticmethod(setup_particle)
7333  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7334  def get_is_setup(*args):
7335  """
7336  get_is_setup(_ParticleAdaptor p) -> bool
7337  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7338  """
7339  return _IMP_atom.Molecule_get_is_setup(*args)
7340 
7341  if _newclass:get_is_setup = staticmethod(get_is_setup)
7342  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7343  def add_attribute(self, *args):
7344  """
7345  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
7346  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
7347  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
7348  add_attribute(Molecule self, StringKey a0, IMP::String a1)
7349  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
7350  add_attribute(Molecule self, ObjectKey a0, IMP::Object * a1)
7351  """
7352  return _IMP_atom.Molecule_add_attribute(self, *args)
7353 
7354  def get_value(self, *args):
7355  """
7356  get_value(Molecule self, FloatKey a0) -> IMP::Float
7357  get_value(Molecule self, IntKey a0) -> IMP::Int
7358  get_value(Molecule self, StringKey a0) -> IMP::String
7359  get_value(Molecule self, ParticleIndexKey a0) -> Particle
7360  get_value(Molecule self, ObjectKey a0) -> IMP::Object *
7361  """
7362  return _IMP_atom.Molecule_get_value(self, *args)
7363 
7364  def set_value(self, *args):
7365  """
7366  set_value(Molecule self, FloatKey a0, IMP::Float a1)
7367  set_value(Molecule self, IntKey a0, IMP::Int a1)
7368  set_value(Molecule self, StringKey a0, IMP::String a1)
7369  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
7370  set_value(Molecule self, ObjectKey a0, IMP::Object * a1)
7371  """
7372  return _IMP_atom.Molecule_set_value(self, *args)
7373 
7374  def remove_attribute(self, *args):
7375  """
7376  remove_attribute(Molecule self, FloatKey a0)
7377  remove_attribute(Molecule self, IntKey a0)
7378  remove_attribute(Molecule self, StringKey a0)
7379  remove_attribute(Molecule self, ParticleIndexKey a0)
7380  remove_attribute(Molecule self, ObjectKey a0)
7381  """
7382  return _IMP_atom.Molecule_remove_attribute(self, *args)
7383 
7384  def has_attribute(self, *args):
7385  """
7386  has_attribute(Molecule self, FloatKey a0) -> bool
7387  has_attribute(Molecule self, IntKey a0) -> bool
7388  has_attribute(Molecule self, StringKey a0) -> bool
7389  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
7390  has_attribute(Molecule self, ObjectKey a0) -> bool
7391  """
7392  return _IMP_atom.Molecule_has_attribute(self, *args)
7393 
7394  def get_derivative(self, *args):
7395  """get_derivative(Molecule self, FloatKey a0) -> double"""
7396  return _IMP_atom.Molecule_get_derivative(self, *args)
7397 
7398  def get_name(self):
7399  """get_name(Molecule self) -> std::string"""
7400  return _IMP_atom.Molecule_get_name(self)
7401 
7402  def clear_caches(self):
7403  """clear_caches(Molecule self)"""
7404  return _IMP_atom.Molecule_clear_caches(self)
7405 
7406  def set_name(self, *args):
7407  """set_name(Molecule self, std::string a0)"""
7408  return _IMP_atom.Molecule_set_name(self, *args)
7409 
7410  def set_check_level(self, *args):
7411  """set_check_level(Molecule self, IMP::base::CheckLevel a0)"""
7412  return _IMP_atom.Molecule_set_check_level(self, *args)
7413 
7414  def add_to_derivative(self, *args):
7415  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7416  return _IMP_atom.Molecule_add_to_derivative(self, *args)
7417 
7418  def set_is_optimized(self, *args):
7419  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
7420  return _IMP_atom.Molecule_set_is_optimized(self, *args)
7421 
7422  def get_is_optimized(self, *args):
7423  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
7424  return _IMP_atom.Molecule_get_is_optimized(self, *args)
7425 
7426  def get_check_level(self):
7427  """get_check_level(Molecule self) -> IMP::base::CheckLevel"""
7428  return _IMP_atom.Molecule_get_check_level(self)
7429 
7430  def __eq__(self, *args):
7431  """
7432  __eq__(Molecule self, Molecule o) -> bool
7433  __eq__(Molecule self, Particle d) -> bool
7434  """
7435  return _IMP_atom.Molecule___eq__(self, *args)
7436 
7437  def __ne__(self, *args):
7438  """
7439  __ne__(Molecule self, Molecule o) -> bool
7440  __ne__(Molecule self, Particle d) -> bool
7441  """
7442  return _IMP_atom.Molecule___ne__(self, *args)
7443 
7444  def __le__(self, *args):
7445  """
7446  __le__(Molecule self, Molecule o) -> bool
7447  __le__(Molecule self, Particle d) -> bool
7448  """
7449  return _IMP_atom.Molecule___le__(self, *args)
7450 
7451  def __lt__(self, *args):
7452  """
7453  __lt__(Molecule self, Molecule o) -> bool
7454  __lt__(Molecule self, Particle d) -> bool
7455  """
7456  return _IMP_atom.Molecule___lt__(self, *args)
7457 
7458  def __ge__(self, *args):
7459  """
7460  __ge__(Molecule self, Molecule o) -> bool
7461  __ge__(Molecule self, Particle d) -> bool
7462  """
7463  return _IMP_atom.Molecule___ge__(self, *args)
7464 
7465  def __gt__(self, *args):
7466  """
7467  __gt__(Molecule self, Molecule o) -> bool
7468  __gt__(Molecule self, Particle d) -> bool
7469  """
7470  return _IMP_atom.Molecule___gt__(self, *args)
7471 
7472  def __str__(self):
7473  """__str__(Molecule self) -> std::string"""
7474  return _IMP_atom.Molecule___str__(self)
7475 
7476  def __repr__(self):
7477  """__repr__(Molecule self) -> std::string"""
7478  return _IMP_atom.Molecule___repr__(self)
7479 
7480  __swig_destroy__ = _IMP_atom.delete_Molecule
7481  __del__ = lambda self : None;
7482 Molecule_swigregister = _IMP_atom.Molecule_swigregister
7483 Molecule_swigregister(Molecule)
7484 
7485 def Molecule_decorate_particle(*args):
7486  """Molecule_decorate_particle(Particle p) -> Molecule"""
7487  return _IMP_atom.Molecule_decorate_particle(*args)
7488 
7489 def Molecule_particle_is_instance(*args):
7490  """
7491  particle_is_instance(Particle p) -> bool
7492  Molecule_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
7493  """
7494  return _IMP_atom.Molecule_particle_is_instance(*args)
7495 
7496 def Molecule_setup_particle(*args):
7497  """
7498  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Molecule
7499  setup_particle(_ParticleAdaptor decorator) -> Molecule
7500  setup_particle(Model m, IMP::kernel::ParticleIndex pi, Molecule other) -> Molecule
7501  Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
7502  """
7503  return _IMP_atom.Molecule_setup_particle(*args)
7504 
7505 def Molecule_get_is_setup(*args):
7506  """
7507  get_is_setup(_ParticleAdaptor p) -> bool
7508  Molecule_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7509  """
7510  return _IMP_atom.Molecule_get_is_setup(*args)
7511 
7512 class Copy(Molecule):
7513  """Proxy of C++ IMP::atom::Copy class"""
7514  __swig_setmethods__ = {}
7515  for _s in [Molecule]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7516  __setattr__ = lambda self, name, value: _swig_setattr(self, Copy, name, value)
7517  __swig_getmethods__ = {}
7518  for _s in [Molecule]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7519  __getattr__ = lambda self, name: _swig_getattr(self, Copy, name)
7520  def get_copy_index_key():
7521  """get_copy_index_key() -> IntKey"""
7522  return _IMP_atom.Copy_get_copy_index_key()
7523 
7524  if _newclass:get_copy_index_key = staticmethod(get_copy_index_key)
7525  __swig_getmethods__["get_copy_index_key"] = lambda x: get_copy_index_key
7526  def __init__(self, *args):
7527  """
7528  __init__(IMP::atom::Copy self) -> Copy
7529  __init__(IMP::atom::Copy self, Model m, ::IMP::kernel::ParticleIndex id) -> Copy
7530  __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
7531  """
7532  this = _IMP_atom.new_Copy(*args)
7533  try: self.this.append(this)
7534  except: self.this = this
7535  def decorate_particle(*args):
7536  """decorate_particle(Particle p) -> Copy"""
7537  return _IMP_atom.Copy_decorate_particle(*args)
7538 
7539  if _newclass:decorate_particle = staticmethod(decorate_particle)
7540  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7541  def particle_is_instance(*args):
7542  """
7543  particle_is_instance(Particle p) -> bool
7544  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
7545  """
7546  return _IMP_atom.Copy_particle_is_instance(*args)
7547 
7548  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
7549  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
7550  def show(self, *args):
7551  """
7552  show(Copy self, _ostream out=std::cout)
7553  show(Copy self)
7554  """
7555  return _IMP_atom.Copy_show(self, *args)
7556 
7557  def setup_particle(*args):
7558  """
7559  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int number) -> Copy
7560  setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
7561  """
7562  return _IMP_atom.Copy_setup_particle(*args)
7563 
7564  if _newclass:setup_particle = staticmethod(setup_particle)
7565  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7566  def get_is_setup(*args):
7567  """
7568  get_is_setup(_ParticleAdaptor p) -> bool
7569  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7570  """
7571  return _IMP_atom.Copy_get_is_setup(*args)
7572 
7573  if _newclass:get_is_setup = staticmethod(get_is_setup)
7574  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
7575  def get_copy_index(self):
7576  """get_copy_index(Copy self) -> int"""
7577  return _IMP_atom.Copy_get_copy_index(self)
7578 
7579  def add_attribute(self, *args):
7580  """
7581  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
7582  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
7583  add_attribute(Copy self, IntKey a0, IMP::Int a1)
7584  add_attribute(Copy self, StringKey a0, IMP::String a1)
7585  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
7586  add_attribute(Copy self, ObjectKey a0, IMP::Object * a1)
7587  """
7588  return _IMP_atom.Copy_add_attribute(self, *args)
7589 
7590  def get_value(self, *args):
7591  """
7592  get_value(Copy self, FloatKey a0) -> IMP::Float
7593  get_value(Copy self, IntKey a0) -> IMP::Int
7594  get_value(Copy self, StringKey a0) -> IMP::String
7595  get_value(Copy self, ParticleIndexKey a0) -> Particle
7596  get_value(Copy self, ObjectKey a0) -> IMP::Object *
7597  """
7598  return _IMP_atom.Copy_get_value(self, *args)
7599 
7600  def set_value(self, *args):
7601  """
7602  set_value(Copy self, FloatKey a0, IMP::Float a1)
7603  set_value(Copy self, IntKey a0, IMP::Int a1)
7604  set_value(Copy self, StringKey a0, IMP::String a1)
7605  set_value(Copy self, ParticleIndexKey a0, Particle a1)
7606  set_value(Copy self, ObjectKey a0, IMP::Object * a1)
7607  """
7608  return _IMP_atom.Copy_set_value(self, *args)
7609 
7610  def remove_attribute(self, *args):
7611  """
7612  remove_attribute(Copy self, FloatKey a0)
7613  remove_attribute(Copy self, IntKey a0)
7614  remove_attribute(Copy self, StringKey a0)
7615  remove_attribute(Copy self, ParticleIndexKey a0)
7616  remove_attribute(Copy self, ObjectKey a0)
7617  """
7618  return _IMP_atom.Copy_remove_attribute(self, *args)
7619 
7620  def has_attribute(self, *args):
7621  """
7622  has_attribute(Copy self, FloatKey a0) -> bool
7623  has_attribute(Copy self, IntKey a0) -> bool
7624  has_attribute(Copy self, StringKey a0) -> bool
7625  has_attribute(Copy self, ParticleIndexKey a0) -> bool
7626  has_attribute(Copy self, ObjectKey a0) -> bool
7627  """
7628  return _IMP_atom.Copy_has_attribute(self, *args)
7629 
7630  def get_derivative(self, *args):
7631  """get_derivative(Copy self, FloatKey a0) -> double"""
7632  return _IMP_atom.Copy_get_derivative(self, *args)
7633 
7634  def get_name(self):
7635  """get_name(Copy self) -> std::string"""
7636  return _IMP_atom.Copy_get_name(self)
7637 
7638  def clear_caches(self):
7639  """clear_caches(Copy self)"""
7640  return _IMP_atom.Copy_clear_caches(self)
7641 
7642  def set_name(self, *args):
7643  """set_name(Copy self, std::string a0)"""
7644  return _IMP_atom.Copy_set_name(self, *args)
7645 
7646  def set_check_level(self, *args):
7647  """set_check_level(Copy self, IMP::base::CheckLevel a0)"""
7648  return _IMP_atom.Copy_set_check_level(self, *args)
7649 
7650  def add_to_derivative(self, *args):
7651  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7652  return _IMP_atom.Copy_add_to_derivative(self, *args)
7653 
7654  def set_is_optimized(self, *args):
7655  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
7656  return _IMP_atom.Copy_set_is_optimized(self, *args)
7657 
7658  def get_is_optimized(self, *args):
7659  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
7660  return _IMP_atom.Copy_get_is_optimized(self, *args)
7661 
7662  def get_check_level(self):
7663  """get_check_level(Copy self) -> IMP::base::CheckLevel"""
7664  return _IMP_atom.Copy_get_check_level(self)
7665 
7666  def __eq__(self, *args):
7667  """
7668  __eq__(Copy self, Copy o) -> bool
7669  __eq__(Copy self, Particle d) -> bool
7670  """
7671  return _IMP_atom.Copy___eq__(self, *args)
7672 
7673  def __ne__(self, *args):
7674  """
7675  __ne__(Copy self, Copy o) -> bool
7676  __ne__(Copy self, Particle d) -> bool
7677  """
7678  return _IMP_atom.Copy___ne__(self, *args)
7679 
7680  def __le__(self, *args):
7681  """
7682  __le__(Copy self, Copy o) -> bool
7683  __le__(Copy self, Particle d) -> bool
7684  """
7685  return _IMP_atom.Copy___le__(self, *args)
7686 
7687  def __lt__(self, *args):
7688  """
7689  __lt__(Copy self, Copy o) -> bool
7690  __lt__(Copy self, Particle d) -> bool
7691  """
7692  return _IMP_atom.Copy___lt__(self, *args)
7693 
7694  def __ge__(self, *args):
7695  """
7696  __ge__(Copy self, Copy o) -> bool
7697  __ge__(Copy self, Particle d) -> bool
7698  """
7699  return _IMP_atom.Copy___ge__(self, *args)
7700 
7701  def __gt__(self, *args):
7702  """
7703  __gt__(Copy self, Copy o) -> bool
7704  __gt__(Copy self, Particle d) -> bool
7705  """
7706  return _IMP_atom.Copy___gt__(self, *args)
7707 
7708  def __str__(self):
7709  """__str__(Copy self) -> std::string"""
7710  return _IMP_atom.Copy___str__(self)
7711 
7712  def __repr__(self):
7713  """__repr__(Copy self) -> std::string"""
7714  return _IMP_atom.Copy___repr__(self)
7715 
7716  __swig_destroy__ = _IMP_atom.delete_Copy
7717  __del__ = lambda self : None;
7718 Copy_swigregister = _IMP_atom.Copy_swigregister
7719 Copy_swigregister(Copy)
7720 
7721 def Copy_get_copy_index_key():
7722  """Copy_get_copy_index_key() -> IntKey"""
7723  return _IMP_atom.Copy_get_copy_index_key()
7724 
7725 def Copy_decorate_particle(*args):
7726  """Copy_decorate_particle(Particle p) -> Copy"""
7727  return _IMP_atom.Copy_decorate_particle(*args)
7728 
7729 def Copy_particle_is_instance(*args):
7730  """
7731  particle_is_instance(Particle p) -> bool
7732  Copy_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
7733  """
7734  return _IMP_atom.Copy_particle_is_instance(*args)
7735 
7736 def Copy_setup_particle(*args):
7737  """
7738  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::Int number) -> Copy
7739  Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
7740  """
7741  return _IMP_atom.Copy_setup_particle(*args)
7742 
7743 def Copy_get_is_setup(*args):
7744  """
7745  get_is_setup(_ParticleAdaptor p) -> bool
7746  Copy_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
7747  """
7748  return _IMP_atom.Copy_get_is_setup(*args)
7749 
7750 
7751 def __lshift__(*args):
7752  """
7753  __lshift__(_ostream out, Bonded n) -> _ostream
7754  __lshift__(_ostream out, Bond n) -> _ostream
7755  __lshift__(_ostream out, Hierarchy n) -> _ostream
7756  __lshift__(_ostream out, Angle n) -> _ostream
7757  __lshift__(_ostream out, Dihedral n) -> _ostream
7758  __lshift__(_ostream out, Diffusion n) -> _ostream
7759  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
7760  __lshift__(_ostream out, Chain n) -> _ostream
7761  __lshift__(_ostream out, Charged n) -> _ostream
7762  __lshift__(_ostream out, Domain n) -> _ostream
7763  __lshift__(_ostream out, LennardJones n) -> _ostream
7764  __lshift__(_ostream out, Fragment n) -> _ostream
7765  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
7766  __lshift__(_ostream out, Atom n) -> _ostream
7767  __lshift__(_ostream out, Residue n) -> _ostream
7768  __lshift__(_ostream out, Molecule n) -> _ostream
7769  __lshift__(_ostream out, Copy n) -> _ostream
7770  """
7771  return _IMP_atom.__lshift__(*args)
7772 class Selection(IMP.kernel._ParticleIndexesAdaptor):
7773  """Proxy of C++ IMP::atom::Selection class"""
7774  __swig_setmethods__ = {}
7775  for _s in [IMP.kernel._ParticleIndexesAdaptor]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7776  __setattr__ = lambda self, name, value: _swig_setattr(self, Selection, name, value)
7777  __swig_getmethods__ = {}
7778  for _s in [IMP.kernel._ParticleIndexesAdaptor]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7779  __getattr__ = lambda self, name: _swig_getattr(self, Selection, name)
7780  NONE = _IMP_atom.Selection_NONE
7781  C = _IMP_atom.Selection_C
7782  N = _IMP_atom.Selection_N
7783  def __init__(self, *args):
7784  """
7785  __init__(IMP::atom::Selection self) -> Selection
7786  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
7787  __init__(IMP::atom::Selection self, Particle h) -> Selection
7788  __init__(IMP::atom::Selection self, Model m, IMP::kernel::ParticleIndexes const & pis) -> Selection
7789  __init__(IMP::atom::Selection self, IMP::kernel::ParticlesTemp const & h) -> Selection
7790  """
7791  this = _IMP_atom.new_Selection(*args)
7792  try: self.this.append(this)
7793  except: self.this = this
7794  def get_hierarchies(self):
7795  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
7796  return _IMP_atom.Selection_get_hierarchies(self)
7797 
7798  def set_molecules(self, *args):
7799  """set_molecules(Selection self, IMP::Strings mols)"""
7800  return _IMP_atom.Selection_set_molecules(self, *args)
7801 
7802  def set_target_radius(self, *args):
7803  """set_target_radius(Selection self, double r)"""
7804  return _IMP_atom.Selection_set_target_radius(self, *args)
7805 
7806  def set_terminus(self, *args):
7807  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
7808  return _IMP_atom.Selection_set_terminus(self, *args)
7809 
7810  def set_chains(self, *args):
7811  """set_chains(Selection self, std::string chains)"""
7812  return _IMP_atom.Selection_set_chains(self, *args)
7813 
7814  def set_residue_indexes(self, *args):
7815  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
7816  return _IMP_atom.Selection_set_residue_indexes(self, *args)
7817 
7818  def set_atom_types(self, *args):
7819  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
7820  return _IMP_atom.Selection_set_atom_types(self, *args)
7821 
7822  def set_residue_types(self, *args):
7823  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
7824  return _IMP_atom.Selection_set_residue_types(self, *args)
7825 
7826  def set_domains(self, *args):
7827  """set_domains(Selection self, IMP::Strings names)"""
7828  return _IMP_atom.Selection_set_domains(self, *args)
7829 
7830  def set_molecule(self, *args):
7831  """set_molecule(Selection self, std::string mol)"""
7832  return _IMP_atom.Selection_set_molecule(self, *args)
7833 
7834  def set_chain(self, *args):
7835  """set_chain(Selection self, char c)"""
7836  return _IMP_atom.Selection_set_chain(self, *args)
7837 
7838  def set_residue_index(self, *args):
7839  """set_residue_index(Selection self, int i)"""
7840  return _IMP_atom.Selection_set_residue_index(self, *args)
7841 
7842  def set_atom_type(self, *args):
7843  """set_atom_type(Selection self, AtomType types)"""
7844  return _IMP_atom.Selection_set_atom_type(self, *args)
7845 
7846  def set_residue_type(self, *args):
7847  """set_residue_type(Selection self, ResidueType type)"""
7848  return _IMP_atom.Selection_set_residue_type(self, *args)
7849 
7850  def set_domain(self, *args):
7851  """set_domain(Selection self, std::string name)"""
7852  return _IMP_atom.Selection_set_domain(self, *args)
7853 
7854  def set_copy_index(self, *args):
7855  """set_copy_index(Selection self, unsigned int copy)"""
7856  return _IMP_atom.Selection_set_copy_index(self, *args)
7857 
7858  def set_copy_indexes(self, *args):
7859  """set_copy_indexes(Selection self, IMP::Ints copies)"""
7860  return _IMP_atom.Selection_set_copy_indexes(self, *args)
7861 
7862  def set_particle_type(self, *args):
7863  """set_particle_type(Selection self, ParticleType t)"""
7864  return _IMP_atom.Selection_set_particle_type(self, *args)
7865 
7866  def set_particle_types(self, *args):
7867  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
7868  return _IMP_atom.Selection_set_particle_types(self, *args)
7869 
7870  def set_hierarchy_types(self, *args):
7871  """set_hierarchy_types(Selection self, IMP::Ints types)"""
7872  return _IMP_atom.Selection_set_hierarchy_types(self, *args)
7873 
7874  def get_selected_particles(self):
7875  """get_selected_particles(Selection self) -> IMP::kernel::ParticlesTemp"""
7876  return _IMP_atom.Selection_get_selected_particles(self)
7877 
7878  def get_selected_particle_indexes(self):
7879  """get_selected_particle_indexes(Selection self) -> IMP::kernel::ParticleIndexes"""
7880  return _IMP_atom.Selection_get_selected_particle_indexes(self)
7881 
7882  def show(self, *args):
7883  """
7884  show(Selection self, _ostream out=std::cout)
7885  show(Selection self)
7886  """
7887  return _IMP_atom.Selection_show(self, *args)
7888 
7889  def __str__(self):
7890  """__str__(Selection self) -> std::string"""
7891  return _IMP_atom.Selection___str__(self)
7892 
7893  def __repr__(self):
7894  """__repr__(Selection self) -> std::string"""
7895  return _IMP_atom.Selection___repr__(self)
7896 
7897  def __init__(self, hierarchy=None,
7898  hierarchies=None, **params):
7899  if hierarchy and hierarchies:
7900  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
7901  if hierarchy:
7902  this = _IMP_atom.new_Selection(hierarchy)
7903  try: self.this.append(this)
7904  except: self.this = this
7905  else:
7906  this = _IMP_atom.new_Selection(hierarchies)
7907  try: self.this.append(this)
7908  except: self.this = this
7909  if "residue_indexes" in params.keys():
7910  out = []
7911  for i in params["residue_indexes"]:
7912  if type(i) == tuple:
7913  print "WARNING, Passing a tuple to residue_indexes in Selection is deprecated as of IMP 2.1, please use range() instead."
7914  out += range(i[0], i[1])
7915  else:
7916  out.append(i)
7917  params["residue_indexes"] = out
7918  for k in params.keys():
7919  eval("self.set_%s(params[k])"%k)
7920 
7921  __swig_destroy__ = _IMP_atom.delete_Selection
7922  __del__ = lambda self : None;
7923 Selection_swigregister = _IMP_atom.Selection_swigregister
7924 Selection_swigregister(Selection)
7925 
7926 
7927 def create_distance_restraint(*args):
7928  """
7929  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint
7930  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
7931  """
7932  return _IMP_atom.create_distance_restraint(*args)
7933 
7935  """
7936  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
7937  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
7938  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
7939  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
7940  """
7941  return _IMP_atom.create_connectivity_restraint(*args)
7942 
7944  """
7945  create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
7946  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
7947  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
7948  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
7949  """
7950  return _IMP_atom.create_internal_connectivity_restraint(*args)
7951 
7952 def create_cover(*args):
7953  """
7954  create_cover(Selection s, std::string name=std::string()) -> XYZR
7955  create_cover(Selection s) -> XYZR
7956  """
7957  return _IMP_atom.create_cover(*args)
7958 
7959 def get_mass(*args):
7960  """get_mass(Selection s) -> double"""
7961  return _IMP_atom.get_mass(*args)
7962 
7963 def get_volume(*args):
7964  """get_volume(Selection s) -> double"""
7965  return _IMP_atom.get_volume(*args)
7966 
7967 def get_surface_area(*args):
7968  """get_surface_area(Selection s) -> double"""
7969  return _IMP_atom.get_surface_area(*args)
7970 
7971 def get_leaves(*args):
7972  """
7973  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
7974  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
7975  get_leaves(Selection h) -> IMP::atom::Hierarchies
7976  """
7977  return _IMP_atom.get_leaves(*args)
7978 class SelectionGeometry(IMP.display.Geometry):
7979  """Proxy of C++ IMP::atom::SelectionGeometry class"""
7980  __swig_setmethods__ = {}
7981  for _s in [IMP.display.Geometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7982  __setattr__ = lambda self, name, value: _swig_setattr(self, SelectionGeometry, name, value)
7983  __swig_getmethods__ = {}
7984  for _s in [IMP.display.Geometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7985  __getattr__ = lambda self, name: _swig_getattr(self, SelectionGeometry, name)
7986  def __init__(self, *args):
7987  """
7988  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry
7989  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
7990  """
7991  this = _IMP_atom.new_SelectionGeometry(*args)
7992  try: self.this.append(this)
7993  except: self.this = this
7994  def get_version_info(self):
7995  """get_version_info(SelectionGeometry self) -> VersionInfo"""
7996  return _IMP_atom.SelectionGeometry_get_version_info(self)
7997 
7998  __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
7999  __del__ = lambda self : None;
8000  def __str__(self):
8001  """__str__(SelectionGeometry self) -> std::string"""
8002  return _IMP_atom.SelectionGeometry___str__(self)
8003 
8004  def __repr__(self):
8005  """__repr__(SelectionGeometry self) -> std::string"""
8006  return _IMP_atom.SelectionGeometry___repr__(self)
8007 
8008  def get_from(o):
8009  return _object_cast_to_SelectionGeometry(o)
8010  get_from = staticmethod(get_from)
8011 
8012 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
8013 SelectionGeometry_swigregister(SelectionGeometry)
8014 
8015 
8016 def get_rmsd(*args):
8017  """
8018  get_rmsd(Selection s0, Selection s1, Transformation3D tr_for_second=IMP::algebra::get_identity_transformation_3d()) -> double
8019  get_rmsd(Selection s0, Selection s1) -> double
8020  """
8021  return _IMP_atom.get_rmsd(*args)
8022 
8023 def get_placement_score(*args):
8024  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
8025  return _IMP_atom.get_placement_score(*args)
8026 
8028  """
8029  get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
8030  IMP::core::XYZs const & mdl2) -> IMP::FloatPair
8031  """
8032  return _IMP_atom.get_component_placement_score(*args)
8033 
8034 def get_pairwise_rmsd_score(*args):
8035  """
8036  get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
8037  IMP::core::XYZs const & mdl2) -> double
8038  """
8039  return _IMP_atom.get_pairwise_rmsd_score(*args)
8040 
8041 def get_radius_of_gyration(*args):
8042  """
8043  get_radius_of_gyration(Selection s) -> double
8044  get_radius_of_gyration(IMP::kernel::ParticlesTemp const & ps) -> double
8045  """
8046  return _IMP_atom.get_radius_of_gyration(*args)
8047 class ForceFieldParameters(IMP.base.Object):
8048  """Proxy of C++ IMP::atom::ForceFieldParameters class"""
8049  __swig_setmethods__ = {}
8050  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8051  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceFieldParameters, name, value)
8052  __swig_getmethods__ = {}
8053  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8054  __getattr__ = lambda self, name: _swig_getattr(self, ForceFieldParameters, name)
8055  def __init__(self):
8056  """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
8057  this = _IMP_atom.new_ForceFieldParameters()
8058  try: self.this.append(this)
8059  except: self.this = this
8060  def get_radius(self, *args):
8061  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
8062  return _IMP_atom.ForceFieldParameters_get_radius(self, *args)
8063 
8064  def get_epsilon(self, *args):
8065  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
8066  return _IMP_atom.ForceFieldParameters_get_epsilon(self, *args)
8067 
8068  def add_radii(self, *args):
8069  """
8070  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius"))
8071  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
8072  add_radii(ForceFieldParameters self, Hierarchy mhd)
8073  """
8074  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
8075 
8076  def add_well_depths(self, *args):
8077  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
8078  return _IMP_atom.ForceFieldParameters_add_well_depths(self, *args)
8079 
8080  def add_bonds(self, *args):
8081  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
8082  return _IMP_atom.ForceFieldParameters_add_bonds(self, *args)
8083 
8084  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
8085  __del__ = lambda self : None;
8086  def __str__(self):
8087  """__str__(ForceFieldParameters self) -> std::string"""
8088  return _IMP_atom.ForceFieldParameters___str__(self)
8089 
8090  def __repr__(self):
8091  """__repr__(ForceFieldParameters self) -> std::string"""
8092  return _IMP_atom.ForceFieldParameters___repr__(self)
8093 
8094  def get_from(o):
8095  return _object_cast_to_ForceFieldParameters(o)
8096  get_from = staticmethod(get_from)
8097 
8098 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
8099 ForceFieldParameters_swigregister(ForceFieldParameters)
8100 
8101 class CHARMMAtomTopology(_object):
8102  """Proxy of C++ IMP::atom::CHARMMAtomTopology class"""
8103  __swig_setmethods__ = {}
8104  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtomTopology, name, value)
8105  __swig_getmethods__ = {}
8106  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtomTopology, name)
8107  def __init__(self, *args):
8108  """
8109  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
8110  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
8111  """
8112  this = _IMP_atom.new_CHARMMAtomTopology(*args)
8113  try: self.this.append(this)
8114  except: self.this = this
8115  def get_name(self):
8116  """get_name(CHARMMAtomTopology self) -> std::string"""
8117  return _IMP_atom.CHARMMAtomTopology_get_name(self)
8118 
8119  def get_charmm_type(self):
8120  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
8121  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
8122 
8123  def get_charge(self):
8124  """get_charge(CHARMMAtomTopology self) -> double"""
8125  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
8126 
8127  def set_charmm_type(self, *args):
8128  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
8129  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, *args)
8130 
8131  def set_charge(self, *args):
8132  """set_charge(CHARMMAtomTopology self, double charge)"""
8133  return _IMP_atom.CHARMMAtomTopology_set_charge(self, *args)
8134 
8135  def show(self, *args):
8136  """
8137  show(CHARMMAtomTopology self, _ostream out=std::cout)
8138  show(CHARMMAtomTopology self)
8139  """
8140  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
8141 
8142  def __str__(self):
8143  """__str__(CHARMMAtomTopology self) -> std::string"""
8144  return _IMP_atom.CHARMMAtomTopology___str__(self)
8145 
8146  def __repr__(self):
8147  """__repr__(CHARMMAtomTopology self) -> std::string"""
8148  return _IMP_atom.CHARMMAtomTopology___repr__(self)
8149 
8150  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
8151  __del__ = lambda self : None;
8152 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
8153 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
8154 
8155 class CHARMMBondEndpoint(_object):
8156  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class"""
8157  __swig_setmethods__ = {}
8158  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondEndpoint, name, value)
8159  __swig_getmethods__ = {}
8160  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondEndpoint, name)
8161  def __init__(self, *args):
8162  """
8163  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=nullptr) -> CHARMMBondEndpoint
8164  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
8165  """
8166  this = _IMP_atom.new_CHARMMBondEndpoint(*args)
8167  try: self.this.append(this)
8168  except: self.this = this
8169  def get_atom_name(self):
8170  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
8171  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
8172 
8173  def get_atom(self, *args):
8174  """
8175  get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue,
8176  std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom
8177  """
8178  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, *args)
8179 
8180  def show(self, *args):
8181  """
8182  show(CHARMMBondEndpoint self, _ostream out=std::cout)
8183  show(CHARMMBondEndpoint self)
8184  """
8185  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
8186 
8187  def __str__(self):
8188  """__str__(CHARMMBondEndpoint self) -> std::string"""
8189  return _IMP_atom.CHARMMBondEndpoint___str__(self)
8190 
8191  def __repr__(self):
8192  """__repr__(CHARMMBondEndpoint self) -> std::string"""
8193  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
8194 
8195  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
8196  __del__ = lambda self : None;
8197 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
8198 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
8199 
8200 class CHARMMDihedral(_object):
8201  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class"""
8202  __swig_setmethods__ = {}
8203  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedral, name, value)
8204  __swig_getmethods__ = {}
8205  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedral, name)
8206  __repr__ = _swig_repr
8207  def __init__(self, *args):
8208  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
8209  this = _IMP_atom.new_CHARMMDihedral(*args)
8210  try: self.this.append(this)
8211  except: self.this = this
8212  def get_endpoint(self, *args):
8213  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
8214  return _IMP_atom.CHARMMDihedral_get_endpoint(self, *args)
8215 
8216  def get_contains_atom(self, *args):
8217  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
8218  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, *args)
8219 
8220  def show(self, *args):
8221  """
8222  show(CHARMMDihedral self, _ostream out=std::cout)
8223  show(CHARMMDihedral self)
8224  """
8225  return _IMP_atom.CHARMMDihedral_show(self, *args)
8226 
8227  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
8228  __del__ = lambda self : None;
8229 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
8230 CHARMMDihedral_swigregister(CHARMMDihedral)
8231 
8232 class CHARMMInternalCoordinate(CHARMMDihedral):
8233  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class"""
8234  __swig_setmethods__ = {}
8235  for _s in [CHARMMDihedral]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8236  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMInternalCoordinate, name, value)
8237  __swig_getmethods__ = {}
8238  for _s in [CHARMMDihedral]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8239  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMInternalCoordinate, name)
8240  def __init__(self, *args):
8241  """
8242  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral,
8243  float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
8244  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::base::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance,
8245  float first_angle, float dihedral, float second_angle, float second_distance,
8246  bool improper) -> CHARMMInternalCoordinate
8247  """
8248  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
8249  try: self.this.append(this)
8250  except: self.this = this
8251  def get_first_distance(self):
8252  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
8253  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
8254 
8255  def get_second_distance(self):
8256  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
8257  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
8258 
8259  def get_first_angle(self):
8260  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
8261  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
8262 
8263  def get_second_angle(self):
8264  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
8265  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
8266 
8267  def get_dihedral(self):
8268  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
8269  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
8270 
8271  def get_improper(self):
8272  """get_improper(CHARMMInternalCoordinate self) -> bool"""
8273  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
8274 
8275  def show(self, *args):
8276  """
8277  show(CHARMMInternalCoordinate self, _ostream out=std::cout)
8278  show(CHARMMInternalCoordinate self)
8279  """
8280  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
8281 
8282  def __str__(self):
8283  """__str__(CHARMMInternalCoordinate self) -> std::string"""
8284  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
8285 
8286  def __repr__(self):
8287  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
8288  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
8289 
8290  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
8291  __del__ = lambda self : None;
8292 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
8293 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
8294 
8295 class CHARMMResidueTopologyBase(IMP.base.Object):
8296  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class"""
8297  __swig_setmethods__ = {}
8298  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8299  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopologyBase, name, value)
8300  __swig_getmethods__ = {}
8301  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8302  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopologyBase, name)
8303  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
8304  def get_type(self):
8305  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
8306  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
8307 
8308  def get_number_of_atoms(self):
8309  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
8310  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
8311 
8312  def add_atom(self, *args):
8313  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
8314  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, *args)
8315 
8316  def get_atom(self, *args):
8317  """
8318  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
8319  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
8320  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
8321  """
8322  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
8323 
8324  def get_number_of_bonds(self):
8325  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
8326  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
8327 
8328  def add_bond(self, *args):
8329  """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
8330  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, *args)
8331 
8332  def get_number_of_angles(self):
8333  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
8334  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
8335 
8336  def add_angle(self, *args):
8337  """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
8338  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, *args)
8339 
8340  def get_number_of_dihedrals(self):
8341  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
8342  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
8343 
8344  def add_dihedral(self, *args):
8345  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8346  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, *args)
8347 
8348  def get_number_of_impropers(self):
8349  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
8350  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
8351 
8352  def add_improper(self, *args):
8353  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8354  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, *args)
8355 
8356  def get_number_of_internal_coordinates(self):
8357  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
8358  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
8359 
8360  def add_internal_coordinate(self, *args):
8361  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
8362  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, *args)
8363 
8364  def get_internal_coordinate(self, *args):
8365  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
8366  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, *args)
8367 
8368  def get_bond(self, *args):
8369  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
8370  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, *args)
8371 
8372  def get_angle(self, *args):
8373  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
8374  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, *args)
8375 
8376  def get_dihedral(self, *args):
8377  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8378  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, *args)
8379 
8380  def get_improper(self, *args):
8381  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8382  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, *args)
8383 
8384  def get_version_info(self):
8385  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
8386  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
8387 
8388  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
8389  __del__ = lambda self : None;
8390  def __str__(self):
8391  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
8392  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
8393 
8394  def __repr__(self):
8395  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
8396  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
8397 
8398  def get_from(o):
8399  return _object_cast_to_CHARMMResidueTopologyBase(o)
8400  get_from = staticmethod(get_from)
8401 
8402 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
8403 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
8404 
8405 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
8406  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class"""
8407  __swig_setmethods__ = {}
8408  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8409  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMIdealResidueTopology, name, value)
8410  __swig_getmethods__ = {}
8411  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8412  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMIdealResidueTopology, name)
8413  def __init__(self, *args):
8414  """
8415  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
8416  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
8417  """
8418  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
8419  try: self.this.append(this)
8420  except: self.this = this
8421  def remove_atom(self, *args):
8422  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
8423  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, *args)
8424 
8425  def set_default_first_patch(self, *args):
8426  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8427  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, *args)
8428 
8429  def set_default_last_patch(self, *args):
8430  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8431  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, *args)
8432 
8433  def get_default_first_patch(self):
8434  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
8435  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
8436 
8437  def get_default_last_patch(self):
8438  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
8439  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
8440 
8441  __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
8442  __del__ = lambda self : None;
8443  def __str__(self):
8444  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
8445  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
8446 
8447  def __repr__(self):
8448  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
8449  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
8450 
8451  def get_from(o):
8452  return _object_cast_to_CHARMMIdealResidueTopology(o)
8453  get_from = staticmethod(get_from)
8454 
8455 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
8456 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
8457 
8458 class CHARMMPatch(CHARMMResidueTopologyBase):
8459  """Proxy of C++ IMP::atom::CHARMMPatch class"""
8460  __swig_setmethods__ = {}
8461  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8462  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMPatch, name, value)
8463  __swig_getmethods__ = {}
8464  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8465  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMPatch, name)
8466  def __init__(self, *args):
8467  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
8468  this = _IMP_atom.new_CHARMMPatch(*args)
8469  try: self.this.append(this)
8470  except: self.this = this
8471  def add_removed_atom(self, *args):
8472  """add_removed_atom(CHARMMPatch self, std::string name)"""
8473  return _IMP_atom.CHARMMPatch_add_removed_atom(self, *args)
8474 
8475  def get_number_of_removed_atoms(self):
8476  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
8477  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
8478 
8479  def get_removed_atom(self, *args):
8480  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
8481  return _IMP_atom.CHARMMPatch_get_removed_atom(self, *args)
8482 
8483  def apply(self, *args):
8484  """
8485  apply(CHARMMPatch self, CHARMMResidueTopology res)
8486  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
8487  """
8488  return _IMP_atom.CHARMMPatch_apply(self, *args)
8489 
8490  __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
8491  __del__ = lambda self : None;
8492  def __str__(self):
8493  """__str__(CHARMMPatch self) -> std::string"""
8494  return _IMP_atom.CHARMMPatch___str__(self)
8495 
8496  def __repr__(self):
8497  """__repr__(CHARMMPatch self) -> std::string"""
8498  return _IMP_atom.CHARMMPatch___repr__(self)
8499 
8500  def get_from(o):
8501  return _object_cast_to_CHARMMPatch(o)
8502  get_from = staticmethod(get_from)
8503 
8504 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
8505 CHARMMPatch_swigregister(CHARMMPatch)
8506 
8507 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
8508  """Proxy of C++ IMP::atom::CHARMMResidueTopology class"""
8509  __swig_setmethods__ = {}
8510  for _s in [CHARMMIdealResidueTopology]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8511  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopology, name, value)
8512  __swig_getmethods__ = {}
8513  for _s in [CHARMMIdealResidueTopology]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8514  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopology, name)
8515  def __init__(self, *args):
8516  """
8517  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
8518  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
8519  """
8520  this = _IMP_atom.new_CHARMMResidueTopology(*args)
8521  try: self.this.append(this)
8522  except: self.this = this
8523  def get_patched(self):
8524  """get_patched(CHARMMResidueTopology self) -> bool"""
8525  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
8526 
8527  def set_patched(self, *args):
8528  """set_patched(CHARMMResidueTopology self, bool patched)"""
8529  return _IMP_atom.CHARMMResidueTopology_set_patched(self, *args)
8530 
8531  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
8532  __del__ = lambda self : None;
8533  def __str__(self):
8534  """__str__(CHARMMResidueTopology self) -> std::string"""
8535  return _IMP_atom.CHARMMResidueTopology___str__(self)
8536 
8537  def __repr__(self):
8538  """__repr__(CHARMMResidueTopology self) -> std::string"""
8539  return _IMP_atom.CHARMMResidueTopology___repr__(self)
8540 
8541  def get_from(o):
8542  return _object_cast_to_CHARMMResidueTopology(o)
8543  get_from = staticmethod(get_from)
8544 
8545 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
8546 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
8547 
8548 class CHARMMAtom(Atom):
8549  """Proxy of C++ IMP::atom::CHARMMAtom class"""
8550  __swig_setmethods__ = {}
8551  for _s in [Atom]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8552  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtom, name, value)
8553  __swig_getmethods__ = {}
8554  for _s in [Atom]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8555  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtom, name)
8556  def __init__(self, *args):
8557  """
8558  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
8559  __init__(IMP::atom::CHARMMAtom self, Model m, ::IMP::kernel::ParticleIndex id) -> CHARMMAtom
8560  __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
8561  """
8562  this = _IMP_atom.new_CHARMMAtom(*args)
8563  try: self.this.append(this)
8564  except: self.this = this
8565  def decorate_particle(*args):
8566  """decorate_particle(Particle p) -> CHARMMAtom"""
8567  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
8568 
8569  if _newclass:decorate_particle = staticmethod(decorate_particle)
8570  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
8571  def particle_is_instance(*args):
8572  """
8573  particle_is_instance(Particle p) -> bool
8574  particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
8575  """
8576  return _IMP_atom.CHARMMAtom_particle_is_instance(*args)
8577 
8578  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
8579  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
8580  def show(self, *args):
8581  """
8582  show(CHARMMAtom self, _ostream out=std::cout)
8583  show(CHARMMAtom self)
8584  """
8585  return _IMP_atom.CHARMMAtom_show(self, *args)
8586 
8587  def setup_particle(*args):
8588  """
8589  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
8590  setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
8591  """
8592  return _IMP_atom.CHARMMAtom_setup_particle(*args)
8593 
8594  if _newclass:setup_particle = staticmethod(setup_particle)
8595  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
8596  def get_charmm_type(self):
8597  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
8598  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
8599 
8600  def set_charmm_type(self, *args):
8601  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
8602  return _IMP_atom.CHARMMAtom_set_charmm_type(self, *args)
8603 
8604  def get_is_setup(*args):
8605  """
8606  get_is_setup(_ParticleAdaptor p) -> bool
8607  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
8608  """
8609  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
8610 
8611  if _newclass:get_is_setup = staticmethod(get_is_setup)
8612  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
8613  def get_charmm_type_key():
8614  """get_charmm_type_key() -> StringKey"""
8615  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
8616 
8617  if _newclass:get_charmm_type_key = staticmethod(get_charmm_type_key)
8618  __swig_getmethods__["get_charmm_type_key"] = lambda x: get_charmm_type_key
8619  def add_attribute(self, *args):
8620  """
8621  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
8622  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8623  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
8624  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
8625  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8626  add_attribute(CHARMMAtom self, ObjectKey a0, IMP::Object * a1)
8627  """
8628  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
8629 
8630  def get_value(self, *args):
8631  """
8632  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
8633  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
8634  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
8635  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
8636  get_value(CHARMMAtom self, ObjectKey a0) -> IMP::Object *
8637  """
8638  return _IMP_atom.CHARMMAtom_get_value(self, *args)
8639 
8640  def set_value(self, *args):
8641  """
8642  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8643  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
8644  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
8645  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8646  set_value(CHARMMAtom self, ObjectKey a0, IMP::Object * a1)
8647  """
8648  return _IMP_atom.CHARMMAtom_set_value(self, *args)
8649 
8650  def remove_attribute(self, *args):
8651  """
8652  remove_attribute(CHARMMAtom self, FloatKey a0)
8653  remove_attribute(CHARMMAtom self, IntKey a0)
8654  remove_attribute(CHARMMAtom self, StringKey a0)
8655  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
8656  remove_attribute(CHARMMAtom self, ObjectKey a0)
8657  """
8658  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
8659 
8660  def has_attribute(self, *args):
8661  """
8662  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
8663  has_attribute(CHARMMAtom self, IntKey a0) -> bool
8664  has_attribute(CHARMMAtom self, StringKey a0) -> bool
8665  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
8666  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
8667  """
8668  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
8669 
8670  def get_derivative(self, *args):
8671  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
8672  return _IMP_atom.CHARMMAtom_get_derivative(self, *args)
8673 
8674  def get_name(self):
8675  """get_name(CHARMMAtom self) -> std::string"""
8676  return _IMP_atom.CHARMMAtom_get_name(self)
8677 
8678  def clear_caches(self):
8679  """clear_caches(CHARMMAtom self)"""
8680  return _IMP_atom.CHARMMAtom_clear_caches(self)
8681 
8682  def set_name(self, *args):
8683  """set_name(CHARMMAtom self, std::string a0)"""
8684  return _IMP_atom.CHARMMAtom_set_name(self, *args)
8685 
8686  def set_check_level(self, *args):
8687  """set_check_level(CHARMMAtom self, IMP::base::CheckLevel a0)"""
8688  return _IMP_atom.CHARMMAtom_set_check_level(self, *args)
8689 
8690  def add_to_derivative(self, *args):
8691  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8692  return _IMP_atom.CHARMMAtom_add_to_derivative(self, *args)
8693 
8694  def set_is_optimized(self, *args):
8695  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
8696  return _IMP_atom.CHARMMAtom_set_is_optimized(self, *args)
8697 
8698  def get_is_optimized(self, *args):
8699  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
8700  return _IMP_atom.CHARMMAtom_get_is_optimized(self, *args)
8701 
8702  def get_check_level(self):
8703  """get_check_level(CHARMMAtom self) -> IMP::base::CheckLevel"""
8704  return _IMP_atom.CHARMMAtom_get_check_level(self)
8705 
8706  def __eq__(self, *args):
8707  """
8708  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
8709  __eq__(CHARMMAtom self, Particle d) -> bool
8710  """
8711  return _IMP_atom.CHARMMAtom___eq__(self, *args)
8712 
8713  def __ne__(self, *args):
8714  """
8715  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
8716  __ne__(CHARMMAtom self, Particle d) -> bool
8717  """
8718  return _IMP_atom.CHARMMAtom___ne__(self, *args)
8719 
8720  def __le__(self, *args):
8721  """
8722  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
8723  __le__(CHARMMAtom self, Particle d) -> bool
8724  """
8725  return _IMP_atom.CHARMMAtom___le__(self, *args)
8726 
8727  def __lt__(self, *args):
8728  """
8729  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
8730  __lt__(CHARMMAtom self, Particle d) -> bool
8731  """
8732  return _IMP_atom.CHARMMAtom___lt__(self, *args)
8733 
8734  def __ge__(self, *args):
8735  """
8736  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
8737  __ge__(CHARMMAtom self, Particle d) -> bool
8738  """
8739  return _IMP_atom.CHARMMAtom___ge__(self, *args)
8740 
8741  def __gt__(self, *args):
8742  """
8743  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
8744  __gt__(CHARMMAtom self, Particle d) -> bool
8745  """
8746  return _IMP_atom.CHARMMAtom___gt__(self, *args)
8747 
8748  def __str__(self):
8749  """__str__(CHARMMAtom self) -> std::string"""
8750  return _IMP_atom.CHARMMAtom___str__(self)
8751 
8752  def __repr__(self):
8753  """__repr__(CHARMMAtom self) -> std::string"""
8754  return _IMP_atom.CHARMMAtom___repr__(self)
8755 
8756  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
8757  __del__ = lambda self : None;
8758 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
8759 CHARMMAtom_swigregister(CHARMMAtom)
8760 
8761 def CHARMMAtom_decorate_particle(*args):
8762  """CHARMMAtom_decorate_particle(Particle p) -> CHARMMAtom"""
8763  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
8764 
8765 def CHARMMAtom_particle_is_instance(*args):
8766  """
8767  particle_is_instance(Particle p) -> bool
8768  CHARMMAtom_particle_is_instance(Model m, IMP::kernel::ParticleIndex pi) -> bool
8769  """
8770  return _IMP_atom.CHARMMAtom_particle_is_instance(*args)
8771 
8772 def CHARMMAtom_setup_particle(*args):
8773  """
8774  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
8775  CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
8776  """
8777  return _IMP_atom.CHARMMAtom_setup_particle(*args)
8778 
8779 def CHARMMAtom_get_is_setup(*args):
8780  """
8781  get_is_setup(_ParticleAdaptor p) -> bool
8782  CHARMMAtom_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
8783  """
8784  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
8785 
8786 def CHARMMAtom_get_charmm_type_key():
8787  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
8788  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
8789 
8790 
8791 def get_charmm_untyped_atoms(*args):
8792  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
8793  return _IMP_atom.get_charmm_untyped_atoms(*args)
8794 
8795 def remove_charmm_untyped_atoms(*args):
8796  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
8797  return _IMP_atom.remove_charmm_untyped_atoms(*args)
8798 class CHARMMBondParameters(_object):
8799  """Proxy of C++ IMP::atom::CHARMMBondParameters class"""
8800  __swig_setmethods__ = {}
8801  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondParameters, name, value)
8802  __swig_getmethods__ = {}
8803  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondParameters, name)
8804  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_set
8805  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_get
8806  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
8807  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_set
8808  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_get
8809  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
8810  def __init__(self):
8811  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
8812  this = _IMP_atom.new_CHARMMBondParameters()
8813  try: self.this.append(this)
8814  except: self.this = this
8815  def show(self, *args):
8816  """
8817  show(CHARMMBondParameters self, _ostream out=std::cout)
8818  show(CHARMMBondParameters self)
8819  """
8820  return _IMP_atom.CHARMMBondParameters_show(self, *args)
8821 
8822  def __str__(self):
8823  """__str__(CHARMMBondParameters self) -> std::string"""
8824  return _IMP_atom.CHARMMBondParameters___str__(self)
8825 
8826  def __repr__(self):
8827  """__repr__(CHARMMBondParameters self) -> std::string"""
8828  return _IMP_atom.CHARMMBondParameters___repr__(self)
8829 
8830  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
8831  __del__ = lambda self : None;
8832 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
8833 CHARMMBondParameters_swigregister(CHARMMBondParameters)
8834 
8835 class CHARMMDihedralParameters(_object):
8836  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class"""
8837  __swig_setmethods__ = {}
8838  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedralParameters, name, value)
8839  __swig_getmethods__ = {}
8840  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedralParameters, name)
8841  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_set
8842  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_get
8843  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
8844  __swig_setmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_set
8845  __swig_getmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_get
8846  if _newclass:multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
8847  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_set
8848  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_get
8849  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
8850  def __init__(self):
8851  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
8852  this = _IMP_atom.new_CHARMMDihedralParameters()
8853  try: self.this.append(this)
8854  except: self.this = this
8855  def show(self, *args):
8856  """
8857  show(CHARMMDihedralParameters self, _ostream out=std::cout)
8858  show(CHARMMDihedralParameters self)
8859  """
8860  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
8861 
8862  def __str__(self):
8863  """__str__(CHARMMDihedralParameters self) -> std::string"""
8864  return _IMP_atom.CHARMMDihedralParameters___str__(self)
8865 
8866  def __repr__(self):
8867  """__repr__(CHARMMDihedralParameters self) -> std::string"""
8868  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
8869 
8870  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
8871  __del__ = lambda self : None;
8872 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
8873 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
8874 
8875 class CHARMMParameters(ForceFieldParameters):
8876  """Proxy of C++ IMP::atom::CHARMMParameters class"""
8877  __swig_setmethods__ = {}
8878  for _s in [ForceFieldParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8879  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMParameters, name, value)
8880  __swig_getmethods__ = {}
8881  for _s in [ForceFieldParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8882  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMParameters, name)
8883  def __init__(self, *args):
8884  """
8885  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters
8886  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput()) -> CHARMMParameters
8887  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
8888  """
8889  this = _IMP_atom.new_CHARMMParameters(*args)
8890  try: self.this.append(this)
8891  except: self.this = this
8892  def add_residue_topology(self, *args):
8893  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
8894  return _IMP_atom.CHARMMParameters_add_residue_topology(self, *args)
8895 
8896  def get_residue_topology(self, *args):
8897  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
8898  return _IMP_atom.CHARMMParameters_get_residue_topology(self, *args)
8899 
8900  def add_patch(self, *args):
8901  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
8902  return _IMP_atom.CHARMMParameters_add_patch(self, *args)
8903 
8904  def get_patch(self, *args):
8905  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
8906  return _IMP_atom.CHARMMParameters_get_patch(self, *args)
8907 
8908  def create_topology(self, *args):
8909  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
8910  return _IMP_atom.CHARMMParameters_create_topology(self, *args)
8911 
8912  def get_bond_parameters(self, *args):
8913  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
8914  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, *args)
8915 
8916  def get_angle_parameters(self, *args):
8917  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
8918  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, *args)
8919 
8920  def get_dihedral_parameters(self, *args):
8921  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
8922  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, *args)
8923 
8924  def get_improper_parameters(self, *args):
8925  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
8926  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, *args)
8927 
8928  def create_angles(self, *args):
8929  """create_angles(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
8930  return _IMP_atom.CHARMMParameters_create_angles(self, *args)
8931 
8932  def create_dihedrals(self, *args):
8933  """create_dihedrals(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
8934  return _IMP_atom.CHARMMParameters_create_dihedrals(self, *args)
8935 
8936  def get_version_info(self):
8937  """get_version_info(CHARMMParameters self) -> VersionInfo"""
8938  return _IMP_atom.CHARMMParameters_get_version_info(self)
8939 
8940  def do_show(self, *args):
8941  """do_show(CHARMMParameters self, _ostream out)"""
8942  return _IMP_atom.CHARMMParameters_do_show(self, *args)
8943 
8944  __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
8945  __del__ = lambda self : None;
8946  def __str__(self):
8947  """__str__(CHARMMParameters self) -> std::string"""
8948  return _IMP_atom.CHARMMParameters___str__(self)
8949 
8950  def __repr__(self):
8951  """__repr__(CHARMMParameters self) -> std::string"""
8952  return _IMP_atom.CHARMMParameters___repr__(self)
8953 
8954  def get_from(o):
8955  return _object_cast_to_CHARMMParameters(o)
8956  get_from = staticmethod(get_from)
8957 
8958 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
8959 CHARMMParameters_swigregister(CHARMMParameters)
8960 
8961 
8963  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
8964  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
8965 
8967  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
8968  return _IMP_atom.get_all_atom_CHARMM_parameters()
8969 class CHARMMSegmentTopology(IMP.base.Object):
8970  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class"""
8971  __swig_setmethods__ = {}
8972  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8973  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMSegmentTopology, name, value)
8974  __swig_getmethods__ = {}
8975  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8976  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMSegmentTopology, name)
8977  def remove_residue(self, *args):
8978  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
8979  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, *args)
8980 
8981  def remove_residues(self, *args):
8982  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
8983  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, *args)
8984 
8985  def set_residues(self, *args):
8986  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
8987  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, *args)
8988 
8989  def set_residues_order(self, *args):
8990  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
8991  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, *args)
8992 
8993  def add_residue(self, *args):
8994  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
8995  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, *args)
8996 
8997  def add_residues(self, *args):
8998  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
8999  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, *args)
9000 
9001  def clear_residues(self):
9002  """clear_residues(CHARMMSegmentTopology self)"""
9003  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
9004 
9005  def get_number_of_residues(self):
9006  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
9007  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
9008 
9009  def get_has_residues(self):
9010  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
9011  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
9012 
9013  def get_residue(self, *args):
9014  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
9015  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, *args)
9016 
9017  def get_residues(self):
9018  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
9019  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
9020 
9021  def reserve_residues(self, *args):
9022  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
9023  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, *args)
9024 
9025  def get_version_info(self):
9026  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
9027  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
9028 
9029  __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
9030  __del__ = lambda self : None;
9031  def __init__(self, name="CHARMM segment topology %1%"):
9032  """
9033  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology
9034  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
9035  """
9036  this = _IMP_atom.new_CHARMMSegmentTopology(name)
9037  try: self.this.append(this)
9038  except: self.this = this
9039  def apply_default_patches(self, *args):
9040  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
9041  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, *args)
9042 
9043  def __str__(self):
9044  """__str__(CHARMMSegmentTopology self) -> std::string"""
9045  return _IMP_atom.CHARMMSegmentTopology___str__(self)
9046 
9047  def __repr__(self):
9048  """__repr__(CHARMMSegmentTopology self) -> std::string"""
9049  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
9050 
9051  def get_from(o):
9052  return _object_cast_to_CHARMMSegmentTopology(o)
9053  get_from = staticmethod(get_from)
9054 
9055 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
9056 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
9057 
9058 class CHARMMTopology(IMP.base.Object):
9059  """Proxy of C++ IMP::atom::CHARMMTopology class"""
9060  __swig_setmethods__ = {}
9061  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9062  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMTopology, name, value)
9063  __swig_getmethods__ = {}
9064  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9065  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMTopology, name)
9066  def __init__(self, *args):
9067  """
9068  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology
9069  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
9070  """
9071  this = _IMP_atom.new_CHARMMTopology(*args)
9072  try: self.this.append(this)
9073  except: self.this = this
9074  def get_parameters(self):
9075  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
9076  return _IMP_atom.CHARMMTopology_get_parameters(self)
9077 
9078  def add_sequence(self, *args):
9079  """add_sequence(CHARMMTopology self, std::string sequence)"""
9080  return _IMP_atom.CHARMMTopology_add_sequence(self, *args)
9081 
9082  def apply_default_patches(self):
9083  """apply_default_patches(CHARMMTopology self)"""
9084  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
9085 
9086  def create_hierarchy(self, *args):
9087  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
9088  return _IMP_atom.CHARMMTopology_create_hierarchy(self, *args)
9089 
9090  def add_atom_types(self, *args):
9091  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
9092  return _IMP_atom.CHARMMTopology_add_atom_types(self, *args)
9093 
9094  def add_coordinates(self, *args):
9095  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
9096  return _IMP_atom.CHARMMTopology_add_coordinates(self, *args)
9097 
9098  def add_missing_atoms(self, *args):
9099  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
9100  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, *args)
9101 
9102  def setup_hierarchy(self, *args):
9103  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
9104  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, *args)
9105 
9106  def add_charges(self, *args):
9107  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
9108  return _IMP_atom.CHARMMTopology_add_charges(self, *args)
9109 
9110  def add_bonds(self, *args):
9111  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9112  return _IMP_atom.CHARMMTopology_add_bonds(self, *args)
9113 
9114  def add_dihedrals(self, *args):
9115  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9116  return _IMP_atom.CHARMMTopology_add_dihedrals(self, *args)
9117 
9118  def add_impropers(self, *args):
9119  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
9120  return _IMP_atom.CHARMMTopology_add_impropers(self, *args)
9121 
9122  def remove_segment(self, *args):
9123  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
9124  return _IMP_atom.CHARMMTopology_remove_segment(self, *args)
9125 
9126  def remove_segments(self, *args):
9127  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
9128  return _IMP_atom.CHARMMTopology_remove_segments(self, *args)
9129 
9130  def set_segments(self, *args):
9131  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
9132  return _IMP_atom.CHARMMTopology_set_segments(self, *args)
9133 
9134  def set_segments_order(self, *args):
9135  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
9136  return _IMP_atom.CHARMMTopology_set_segments_order(self, *args)
9137 
9138  def add_segment(self, *args):
9139  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
9140  return _IMP_atom.CHARMMTopology_add_segment(self, *args)
9141 
9142  def add_segments(self, *args):
9143  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
9144  return _IMP_atom.CHARMMTopology_add_segments(self, *args)
9145 
9146  def clear_segments(self):
9147  """clear_segments(CHARMMTopology self)"""
9148  return _IMP_atom.CHARMMTopology_clear_segments(self)
9149 
9150  def get_number_of_segments(self):
9151  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
9152  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
9153 
9154  def get_has_segments(self):
9155  """get_has_segments(CHARMMTopology self) -> bool"""
9156  return _IMP_atom.CHARMMTopology_get_has_segments(self)
9157 
9158  def get_segment(self, *args):
9159  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
9160  return _IMP_atom.CHARMMTopology_get_segment(self, *args)
9161 
9162  def get_segments(self):
9163  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
9164  return _IMP_atom.CHARMMTopology_get_segments(self)
9165 
9166  def reserve_segments(self, *args):
9167  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
9168  return _IMP_atom.CHARMMTopology_reserve_segments(self, *args)
9169 
9170  def get_version_info(self):
9171  """get_version_info(CHARMMTopology self) -> VersionInfo"""
9172  return _IMP_atom.CHARMMTopology_get_version_info(self)
9173 
9174  __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
9175  __del__ = lambda self : None;
9176  def __str__(self):
9177  """__str__(CHARMMTopology self) -> std::string"""
9178  return _IMP_atom.CHARMMTopology___str__(self)
9179 
9180  def __repr__(self):
9181  """__repr__(CHARMMTopology self) -> std::string"""
9182  return _IMP_atom.CHARMMTopology___repr__(self)
9183 
9184  def get_from(o):
9185  return _object_cast_to_CHARMMTopology(o)
9186  get_from = staticmethod(get_from)
9187 
9188 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
9189 CHARMMTopology_swigregister(CHARMMTopology)
9190 
9191 class CHARMMStereochemistryRestraint(IMP.kernel.Restraint):
9192  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class"""
9193  __swig_setmethods__ = {}
9194  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9195  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMStereochemistryRestraint, name, value)
9196  __swig_getmethods__ = {}
9197  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9198  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMStereochemistryRestraint, name)
9199  def __init__(self, *args):
9200  """__init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint"""
9201  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
9202  try: self.this.append(this)
9203  except: self.this = this
9204  def get_pair_filter(self):
9205  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
9206  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
9207 
9208  def do_get_inputs(self):
9209  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::kernel::ModelObjectsTemp"""
9210  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
9211 
9212  def get_version_info(self):
9213  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
9214  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
9215 
9216  __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
9217  __del__ = lambda self : None;
9218  def __str__(self):
9219  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
9220  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
9221 
9222  def __repr__(self):
9223  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
9224  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
9225 
9226  def get_from(o):
9227  return _object_cast_to_CHARMMStereochemistryRestraint(o)
9228  get_from = staticmethod(get_from)
9229 
9230 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
9231 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
9232 
9233 
9234 def add_bonds(*args):
9235  """
9236  add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
9237  add_bonds(Hierarchy d)
9238  """
9239  return _IMP_atom.add_bonds(*args)
9240 
9241 def add_radii(*args):
9242  """
9243  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(),
9244  FloatKey radius_key=FloatKey("radius"))
9245  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
9246  add_radii(Hierarchy d)
9247  """
9248  return _IMP_atom.add_radii(*args)
9249 ALBER = _IMP_atom.ALBER
9250 HARPAZ = _IMP_atom.HARPAZ
9251 ANDERSSON = _IMP_atom.ANDERSSON
9252 TSAI = _IMP_atom.TSAI
9253 QUILLIN = _IMP_atom.QUILLIN
9254 SQUIRE = _IMP_atom.SQUIRE
9255 
9257  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
9258  return _IMP_atom.get_protein_density_from_reference(*args)
9259 
9260 def get_volume_from_mass(*args):
9261  """
9262  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double
9263  get_volume_from_mass(double m) -> double
9264  """
9265  return _IMP_atom.get_volume_from_mass(*args)
9266 
9267 def get_mass_from_volume(*args):
9268  """
9269  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double
9270  get_mass_from_volume(double v) -> double
9271  """
9272  return _IMP_atom.get_mass_from_volume(*args)
9273 
9275  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
9276  return _IMP_atom.get_mass_from_number_of_residues(*args)
9277 
9278 def get_volume_from_residue_type(*args):
9279  """get_volume_from_residue_type(ResidueType rt) -> double"""
9280  return _IMP_atom.get_volume_from_residue_type(*args)
9281 
9282 def get_molarity(*args):
9283  """get_molarity(double n, double volume) -> double"""
9284  return _IMP_atom.get_molarity(*args)
9285 
9286 def get_kd(*args):
9287  """get_kd(double na, double nb, double nab, double volume) -> double"""
9288  return _IMP_atom.get_kd(*args)
9289 
9291  """get_einstein_diffusion_coefficient(double r) -> double"""
9292  return _IMP_atom.get_einstein_diffusion_coefficient(*args)
9293 
9295  """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
9296  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(*args)
9297 
9298 def get_diffusion_length(*args):
9299  """
9300  get_diffusion_length(double D, double t) -> double
9301  get_diffusion_length(double D, double force, double t, double temp=273) -> double
9302  get_diffusion_length(double D, double force, double t) -> double
9303  """
9304  return _IMP_atom.get_diffusion_length(*args)
9305 
9306 def get_diffusion_angle(*args):
9307  """get_diffusion_angle(double D, double dtfs) -> double"""
9308  return _IMP_atom.get_diffusion_angle(*args)
9309 
9310 def get_diffusion_coefficient(*args):
9311  """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
9312  return _IMP_atom.get_diffusion_coefficient(*args)
9313 
9315  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
9316  return _IMP_atom.get_rotational_diffusion_coefficient(*args)
9317 class EzRestraint(IMP.kernel.Restraint):
9318  """Proxy of C++ IMP::atom::EzRestraint class"""
9319  __swig_setmethods__ = {}
9320  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9321  __setattr__ = lambda self, name, value: _swig_setattr(self, EzRestraint, name, value)
9322  __swig_getmethods__ = {}
9323  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9324  __getattr__ = lambda self, name: _swig_getattr(self, EzRestraint, name)
9325  def __init__(self, *args):
9326  """__init__(IMP::atom::EzRestraint self, IMP::kernel::Particles ps) -> EzRestraint"""
9327  this = _IMP_atom.new_EzRestraint(*args)
9328  try: self.this.append(this)
9329  except: self.this = this
9330  def get_version_info(self):
9331  """get_version_info(EzRestraint self) -> VersionInfo"""
9332  return _IMP_atom.EzRestraint_get_version_info(self)
9333 
9334  __swig_destroy__ = _IMP_atom.delete_EzRestraint
9335  __del__ = lambda self : None;
9336  def __str__(self):
9337  """__str__(EzRestraint self) -> std::string"""
9338  return _IMP_atom.EzRestraint___str__(self)
9339 
9340  def __repr__(self):
9341  """__repr__(EzRestraint self) -> std::string"""
9342  return _IMP_atom.EzRestraint___repr__(self)
9343 
9344  def get_from(o):
9345  return _object_cast_to_EzRestraint(o)
9346  get_from = staticmethod(get_from)
9347 
9348 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
9349 EzRestraint_swigregister(EzRestraint)
9350 
9351 
9352 def create_protein(*args):
9353  """
9354  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0,
9355  double volume=-1, bool ismol=True) -> Hierarchy
9356  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0,
9357  double volume=-1) -> Hierarchy
9358  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0) -> Hierarchy
9359  create_protein(Model m, std::string name, double resolution, int number_of_residues) -> Hierarchy
9360  create_protein(Model m, std::string name, double resolution, IMP::Ints const domain_boundaries) -> Hierarchy
9361  """
9362  return _IMP_atom.create_protein(*args)
9363 
9365  """
9366  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
9367  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
9368  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
9369  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
9370  """
9371  return _IMP_atom.create_simplified_along_backbone(*args)
9372 
9373 def get_molecule_name(*args):
9374  """get_molecule_name(Hierarchy h) -> std::string"""
9375  return _IMP_atom.get_molecule_name(*args)
9376 
9377 def get_residue_indexes(*args):
9378  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
9379  return _IMP_atom.get_residue_indexes(*args)
9380 
9381 def get_residue_type(*args):
9382  """
9383  get_residue_type(char c) -> ResidueType
9384  get_residue_type(Hierarchy h) -> ResidueType
9385  """
9386  return _IMP_atom.get_residue_type(*args)
9387 
9388 def get_chain_id(*args):
9389  """get_chain_id(Hierarchy h) -> int"""
9390  return _IMP_atom.get_chain_id(*args)
9391 
9392 def get_atom_type(*args):
9393  """get_atom_type(Hierarchy h) -> AtomType"""
9394  return _IMP_atom.get_atom_type(*args)
9395 
9396 def get_domain_name(*args):
9397  """get_domain_name(Hierarchy h) -> std::string"""
9398  return _IMP_atom.get_domain_name(*args)
9399 
9400 def get_copy_index(*args):
9401  """get_copy_index(Hierarchy h) -> int"""
9402  return _IMP_atom.get_copy_index(*args)
9403 
9405  """
9406  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
9407  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
9408  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
9409  """
9410  return _IMP_atom.create_excluded_volume_restraint(*args)
9411 
9412 def setup_as_approximation(*args):
9413  """
9414  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other, double resolution=-1)
9415  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other)
9416  setup_as_approximation(Hierarchy h, double resolution=-1)
9417  setup_as_approximation(Hierarchy h)
9418  """
9419  return _IMP_atom.setup_as_approximation(*args)
9420 
9421 def transform(*args):
9422  """transform(Hierarchy h, Transformation3D tr)"""
9423  return _IMP_atom.transform(*args)
9424 class _HierarchyTreeVertexIndex(_object):
9425  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class"""
9426  __swig_setmethods__ = {}
9427  __setattr__ = lambda self, name, value: _swig_setattr(self, _HierarchyTreeVertexIndex, name, value)
9428  __swig_getmethods__ = {}
9429  __getattr__ = lambda self, name: _swig_getattr(self, _HierarchyTreeVertexIndex, name)
9430  __repr__ = _swig_repr
9431  def __init__(self):
9432  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
9433  this = _IMP_atom.new__HierarchyTreeVertexIndex()
9434  try: self.this.append(this)
9435  except: self.this = this
9436  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
9437  __del__ = lambda self : None;
9438 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
9439 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
9440 
9441 
9442 def show_as_graphviz(*args):
9443  """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
9444  return _IMP_atom.show_as_graphviz(*args)
9445 
9446 def get_vertex_index(*args):
9447  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
9448  return _IMP_atom.get_vertex_index(*args)
9449 
9450 def get_hierarchy_tree(*args):
9451  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
9452  return _IMP_atom.get_hierarchy_tree(*args)
9453 class HierarchyGeometry(IMP.display.SingletonGeometry):
9454  """Proxy of C++ IMP::atom::HierarchyGeometry class"""
9455  __swig_setmethods__ = {}
9456  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9457  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyGeometry, name, value)
9458  __swig_getmethods__ = {}
9459  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9460  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyGeometry, name)
9461  def __init__(self, *args):
9462  """
9463  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=-1) -> HierarchyGeometry
9464  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
9465  """
9466  this = _IMP_atom.new_HierarchyGeometry(*args)
9467  try: self.this.append(this)
9468  except: self.this = this
9469  def get_version_info(self):
9470  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
9471  return _IMP_atom.HierarchyGeometry_get_version_info(self)
9472 
9473  __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
9474  __del__ = lambda self : None;
9475  def __str__(self):
9476  """__str__(HierarchyGeometry self) -> std::string"""
9477  return _IMP_atom.HierarchyGeometry___str__(self)
9478 
9479  def __repr__(self):
9480  """__repr__(HierarchyGeometry self) -> std::string"""
9481  return _IMP_atom.HierarchyGeometry___repr__(self)
9482 
9483  def get_from(o):
9484  return _object_cast_to_HierarchyGeometry(o)
9485  get_from = staticmethod(get_from)
9486 
9487 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
9488 HierarchyGeometry_swigregister(HierarchyGeometry)
9489 
9490 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
9491  """Proxy of C++ IMP::atom::HierarchiesGeometry class"""
9492  __swig_setmethods__ = {}
9493  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9494  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchiesGeometry, name, value)
9495  __swig_getmethods__ = {}
9496  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9497  __getattr__ = lambda self, name: _swig_getattr(self, HierarchiesGeometry, name)
9498  def __init__(self, *args):
9499  """
9500  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
9501  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
9502  """
9503  this = _IMP_atom.new_HierarchiesGeometry(*args)
9504  try: self.this.append(this)
9505  except: self.this = this
9506  def get_version_info(self):
9507  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
9508  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
9509 
9510  __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
9511  __del__ = lambda self : None;
9512  def __str__(self):
9513  """__str__(HierarchiesGeometry self) -> std::string"""
9514  return _IMP_atom.HierarchiesGeometry___str__(self)
9515 
9516  def __repr__(self):
9517  """__repr__(HierarchiesGeometry self) -> std::string"""
9518  return _IMP_atom.HierarchiesGeometry___repr__(self)
9519 
9520  def get_from(o):
9521  return _object_cast_to_HierarchiesGeometry(o)
9522  get_from = staticmethod(get_from)
9523 
9524 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
9525 HierarchiesGeometry_swigregister(HierarchiesGeometry)
9526 
9527 class DopePairScore(_ADopeBase):
9528  """Proxy of C++ IMP::atom::DopePairScore class"""
9529  __swig_setmethods__ = {}
9530  for _s in [_ADopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9531  __setattr__ = lambda self, name, value: _swig_setattr(self, DopePairScore, name, value)
9532  __swig_getmethods__ = {}
9533  for _s in [_ADopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9534  __getattr__ = lambda self, name: _swig_getattr(self, DopePairScore, name)
9535  def __init__(self, *args):
9536  """
9537  __init__(IMP::atom::DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
9538  __init__(IMP::atom::DopePairScore self) -> DopePairScore
9539  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
9540  """
9541  this = _IMP_atom.new_DopePairScore(*args)
9542  try: self.this.append(this)
9543  except: self.this = this
9544  def __str__(self):
9545  """__str__(DopePairScore self) -> std::string"""
9546  return _IMP_atom.DopePairScore___str__(self)
9547 
9548  def __repr__(self):
9549  """__repr__(DopePairScore self) -> std::string"""
9550  return _IMP_atom.DopePairScore___repr__(self)
9551 
9552  def get_from(o):
9553  return _object_cast_to_DopePairScore(o)
9554  get_from = staticmethod(get_from)
9555 
9556  __swig_destroy__ = _IMP_atom.delete_DopePairScore
9557  __del__ = lambda self : None;
9558 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
9559 DopePairScore_swigregister(DopePairScore)
9560 
9561 
9562 def add_dope_score_data(*args):
9563  """add_dope_score_data(Hierarchy h)"""
9564  return _IMP_atom.add_dope_score_data(*args)
9565 class SameResiduePairFilter(IMP.kernel.PairPredicate):
9566  """Proxy of C++ IMP::atom::SameResiduePairFilter class"""
9567  __swig_setmethods__ = {}
9568  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9569  __setattr__ = lambda self, name, value: _swig_setattr(self, SameResiduePairFilter, name, value)
9570  __swig_getmethods__ = {}
9571  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9572  __getattr__ = lambda self, name: _swig_getattr(self, SameResiduePairFilter, name)
9573  def __init__(self):
9574  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
9575  this = _IMP_atom.new_SameResiduePairFilter()
9576  try: self.this.append(this)
9577  except: self.this = this
9578  def do_get_inputs(self, *args):
9579  """do_get_inputs(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexes const & pis) -> IMP::kernel::ModelObjectsTemp"""
9580  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, *args)
9581 
9582  def get_value(self, *args):
9583  """
9584  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePair const & a) -> int
9585  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
9586  """
9587  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
9588 
9589  def get_value_index(self, *args):
9590  """
9591  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPair const & p) -> int
9592  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
9593  """
9594  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
9595 
9596  def get_version_info(self):
9597  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
9598  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
9599 
9600  __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
9601  __del__ = lambda self : None;
9602  def __str__(self):
9603  """__str__(SameResiduePairFilter self) -> std::string"""
9604  return _IMP_atom.SameResiduePairFilter___str__(self)
9605 
9606  def __repr__(self):
9607  """__repr__(SameResiduePairFilter self) -> std::string"""
9608  return _IMP_atom.SameResiduePairFilter___repr__(self)
9609 
9610  def get_from(o):
9611  return _object_cast_to_SameResiduePairFilter(o)
9612  get_from = staticmethod(get_from)
9613 
9614 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
9615 SameResiduePairFilter_swigregister(SameResiduePairFilter)
9616 
9617 class RemoveRigidMotionOptimizerState(IMP.kernel.OptimizerState):
9618  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class"""
9619  __swig_setmethods__ = {}
9620  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9621  __setattr__ = lambda self, name, value: _swig_setattr(self, RemoveRigidMotionOptimizerState, name, value)
9622  __swig_getmethods__ = {}
9623  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9624  __getattr__ = lambda self, name: _swig_getattr(self, RemoveRigidMotionOptimizerState, name)
9625  def __init__(self, *args):
9626  """
9627  __init__(IMP::atom::RemoveRigidMotionOptimizerState self, IMP::kernel::ParticlesTemp const & pis, unsigned int skip_steps) -> RemoveRigidMotionOptimizerState
9628  __init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState
9629  """
9630  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(*args)
9631  try: self.this.append(this)
9632  except: self.this = this
9633  def set_particles(self, *args):
9634  """set_particles(RemoveRigidMotionOptimizerState self, IMP::kernel::Particles const & pis)"""
9635  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, *args)
9636 
9637  def remove_rigid_motion(self):
9638  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
9639  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
9640 
9641  def get_version_info(self):
9642  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
9643  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
9644 
9645  __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
9646  __del__ = lambda self : None;
9647  def __str__(self):
9648  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
9649  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
9650 
9651  def __repr__(self):
9652  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
9653  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
9654 
9655  def get_from(o):
9656  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
9657  get_from = staticmethod(get_from)
9658 
9659 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
9660 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
9661 
9662 class BerendsenThermostatOptimizerState(IMP.kernel.OptimizerState):
9663  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class"""
9664  __swig_setmethods__ = {}
9665  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9666  __setattr__ = lambda self, name, value: _swig_setattr(self, BerendsenThermostatOptimizerState, name, value)
9667  __swig_getmethods__ = {}
9668  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9669  __getattr__ = lambda self, name: _swig_getattr(self, BerendsenThermostatOptimizerState, name)
9670  def __init__(self, *args):
9671  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
9672  this = _IMP_atom.new_BerendsenThermostatOptimizerState(*args)
9673  try: self.this.append(this)
9674  except: self.this = this
9675  def set_particles(self, *args):
9676  """set_particles(BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9677  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, *args)
9678 
9679  def get_temperature(self):
9680  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
9681  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
9682 
9683  def get_tau(self):
9684  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
9685  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
9686 
9687  def set_temperature(self, *args):
9688  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
9689  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, *args)
9690 
9691  def set_tau(self, *args):
9692  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
9693  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, *args)
9694 
9695  def rescale_velocities(self):
9696  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
9697  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
9698 
9699  def get_version_info(self):
9700  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
9701  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
9702 
9703  __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
9704  __del__ = lambda self : None;
9705  def __str__(self):
9706  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
9707  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
9708 
9709  def __repr__(self):
9710  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
9711  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
9712 
9713  def get_from(o):
9714  return _object_cast_to_BerendsenThermostatOptimizerState(o)
9715  get_from = staticmethod(get_from)
9716 
9717 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
9718 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
9719 
9720 class LangevinThermostatOptimizerState(IMP.kernel.OptimizerState):
9721  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class"""
9722  __swig_setmethods__ = {}
9723  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9724  __setattr__ = lambda self, name, value: _swig_setattr(self, LangevinThermostatOptimizerState, name, value)
9725  __swig_getmethods__ = {}
9726  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9727  __getattr__ = lambda self, name: _swig_getattr(self, LangevinThermostatOptimizerState, name)
9728  def __init__(self, *args):
9729  """
9730  __init__(IMP::atom::LangevinThermostatOptimizerState self, IMP::kernel::ParticlesTemp const & pis, double temperature, double gamma) -> LangevinThermostatOptimizerState
9731  __init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState
9732  """
9733  this = _IMP_atom.new_LangevinThermostatOptimizerState(*args)
9734  try: self.this.append(this)
9735  except: self.this = this
9736  def set_particles(self, *args):
9737  """set_particles(LangevinThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9738  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, *args)
9739 
9740  def get_temperature(self):
9741  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
9742  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
9743 
9744  def get_gamma(self):
9745  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
9746  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
9747 
9748  def set_temperature(self, *args):
9749  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
9750  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, *args)
9751 
9752  def set_gamma(self, *args):
9753  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
9754  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, *args)
9755 
9756  def rescale_velocities(self):
9757  """rescale_velocities(LangevinThermostatOptimizerState self)"""
9758  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
9759 
9760  def get_version_info(self):
9761  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
9762  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
9763 
9764  __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
9765  __del__ = lambda self : None;
9766  def __str__(self):
9767  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
9768  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
9769 
9770  def __repr__(self):
9771  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
9772  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
9773 
9774  def get_from(o):
9775  return _object_cast_to_LangevinThermostatOptimizerState(o)
9776  get_from = staticmethod(get_from)
9777 
9778 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
9779 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
9780 
9781 class PDBSelector(IMP.base.Object):
9782  """Proxy of C++ IMP::atom::PDBSelector class"""
9783  __swig_setmethods__ = {}
9784  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9785  __setattr__ = lambda self, name, value: _swig_setattr(self, PDBSelector, name, value)
9786  __swig_getmethods__ = {}
9787  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9788  __getattr__ = lambda self, name: _swig_getattr(self, PDBSelector, name)
9789  def __init__(self, *args):
9790  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
9791  if self.__class__ == PDBSelector:
9792  _self = None
9793  else:
9794  _self = self
9795  this = _IMP_atom.new_PDBSelector(_self, *args)
9796  try: self.this.append(this)
9797  except: self.this = this
9798  if self.__class__ != PDBSelector:
9799  import IMP.base
9800  IMP.base._director_objects.register(self)
9801 
9802 
9803 
9804  def get_is_selected(self, *args):
9805  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
9806  return _IMP_atom.PDBSelector_get_is_selected(self, *args)
9807 
9808  __swig_destroy__ = _IMP_atom.delete_PDBSelector
9809  __del__ = lambda self : None;
9810  def __str__(self):
9811  """__str__(PDBSelector self) -> std::string"""
9812  return _IMP_atom.PDBSelector___str__(self)
9813 
9814  def __repr__(self):
9815  """__repr__(PDBSelector self) -> std::string"""
9816  return _IMP_atom.PDBSelector___repr__(self)
9817 
9818  def get_from(o):
9819  return _object_cast_to_PDBSelector(o)
9820  get_from = staticmethod(get_from)
9821 
9822  def get_type_name(self):
9823  return self.__class__.__name__
9824  def do_show(self, out):
9825  pass
9826  def get_version_info(self):
9827  if"IMP::atom" == "IMP":
9828  return VersionInfo("python", "0")
9829  else:
9830  return IMP.VersionInfo("python", "0")
9831  def get_from(o):
9832  return _object_cast_to_PDBSelector(o)
9833  get_from = staticmethod(get_from)
9834 
9835  def __disown__(self):
9836  self.this.disown()
9837  _IMP_atom.disown_PDBSelector(self)
9838  return weakref_proxy(self)
9839 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
9840 PDBSelector_swigregister(PDBSelector)
9841 
9842 class NonAlternativePDBSelector(PDBSelector):
9843  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class"""
9844  __swig_setmethods__ = {}
9845  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9846  __setattr__ = lambda self, name, value: _swig_setattr(self, NonAlternativePDBSelector, name, value)
9847  __swig_getmethods__ = {}
9848  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9849  __getattr__ = lambda self, name: _swig_getattr(self, NonAlternativePDBSelector, name)
9850  def __init__(self, name="NonAlternativePDBSelector%1%"):
9851  """
9852  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector
9853  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
9854  """
9855  this = _IMP_atom.new_NonAlternativePDBSelector(name)
9856  try: self.this.append(this)
9857  except: self.this = this
9858  def get_version_info(self):
9859  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
9860  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
9861 
9862  __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
9863  __del__ = lambda self : None;
9864  def __str__(self):
9865  """__str__(NonAlternativePDBSelector self) -> std::string"""
9866  return _IMP_atom.NonAlternativePDBSelector___str__(self)
9867 
9868  def __repr__(self):
9869  """__repr__(NonAlternativePDBSelector self) -> std::string"""
9870  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
9871 
9872  def get_from(o):
9873  return _object_cast_to_NonAlternativePDBSelector(o)
9874  get_from = staticmethod(get_from)
9875 
9876 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
9877 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
9878 
9879 class ATOMPDBSelector(NonAlternativePDBSelector):
9880  """Proxy of C++ IMP::atom::ATOMPDBSelector class"""
9881  __swig_setmethods__ = {}
9882  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9883  __setattr__ = lambda self, name, value: _swig_setattr(self, ATOMPDBSelector, name, value)
9884  __swig_getmethods__ = {}
9885  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9886  __getattr__ = lambda self, name: _swig_getattr(self, ATOMPDBSelector, name)
9887  def __init__(self, name="ATOMPDBSelector%1%"):
9888  """
9889  __init__(IMP::atom::ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector
9890  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
9891  """
9892  this = _IMP_atom.new_ATOMPDBSelector(name)
9893  try: self.this.append(this)
9894  except: self.this = this
9895  __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
9896  __del__ = lambda self : None;
9897  def __str__(self):
9898  """__str__(ATOMPDBSelector self) -> std::string"""
9899  return _IMP_atom.ATOMPDBSelector___str__(self)
9900 
9901  def __repr__(self):
9902  """__repr__(ATOMPDBSelector self) -> std::string"""
9903  return _IMP_atom.ATOMPDBSelector___repr__(self)
9904 
9905  def get_from(o):
9906  return _object_cast_to_ATOMPDBSelector(o)
9907  get_from = staticmethod(get_from)
9908 
9909 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
9910 ATOMPDBSelector_swigregister(ATOMPDBSelector)
9911 
9912 class CAlphaPDBSelector(NonAlternativePDBSelector):
9913  """Proxy of C++ IMP::atom::CAlphaPDBSelector class"""
9914  __swig_setmethods__ = {}
9915  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9916  __setattr__ = lambda self, name, value: _swig_setattr(self, CAlphaPDBSelector, name, value)
9917  __swig_getmethods__ = {}
9918  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9919  __getattr__ = lambda self, name: _swig_getattr(self, CAlphaPDBSelector, name)
9920  def __init__(self, name="CAlphaPDBSelector%1%"):
9921  """
9922  __init__(IMP::atom::CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector
9923  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
9924  """
9925  this = _IMP_atom.new_CAlphaPDBSelector(name)
9926  try: self.this.append(this)
9927  except: self.this = this
9928  __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
9929  __del__ = lambda self : None;
9930  def __str__(self):
9931  """__str__(CAlphaPDBSelector self) -> std::string"""
9932  return _IMP_atom.CAlphaPDBSelector___str__(self)
9933 
9934  def __repr__(self):
9935  """__repr__(CAlphaPDBSelector self) -> std::string"""
9936  return _IMP_atom.CAlphaPDBSelector___repr__(self)
9937 
9938  def get_from(o):
9939  return _object_cast_to_CAlphaPDBSelector(o)
9940  get_from = staticmethod(get_from)
9941 
9942 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
9943 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
9944 
9945 class CBetaPDBSelector(NonAlternativePDBSelector):
9946  """Proxy of C++ IMP::atom::CBetaPDBSelector class"""
9947  __swig_setmethods__ = {}
9948  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9949  __setattr__ = lambda self, name, value: _swig_setattr(self, CBetaPDBSelector, name, value)
9950  __swig_getmethods__ = {}
9951  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9952  __getattr__ = lambda self, name: _swig_getattr(self, CBetaPDBSelector, name)
9953  def __init__(self, name="CBetaPDBSelector%1%"):
9954  """
9955  __init__(IMP::atom::CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector
9956  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
9957  """
9958  this = _IMP_atom.new_CBetaPDBSelector(name)
9959  try: self.this.append(this)
9960  except: self.this = this
9961  __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
9962  __del__ = lambda self : None;
9963  def __str__(self):
9964  """__str__(CBetaPDBSelector self) -> std::string"""
9965  return _IMP_atom.CBetaPDBSelector___str__(self)
9966 
9967  def __repr__(self):
9968  """__repr__(CBetaPDBSelector self) -> std::string"""
9969  return _IMP_atom.CBetaPDBSelector___repr__(self)
9970 
9971  def get_from(o):
9972  return _object_cast_to_CBetaPDBSelector(o)
9973  get_from = staticmethod(get_from)
9974 
9975 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
9976 CBetaPDBSelector_swigregister(CBetaPDBSelector)
9977 
9978 class CPDBSelector(NonAlternativePDBSelector):
9979  """Proxy of C++ IMP::atom::CPDBSelector class"""
9980  __swig_setmethods__ = {}
9981  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9982  __setattr__ = lambda self, name, value: _swig_setattr(self, CPDBSelector, name, value)
9983  __swig_getmethods__ = {}
9984  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9985  __getattr__ = lambda self, name: _swig_getattr(self, CPDBSelector, name)
9986  def __init__(self, name="CPDBSelector%1%"):
9987  """
9988  __init__(IMP::atom::CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector
9989  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
9990  """
9991  this = _IMP_atom.new_CPDBSelector(name)
9992  try: self.this.append(this)
9993  except: self.this = this
9994  __swig_destroy__ = _IMP_atom.delete_CPDBSelector
9995  __del__ = lambda self : None;
9996  def __str__(self):
9997  """__str__(CPDBSelector self) -> std::string"""
9998  return _IMP_atom.CPDBSelector___str__(self)
9999 
10000  def __repr__(self):
10001  """__repr__(CPDBSelector self) -> std::string"""
10002  return _IMP_atom.CPDBSelector___repr__(self)
10003 
10004  def get_from(o):
10005  return _object_cast_to_CPDBSelector(o)
10006  get_from = staticmethod(get_from)
10007 
10008 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
10009 CPDBSelector_swigregister(CPDBSelector)
10010 
10011 class NPDBSelector(NonAlternativePDBSelector):
10012  """Proxy of C++ IMP::atom::NPDBSelector class"""
10013  __swig_setmethods__ = {}
10014  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10015  __setattr__ = lambda self, name, value: _swig_setattr(self, NPDBSelector, name, value)
10016  __swig_getmethods__ = {}
10017  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10018  __getattr__ = lambda self, name: _swig_getattr(self, NPDBSelector, name)
10019  def __init__(self, name="NPDBSelector%1%"):
10020  """
10021  __init__(IMP::atom::NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector
10022  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
10023  """
10024  this = _IMP_atom.new_NPDBSelector(name)
10025  try: self.this.append(this)
10026  except: self.this = this
10027  __swig_destroy__ = _IMP_atom.delete_NPDBSelector
10028  __del__ = lambda self : None;
10029  def __str__(self):
10030  """__str__(NPDBSelector self) -> std::string"""
10031  return _IMP_atom.NPDBSelector___str__(self)
10032 
10033  def __repr__(self):
10034  """__repr__(NPDBSelector self) -> std::string"""
10035  return _IMP_atom.NPDBSelector___repr__(self)
10036 
10037  def get_from(o):
10038  return _object_cast_to_NPDBSelector(o)
10039  get_from = staticmethod(get_from)
10040 
10041 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
10042 NPDBSelector_swigregister(NPDBSelector)
10043 
10044 class AllPDBSelector(PDBSelector):
10045  """Proxy of C++ IMP::atom::AllPDBSelector class"""
10046  __swig_setmethods__ = {}
10047  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10048  __setattr__ = lambda self, name, value: _swig_setattr(self, AllPDBSelector, name, value)
10049  __swig_getmethods__ = {}
10050  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10051  __getattr__ = lambda self, name: _swig_getattr(self, AllPDBSelector, name)
10052  def __init__(self, name="AllPDBSelector%1%"):
10053  """
10054  __init__(IMP::atom::AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector
10055  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
10056  """
10057  this = _IMP_atom.new_AllPDBSelector(name)
10058  try: self.this.append(this)
10059  except: self.this = this
10060  def get_version_info(self):
10061  """get_version_info(AllPDBSelector self) -> VersionInfo"""
10062  return _IMP_atom.AllPDBSelector_get_version_info(self)
10063 
10064  __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
10065  __del__ = lambda self : None;
10066  def __str__(self):
10067  """__str__(AllPDBSelector self) -> std::string"""
10068  return _IMP_atom.AllPDBSelector___str__(self)
10069 
10070  def __repr__(self):
10071  """__repr__(AllPDBSelector self) -> std::string"""
10072  return _IMP_atom.AllPDBSelector___repr__(self)
10073 
10074  def get_from(o):
10075  return _object_cast_to_AllPDBSelector(o)
10076  get_from = staticmethod(get_from)
10077 
10078 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
10079 AllPDBSelector_swigregister(AllPDBSelector)
10080 
10081 class ChainPDBSelector(NonAlternativePDBSelector):
10082  """Proxy of C++ IMP::atom::ChainPDBSelector class"""
10083  __swig_setmethods__ = {}
10084  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10085  __setattr__ = lambda self, name, value: _swig_setattr(self, ChainPDBSelector, name, value)
10086  __swig_getmethods__ = {}
10087  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10088  __getattr__ = lambda self, name: _swig_getattr(self, ChainPDBSelector, name)
10089  __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
10090  __del__ = lambda self : None;
10091  def __init__(self, *args):
10092  """
10093  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
10094  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
10095  """
10096  this = _IMP_atom.new_ChainPDBSelector(*args)
10097  try: self.this.append(this)
10098  except: self.this = this
10099  def __str__(self):
10100  """__str__(ChainPDBSelector self) -> std::string"""
10101  return _IMP_atom.ChainPDBSelector___str__(self)
10102 
10103  def __repr__(self):
10104  """__repr__(ChainPDBSelector self) -> std::string"""
10105  return _IMP_atom.ChainPDBSelector___repr__(self)
10106 
10107  def get_from(o):
10108  return _object_cast_to_ChainPDBSelector(o)
10109  get_from = staticmethod(get_from)
10110 
10111 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
10112 ChainPDBSelector_swigregister(ChainPDBSelector)
10113 
10114 class WaterPDBSelector(NonAlternativePDBSelector):
10115  """Proxy of C++ IMP::atom::WaterPDBSelector class"""
10116  __swig_setmethods__ = {}
10117  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10118  __setattr__ = lambda self, name, value: _swig_setattr(self, WaterPDBSelector, name, value)
10119  __swig_getmethods__ = {}
10120  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10121  __getattr__ = lambda self, name: _swig_getattr(self, WaterPDBSelector, name)
10122  def __init__(self, name="WaterPDBSelector%1%"):
10123  """
10124  __init__(IMP::atom::WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector
10125  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
10126  """
10127  this = _IMP_atom.new_WaterPDBSelector(name)
10128  try: self.this.append(this)
10129  except: self.this = this
10130  __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
10131  __del__ = lambda self : None;
10132  def __str__(self):
10133  """__str__(WaterPDBSelector self) -> std::string"""
10134  return _IMP_atom.WaterPDBSelector___str__(self)
10135 
10136  def __repr__(self):
10137  """__repr__(WaterPDBSelector self) -> std::string"""
10138  return _IMP_atom.WaterPDBSelector___repr__(self)
10139 
10140  def get_from(o):
10141  return _object_cast_to_WaterPDBSelector(o)
10142  get_from = staticmethod(get_from)
10143 
10144 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
10145 WaterPDBSelector_swigregister(WaterPDBSelector)
10146 
10147 class HydrogenPDBSelector(NonAlternativePDBSelector):
10148  """Proxy of C++ IMP::atom::HydrogenPDBSelector class"""
10149  __swig_setmethods__ = {}
10150  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10151  __setattr__ = lambda self, name, value: _swig_setattr(self, HydrogenPDBSelector, name, value)
10152  __swig_getmethods__ = {}
10153  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10154  __getattr__ = lambda self, name: _swig_getattr(self, HydrogenPDBSelector, name)
10155  def __init__(self, name="HydrogenPDBSelector%1%"):
10156  """
10157  __init__(IMP::atom::HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector
10158  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
10159  """
10160  this = _IMP_atom.new_HydrogenPDBSelector(name)
10161  try: self.this.append(this)
10162  except: self.this = this
10163  __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
10164  __del__ = lambda self : None;
10165  def __str__(self):
10166  """__str__(HydrogenPDBSelector self) -> std::string"""
10167  return _IMP_atom.HydrogenPDBSelector___str__(self)
10168 
10169  def __repr__(self):
10170  """__repr__(HydrogenPDBSelector self) -> std::string"""
10171  return _IMP_atom.HydrogenPDBSelector___repr__(self)
10172 
10173  def get_from(o):
10174  return _object_cast_to_HydrogenPDBSelector(o)
10175  get_from = staticmethod(get_from)
10176 
10177 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
10178 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
10179 
10180 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
10181  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class"""
10182  __swig_setmethods__ = {}
10183  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10184  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterNonHydrogenPDBSelector, name, value)
10185  __swig_getmethods__ = {}
10186  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10187  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterNonHydrogenPDBSelector, name)
10188  __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
10189  __del__ = lambda self : None;
10190  def __init__(self, *args):
10191  """
10192  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
10193  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
10194  """
10195  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
10196  try: self.this.append(this)
10197  except: self.this = this
10198  def __str__(self):
10199  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
10200  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
10201 
10202  def __repr__(self):
10203  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
10204  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
10205 
10206  def get_from(o):
10207  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
10208  get_from = staticmethod(get_from)
10209 
10210 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
10211 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
10212 
10213 class NonWaterPDBSelector(NonAlternativePDBSelector):
10214  """Proxy of C++ IMP::atom::NonWaterPDBSelector class"""
10215  __swig_setmethods__ = {}
10216  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10217  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterPDBSelector, name, value)
10218  __swig_getmethods__ = {}
10219  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10220  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterPDBSelector, name)
10221  __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
10222  __del__ = lambda self : None;
10223  def __init__(self, *args):
10224  """
10225  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
10226  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
10227  """
10228  this = _IMP_atom.new_NonWaterPDBSelector(*args)
10229  try: self.this.append(this)
10230  except: self.this = this
10231  def __str__(self):
10232  """__str__(NonWaterPDBSelector self) -> std::string"""
10233  return _IMP_atom.NonWaterPDBSelector___str__(self)
10234 
10235  def __repr__(self):
10236  """__repr__(NonWaterPDBSelector self) -> std::string"""
10237  return _IMP_atom.NonWaterPDBSelector___repr__(self)
10238 
10239  def get_from(o):
10240  return _object_cast_to_NonWaterPDBSelector(o)
10241  get_from = staticmethod(get_from)
10242 
10243 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
10244 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
10245 
10246 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
10247  """Proxy of C++ IMP::atom::BackbonePDBSelector class"""
10248  __swig_setmethods__ = {}
10249  for _s in [NonWaterNonHydrogenPDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10250  __setattr__ = lambda self, name, value: _swig_setattr(self, BackbonePDBSelector, name, value)
10251  __swig_getmethods__ = {}
10252  for _s in [NonWaterNonHydrogenPDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10253  __getattr__ = lambda self, name: _swig_getattr(self, BackbonePDBSelector, name)
10254  def __init__(self, name="BackbonePDBSelector%1%"):
10255  """
10256  __init__(IMP::atom::BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector
10257  __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
10258  """
10259  this = _IMP_atom.new_BackbonePDBSelector(name)
10260  try: self.this.append(this)
10261  except: self.this = this
10262  __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
10263  __del__ = lambda self : None;
10264  def __str__(self):
10265  """__str__(BackbonePDBSelector self) -> std::string"""
10266  return _IMP_atom.BackbonePDBSelector___str__(self)
10267 
10268  def __repr__(self):
10269  """__repr__(BackbonePDBSelector self) -> std::string"""
10270  return _IMP_atom.BackbonePDBSelector___repr__(self)
10271 
10272  def get_from(o):
10273  return _object_cast_to_BackbonePDBSelector(o)
10274  get_from = staticmethod(get_from)
10275 
10276 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
10277 BackbonePDBSelector_swigregister(BackbonePDBSelector)
10278 
10279 class PPDBSelector(NonAlternativePDBSelector):
10280  """Proxy of C++ IMP::atom::PPDBSelector class"""
10281  __swig_setmethods__ = {}
10282  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10283  __setattr__ = lambda self, name, value: _swig_setattr(self, PPDBSelector, name, value)
10284  __swig_getmethods__ = {}
10285  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10286  __getattr__ = lambda self, name: _swig_getattr(self, PPDBSelector, name)
10287  def __init__(self, name="PPDBSelector%1%"):
10288  """
10289  __init__(IMP::atom::PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector
10290  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
10291  """
10292  this = _IMP_atom.new_PPDBSelector(name)
10293  try: self.this.append(this)
10294  except: self.this = this
10295  __swig_destroy__ = _IMP_atom.delete_PPDBSelector
10296  __del__ = lambda self : None;
10297  def __str__(self):
10298  """__str__(PPDBSelector self) -> std::string"""
10299  return _IMP_atom.PPDBSelector___str__(self)
10300 
10301  def __repr__(self):
10302  """__repr__(PPDBSelector self) -> std::string"""
10303  return _IMP_atom.PPDBSelector___repr__(self)
10304 
10305  def get_from(o):
10306  return _object_cast_to_PPDBSelector(o)
10307  get_from = staticmethod(get_from)
10308 
10309 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
10310 PPDBSelector_swigregister(PPDBSelector)
10311 
10312 class AndPDBSelector(PDBSelector):
10313  """Proxy of C++ IMP::atom::AndPDBSelector class"""
10314  __swig_setmethods__ = {}
10315  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10316  __setattr__ = lambda self, name, value: _swig_setattr(self, AndPDBSelector, name, value)
10317  __swig_getmethods__ = {}
10318  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10319  __getattr__ = lambda self, name: _swig_getattr(self, AndPDBSelector, name)
10320  def get_version_info(self):
10321  """get_version_info(AndPDBSelector self) -> VersionInfo"""
10322  return _IMP_atom.AndPDBSelector_get_version_info(self)
10323 
10324  __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
10325  __del__ = lambda self : None;
10326  def __init__(self, *args):
10327  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
10328  this = _IMP_atom.new_AndPDBSelector(*args)
10329  try: self.this.append(this)
10330  except: self.this = this
10331  def __str__(self):
10332  """__str__(AndPDBSelector self) -> std::string"""
10333  return _IMP_atom.AndPDBSelector___str__(self)
10334 
10335  def __repr__(self):
10336  """__repr__(AndPDBSelector self) -> std::string"""
10337  return _IMP_atom.AndPDBSelector___repr__(self)
10338 
10339  def get_from(o):
10340  return _object_cast_to_AndPDBSelector(o)
10341  get_from = staticmethod(get_from)
10342 
10343 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
10344 AndPDBSelector_swigregister(AndPDBSelector)
10345 
10346 class OrPDBSelector(PDBSelector):
10347  """Proxy of C++ IMP::atom::OrPDBSelector class"""
10348  __swig_setmethods__ = {}
10349  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10350  __setattr__ = lambda self, name, value: _swig_setattr(self, OrPDBSelector, name, value)
10351  __swig_getmethods__ = {}
10352  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10353  __getattr__ = lambda self, name: _swig_getattr(self, OrPDBSelector, name)
10354  def get_version_info(self):
10355  """get_version_info(OrPDBSelector self) -> VersionInfo"""
10356  return _IMP_atom.OrPDBSelector_get_version_info(self)
10357 
10358  __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
10359  __del__ = lambda self : None;
10360  def __init__(self, *args):
10361  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
10362  this = _IMP_atom.new_OrPDBSelector(*args)
10363  try: self.this.append(this)
10364  except: self.this = this
10365  def __str__(self):
10366  """__str__(OrPDBSelector self) -> std::string"""
10367  return _IMP_atom.OrPDBSelector___str__(self)
10368 
10369  def __repr__(self):
10370  """__repr__(OrPDBSelector self) -> std::string"""
10371  return _IMP_atom.OrPDBSelector___repr__(self)
10372 
10373  def get_from(o):
10374  return _object_cast_to_OrPDBSelector(o)
10375  get_from = staticmethod(get_from)
10376 
10377 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
10378 OrPDBSelector_swigregister(OrPDBSelector)
10379 
10380 class NotPDBSelector(PDBSelector):
10381  """Proxy of C++ IMP::atom::NotPDBSelector class"""
10382  __swig_setmethods__ = {}
10383  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10384  __setattr__ = lambda self, name, value: _swig_setattr(self, NotPDBSelector, name, value)
10385  __swig_getmethods__ = {}
10386  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10387  __getattr__ = lambda self, name: _swig_getattr(self, NotPDBSelector, name)
10388  def get_version_info(self):
10389  """get_version_info(NotPDBSelector self) -> VersionInfo"""
10390  return _IMP_atom.NotPDBSelector_get_version_info(self)
10391 
10392  __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
10393  __del__ = lambda self : None;
10394  def __init__(self, *args):
10395  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
10396  this = _IMP_atom.new_NotPDBSelector(*args)
10397  try: self.this.append(this)
10398  except: self.this = this
10399  def __str__(self):
10400  """__str__(NotPDBSelector self) -> std::string"""
10401  return _IMP_atom.NotPDBSelector___str__(self)
10402 
10403  def __repr__(self):
10404  """__repr__(NotPDBSelector self) -> std::string"""
10405  return _IMP_atom.NotPDBSelector___repr__(self)
10406 
10407  def get_from(o):
10408  return _object_cast_to_NotPDBSelector(o)
10409  get_from = staticmethod(get_from)
10410 
10411 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
10412 NotPDBSelector_swigregister(NotPDBSelector)
10413 
10414 
10415 def get_default_pdb_selector():
10416  """get_default_pdb_selector() -> PDBSelector"""
10417  return _IMP_atom.get_default_pdb_selector()
10418 
10419 def read_pdb(*args):
10420  """
10421  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10422  bool select_first_model=True, bool no_radii=False) -> Hierarchy
10423  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10424  bool select_first_model=True) -> Hierarchy
10425  read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector()) -> Hierarchy
10426  read_pdb(TextInput input, Model model) -> Hierarchy
10427  read_pdb(TextInput input, int model, Hierarchy h)
10428  """
10429  return _IMP_atom.read_pdb(*args)
10430 
10431 def read_multimodel_pdb(*args):
10432  """
10433  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(),
10434  bool noradii=False) -> IMP::atom::Hierarchies
10435  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector()) -> IMP::atom::Hierarchies
10436  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
10437  """
10438  return _IMP_atom.read_multimodel_pdb(*args)
10439 
10440 def write_pdb(*args):
10441  """
10442  write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
10443  write_pdb(Selection mhd, TextOutput out)
10444  """
10445  return _IMP_atom.write_pdb(*args)
10446 
10447 def write_pdb_of_c_alphas(*args):
10448  """
10449  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
10450  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
10451  """
10452  return _IMP_atom.write_pdb_of_c_alphas(*args)
10453 
10454 def write_multimodel_pdb(*args):
10455  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
10456  return _IMP_atom.write_multimodel_pdb(*args)
10457 
10458 def get_pdb_string(*args):
10459  """
10460  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10461  char res_icode=' ', double occpancy=1.00, double tempFactor=0.00,
10462  IMP::atom::Element e=C) -> std::string
10463  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10464  char res_icode=' ', double occpancy=1.00, double tempFactor=0.00) -> std::string
10465  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10466  char res_icode=' ', double occpancy=1.00) -> std::string
10467  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10468  char res_icode=' ') -> std::string
10469  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1) -> std::string
10470  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ') -> std::string
10471  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA) -> std::string
10472  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C) -> std::string
10473  get_pdb_string(Vector3D v, int index=-1) -> std::string
10474  get_pdb_string(Vector3D v) -> std::string
10475  """
10476  return _IMP_atom.get_pdb_string(*args)
10477 
10478 def get_pdb_conect_record_string(*args):
10479  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
10480  return _IMP_atom.get_pdb_conect_record_string(*args)
10481 class WritePDBOptimizerState(IMP.kernel.OptimizerState):
10482  """Proxy of C++ IMP::atom::WritePDBOptimizerState class"""
10483  __swig_setmethods__ = {}
10484  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10485  __setattr__ = lambda self, name, value: _swig_setattr(self, WritePDBOptimizerState, name, value)
10486  __swig_getmethods__ = {}
10487  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10488  __getattr__ = lambda self, name: _swig_getattr(self, WritePDBOptimizerState, name)
10489  def __init__(self, *args):
10490  """
10491  __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
10492  __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
10493  """
10494  this = _IMP_atom.new_WritePDBOptimizerState(*args)
10495  try: self.this.append(this)
10496  except: self.this = this
10497  def get_version_info(self):
10498  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
10499  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
10500 
10501  __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
10502  __del__ = lambda self : None;
10503  def __str__(self):
10504  """__str__(WritePDBOptimizerState self) -> std::string"""
10505  return _IMP_atom.WritePDBOptimizerState___str__(self)
10506 
10507  def __repr__(self):
10508  """__repr__(WritePDBOptimizerState self) -> std::string"""
10509  return _IMP_atom.WritePDBOptimizerState___repr__(self)
10510 
10511  def get_from(o):
10512  return _object_cast_to_WritePDBOptimizerState(o)
10513  get_from = staticmethod(get_from)
10514 
10515 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
10516 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
10517 
10518 
10519 def get_kt(*args):
10520  """get_kt(double T) -> double"""
10521  return _IMP_atom.get_kt(*args)
10522 
10523 def show_molecular_hierarchy(*args):
10524  """
10525  show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream
10526  show_molecular_hierarchy(Hierarchy h) -> _ostream
10527  """
10528  return _IMP_atom.show_molecular_hierarchy(*args)
10529 class CHARMMBond(_object):
10530  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class"""
10531  __swig_setmethods__ = {}
10532  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBond, name, value)
10533  __swig_getmethods__ = {}
10534  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBond, name)
10535  __repr__ = _swig_repr
10536  def __init__(self, *args):
10537  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
10538  this = _IMP_atom.new_CHARMMBond(*args)
10539  try: self.this.append(this)
10540  except: self.this = this
10541  def get_endpoint(self, *args):
10542  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
10543  return _IMP_atom.CHARMMBond_get_endpoint(self, *args)
10544 
10545  def get_contains_atom(self, *args):
10546  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
10547  return _IMP_atom.CHARMMBond_get_contains_atom(self, *args)
10548 
10549  def show(self, *args):
10550  """
10551  show(CHARMMBond self, _ostream out=std::cout)
10552  show(CHARMMBond self)
10553  """
10554  return _IMP_atom.CHARMMBond_show(self, *args)
10555 
10556  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
10557  __del__ = lambda self : None;
10558 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
10559 CHARMMBond_swigregister(CHARMMBond)
10560 
10561 class CHARMMAngle(_object):
10562  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class"""
10563  __swig_setmethods__ = {}
10564  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAngle, name, value)
10565  __swig_getmethods__ = {}
10566  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAngle, name)
10567  __repr__ = _swig_repr
10568  def __init__(self, *args):
10569  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
10570  this = _IMP_atom.new_CHARMMAngle(*args)
10571  try: self.this.append(this)
10572  except: self.this = this
10573  def get_endpoint(self, *args):
10574  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
10575  return _IMP_atom.CHARMMAngle_get_endpoint(self, *args)
10576 
10577  def get_contains_atom(self, *args):
10578  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
10579  return _IMP_atom.CHARMMAngle_get_contains_atom(self, *args)
10580 
10581  def show(self, *args):
10582  """
10583  show(CHARMMAngle self, _ostream out=std::cout)
10584  show(CHARMMAngle self)
10585  """
10586  return _IMP_atom.CHARMMAngle_show(self, *args)
10587 
10588  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
10589  __del__ = lambda self : None;
10590 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
10591 CHARMMAngle_swigregister(CHARMMAngle)
10592 
10593 
10594 def _get_rmsd_cpp(*args):
10595  """
10596  _get_rmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10597  Transformation3D tr_for_second=IMP::algebra::get_identity_transformation_3d()) -> double
10598  _get_rmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double
10599  """
10600  return _IMP_atom._get_rmsd_cpp(*args)
10601 
10602 def _get_native_overlap_cpp(*args):
10603  """
10604  _get_native_overlap_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10605  double threshold) -> double
10606  """
10607  return _IMP_atom._get_native_overlap_cpp(*args)
10608 
10609 def _get_drmsd_cpp(*args):
10610  """_get_drmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
10611  return _IMP_atom._get_drmsd_cpp(*args)
10612 
10613 def _get_drms_cpp(*args):
10614  """_get_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
10615  return _IMP_atom._get_drms_cpp(*args)
10616 
10617 def _get_rigid_bodies_drms_cpp(*args):
10618  """
10619  _get_rigid_bodies_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10620  IMP::IntRanges const & ranges) -> double
10621  """
10622  return _IMP_atom._get_rigid_bodies_drms_cpp(*args)
10623 def get_rmsd(a, b):
10624  va= [IMP.algebra.get_vector(x) for x in a]
10625  vb= [IMP.algebra.get_vector(x) for x in b]
10626  return _get_rmsd_cpp(va, vb)
10627 def get_native_overlap(a, b, d):
10628  va= [IMP.algebra.get_vector(x) for x in a]
10629  vb= [IMP.algebra.get_vector(x) for x in b]
10630  return _get_native_overlap_cpp(va, vb, d)
10631 
10632 def get_drmsd(a, b):
10633  va= [IMP.algebra.get_vector(x) for x in a]
10634  vb= [IMP.algebra.get_vector(x) for x in b]
10635  return _get_drmsd_cpp(va, vb)
10636 
10637 def get_drms(a, b):
10638  va= [IMP.algebra.get_vector(x) for x in a]
10639  vb= [IMP.algebra.get_vector(x) for x in b]
10640  return _get_drms_cpp(va, vb)
10641 
10642 def get_rigid_bodies_drms(a, b, ranges):
10643  va= [IMP.algebra.get_vector(x) for x in a]
10644  vb= [IMP.algebra.get_vector(x) for x in b]
10645  #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
10646  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
10647 
10648 
10649 
10650 def get_module_version():
10651  """get_module_version() -> std::string const"""
10652  return _IMP_atom.get_module_version()
10653 
10654 def get_example_path(*args):
10655  """get_example_path(std::string fname) -> std::string"""
10656  return _IMP_atom.get_example_path(*args)
10657 
10658 def get_data_path(*args):
10659  """get_data_path(std::string fname) -> std::string"""
10660  return _IMP_atom.get_data_path(*args)
10661 import _version_check
10662 _version_check.check_version(get_module_version())
10663 
10664 # This file is compatible with both classic and new-style classes.
10665 
10666 
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)
Definition: distance.h:152
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)
Definition: distance.h:121
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)
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)
Hierarchies read_multimodel_pdb(base::TextInput input, kernel::Model *model, PDBSelector *selector=)
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Definition: distance.h:98
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: distance.h:63
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.
Definition: XYZ.h:143
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
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)
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::algebra::Transformation3D &tr_for_second=IMP::algebra::get_identity_transformation_3d())
Calculate the root mean square deviation between two sets of 3D points.
Definition: distance.h:28
Vector3Ds get_vertices(const BoundingBoxD< 3 > &bb)
Return a list of the 8 bounding points for the bounding box.
Definition: BoundingBoxD.h:255
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 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)
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:32
void write_mol2(Hierarchy rhd, base::TextOutput file_name)
Write a lignand hierarchy as a mol2 file.
Abstract predicate function.
Common base class for heavy weight IMP objects.
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)
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)
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
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)
void add_particle(RMF::FileHandle fh, kernel::Particle *hs)
See IMP.display for more information.
Definition: BildWriter.h:20
CheckLevel get_check_level()
Get the current audit mode.
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.
Hierarchy create_protein(kernel::Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
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