IMP  2.0.0
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.8
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 from sys import version_info
10 if version_info >= (2,6,0):
11  def swig_import_helper():
12  from os.path import dirname
13  import imp
14  fp = None
15  try:
16  fp, pathname, description = imp.find_module('_IMP_atom', [dirname(__file__)])
17  except ImportError:
18  import _IMP_atom
19  return _IMP_atom
20  if fp is not None:
21  try:
22  _mod = imp.load_module('_IMP_atom', fp, pathname, description)
23  finally:
24  fp.close()
25  return _mod
26  _IMP_atom = swig_import_helper()
27  del swig_import_helper
28 else:
29  import _IMP_atom
30 del version_info
31 try:
32  _swig_property = property
33 except NameError:
34  pass # Python < 2.2 doesn't have 'property'.
35 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
36  if (name == "thisown"): return self.this.own(value)
37  if (name == "this"):
38  if type(value).__name__ == 'SwigPyObject':
39  self.__dict__[name] = value
40  return
41  method = class_type.__swig_setmethods__.get(name,None)
42  if method: return method(self,value)
43  if (not static):
44  self.__dict__[name] = value
45  else:
46  raise AttributeError("You cannot add attributes to %s" % self)
47 
48 def _swig_setattr(self,class_type,name,value):
49  return _swig_setattr_nondynamic(self,class_type,name,value,0)
50 
51 def _swig_getattr(self,class_type,name):
52  if (name == "thisown"): return self.this.own()
53  method = class_type.__swig_getmethods__.get(name,None)
54  if method: return method(self)
55  raise AttributeError(name)
56 
57 def _swig_repr(self):
58  try: strthis = "proxy of " + self.this.__repr__()
59  except: strthis = ""
60  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
61 
62 try:
63  _object = object
64  _newclass = 1
65 except AttributeError:
66  class _object : pass
67  _newclass = 0
68 
69 
70 try:
71  import weakref
72  weakref_proxy = weakref.proxy
73 except:
74  weakref_proxy = lambda x: x
75 
76 
77 class IMP_ATOM_SwigPyIterator(_object):
78  """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class"""
79  __swig_setmethods__ = {}
80  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_ATOM_SwigPyIterator, name, value)
81  __swig_getmethods__ = {}
82  __getattr__ = lambda self, name: _swig_getattr(self, IMP_ATOM_SwigPyIterator, name)
83  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
84  __repr__ = _swig_repr
85  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
86  __del__ = lambda self : None;
87  def value(self):
88  """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
89  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
90 
91  def incr(self, n=1):
92  """
93  incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
94  incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
95  """
96  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
97 
98  def decr(self, n=1):
99  """
100  decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
101  decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
102  """
103  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
104 
105  def distance(self, *args):
106  """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
107  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, *args)
108 
109  def equal(self, *args):
110  """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
111  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, *args)
112 
113  def copy(self):
114  """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
115  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
116 
117  def next(self):
118  """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
119  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
120 
121  def __next__(self):
122  """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
123  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
124 
125  def previous(self):
126  """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
127  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
128 
129  def advance(self, *args):
130  """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
131  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, *args)
132 
133  def __eq__(self, *args):
134  """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
135  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, *args)
136 
137  def __ne__(self, *args):
138  """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
139  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, *args)
140 
141  def __iadd__(self, *args):
142  """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
143  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, *args)
144 
145  def __isub__(self, *args):
146  """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
147  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, *args)
148 
149  def __add__(self, *args):
150  """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
151  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, *args)
152 
153  def __sub__(self, *args):
154  """
155  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
156  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
157  """
158  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
159 
160  def __iter__(self): return self
161 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
162 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
163 
164 _value_types=[]
165 _object_types=[]
166 _raii_types=[]
167 _plural_types=[]
168 
169 IMP_HAS_DEPRECATED = _IMP_atom.IMP_HAS_DEPRECATED
170 IMP_DEBUG = _IMP_atom.IMP_DEBUG
171 IMP_RELEASE = _IMP_atom.IMP_RELEASE
172 IMP_SILENT = _IMP_atom.IMP_SILENT
173 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
174 IMP_TERSE = _IMP_atom.IMP_TERSE
175 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
176 IMP_NONE = _IMP_atom.IMP_NONE
177 IMP_USAGE = _IMP_atom.IMP_USAGE
178 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
179 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
180 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
181 IMP_COMPILER_HAS_NULLPTR = _IMP_atom.IMP_COMPILER_HAS_NULLPTR
182 IMP_BASE_HAS_BOOST_RANDOM = _IMP_atom.IMP_BASE_HAS_BOOST_RANDOM
183 IMP_BASE_HAS_GPERFTOOLS = _IMP_atom.IMP_BASE_HAS_GPERFTOOLS
184 IMP_BASE_HAS_LOG4CXX = _IMP_atom.IMP_BASE_HAS_LOG4CXX
185 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
186 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
187 import sys
188 class _DirectorObjects(object):
189  """@internal Simple class to keep references to director objects
190  to prevent premature deletion."""
191  def __init__(self):
192  self._objects = []
193  def register(self, obj):
194  """Take a reference to a director object; will only work for
195  refcounted C++ classes"""
196  if hasattr(obj, 'get_ref_count'):
197  self._objects.append(obj)
198  def cleanup(self):
199  """Only drop our reference and allow cleanup by Python if no other
200  Python references exist (we hold 3 references: one in self._objects,
201  one in x, and one in the argument list for getrefcount) *and* no
202  other C++ references exist (the Python object always holds one)"""
203  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
204  or x.get_ref_count() > 1]
205 
206 
207  self._objects = objs
208  def get_object_count(self):
209  """Get number of director objects (useful for testing only)"""
210  return len(self._objects)
211 _director_objects = _DirectorObjects()
212 
213 DEFAULT_CHECK = _IMP_atom.DEFAULT_CHECK
214 NONE = _IMP_atom.NONE
215 USAGE = _IMP_atom.USAGE
216 USAGE_AND_INTERNAL = _IMP_atom.USAGE_AND_INTERNAL
217 
218 def set_check_level(*args):
219  """set_check_level(IMP::base::CheckLevel tf)"""
220  return _IMP_atom.set_check_level(*args)
221 
222 def get_check_level():
223  """get_check_level() -> IMP::base::CheckLevel"""
224  return _IMP_atom.get_check_level()
225 class _ostream(_object):
226  """Proxy of C++ std::ostream class"""
227  __swig_setmethods__ = {}
228  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
229  __swig_getmethods__ = {}
230  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
231  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
232  __repr__ = _swig_repr
233  def write(self, *args):
234  """write(_ostream self, char const * osa_buf)"""
235  return _IMP_atom._ostream_write(self, *args)
236 
237 _ostream_swigregister = _IMP_atom._ostream_swigregister
238 _ostream_swigregister(_ostream)
239 
240 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
241 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
242 import IMP.base
243 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
247 import IMP.cgal
248 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
249 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
250 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
251 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
252 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
253 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
254 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
255 import IMP.algebra
256 IMP_KERNEL_HAS_IMP_CGAL = _IMP_atom.IMP_KERNEL_HAS_IMP_CGAL
257 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
258 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
259 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_KERNEL_HAS_BOOST_SYSTEM
260 IMP_KERNEL_HAS_CGAL = _IMP_atom.IMP_KERNEL_HAS_CGAL
261 import IMP.kernel
262 IMP_DISPLAY_HAS_IMP_BASE = _IMP_atom.IMP_DISPLAY_HAS_IMP_BASE
263 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
264 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
265 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
266 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
267 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
268 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
269 import IMP.display
270 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
271 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
272 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
273 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
274 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
275 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
276 import IMP.score_functor
277 IMP_CORE_HAS_IMP_BASE = _IMP_atom.IMP_CORE_HAS_IMP_BASE
278 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
279 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
280 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
281 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
282 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
283 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
284 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
285 import IMP.core
286 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
287 IMP_CONTAINER_HAS_IMP_BASE = _IMP_atom.IMP_CONTAINER_HAS_IMP_BASE
288 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
289 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
290 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
291 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
292 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
293 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
294 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
295 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
296 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
297 import IMP.container
298 IMP_ATOM_HAS_IMP_BASE = _IMP_atom.IMP_ATOM_HAS_IMP_BASE
299 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
300 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
301 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
302 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
303 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
304 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
305 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
306 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
307 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
308 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
309 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
311  """Proxy of C++ IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy)> class"""
312  __swig_setmethods__ = {}
313  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
314  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyTree, name, value)
315  __swig_getmethods__ = {}
316  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
317  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyTree, name)
318  __repr__ = _swig_repr
319  def __init__(self):
320  """__init__(IMP::base::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy)> self) -> HierarchyTree"""
321  this = _IMP_atom.new_HierarchyTree()
322  try: self.this.append(this)
323  except: self.this = this
324  def get_graph(self):
325  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
326  return _IMP_atom.HierarchyTree_get_graph(self)
327 
328  def get_vertices(self):
329  """get_vertices(HierarchyTree self) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptors"""
330  return _IMP_atom.HierarchyTree_get_vertices(self)
331 
332  def get_vertex_name(self, *args):
333  """get_vertex_name(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor i) -> Hierarchy"""
334  return _IMP_atom.HierarchyTree_get_vertex_name(self, *args)
335 
336  def get_in_neighbors(self, *args):
337  """get_in_neighbors(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor v) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptors"""
338  return _IMP_atom.HierarchyTree_get_in_neighbors(self, *args)
339 
340  def get_out_neighbors(self, *args):
341  """get_out_neighbors(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor v) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptors"""
342  return _IMP_atom.HierarchyTree_get_out_neighbors(self, *args)
343 
344  def do_show(self, *args):
345  """do_show(HierarchyTree self, _ostream out)"""
346  return _IMP_atom.HierarchyTree_do_show(self, *args)
347 
348  def show_graphviz(self, *args):
349  """
350  show_graphviz(HierarchyTree self, _ostream out=std::cout)
351  show_graphviz(HierarchyTree self)
352  """
353  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
354 
355  def get_graphviz_string(self):
356  """get_graphviz_string(HierarchyTree self) -> std::string"""
357  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
358 
359  def get_type_name(self):
360  """get_type_name(HierarchyTree self) -> std::string"""
361  return _IMP_atom.HierarchyTree_get_type_name(self)
362 
363  def add_edge(self, *args):
364  """
365  add_edge(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor v0,
366  IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor v1)
367  """
368  return _IMP_atom.HierarchyTree_add_edge(self, *args)
369 
370  def add_vertex(self, *args):
371  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor"""
372  return _IMP_atom.HierarchyTree_add_vertex(self, *args)
373 
374  def remove_vertex(self, *args):
375  """remove_vertex(HierarchyTree self, IMP::base::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy >::VertexDescriptor l)"""
376  return _IMP_atom.HierarchyTree_remove_vertex(self, *args)
377 
378  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
379  __del__ = lambda self : None;
380 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
381 HierarchyTree_swigregister(HierarchyTree)
382 
383 _value_types.append("HierarchyTree")
384 
385 _object_types.append("PDBSelector")
386 
387 
388 def _object_cast_to_PDBSelector(*args):
389  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
390  return _IMP_atom._object_cast_to_PDBSelector(*args)
391 def Angles(l=[]):
392  return [Angle(x) for x in l]
393 _plural_types.append("Angles")
394 
395 _value_types.append("Angle")
396 
397 def Atoms(l=[]):
398  return [Atom(x) for x in l]
399 _plural_types.append("Atoms")
400 
401 _value_types.append("Atom")
402 
403 def Bonds(l=[]):
404  return [Bond(x) for x in l]
405 _plural_types.append("Bonds")
406 
407 _value_types.append("Bond")
408 
409 def Bondeds(l=[]):
410  return [Bonded(x) for x in l]
411 _plural_types.append("Bondeds")
412 
413 _value_types.append("Bonded")
414 
415 def CHARMMAtomList(l=[]):
416  return [CHARMMAtom(x) for x in l]
417 _plural_types.append("CHARMMAtomList")
418 
419 _value_types.append("CHARMMAtom")
420 
421 def Chains(l=[]):
422  return [Chain(x) for x in l]
423 _plural_types.append("Chains")
424 
425 _value_types.append("Chain")
426 
427 def Chargeds(l=[]):
428  return [Charged(x) for x in l]
429 _plural_types.append("Chargeds")
430 
431 _value_types.append("Charged")
432 
433 def Diffusions(l=[]):
434  return [Diffusion(x) for x in l]
435 _plural_types.append("Diffusions")
436 
437 _value_types.append("Diffusion")
438 
439 def RigidBodyDiffusions(l=[]):
440  return [RigidBodyDiffusion(x) for x in l]
441 _plural_types.append("RigidBodyDiffusions")
442 
443 _value_types.append("RigidBodyDiffusion")
444 
445 def Dihedrals(l=[]):
446  return [Dihedral(x) for x in l]
447 _plural_types.append("Dihedrals")
448 
449 _value_types.append("Dihedral")
450 
451 def Domains(l=[]):
452  return [Domain(x) for x in l]
453 _plural_types.append("Domains")
454 
455 _value_types.append("Domain")
456 
457 def Fragments(l=[]):
458  return [Fragment(x) for x in l]
459 _plural_types.append("Fragments")
460 
461 _value_types.append("Fragment")
462 
463 def Hierarchies(l=[]):
464  return [Hierarchy(x) for x in l]
465 _plural_types.append("Hierarchies")
466 
467 _value_types.append("Hierarchy")
468 
469 def LennardJonesList(l=[]):
470  return [LennardJones(x) for x in l]
471 _plural_types.append("LennardJonesList")
472 
473 _value_types.append("LennardJones")
474 
475 def Masses(l=[]):
476  return [Mass(x) for x in l]
477 _plural_types.append("Masses")
478 
479 _value_types.append("Mass")
480 
481 def Molecules(l=[]):
482  return [Molecule(x) for x in l]
483 _plural_types.append("Molecules")
484 
485 _value_types.append("Molecule")
486 
487 def Residues(l=[]):
488  return [Residue(x) for x in l]
489 _plural_types.append("Residues")
490 
491 _value_types.append("Residue")
492 
493 def Copies(l=[]):
494  return [Copy(x) for x in l]
495 _plural_types.append("Copies")
496 
497 _value_types.append("Copy")
498 
499 def SecondaryStructureResidues(l=[]):
500  return [SecondaryStructureResidue(x) for x in l]
501 _plural_types.append("SecondaryStructureResidues")
502 
503 _value_types.append("SecondaryStructureResidue")
504 
505 _object_types.append("Simulator")
506 
507 
508 def _object_cast_to_Simulator(*args):
509  """_object_cast_to_Simulator(Object o) -> Simulator"""
510  return _IMP_atom._object_cast_to_Simulator(*args)
511 _object_types.append("ATOMPDBSelector")
512 
513 
514 def _object_cast_to_ATOMPDBSelector(*args):
515  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
516  return _IMP_atom._object_cast_to_ATOMPDBSelector(*args)
517 _object_types.append("AllMol2Selector")
518 
519 
520 def _object_cast_to_AllMol2Selector(*args):
521  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
522  return _IMP_atom._object_cast_to_AllMol2Selector(*args)
523 _object_types.append("AllPDBSelector")
524 
525 
526 def _object_cast_to_AllPDBSelector(*args):
527  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
528  return _IMP_atom._object_cast_to_AllPDBSelector(*args)
529 _object_types.append("AndPDBSelector")
530 
531 
532 def _object_cast_to_AndPDBSelector(*args):
533  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
534  return _IMP_atom._object_cast_to_AndPDBSelector(*args)
535 _object_types.append("AngleSingletonScore")
536 
537 
538 def _object_cast_to_AngleSingletonScore(*args):
539  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
540  return _IMP_atom._object_cast_to_AngleSingletonScore(*args)
541 _object_types.append("BondEndpointsRefiner")
542 
543 
544 def _object_cast_to_BondEndpointsRefiner(*args):
545  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
546  return _IMP_atom._object_cast_to_BondEndpointsRefiner(*args)
547 _object_types.append("BondPairContainer")
548 
549 
550 def _object_cast_to_BondPairContainer(*args):
551  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
552  return _IMP_atom._object_cast_to_BondPairContainer(*args)
553 _object_types.append("BondSingletonScore")
554 
555 
556 def _object_cast_to_BondSingletonScore(*args):
557  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
558  return _IMP_atom._object_cast_to_BondSingletonScore(*args)
559 _object_types.append("BondedPairFilter")
560 
561 
562 def _object_cast_to_BondedPairFilter(*args):
563  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
564  return _IMP_atom._object_cast_to_BondedPairFilter(*args)
565 _object_types.append("BrownianDynamics")
566 
567 
568 def _object_cast_to_BrownianDynamics(*args):
569  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
570  return _IMP_atom._object_cast_to_BrownianDynamics(*args)
571 _object_types.append("CAlphaPDBSelector")
572 
573 
574 def _object_cast_to_CAlphaPDBSelector(*args):
575  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
576  return _IMP_atom._object_cast_to_CAlphaPDBSelector(*args)
577 _object_types.append("CBetaPDBSelector")
578 
579 
580 def _object_cast_to_CBetaPDBSelector(*args):
581  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
582  return _IMP_atom._object_cast_to_CBetaPDBSelector(*args)
583 _object_types.append("CHARMMParameters")
584 
585 
586 def _object_cast_to_CHARMMParameters(*args):
587  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
588  return _IMP_atom._object_cast_to_CHARMMParameters(*args)
589 _object_types.append("CHARMMResidueTopology")
590 
591 
592 def _object_cast_to_CHARMMResidueTopology(*args):
593  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
594  return _IMP_atom._object_cast_to_CHARMMResidueTopology(*args)
595 _object_types.append("CHARMMSegmentTopology")
596 
597 
598 def _object_cast_to_CHARMMSegmentTopology(*args):
599  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
600  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(*args)
601 _object_types.append("CHARMMStereochemistryRestraint")
602 
603 
604 def _object_cast_to_CHARMMStereochemistryRestraint(*args):
605  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
606  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(*args)
607 _object_types.append("CHARMMTopology")
608 
609 
610 def _object_cast_to_CHARMMTopology(*args):
611  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
612  return _IMP_atom._object_cast_to_CHARMMTopology(*args)
613 _object_types.append("CPDBSelector")
614 
615 
616 def _object_cast_to_CPDBSelector(*args):
617  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
618  return _IMP_atom._object_cast_to_CPDBSelector(*args)
619 _object_types.append("ChainPDBSelector")
620 
621 
622 def _object_cast_to_ChainPDBSelector(*args):
623  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
624  return _IMP_atom._object_cast_to_ChainPDBSelector(*args)
625 _object_types.append("CoulombPairScore")
626 
627 
628 def _object_cast_to_CoulombPairScore(*args):
629  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
630  return _IMP_atom._object_cast_to_CoulombPairScore(*args)
631 _object_types.append("CoverBond")
632 
633 
634 def _object_cast_to_CoverBond(*args):
635  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
636  return _IMP_atom._object_cast_to_CoverBond(*args)
637 _object_types.append("DihedralSingletonScore")
638 
639 
640 def _object_cast_to_DihedralSingletonScore(*args):
641  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
642  return _IMP_atom._object_cast_to_DihedralSingletonScore(*args)
643 _object_types.append("DopePairScore")
644 
645 
646 def _object_cast_to_DopePairScore(*args):
647  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
648  return _IMP_atom._object_cast_to_DopePairScore(*args)
649 _object_types.append("ForceFieldParameters")
650 
651 
652 def _object_cast_to_ForceFieldParameters(*args):
653  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
654  return _IMP_atom._object_cast_to_ForceFieldParameters(*args)
655 _object_types.append("ForceSwitch")
656 
657 
658 def _object_cast_to_ForceSwitch(*args):
659  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
660  return _IMP_atom._object_cast_to_ForceSwitch(*args)
661 _object_types.append("HydrogenPDBSelector")
662 
663 
664 def _object_cast_to_HydrogenPDBSelector(*args):
665  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
666  return _IMP_atom._object_cast_to_HydrogenPDBSelector(*args)
667 _object_types.append("ImproperSingletonScore")
668 
669 
670 def _object_cast_to_ImproperSingletonScore(*args):
671  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
672  return _IMP_atom._object_cast_to_ImproperSingletonScore(*args)
673 _object_types.append("LennardJonesPairScore")
674 
675 
676 def _object_cast_to_LennardJonesPairScore(*args):
677  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
678  return _IMP_atom._object_cast_to_LennardJonesPairScore(*args)
679 _object_types.append("Mol2Selector")
680 
681 
682 def _object_cast_to_Mol2Selector(*args):
683  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
684  return _IMP_atom._object_cast_to_Mol2Selector(*args)
685 _object_types.append("MolecularDynamics")
686 
687 
688 def _object_cast_to_MolecularDynamics(*args):
689  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
690  return _IMP_atom._object_cast_to_MolecularDynamics(*args)
691 _object_types.append("NPDBSelector")
692 
693 
694 def _object_cast_to_NPDBSelector(*args):
695  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
696  return _IMP_atom._object_cast_to_NPDBSelector(*args)
697 _object_types.append("NonAlternativePDBSelector")
698 
699 
700 def _object_cast_to_NonAlternativePDBSelector(*args):
701  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
702  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(*args)
703 _object_types.append("NonHydrogenMol2Selector")
704 
705 
706 def _object_cast_to_NonHydrogenMol2Selector(*args):
707  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
708  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(*args)
709 _object_types.append("NonWaterNonHydrogenPDBSelector")
710 
711 
712 def _object_cast_to_NonWaterNonHydrogenPDBSelector(*args):
713  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
714  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(*args)
715 _object_types.append("NonWaterPDBSelector")
716 
717 
718 def _object_cast_to_NonWaterPDBSelector(*args):
719  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
720  return _IMP_atom._object_cast_to_NonWaterPDBSelector(*args)
721 _object_types.append("NotPDBSelector")
722 
723 
724 def _object_cast_to_NotPDBSelector(*args):
725  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
726  return _IMP_atom._object_cast_to_NotPDBSelector(*args)
727 _object_types.append("OrPDBSelector")
728 
729 
730 def _object_cast_to_OrPDBSelector(*args):
731  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
732  return _IMP_atom._object_cast_to_OrPDBSelector(*args)
733 _object_types.append("PPDBSelector")
734 
735 
736 def _object_cast_to_PPDBSelector(*args):
737  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
738  return _IMP_atom._object_cast_to_PPDBSelector(*args)
739 _object_types.append("ProteinLigandAtomPairScore")
740 
741 
742 def _object_cast_to_ProteinLigandAtomPairScore(*args):
743  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
744  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(*args)
745 _object_types.append("ProteinLigandRestraint")
746 
747 
748 def _object_cast_to_ProteinLigandRestraint(*args):
749  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
750  return _IMP_atom._object_cast_to_ProteinLigandRestraint(*args)
751 _object_types.append("SameResiduePairFilter")
752 
753 
754 def _object_cast_to_SameResiduePairFilter(*args):
755  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
756  return _IMP_atom._object_cast_to_SameResiduePairFilter(*args)
757 _object_types.append("SmoothingFunction")
758 
759 
760 def _object_cast_to_SmoothingFunction(*args):
761  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
762  return _IMP_atom._object_cast_to_SmoothingFunction(*args)
763 _object_types.append("StereochemistryPairFilter")
764 
765 
766 def _object_cast_to_StereochemistryPairFilter(*args):
767  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
768  return _IMP_atom._object_cast_to_StereochemistryPairFilter(*args)
769 _object_types.append("VelocityScalingOptimizerState")
770 
771 
772 def _object_cast_to_VelocityScalingOptimizerState(*args):
773  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
774  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(*args)
775 _object_types.append("WaterPDBSelector")
776 
777 
778 def _object_cast_to_WaterPDBSelector(*args):
779  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
780  return _IMP_atom._object_cast_to_WaterPDBSelector(*args)
781 _object_types.append("WritePDBOptimizerState")
782 
783 
784 def _object_cast_to_WritePDBOptimizerState(*args):
785  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
786  return _IMP_atom._object_cast_to_WritePDBOptimizerState(*args)
787 AtomTypes=list
788 _plural_types.append("AtomTypes")
789 _value_types.append("AtomType")
790 
791 CHARMMAtomTopologies=list
792 _plural_types.append("CHARMMAtomTopologies")
793 _value_types.append("CHARMMAtomTopology")
794 
795 CHARMMBondEndpoints=list
796 _plural_types.append("CHARMMBondEndpoints")
797 _value_types.append("CHARMMBondEndpoint")
798 
799 CHARMMBondParametersList=list
800 _plural_types.append("CHARMMBondParametersList")
801 _value_types.append("CHARMMBondParameters")
802 
803 CHARMMDihedralParametersList=list
804 _plural_types.append("CHARMMDihedralParametersList")
805 _value_types.append("CHARMMDihedralParameters")
806 
807 _object_types.append("CHARMMIdealResidueTopology")
808 
809 
810 def _object_cast_to_CHARMMIdealResidueTopology(*args):
811  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
812  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(*args)
813 CHARMMInternalCoordinates=list
814 _plural_types.append("CHARMMInternalCoordinates")
815 _value_types.append("CHARMMInternalCoordinate")
816 
817 _object_types.append("CHARMMPatch")
818 
819 
820 def _object_cast_to_CHARMMPatch(*args):
821  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
822  return _IMP_atom._object_cast_to_CHARMMPatch(*args)
823 _object_types.append("CHARMMResidueTopologyBase")
824 
825 
826 def _object_cast_to_CHARMMResidueTopologyBase(*args):
827  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
828  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(*args)
829 RMSDCalculators=list
830 _plural_types.append("RMSDCalculators")
831 _value_types.append("RMSDCalculator")
832 
833 ResidueTypes=list
834 _plural_types.append("ResidueTypes")
835 _value_types.append("ResidueType")
836 
837 Selections=list
838 _plural_types.append("Selections")
839 _value_types.append("Selection")
840 
841 _object_types.append("RemoveRigidMotionOptimizerState")
842 
843 
844 def _object_cast_to_RemoveRigidMotionOptimizerState(*args):
845  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
846  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(*args)
847 _object_types.append("BerendsenThermostatOptimizerState")
848 
849 
850 def _object_cast_to_BerendsenThermostatOptimizerState(*args):
851  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
852  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(*args)
853 _object_types.append("LangevinThermostatOptimizerState")
854 
855 
856 def _object_cast_to_LangevinThermostatOptimizerState(*args):
857  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
858  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(*args)
859 _object_types.append("SelectionGeometry")
860 
861 
862 def _object_cast_to_SelectionGeometry(*args):
863  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
864  return _IMP_atom._object_cast_to_SelectionGeometry(*args)
865 _object_types.append("HierarchyGeometry")
866 
867 
868 def _object_cast_to_HierarchyGeometry(*args):
869  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
870  return _IMP_atom._object_cast_to_HierarchyGeometry(*args)
871 _object_types.append("HierarchiesGeometry")
872 
873 
874 def _object_cast_to_HierarchiesGeometry(*args):
875  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
876  return _IMP_atom._object_cast_to_HierarchiesGeometry(*args)
877 _object_types.append("BondGeometry")
878 
879 
880 def _object_cast_to_BondGeometry(*args):
881  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
882  return _IMP_atom._object_cast_to_BondGeometry(*args)
883 _object_types.append("BondsGeometry")
884 
885 
886 def _object_cast_to_BondsGeometry(*args):
887  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
888  return _IMP_atom._object_cast_to_BondsGeometry(*args)
889 CHARMMDihedrals=list
890 _plural_types.append("CHARMMDihedrals")
891 _value_types.append("CHARMMDihedral")
892 
893 CHARMMBonds=list
894 _plural_types.append("CHARMMBonds")
895 _value_types.append("CHARMMBond")
896 
897 CHARMMAngles=list
898 _plural_types.append("CHARMMAngles")
899 _value_types.append("CHARMMAngle")
900 
901 class Bond(IMP.kernel.Decorator):
902  """Proxy of C++ IMP::atom::Bond class"""
903  __swig_setmethods__ = {}
904  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
905  __setattr__ = lambda self, name, value: _swig_setattr(self, Bond, name, value)
906  __swig_getmethods__ = {}
907  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
908  __getattr__ = lambda self, name: _swig_getattr(self, Bond, name)
909  def __init__(self, *args):
910  """
911  __init__(IMP::atom::Bond self) -> Bond
912  __init__(IMP::atom::Bond self, Model m, IMP::kernel::ParticleIndex id) -> Bond
913  __init__(IMP::atom::Bond self, Particle p) -> Bond
914  """
915  this = _IMP_atom.new_Bond(*args)
916  try: self.this.append(this)
917  except: self.this = this
918  def decorate_particle(*args):
919  """decorate_particle(Particle p) -> Bond"""
920  return _IMP_atom.Bond_decorate_particle(*args)
921 
922  if _newclass:decorate_particle = staticmethod(decorate_particle)
923  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
924  def show(self, *args):
925  """
926  show(Bond self, _ostream out=std::cout)
927  show(Bond self)
928  """
929  return _IMP_atom.Bond_show(self, *args)
930 
931  def particle_is_instance(*args):
932  """particle_is_instance(Particle p) -> bool"""
933  return _IMP_atom.Bond_particle_is_instance(*args)
934 
935  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
936  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
937  UNKNOWN = _IMP_atom.Bond_UNKNOWN
938  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
939  SINGLE = _IMP_atom.Bond_SINGLE
940  DOUBLE = _IMP_atom.Bond_DOUBLE
941  TRIPLE = _IMP_atom.Bond_TRIPLE
942  HYDROGEN = _IMP_atom.Bond_HYDROGEN
943  SALT = _IMP_atom.Bond_SALT
944  PEPTIDE = _IMP_atom.Bond_PEPTIDE
945  AMIDE = _IMP_atom.Bond_AMIDE
946  AROMATIC = _IMP_atom.Bond_AROMATIC
947  def get_bonded(self, *args):
948  """get_bonded(Bond self, unsigned int i) -> Bonded"""
949  return _IMP_atom.Bond_get_bonded(self, *args)
950 
951  def get_type(self):
952  """get_type(Bond self) -> IMP::Int"""
953  return _IMP_atom.Bond_get_type(self)
954 
955  def set_type(self, *args):
956  """set_type(Bond self, IMP::Int t)"""
957  return _IMP_atom.Bond_set_type(self, *args)
958 
959  def get_order(self):
960  """get_order(Bond self) -> IMP::Int"""
961  return _IMP_atom.Bond_get_order(self)
962 
963  def set_order(self, *args):
964  """set_order(Bond self, IMP::Int t)"""
965  return _IMP_atom.Bond_set_order(self, *args)
966 
967  def get_length(self):
968  """get_length(Bond self) -> IMP::Float"""
969  return _IMP_atom.Bond_get_length(self)
970 
971  def set_length(self, *args):
972  """set_length(Bond self, IMP::Float t)"""
973  return _IMP_atom.Bond_set_length(self, *args)
974 
975  def get_stiffness(self):
976  """get_stiffness(Bond self) -> IMP::Float"""
977  return _IMP_atom.Bond_get_stiffness(self)
978 
979  def set_stiffness(self, *args):
980  """set_stiffness(Bond self, IMP::Float t)"""
981  return _IMP_atom.Bond_set_stiffness(self, *args)
982 
983  def get_length_key():
984  """get_length_key() -> FloatKey"""
985  return _IMP_atom.Bond_get_length_key()
986 
987  if _newclass:get_length_key = staticmethod(get_length_key)
988  __swig_getmethods__["get_length_key"] = lambda x: get_length_key
989  def add_attribute(self, *args):
990  """
991  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
992  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
993  add_attribute(Bond self, IntKey a0, IMP::Int a1)
994  add_attribute(Bond self, StringKey a0, IMP::String a1)
995  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
996  add_attribute(Bond self, ObjectKey a0, IMP::Object * a1)
997  """
998  return _IMP_atom.Bond_add_attribute(self, *args)
999 
1000  def get_value(self, *args):
1001  """
1002  get_value(Bond self, FloatKey a0) -> IMP::Float
1003  get_value(Bond self, IntKey a0) -> IMP::Int
1004  get_value(Bond self, StringKey a0) -> IMP::String
1005  get_value(Bond self, ParticleIndexKey a0) -> Particle
1006  get_value(Bond self, ObjectKey a0) -> IMP::Object *
1007  """
1008  return _IMP_atom.Bond_get_value(self, *args)
1009 
1010  def set_value(self, *args):
1011  """
1012  set_value(Bond self, FloatKey a0, IMP::Float a1)
1013  set_value(Bond self, IntKey a0, IMP::Int a1)
1014  set_value(Bond self, StringKey a0, IMP::String a1)
1015  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1016  set_value(Bond self, ObjectKey a0, IMP::Object * a1)
1017  """
1018  return _IMP_atom.Bond_set_value(self, *args)
1019 
1020  def remove_attribute(self, *args):
1021  """
1022  remove_attribute(Bond self, FloatKey a0)
1023  remove_attribute(Bond self, IntKey a0)
1024  remove_attribute(Bond self, StringKey a0)
1025  remove_attribute(Bond self, ParticleIndexKey a0)
1026  remove_attribute(Bond self, ObjectKey a0)
1027  """
1028  return _IMP_atom.Bond_remove_attribute(self, *args)
1029 
1030  def has_attribute(self, *args):
1031  """
1032  has_attribute(Bond self, FloatKey a0) -> bool
1033  has_attribute(Bond self, IntKey a0) -> bool
1034  has_attribute(Bond self, StringKey a0) -> bool
1035  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1036  has_attribute(Bond self, ObjectKey a0) -> bool
1037  """
1038  return _IMP_atom.Bond_has_attribute(self, *args)
1039 
1040  def get_derivative(self, *args):
1041  """get_derivative(Bond self, FloatKey a0) -> double"""
1042  return _IMP_atom.Bond_get_derivative(self, *args)
1043 
1044  def get_name(self):
1045  """get_name(Bond self) -> std::string"""
1046  return _IMP_atom.Bond_get_name(self)
1047 
1048  def clear_caches(self):
1049  """clear_caches(Bond self)"""
1050  return _IMP_atom.Bond_clear_caches(self)
1051 
1052  def set_name(self, *args):
1053  """set_name(Bond self, std::string a0)"""
1054  return _IMP_atom.Bond_set_name(self, *args)
1055 
1056  def set_check_level(self, *args):
1057  """set_check_level(Bond self, IMP::base::CheckLevel a0)"""
1058  return _IMP_atom.Bond_set_check_level(self, *args)
1059 
1060  def add_to_derivative(self, *args):
1061  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1062  return _IMP_atom.Bond_add_to_derivative(self, *args)
1063 
1064  def set_is_optimized(self, *args):
1065  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1066  return _IMP_atom.Bond_set_is_optimized(self, *args)
1067 
1068  def get_is_optimized(self, *args):
1069  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1070  return _IMP_atom.Bond_get_is_optimized(self, *args)
1071 
1072  def get_check_level(self):
1073  """get_check_level(Bond self) -> IMP::base::CheckLevel"""
1074  return _IMP_atom.Bond_get_check_level(self)
1075 
1076  def __eq__(self, *args):
1077  """
1078  __eq__(Bond self, Bond o) -> bool
1079  __eq__(Bond self, Particle d) -> bool
1080  """
1081  return _IMP_atom.Bond___eq__(self, *args)
1082 
1083  def __ne__(self, *args):
1084  """
1085  __ne__(Bond self, Bond o) -> bool
1086  __ne__(Bond self, Particle d) -> bool
1087  """
1088  return _IMP_atom.Bond___ne__(self, *args)
1089 
1090  def __le__(self, *args):
1091  """
1092  __le__(Bond self, Bond o) -> bool
1093  __le__(Bond self, Particle d) -> bool
1094  """
1095  return _IMP_atom.Bond___le__(self, *args)
1096 
1097  def __lt__(self, *args):
1098  """
1099  __lt__(Bond self, Bond o) -> bool
1100  __lt__(Bond self, Particle d) -> bool
1101  """
1102  return _IMP_atom.Bond___lt__(self, *args)
1103 
1104  def __ge__(self, *args):
1105  """
1106  __ge__(Bond self, Bond o) -> bool
1107  __ge__(Bond self, Particle d) -> bool
1108  """
1109  return _IMP_atom.Bond___ge__(self, *args)
1110 
1111  def __gt__(self, *args):
1112  """
1113  __gt__(Bond self, Bond o) -> bool
1114  __gt__(Bond self, Particle d) -> bool
1115  """
1116  return _IMP_atom.Bond___gt__(self, *args)
1117 
1118  def __str__(self):
1119  """__str__(Bond self) -> std::string"""
1120  return _IMP_atom.Bond___str__(self)
1121 
1122  def __repr__(self):
1123  """__repr__(Bond self) -> std::string"""
1124  return _IMP_atom.Bond___repr__(self)
1125 
1126  __swig_destroy__ = _IMP_atom.delete_Bond
1127  __del__ = lambda self : None;
1128 Bond_swigregister = _IMP_atom.Bond_swigregister
1129 Bond_swigregister(Bond)
1130 
1131 def Bond_decorate_particle(*args):
1132  """Bond_decorate_particle(Particle p) -> Bond"""
1133  return _IMP_atom.Bond_decorate_particle(*args)
1134 
1135 def Bond_particle_is_instance(*args):
1136  """Bond_particle_is_instance(Particle p) -> bool"""
1137  return _IMP_atom.Bond_particle_is_instance(*args)
1138 
1139 def Bond_get_length_key():
1140  """Bond_get_length_key() -> FloatKey"""
1141  return _IMP_atom.Bond_get_length_key()
1142 
1143 class Bonded(IMP.kernel.Decorator):
1144  """Proxy of C++ IMP::atom::Bonded class"""
1145  __swig_setmethods__ = {}
1146  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1147  __setattr__ = lambda self, name, value: _swig_setattr(self, Bonded, name, value)
1148  __swig_getmethods__ = {}
1149  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1150  __getattr__ = lambda self, name: _swig_getattr(self, Bonded, name)
1151  def __init__(self, *args):
1152  """
1153  __init__(IMP::atom::Bonded self) -> Bonded
1154  __init__(IMP::atom::Bonded self, Model m, IMP::kernel::ParticleIndex id) -> Bonded
1155  __init__(IMP::atom::Bonded self, Particle p) -> Bonded
1156  """
1157  this = _IMP_atom.new_Bonded(*args)
1158  try: self.this.append(this)
1159  except: self.this = this
1160  def decorate_particle(*args):
1161  """decorate_particle(Particle p) -> Bonded"""
1162  return _IMP_atom.Bonded_decorate_particle(*args)
1163 
1164  if _newclass:decorate_particle = staticmethod(decorate_particle)
1165  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1166  def show(self, *args):
1167  """
1168  show(Bonded self, _ostream out=std::cout)
1169  show(Bonded self)
1170  """
1171  return _IMP_atom.Bonded_show(self, *args)
1172 
1173  def particle_is_instance(*args):
1174  """particle_is_instance(Particle p) -> bool"""
1175  return _IMP_atom.Bonded_particle_is_instance(*args)
1176 
1177  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1178  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1179  def setup_particle(*args):
1180  """setup_particle(Particle p) -> Bonded"""
1181  return _IMP_atom.Bonded_setup_particle(*args)
1182 
1183  if _newclass:setup_particle = staticmethod(setup_particle)
1184  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1185  def get_number_of_bonds(self):
1186  """get_number_of_bonds(Bonded self) -> unsigned int"""
1187  return _IMP_atom.Bonded_get_number_of_bonds(self)
1188 
1189  def get_bonds(self):
1190  """get_bonds(Bonded self) -> IMP::kernel::ParticleIndexes"""
1191  return _IMP_atom.Bonded_get_bonds(self)
1192 
1193  def get_bond(self, *args):
1194  """get_bond(Bonded self, unsigned int i) -> Bond"""
1195  return _IMP_atom.Bonded_get_bond(self, *args)
1196 
1197  def get_bonded(self, *args):
1198  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1199  return _IMP_atom.Bonded_get_bonded(self, *args)
1200 
1201  def add_attribute(self, *args):
1202  """
1203  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1204  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1205  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1206  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1207  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1208  add_attribute(Bonded self, ObjectKey a0, IMP::Object * a1)
1209  """
1210  return _IMP_atom.Bonded_add_attribute(self, *args)
1211 
1212  def get_value(self, *args):
1213  """
1214  get_value(Bonded self, FloatKey a0) -> IMP::Float
1215  get_value(Bonded self, IntKey a0) -> IMP::Int
1216  get_value(Bonded self, StringKey a0) -> IMP::String
1217  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1218  get_value(Bonded self, ObjectKey a0) -> IMP::Object *
1219  """
1220  return _IMP_atom.Bonded_get_value(self, *args)
1221 
1222  def set_value(self, *args):
1223  """
1224  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1225  set_value(Bonded self, IntKey a0, IMP::Int a1)
1226  set_value(Bonded self, StringKey a0, IMP::String a1)
1227  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1228  set_value(Bonded self, ObjectKey a0, IMP::Object * a1)
1229  """
1230  return _IMP_atom.Bonded_set_value(self, *args)
1231 
1232  def remove_attribute(self, *args):
1233  """
1234  remove_attribute(Bonded self, FloatKey a0)
1235  remove_attribute(Bonded self, IntKey a0)
1236  remove_attribute(Bonded self, StringKey a0)
1237  remove_attribute(Bonded self, ParticleIndexKey a0)
1238  remove_attribute(Bonded self, ObjectKey a0)
1239  """
1240  return _IMP_atom.Bonded_remove_attribute(self, *args)
1241 
1242  def has_attribute(self, *args):
1243  """
1244  has_attribute(Bonded self, FloatKey a0) -> bool
1245  has_attribute(Bonded self, IntKey a0) -> bool
1246  has_attribute(Bonded self, StringKey a0) -> bool
1247  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1248  has_attribute(Bonded self, ObjectKey a0) -> bool
1249  """
1250  return _IMP_atom.Bonded_has_attribute(self, *args)
1251 
1252  def get_derivative(self, *args):
1253  """get_derivative(Bonded self, FloatKey a0) -> double"""
1254  return _IMP_atom.Bonded_get_derivative(self, *args)
1255 
1256  def get_name(self):
1257  """get_name(Bonded self) -> std::string"""
1258  return _IMP_atom.Bonded_get_name(self)
1259 
1260  def clear_caches(self):
1261  """clear_caches(Bonded self)"""
1262  return _IMP_atom.Bonded_clear_caches(self)
1263 
1264  def set_name(self, *args):
1265  """set_name(Bonded self, std::string a0)"""
1266  return _IMP_atom.Bonded_set_name(self, *args)
1267 
1268  def set_check_level(self, *args):
1269  """set_check_level(Bonded self, IMP::base::CheckLevel a0)"""
1270  return _IMP_atom.Bonded_set_check_level(self, *args)
1271 
1272  def add_to_derivative(self, *args):
1273  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1274  return _IMP_atom.Bonded_add_to_derivative(self, *args)
1275 
1276  def set_is_optimized(self, *args):
1277  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1278  return _IMP_atom.Bonded_set_is_optimized(self, *args)
1279 
1280  def get_is_optimized(self, *args):
1281  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1282  return _IMP_atom.Bonded_get_is_optimized(self, *args)
1283 
1284  def get_check_level(self):
1285  """get_check_level(Bonded self) -> IMP::base::CheckLevel"""
1286  return _IMP_atom.Bonded_get_check_level(self)
1287 
1288  def __eq__(self, *args):
1289  """
1290  __eq__(Bonded self, Bonded o) -> bool
1291  __eq__(Bonded self, Particle d) -> bool
1292  """
1293  return _IMP_atom.Bonded___eq__(self, *args)
1294 
1295  def __ne__(self, *args):
1296  """
1297  __ne__(Bonded self, Bonded o) -> bool
1298  __ne__(Bonded self, Particle d) -> bool
1299  """
1300  return _IMP_atom.Bonded___ne__(self, *args)
1301 
1302  def __le__(self, *args):
1303  """
1304  __le__(Bonded self, Bonded o) -> bool
1305  __le__(Bonded self, Particle d) -> bool
1306  """
1307  return _IMP_atom.Bonded___le__(self, *args)
1308 
1309  def __lt__(self, *args):
1310  """
1311  __lt__(Bonded self, Bonded o) -> bool
1312  __lt__(Bonded self, Particle d) -> bool
1313  """
1314  return _IMP_atom.Bonded___lt__(self, *args)
1315 
1316  def __ge__(self, *args):
1317  """
1318  __ge__(Bonded self, Bonded o) -> bool
1319  __ge__(Bonded self, Particle d) -> bool
1320  """
1321  return _IMP_atom.Bonded___ge__(self, *args)
1322 
1323  def __gt__(self, *args):
1324  """
1325  __gt__(Bonded self, Bonded o) -> bool
1326  __gt__(Bonded self, Particle d) -> bool
1327  """
1328  return _IMP_atom.Bonded___gt__(self, *args)
1329 
1330  def __str__(self):
1331  """__str__(Bonded self) -> std::string"""
1332  return _IMP_atom.Bonded___str__(self)
1333 
1334  def __repr__(self):
1335  """__repr__(Bonded self) -> std::string"""
1336  return _IMP_atom.Bonded___repr__(self)
1337 
1338  __swig_destroy__ = _IMP_atom.delete_Bonded
1339  __del__ = lambda self : None;
1340 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1341 Bonded_swigregister(Bonded)
1342 
1343 def Bonded_decorate_particle(*args):
1344  """Bonded_decorate_particle(Particle p) -> Bonded"""
1345  return _IMP_atom.Bonded_decorate_particle(*args)
1346 
1347 def Bonded_particle_is_instance(*args):
1348  """Bonded_particle_is_instance(Particle p) -> bool"""
1349  return _IMP_atom.Bonded_particle_is_instance(*args)
1350 
1351 def Bonded_setup_particle(*args):
1352  """Bonded_setup_particle(Particle p) -> Bonded"""
1353  return _IMP_atom.Bonded_setup_particle(*args)
1354 
1355 
1356 def create_custom_bond(*args):
1357  """
1358  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1359  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1360  """
1361  return _IMP_atom.create_custom_bond(*args)
1362 
1363 def create_bond(*args):
1364  """
1365  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1366  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1367  """
1368  return _IMP_atom.create_bond(*args)
1369 
1370 def destroy_bond(*args):
1371  """destroy_bond(Bond b)"""
1372  return _IMP_atom.destroy_bond(*args)
1373 
1374 def get_bond(*args):
1375  """get_bond(Bonded a, Bonded b) -> Bond"""
1376  return _IMP_atom.get_bond(*args)
1377 class BondGeometry(IMP.display.SingletonGeometry):
1378  """Proxy of C++ IMP::atom::BondGeometry class"""
1379  __swig_setmethods__ = {}
1380  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1381  __setattr__ = lambda self, name, value: _swig_setattr(self, BondGeometry, name, value)
1382  __swig_getmethods__ = {}
1383  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1384  __getattr__ = lambda self, name: _swig_getattr(self, BondGeometry, name)
1385  def __init__(self, *args):
1386  """
1387  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1388  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1389  """
1390  this = _IMP_atom.new_BondGeometry(*args)
1391  try: self.this.append(this)
1392  except: self.this = this
1393  def get_version_info(self):
1394  """get_version_info(BondGeometry self) -> VersionInfo"""
1395  return _IMP_atom.BondGeometry_get_version_info(self)
1396 
1397  __swig_destroy__ = _IMP_atom.delete_BondGeometry
1398  __del__ = lambda self : None;
1399  def __str__(self):
1400  """__str__(BondGeometry self) -> std::string"""
1401  return _IMP_atom.BondGeometry___str__(self)
1402 
1403  def __repr__(self):
1404  """__repr__(BondGeometry self) -> std::string"""
1405  return _IMP_atom.BondGeometry___repr__(self)
1406 
1407  def get_from(o):
1408  return _object_cast_to_BondGeometry(o)
1409  get_from = staticmethod(get_from)
1410 
1411 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1412 BondGeometry_swigregister(BondGeometry)
1413 
1414 class BondsGeometry(IMP.display.SingletonsGeometry):
1415  """Proxy of C++ IMP::atom::BondsGeometry class"""
1416  __swig_setmethods__ = {}
1417  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1418  __setattr__ = lambda self, name, value: _swig_setattr(self, BondsGeometry, name, value)
1419  __swig_getmethods__ = {}
1420  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1421  __getattr__ = lambda self, name: _swig_getattr(self, BondsGeometry, name)
1422  def __init__(self, *args):
1423  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1424  this = _IMP_atom.new_BondsGeometry(*args)
1425  try: self.this.append(this)
1426  except: self.this = this
1427  def get_version_info(self):
1428  """get_version_info(BondsGeometry self) -> VersionInfo"""
1429  return _IMP_atom.BondsGeometry_get_version_info(self)
1430 
1431  __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1432  __del__ = lambda self : None;
1433  def __str__(self):
1434  """__str__(BondsGeometry self) -> std::string"""
1435  return _IMP_atom.BondsGeometry___str__(self)
1436 
1437  def __repr__(self):
1438  """__repr__(BondsGeometry self) -> std::string"""
1439  return _IMP_atom.BondsGeometry___repr__(self)
1440 
1441  def get_from(o):
1442  return _object_cast_to_BondsGeometry(o)
1443  get_from = staticmethod(get_from)
1444 
1445 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1446 BondsGeometry_swigregister(BondsGeometry)
1447 
1448 class Hierarchy(IMP.core.Hierarchy):
1449  """Proxy of C++ IMP::atom::Hierarchy class"""
1450  __swig_setmethods__ = {}
1451  for _s in [IMP.core.Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1452  __setattr__ = lambda self, name, value: _swig_setattr(self, Hierarchy, name, value)
1453  __swig_getmethods__ = {}
1454  for _s in [IMP.core.Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1455  __getattr__ = lambda self, name: _swig_getattr(self, Hierarchy, name)
1456  def decorate_particle(*args):
1457  """decorate_particle(Particle p) -> Hierarchy"""
1458  return _IMP_atom.Hierarchy_decorate_particle(*args)
1459 
1460  if _newclass:decorate_particle = staticmethod(decorate_particle)
1461  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1462  def __init__(self, *args):
1463  """
1464  __init__(IMP::atom::Hierarchy self, Particle p) -> Hierarchy
1465  __init__(IMP::atom::Hierarchy self, Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1466  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1467  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1468  """
1469  this = _IMP_atom.new_Hierarchy(*args)
1470  try: self.this.append(this)
1471  except: self.this = this
1472  def setup_particle(*args):
1473  """
1474  setup_particle(Particle p, IMP::kernel::ParticlesTemp const & children) -> Hierarchy
1475  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::kernel::ParticlesTemp const & children=IMP::kernel::ParticlesTemp()) -> Hierarchy
1476  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1477  setup_particle(Particle p) -> Hierarchy
1478  """
1479  return _IMP_atom.Hierarchy_setup_particle(*args)
1480 
1481  if _newclass:setup_particle = staticmethod(setup_particle)
1482  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1483  def particle_is_instance(*args):
1484  """
1485  particle_is_instance(Particle p) -> bool
1486  particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1487  """
1488  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1489 
1490  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1491  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1492  def get_is_valid(self, *args):
1493  """get_is_valid(Hierarchy self, bool print_info) -> bool"""
1494  return _IMP_atom.Hierarchy_get_is_valid(self, *args)
1495 
1496  def add_child(self, *args):
1497  """add_child(Hierarchy self, Hierarchy o)"""
1498  return _IMP_atom.Hierarchy_add_child(self, *args)
1499 
1500  def get_child(self, *args):
1501  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1502  return _IMP_atom.Hierarchy_get_child(self, *args)
1503 
1504  def get_children(self):
1505  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1506  return _IMP_atom.Hierarchy_get_children(self)
1507 
1508  def get_parent(self):
1509  """get_parent(Hierarchy self) -> Hierarchy"""
1510  return _IMP_atom.Hierarchy_get_parent(self)
1511 
1512  def get_as_atom(self):
1513  """get_as_atom(Hierarchy self) -> Atom"""
1514  return _IMP_atom.Hierarchy_get_as_atom(self)
1515 
1516  def get_as_residue(self):
1517  """get_as_residue(Hierarchy self) -> Residue"""
1518  return _IMP_atom.Hierarchy_get_as_residue(self)
1519 
1520  def get_as_chain(self):
1521  """get_as_chain(Hierarchy self) -> Chain"""
1522  return _IMP_atom.Hierarchy_get_as_chain(self)
1523 
1524  def get_as_molecule(self):
1525  """get_as_molecule(Hierarchy self) -> Molecule"""
1526  return _IMP_atom.Hierarchy_get_as_molecule(self)
1527 
1528  def get_as_domain(self):
1529  """get_as_domain(Hierarchy self) -> Domain"""
1530  return _IMP_atom.Hierarchy_get_as_domain(self)
1531 
1532  def get_as_fragment(self):
1533  """get_as_fragment(Hierarchy self) -> Fragment"""
1534  return _IMP_atom.Hierarchy_get_as_fragment(self)
1535 
1536  def get_as_xyz(self):
1537  """get_as_xyz(Hierarchy self) -> XYZ"""
1538  return _IMP_atom.Hierarchy_get_as_xyz(self)
1539 
1540  def get_as_xyzr(self):
1541  """get_as_xyzr(Hierarchy self) -> XYZR"""
1542  return _IMP_atom.Hierarchy_get_as_xyzr(self)
1543 
1544  def get_as_mass(self):
1545  """get_as_mass(Hierarchy self) -> Mass"""
1546  return _IMP_atom.Hierarchy_get_as_mass(self)
1547 
1548  def get_traits():
1549  """get_traits() -> HierarchyTraits"""
1550  return _IMP_atom.Hierarchy_get_traits()
1551 
1552  if _newclass:get_traits = staticmethod(get_traits)
1553  __swig_getmethods__["get_traits"] = lambda x: get_traits
1554  def show(self, *args):
1555  """
1556  show(Hierarchy self, _ostream out=std::cout)
1557  show(Hierarchy self)
1558  """
1559  return _IMP_atom.Hierarchy_show(self, *args)
1560 
1561  def add_attribute(self, *args):
1562  """
1563  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1564  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1565  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1566  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1567  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1568  add_attribute(Hierarchy self, ObjectKey a0, IMP::Object * a1)
1569  """
1570  return _IMP_atom.Hierarchy_add_attribute(self, *args)
1571 
1572  def get_value(self, *args):
1573  """
1574  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1575  get_value(Hierarchy self, IntKey a0) -> IMP::Int
1576  get_value(Hierarchy self, StringKey a0) -> IMP::String
1577  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1578  get_value(Hierarchy self, ObjectKey a0) -> IMP::Object *
1579  """
1580  return _IMP_atom.Hierarchy_get_value(self, *args)
1581 
1582  def set_value(self, *args):
1583  """
1584  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1585  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1586  set_value(Hierarchy self, StringKey a0, IMP::String a1)
1587  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1588  set_value(Hierarchy self, ObjectKey a0, IMP::Object * a1)
1589  """
1590  return _IMP_atom.Hierarchy_set_value(self, *args)
1591 
1592  def remove_attribute(self, *args):
1593  """
1594  remove_attribute(Hierarchy self, FloatKey a0)
1595  remove_attribute(Hierarchy self, IntKey a0)
1596  remove_attribute(Hierarchy self, StringKey a0)
1597  remove_attribute(Hierarchy self, ParticleIndexKey a0)
1598  remove_attribute(Hierarchy self, ObjectKey a0)
1599  """
1600  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1601 
1602  def has_attribute(self, *args):
1603  """
1604  has_attribute(Hierarchy self, FloatKey a0) -> bool
1605  has_attribute(Hierarchy self, IntKey a0) -> bool
1606  has_attribute(Hierarchy self, StringKey a0) -> bool
1607  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1608  has_attribute(Hierarchy self, ObjectKey a0) -> bool
1609  """
1610  return _IMP_atom.Hierarchy_has_attribute(self, *args)
1611 
1612  def get_derivative(self, *args):
1613  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
1614  return _IMP_atom.Hierarchy_get_derivative(self, *args)
1615 
1616  def get_name(self):
1617  """get_name(Hierarchy self) -> std::string"""
1618  return _IMP_atom.Hierarchy_get_name(self)
1619 
1620  def clear_caches(self):
1621  """clear_caches(Hierarchy self)"""
1622  return _IMP_atom.Hierarchy_clear_caches(self)
1623 
1624  def set_name(self, *args):
1625  """set_name(Hierarchy self, std::string a0)"""
1626  return _IMP_atom.Hierarchy_set_name(self, *args)
1627 
1628  def set_check_level(self, *args):
1629  """set_check_level(Hierarchy self, IMP::base::CheckLevel a0)"""
1630  return _IMP_atom.Hierarchy_set_check_level(self, *args)
1631 
1632  def add_to_derivative(self, *args):
1633  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1634  return _IMP_atom.Hierarchy_add_to_derivative(self, *args)
1635 
1636  def set_is_optimized(self, *args):
1637  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1638  return _IMP_atom.Hierarchy_set_is_optimized(self, *args)
1639 
1640  def get_is_optimized(self, *args):
1641  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1642  return _IMP_atom.Hierarchy_get_is_optimized(self, *args)
1643 
1644  def get_check_level(self):
1645  """get_check_level(Hierarchy self) -> IMP::base::CheckLevel"""
1646  return _IMP_atom.Hierarchy_get_check_level(self)
1647 
1648  def __eq__(self, *args):
1649  """
1650  __eq__(Hierarchy self, Hierarchy o) -> bool
1651  __eq__(Hierarchy self, Particle d) -> bool
1652  """
1653  return _IMP_atom.Hierarchy___eq__(self, *args)
1654 
1655  def __ne__(self, *args):
1656  """
1657  __ne__(Hierarchy self, Hierarchy o) -> bool
1658  __ne__(Hierarchy self, Particle d) -> bool
1659  """
1660  return _IMP_atom.Hierarchy___ne__(self, *args)
1661 
1662  def __le__(self, *args):
1663  """
1664  __le__(Hierarchy self, Hierarchy o) -> bool
1665  __le__(Hierarchy self, Particle d) -> bool
1666  """
1667  return _IMP_atom.Hierarchy___le__(self, *args)
1668 
1669  def __lt__(self, *args):
1670  """
1671  __lt__(Hierarchy self, Hierarchy o) -> bool
1672  __lt__(Hierarchy self, Particle d) -> bool
1673  """
1674  return _IMP_atom.Hierarchy___lt__(self, *args)
1675 
1676  def __ge__(self, *args):
1677  """
1678  __ge__(Hierarchy self, Hierarchy o) -> bool
1679  __ge__(Hierarchy self, Particle d) -> bool
1680  """
1681  return _IMP_atom.Hierarchy___ge__(self, *args)
1682 
1683  def __gt__(self, *args):
1684  """
1685  __gt__(Hierarchy self, Hierarchy o) -> bool
1686  __gt__(Hierarchy self, Particle d) -> bool
1687  """
1688  return _IMP_atom.Hierarchy___gt__(self, *args)
1689 
1690  def __str__(self):
1691  """__str__(Hierarchy self) -> std::string"""
1692  return _IMP_atom.Hierarchy___str__(self)
1693 
1694  def __repr__(self):
1695  """__repr__(Hierarchy self) -> std::string"""
1696  return _IMP_atom.Hierarchy___repr__(self)
1697 
1698  __swig_destroy__ = _IMP_atom.delete_Hierarchy
1699  __del__ = lambda self : None;
1700 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
1701 Hierarchy_swigregister(Hierarchy)
1702 
1703 def Hierarchy_decorate_particle(*args):
1704  """Hierarchy_decorate_particle(Particle p) -> Hierarchy"""
1705  return _IMP_atom.Hierarchy_decorate_particle(*args)
1706 
1707 def Hierarchy_setup_particle(*args):
1708  """
1709  setup_particle(Particle p, IMP::kernel::ParticlesTemp const & children) -> Hierarchy
1710  setup_particle(Model m, IMP::kernel::ParticleIndex pi, IMP::kernel::ParticlesTemp const & children=IMP::kernel::ParticlesTemp()) -> Hierarchy
1711  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Hierarchy
1712  Hierarchy_setup_particle(Particle p) -> Hierarchy
1713  """
1714  return _IMP_atom.Hierarchy_setup_particle(*args)
1715 
1716 def Hierarchy_particle_is_instance(*args):
1717  """
1718  particle_is_instance(Particle p) -> bool
1719  Hierarchy_particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
1720  """
1721  return _IMP_atom.Hierarchy_particle_is_instance(*args)
1722 
1723 def Hierarchy_get_traits():
1724  """Hierarchy_get_traits() -> HierarchyTraits"""
1725  return _IMP_atom.Hierarchy_get_traits()
1726 
1727 ATOM_TYPE = _IMP_atom.ATOM_TYPE
1728 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
1729 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
1730 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
1731 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
1732 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
1733 XYZ_TYPE = _IMP_atom.XYZ_TYPE
1734 XYZR_TYPE = _IMP_atom.XYZR_TYPE
1735 MASS_TYPE = _IMP_atom.MASS_TYPE
1736 
1737 def get_by_type(*args):
1738  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
1739  return _IMP_atom.get_by_type(*args)
1740 
1741 def create_fragment(*args):
1742  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
1743  return _IMP_atom.create_fragment(*args)
1744 
1745 def get_internal_bonds(*args):
1746  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
1747  return _IMP_atom.get_internal_bonds(*args)
1748 
1749 def get_root(*args):
1750  """get_root(Hierarchy h) -> Hierarchy"""
1751  return _IMP_atom.get_root(*args)
1752 
1753 def show(*args):
1754  """
1755  show(Hierarchy h, _ostream out=std::cout)
1756  show(Hierarchy h)
1757  """
1758  return _IMP_atom.show(*args)
1759 
1760 def create_rigid_body(*args):
1761  """
1762  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
1763  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
1764  create_rigid_body(Hierarchy h) -> RigidBody
1765  """
1766  return _IMP_atom.create_rigid_body(*args)
1767 
1768 def create_compatible_rigid_body(*args):
1769  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
1770  return _IMP_atom.create_compatible_rigid_body(*args)
1771 
1772 def setup_as_rigid_body(*args):
1773  """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
1774  return _IMP_atom.setup_as_rigid_body(*args)
1775 
1776 def get_is_heterogen(*args):
1777  """get_is_heterogen(Hierarchy h) -> bool"""
1778  return _IMP_atom.get_is_heterogen(*args)
1779 
1780 def create_clone(*args):
1781  """create_clone(Hierarchy d) -> Hierarchy"""
1782  return _IMP_atom.create_clone(*args)
1783 
1784 def create_clone_one(*args):
1785  """create_clone_one(Hierarchy d) -> Hierarchy"""
1786  return _IMP_atom.create_clone_one(*args)
1787 
1788 def destroy(*args):
1789  """destroy(Hierarchy d)"""
1790  return _IMP_atom.destroy(*args)
1791 
1792 def get_bounding_box(*args):
1793  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
1794  return _IMP_atom.get_bounding_box(*args)
1795 
1796 def get_bounding_sphere(*args):
1797  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
1798  return _IMP_atom.get_bounding_sphere(*args)
1799 class Angle(IMP.kernel.Decorator):
1800  """Proxy of C++ IMP::atom::Angle class"""
1801  __swig_setmethods__ = {}
1802  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1803  __setattr__ = lambda self, name, value: _swig_setattr(self, Angle, name, value)
1804  __swig_getmethods__ = {}
1805  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1806  __getattr__ = lambda self, name: _swig_getattr(self, Angle, name)
1807  def __init__(self, *args):
1808  """
1809  __init__(IMP::atom::Angle self) -> Angle
1810  __init__(IMP::atom::Angle self, Model m, IMP::kernel::ParticleIndex id) -> Angle
1811  __init__(IMP::atom::Angle self, Particle p) -> Angle
1812  """
1813  this = _IMP_atom.new_Angle(*args)
1814  try: self.this.append(this)
1815  except: self.this = this
1816  def decorate_particle(*args):
1817  """decorate_particle(Particle p) -> Angle"""
1818  return _IMP_atom.Angle_decorate_particle(*args)
1819 
1820  if _newclass:decorate_particle = staticmethod(decorate_particle)
1821  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1822  def show(self, *args):
1823  """
1824  show(Angle self, _ostream out=std::cout)
1825  show(Angle self)
1826  """
1827  return _IMP_atom.Angle_show(self, *args)
1828 
1829  def setup_particle(*args):
1830  """setup_particle(Particle p, XYZ a, XYZ b, XYZ c) -> Angle"""
1831  return _IMP_atom.Angle_setup_particle(*args)
1832 
1833  if _newclass:setup_particle = staticmethod(setup_particle)
1834  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1835  def particle_is_instance(*args):
1836  """particle_is_instance(Particle p) -> bool"""
1837  return _IMP_atom.Angle_particle_is_instance(*args)
1838 
1839  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
1840  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
1841  def get_particle(self, *args):
1842  """
1843  get_particle(Angle self) -> Particle
1844  get_particle(Angle self, unsigned int i) -> Particle
1845  """
1846  return _IMP_atom.Angle_get_particle(self, *args)
1847 
1848  def get_ideal(self):
1849  """get_ideal(Angle self) -> IMP::Float"""
1850  return _IMP_atom.Angle_get_ideal(self)
1851 
1852  def set_ideal(self, *args):
1853  """set_ideal(Angle self, IMP::Float t)"""
1854  return _IMP_atom.Angle_set_ideal(self, *args)
1855 
1856  def get_stiffness(self):
1857  """get_stiffness(Angle self) -> IMP::Float"""
1858  return _IMP_atom.Angle_get_stiffness(self)
1859 
1860  def set_stiffness(self, *args):
1861  """set_stiffness(Angle self, IMP::Float t)"""
1862  return _IMP_atom.Angle_set_stiffness(self, *args)
1863 
1864  def get_particle_key(*args):
1865  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
1866  return _IMP_atom.Angle_get_particle_key(*args)
1867 
1868  if _newclass:get_particle_key = staticmethod(get_particle_key)
1869  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
1870  def get_ideal_key():
1871  """get_ideal_key() -> FloatKey"""
1872  return _IMP_atom.Angle_get_ideal_key()
1873 
1874  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
1875  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
1876  def get_stiffness_key():
1877  """get_stiffness_key() -> FloatKey"""
1878  return _IMP_atom.Angle_get_stiffness_key()
1879 
1880  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
1881  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
1882  def add_attribute(self, *args):
1883  """
1884  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
1885  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
1886  add_attribute(Angle self, IntKey a0, IMP::Int a1)
1887  add_attribute(Angle self, StringKey a0, IMP::String a1)
1888  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
1889  add_attribute(Angle self, ObjectKey a0, IMP::Object * a1)
1890  """
1891  return _IMP_atom.Angle_add_attribute(self, *args)
1892 
1893  def get_value(self, *args):
1894  """
1895  get_value(Angle self, FloatKey a0) -> IMP::Float
1896  get_value(Angle self, IntKey a0) -> IMP::Int
1897  get_value(Angle self, StringKey a0) -> IMP::String
1898  get_value(Angle self, ParticleIndexKey a0) -> Particle
1899  get_value(Angle self, ObjectKey a0) -> IMP::Object *
1900  """
1901  return _IMP_atom.Angle_get_value(self, *args)
1902 
1903  def set_value(self, *args):
1904  """
1905  set_value(Angle self, FloatKey a0, IMP::Float a1)
1906  set_value(Angle self, IntKey a0, IMP::Int a1)
1907  set_value(Angle self, StringKey a0, IMP::String a1)
1908  set_value(Angle self, ParticleIndexKey a0, Particle a1)
1909  set_value(Angle self, ObjectKey a0, IMP::Object * a1)
1910  """
1911  return _IMP_atom.Angle_set_value(self, *args)
1912 
1913  def remove_attribute(self, *args):
1914  """
1915  remove_attribute(Angle self, FloatKey a0)
1916  remove_attribute(Angle self, IntKey a0)
1917  remove_attribute(Angle self, StringKey a0)
1918  remove_attribute(Angle self, ParticleIndexKey a0)
1919  remove_attribute(Angle self, ObjectKey a0)
1920  """
1921  return _IMP_atom.Angle_remove_attribute(self, *args)
1922 
1923  def has_attribute(self, *args):
1924  """
1925  has_attribute(Angle self, FloatKey a0) -> bool
1926  has_attribute(Angle self, IntKey a0) -> bool
1927  has_attribute(Angle self, StringKey a0) -> bool
1928  has_attribute(Angle self, ParticleIndexKey a0) -> bool
1929  has_attribute(Angle self, ObjectKey a0) -> bool
1930  """
1931  return _IMP_atom.Angle_has_attribute(self, *args)
1932 
1933  def get_derivative(self, *args):
1934  """get_derivative(Angle self, FloatKey a0) -> double"""
1935  return _IMP_atom.Angle_get_derivative(self, *args)
1936 
1937  def get_name(self):
1938  """get_name(Angle self) -> std::string"""
1939  return _IMP_atom.Angle_get_name(self)
1940 
1941  def clear_caches(self):
1942  """clear_caches(Angle self)"""
1943  return _IMP_atom.Angle_clear_caches(self)
1944 
1945  def set_name(self, *args):
1946  """set_name(Angle self, std::string a0)"""
1947  return _IMP_atom.Angle_set_name(self, *args)
1948 
1949  def set_check_level(self, *args):
1950  """set_check_level(Angle self, IMP::base::CheckLevel a0)"""
1951  return _IMP_atom.Angle_set_check_level(self, *args)
1952 
1953  def add_to_derivative(self, *args):
1954  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1955  return _IMP_atom.Angle_add_to_derivative(self, *args)
1956 
1957  def set_is_optimized(self, *args):
1958  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
1959  return _IMP_atom.Angle_set_is_optimized(self, *args)
1960 
1961  def get_is_optimized(self, *args):
1962  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
1963  return _IMP_atom.Angle_get_is_optimized(self, *args)
1964 
1965  def get_check_level(self):
1966  """get_check_level(Angle self) -> IMP::base::CheckLevel"""
1967  return _IMP_atom.Angle_get_check_level(self)
1968 
1969  def __eq__(self, *args):
1970  """
1971  __eq__(Angle self, Angle o) -> bool
1972  __eq__(Angle self, Particle d) -> bool
1973  """
1974  return _IMP_atom.Angle___eq__(self, *args)
1975 
1976  def __ne__(self, *args):
1977  """
1978  __ne__(Angle self, Angle o) -> bool
1979  __ne__(Angle self, Particle d) -> bool
1980  """
1981  return _IMP_atom.Angle___ne__(self, *args)
1982 
1983  def __le__(self, *args):
1984  """
1985  __le__(Angle self, Angle o) -> bool
1986  __le__(Angle self, Particle d) -> bool
1987  """
1988  return _IMP_atom.Angle___le__(self, *args)
1989 
1990  def __lt__(self, *args):
1991  """
1992  __lt__(Angle self, Angle o) -> bool
1993  __lt__(Angle self, Particle d) -> bool
1994  """
1995  return _IMP_atom.Angle___lt__(self, *args)
1996 
1997  def __ge__(self, *args):
1998  """
1999  __ge__(Angle self, Angle o) -> bool
2000  __ge__(Angle self, Particle d) -> bool
2001  """
2002  return _IMP_atom.Angle___ge__(self, *args)
2003 
2004  def __gt__(self, *args):
2005  """
2006  __gt__(Angle self, Angle o) -> bool
2007  __gt__(Angle self, Particle d) -> bool
2008  """
2009  return _IMP_atom.Angle___gt__(self, *args)
2010 
2011  def __str__(self):
2012  """__str__(Angle self) -> std::string"""
2013  return _IMP_atom.Angle___str__(self)
2014 
2015  def __repr__(self):
2016  """__repr__(Angle self) -> std::string"""
2017  return _IMP_atom.Angle___repr__(self)
2018 
2019  __swig_destroy__ = _IMP_atom.delete_Angle
2020  __del__ = lambda self : None;
2021 Angle_swigregister = _IMP_atom.Angle_swigregister
2022 Angle_swigregister(Angle)
2023 
2024 def Angle_decorate_particle(*args):
2025  """Angle_decorate_particle(Particle p) -> Angle"""
2026  return _IMP_atom.Angle_decorate_particle(*args)
2027 
2028 def Angle_setup_particle(*args):
2029  """Angle_setup_particle(Particle p, XYZ a, XYZ b, XYZ c) -> Angle"""
2030  return _IMP_atom.Angle_setup_particle(*args)
2031 
2032 def Angle_particle_is_instance(*args):
2033  """Angle_particle_is_instance(Particle p) -> bool"""
2034  return _IMP_atom.Angle_particle_is_instance(*args)
2035 
2036 def Angle_get_particle_key(*args):
2037  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2038  return _IMP_atom.Angle_get_particle_key(*args)
2039 
2040 def Angle_get_ideal_key():
2041  """Angle_get_ideal_key() -> FloatKey"""
2042  return _IMP_atom.Angle_get_ideal_key()
2043 
2044 def Angle_get_stiffness_key():
2045  """Angle_get_stiffness_key() -> FloatKey"""
2046  return _IMP_atom.Angle_get_stiffness_key()
2047 
2048 class Dihedral(IMP.kernel.Decorator):
2049  """Proxy of C++ IMP::atom::Dihedral class"""
2050  __swig_setmethods__ = {}
2051  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2052  __setattr__ = lambda self, name, value: _swig_setattr(self, Dihedral, name, value)
2053  __swig_getmethods__ = {}
2054  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2055  __getattr__ = lambda self, name: _swig_getattr(self, Dihedral, name)
2056  def __init__(self, *args):
2057  """
2058  __init__(IMP::atom::Dihedral self) -> Dihedral
2059  __init__(IMP::atom::Dihedral self, Model m, IMP::kernel::ParticleIndex id) -> Dihedral
2060  __init__(IMP::atom::Dihedral self, Particle p) -> Dihedral
2061  """
2062  this = _IMP_atom.new_Dihedral(*args)
2063  try: self.this.append(this)
2064  except: self.this = this
2065  def decorate_particle(*args):
2066  """decorate_particle(Particle p) -> Dihedral"""
2067  return _IMP_atom.Dihedral_decorate_particle(*args)
2068 
2069  if _newclass:decorate_particle = staticmethod(decorate_particle)
2070  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
2071  def show(self, *args):
2072  """
2073  show(Dihedral self, _ostream out=std::cout)
2074  show(Dihedral self)
2075  """
2076  return _IMP_atom.Dihedral_show(self, *args)
2077 
2078  def setup_particle(*args):
2079  """setup_particle(Particle p, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral"""
2080  return _IMP_atom.Dihedral_setup_particle(*args)
2081 
2082  if _newclass:setup_particle = staticmethod(setup_particle)
2083  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
2084  def particle_is_instance(*args):
2085  """particle_is_instance(Particle p) -> bool"""
2086  return _IMP_atom.Dihedral_particle_is_instance(*args)
2087 
2088  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
2089  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
2090  def get_particle(self, *args):
2091  """
2092  get_particle(Dihedral self) -> Particle
2093  get_particle(Dihedral self, unsigned int i) -> Particle
2094  """
2095  return _IMP_atom.Dihedral_get_particle(self, *args)
2096 
2097  def get_ideal(self):
2098  """get_ideal(Dihedral self) -> IMP::Float"""
2099  return _IMP_atom.Dihedral_get_ideal(self)
2100 
2101  def set_ideal(self, *args):
2102  """set_ideal(Dihedral self, IMP::Float t)"""
2103  return _IMP_atom.Dihedral_set_ideal(self, *args)
2104 
2105  def get_multiplicity(self):
2106  """get_multiplicity(Dihedral self) -> IMP::Int"""
2107  return _IMP_atom.Dihedral_get_multiplicity(self)
2108 
2109  def set_multiplicity(self, *args):
2110  """set_multiplicity(Dihedral self, IMP::Int t)"""
2111  return _IMP_atom.Dihedral_set_multiplicity(self, *args)
2112 
2113  def get_stiffness(self):
2114  """get_stiffness(Dihedral self) -> IMP::Float"""
2115  return _IMP_atom.Dihedral_get_stiffness(self)
2116 
2117  def set_stiffness(self, *args):
2118  """set_stiffness(Dihedral self, IMP::Float t)"""
2119  return _IMP_atom.Dihedral_set_stiffness(self, *args)
2120 
2121  def get_particle_key(*args):
2122  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2123  return _IMP_atom.Dihedral_get_particle_key(*args)
2124 
2125  if _newclass:get_particle_key = staticmethod(get_particle_key)
2126  __swig_getmethods__["get_particle_key"] = lambda x: get_particle_key
2127  def get_ideal_key():
2128  """get_ideal_key() -> FloatKey"""
2129  return _IMP_atom.Dihedral_get_ideal_key()
2130 
2131  if _newclass:get_ideal_key = staticmethod(get_ideal_key)
2132  __swig_getmethods__["get_ideal_key"] = lambda x: get_ideal_key
2133  def get_multiplicity_key():
2134  """get_multiplicity_key() -> IntKey"""
2135  return _IMP_atom.Dihedral_get_multiplicity_key()
2136 
2137  if _newclass:get_multiplicity_key = staticmethod(get_multiplicity_key)
2138  __swig_getmethods__["get_multiplicity_key"] = lambda x: get_multiplicity_key
2139  def get_stiffness_key():
2140  """get_stiffness_key() -> FloatKey"""
2141  return _IMP_atom.Dihedral_get_stiffness_key()
2142 
2143  if _newclass:get_stiffness_key = staticmethod(get_stiffness_key)
2144  __swig_getmethods__["get_stiffness_key"] = lambda x: get_stiffness_key
2145  def add_attribute(self, *args):
2146  """
2147  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2148  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2149  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2150  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2151  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2152  add_attribute(Dihedral self, ObjectKey a0, IMP::Object * a1)
2153  """
2154  return _IMP_atom.Dihedral_add_attribute(self, *args)
2155 
2156  def get_value(self, *args):
2157  """
2158  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2159  get_value(Dihedral self, IntKey a0) -> IMP::Int
2160  get_value(Dihedral self, StringKey a0) -> IMP::String
2161  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2162  get_value(Dihedral self, ObjectKey a0) -> IMP::Object *
2163  """
2164  return _IMP_atom.Dihedral_get_value(self, *args)
2165 
2166  def set_value(self, *args):
2167  """
2168  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2169  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2170  set_value(Dihedral self, StringKey a0, IMP::String a1)
2171  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2172  set_value(Dihedral self, ObjectKey a0, IMP::Object * a1)
2173  """
2174  return _IMP_atom.Dihedral_set_value(self, *args)
2175 
2176  def remove_attribute(self, *args):
2177  """
2178  remove_attribute(Dihedral self, FloatKey a0)
2179  remove_attribute(Dihedral self, IntKey a0)
2180  remove_attribute(Dihedral self, StringKey a0)
2181  remove_attribute(Dihedral self, ParticleIndexKey a0)
2182  remove_attribute(Dihedral self, ObjectKey a0)
2183  """
2184  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2185 
2186  def has_attribute(self, *args):
2187  """
2188  has_attribute(Dihedral self, FloatKey a0) -> bool
2189  has_attribute(Dihedral self, IntKey a0) -> bool
2190  has_attribute(Dihedral self, StringKey a0) -> bool
2191  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2192  has_attribute(Dihedral self, ObjectKey a0) -> bool
2193  """
2194  return _IMP_atom.Dihedral_has_attribute(self, *args)
2195 
2196  def get_derivative(self, *args):
2197  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2198  return _IMP_atom.Dihedral_get_derivative(self, *args)
2199 
2200  def get_name(self):
2201  """get_name(Dihedral self) -> std::string"""
2202  return _IMP_atom.Dihedral_get_name(self)
2203 
2204  def clear_caches(self):
2205  """clear_caches(Dihedral self)"""
2206  return _IMP_atom.Dihedral_clear_caches(self)
2207 
2208  def set_name(self, *args):
2209  """set_name(Dihedral self, std::string a0)"""
2210  return _IMP_atom.Dihedral_set_name(self, *args)
2211 
2212  def set_check_level(self, *args):
2213  """set_check_level(Dihedral self, IMP::base::CheckLevel a0)"""
2214  return _IMP_atom.Dihedral_set_check_level(self, *args)
2215 
2216  def add_to_derivative(self, *args):
2217  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2218  return _IMP_atom.Dihedral_add_to_derivative(self, *args)
2219 
2220  def set_is_optimized(self, *args):
2221  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2222  return _IMP_atom.Dihedral_set_is_optimized(self, *args)
2223 
2224  def get_is_optimized(self, *args):
2225  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2226  return _IMP_atom.Dihedral_get_is_optimized(self, *args)
2227 
2228  def get_check_level(self):
2229  """get_check_level(Dihedral self) -> IMP::base::CheckLevel"""
2230  return _IMP_atom.Dihedral_get_check_level(self)
2231 
2232  def __eq__(self, *args):
2233  """
2234  __eq__(Dihedral self, Dihedral o) -> bool
2235  __eq__(Dihedral self, Particle d) -> bool
2236  """
2237  return _IMP_atom.Dihedral___eq__(self, *args)
2238 
2239  def __ne__(self, *args):
2240  """
2241  __ne__(Dihedral self, Dihedral o) -> bool
2242  __ne__(Dihedral self, Particle d) -> bool
2243  """
2244  return _IMP_atom.Dihedral___ne__(self, *args)
2245 
2246  def __le__(self, *args):
2247  """
2248  __le__(Dihedral self, Dihedral o) -> bool
2249  __le__(Dihedral self, Particle d) -> bool
2250  """
2251  return _IMP_atom.Dihedral___le__(self, *args)
2252 
2253  def __lt__(self, *args):
2254  """
2255  __lt__(Dihedral self, Dihedral o) -> bool
2256  __lt__(Dihedral self, Particle d) -> bool
2257  """
2258  return _IMP_atom.Dihedral___lt__(self, *args)
2259 
2260  def __ge__(self, *args):
2261  """
2262  __ge__(Dihedral self, Dihedral o) -> bool
2263  __ge__(Dihedral self, Particle d) -> bool
2264  """
2265  return _IMP_atom.Dihedral___ge__(self, *args)
2266 
2267  def __gt__(self, *args):
2268  """
2269  __gt__(Dihedral self, Dihedral o) -> bool
2270  __gt__(Dihedral self, Particle d) -> bool
2271  """
2272  return _IMP_atom.Dihedral___gt__(self, *args)
2273 
2274  def __str__(self):
2275  """__str__(Dihedral self) -> std::string"""
2276  return _IMP_atom.Dihedral___str__(self)
2277 
2278  def __repr__(self):
2279  """__repr__(Dihedral self) -> std::string"""
2280  return _IMP_atom.Dihedral___repr__(self)
2281 
2282  __swig_destroy__ = _IMP_atom.delete_Dihedral
2283  __del__ = lambda self : None;
2284 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2285 Dihedral_swigregister(Dihedral)
2286 
2287 def Dihedral_decorate_particle(*args):
2288  """Dihedral_decorate_particle(Particle p) -> Dihedral"""
2289  return _IMP_atom.Dihedral_decorate_particle(*args)
2290 
2291 def Dihedral_setup_particle(*args):
2292  """Dihedral_setup_particle(Particle p, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral"""
2293  return _IMP_atom.Dihedral_setup_particle(*args)
2294 
2295 def Dihedral_particle_is_instance(*args):
2296  """Dihedral_particle_is_instance(Particle p) -> bool"""
2297  return _IMP_atom.Dihedral_particle_is_instance(*args)
2298 
2299 def Dihedral_get_particle_key(*args):
2300  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2301  return _IMP_atom.Dihedral_get_particle_key(*args)
2302 
2303 def Dihedral_get_ideal_key():
2304  """Dihedral_get_ideal_key() -> FloatKey"""
2305  return _IMP_atom.Dihedral_get_ideal_key()
2306 
2307 def Dihedral_get_multiplicity_key():
2308  """Dihedral_get_multiplicity_key() -> IntKey"""
2309  return _IMP_atom.Dihedral_get_multiplicity_key()
2310 
2311 def Dihedral_get_stiffness_key():
2312  """Dihedral_get_stiffness_key() -> FloatKey"""
2313  return _IMP_atom.Dihedral_get_stiffness_key()
2314 
2315 class SmoothingFunction(IMP.base.Object):
2316  """Proxy of C++ IMP::atom::SmoothingFunction class"""
2317  __swig_setmethods__ = {}
2318  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2319  __setattr__ = lambda self, name, value: _swig_setattr(self, SmoothingFunction, name, value)
2320  __swig_getmethods__ = {}
2321  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2322  __getattr__ = lambda self, name: _swig_getattr(self, SmoothingFunction, name)
2323  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
2324  def __call__(self, *args):
2325  """
2326  __call__(SmoothingFunction self, double score, double distance) -> double
2327  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2328  """
2329  return _IMP_atom.SmoothingFunction___call__(self, *args)
2330 
2331  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2332  __del__ = lambda self : None;
2333  def __str__(self):
2334  """__str__(SmoothingFunction self) -> std::string"""
2335  return _IMP_atom.SmoothingFunction___str__(self)
2336 
2337  def __repr__(self):
2338  """__repr__(SmoothingFunction self) -> std::string"""
2339  return _IMP_atom.SmoothingFunction___repr__(self)
2340 
2341  def get_from(o):
2342  return _object_cast_to_SmoothingFunction(o)
2343  get_from = staticmethod(get_from)
2344 
2345 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2346 SmoothingFunction_swigregister(SmoothingFunction)
2347 
2348 class ForceSwitch(SmoothingFunction):
2349  """Proxy of C++ IMP::atom::ForceSwitch class"""
2350  __swig_setmethods__ = {}
2351  for _s in [SmoothingFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2352  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceSwitch, name, value)
2353  __swig_getmethods__ = {}
2354  for _s in [SmoothingFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2355  __getattr__ = lambda self, name: _swig_getattr(self, ForceSwitch, name)
2356  def __init__(self, *args):
2357  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2358  this = _IMP_atom.new_ForceSwitch(*args)
2359  try: self.this.append(this)
2360  except: self.this = this
2361  def __call__(self, *args):
2362  """
2363  __call__(ForceSwitch self, double score, double distance) -> double
2364  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2365  """
2366  return _IMP_atom.ForceSwitch___call__(self, *args)
2367 
2368  def get_version_info(self):
2369  """get_version_info(ForceSwitch self) -> VersionInfo"""
2370  return _IMP_atom.ForceSwitch_get_version_info(self)
2371 
2372  def do_show(self, *args):
2373  """do_show(ForceSwitch self, _ostream out)"""
2374  return _IMP_atom.ForceSwitch_do_show(self, *args)
2375 
2376  __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2377  __del__ = lambda self : None;
2378  def __str__(self):
2379  """__str__(ForceSwitch self) -> std::string"""
2380  return _IMP_atom.ForceSwitch___str__(self)
2381 
2382  def __repr__(self):
2383  """__repr__(ForceSwitch self) -> std::string"""
2384  return _IMP_atom.ForceSwitch___repr__(self)
2385 
2386  def get_from(o):
2387  return _object_cast_to_ForceSwitch(o)
2388  get_from = staticmethod(get_from)
2389 
2390 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2391 ForceSwitch_swigregister(ForceSwitch)
2392 
2393 class AngleSingletonScore(IMP.kernel.SingletonScore):
2394  """Proxy of C++ IMP::atom::AngleSingletonScore class"""
2395  __swig_setmethods__ = {}
2396  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2397  __setattr__ = lambda self, name, value: _swig_setattr(self, AngleSingletonScore, name, value)
2398  __swig_getmethods__ = {}
2399  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2400  __getattr__ = lambda self, name: _swig_getattr(self, AngleSingletonScore, name)
2401  def __init__(self, *args):
2402  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2403  this = _IMP_atom.new_AngleSingletonScore(*args)
2404  try: self.this.append(this)
2405  except: self.this = this
2406  def get_input_particles(self, *args):
2407  """get_input_particles(AngleSingletonScore self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2408  return _IMP_atom.AngleSingletonScore_get_input_particles(self, *args)
2409 
2410  def get_input_containers(self, *args):
2411  """get_input_containers(AngleSingletonScore self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2412  return _IMP_atom.AngleSingletonScore_get_input_containers(self, *args)
2413 
2414  def get_version_info(self):
2415  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2416  return _IMP_atom.AngleSingletonScore_get_version_info(self)
2417 
2418  def do_show(self, *args):
2419  """do_show(AngleSingletonScore self, _ostream out)"""
2420  return _IMP_atom.AngleSingletonScore_do_show(self, *args)
2421 
2422  __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2423  __del__ = lambda self : None;
2424  def __str__(self):
2425  """__str__(AngleSingletonScore self) -> std::string"""
2426  return _IMP_atom.AngleSingletonScore___str__(self)
2427 
2428  def __repr__(self):
2429  """__repr__(AngleSingletonScore self) -> std::string"""
2430  return _IMP_atom.AngleSingletonScore___repr__(self)
2431 
2432  def get_from(o):
2433  return _object_cast_to_AngleSingletonScore(o)
2434  get_from = staticmethod(get_from)
2435 
2436 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2437 AngleSingletonScore_swigregister(AngleSingletonScore)
2438 
2439 class BondEndpointsRefiner(IMP.kernel.Refiner):
2440  """Proxy of C++ IMP::atom::BondEndpointsRefiner class"""
2441  __swig_setmethods__ = {}
2442  for _s in [IMP.kernel.Refiner]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2443  __setattr__ = lambda self, name, value: _swig_setattr(self, BondEndpointsRefiner, name, value)
2444  __swig_getmethods__ = {}
2445  for _s in [IMP.kernel.Refiner]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2446  __getattr__ = lambda self, name: _swig_getattr(self, BondEndpointsRefiner, name)
2447  def __init__(self):
2448  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2449  this = _IMP_atom.new_BondEndpointsRefiner()
2450  try: self.this.append(this)
2451  except: self.this = this
2452  def get_refined(self, *args):
2453  """
2454  get_refined(BondEndpointsRefiner self, Particle arg2) -> IMP::kernel::ParticlesTemp const
2455  get_refined(BondEndpointsRefiner self, Particle arg2, unsigned int arg3) -> Particle
2456  """
2457  return _IMP_atom.BondEndpointsRefiner_get_refined(self, *args)
2458 
2459  def get_input_particles(self, *args):
2460  """get_input_particles(BondEndpointsRefiner self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2461  return _IMP_atom.BondEndpointsRefiner_get_input_particles(self, *args)
2462 
2463  def get_input_containers(self, *args):
2464  """get_input_containers(BondEndpointsRefiner self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2465  return _IMP_atom.BondEndpointsRefiner_get_input_containers(self, *args)
2466 
2467  def get_version_info(self):
2468  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2469  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2470 
2471  def do_show(self, *args):
2472  """do_show(BondEndpointsRefiner self, _ostream out)"""
2473  return _IMP_atom.BondEndpointsRefiner_do_show(self, *args)
2474 
2475  __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2476  __del__ = lambda self : None;
2477  def __str__(self):
2478  """__str__(BondEndpointsRefiner self) -> std::string"""
2479  return _IMP_atom.BondEndpointsRefiner___str__(self)
2480 
2481  def __repr__(self):
2482  """__repr__(BondEndpointsRefiner self) -> std::string"""
2483  return _IMP_atom.BondEndpointsRefiner___repr__(self)
2484 
2485  def get_from(o):
2486  return _object_cast_to_BondEndpointsRefiner(o)
2487  get_from = staticmethod(get_from)
2488 
2489 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2490 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2491 
2492 class BondPairContainer(IMP.kernel.PairContainer):
2493  """Proxy of C++ IMP::atom::BondPairContainer class"""
2494  __swig_setmethods__ = {}
2495  for _s in [IMP.kernel.PairContainer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2496  __setattr__ = lambda self, name, value: _swig_setattr(self, BondPairContainer, name, value)
2497  __swig_getmethods__ = {}
2498  for _s in [IMP.kernel.PairContainer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2499  __getattr__ = lambda self, name: _swig_getattr(self, BondPairContainer, name)
2500  def __init__(self, *args):
2501  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2502  this = _IMP_atom.new_BondPairContainer(*args)
2503  try: self.this.append(this)
2504  except: self.this = this
2505  def do_before_evaluate(self):
2506  """do_before_evaluate(BondPairContainer self)"""
2507  return _IMP_atom.BondPairContainer_do_before_evaluate(self)
2508 
2509  def do_get_inputs(self):
2510  """do_get_inputs(BondPairContainer self) -> IMP::kernel::ModelObjectsTemp"""
2511  return _IMP_atom.BondPairContainer_do_get_inputs(self)
2512 
2513  def do_apply(self, *args):
2514  """do_apply(BondPairContainer self, PairModifier sm)"""
2515  return _IMP_atom.BondPairContainer_do_apply(self, *args)
2516 
2517  def get_version_info(self):
2518  """get_version_info(BondPairContainer self) -> VersionInfo"""
2519  return _IMP_atom.BondPairContainer_get_version_info(self)
2520 
2521  def do_show(self, *args):
2522  """do_show(BondPairContainer self, _ostream out)"""
2523  return _IMP_atom.BondPairContainer_do_show(self, *args)
2524 
2525  __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2526  __del__ = lambda self : None;
2527  def __str__(self):
2528  """__str__(BondPairContainer self) -> std::string"""
2529  return _IMP_atom.BondPairContainer___str__(self)
2530 
2531  def __repr__(self):
2532  """__repr__(BondPairContainer self) -> std::string"""
2533  return _IMP_atom.BondPairContainer___repr__(self)
2534 
2535  def get_from(o):
2536  return _object_cast_to_BondPairContainer(o)
2537  get_from = staticmethod(get_from)
2538 
2539 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
2540 BondPairContainer_swigregister(BondPairContainer)
2541 
2542 class BondSingletonScore(IMP.kernel.SingletonScore):
2543  """Proxy of C++ IMP::atom::BondSingletonScore class"""
2544  __swig_setmethods__ = {}
2545  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2546  __setattr__ = lambda self, name, value: _swig_setattr(self, BondSingletonScore, name, value)
2547  __swig_getmethods__ = {}
2548  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2549  __getattr__ = lambda self, name: _swig_getattr(self, BondSingletonScore, name)
2550  def __init__(self, *args):
2551  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2552  this = _IMP_atom.new_BondSingletonScore(*args)
2553  try: self.this.append(this)
2554  except: self.this = this
2555  def get_unary_function(self):
2556  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2557  return _IMP_atom.BondSingletonScore_get_unary_function(self)
2558 
2559  def get_input_particles(self, *args):
2560  """get_input_particles(BondSingletonScore self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2561  return _IMP_atom.BondSingletonScore_get_input_particles(self, *args)
2562 
2563  def get_input_containers(self, *args):
2564  """get_input_containers(BondSingletonScore self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2565  return _IMP_atom.BondSingletonScore_get_input_containers(self, *args)
2566 
2567  def get_version_info(self):
2568  """get_version_info(BondSingletonScore self) -> VersionInfo"""
2569  return _IMP_atom.BondSingletonScore_get_version_info(self)
2570 
2571  def do_show(self, *args):
2572  """do_show(BondSingletonScore self, _ostream out)"""
2573  return _IMP_atom.BondSingletonScore_do_show(self, *args)
2574 
2575  __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2576  __del__ = lambda self : None;
2577  def __str__(self):
2578  """__str__(BondSingletonScore self) -> std::string"""
2579  return _IMP_atom.BondSingletonScore___str__(self)
2580 
2581  def __repr__(self):
2582  """__repr__(BondSingletonScore self) -> std::string"""
2583  return _IMP_atom.BondSingletonScore___repr__(self)
2584 
2585  def get_from(o):
2586  return _object_cast_to_BondSingletonScore(o)
2587  get_from = staticmethod(get_from)
2588 
2589 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
2590 BondSingletonScore_swigregister(BondSingletonScore)
2591 
2592 class DihedralSingletonScore(IMP.kernel.SingletonScore):
2593  """Proxy of C++ IMP::atom::DihedralSingletonScore class"""
2594  __swig_setmethods__ = {}
2595  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2596  __setattr__ = lambda self, name, value: _swig_setattr(self, DihedralSingletonScore, name, value)
2597  __swig_getmethods__ = {}
2598  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2599  __getattr__ = lambda self, name: _swig_getattr(self, DihedralSingletonScore, name)
2600  def __init__(self):
2601  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
2602  this = _IMP_atom.new_DihedralSingletonScore()
2603  try: self.this.append(this)
2604  except: self.this = this
2605  def get_input_particles(self, *args):
2606  """get_input_particles(DihedralSingletonScore self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2607  return _IMP_atom.DihedralSingletonScore_get_input_particles(self, *args)
2608 
2609  def get_input_containers(self, *args):
2610  """get_input_containers(DihedralSingletonScore self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2611  return _IMP_atom.DihedralSingletonScore_get_input_containers(self, *args)
2612 
2613  def get_version_info(self):
2614  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2615  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2616 
2617  def do_show(self, *args):
2618  """do_show(DihedralSingletonScore self, _ostream out)"""
2619  return _IMP_atom.DihedralSingletonScore_do_show(self, *args)
2620 
2621  __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
2622  __del__ = lambda self : None;
2623  def __str__(self):
2624  """__str__(DihedralSingletonScore self) -> std::string"""
2625  return _IMP_atom.DihedralSingletonScore___str__(self)
2626 
2627  def __repr__(self):
2628  """__repr__(DihedralSingletonScore self) -> std::string"""
2629  return _IMP_atom.DihedralSingletonScore___repr__(self)
2630 
2631  def get_from(o):
2632  return _object_cast_to_DihedralSingletonScore(o)
2633  get_from = staticmethod(get_from)
2634 
2635 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
2636 DihedralSingletonScore_swigregister(DihedralSingletonScore)
2637 
2638 class ImproperSingletonScore(IMP.kernel.SingletonScore):
2639  """Proxy of C++ IMP::atom::ImproperSingletonScore class"""
2640  __swig_setmethods__ = {}
2641  for _s in [IMP.kernel.SingletonScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2642  __setattr__ = lambda self, name, value: _swig_setattr(self, ImproperSingletonScore, name, value)
2643  __swig_getmethods__ = {}
2644  for _s in [IMP.kernel.SingletonScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2645  __getattr__ = lambda self, name: _swig_getattr(self, ImproperSingletonScore, name)
2646  def __init__(self, *args):
2647  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
2648  this = _IMP_atom.new_ImproperSingletonScore(*args)
2649  try: self.this.append(this)
2650  except: self.this = this
2651  def get_input_particles(self, *args):
2652  """get_input_particles(ImproperSingletonScore self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2653  return _IMP_atom.ImproperSingletonScore_get_input_particles(self, *args)
2654 
2655  def get_input_containers(self, *args):
2656  """get_input_containers(ImproperSingletonScore self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2657  return _IMP_atom.ImproperSingletonScore_get_input_containers(self, *args)
2658 
2659  def get_version_info(self):
2660  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
2661  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
2662 
2663  def do_show(self, *args):
2664  """do_show(ImproperSingletonScore self, _ostream out)"""
2665  return _IMP_atom.ImproperSingletonScore_do_show(self, *args)
2666 
2667  __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
2668  __del__ = lambda self : None;
2669  def __str__(self):
2670  """__str__(ImproperSingletonScore self) -> std::string"""
2671  return _IMP_atom.ImproperSingletonScore___str__(self)
2672 
2673  def __repr__(self):
2674  """__repr__(ImproperSingletonScore self) -> std::string"""
2675  return _IMP_atom.ImproperSingletonScore___repr__(self)
2676 
2677  def get_from(o):
2678  return _object_cast_to_ImproperSingletonScore(o)
2679  get_from = staticmethod(get_from)
2680 
2681 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
2682 ImproperSingletonScore_swigregister(ImproperSingletonScore)
2683 
2684 class CoverBond(IMP.kernel.SingletonModifier):
2685  """Proxy of C++ IMP::atom::CoverBond class"""
2686  __swig_setmethods__ = {}
2687  for _s in [IMP.kernel.SingletonModifier]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2688  __setattr__ = lambda self, name, value: _swig_setattr(self, CoverBond, name, value)
2689  __swig_getmethods__ = {}
2690  for _s in [IMP.kernel.SingletonModifier]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2691  __getattr__ = lambda self, name: _swig_getattr(self, CoverBond, name)
2692  def __init__(self):
2693  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
2694  this = _IMP_atom.new_CoverBond()
2695  try: self.this.append(this)
2696  except: self.this = this
2697  def get_input_particles(self, *args):
2698  """get_input_particles(CoverBond self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2699  return _IMP_atom.CoverBond_get_input_particles(self, *args)
2700 
2701  def get_input_containers(self, *args):
2702  """get_input_containers(CoverBond self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2703  return _IMP_atom.CoverBond_get_input_containers(self, *args)
2704 
2705  def get_output_particles(self, *args):
2706  """get_output_particles(CoverBond self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
2707  return _IMP_atom.CoverBond_get_output_particles(self, *args)
2708 
2709  def get_output_containers(self, *args):
2710  """get_output_containers(CoverBond self, Particle arg2) -> IMP::kernel::ContainersTemp"""
2711  return _IMP_atom.CoverBond_get_output_containers(self, *args)
2712 
2713  def get_version_info(self):
2714  """get_version_info(CoverBond self) -> VersionInfo"""
2715  return _IMP_atom.CoverBond_get_version_info(self)
2716 
2717  def do_show(self, *args):
2718  """do_show(CoverBond self, _ostream out)"""
2719  return _IMP_atom.CoverBond_do_show(self, *args)
2720 
2721  __swig_destroy__ = _IMP_atom.delete_CoverBond
2722  __del__ = lambda self : None;
2723  def __str__(self):
2724  """__str__(CoverBond self) -> std::string"""
2725  return _IMP_atom.CoverBond___str__(self)
2726 
2727  def __repr__(self):
2728  """__repr__(CoverBond self) -> std::string"""
2729  return _IMP_atom.CoverBond___repr__(self)
2730 
2731  def get_from(o):
2732  return _object_cast_to_CoverBond(o)
2733  get_from = staticmethod(get_from)
2734 
2735 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
2736 CoverBond_swigregister(CoverBond)
2737 
2738 class Simulator(IMP.kernel.Optimizer):
2739  """Proxy of C++ IMP::atom::Simulator class"""
2740  __swig_setmethods__ = {}
2741  for _s in [IMP.kernel.Optimizer]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2742  __setattr__ = lambda self, name, value: _swig_setattr(self, Simulator, name, value)
2743  __swig_getmethods__ = {}
2744  for _s in [IMP.kernel.Optimizer]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2745  __getattr__ = lambda self, name: _swig_getattr(self, Simulator, name)
2746  def __init__(self, *args):
2747  """
2748  __init__(IMP::atom::Simulator self, Model m, std::string name="Simulator %1%") -> Simulator
2749  __init__(IMP::atom::Simulator self, Model m) -> Simulator
2750  """
2751  if self.__class__ == Simulator:
2752  _self = None
2753  else:
2754  _self = self
2755  this = _IMP_atom.new_Simulator(_self, *args)
2756  try: self.this.append(this)
2757  except: self.this = this
2758  if self.__class__ != Simulator:
2759  import IMP.base
2760  IMP.base._director_objects.register(self)
2761 
2762 
2763 
2764  def simulate(self, *args):
2765  """simulate(Simulator self, double time_in_fs) -> double"""
2766  return _IMP_atom.Simulator_simulate(self, *args)
2767 
2768  def get_temperature(self):
2769  """get_temperature(Simulator self) -> double"""
2770  return _IMP_atom.Simulator_get_temperature(self)
2771 
2772  def set_temperature(self, *args):
2773  """set_temperature(Simulator self, double d)"""
2774  return _IMP_atom.Simulator_set_temperature(self, *args)
2775 
2776  def set_maximum_time_step(self, *args):
2777  """set_maximum_time_step(Simulator self, double ts)"""
2778  return _IMP_atom.Simulator_set_maximum_time_step(self, *args)
2779 
2780  def get_maximum_time_step(self):
2781  """get_maximum_time_step(Simulator self) -> double"""
2782  return _IMP_atom.Simulator_get_maximum_time_step(self)
2783 
2784  def get_last_time_step(self):
2785  """get_last_time_step(Simulator self) -> double"""
2786  return _IMP_atom.Simulator_get_last_time_step(self)
2787 
2788  def set_time_step(self, *args):
2789  """set_time_step(Simulator self, double ts)"""
2790  return _IMP_atom.Simulator_set_time_step(self, *args)
2791 
2792  def get_kt(self):
2793  """get_kt(Simulator self) -> double"""
2794  return _IMP_atom.Simulator_get_kt(self)
2795 
2796  def get_current_time(self):
2797  """get_current_time(Simulator self) -> double"""
2798  return _IMP_atom.Simulator_get_current_time(self)
2799 
2800  def set_current_time(self, *args):
2801  """set_current_time(Simulator self, double ct)"""
2802  return _IMP_atom.Simulator_set_current_time(self, *args)
2803 
2804  def get_simulation_particles(self):
2805  """get_simulation_particles(Simulator self) -> IMP::kernel::ParticlesTemp"""
2806  return _IMP_atom.Simulator_get_simulation_particles(self)
2807 
2808  def get_simulation_particle_indexes(self):
2809  """get_simulation_particle_indexes(Simulator self) -> IMP::kernel::ParticleIndexes"""
2810  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
2811 
2812  def remove_particle(self, *args):
2813  """remove_particle(Simulator self, Particle d)"""
2814  return _IMP_atom.Simulator_remove_particle(self, *args)
2815 
2816  def remove_particles(self, *args):
2817  """remove_particles(Simulator self, IMP::kernel::Particles const & d)"""
2818  return _IMP_atom.Simulator_remove_particles(self, *args)
2819 
2820  def set_particles(self, *args):
2821  """set_particles(Simulator self, IMP::kernel::Particles const & ps)"""
2822  return _IMP_atom.Simulator_set_particles(self, *args)
2823 
2824  def set_particles_order(self, *args):
2825  """set_particles_order(Simulator self, IMP::kernel::Particles const & objs)"""
2826  return _IMP_atom.Simulator_set_particles_order(self, *args)
2827 
2828  def add_particle(self, *args):
2829  """add_particle(Simulator self, Particle obj) -> unsigned int"""
2830  return _IMP_atom.Simulator_add_particle(self, *args)
2831 
2832  def add_particles(self, *args):
2833  """add_particles(Simulator self, IMP::kernel::Particles const & objs)"""
2834  return _IMP_atom.Simulator_add_particles(self, *args)
2835 
2836  def clear_particles(self):
2837  """clear_particles(Simulator self)"""
2838  return _IMP_atom.Simulator_clear_particles(self)
2839 
2840  def get_number_of_particles(self):
2841  """get_number_of_particles(Simulator self) -> unsigned int"""
2842  return _IMP_atom.Simulator_get_number_of_particles(self)
2843 
2844  def get_has_particles(self):
2845  """get_has_particles(Simulator self) -> bool"""
2846  return _IMP_atom.Simulator_get_has_particles(self)
2847 
2848  def get_particle(self, *args):
2849  """get_particle(Simulator self, unsigned int i) -> Particle"""
2850  return _IMP_atom.Simulator_get_particle(self, *args)
2851 
2852  def get_particles(self):
2853  """get_particles(Simulator self) -> IMP::kernel::Particles"""
2854  return _IMP_atom.Simulator_get_particles(self)
2855 
2856  def reserve_particles(self, *args):
2857  """reserve_particles(Simulator self, unsigned int sz)"""
2858  return _IMP_atom.Simulator_reserve_particles(self, *args)
2859 
2860  def do_optimize(self, *args):
2861  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
2862  return _IMP_atom.Simulator_do_optimize(self, *args)
2863 
2864  def get_version_info(self):
2865  """get_version_info(Simulator self) -> VersionInfo"""
2866  return _IMP_atom.Simulator_get_version_info(self)
2867 
2868  def do_show(self, *args):
2869  """do_show(Simulator self, _ostream out)"""
2870  return _IMP_atom.Simulator_do_show(self, *args)
2871 
2872  __swig_destroy__ = _IMP_atom.delete_Simulator
2873  __del__ = lambda self : None;
2874  def setup(self, *args):
2875  """setup(Simulator self, IMP::kernel::ParticleIndexes const & arg0)"""
2876  return _IMP_atom.Simulator_setup(self, *args)
2877 
2878  def do_step(self, *args):
2879  """do_step(Simulator self, IMP::kernel::ParticleIndexes const & sc, double dt) -> double"""
2880  return _IMP_atom.Simulator_do_step(self, *args)
2881 
2882  def get_is_simulation_particle(self, *args):
2883  """get_is_simulation_particle(Simulator self, IMP::kernel::ParticleIndex p) -> bool"""
2884  return _IMP_atom.Simulator_get_is_simulation_particle(self, *args)
2885 
2886  def __str__(self):
2887  """__str__(Simulator self) -> std::string"""
2888  return _IMP_atom.Simulator___str__(self)
2889 
2890  def __repr__(self):
2891  """__repr__(Simulator self) -> std::string"""
2892  return _IMP_atom.Simulator___repr__(self)
2893 
2894  def get_from(o):
2895  return _object_cast_to_Simulator(o)
2896  get_from = staticmethod(get_from)
2897 
2898  def get_type_name(self):
2899  return self.__class__.__name__
2900  def do_show(self, out):
2901  pass
2902  def get_version_info(self):
2903  if"IMP::atom" == "IMP":
2904  return VersionInfo("python", "0")
2905  else:
2906  return IMP.VersionInfo("python", "0")
2907  def get_from(o):
2908  return _object_cast_to_Simulator(o)
2909  get_from = staticmethod(get_from)
2910 
2911  def __disown__(self):
2912  self.this.disown()
2913  _IMP_atom.disown_Simulator(self)
2914  return weakref_proxy(self)
2915 Simulator_swigregister = _IMP_atom.Simulator_swigregister
2916 Simulator_swigregister(Simulator)
2917 
2918 
2919 def get_energy_in_femto_joules(*args):
2920  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
2921  return _IMP_atom.get_energy_in_femto_joules(*args)
2922 
2923 def get_force_in_femto_newtons(*args):
2924  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
2925  return _IMP_atom.get_force_in_femto_newtons(*args)
2926 
2927 def get_spring_constant_in_femto_newtons_per_angstrom(*args):
2928  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
2929  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(*args)
2930 class BrownianDynamics(Simulator):
2931  """Proxy of C++ IMP::atom::BrownianDynamics class"""
2932  __swig_setmethods__ = {}
2933  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2934  __setattr__ = lambda self, name, value: _swig_setattr(self, BrownianDynamics, name, value)
2935  __swig_getmethods__ = {}
2936  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2937  __getattr__ = lambda self, name: _swig_getattr(self, BrownianDynamics, name)
2938  def __init__(self, *args):
2939  """
2940  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%") -> BrownianDynamics
2941  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
2942  """
2943  this = _IMP_atom.new_BrownianDynamics(*args)
2944  try: self.this.append(this)
2945  except: self.this = this
2946  def set_maximum_move(self, *args):
2947  """set_maximum_move(BrownianDynamics self, double ms)"""
2948  return _IMP_atom.BrownianDynamics_set_maximum_move(self, *args)
2949 
2950  def set_use_stochastic_runge_kutta(self, *args):
2951  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
2952  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, *args)
2953 
2954  def __str__(self):
2955  """__str__(BrownianDynamics self) -> std::string"""
2956  return _IMP_atom.BrownianDynamics___str__(self)
2957 
2958  def __repr__(self):
2959  """__repr__(BrownianDynamics self) -> std::string"""
2960  return _IMP_atom.BrownianDynamics___repr__(self)
2961 
2962  def get_from(o):
2963  return _object_cast_to_BrownianDynamics(o)
2964  get_from = staticmethod(get_from)
2965 
2966  __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
2967  __del__ = lambda self : None;
2968 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
2969 BrownianDynamics_swigregister(BrownianDynamics)
2970 
2971 
2973  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
2974  return _IMP_atom.get_maximum_time_step_estimate(*args)
2975 
2976 def get_harmonic_sigma(*args):
2977  """get_harmonic_sigma(double D, double f) -> double"""
2978  return _IMP_atom.get_harmonic_sigma(*args)
2979 class Diffusion(IMP.core.XYZ):
2980  """Proxy of C++ IMP::atom::Diffusion class"""
2981  __swig_setmethods__ = {}
2982  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2983  __setattr__ = lambda self, name, value: _swig_setattr(self, Diffusion, name, value)
2984  __swig_getmethods__ = {}
2985  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2986  __getattr__ = lambda self, name: _swig_getattr(self, Diffusion, name)
2987  def __init__(self, *args):
2988  """
2989  __init__(IMP::atom::Diffusion self) -> Diffusion
2990  __init__(IMP::atom::Diffusion self, Model m, IMP::kernel::ParticleIndex id) -> Diffusion
2991  __init__(IMP::atom::Diffusion self, Particle p) -> Diffusion
2992  """
2993  this = _IMP_atom.new_Diffusion(*args)
2994  try: self.this.append(this)
2995  except: self.this = this
2996  def decorate_particle(*args):
2997  """decorate_particle(Particle p) -> Diffusion"""
2998  return _IMP_atom.Diffusion_decorate_particle(*args)
2999 
3000  if _newclass:decorate_particle = staticmethod(decorate_particle)
3001  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3002  def show(self, *args):
3003  """
3004  show(Diffusion self, _ostream out=std::cout)
3005  show(Diffusion self)
3006  """
3007  return _IMP_atom.Diffusion_show(self, *args)
3008 
3009  def setup_particle(*args):
3010  """
3011  setup_particle(Particle p, Vector3D v, IMP::Float D) -> Diffusion
3012  setup_particle(Particle p, IMP::Float D) -> Diffusion
3013  setup_particle(Particle p) -> Diffusion
3014  """
3015  return _IMP_atom.Diffusion_setup_particle(*args)
3016 
3017  if _newclass:setup_particle = staticmethod(setup_particle)
3018  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3019  def particle_is_instance(*args):
3020  """
3021  particle_is_instance(Particle p) -> bool
3022  particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
3023  """
3024  return _IMP_atom.Diffusion_particle_is_instance(*args)
3025 
3026  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3027  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3028  def set_d(self, *args):
3029  """set_d(Diffusion self, double d)"""
3030  return _IMP_atom.Diffusion_set_d(self, *args)
3031 
3032  def get_d(self):
3033  """get_d(Diffusion self) -> double"""
3034  return _IMP_atom.Diffusion_get_d(self)
3035 
3036  def set_diffusion_coefficient(self, *args):
3037  """set_diffusion_coefficient(Diffusion self, double d)"""
3038  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, *args)
3039 
3040  def get_diffusion_coefficient(self):
3041  """get_diffusion_coefficient(Diffusion self) -> double"""
3042  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3043 
3044  def get_diffusion_coefficient_key():
3045  """get_diffusion_coefficient_key() -> FloatKey"""
3046  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3047 
3048  if _newclass:get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3049  __swig_getmethods__["get_diffusion_coefficient_key"] = lambda x: get_diffusion_coefficient_key
3050  def add_attribute(self, *args):
3051  """
3052  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3053  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3054  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3055  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3056  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3057  add_attribute(Diffusion self, ObjectKey a0, IMP::Object * a1)
3058  """
3059  return _IMP_atom.Diffusion_add_attribute(self, *args)
3060 
3061  def get_value(self, *args):
3062  """
3063  get_value(Diffusion self, FloatKey a0) -> IMP::Float
3064  get_value(Diffusion self, IntKey a0) -> IMP::Int
3065  get_value(Diffusion self, StringKey a0) -> IMP::String
3066  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3067  get_value(Diffusion self, ObjectKey a0) -> IMP::Object *
3068  """
3069  return _IMP_atom.Diffusion_get_value(self, *args)
3070 
3071  def set_value(self, *args):
3072  """
3073  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3074  set_value(Diffusion self, IntKey a0, IMP::Int a1)
3075  set_value(Diffusion self, StringKey a0, IMP::String a1)
3076  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3077  set_value(Diffusion self, ObjectKey a0, IMP::Object * a1)
3078  """
3079  return _IMP_atom.Diffusion_set_value(self, *args)
3080 
3081  def remove_attribute(self, *args):
3082  """
3083  remove_attribute(Diffusion self, FloatKey a0)
3084  remove_attribute(Diffusion self, IntKey a0)
3085  remove_attribute(Diffusion self, StringKey a0)
3086  remove_attribute(Diffusion self, ParticleIndexKey a0)
3087  remove_attribute(Diffusion self, ObjectKey a0)
3088  """
3089  return _IMP_atom.Diffusion_remove_attribute(self, *args)
3090 
3091  def has_attribute(self, *args):
3092  """
3093  has_attribute(Diffusion self, FloatKey a0) -> bool
3094  has_attribute(Diffusion self, IntKey a0) -> bool
3095  has_attribute(Diffusion self, StringKey a0) -> bool
3096  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3097  has_attribute(Diffusion self, ObjectKey a0) -> bool
3098  """
3099  return _IMP_atom.Diffusion_has_attribute(self, *args)
3100 
3101  def get_derivative(self, *args):
3102  """get_derivative(Diffusion self, FloatKey a0) -> double"""
3103  return _IMP_atom.Diffusion_get_derivative(self, *args)
3104 
3105  def get_name(self):
3106  """get_name(Diffusion self) -> std::string"""
3107  return _IMP_atom.Diffusion_get_name(self)
3108 
3109  def clear_caches(self):
3110  """clear_caches(Diffusion self)"""
3111  return _IMP_atom.Diffusion_clear_caches(self)
3112 
3113  def set_name(self, *args):
3114  """set_name(Diffusion self, std::string a0)"""
3115  return _IMP_atom.Diffusion_set_name(self, *args)
3116 
3117  def set_check_level(self, *args):
3118  """set_check_level(Diffusion self, IMP::base::CheckLevel a0)"""
3119  return _IMP_atom.Diffusion_set_check_level(self, *args)
3120 
3121  def add_to_derivative(self, *args):
3122  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3123  return _IMP_atom.Diffusion_add_to_derivative(self, *args)
3124 
3125  def set_is_optimized(self, *args):
3126  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3127  return _IMP_atom.Diffusion_set_is_optimized(self, *args)
3128 
3129  def get_is_optimized(self, *args):
3130  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3131  return _IMP_atom.Diffusion_get_is_optimized(self, *args)
3132 
3133  def get_check_level(self):
3134  """get_check_level(Diffusion self) -> IMP::base::CheckLevel"""
3135  return _IMP_atom.Diffusion_get_check_level(self)
3136 
3137  def __eq__(self, *args):
3138  """
3139  __eq__(Diffusion self, Diffusion o) -> bool
3140  __eq__(Diffusion self, Particle d) -> bool
3141  """
3142  return _IMP_atom.Diffusion___eq__(self, *args)
3143 
3144  def __ne__(self, *args):
3145  """
3146  __ne__(Diffusion self, Diffusion o) -> bool
3147  __ne__(Diffusion self, Particle d) -> bool
3148  """
3149  return _IMP_atom.Diffusion___ne__(self, *args)
3150 
3151  def __le__(self, *args):
3152  """
3153  __le__(Diffusion self, Diffusion o) -> bool
3154  __le__(Diffusion self, Particle d) -> bool
3155  """
3156  return _IMP_atom.Diffusion___le__(self, *args)
3157 
3158  def __lt__(self, *args):
3159  """
3160  __lt__(Diffusion self, Diffusion o) -> bool
3161  __lt__(Diffusion self, Particle d) -> bool
3162  """
3163  return _IMP_atom.Diffusion___lt__(self, *args)
3164 
3165  def __ge__(self, *args):
3166  """
3167  __ge__(Diffusion self, Diffusion o) -> bool
3168  __ge__(Diffusion self, Particle d) -> bool
3169  """
3170  return _IMP_atom.Diffusion___ge__(self, *args)
3171 
3172  def __gt__(self, *args):
3173  """
3174  __gt__(Diffusion self, Diffusion o) -> bool
3175  __gt__(Diffusion self, Particle d) -> bool
3176  """
3177  return _IMP_atom.Diffusion___gt__(self, *args)
3178 
3179  def __str__(self):
3180  """__str__(Diffusion self) -> std::string"""
3181  return _IMP_atom.Diffusion___str__(self)
3182 
3183  def __repr__(self):
3184  """__repr__(Diffusion self) -> std::string"""
3185  return _IMP_atom.Diffusion___repr__(self)
3186 
3187  __swig_destroy__ = _IMP_atom.delete_Diffusion
3188  __del__ = lambda self : None;
3189 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
3190 Diffusion_swigregister(Diffusion)
3191 
3192 def Diffusion_decorate_particle(*args):
3193  """Diffusion_decorate_particle(Particle p) -> Diffusion"""
3194  return _IMP_atom.Diffusion_decorate_particle(*args)
3195 
3196 def Diffusion_setup_particle(*args):
3197  """
3198  setup_particle(Particle p, Vector3D v, IMP::Float D) -> Diffusion
3199  setup_particle(Particle p, IMP::Float D) -> Diffusion
3200  Diffusion_setup_particle(Particle p) -> Diffusion
3201  """
3202  return _IMP_atom.Diffusion_setup_particle(*args)
3203 
3204 def Diffusion_particle_is_instance(*args):
3205  """
3206  particle_is_instance(Particle p) -> bool
3207  Diffusion_particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
3208  """
3209  return _IMP_atom.Diffusion_particle_is_instance(*args)
3210 
3211 def Diffusion_get_diffusion_coefficient_key():
3212  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
3213  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3214 
3215 
3216 def get_diffusion_coefficient_from_cm2_per_second(*args):
3217  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3218  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(*args)
3219 class RigidBodyDiffusion(Diffusion):
3220  """Proxy of C++ IMP::atom::RigidBodyDiffusion class"""
3221  __swig_setmethods__ = {}
3222  for _s in [Diffusion]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3223  __setattr__ = lambda self, name, value: _swig_setattr(self, RigidBodyDiffusion, name, value)
3224  __swig_getmethods__ = {}
3225  for _s in [Diffusion]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3226  __getattr__ = lambda self, name: _swig_getattr(self, RigidBodyDiffusion, name)
3227  def __init__(self, *args):
3228  """
3229  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
3230  __init__(IMP::atom::RigidBodyDiffusion self, Model m, IMP::kernel::ParticleIndex id) -> RigidBodyDiffusion
3231  __init__(IMP::atom::RigidBodyDiffusion self, Particle p) -> RigidBodyDiffusion
3232  """
3233  this = _IMP_atom.new_RigidBodyDiffusion(*args)
3234  try: self.this.append(this)
3235  except: self.this = this
3236  def decorate_particle(*args):
3237  """decorate_particle(Particle p) -> RigidBodyDiffusion"""
3238  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3239 
3240  if _newclass:decorate_particle = staticmethod(decorate_particle)
3241  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3242  def show(self, *args):
3243  """
3244  show(RigidBodyDiffusion self, _ostream out=std::cout)
3245  show(RigidBodyDiffusion self)
3246  """
3247  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3248 
3249  def setup_particle(*args):
3250  """setup_particle(Particle p) -> RigidBodyDiffusion"""
3251  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3252 
3253  if _newclass:setup_particle = staticmethod(setup_particle)
3254  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3256  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3257  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3258 
3259  def set_rotational_diffusion_coefficient(self, *args):
3260  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3261  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, *args)
3262 
3263  def particle_is_instance(*args):
3264  """
3265  particle_is_instance(Particle p) -> bool
3266  particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
3267  """
3268  return _IMP_atom.RigidBodyDiffusion_particle_is_instance(*args)
3269 
3270  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3271  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3272  def get_rotational_diffusion_coefficient_key():
3273  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
3274  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3275 
3276  if _newclass:get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
3277  __swig_getmethods__["get_rotational_diffusion_coefficient_key"] = lambda x: get_rotational_diffusion_coefficient_key
3278  def add_attribute(self, *args):
3279  """
3280  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3281  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3282  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3283  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3284  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3285  add_attribute(RigidBodyDiffusion self, ObjectKey a0, IMP::Object * a1)
3286  """
3287  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3288 
3289  def get_value(self, *args):
3290  """
3291  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3292  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3293  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3294  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3295  get_value(RigidBodyDiffusion self, ObjectKey a0) -> IMP::Object *
3296  """
3297  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3298 
3299  def set_value(self, *args):
3300  """
3301  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3302  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3303  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3304  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3305  set_value(RigidBodyDiffusion self, ObjectKey a0, IMP::Object * a1)
3306  """
3307  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3308 
3309  def remove_attribute(self, *args):
3310  """
3311  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3312  remove_attribute(RigidBodyDiffusion self, IntKey a0)
3313  remove_attribute(RigidBodyDiffusion self, StringKey a0)
3314  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3315  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3316  """
3317  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3318 
3319  def has_attribute(self, *args):
3320  """
3321  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3322  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3323  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3324  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3325  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3326  """
3327  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3328 
3329  def get_derivative(self, *args):
3330  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3331  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, *args)
3332 
3333  def get_name(self):
3334  """get_name(RigidBodyDiffusion self) -> std::string"""
3335  return _IMP_atom.RigidBodyDiffusion_get_name(self)
3336 
3337  def clear_caches(self):
3338  """clear_caches(RigidBodyDiffusion self)"""
3339  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
3340 
3341  def set_name(self, *args):
3342  """set_name(RigidBodyDiffusion self, std::string a0)"""
3343  return _IMP_atom.RigidBodyDiffusion_set_name(self, *args)
3344 
3345  def set_check_level(self, *args):
3346  """set_check_level(RigidBodyDiffusion self, IMP::base::CheckLevel a0)"""
3347  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, *args)
3348 
3349  def add_to_derivative(self, *args):
3350  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3351  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, *args)
3352 
3353  def set_is_optimized(self, *args):
3354  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
3355  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, *args)
3356 
3357  def get_is_optimized(self, *args):
3358  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
3359  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, *args)
3360 
3361  def get_check_level(self):
3362  """get_check_level(RigidBodyDiffusion self) -> IMP::base::CheckLevel"""
3363  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
3364 
3365  def __eq__(self, *args):
3366  """
3367  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3368  __eq__(RigidBodyDiffusion self, Particle d) -> bool
3369  """
3370  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
3371 
3372  def __ne__(self, *args):
3373  """
3374  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3375  __ne__(RigidBodyDiffusion self, Particle d) -> bool
3376  """
3377  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
3378 
3379  def __le__(self, *args):
3380  """
3381  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3382  __le__(RigidBodyDiffusion self, Particle d) -> bool
3383  """
3384  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
3385 
3386  def __lt__(self, *args):
3387  """
3388  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3389  __lt__(RigidBodyDiffusion self, Particle d) -> bool
3390  """
3391  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
3392 
3393  def __ge__(self, *args):
3394  """
3395  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3396  __ge__(RigidBodyDiffusion self, Particle d) -> bool
3397  """
3398  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
3399 
3400  def __gt__(self, *args):
3401  """
3402  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3403  __gt__(RigidBodyDiffusion self, Particle d) -> bool
3404  """
3405  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
3406 
3407  def __str__(self):
3408  """__str__(RigidBodyDiffusion self) -> std::string"""
3409  return _IMP_atom.RigidBodyDiffusion___str__(self)
3410 
3411  def __repr__(self):
3412  """__repr__(RigidBodyDiffusion self) -> std::string"""
3413  return _IMP_atom.RigidBodyDiffusion___repr__(self)
3414 
3415  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
3416  __del__ = lambda self : None;
3417 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
3418 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
3419 
3420 def RigidBodyDiffusion_decorate_particle(*args):
3421  """RigidBodyDiffusion_decorate_particle(Particle p) -> RigidBodyDiffusion"""
3422  return _IMP_atom.RigidBodyDiffusion_decorate_particle(*args)
3423 
3424 def RigidBodyDiffusion_setup_particle(*args):
3425  """RigidBodyDiffusion_setup_particle(Particle p) -> RigidBodyDiffusion"""
3426  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3427 
3428 def RigidBodyDiffusion_particle_is_instance(*args):
3429  """
3430  particle_is_instance(Particle p) -> bool
3431  RigidBodyDiffusion_particle_is_instance(Model m, IMP::kernel::ParticleIndex p) -> bool
3432  """
3433  return _IMP_atom.RigidBodyDiffusion_particle_is_instance(*args)
3434 
3435 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
3436  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
3437  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3438 
3439 class Chain(Hierarchy):
3440  """Proxy of C++ IMP::atom::Chain class"""
3441  __swig_setmethods__ = {}
3442  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3443  __setattr__ = lambda self, name, value: _swig_setattr(self, Chain, name, value)
3444  __swig_getmethods__ = {}
3445  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3446  __getattr__ = lambda self, name: _swig_getattr(self, Chain, name)
3447  def __init__(self, *args):
3448  """
3449  __init__(IMP::atom::Chain self) -> Chain
3450  __init__(IMP::atom::Chain self, Model m, IMP::kernel::ParticleIndex id) -> Chain
3451  __init__(IMP::atom::Chain self, Particle p) -> Chain
3452  """
3453  this = _IMP_atom.new_Chain(*args)
3454  try: self.this.append(this)
3455  except: self.this = this
3456  def decorate_particle(*args):
3457  """decorate_particle(Particle p) -> Chain"""
3458  return _IMP_atom.Chain_decorate_particle(*args)
3459 
3460  if _newclass:decorate_particle = staticmethod(decorate_particle)
3461  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3462  def show(self, *args):
3463  """
3464  show(Chain self, _ostream out=std::cout)
3465  show(Chain self)
3466  """
3467  return _IMP_atom.Chain_show(self, *args)
3468 
3469  def setup_particle(*args):
3470  """
3471  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3472  setup_particle(Particle p, char id) -> Chain
3473  setup_particle(Particle p, Chain o) -> Chain
3474  """
3475  return _IMP_atom.Chain_setup_particle(*args)
3476 
3477  if _newclass:setup_particle = staticmethod(setup_particle)
3478  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3479  def particle_is_instance(*args):
3480  """particle_is_instance(Particle p) -> bool"""
3481  return _IMP_atom.Chain_particle_is_instance(*args)
3482 
3483  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3484  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3485  def get_id(self):
3486  """get_id(Chain self) -> char"""
3487  return _IMP_atom.Chain_get_id(self)
3488 
3489  def set_id(self, *args):
3490  """set_id(Chain self, char c)"""
3491  return _IMP_atom.Chain_set_id(self, *args)
3492 
3493  def get_id_key():
3494  """get_id_key() -> IntKey"""
3495  return _IMP_atom.Chain_get_id_key()
3496 
3497  if _newclass:get_id_key = staticmethod(get_id_key)
3498  __swig_getmethods__["get_id_key"] = lambda x: get_id_key
3499  def add_attribute(self, *args):
3500  """
3501  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
3502  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
3503  add_attribute(Chain self, IntKey a0, IMP::Int a1)
3504  add_attribute(Chain self, StringKey a0, IMP::String a1)
3505  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
3506  add_attribute(Chain self, ObjectKey a0, IMP::Object * a1)
3507  """
3508  return _IMP_atom.Chain_add_attribute(self, *args)
3509 
3510  def get_value(self, *args):
3511  """
3512  get_value(Chain self, FloatKey a0) -> IMP::Float
3513  get_value(Chain self, IntKey a0) -> IMP::Int
3514  get_value(Chain self, StringKey a0) -> IMP::String
3515  get_value(Chain self, ParticleIndexKey a0) -> Particle
3516  get_value(Chain self, ObjectKey a0) -> IMP::Object *
3517  """
3518  return _IMP_atom.Chain_get_value(self, *args)
3519 
3520  def set_value(self, *args):
3521  """
3522  set_value(Chain self, FloatKey a0, IMP::Float a1)
3523  set_value(Chain self, IntKey a0, IMP::Int a1)
3524  set_value(Chain self, StringKey a0, IMP::String a1)
3525  set_value(Chain self, ParticleIndexKey a0, Particle a1)
3526  set_value(Chain self, ObjectKey a0, IMP::Object * a1)
3527  """
3528  return _IMP_atom.Chain_set_value(self, *args)
3529 
3530  def remove_attribute(self, *args):
3531  """
3532  remove_attribute(Chain self, FloatKey a0)
3533  remove_attribute(Chain self, IntKey a0)
3534  remove_attribute(Chain self, StringKey a0)
3535  remove_attribute(Chain self, ParticleIndexKey a0)
3536  remove_attribute(Chain self, ObjectKey a0)
3537  """
3538  return _IMP_atom.Chain_remove_attribute(self, *args)
3539 
3540  def has_attribute(self, *args):
3541  """
3542  has_attribute(Chain self, FloatKey a0) -> bool
3543  has_attribute(Chain self, IntKey a0) -> bool
3544  has_attribute(Chain self, StringKey a0) -> bool
3545  has_attribute(Chain self, ParticleIndexKey a0) -> bool
3546  has_attribute(Chain self, ObjectKey a0) -> bool
3547  """
3548  return _IMP_atom.Chain_has_attribute(self, *args)
3549 
3550  def get_derivative(self, *args):
3551  """get_derivative(Chain self, FloatKey a0) -> double"""
3552  return _IMP_atom.Chain_get_derivative(self, *args)
3553 
3554  def get_name(self):
3555  """get_name(Chain self) -> std::string"""
3556  return _IMP_atom.Chain_get_name(self)
3557 
3558  def clear_caches(self):
3559  """clear_caches(Chain self)"""
3560  return _IMP_atom.Chain_clear_caches(self)
3561 
3562  def set_name(self, *args):
3563  """set_name(Chain self, std::string a0)"""
3564  return _IMP_atom.Chain_set_name(self, *args)
3565 
3566  def set_check_level(self, *args):
3567  """set_check_level(Chain self, IMP::base::CheckLevel a0)"""
3568  return _IMP_atom.Chain_set_check_level(self, *args)
3569 
3570  def add_to_derivative(self, *args):
3571  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3572  return _IMP_atom.Chain_add_to_derivative(self, *args)
3573 
3574  def set_is_optimized(self, *args):
3575  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
3576  return _IMP_atom.Chain_set_is_optimized(self, *args)
3577 
3578  def get_is_optimized(self, *args):
3579  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
3580  return _IMP_atom.Chain_get_is_optimized(self, *args)
3581 
3582  def get_check_level(self):
3583  """get_check_level(Chain self) -> IMP::base::CheckLevel"""
3584  return _IMP_atom.Chain_get_check_level(self)
3585 
3586  def __eq__(self, *args):
3587  """
3588  __eq__(Chain self, Chain o) -> bool
3589  __eq__(Chain self, Particle d) -> bool
3590  """
3591  return _IMP_atom.Chain___eq__(self, *args)
3592 
3593  def __ne__(self, *args):
3594  """
3595  __ne__(Chain self, Chain o) -> bool
3596  __ne__(Chain self, Particle d) -> bool
3597  """
3598  return _IMP_atom.Chain___ne__(self, *args)
3599 
3600  def __le__(self, *args):
3601  """
3602  __le__(Chain self, Chain o) -> bool
3603  __le__(Chain self, Particle d) -> bool
3604  """
3605  return _IMP_atom.Chain___le__(self, *args)
3606 
3607  def __lt__(self, *args):
3608  """
3609  __lt__(Chain self, Chain o) -> bool
3610  __lt__(Chain self, Particle d) -> bool
3611  """
3612  return _IMP_atom.Chain___lt__(self, *args)
3613 
3614  def __ge__(self, *args):
3615  """
3616  __ge__(Chain self, Chain o) -> bool
3617  __ge__(Chain self, Particle d) -> bool
3618  """
3619  return _IMP_atom.Chain___ge__(self, *args)
3620 
3621  def __gt__(self, *args):
3622  """
3623  __gt__(Chain self, Chain o) -> bool
3624  __gt__(Chain self, Particle d) -> bool
3625  """
3626  return _IMP_atom.Chain___gt__(self, *args)
3627 
3628  def __str__(self):
3629  """__str__(Chain self) -> std::string"""
3630  return _IMP_atom.Chain___str__(self)
3631 
3632  def __repr__(self):
3633  """__repr__(Chain self) -> std::string"""
3634  return _IMP_atom.Chain___repr__(self)
3635 
3636  __swig_destroy__ = _IMP_atom.delete_Chain
3637  __del__ = lambda self : None;
3638 Chain_swigregister = _IMP_atom.Chain_swigregister
3639 Chain_swigregister(Chain)
3640 
3641 def Chain_decorate_particle(*args):
3642  """Chain_decorate_particle(Particle p) -> Chain"""
3643  return _IMP_atom.Chain_decorate_particle(*args)
3644 
3645 def Chain_setup_particle(*args):
3646  """
3647  setup_particle(Model m, IMP::kernel::ParticleIndex pi, char id) -> Chain
3648  setup_particle(Particle p, char id) -> Chain
3649  Chain_setup_particle(Particle p, Chain o) -> Chain
3650  """
3651  return _IMP_atom.Chain_setup_particle(*args)
3652 
3653 def Chain_particle_is_instance(*args):
3654  """Chain_particle_is_instance(Particle p) -> bool"""
3655  return _IMP_atom.Chain_particle_is_instance(*args)
3656 
3657 def Chain_get_id_key():
3658  """Chain_get_id_key() -> IntKey"""
3659  return _IMP_atom.Chain_get_id_key()
3660 
3661 
3662 def get_chain(*args):
3663  """get_chain(Hierarchy h) -> Chain"""
3664  return _IMP_atom.get_chain(*args)
3665 class Charged(IMP.core.XYZ):
3666  """Proxy of C++ IMP::atom::Charged class"""
3667  __swig_setmethods__ = {}
3668  for _s in [IMP.core.XYZ]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3669  __setattr__ = lambda self, name, value: _swig_setattr(self, Charged, name, value)
3670  __swig_getmethods__ = {}
3671  for _s in [IMP.core.XYZ]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3672  __getattr__ = lambda self, name: _swig_getattr(self, Charged, name)
3673  def __init__(self, *args):
3674  """
3675  __init__(IMP::atom::Charged self) -> Charged
3676  __init__(IMP::atom::Charged self, Model m, IMP::kernel::ParticleIndex id) -> Charged
3677  __init__(IMP::atom::Charged self, Particle p) -> Charged
3678  """
3679  this = _IMP_atom.new_Charged(*args)
3680  try: self.this.append(this)
3681  except: self.this = this
3682  def decorate_particle(*args):
3683  """decorate_particle(Particle p) -> Charged"""
3684  return _IMP_atom.Charged_decorate_particle(*args)
3685 
3686  if _newclass:decorate_particle = staticmethod(decorate_particle)
3687  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3688  def show(self, *args):
3689  """
3690  show(Charged self, _ostream out=std::cout)
3691  show(Charged self)
3692  """
3693  return _IMP_atom.Charged_show(self, *args)
3694 
3695  def setup_particle(*args):
3696  """
3697  setup_particle(Particle p, Vector3D v, IMP::Float charge) -> Charged
3698  setup_particle(Particle p, IMP::Float charge=0) -> Charged
3699  setup_particle(Particle p) -> Charged
3700  """
3701  return _IMP_atom.Charged_setup_particle(*args)
3702 
3703  if _newclass:setup_particle = staticmethod(setup_particle)
3704  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3705  def get_charge(self):
3706  """get_charge(Charged self) -> IMP::Float"""
3707  return _IMP_atom.Charged_get_charge(self)
3708 
3709  def set_charge(self, *args):
3710  """set_charge(Charged self, IMP::Float t)"""
3711  return _IMP_atom.Charged_set_charge(self, *args)
3712 
3713  def particle_is_instance(*args):
3714  """particle_is_instance(Particle p) -> bool"""
3715  return _IMP_atom.Charged_particle_is_instance(*args)
3716 
3717  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3718  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3719  def get_charge_key():
3720  """get_charge_key() -> FloatKey"""
3721  return _IMP_atom.Charged_get_charge_key()
3722 
3723  if _newclass:get_charge_key = staticmethod(get_charge_key)
3724  __swig_getmethods__["get_charge_key"] = lambda x: get_charge_key
3725  def add_attribute(self, *args):
3726  """
3727  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
3728  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
3729  add_attribute(Charged self, IntKey a0, IMP::Int a1)
3730  add_attribute(Charged self, StringKey a0, IMP::String a1)
3731  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
3732  add_attribute(Charged self, ObjectKey a0, IMP::Object * a1)
3733  """
3734  return _IMP_atom.Charged_add_attribute(self, *args)
3735 
3736  def get_value(self, *args):
3737  """
3738  get_value(Charged self, FloatKey a0) -> IMP::Float
3739  get_value(Charged self, IntKey a0) -> IMP::Int
3740  get_value(Charged self, StringKey a0) -> IMP::String
3741  get_value(Charged self, ParticleIndexKey a0) -> Particle
3742  get_value(Charged self, ObjectKey a0) -> IMP::Object *
3743  """
3744  return _IMP_atom.Charged_get_value(self, *args)
3745 
3746  def set_value(self, *args):
3747  """
3748  set_value(Charged self, FloatKey a0, IMP::Float a1)
3749  set_value(Charged self, IntKey a0, IMP::Int a1)
3750  set_value(Charged self, StringKey a0, IMP::String a1)
3751  set_value(Charged self, ParticleIndexKey a0, Particle a1)
3752  set_value(Charged self, ObjectKey a0, IMP::Object * a1)
3753  """
3754  return _IMP_atom.Charged_set_value(self, *args)
3755 
3756  def remove_attribute(self, *args):
3757  """
3758  remove_attribute(Charged self, FloatKey a0)
3759  remove_attribute(Charged self, IntKey a0)
3760  remove_attribute(Charged self, StringKey a0)
3761  remove_attribute(Charged self, ParticleIndexKey a0)
3762  remove_attribute(Charged self, ObjectKey a0)
3763  """
3764  return _IMP_atom.Charged_remove_attribute(self, *args)
3765 
3766  def has_attribute(self, *args):
3767  """
3768  has_attribute(Charged self, FloatKey a0) -> bool
3769  has_attribute(Charged self, IntKey a0) -> bool
3770  has_attribute(Charged self, StringKey a0) -> bool
3771  has_attribute(Charged self, ParticleIndexKey a0) -> bool
3772  has_attribute(Charged self, ObjectKey a0) -> bool
3773  """
3774  return _IMP_atom.Charged_has_attribute(self, *args)
3775 
3776  def get_derivative(self, *args):
3777  """get_derivative(Charged self, FloatKey a0) -> double"""
3778  return _IMP_atom.Charged_get_derivative(self, *args)
3779 
3780  def get_name(self):
3781  """get_name(Charged self) -> std::string"""
3782  return _IMP_atom.Charged_get_name(self)
3783 
3784  def clear_caches(self):
3785  """clear_caches(Charged self)"""
3786  return _IMP_atom.Charged_clear_caches(self)
3787 
3788  def set_name(self, *args):
3789  """set_name(Charged self, std::string a0)"""
3790  return _IMP_atom.Charged_set_name(self, *args)
3791 
3792  def set_check_level(self, *args):
3793  """set_check_level(Charged self, IMP::base::CheckLevel a0)"""
3794  return _IMP_atom.Charged_set_check_level(self, *args)
3795 
3796  def add_to_derivative(self, *args):
3797  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3798  return _IMP_atom.Charged_add_to_derivative(self, *args)
3799 
3800  def set_is_optimized(self, *args):
3801  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
3802  return _IMP_atom.Charged_set_is_optimized(self, *args)
3803 
3804  def get_is_optimized(self, *args):
3805  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
3806  return _IMP_atom.Charged_get_is_optimized(self, *args)
3807 
3808  def get_check_level(self):
3809  """get_check_level(Charged self) -> IMP::base::CheckLevel"""
3810  return _IMP_atom.Charged_get_check_level(self)
3811 
3812  def __eq__(self, *args):
3813  """
3814  __eq__(Charged self, Charged o) -> bool
3815  __eq__(Charged self, Particle d) -> bool
3816  """
3817  return _IMP_atom.Charged___eq__(self, *args)
3818 
3819  def __ne__(self, *args):
3820  """
3821  __ne__(Charged self, Charged o) -> bool
3822  __ne__(Charged self, Particle d) -> bool
3823  """
3824  return _IMP_atom.Charged___ne__(self, *args)
3825 
3826  def __le__(self, *args):
3827  """
3828  __le__(Charged self, Charged o) -> bool
3829  __le__(Charged self, Particle d) -> bool
3830  """
3831  return _IMP_atom.Charged___le__(self, *args)
3832 
3833  def __lt__(self, *args):
3834  """
3835  __lt__(Charged self, Charged o) -> bool
3836  __lt__(Charged self, Particle d) -> bool
3837  """
3838  return _IMP_atom.Charged___lt__(self, *args)
3839 
3840  def __ge__(self, *args):
3841  """
3842  __ge__(Charged self, Charged o) -> bool
3843  __ge__(Charged self, Particle d) -> bool
3844  """
3845  return _IMP_atom.Charged___ge__(self, *args)
3846 
3847  def __gt__(self, *args):
3848  """
3849  __gt__(Charged self, Charged o) -> bool
3850  __gt__(Charged self, Particle d) -> bool
3851  """
3852  return _IMP_atom.Charged___gt__(self, *args)
3853 
3854  def __str__(self):
3855  """__str__(Charged self) -> std::string"""
3856  return _IMP_atom.Charged___str__(self)
3857 
3858  def __repr__(self):
3859  """__repr__(Charged self) -> std::string"""
3860  return _IMP_atom.Charged___repr__(self)
3861 
3862  __swig_destroy__ = _IMP_atom.delete_Charged
3863  __del__ = lambda self : None;
3864 Charged_swigregister = _IMP_atom.Charged_swigregister
3865 Charged_swigregister(Charged)
3866 
3867 def Charged_decorate_particle(*args):
3868  """Charged_decorate_particle(Particle p) -> Charged"""
3869  return _IMP_atom.Charged_decorate_particle(*args)
3870 
3871 def Charged_setup_particle(*args):
3872  """
3873  setup_particle(Particle p, Vector3D v, IMP::Float charge) -> Charged
3874  setup_particle(Particle p, IMP::Float charge=0) -> Charged
3875  Charged_setup_particle(Particle p) -> Charged
3876  """
3877  return _IMP_atom.Charged_setup_particle(*args)
3878 
3879 def Charged_particle_is_instance(*args):
3880  """Charged_particle_is_instance(Particle p) -> bool"""
3881  return _IMP_atom.Charged_particle_is_instance(*args)
3882 
3883 def Charged_get_charge_key():
3884  """Charged_get_charge_key() -> FloatKey"""
3885  return _IMP_atom.Charged_get_charge_key()
3886 
3887 class CoulombPairScore(IMP.kernel.PairScore):
3888  """Proxy of C++ IMP::atom::CoulombPairScore class"""
3889  __swig_setmethods__ = {}
3890  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3891  __setattr__ = lambda self, name, value: _swig_setattr(self, CoulombPairScore, name, value)
3892  __swig_getmethods__ = {}
3893  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3894  __getattr__ = lambda self, name: _swig_getattr(self, CoulombPairScore, name)
3895  def __init__(self, *args):
3896  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
3897  this = _IMP_atom.new_CoulombPairScore(*args)
3898  try: self.this.append(this)
3899  except: self.this = this
3900  def set_relative_dielectric(self, *args):
3901  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
3902  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, *args)
3903 
3904  def get_relative_dielectric(self):
3905  """get_relative_dielectric(CoulombPairScore self) -> double"""
3906  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
3907 
3908  def do_create_current_decomposition(self, *args):
3909  """do_create_current_decomposition(CoulombPairScore self, Model m, IMP::kernel::ParticleIndexPair const & vt) -> IMP::kernel::Restraints"""
3910  return _IMP_atom.CoulombPairScore_do_create_current_decomposition(self, *args)
3911 
3912  def get_version_info(self):
3913  """get_version_info(CoulombPairScore self) -> VersionInfo"""
3914  return _IMP_atom.CoulombPairScore_get_version_info(self)
3915 
3916  def do_show(self, *args):
3917  """do_show(CoulombPairScore self, _ostream out)"""
3918  return _IMP_atom.CoulombPairScore_do_show(self, *args)
3919 
3920  __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
3921  __del__ = lambda self : None;
3922  def __str__(self):
3923  """__str__(CoulombPairScore self) -> std::string"""
3924  return _IMP_atom.CoulombPairScore___str__(self)
3925 
3926  def __repr__(self):
3927  """__repr__(CoulombPairScore self) -> std::string"""
3928  return _IMP_atom.CoulombPairScore___repr__(self)
3929 
3930  def get_from(o):
3931  return _object_cast_to_CoulombPairScore(o)
3932  get_from = staticmethod(get_from)
3933 
3934 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
3935 CoulombPairScore_swigregister(CoulombPairScore)
3936 
3937 class Domain(Hierarchy):
3938  """Proxy of C++ IMP::atom::Domain class"""
3939  __swig_setmethods__ = {}
3940  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3941  __setattr__ = lambda self, name, value: _swig_setattr(self, Domain, name, value)
3942  __swig_getmethods__ = {}
3943  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3944  __getattr__ = lambda self, name: _swig_getattr(self, Domain, name)
3945  def setup_particle(*args):
3946  """
3947  setup_particle(Particle p, IMP::Int b, IMP::Int e) -> Domain
3948  setup_particle(Particle p, IMP::IntRange r) -> Domain
3949  setup_particle(Particle p, Domain o) -> Domain
3950  """
3951  return _IMP_atom.Domain_setup_particle(*args)
3952 
3953  if _newclass:setup_particle = staticmethod(setup_particle)
3954  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
3955  __swig_destroy__ = _IMP_atom.delete_Domain
3956  __del__ = lambda self : None;
3957  def particle_is_instance(*args):
3958  """particle_is_instance(Particle p) -> bool"""
3959  return _IMP_atom.Domain_particle_is_instance(*args)
3960 
3961  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
3962  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
3963  def set_index_range(self, *args):
3964  """set_index_range(Domain self, IMP::IntRange ir)"""
3965  return _IMP_atom.Domain_set_index_range(self, *args)
3966 
3967  def get_index_range(self):
3968  """get_index_range(Domain self) -> IMP::IntRange"""
3969  return _IMP_atom.Domain_get_index_range(self)
3970 
3971  def get_begin_index(self):
3972  """get_begin_index(Domain self) -> IMP::Int"""
3973  return _IMP_atom.Domain_get_begin_index(self)
3974 
3975  def get_end_index(self):
3976  """get_end_index(Domain self) -> IMP::Int"""
3977  return _IMP_atom.Domain_get_end_index(self)
3978 
3979  def __init__(self, *args):
3980  """
3981  __init__(IMP::atom::Domain self) -> Domain
3982  __init__(IMP::atom::Domain self, Model m, IMP::kernel::ParticleIndex id) -> Domain
3983  __init__(IMP::atom::Domain self, Particle p) -> Domain
3984  """
3985  this = _IMP_atom.new_Domain(*args)
3986  try: self.this.append(this)
3987  except: self.this = this
3988  def decorate_particle(*args):
3989  """decorate_particle(Particle p) -> Domain"""
3990  return _IMP_atom.Domain_decorate_particle(*args)
3991 
3992  if _newclass:decorate_particle = staticmethod(decorate_particle)
3993  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
3994  def show(self, *args):
3995  """
3996  show(Domain self, _ostream out=std::cout)
3997  show(Domain self)
3998  """
3999  return _IMP_atom.Domain_show(self, *args)
4000 
4001  def add_attribute(self, *args):
4002  """
4003  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4004  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4005  add_attribute(Domain self, IntKey a0, IMP::Int a1)
4006  add_attribute(Domain self, StringKey a0, IMP::String a1)
4007  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4008  add_attribute(Domain self, ObjectKey a0, IMP::Object * a1)
4009  """
4010  return _IMP_atom.Domain_add_attribute(self, *args)
4011 
4012  def get_value(self, *args):
4013  """
4014  get_value(Domain self, FloatKey a0) -> IMP::Float
4015  get_value(Domain self, IntKey a0) -> IMP::Int
4016  get_value(Domain self, StringKey a0) -> IMP::String
4017  get_value(Domain self, ParticleIndexKey a0) -> Particle
4018  get_value(Domain self, ObjectKey a0) -> IMP::Object *
4019  """
4020  return _IMP_atom.Domain_get_value(self, *args)
4021 
4022  def set_value(self, *args):
4023  """
4024  set_value(Domain self, FloatKey a0, IMP::Float a1)
4025  set_value(Domain self, IntKey a0, IMP::Int a1)
4026  set_value(Domain self, StringKey a0, IMP::String a1)
4027  set_value(Domain self, ParticleIndexKey a0, Particle a1)
4028  set_value(Domain self, ObjectKey a0, IMP::Object * a1)
4029  """
4030  return _IMP_atom.Domain_set_value(self, *args)
4031 
4032  def remove_attribute(self, *args):
4033  """
4034  remove_attribute(Domain self, FloatKey a0)
4035  remove_attribute(Domain self, IntKey a0)
4036  remove_attribute(Domain self, StringKey a0)
4037  remove_attribute(Domain self, ParticleIndexKey a0)
4038  remove_attribute(Domain self, ObjectKey a0)
4039  """
4040  return _IMP_atom.Domain_remove_attribute(self, *args)
4041 
4042  def has_attribute(self, *args):
4043  """
4044  has_attribute(Domain self, FloatKey a0) -> bool
4045  has_attribute(Domain self, IntKey a0) -> bool
4046  has_attribute(Domain self, StringKey a0) -> bool
4047  has_attribute(Domain self, ParticleIndexKey a0) -> bool
4048  has_attribute(Domain self, ObjectKey a0) -> bool
4049  """
4050  return _IMP_atom.Domain_has_attribute(self, *args)
4051 
4052  def get_derivative(self, *args):
4053  """get_derivative(Domain self, FloatKey a0) -> double"""
4054  return _IMP_atom.Domain_get_derivative(self, *args)
4055 
4056  def get_name(self):
4057  """get_name(Domain self) -> std::string"""
4058  return _IMP_atom.Domain_get_name(self)
4059 
4060  def clear_caches(self):
4061  """clear_caches(Domain self)"""
4062  return _IMP_atom.Domain_clear_caches(self)
4063 
4064  def set_name(self, *args):
4065  """set_name(Domain self, std::string a0)"""
4066  return _IMP_atom.Domain_set_name(self, *args)
4067 
4068  def set_check_level(self, *args):
4069  """set_check_level(Domain self, IMP::base::CheckLevel a0)"""
4070  return _IMP_atom.Domain_set_check_level(self, *args)
4071 
4072  def add_to_derivative(self, *args):
4073  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4074  return _IMP_atom.Domain_add_to_derivative(self, *args)
4075 
4076  def set_is_optimized(self, *args):
4077  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4078  return _IMP_atom.Domain_set_is_optimized(self, *args)
4079 
4080  def get_is_optimized(self, *args):
4081  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
4082  return _IMP_atom.Domain_get_is_optimized(self, *args)
4083 
4084  def get_check_level(self):
4085  """get_check_level(Domain self) -> IMP::base::CheckLevel"""
4086  return _IMP_atom.Domain_get_check_level(self)
4087 
4088  def __eq__(self, *args):
4089  """
4090  __eq__(Domain self, Domain o) -> bool
4091  __eq__(Domain self, Particle d) -> bool
4092  """
4093  return _IMP_atom.Domain___eq__(self, *args)
4094 
4095  def __ne__(self, *args):
4096  """
4097  __ne__(Domain self, Domain o) -> bool
4098  __ne__(Domain self, Particle d) -> bool
4099  """
4100  return _IMP_atom.Domain___ne__(self, *args)
4101 
4102  def __le__(self, *args):
4103  """
4104  __le__(Domain self, Domain o) -> bool
4105  __le__(Domain self, Particle d) -> bool
4106  """
4107  return _IMP_atom.Domain___le__(self, *args)
4108 
4109  def __lt__(self, *args):
4110  """
4111  __lt__(Domain self, Domain o) -> bool
4112  __lt__(Domain self, Particle d) -> bool
4113  """
4114  return _IMP_atom.Domain___lt__(self, *args)
4115 
4116  def __ge__(self, *args):
4117  """
4118  __ge__(Domain self, Domain o) -> bool
4119  __ge__(Domain self, Particle d) -> bool
4120  """
4121  return _IMP_atom.Domain___ge__(self, *args)
4122 
4123  def __gt__(self, *args):
4124  """
4125  __gt__(Domain self, Domain o) -> bool
4126  __gt__(Domain self, Particle d) -> bool
4127  """
4128  return _IMP_atom.Domain___gt__(self, *args)
4129 
4130  def __str__(self):
4131  """__str__(Domain self) -> std::string"""
4132  return _IMP_atom.Domain___str__(self)
4133 
4134  def __repr__(self):
4135  """__repr__(Domain self) -> std::string"""
4136  return _IMP_atom.Domain___repr__(self)
4137 
4138 Domain_swigregister = _IMP_atom.Domain_swigregister
4139 Domain_swigregister(Domain)
4140 
4141 def Domain_setup_particle(*args):
4142  """
4143  setup_particle(Particle p, IMP::Int b, IMP::Int e) -> Domain
4144  setup_particle(Particle p, IMP::IntRange r) -> Domain
4145  Domain_setup_particle(Particle p, Domain o) -> Domain
4146  """
4147  return _IMP_atom.Domain_setup_particle(*args)
4148 
4149 def Domain_particle_is_instance(*args):
4150  """Domain_particle_is_instance(Particle p) -> bool"""
4151  return _IMP_atom.Domain_particle_is_instance(*args)
4152 
4153 def Domain_decorate_particle(*args):
4154  """Domain_decorate_particle(Particle p) -> Domain"""
4155  return _IMP_atom.Domain_decorate_particle(*args)
4156 
4157 class LennardJones(IMP.core.XYZR):
4158  """Proxy of C++ IMP::atom::LennardJones class"""
4159  __swig_setmethods__ = {}
4160  for _s in [IMP.core.XYZR]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4161  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJones, name, value)
4162  __swig_getmethods__ = {}
4163  for _s in [IMP.core.XYZR]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4164  __getattr__ = lambda self, name: _swig_getattr(self, LennardJones, name)
4165  def __init__(self, *args):
4166  """
4167  __init__(IMP::atom::LennardJones self) -> LennardJones
4168  __init__(IMP::atom::LennardJones self, Model m, IMP::kernel::ParticleIndex id) -> LennardJones
4169  __init__(IMP::atom::LennardJones self, Particle p) -> LennardJones
4170  """
4171  this = _IMP_atom.new_LennardJones(*args)
4172  try: self.this.append(this)
4173  except: self.this = this
4174  def decorate_particle(*args):
4175  """decorate_particle(Particle p) -> LennardJones"""
4176  return _IMP_atom.LennardJones_decorate_particle(*args)
4177 
4178  if _newclass:decorate_particle = staticmethod(decorate_particle)
4179  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4180  def show(self, *args):
4181  """
4182  show(LennardJones self, _ostream out=std::cout)
4183  show(LennardJones self)
4184  """
4185  return _IMP_atom.LennardJones_show(self, *args)
4186 
4187  def setup_particle(*args):
4188  """
4189  setup_particle(Particle p, IMP::Float well_depth=0) -> LennardJones
4190  setup_particle(Particle p) -> LennardJones
4191  """
4192  return _IMP_atom.LennardJones_setup_particle(*args)
4193 
4194  if _newclass:setup_particle = staticmethod(setup_particle)
4195  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4196  def get_well_depth(self):
4197  """get_well_depth(LennardJones self) -> IMP::Float"""
4198  return _IMP_atom.LennardJones_get_well_depth(self)
4199 
4200  def set_well_depth(self, *args):
4201  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
4202  return _IMP_atom.LennardJones_set_well_depth(self, *args)
4203 
4204  def particle_is_instance(*args):
4205  """particle_is_instance(Particle p) -> bool"""
4206  return _IMP_atom.LennardJones_particle_is_instance(*args)
4207 
4208  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4209  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4210  def get_well_depth_key():
4211  """get_well_depth_key() -> FloatKey"""
4212  return _IMP_atom.LennardJones_get_well_depth_key()
4213 
4214  if _newclass:get_well_depth_key = staticmethod(get_well_depth_key)
4215  __swig_getmethods__["get_well_depth_key"] = lambda x: get_well_depth_key
4216  def add_attribute(self, *args):
4217  """
4218  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
4219  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
4220  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
4221  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
4222  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
4223  add_attribute(LennardJones self, ObjectKey a0, IMP::Object * a1)
4224  """
4225  return _IMP_atom.LennardJones_add_attribute(self, *args)
4226 
4227  def get_value(self, *args):
4228  """
4229  get_value(LennardJones self, FloatKey a0) -> IMP::Float
4230  get_value(LennardJones self, IntKey a0) -> IMP::Int
4231  get_value(LennardJones self, StringKey a0) -> IMP::String
4232  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
4233  get_value(LennardJones self, ObjectKey a0) -> IMP::Object *
4234  """
4235  return _IMP_atom.LennardJones_get_value(self, *args)
4236 
4237  def set_value(self, *args):
4238  """
4239  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
4240  set_value(LennardJones self, IntKey a0, IMP::Int a1)
4241  set_value(LennardJones self, StringKey a0, IMP::String a1)
4242  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
4243  set_value(LennardJones self, ObjectKey a0, IMP::Object * a1)
4244  """
4245  return _IMP_atom.LennardJones_set_value(self, *args)
4246 
4247  def remove_attribute(self, *args):
4248  """
4249  remove_attribute(LennardJones self, FloatKey a0)
4250  remove_attribute(LennardJones self, IntKey a0)
4251  remove_attribute(LennardJones self, StringKey a0)
4252  remove_attribute(LennardJones self, ParticleIndexKey a0)
4253  remove_attribute(LennardJones self, ObjectKey a0)
4254  """
4255  return _IMP_atom.LennardJones_remove_attribute(self, *args)
4256 
4257  def has_attribute(self, *args):
4258  """
4259  has_attribute(LennardJones self, FloatKey a0) -> bool
4260  has_attribute(LennardJones self, IntKey a0) -> bool
4261  has_attribute(LennardJones self, StringKey a0) -> bool
4262  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
4263  has_attribute(LennardJones self, ObjectKey a0) -> bool
4264  """
4265  return _IMP_atom.LennardJones_has_attribute(self, *args)
4266 
4267  def get_derivative(self, *args):
4268  """get_derivative(LennardJones self, FloatKey a0) -> double"""
4269  return _IMP_atom.LennardJones_get_derivative(self, *args)
4270 
4271  def get_name(self):
4272  """get_name(LennardJones self) -> std::string"""
4273  return _IMP_atom.LennardJones_get_name(self)
4274 
4275  def clear_caches(self):
4276  """clear_caches(LennardJones self)"""
4277  return _IMP_atom.LennardJones_clear_caches(self)
4278 
4279  def set_name(self, *args):
4280  """set_name(LennardJones self, std::string a0)"""
4281  return _IMP_atom.LennardJones_set_name(self, *args)
4282 
4283  def set_check_level(self, *args):
4284  """set_check_level(LennardJones self, IMP::base::CheckLevel a0)"""
4285  return _IMP_atom.LennardJones_set_check_level(self, *args)
4286 
4287  def add_to_derivative(self, *args):
4288  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4289  return _IMP_atom.LennardJones_add_to_derivative(self, *args)
4290 
4291  def set_is_optimized(self, *args):
4292  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
4293  return _IMP_atom.LennardJones_set_is_optimized(self, *args)
4294 
4295  def get_is_optimized(self, *args):
4296  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
4297  return _IMP_atom.LennardJones_get_is_optimized(self, *args)
4298 
4299  def get_check_level(self):
4300  """get_check_level(LennardJones self) -> IMP::base::CheckLevel"""
4301  return _IMP_atom.LennardJones_get_check_level(self)
4302 
4303  def __eq__(self, *args):
4304  """
4305  __eq__(LennardJones self, LennardJones o) -> bool
4306  __eq__(LennardJones self, Particle d) -> bool
4307  """
4308  return _IMP_atom.LennardJones___eq__(self, *args)
4309 
4310  def __ne__(self, *args):
4311  """
4312  __ne__(LennardJones self, LennardJones o) -> bool
4313  __ne__(LennardJones self, Particle d) -> bool
4314  """
4315  return _IMP_atom.LennardJones___ne__(self, *args)
4316 
4317  def __le__(self, *args):
4318  """
4319  __le__(LennardJones self, LennardJones o) -> bool
4320  __le__(LennardJones self, Particle d) -> bool
4321  """
4322  return _IMP_atom.LennardJones___le__(self, *args)
4323 
4324  def __lt__(self, *args):
4325  """
4326  __lt__(LennardJones self, LennardJones o) -> bool
4327  __lt__(LennardJones self, Particle d) -> bool
4328  """
4329  return _IMP_atom.LennardJones___lt__(self, *args)
4330 
4331  def __ge__(self, *args):
4332  """
4333  __ge__(LennardJones self, LennardJones o) -> bool
4334  __ge__(LennardJones self, Particle d) -> bool
4335  """
4336  return _IMP_atom.LennardJones___ge__(self, *args)
4337 
4338  def __gt__(self, *args):
4339  """
4340  __gt__(LennardJones self, LennardJones o) -> bool
4341  __gt__(LennardJones self, Particle d) -> bool
4342  """
4343  return _IMP_atom.LennardJones___gt__(self, *args)
4344 
4345  def __str__(self):
4346  """__str__(LennardJones self) -> std::string"""
4347  return _IMP_atom.LennardJones___str__(self)
4348 
4349  def __repr__(self):
4350  """__repr__(LennardJones self) -> std::string"""
4351  return _IMP_atom.LennardJones___repr__(self)
4352 
4353  __swig_destroy__ = _IMP_atom.delete_LennardJones
4354  __del__ = lambda self : None;
4355 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
4356 LennardJones_swigregister(LennardJones)
4357 
4358 def LennardJones_decorate_particle(*args):
4359  """LennardJones_decorate_particle(Particle p) -> LennardJones"""
4360  return _IMP_atom.LennardJones_decorate_particle(*args)
4361 
4362 def LennardJones_setup_particle(*args):
4363  """
4364  setup_particle(Particle p, IMP::Float well_depth=0) -> LennardJones
4365  LennardJones_setup_particle(Particle p) -> LennardJones
4366  """
4367  return _IMP_atom.LennardJones_setup_particle(*args)
4368 
4369 def LennardJones_particle_is_instance(*args):
4370  """LennardJones_particle_is_instance(Particle p) -> bool"""
4371  return _IMP_atom.LennardJones_particle_is_instance(*args)
4372 
4373 def LennardJones_get_well_depth_key():
4374  """LennardJones_get_well_depth_key() -> FloatKey"""
4375  return _IMP_atom.LennardJones_get_well_depth_key()
4376 
4377 class LennardJonesPairScore(IMP.kernel.PairScore):
4378  """Proxy of C++ IMP::atom::LennardJonesPairScore class"""
4379  __swig_setmethods__ = {}
4380  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4381  __setattr__ = lambda self, name, value: _swig_setattr(self, LennardJonesPairScore, name, value)
4382  __swig_getmethods__ = {}
4383  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4384  __getattr__ = lambda self, name: _swig_getattr(self, LennardJonesPairScore, name)
4385  def __init__(self, *args):
4386  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
4387  this = _IMP_atom.new_LennardJonesPairScore(*args)
4388  try: self.this.append(this)
4389  except: self.this = this
4390  def set_repulsive_weight(self, *args):
4391  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
4392  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, *args)
4393 
4394  def get_repulsive_weight(self):
4395  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
4396  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
4397 
4398  def set_attractive_weight(self, *args):
4399  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
4400  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, *args)
4401 
4402  def get_attractive_weight(self):
4403  """get_attractive_weight(LennardJonesPairScore self) -> double"""
4404  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
4405 
4406  def do_create_current_decomposition(self, *args):
4407  """do_create_current_decomposition(LennardJonesPairScore self, Model m, IMP::kernel::ParticleIndexPair const & vt) -> IMP::kernel::Restraints"""
4408  return _IMP_atom.LennardJonesPairScore_do_create_current_decomposition(self, *args)
4409 
4410  def get_version_info(self):
4411  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
4412  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
4413 
4414  def do_show(self, *args):
4415  """do_show(LennardJonesPairScore self, _ostream out)"""
4416  return _IMP_atom.LennardJonesPairScore_do_show(self, *args)
4417 
4418  __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
4419  __del__ = lambda self : None;
4420  def __str__(self):
4421  """__str__(LennardJonesPairScore self) -> std::string"""
4422  return _IMP_atom.LennardJonesPairScore___str__(self)
4423 
4424  def __repr__(self):
4425  """__repr__(LennardJonesPairScore self) -> std::string"""
4426  return _IMP_atom.LennardJonesPairScore___repr__(self)
4427 
4428  def get_from(o):
4429  return _object_cast_to_LennardJonesPairScore(o)
4430  get_from = staticmethod(get_from)
4431 
4432 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
4433 LennardJonesPairScore_swigregister(LennardJonesPairScore)
4434 
4435 class MolecularDynamics(Simulator):
4436  """Proxy of C++ IMP::atom::MolecularDynamics class"""
4437  __swig_setmethods__ = {}
4438  for _s in [Simulator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4439  __setattr__ = lambda self, name, value: _swig_setattr(self, MolecularDynamics, name, value)
4440  __swig_getmethods__ = {}
4441  for _s in [Simulator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4442  __getattr__ = lambda self, name: _swig_getattr(self, MolecularDynamics, name)
4443  def __init__(self, *args):
4444  """
4445  __init__(IMP::atom::MolecularDynamics self, Model m=nullptr) -> MolecularDynamics
4446  __init__(IMP::atom::MolecularDynamics self) -> MolecularDynamics
4447  """
4448  this = _IMP_atom.new_MolecularDynamics(*args)
4449  try: self.this.append(this)
4450  except: self.this = this
4451  def get_kinetic_energy(self):
4452  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
4453  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
4454 
4455  def get_kinetic_temperature(self, *args):
4456  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
4457  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, *args)
4458 
4459  def set_velocity_cap(self, *args):
4460  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
4461  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, *args)
4462 
4463  def assign_velocities(self, *args):
4464  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
4465  return _IMP_atom.MolecularDynamics_assign_velocities(self, *args)
4466 
4467  def __str__(self):
4468  """__str__(MolecularDynamics self) -> std::string"""
4469  return _IMP_atom.MolecularDynamics___str__(self)
4470 
4471  def __repr__(self):
4472  """__repr__(MolecularDynamics self) -> std::string"""
4473  return _IMP_atom.MolecularDynamics___repr__(self)
4474 
4475  def get_from(o):
4476  return _object_cast_to_MolecularDynamics(o)
4477  get_from = staticmethod(get_from)
4478 
4479  __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
4480  __del__ = lambda self : None;
4481 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
4482 MolecularDynamics_swigregister(MolecularDynamics)
4483 
4484 class VelocityScalingOptimizerState(IMP.kernel.OptimizerState):
4485  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class"""
4486  __swig_setmethods__ = {}
4487  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4488  __setattr__ = lambda self, name, value: _swig_setattr(self, VelocityScalingOptimizerState, name, value)
4489  __swig_getmethods__ = {}
4490  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4491  __getattr__ = lambda self, name: _swig_getattr(self, VelocityScalingOptimizerState, name)
4492  def __init__(self, *args):
4493  """__init__(IMP::atom::VelocityScalingOptimizerState self, IMP::kernel::Particles const & pis, IMP::Float temperature, unsigned int skip_steps) -> VelocityScalingOptimizerState"""
4494  this = _IMP_atom.new_VelocityScalingOptimizerState(*args)
4495  try: self.this.append(this)
4496  except: self.this = this
4497  def set_skip_steps(self, *args):
4498  """set_skip_steps(VelocityScalingOptimizerState self, unsigned int skip_steps)"""
4499  return _IMP_atom.VelocityScalingOptimizerState_set_skip_steps(self, *args)
4500 
4501  def set_particles(self, *args):
4502  """set_particles(VelocityScalingOptimizerState self, IMP::kernel::Particles const & pis)"""
4503  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, *args)
4504 
4505  def set_temperature(self, *args):
4506  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
4507  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, *args)
4508 
4509  def rescale_velocities(self):
4510  """rescale_velocities(VelocityScalingOptimizerState self)"""
4511  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
4512 
4513  def get_version_info(self):
4514  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
4515  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
4516 
4517  def do_show(self, *args):
4518  """do_show(VelocityScalingOptimizerState self, _ostream out)"""
4519  return _IMP_atom.VelocityScalingOptimizerState_do_show(self, *args)
4520 
4521  __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
4522  __del__ = lambda self : None;
4523  def __str__(self):
4524  """__str__(VelocityScalingOptimizerState self) -> std::string"""
4525  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
4526 
4527  def __repr__(self):
4528  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
4529  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
4530 
4531  def get_from(o):
4532  return _object_cast_to_VelocityScalingOptimizerState(o)
4533  get_from = staticmethod(get_from)
4534 
4535 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
4536 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
4537 
4538 class Fragment(Hierarchy):
4539  """Proxy of C++ IMP::atom::Fragment class"""
4540  __swig_setmethods__ = {}
4541  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4542  __setattr__ = lambda self, name, value: _swig_setattr(self, Fragment, name, value)
4543  __swig_getmethods__ = {}
4544  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4545  __getattr__ = lambda self, name: _swig_getattr(self, Fragment, name)
4546  def setup_particle(*args):
4547  """
4548  setup_particle(Particle p, IMP::Ints const & ris=IMP::Ints()) -> Fragment
4549  setup_particle(Particle p) -> Fragment
4550  setup_particle(Particle p, Fragment o) -> Fragment
4551  """
4552  return _IMP_atom.Fragment_setup_particle(*args)
4553 
4554  if _newclass:setup_particle = staticmethod(setup_particle)
4555  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4556  __swig_destroy__ = _IMP_atom.delete_Fragment
4557  __del__ = lambda self : None;
4558  def particle_is_instance(*args):
4559  """particle_is_instance(Particle p) -> bool"""
4560  return _IMP_atom.Fragment_particle_is_instance(*args)
4561 
4562  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4563  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4564  def set_residue_indexes(self, *args):
4565  """set_residue_indexes(Fragment self, IMP::Ints o)"""
4566  return _IMP_atom.Fragment_set_residue_indexes(self, *args)
4567 
4568  def get_residue_indexes(self):
4569  """get_residue_indexes(Fragment self) -> IMP::Ints"""
4570  return _IMP_atom.Fragment_get_residue_indexes(self)
4571 
4572  def get_residue_index_ranges(self):
4573  """get_residue_index_ranges(Fragment self) -> IMP::IntPairs"""
4574  return _IMP_atom.Fragment_get_residue_index_ranges(self)
4575 
4576  def get_contains_residue(self, *args):
4577  """get_contains_residue(Fragment self, int rindex) -> bool"""
4578  return _IMP_atom.Fragment_get_contains_residue(self, *args)
4579 
4580  def __init__(self, *args):
4581  """
4582  __init__(IMP::atom::Fragment self) -> Fragment
4583  __init__(IMP::atom::Fragment self, Model m, IMP::kernel::ParticleIndex id) -> Fragment
4584  __init__(IMP::atom::Fragment self, Particle p) -> Fragment
4585  """
4586  this = _IMP_atom.new_Fragment(*args)
4587  try: self.this.append(this)
4588  except: self.this = this
4589  def decorate_particle(*args):
4590  """decorate_particle(Particle p) -> Fragment"""
4591  return _IMP_atom.Fragment_decorate_particle(*args)
4592 
4593  if _newclass:decorate_particle = staticmethod(decorate_particle)
4594  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4595  def show(self, *args):
4596  """
4597  show(Fragment self, _ostream out=std::cout)
4598  show(Fragment self)
4599  """
4600  return _IMP_atom.Fragment_show(self, *args)
4601 
4602  def add_attribute(self, *args):
4603  """
4604  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
4605  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
4606  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
4607  add_attribute(Fragment self, StringKey a0, IMP::String a1)
4608  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
4609  add_attribute(Fragment self, ObjectKey a0, IMP::Object * a1)
4610  """
4611  return _IMP_atom.Fragment_add_attribute(self, *args)
4612 
4613  def get_value(self, *args):
4614  """
4615  get_value(Fragment self, FloatKey a0) -> IMP::Float
4616  get_value(Fragment self, IntKey a0) -> IMP::Int
4617  get_value(Fragment self, StringKey a0) -> IMP::String
4618  get_value(Fragment self, ParticleIndexKey a0) -> Particle
4619  get_value(Fragment self, ObjectKey a0) -> IMP::Object *
4620  """
4621  return _IMP_atom.Fragment_get_value(self, *args)
4622 
4623  def set_value(self, *args):
4624  """
4625  set_value(Fragment self, FloatKey a0, IMP::Float a1)
4626  set_value(Fragment self, IntKey a0, IMP::Int a1)
4627  set_value(Fragment self, StringKey a0, IMP::String a1)
4628  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
4629  set_value(Fragment self, ObjectKey a0, IMP::Object * a1)
4630  """
4631  return _IMP_atom.Fragment_set_value(self, *args)
4632 
4633  def remove_attribute(self, *args):
4634  """
4635  remove_attribute(Fragment self, FloatKey a0)
4636  remove_attribute(Fragment self, IntKey a0)
4637  remove_attribute(Fragment self, StringKey a0)
4638  remove_attribute(Fragment self, ParticleIndexKey a0)
4639  remove_attribute(Fragment self, ObjectKey a0)
4640  """
4641  return _IMP_atom.Fragment_remove_attribute(self, *args)
4642 
4643  def has_attribute(self, *args):
4644  """
4645  has_attribute(Fragment self, FloatKey a0) -> bool
4646  has_attribute(Fragment self, IntKey a0) -> bool
4647  has_attribute(Fragment self, StringKey a0) -> bool
4648  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
4649  has_attribute(Fragment self, ObjectKey a0) -> bool
4650  """
4651  return _IMP_atom.Fragment_has_attribute(self, *args)
4652 
4653  def get_derivative(self, *args):
4654  """get_derivative(Fragment self, FloatKey a0) -> double"""
4655  return _IMP_atom.Fragment_get_derivative(self, *args)
4656 
4657  def get_name(self):
4658  """get_name(Fragment self) -> std::string"""
4659  return _IMP_atom.Fragment_get_name(self)
4660 
4661  def clear_caches(self):
4662  """clear_caches(Fragment self)"""
4663  return _IMP_atom.Fragment_clear_caches(self)
4664 
4665  def set_name(self, *args):
4666  """set_name(Fragment self, std::string a0)"""
4667  return _IMP_atom.Fragment_set_name(self, *args)
4668 
4669  def set_check_level(self, *args):
4670  """set_check_level(Fragment self, IMP::base::CheckLevel a0)"""
4671  return _IMP_atom.Fragment_set_check_level(self, *args)
4672 
4673  def add_to_derivative(self, *args):
4674  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4675  return _IMP_atom.Fragment_add_to_derivative(self, *args)
4676 
4677  def set_is_optimized(self, *args):
4678  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
4679  return _IMP_atom.Fragment_set_is_optimized(self, *args)
4680 
4681  def get_is_optimized(self, *args):
4682  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
4683  return _IMP_atom.Fragment_get_is_optimized(self, *args)
4684 
4685  def get_check_level(self):
4686  """get_check_level(Fragment self) -> IMP::base::CheckLevel"""
4687  return _IMP_atom.Fragment_get_check_level(self)
4688 
4689  def __eq__(self, *args):
4690  """
4691  __eq__(Fragment self, Fragment o) -> bool
4692  __eq__(Fragment self, Particle d) -> bool
4693  """
4694  return _IMP_atom.Fragment___eq__(self, *args)
4695 
4696  def __ne__(self, *args):
4697  """
4698  __ne__(Fragment self, Fragment o) -> bool
4699  __ne__(Fragment self, Particle d) -> bool
4700  """
4701  return _IMP_atom.Fragment___ne__(self, *args)
4702 
4703  def __le__(self, *args):
4704  """
4705  __le__(Fragment self, Fragment o) -> bool
4706  __le__(Fragment self, Particle d) -> bool
4707  """
4708  return _IMP_atom.Fragment___le__(self, *args)
4709 
4710  def __lt__(self, *args):
4711  """
4712  __lt__(Fragment self, Fragment o) -> bool
4713  __lt__(Fragment self, Particle d) -> bool
4714  """
4715  return _IMP_atom.Fragment___lt__(self, *args)
4716 
4717  def __ge__(self, *args):
4718  """
4719  __ge__(Fragment self, Fragment o) -> bool
4720  __ge__(Fragment self, Particle d) -> bool
4721  """
4722  return _IMP_atom.Fragment___ge__(self, *args)
4723 
4724  def __gt__(self, *args):
4725  """
4726  __gt__(Fragment self, Fragment o) -> bool
4727  __gt__(Fragment self, Particle d) -> bool
4728  """
4729  return _IMP_atom.Fragment___gt__(self, *args)
4730 
4731  def __str__(self):
4732  """__str__(Fragment self) -> std::string"""
4733  return _IMP_atom.Fragment___str__(self)
4734 
4735  def __repr__(self):
4736  """__repr__(Fragment self) -> std::string"""
4737  return _IMP_atom.Fragment___repr__(self)
4738 
4739 Fragment_swigregister = _IMP_atom.Fragment_swigregister
4740 Fragment_swigregister(Fragment)
4741 
4742 def Fragment_setup_particle(*args):
4743  """
4744  setup_particle(Particle p, IMP::Ints const & ris=IMP::Ints()) -> Fragment
4745  setup_particle(Particle p) -> Fragment
4746  Fragment_setup_particle(Particle p, Fragment o) -> Fragment
4747  """
4748  return _IMP_atom.Fragment_setup_particle(*args)
4749 
4750 def Fragment_particle_is_instance(*args):
4751  """Fragment_particle_is_instance(Particle p) -> bool"""
4752  return _IMP_atom.Fragment_particle_is_instance(*args)
4753 
4754 def Fragment_decorate_particle(*args):
4755  """Fragment_decorate_particle(Particle p) -> Fragment"""
4756  return _IMP_atom.Fragment_decorate_particle(*args)
4757 
4758 class StereochemistryPairFilter(IMP.kernel.PairPredicate):
4759  """Proxy of C++ IMP::atom::StereochemistryPairFilter class"""
4760  __swig_setmethods__ = {}
4761  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4762  __setattr__ = lambda self, name, value: _swig_setattr(self, StereochemistryPairFilter, name, value)
4763  __swig_getmethods__ = {}
4764  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4765  __getattr__ = lambda self, name: _swig_getattr(self, StereochemistryPairFilter, name)
4766  def __init__(self):
4767  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
4768  this = _IMP_atom.new_StereochemistryPairFilter()
4769  try: self.this.append(this)
4770  except: self.this = this
4771  def set_bonds(self, *args):
4772  """set_bonds(StereochemistryPairFilter self, IMP::kernel::Particles const & bonds)"""
4773  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, *args)
4774 
4775  def set_angles(self, *args):
4776  """set_angles(StereochemistryPairFilter self, IMP::kernel::Particles const & angles)"""
4777  return _IMP_atom.StereochemistryPairFilter_set_angles(self, *args)
4778 
4779  def set_dihedrals(self, *args):
4780  """set_dihedrals(StereochemistryPairFilter self, IMP::kernel::Particles const & dihedrals)"""
4781  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, *args)
4782 
4783  def get_value(self, *args):
4784  """
4785  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePair const & a) -> int
4786  get_value(StereochemistryPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
4787  """
4788  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
4789 
4790  def get_value_index(self, *args):
4791  """
4792  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & vt) -> int
4793  get_value_index(StereochemistryPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
4794  """
4795  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
4796 
4797  def get_input_particles(self, *args):
4798  """get_input_particles(StereochemistryPairFilter self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
4799  return _IMP_atom.StereochemistryPairFilter_get_input_particles(self, *args)
4800 
4801  def get_input_containers(self, *args):
4802  """get_input_containers(StereochemistryPairFilter self, Particle arg2) -> IMP::kernel::ContainersTemp"""
4803  return _IMP_atom.StereochemistryPairFilter_get_input_containers(self, *args)
4804 
4805  def get_version_info(self):
4806  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
4807  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
4808 
4809  def do_show(self, *args):
4810  """do_show(StereochemistryPairFilter self, _ostream out)"""
4811  return _IMP_atom.StereochemistryPairFilter_do_show(self, *args)
4812 
4813  __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
4814  __del__ = lambda self : None;
4815  def __str__(self):
4816  """__str__(StereochemistryPairFilter self) -> std::string"""
4817  return _IMP_atom.StereochemistryPairFilter___str__(self)
4818 
4819  def __repr__(self):
4820  """__repr__(StereochemistryPairFilter self) -> std::string"""
4821  return _IMP_atom.StereochemistryPairFilter___repr__(self)
4822 
4823  def get_from(o):
4824  return _object_cast_to_StereochemistryPairFilter(o)
4825  get_from = staticmethod(get_from)
4826 
4827 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
4828 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
4829 
4830 class Mass(IMP.kernel.Decorator):
4831  """Proxy of C++ IMP::atom::Mass class"""
4832  __swig_setmethods__ = {}
4833  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
4834  __setattr__ = lambda self, name, value: _swig_setattr(self, Mass, name, value)
4835  __swig_getmethods__ = {}
4836  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
4837  __getattr__ = lambda self, name: _swig_getattr(self, Mass, name)
4838  def setup_particle(*args):
4839  """setup_particle(Particle p, double mass) -> Mass"""
4840  return _IMP_atom.Mass_setup_particle(*args)
4841 
4842  if _newclass:setup_particle = staticmethod(setup_particle)
4843  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
4844  def particle_is_instance(*args):
4845  """particle_is_instance(Particle p) -> bool"""
4846  return _IMP_atom.Mass_particle_is_instance(*args)
4847 
4848  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
4849  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
4850  def get_mass(self):
4851  """get_mass(Mass self) -> IMP::Float"""
4852  return _IMP_atom.Mass_get_mass(self)
4853 
4854  def set_mass(self, *args):
4855  """set_mass(Mass self, IMP::Float d)"""
4856  return _IMP_atom.Mass_set_mass(self, *args)
4857 
4858  def __init__(self, *args):
4859  """
4860  __init__(IMP::atom::Mass self) -> Mass
4861  __init__(IMP::atom::Mass self, Model m, IMP::kernel::ParticleIndex id) -> Mass
4862  __init__(IMP::atom::Mass self, Particle p) -> Mass
4863  """
4864  this = _IMP_atom.new_Mass(*args)
4865  try: self.this.append(this)
4866  except: self.this = this
4867  def decorate_particle(*args):
4868  """decorate_particle(Particle p) -> Mass"""
4869  return _IMP_atom.Mass_decorate_particle(*args)
4870 
4871  if _newclass:decorate_particle = staticmethod(decorate_particle)
4872  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
4873  def show(self, *args):
4874  """
4875  show(Mass self, _ostream out=std::cout)
4876  show(Mass self)
4877  """
4878  return _IMP_atom.Mass_show(self, *args)
4879 
4880  def get_mass_key():
4881  """get_mass_key() -> FloatKey"""
4882  return _IMP_atom.Mass_get_mass_key()
4883 
4884  if _newclass:get_mass_key = staticmethod(get_mass_key)
4885  __swig_getmethods__["get_mass_key"] = lambda x: get_mass_key
4886  def add_attribute(self, *args):
4887  """
4888  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
4889  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
4890  add_attribute(Mass self, IntKey a0, IMP::Int a1)
4891  add_attribute(Mass self, StringKey a0, IMP::String a1)
4892  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
4893  add_attribute(Mass self, ObjectKey a0, IMP::Object * a1)
4894  """
4895  return _IMP_atom.Mass_add_attribute(self, *args)
4896 
4897  def get_value(self, *args):
4898  """
4899  get_value(Mass self, FloatKey a0) -> IMP::Float
4900  get_value(Mass self, IntKey a0) -> IMP::Int
4901  get_value(Mass self, StringKey a0) -> IMP::String
4902  get_value(Mass self, ParticleIndexKey a0) -> Particle
4903  get_value(Mass self, ObjectKey a0) -> IMP::Object *
4904  """
4905  return _IMP_atom.Mass_get_value(self, *args)
4906 
4907  def set_value(self, *args):
4908  """
4909  set_value(Mass self, FloatKey a0, IMP::Float a1)
4910  set_value(Mass self, IntKey a0, IMP::Int a1)
4911  set_value(Mass self, StringKey a0, IMP::String a1)
4912  set_value(Mass self, ParticleIndexKey a0, Particle a1)
4913  set_value(Mass self, ObjectKey a0, IMP::Object * a1)
4914  """
4915  return _IMP_atom.Mass_set_value(self, *args)
4916 
4917  def remove_attribute(self, *args):
4918  """
4919  remove_attribute(Mass self, FloatKey a0)
4920  remove_attribute(Mass self, IntKey a0)
4921  remove_attribute(Mass self, StringKey a0)
4922  remove_attribute(Mass self, ParticleIndexKey a0)
4923  remove_attribute(Mass self, ObjectKey a0)
4924  """
4925  return _IMP_atom.Mass_remove_attribute(self, *args)
4926 
4927  def has_attribute(self, *args):
4928  """
4929  has_attribute(Mass self, FloatKey a0) -> bool
4930  has_attribute(Mass self, IntKey a0) -> bool
4931  has_attribute(Mass self, StringKey a0) -> bool
4932  has_attribute(Mass self, ParticleIndexKey a0) -> bool
4933  has_attribute(Mass self, ObjectKey a0) -> bool
4934  """
4935  return _IMP_atom.Mass_has_attribute(self, *args)
4936 
4937  def get_derivative(self, *args):
4938  """get_derivative(Mass self, FloatKey a0) -> double"""
4939  return _IMP_atom.Mass_get_derivative(self, *args)
4940 
4941  def get_name(self):
4942  """get_name(Mass self) -> std::string"""
4943  return _IMP_atom.Mass_get_name(self)
4944 
4945  def clear_caches(self):
4946  """clear_caches(Mass self)"""
4947  return _IMP_atom.Mass_clear_caches(self)
4948 
4949  def set_name(self, *args):
4950  """set_name(Mass self, std::string a0)"""
4951  return _IMP_atom.Mass_set_name(self, *args)
4952 
4953  def set_check_level(self, *args):
4954  """set_check_level(Mass self, IMP::base::CheckLevel a0)"""
4955  return _IMP_atom.Mass_set_check_level(self, *args)
4956 
4957  def add_to_derivative(self, *args):
4958  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4959  return _IMP_atom.Mass_add_to_derivative(self, *args)
4960 
4961  def set_is_optimized(self, *args):
4962  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
4963  return _IMP_atom.Mass_set_is_optimized(self, *args)
4964 
4965  def get_is_optimized(self, *args):
4966  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
4967  return _IMP_atom.Mass_get_is_optimized(self, *args)
4968 
4969  def get_check_level(self):
4970  """get_check_level(Mass self) -> IMP::base::CheckLevel"""
4971  return _IMP_atom.Mass_get_check_level(self)
4972 
4973  def __eq__(self, *args):
4974  """
4975  __eq__(Mass self, Mass o) -> bool
4976  __eq__(Mass self, Particle d) -> bool
4977  """
4978  return _IMP_atom.Mass___eq__(self, *args)
4979 
4980  def __ne__(self, *args):
4981  """
4982  __ne__(Mass self, Mass o) -> bool
4983  __ne__(Mass self, Particle d) -> bool
4984  """
4985  return _IMP_atom.Mass___ne__(self, *args)
4986 
4987  def __le__(self, *args):
4988  """
4989  __le__(Mass self, Mass o) -> bool
4990  __le__(Mass self, Particle d) -> bool
4991  """
4992  return _IMP_atom.Mass___le__(self, *args)
4993 
4994  def __lt__(self, *args):
4995  """
4996  __lt__(Mass self, Mass o) -> bool
4997  __lt__(Mass self, Particle d) -> bool
4998  """
4999  return _IMP_atom.Mass___lt__(self, *args)
5000 
5001  def __ge__(self, *args):
5002  """
5003  __ge__(Mass self, Mass o) -> bool
5004  __ge__(Mass self, Particle d) -> bool
5005  """
5006  return _IMP_atom.Mass___ge__(self, *args)
5007 
5008  def __gt__(self, *args):
5009  """
5010  __gt__(Mass self, Mass o) -> bool
5011  __gt__(Mass self, Particle d) -> bool
5012  """
5013  return _IMP_atom.Mass___gt__(self, *args)
5014 
5015  def __str__(self):
5016  """__str__(Mass self) -> std::string"""
5017  return _IMP_atom.Mass___str__(self)
5018 
5019  def __repr__(self):
5020  """__repr__(Mass self) -> std::string"""
5021  return _IMP_atom.Mass___repr__(self)
5022 
5023  __swig_destroy__ = _IMP_atom.delete_Mass
5024  __del__ = lambda self : None;
5025 Mass_swigregister = _IMP_atom.Mass_swigregister
5026 Mass_swigregister(Mass)
5027 
5028 def Mass_setup_particle(*args):
5029  """Mass_setup_particle(Particle p, double mass) -> Mass"""
5030  return _IMP_atom.Mass_setup_particle(*args)
5031 
5032 def Mass_particle_is_instance(*args):
5033  """Mass_particle_is_instance(Particle p) -> bool"""
5034  return _IMP_atom.Mass_particle_is_instance(*args)
5035 
5036 def Mass_decorate_particle(*args):
5037  """Mass_decorate_particle(Particle p) -> Mass"""
5038  return _IMP_atom.Mass_decorate_particle(*args)
5039 
5040 def Mass_get_mass_key():
5041  """Mass_get_mass_key() -> FloatKey"""
5042  return _IMP_atom.Mass_get_mass_key()
5043 
5044 class BondedPairFilter(IMP.kernel.PairPredicate):
5045  """Proxy of C++ IMP::atom::BondedPairFilter class"""
5046  __swig_setmethods__ = {}
5047  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5048  __setattr__ = lambda self, name, value: _swig_setattr(self, BondedPairFilter, name, value)
5049  __swig_getmethods__ = {}
5050  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5051  __getattr__ = lambda self, name: _swig_getattr(self, BondedPairFilter, name)
5052  def __init__(self):
5053  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
5054  this = _IMP_atom.new_BondedPairFilter()
5055  try: self.this.append(this)
5056  except: self.this = this
5057  def get_value(self, *args):
5058  """
5059  get_value(BondedPairFilter self, IMP::kernel::ParticlePair const & a) -> int
5060  get_value(BondedPairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
5061  """
5062  return _IMP_atom.BondedPairFilter_get_value(self, *args)
5063 
5064  def get_value_index(self, *args):
5065  """
5066  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPair const & vt) -> int
5067  get_value_index(BondedPairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
5068  """
5069  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
5070 
5071  def get_input_particles(self, *args):
5072  """get_input_particles(BondedPairFilter self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
5073  return _IMP_atom.BondedPairFilter_get_input_particles(self, *args)
5074 
5075  def get_input_containers(self, *args):
5076  """get_input_containers(BondedPairFilter self, Particle arg2) -> IMP::kernel::ContainersTemp"""
5077  return _IMP_atom.BondedPairFilter_get_input_containers(self, *args)
5078 
5079  def get_version_info(self):
5080  """get_version_info(BondedPairFilter self) -> VersionInfo"""
5081  return _IMP_atom.BondedPairFilter_get_version_info(self)
5082 
5083  def do_show(self, *args):
5084  """do_show(BondedPairFilter self, _ostream out)"""
5085  return _IMP_atom.BondedPairFilter_do_show(self, *args)
5086 
5087  __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
5088  __del__ = lambda self : None;
5089  def __str__(self):
5090  """__str__(BondedPairFilter self) -> std::string"""
5091  return _IMP_atom.BondedPairFilter___str__(self)
5092 
5093  def __repr__(self):
5094  """__repr__(BondedPairFilter self) -> std::string"""
5095  return _IMP_atom.BondedPairFilter___repr__(self)
5096 
5097  def get_from(o):
5098  return _object_cast_to_BondedPairFilter(o)
5099  get_from = staticmethod(get_from)
5100 
5101 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
5102 BondedPairFilter_swigregister(BondedPairFilter)
5103 
5104 class Mol2Selector(IMP.base.Object):
5105  """Proxy of C++ IMP::atom::Mol2Selector class"""
5106  __swig_setmethods__ = {}
5107  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5108  __setattr__ = lambda self, name, value: _swig_setattr(self, Mol2Selector, name, value)
5109  __swig_getmethods__ = {}
5110  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5111  __getattr__ = lambda self, name: _swig_getattr(self, Mol2Selector, name)
5112  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
5113  def get_is_selected(self, *args):
5114  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
5115  return _IMP_atom.Mol2Selector_get_is_selected(self, *args)
5116 
5117  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
5118  __del__ = lambda self : None;
5119  def __str__(self):
5120  """__str__(Mol2Selector self) -> std::string"""
5121  return _IMP_atom.Mol2Selector___str__(self)
5122 
5123  def __repr__(self):
5124  """__repr__(Mol2Selector self) -> std::string"""
5125  return _IMP_atom.Mol2Selector___repr__(self)
5126 
5127  def get_from(o):
5128  return _object_cast_to_Mol2Selector(o)
5129  get_from = staticmethod(get_from)
5130 
5131 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
5132 Mol2Selector_swigregister(Mol2Selector)
5133 
5134 class AllMol2Selector(Mol2Selector):
5135  """Proxy of C++ IMP::atom::AllMol2Selector class"""
5136  __swig_setmethods__ = {}
5137  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5138  __setattr__ = lambda self, name, value: _swig_setattr(self, AllMol2Selector, name, value)
5139  __swig_getmethods__ = {}
5140  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5141  __getattr__ = lambda self, name: _swig_getattr(self, AllMol2Selector, name)
5142  def get_version_info(self):
5143  """get_version_info(AllMol2Selector self) -> VersionInfo"""
5144  return _IMP_atom.AllMol2Selector_get_version_info(self)
5145 
5146  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
5147  __del__ = lambda self : None;
5148  def __str__(self):
5149  """__str__(AllMol2Selector self) -> std::string"""
5150  return _IMP_atom.AllMol2Selector___str__(self)
5151 
5152  def __repr__(self):
5153  """__repr__(AllMol2Selector self) -> std::string"""
5154  return _IMP_atom.AllMol2Selector___repr__(self)
5155 
5156  def get_from(o):
5157  return _object_cast_to_AllMol2Selector(o)
5158  get_from = staticmethod(get_from)
5159 
5160  def __init__(self):
5161  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
5162  this = _IMP_atom.new_AllMol2Selector()
5163  try: self.this.append(this)
5164  except: self.this = this
5165 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
5166 AllMol2Selector_swigregister(AllMol2Selector)
5167 
5168 class NonHydrogenMol2Selector(Mol2Selector):
5169  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class"""
5170  __swig_setmethods__ = {}
5171  for _s in [Mol2Selector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5172  __setattr__ = lambda self, name, value: _swig_setattr(self, NonHydrogenMol2Selector, name, value)
5173  __swig_getmethods__ = {}
5174  for _s in [Mol2Selector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5175  __getattr__ = lambda self, name: _swig_getattr(self, NonHydrogenMol2Selector, name)
5176  def get_version_info(self):
5177  """get_version_info(NonHydrogenMol2Selector self) -> VersionInfo"""
5178  return _IMP_atom.NonHydrogenMol2Selector_get_version_info(self)
5179 
5180  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
5181  __del__ = lambda self : None;
5182  def __str__(self):
5183  """__str__(NonHydrogenMol2Selector self) -> std::string"""
5184  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
5185 
5186  def __repr__(self):
5187  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
5188  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
5189 
5190  def get_from(o):
5191  return _object_cast_to_NonHydrogenMol2Selector(o)
5192  get_from = staticmethod(get_from)
5193 
5194  def __init__(self):
5195  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
5196  this = _IMP_atom.new_NonHydrogenMol2Selector()
5197  try: self.this.append(this)
5198  except: self.this = this
5199 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
5200 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
5201 
5202 
5203 def read_mol2(*args):
5204  """
5205  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=nullptr) -> Hierarchy
5206  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
5207  """
5208  return _IMP_atom.read_mol2(*args)
5209 
5210 def write_mol2(*args):
5211  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
5212  return _IMP_atom.write_mol2(*args)
5213 class SecondaryStructureResidue(IMP.kernel.Decorator):
5214  """Proxy of C++ IMP::atom::SecondaryStructureResidue class"""
5215  __swig_setmethods__ = {}
5216  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5217  __setattr__ = lambda self, name, value: _swig_setattr(self, SecondaryStructureResidue, name, value)
5218  __swig_getmethods__ = {}
5219  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5220  __getattr__ = lambda self, name: _swig_getattr(self, SecondaryStructureResidue, name)
5221  def __init__(self, *args):
5222  """
5223  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
5224  __init__(IMP::atom::SecondaryStructureResidue self, Model m, IMP::kernel::ParticleIndex id) -> SecondaryStructureResidue
5225  __init__(IMP::atom::SecondaryStructureResidue self, Particle p) -> SecondaryStructureResidue
5226  """
5227  this = _IMP_atom.new_SecondaryStructureResidue(*args)
5228  try: self.this.append(this)
5229  except: self.this = this
5230  def decorate_particle(*args):
5231  """decorate_particle(Particle p) -> SecondaryStructureResidue"""
5232  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5233 
5234  if _newclass:decorate_particle = staticmethod(decorate_particle)
5235  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
5236  def show(self, *args):
5237  """
5238  show(SecondaryStructureResidue self, _ostream out=std::cout)
5239  show(SecondaryStructureResidue self)
5240  """
5241  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
5242 
5243  def setup_particle(*args):
5244  """
5245  setup_particle(Particle res_p, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5246  setup_particle(Particle res_p) -> SecondaryStructureResidue
5247  """
5248  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5249 
5250  if _newclass:setup_particle = staticmethod(setup_particle)
5251  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
5252  def particle_is_instance(*args):
5253  """particle_is_instance(Particle p) -> bool"""
5254  return _IMP_atom.SecondaryStructureResidue_particle_is_instance(*args)
5255 
5256  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
5257  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
5258  def get_particle(self):
5259  """get_particle(SecondaryStructureResidue self) -> Particle"""
5260  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
5261 
5262  def get_all_probabilities(self):
5263  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
5264  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
5265 
5266  def get_prob_helix(self):
5267  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
5268  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
5269 
5270  def set_prob_helix(self, *args):
5271  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
5272  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, *args)
5273 
5274  def get_prob_strand(self):
5275  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
5276  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
5277 
5278  def set_prob_strand(self, *args):
5279  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
5280  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, *args)
5281 
5282  def get_prob_coil(self):
5283  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
5284  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
5285 
5286  def set_prob_coil(self, *args):
5287  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
5288  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, *args)
5289 
5290  def get_prob_helix_key():
5291  """get_prob_helix_key() -> FloatKey"""
5292  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5293 
5294  if _newclass:get_prob_helix_key = staticmethod(get_prob_helix_key)
5295  __swig_getmethods__["get_prob_helix_key"] = lambda x: get_prob_helix_key
5296  def get_prob_strand_key():
5297  """get_prob_strand_key() -> FloatKey"""
5298  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5299 
5300  if _newclass:get_prob_strand_key = staticmethod(get_prob_strand_key)
5301  __swig_getmethods__["get_prob_strand_key"] = lambda x: get_prob_strand_key
5302  def get_prob_coil_key():
5303  """get_prob_coil_key() -> FloatKey"""
5304  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5305 
5306  if _newclass:get_prob_coil_key = staticmethod(get_prob_coil_key)
5307  __swig_getmethods__["get_prob_coil_key"] = lambda x: get_prob_coil_key
5308  def add_attribute(self, *args):
5309  """
5310  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
5311  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5312  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5313  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5314  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5315  add_attribute(SecondaryStructureResidue self, ObjectKey a0, IMP::Object * a1)
5316  """
5317  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
5318 
5319  def get_value(self, *args):
5320  """
5321  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
5322  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
5323  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
5324  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
5325  get_value(SecondaryStructureResidue self, ObjectKey a0) -> IMP::Object *
5326  """
5327  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
5328 
5329  def set_value(self, *args):
5330  """
5331  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
5332  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
5333  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
5334  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
5335  set_value(SecondaryStructureResidue self, ObjectKey a0, IMP::Object * a1)
5336  """
5337  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
5338 
5339  def remove_attribute(self, *args):
5340  """
5341  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
5342  remove_attribute(SecondaryStructureResidue self, IntKey a0)
5343  remove_attribute(SecondaryStructureResidue self, StringKey a0)
5344  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
5345  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
5346  """
5347  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
5348 
5349  def has_attribute(self, *args):
5350  """
5351  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
5352  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
5353  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
5354  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
5355  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
5356  """
5357  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
5358 
5359  def get_derivative(self, *args):
5360  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
5361  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, *args)
5362 
5363  def get_name(self):
5364  """get_name(SecondaryStructureResidue self) -> std::string"""
5365  return _IMP_atom.SecondaryStructureResidue_get_name(self)
5366 
5367  def clear_caches(self):
5368  """clear_caches(SecondaryStructureResidue self)"""
5369  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
5370 
5371  def set_name(self, *args):
5372  """set_name(SecondaryStructureResidue self, std::string a0)"""
5373  return _IMP_atom.SecondaryStructureResidue_set_name(self, *args)
5374 
5375  def set_check_level(self, *args):
5376  """set_check_level(SecondaryStructureResidue self, IMP::base::CheckLevel a0)"""
5377  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, *args)
5378 
5379  def add_to_derivative(self, *args):
5380  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5381  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, *args)
5382 
5383  def set_is_optimized(self, *args):
5384  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
5385  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, *args)
5386 
5387  def get_is_optimized(self, *args):
5388  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
5389  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, *args)
5390 
5391  def get_check_level(self):
5392  """get_check_level(SecondaryStructureResidue self) -> IMP::base::CheckLevel"""
5393  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
5394 
5395  def __eq__(self, *args):
5396  """
5397  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5398  __eq__(SecondaryStructureResidue self, Particle d) -> bool
5399  """
5400  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
5401 
5402  def __ne__(self, *args):
5403  """
5404  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5405  __ne__(SecondaryStructureResidue self, Particle d) -> bool
5406  """
5407  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
5408 
5409  def __le__(self, *args):
5410  """
5411  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5412  __le__(SecondaryStructureResidue self, Particle d) -> bool
5413  """
5414  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
5415 
5416  def __lt__(self, *args):
5417  """
5418  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5419  __lt__(SecondaryStructureResidue self, Particle d) -> bool
5420  """
5421  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
5422 
5423  def __ge__(self, *args):
5424  """
5425  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5426  __ge__(SecondaryStructureResidue self, Particle d) -> bool
5427  """
5428  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
5429 
5430  def __gt__(self, *args):
5431  """
5432  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
5433  __gt__(SecondaryStructureResidue self, Particle d) -> bool
5434  """
5435  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
5436 
5437  def __str__(self):
5438  """__str__(SecondaryStructureResidue self) -> std::string"""
5439  return _IMP_atom.SecondaryStructureResidue___str__(self)
5440 
5441  def __repr__(self):
5442  """__repr__(SecondaryStructureResidue self) -> std::string"""
5443  return _IMP_atom.SecondaryStructureResidue___repr__(self)
5444 
5445  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
5446  __del__ = lambda self : None;
5447 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
5448 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
5449 
5450 def SecondaryStructureResidue_decorate_particle(*args):
5451  """SecondaryStructureResidue_decorate_particle(Particle p) -> SecondaryStructureResidue"""
5452  return _IMP_atom.SecondaryStructureResidue_decorate_particle(*args)
5453 
5454 def SecondaryStructureResidue_setup_particle(*args):
5455  """
5456  setup_particle(Particle res_p, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
5457  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
5458  """
5459  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
5460 
5461 def SecondaryStructureResidue_particle_is_instance(*args):
5462  """SecondaryStructureResidue_particle_is_instance(Particle p) -> bool"""
5463  return _IMP_atom.SecondaryStructureResidue_particle_is_instance(*args)
5464 
5465 def SecondaryStructureResidue_get_prob_helix_key():
5466  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
5467  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
5468 
5469 def SecondaryStructureResidue_get_prob_strand_key():
5470  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
5471  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
5472 
5473 def SecondaryStructureResidue_get_prob_coil_key():
5474  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
5475  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
5476 
5477 
5479  """
5480  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
5481  setup_coarse_secondary_structure_residue(IMP::kernel::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
5482  """
5483  return _IMP_atom.setup_coarse_secondary_structure_residue(*args)
5484 
5486  """
5487  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num,
5488  bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues
5489  setup_coarse_secondary_structure_residues(IMP::kernel::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
5490  """
5491  return _IMP_atom.setup_coarse_secondary_structure_residues(*args)
5492 
5494  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
5495  return _IMP_atom.get_secondary_structure_match_score(*args)
5496 
5497 def read_psipred(*args):
5498  """
5499  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
5500  read_psipred(TextInput inf, IMP::kernel::Particles ps) -> IMP::atom::SecondaryStructureResidues
5501  """
5502  return _IMP_atom.read_psipred(*args)
5503 class _ADopeBase(IMP.kernel.PairScore):
5504  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class"""
5505  __swig_setmethods__ = {}
5506  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5507  __setattr__ = lambda self, name, value: _swig_setattr(self, _ADopeBase, name, value)
5508  __swig_getmethods__ = {}
5509  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5510  __getattr__ = lambda self, name: _swig_getattr(self, _ADopeBase, name)
5511  __repr__ = _swig_repr
5512  def __init__(self, *args):
5513  """
5514  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
5515  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
5516  """
5517  this = _IMP_atom.new__ADopeBase(*args)
5518  try: self.this.append(this)
5519  except: self.this = this
5520  def get_version_info(self):
5521  """get_version_info(_ADopeBase self) -> VersionInfo"""
5522  return _IMP_atom._ADopeBase_get_version_info(self)
5523 
5524  def do_show(self, *args):
5525  """do_show(_ADopeBase self, _ostream out)"""
5526  return _IMP_atom._ADopeBase_do_show(self, *args)
5527 
5528  __swig_destroy__ = _IMP_atom.delete__ADopeBase
5529  __del__ = lambda self : None;
5530 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
5531 _ADopeBase_swigregister(_ADopeBase)
5532 
5533 class _BDopeBase(IMP.kernel.PairScore):
5534  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class"""
5535  __swig_setmethods__ = {}
5536  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5537  __setattr__ = lambda self, name, value: _swig_setattr(self, _BDopeBase, name, value)
5538  __swig_getmethods__ = {}
5539  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5540  __getattr__ = lambda self, name: _swig_getattr(self, _BDopeBase, name)
5541  __repr__ = _swig_repr
5542  def __init__(self, *args):
5543  """
5544  __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,
5545  std::string name="FunctorDistancePairScore %1%") -> _BDopeBase
5546  __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
5547  """
5548  this = _IMP_atom.new__BDopeBase(*args)
5549  try: self.this.append(this)
5550  except: self.this = this
5551  def get_version_info(self):
5552  """get_version_info(_BDopeBase self) -> VersionInfo"""
5553  return _IMP_atom._BDopeBase_get_version_info(self)
5554 
5555  def do_show(self, *args):
5556  """do_show(_BDopeBase self, _ostream out)"""
5557  return _IMP_atom._BDopeBase_do_show(self, *args)
5558 
5559  __swig_destroy__ = _IMP_atom.delete__BDopeBase
5560  __del__ = lambda self : None;
5561 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
5562 _BDopeBase_swigregister(_BDopeBase)
5563 
5564 class _SPSFTB(IMP.kernel.PairScore):
5565  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class"""
5566  __swig_setmethods__ = {}
5567  for _s in [IMP.kernel.PairScore]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5568  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFTB, name, value)
5569  __swig_getmethods__ = {}
5570  for _s in [IMP.kernel.PairScore]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5571  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFTB, name)
5572  __repr__ = _swig_repr
5573  def __init__(self, *args):
5574  """
5575  __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,
5576  std::string name="FunctorDistancePairScore %1%") -> _SPSFTB
5577  __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
5578  """
5579  this = _IMP_atom.new__SPSFTB(*args)
5580  try: self.this.append(this)
5581  except: self.this = this
5582  def get_version_info(self):
5583  """get_version_info(_SPSFTB self) -> VersionInfo"""
5584  return _IMP_atom._SPSFTB_get_version_info(self)
5585 
5586  def do_show(self, *args):
5587  """do_show(_SPSFTB self, _ostream out)"""
5588  return _IMP_atom._SPSFTB_do_show(self, *args)
5589 
5590  __swig_destroy__ = _IMP_atom.delete__SPSFTB
5591  __del__ = lambda self : None;
5592 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
5593 _SPSFTB_swigregister(_SPSFTB)
5594 
5595 class _SPSTF(_SPSFTB):
5596  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class"""
5597  __swig_setmethods__ = {}
5598  for _s in [_SPSFTB]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5599  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSTF, name, value)
5600  __swig_getmethods__ = {}
5601  for _s in [_SPSFTB]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5602  __getattr__ = lambda self, name: _swig_getattr(self, _SPSTF, name)
5603  __repr__ = _swig_repr
5604  def __init__(self, *args):
5605  """
5606  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
5607  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
5608  """
5609  this = _IMP_atom.new__SPSTF(*args)
5610  try: self.this.append(this)
5611  except: self.this = this
5612  __swig_destroy__ = _IMP_atom.delete__SPSTF
5613  __del__ = lambda self : None;
5614 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
5615 _SPSTF_swigregister(_SPSTF)
5616 
5617 class _SPSFT(_BDopeBase):
5618  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class"""
5619  __swig_setmethods__ = {}
5620  for _s in [_BDopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5621  __setattr__ = lambda self, name, value: _swig_setattr(self, _SPSFT, name, value)
5622  __swig_getmethods__ = {}
5623  for _s in [_BDopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5624  __getattr__ = lambda self, name: _swig_getattr(self, _SPSFT, name)
5625  __repr__ = _swig_repr
5626  def __init__(self, *args):
5627  """
5628  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
5629  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
5630  """
5631  this = _IMP_atom.new__SPSFT(*args)
5632  try: self.this.append(this)
5633  except: self.this = this
5634  __swig_destroy__ = _IMP_atom.delete__SPSFT
5635  __del__ = lambda self : None;
5636 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
5637 _SPSFT_swigregister(_SPSFT)
5638 
5639 class ProteinLigandAtomPairScore(_SPSTF):
5640  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class"""
5641  __swig_setmethods__ = {}
5642  for _s in [_SPSTF]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5643  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandAtomPairScore, name, value)
5644  __swig_getmethods__ = {}
5645  for _s in [_SPSTF]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5646  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandAtomPairScore, name)
5647  def __init__(self, *args):
5648  """
5649  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
5650  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
5651  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
5652  """
5653  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
5654  try: self.this.append(this)
5655  except: self.this = this
5656  def get_maximum_distance(self):
5657  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
5658  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
5659 
5660  def __str__(self):
5661  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
5662  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
5663 
5664  def __repr__(self):
5665  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
5666  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
5667 
5668  def get_from(o):
5669  return _object_cast_to_ProteinLigandAtomPairScore(o)
5670  get_from = staticmethod(get_from)
5671 
5672  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
5673  __del__ = lambda self : None;
5674 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
5675 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
5676 
5677 class ProteinLigandRestraint(IMP.container.PairsRestraint):
5678  """Proxy of C++ IMP::atom::ProteinLigandRestraint class"""
5679  __swig_setmethods__ = {}
5680  for _s in [IMP.container.PairsRestraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5681  __setattr__ = lambda self, name, value: _swig_setattr(self, ProteinLigandRestraint, name, value)
5682  __swig_getmethods__ = {}
5683  for _s in [IMP.container.PairsRestraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5684  __getattr__ = lambda self, name: _swig_getattr(self, ProteinLigandRestraint, name)
5685  def __init__(self, *args):
5686  """
5687  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
5688  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
5689  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
5690  """
5691  this = _IMP_atom.new_ProteinLigandRestraint(*args)
5692  try: self.this.append(this)
5693  except: self.this = this
5694  def __str__(self):
5695  """__str__(ProteinLigandRestraint self) -> std::string"""
5696  return _IMP_atom.ProteinLigandRestraint___str__(self)
5697 
5698  def __repr__(self):
5699  """__repr__(ProteinLigandRestraint self) -> std::string"""
5700  return _IMP_atom.ProteinLigandRestraint___repr__(self)
5701 
5702  def get_from(o):
5703  return _object_cast_to_ProteinLigandRestraint(o)
5704  get_from = staticmethod(get_from)
5705 
5706  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
5707  __del__ = lambda self : None;
5708 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
5709 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
5710 
5711 
5712 def add_protein_ligand_score_data(*args):
5713  """add_protein_ligand_score_data(Hierarchy h)"""
5714  return _IMP_atom.add_protein_ligand_score_data(*args)
5715 class AtomType(IMP.base._Value):
5716  """Proxy of C++ IMP::Key<(8974343,false)> class"""
5717  __swig_setmethods__ = {}
5718  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5719  __setattr__ = lambda self, name, value: _swig_setattr(self, AtomType, name, value)
5720  __swig_getmethods__ = {}
5721  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5722  __getattr__ = lambda self, name: _swig_getattr(self, AtomType, name)
5723  def __init__(self, *args):
5724  """
5725  __init__(IMP::Key<(8974343,false)> self) -> AtomType
5726  __init__(IMP::Key<(8974343,false)> self, std::string c) -> AtomType
5727  __init__(IMP::Key<(8974343,false)> self, unsigned int i) -> AtomType
5728  """
5729  this = _IMP_atom.new_AtomType(*args)
5730  try: self.this.append(this)
5731  except: self.this = this
5732  def add_key(*args):
5733  """add_key(std::string sc) -> unsigned int"""
5734  return _IMP_atom.AtomType_add_key(*args)
5735 
5736  if _newclass:add_key = staticmethod(add_key)
5737  __swig_getmethods__["add_key"] = lambda x: add_key
5738  def get_key_exists(*args):
5739  """get_key_exists(std::string sc) -> bool"""
5740  return _IMP_atom.AtomType_get_key_exists(*args)
5741 
5742  if _newclass:get_key_exists = staticmethod(get_key_exists)
5743  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
5744  def get_string(self):
5745  """get_string(AtomType self) -> std::string const"""
5746  return _IMP_atom.AtomType_get_string(self)
5747 
5748  def __eq__(self, *args):
5749  """__eq__(AtomType self, AtomType o) -> bool"""
5750  return _IMP_atom.AtomType___eq__(self, *args)
5751 
5752  def __ne__(self, *args):
5753  """__ne__(AtomType self, AtomType o) -> bool"""
5754  return _IMP_atom.AtomType___ne__(self, *args)
5755 
5756  def __lt__(self, *args):
5757  """__lt__(AtomType self, AtomType o) -> bool"""
5758  return _IMP_atom.AtomType___lt__(self, *args)
5759 
5760  def __gt__(self, *args):
5761  """__gt__(AtomType self, AtomType o) -> bool"""
5762  return _IMP_atom.AtomType___gt__(self, *args)
5763 
5764  def __ge__(self, *args):
5765  """__ge__(AtomType self, AtomType o) -> bool"""
5766  return _IMP_atom.AtomType___ge__(self, *args)
5767 
5768  def __le__(self, *args):
5769  """__le__(AtomType self, AtomType o) -> bool"""
5770  return _IMP_atom.AtomType___le__(self, *args)
5771 
5772  def __hash__(self):
5773  """__hash__(AtomType self) -> std::size_t"""
5774  return _IMP_atom.AtomType___hash__(self)
5775 
5776  def show(self, *args):
5777  """
5778  show(AtomType self, _ostream out=std::cout)
5779  show(AtomType self)
5780  """
5781  return _IMP_atom.AtomType_show(self, *args)
5782 
5783  def add_alias(*args):
5784  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
5785  return _IMP_atom.AtomType_add_alias(*args)
5786 
5787  if _newclass:add_alias = staticmethod(add_alias)
5788  __swig_getmethods__["add_alias"] = lambda x: add_alias
5789  def get_index(self):
5790  """get_index(AtomType self) -> unsigned int"""
5791  return _IMP_atom.AtomType_get_index(self)
5792 
5793  def show_all(*args):
5794  """show_all(_ostream out)"""
5795  return _IMP_atom.AtomType_show_all(*args)
5796 
5797  if _newclass:show_all = staticmethod(show_all)
5798  __swig_getmethods__["show_all"] = lambda x: show_all
5799  def get_all_strings():
5800  """get_all_strings() -> IMP::base::Vector< std::string >"""
5801  return _IMP_atom.AtomType_get_all_strings()
5802 
5803  if _newclass:get_all_strings = staticmethod(get_all_strings)
5804  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
5805  def get_number_unique():
5806  """get_number_unique() -> unsigned int"""
5807  return _IMP_atom.AtomType_get_number_unique()
5808 
5809  if _newclass:get_number_unique = staticmethod(get_number_unique)
5810  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
5811  def __str__(self):
5812  """__str__(AtomType self) -> std::string"""
5813  return _IMP_atom.AtomType___str__(self)
5814 
5815  def __repr__(self):
5816  """__repr__(AtomType self) -> std::string"""
5817  return _IMP_atom.AtomType___repr__(self)
5818 
5819  __swig_destroy__ = _IMP_atom.delete_AtomType
5820  __del__ = lambda self : None;
5821 AtomType_swigregister = _IMP_atom.AtomType_swigregister
5822 AtomType_swigregister(AtomType)
5823 
5824 def AtomType_add_key(*args):
5825  """AtomType_add_key(std::string sc) -> unsigned int"""
5826  return _IMP_atom.AtomType_add_key(*args)
5827 
5828 def AtomType_get_key_exists(*args):
5829  """AtomType_get_key_exists(std::string sc) -> bool"""
5830  return _IMP_atom.AtomType_get_key_exists(*args)
5831 
5832 def AtomType_add_alias(*args):
5833  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
5834  return _IMP_atom.AtomType_add_alias(*args)
5835 
5836 def AtomType_show_all(*args):
5837  """AtomType_show_all(_ostream out)"""
5838  return _IMP_atom.AtomType_show_all(*args)
5839 
5840 def AtomType_get_all_strings():
5841  """AtomType_get_all_strings() -> IMP::base::Vector< std::string >"""
5842  return _IMP_atom.AtomType_get_all_strings()
5843 
5844 def AtomType_get_number_unique():
5845  """AtomType_get_number_unique() -> unsigned int"""
5846  return _IMP_atom.AtomType_get_number_unique()
5847 
5848 class ResidueType(IMP.base._Value):
5849  """Proxy of C++ IMP::Key<(90784334,true)> class"""
5850  __swig_setmethods__ = {}
5851  for _s in [IMP.base._Value]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
5852  __setattr__ = lambda self, name, value: _swig_setattr(self, ResidueType, name, value)
5853  __swig_getmethods__ = {}
5854  for _s in [IMP.base._Value]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
5855  __getattr__ = lambda self, name: _swig_getattr(self, ResidueType, name)
5856  def __init__(self, *args):
5857  """
5858  __init__(IMP::Key<(90784334,true)> self) -> ResidueType
5859  __init__(IMP::Key<(90784334,true)> self, std::string c) -> ResidueType
5860  __init__(IMP::Key<(90784334,true)> self, unsigned int i) -> ResidueType
5861  """
5862  this = _IMP_atom.new_ResidueType(*args)
5863  try: self.this.append(this)
5864  except: self.this = this
5865  def add_key(*args):
5866  """add_key(std::string sc) -> unsigned int"""
5867  return _IMP_atom.ResidueType_add_key(*args)
5868 
5869  if _newclass:add_key = staticmethod(add_key)
5870  __swig_getmethods__["add_key"] = lambda x: add_key
5871  def get_key_exists(*args):
5872  """get_key_exists(std::string sc) -> bool"""
5873  return _IMP_atom.ResidueType_get_key_exists(*args)
5874 
5875  if _newclass:get_key_exists = staticmethod(get_key_exists)
5876  __swig_getmethods__["get_key_exists"] = lambda x: get_key_exists
5877  def get_string(self):
5878  """get_string(ResidueType self) -> std::string const"""
5879  return _IMP_atom.ResidueType_get_string(self)
5880 
5881  def __eq__(self, *args):
5882  """__eq__(ResidueType self, ResidueType o) -> bool"""
5883  return _IMP_atom.ResidueType___eq__(self, *args)
5884 
5885  def __ne__(self, *args):
5886  """__ne__(ResidueType self, ResidueType o) -> bool"""
5887  return _IMP_atom.ResidueType___ne__(self, *args)
5888 
5889  def __lt__(self, *args):
5890  """__lt__(ResidueType self, ResidueType o) -> bool"""
5891  return _IMP_atom.ResidueType___lt__(self, *args)
5892 
5893  def __gt__(self, *args):
5894  """__gt__(ResidueType self, ResidueType o) -> bool"""
5895  return _IMP_atom.ResidueType___gt__(self, *args)
5896 
5897  def __ge__(self, *args):
5898  """__ge__(ResidueType self, ResidueType o) -> bool"""
5899  return _IMP_atom.ResidueType___ge__(self, *args)
5900 
5901  def __le__(self, *args):
5902  """__le__(ResidueType self, ResidueType o) -> bool"""
5903  return _IMP_atom.ResidueType___le__(self, *args)
5904 
5905  def __hash__(self):
5906  """__hash__(ResidueType self) -> std::size_t"""
5907  return _IMP_atom.ResidueType___hash__(self)
5908 
5909  def show(self, *args):
5910  """
5911  show(ResidueType self, _ostream out=std::cout)
5912  show(ResidueType self)
5913  """
5914  return _IMP_atom.ResidueType_show(self, *args)
5915 
5916  def add_alias(*args):
5917  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
5918  return _IMP_atom.ResidueType_add_alias(*args)
5919 
5920  if _newclass:add_alias = staticmethod(add_alias)
5921  __swig_getmethods__["add_alias"] = lambda x: add_alias
5922  def get_index(self):
5923  """get_index(ResidueType self) -> unsigned int"""
5924  return _IMP_atom.ResidueType_get_index(self)
5925 
5926  def show_all(*args):
5927  """show_all(_ostream out)"""
5928  return _IMP_atom.ResidueType_show_all(*args)
5929 
5930  if _newclass:show_all = staticmethod(show_all)
5931  __swig_getmethods__["show_all"] = lambda x: show_all
5932  def get_all_strings():
5933  """get_all_strings() -> IMP::base::Vector< std::string >"""
5934  return _IMP_atom.ResidueType_get_all_strings()
5935 
5936  if _newclass:get_all_strings = staticmethod(get_all_strings)
5937  __swig_getmethods__["get_all_strings"] = lambda x: get_all_strings
5938  def get_number_unique():
5939  """get_number_unique() -> unsigned int"""
5940  return _IMP_atom.ResidueType_get_number_unique()
5941 
5942  if _newclass:get_number_unique = staticmethod(get_number_unique)
5943  __swig_getmethods__["get_number_unique"] = lambda x: get_number_unique
5944  def __str__(self):
5945  """__str__(ResidueType self) -> std::string"""
5946  return _IMP_atom.ResidueType___str__(self)
5947 
5948  def __repr__(self):
5949  """__repr__(ResidueType self) -> std::string"""
5950  return _IMP_atom.ResidueType___repr__(self)
5951 
5952  __swig_destroy__ = _IMP_atom.delete_ResidueType
5953  __del__ = lambda self : None;
5954 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
5955 ResidueType_swigregister(ResidueType)
5956 
5957 def ResidueType_add_key(*args):
5958  """ResidueType_add_key(std::string sc) -> unsigned int"""
5959  return _IMP_atom.ResidueType_add_key(*args)
5960 
5961 def ResidueType_get_key_exists(*args):
5962  """ResidueType_get_key_exists(std::string sc) -> bool"""
5963  return _IMP_atom.ResidueType_get_key_exists(*args)
5964 
5965 def ResidueType_add_alias(*args):
5966  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
5967  return _IMP_atom.ResidueType_add_alias(*args)
5968 
5969 def ResidueType_show_all(*args):
5970  """ResidueType_show_all(_ostream out)"""
5971  return _IMP_atom.ResidueType_show_all(*args)
5972 
5973 def ResidueType_get_all_strings():
5974  """ResidueType_get_all_strings() -> IMP::base::Vector< std::string >"""
5975  return _IMP_atom.ResidueType_get_all_strings()
5976 
5977 def ResidueType_get_number_unique():
5978  """ResidueType_get_number_unique() -> unsigned int"""
5979  return _IMP_atom.ResidueType_get_number_unique()
5980 
5981 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
5982 OH = _IMP_atom.OH
5983 H2O = _IMP_atom.H2O
5984 H = _IMP_atom.H
5985 He = _IMP_atom.He
5986 Li = _IMP_atom.Li
5987 Be = _IMP_atom.Be
5988 B = _IMP_atom.B
5989 C = _IMP_atom.C
5990 N = _IMP_atom.N
5991 O = _IMP_atom.O
5992 F = _IMP_atom.F
5993 Ne = _IMP_atom.Ne
5994 Na = _IMP_atom.Na
5995 Mg = _IMP_atom.Mg
5996 Al = _IMP_atom.Al
5997 Si = _IMP_atom.Si
5998 P = _IMP_atom.P
5999 S = _IMP_atom.S
6000 Cl = _IMP_atom.Cl
6001 Ar = _IMP_atom.Ar
6002 K = _IMP_atom.K
6003 Ca = _IMP_atom.Ca
6004 Sc = _IMP_atom.Sc
6005 Ti = _IMP_atom.Ti
6006 V = _IMP_atom.V
6007 Cr = _IMP_atom.Cr
6008 Mn = _IMP_atom.Mn
6009 Fe = _IMP_atom.Fe
6010 Co = _IMP_atom.Co
6011 Ni = _IMP_atom.Ni
6012 Cu = _IMP_atom.Cu
6013 Zn = _IMP_atom.Zn
6014 Ga = _IMP_atom.Ga
6015 Ge = _IMP_atom.Ge
6016 As = _IMP_atom.As
6017 Se = _IMP_atom.Se
6018 Br = _IMP_atom.Br
6019 Kr = _IMP_atom.Kr
6020 Rb = _IMP_atom.Rb
6021 Sr = _IMP_atom.Sr
6022 Y = _IMP_atom.Y
6023 Zr = _IMP_atom.Zr
6024 Nb = _IMP_atom.Nb
6025 Mo = _IMP_atom.Mo
6026 Tc = _IMP_atom.Tc
6027 Ru = _IMP_atom.Ru
6028 Rh = _IMP_atom.Rh
6029 Pd = _IMP_atom.Pd
6030 Ag = _IMP_atom.Ag
6031 Cd = _IMP_atom.Cd
6032 In = _IMP_atom.In
6033 Sn = _IMP_atom.Sn
6034 Sb = _IMP_atom.Sb
6035 Te = _IMP_atom.Te
6036 I = _IMP_atom.I
6037 Xe = _IMP_atom.Xe
6038 Cs = _IMP_atom.Cs
6039 Ba = _IMP_atom.Ba
6040 La = _IMP_atom.La
6041 Ce = _IMP_atom.Ce
6042 Pr = _IMP_atom.Pr
6043 Nd = _IMP_atom.Nd
6044 Pm = _IMP_atom.Pm
6045 Sm = _IMP_atom.Sm
6046 Eu = _IMP_atom.Eu
6047 Gd = _IMP_atom.Gd
6048 Tb = _IMP_atom.Tb
6049 Dy = _IMP_atom.Dy
6050 Ho = _IMP_atom.Ho
6051 Er = _IMP_atom.Er
6052 Tm = _IMP_atom.Tm
6053 Yb = _IMP_atom.Yb
6054 Lu = _IMP_atom.Lu
6055 Hf = _IMP_atom.Hf
6056 Ta = _IMP_atom.Ta
6057 W = _IMP_atom.W
6058 Re = _IMP_atom.Re
6059 Os = _IMP_atom.Os
6060 Ir = _IMP_atom.Ir
6061 Pt = _IMP_atom.Pt
6062 Au = _IMP_atom.Au
6063 Hg = _IMP_atom.Hg
6064 Tl = _IMP_atom.Tl
6065 Pb = _IMP_atom.Pb
6066 Bi = _IMP_atom.Bi
6067 Po = _IMP_atom.Po
6068 At = _IMP_atom.At
6069 Rn = _IMP_atom.Rn
6070 Fr = _IMP_atom.Fr
6071 Ra = _IMP_atom.Ra
6072 Ac = _IMP_atom.Ac
6073 Th = _IMP_atom.Th
6074 Pa = _IMP_atom.Pa
6075 U = _IMP_atom.U
6076 Np = _IMP_atom.Np
6077 Pu = _IMP_atom.Pu
6078 Am = _IMP_atom.Am
6079 Cm = _IMP_atom.Cm
6080 Bk = _IMP_atom.Bk
6081 Cf = _IMP_atom.Cf
6082 Es = _IMP_atom.Es
6083 Fm = _IMP_atom.Fm
6084 Md = _IMP_atom.Md
6085 No = _IMP_atom.No
6086 Lr = _IMP_atom.Lr
6087 Db = _IMP_atom.Db
6088 Jl = _IMP_atom.Jl
6089 Rf = _IMP_atom.Rf
6090 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
6091 
6092 def hash_value(*args):
6093  """hash_value(IMP::atom::Element e) -> size_t"""
6094  return _IMP_atom.hash_value(*args)
6095 class ElementTable(_object):
6096  """Proxy of C++ IMP::atom::ElementTable class"""
6097  __swig_setmethods__ = {}
6098  __setattr__ = lambda self, name, value: _swig_setattr(self, ElementTable, name, value)
6099  __swig_getmethods__ = {}
6100  __getattr__ = lambda self, name: _swig_getattr(self, ElementTable, name)
6101  __repr__ = _swig_repr
6102  def __init__(self):
6103  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
6104  this = _IMP_atom.new_ElementTable()
6105  try: self.this.append(this)
6106  except: self.this = this
6107  def get_element(self, *args):
6108  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
6109  return _IMP_atom.ElementTable_get_element(self, *args)
6110 
6111  def get_name(self, *args):
6112  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
6113  return _IMP_atom.ElementTable_get_name(self, *args)
6114 
6115  def get_mass(self, *args):
6116  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
6117  return _IMP_atom.ElementTable_get_mass(self, *args)
6118 
6119  __swig_destroy__ = _IMP_atom.delete_ElementTable
6120  __del__ = lambda self : None;
6121 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
6122 ElementTable_swigregister(ElementTable)
6123 
6124 
6125 def get_element_table():
6126  """get_element_table() -> ElementTable"""
6127  return _IMP_atom.get_element_table()
6128 class Atom(Hierarchy):
6129  """Proxy of C++ IMP::atom::Atom class"""
6130  __swig_setmethods__ = {}
6131  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6132  __setattr__ = lambda self, name, value: _swig_setattr(self, Atom, name, value)
6133  __swig_getmethods__ = {}
6134  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6135  __getattr__ = lambda self, name: _swig_getattr(self, Atom, name)
6136  def __init__(self, *args):
6137  """
6138  __init__(IMP::atom::Atom self) -> Atom
6139  __init__(IMP::atom::Atom self, Model m, IMP::kernel::ParticleIndex id) -> Atom
6140  __init__(IMP::atom::Atom self, Particle p) -> Atom
6141  """
6142  this = _IMP_atom.new_Atom(*args)
6143  try: self.this.append(this)
6144  except: self.this = this
6145  def decorate_particle(*args):
6146  """decorate_particle(Particle p) -> Atom"""
6147  return _IMP_atom.Atom_decorate_particle(*args)
6148 
6149  if _newclass:decorate_particle = staticmethod(decorate_particle)
6150  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6151  def show(self, *args):
6152  """
6153  show(Atom self, _ostream out=std::cout)
6154  show(Atom self)
6155  """
6156  return _IMP_atom.Atom_show(self, *args)
6157 
6158  def get_particle(self):
6159  """get_particle(Atom self) -> Particle"""
6160  return _IMP_atom.Atom_get_particle(self)
6161 
6162  def setup_particle(*args):
6163  """
6164  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType t) -> Atom
6165  setup_particle(Particle p, AtomType t) -> Atom
6166  setup_particle(Particle p, Atom o) -> Atom
6167  """
6168  return _IMP_atom.Atom_setup_particle(*args)
6169 
6170  if _newclass:setup_particle = staticmethod(setup_particle)
6171  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6172  def particle_is_instance(*args):
6173  """particle_is_instance(Particle p) -> bool"""
6174  return _IMP_atom.Atom_particle_is_instance(*args)
6175 
6176  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
6177  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
6178  def get_atom_type(self):
6179  """get_atom_type(Atom self) -> AtomType"""
6180  return _IMP_atom.Atom_get_atom_type(self)
6181 
6182  def set_atom_type(self, *args):
6183  """set_atom_type(Atom self, AtomType t)"""
6184  return _IMP_atom.Atom_set_atom_type(self, *args)
6185 
6186  def get_element(self):
6187  """get_element(Atom self) -> IMP::atom::Element"""
6188  return _IMP_atom.Atom_get_element(self)
6189 
6190  def set_element(self, *args):
6191  """set_element(Atom self, IMP::atom::Element e)"""
6192  return _IMP_atom.Atom_set_element(self, *args)
6193 
6194  def get_occupancy(self):
6195  """get_occupancy(Atom self) -> double"""
6196  return _IMP_atom.Atom_get_occupancy(self)
6197 
6198  def set_occupancy(self, *args):
6199  """set_occupancy(Atom self, double occupancy)"""
6200  return _IMP_atom.Atom_set_occupancy(self, *args)
6201 
6202  def get_temperature_factor(self):
6203  """get_temperature_factor(Atom self) -> double"""
6204  return _IMP_atom.Atom_get_temperature_factor(self)
6205 
6206  def set_temperature_factor(self, *args):
6207  """set_temperature_factor(Atom self, double tempFactor)"""
6208  return _IMP_atom.Atom_set_temperature_factor(self, *args)
6209 
6210  def get_input_index(self):
6211  """get_input_index(Atom self) -> IMP::Int"""
6212  return _IMP_atom.Atom_get_input_index(self)
6213 
6214  def set_input_index(self, *args):
6215  """set_input_index(Atom self, IMP::Int t)"""
6216  return _IMP_atom.Atom_set_input_index(self, *args)
6217 
6218  def get_atom_type_key():
6219  """get_atom_type_key() -> IntKey"""
6220  return _IMP_atom.Atom_get_atom_type_key()
6221 
6222  if _newclass:get_atom_type_key = staticmethod(get_atom_type_key)
6223  __swig_getmethods__["get_atom_type_key"] = lambda x: get_atom_type_key
6224  def get_element_key():
6225  """get_element_key() -> IntKey"""
6226  return _IMP_atom.Atom_get_element_key()
6227 
6228  if _newclass:get_element_key = staticmethod(get_element_key)
6229  __swig_getmethods__["get_element_key"] = lambda x: get_element_key
6230  def get_input_index_key():
6231  """get_input_index_key() -> IntKey"""
6232  return _IMP_atom.Atom_get_input_index_key()
6233 
6234  if _newclass:get_input_index_key = staticmethod(get_input_index_key)
6235  __swig_getmethods__["get_input_index_key"] = lambda x: get_input_index_key
6236  def get_occupancy_key():
6237  """get_occupancy_key() -> FloatKey"""
6238  return _IMP_atom.Atom_get_occupancy_key()
6239 
6240  if _newclass:get_occupancy_key = staticmethod(get_occupancy_key)
6241  __swig_getmethods__["get_occupancy_key"] = lambda x: get_occupancy_key
6242  def get_temperature_factor_key():
6243  """get_temperature_factor_key() -> FloatKey"""
6244  return _IMP_atom.Atom_get_temperature_factor_key()
6245 
6246  if _newclass:get_temperature_factor_key = staticmethod(get_temperature_factor_key)
6247  __swig_getmethods__["get_temperature_factor_key"] = lambda x: get_temperature_factor_key
6248  def add_attribute(self, *args):
6249  """
6250  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
6251  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
6252  add_attribute(Atom self, IntKey a0, IMP::Int a1)
6253  add_attribute(Atom self, StringKey a0, IMP::String a1)
6254  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
6255  add_attribute(Atom self, ObjectKey a0, IMP::Object * a1)
6256  """
6257  return _IMP_atom.Atom_add_attribute(self, *args)
6258 
6259  def get_value(self, *args):
6260  """
6261  get_value(Atom self, FloatKey a0) -> IMP::Float
6262  get_value(Atom self, IntKey a0) -> IMP::Int
6263  get_value(Atom self, StringKey a0) -> IMP::String
6264  get_value(Atom self, ParticleIndexKey a0) -> Particle
6265  get_value(Atom self, ObjectKey a0) -> IMP::Object *
6266  """
6267  return _IMP_atom.Atom_get_value(self, *args)
6268 
6269  def set_value(self, *args):
6270  """
6271  set_value(Atom self, FloatKey a0, IMP::Float a1)
6272  set_value(Atom self, IntKey a0, IMP::Int a1)
6273  set_value(Atom self, StringKey a0, IMP::String a1)
6274  set_value(Atom self, ParticleIndexKey a0, Particle a1)
6275  set_value(Atom self, ObjectKey a0, IMP::Object * a1)
6276  """
6277  return _IMP_atom.Atom_set_value(self, *args)
6278 
6279  def remove_attribute(self, *args):
6280  """
6281  remove_attribute(Atom self, FloatKey a0)
6282  remove_attribute(Atom self, IntKey a0)
6283  remove_attribute(Atom self, StringKey a0)
6284  remove_attribute(Atom self, ParticleIndexKey a0)
6285  remove_attribute(Atom self, ObjectKey a0)
6286  """
6287  return _IMP_atom.Atom_remove_attribute(self, *args)
6288 
6289  def has_attribute(self, *args):
6290  """
6291  has_attribute(Atom self, FloatKey a0) -> bool
6292  has_attribute(Atom self, IntKey a0) -> bool
6293  has_attribute(Atom self, StringKey a0) -> bool
6294  has_attribute(Atom self, ParticleIndexKey a0) -> bool
6295  has_attribute(Atom self, ObjectKey a0) -> bool
6296  """
6297  return _IMP_atom.Atom_has_attribute(self, *args)
6298 
6299  def get_derivative(self, *args):
6300  """get_derivative(Atom self, FloatKey a0) -> double"""
6301  return _IMP_atom.Atom_get_derivative(self, *args)
6302 
6303  def get_name(self):
6304  """get_name(Atom self) -> std::string"""
6305  return _IMP_atom.Atom_get_name(self)
6306 
6307  def clear_caches(self):
6308  """clear_caches(Atom self)"""
6309  return _IMP_atom.Atom_clear_caches(self)
6310 
6311  def set_name(self, *args):
6312  """set_name(Atom self, std::string a0)"""
6313  return _IMP_atom.Atom_set_name(self, *args)
6314 
6315  def set_check_level(self, *args):
6316  """set_check_level(Atom self, IMP::base::CheckLevel a0)"""
6317  return _IMP_atom.Atom_set_check_level(self, *args)
6318 
6319  def add_to_derivative(self, *args):
6320  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6321  return _IMP_atom.Atom_add_to_derivative(self, *args)
6322 
6323  def set_is_optimized(self, *args):
6324  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
6325  return _IMP_atom.Atom_set_is_optimized(self, *args)
6326 
6327  def get_is_optimized(self, *args):
6328  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
6329  return _IMP_atom.Atom_get_is_optimized(self, *args)
6330 
6331  def get_check_level(self):
6332  """get_check_level(Atom self) -> IMP::base::CheckLevel"""
6333  return _IMP_atom.Atom_get_check_level(self)
6334 
6335  def __eq__(self, *args):
6336  """
6337  __eq__(Atom self, Atom o) -> bool
6338  __eq__(Atom self, Particle d) -> bool
6339  """
6340  return _IMP_atom.Atom___eq__(self, *args)
6341 
6342  def __ne__(self, *args):
6343  """
6344  __ne__(Atom self, Atom o) -> bool
6345  __ne__(Atom self, Particle d) -> bool
6346  """
6347  return _IMP_atom.Atom___ne__(self, *args)
6348 
6349  def __le__(self, *args):
6350  """
6351  __le__(Atom self, Atom o) -> bool
6352  __le__(Atom self, Particle d) -> bool
6353  """
6354  return _IMP_atom.Atom___le__(self, *args)
6355 
6356  def __lt__(self, *args):
6357  """
6358  __lt__(Atom self, Atom o) -> bool
6359  __lt__(Atom self, Particle d) -> bool
6360  """
6361  return _IMP_atom.Atom___lt__(self, *args)
6362 
6363  def __ge__(self, *args):
6364  """
6365  __ge__(Atom self, Atom o) -> bool
6366  __ge__(Atom self, Particle d) -> bool
6367  """
6368  return _IMP_atom.Atom___ge__(self, *args)
6369 
6370  def __gt__(self, *args):
6371  """
6372  __gt__(Atom self, Atom o) -> bool
6373  __gt__(Atom self, Particle d) -> bool
6374  """
6375  return _IMP_atom.Atom___gt__(self, *args)
6376 
6377  def __str__(self):
6378  """__str__(Atom self) -> std::string"""
6379  return _IMP_atom.Atom___str__(self)
6380 
6381  def __repr__(self):
6382  """__repr__(Atom self) -> std::string"""
6383  return _IMP_atom.Atom___repr__(self)
6384 
6385  __swig_destroy__ = _IMP_atom.delete_Atom
6386  __del__ = lambda self : None;
6387 Atom_swigregister = _IMP_atom.Atom_swigregister
6388 Atom_swigregister(Atom)
6389 cvar = _IMP_atom.cvar
6390 AT_UNKNOWN = cvar.AT_UNKNOWN
6391 AT_N = cvar.AT_N
6392 AT_CA = cvar.AT_CA
6393 AT_C = cvar.AT_C
6394 AT_O = cvar.AT_O
6395 AT_H = cvar.AT_H
6396 AT_H1 = cvar.AT_H1
6397 AT_H2 = cvar.AT_H2
6398 AT_H3 = cvar.AT_H3
6399 AT_HA = cvar.AT_HA
6400 AT_HA1 = cvar.AT_HA1
6401 AT_HA2 = cvar.AT_HA2
6402 AT_HA3 = cvar.AT_HA3
6403 AT_CB = cvar.AT_CB
6404 AT_HB = cvar.AT_HB
6405 AT_HB1 = cvar.AT_HB1
6406 AT_HB2 = cvar.AT_HB2
6407 AT_HB3 = cvar.AT_HB3
6408 AT_OXT = cvar.AT_OXT
6409 AT_CH3 = cvar.AT_CH3
6410 AT_CH = cvar.AT_CH
6411 AT_CG = cvar.AT_CG
6412 AT_CG1 = cvar.AT_CG1
6413 AT_CG2 = cvar.AT_CG2
6414 AT_HG = cvar.AT_HG
6415 AT_HG1 = cvar.AT_HG1
6416 AT_HG2 = cvar.AT_HG2
6417 AT_HG3 = cvar.AT_HG3
6418 AT_HG11 = cvar.AT_HG11
6419 AT_HG21 = cvar.AT_HG21
6420 AT_HG31 = cvar.AT_HG31
6421 AT_HG12 = cvar.AT_HG12
6422 AT_HG13 = cvar.AT_HG13
6423 AT_HG22 = cvar.AT_HG22
6424 AT_HG23 = cvar.AT_HG23
6425 AT_HG32 = cvar.AT_HG32
6426 AT_OG = cvar.AT_OG
6427 AT_OG1 = cvar.AT_OG1
6428 AT_SG = cvar.AT_SG
6429 AT_CD = cvar.AT_CD
6430 AT_CD1 = cvar.AT_CD1
6431 AT_CD2 = cvar.AT_CD2
6432 AT_HD = cvar.AT_HD
6433 AT_HD1 = cvar.AT_HD1
6434 AT_HD2 = cvar.AT_HD2
6435 AT_HD3 = cvar.AT_HD3
6436 AT_HD11 = cvar.AT_HD11
6437 AT_HD21 = cvar.AT_HD21
6438 AT_HD31 = cvar.AT_HD31
6439 AT_HD12 = cvar.AT_HD12
6440 AT_HD13 = cvar.AT_HD13
6441 AT_HD22 = cvar.AT_HD22
6442 AT_HD23 = cvar.AT_HD23
6443 AT_HD32 = cvar.AT_HD32
6444 AT_SD = cvar.AT_SD
6445 AT_OD1 = cvar.AT_OD1
6446 AT_OD2 = cvar.AT_OD2
6447 AT_ND1 = cvar.AT_ND1
6448 AT_ND2 = cvar.AT_ND2
6449 AT_CE = cvar.AT_CE
6450 AT_CE1 = cvar.AT_CE1
6451 AT_CE2 = cvar.AT_CE2
6452 AT_CE3 = cvar.AT_CE3
6453 AT_HE = cvar.AT_HE
6454 AT_HE1 = cvar.AT_HE1
6455 AT_HE2 = cvar.AT_HE2
6456 AT_HE3 = cvar.AT_HE3
6457 AT_HE21 = cvar.AT_HE21
6458 AT_HE22 = cvar.AT_HE22
6459 AT_OE1 = cvar.AT_OE1
6460 AT_OE2 = cvar.AT_OE2
6461 AT_NE = cvar.AT_NE
6462 AT_NE1 = cvar.AT_NE1
6463 AT_NE2 = cvar.AT_NE2
6464 AT_CZ = cvar.AT_CZ
6465 AT_CZ2 = cvar.AT_CZ2
6466 AT_CZ3 = cvar.AT_CZ3
6467 AT_NZ = cvar.AT_NZ
6468 AT_HZ = cvar.AT_HZ
6469 AT_HZ1 = cvar.AT_HZ1
6470 AT_HZ2 = cvar.AT_HZ2
6471 AT_HZ3 = cvar.AT_HZ3
6472 AT_CH2 = cvar.AT_CH2
6473 AT_NH1 = cvar.AT_NH1
6474 AT_NH2 = cvar.AT_NH2
6475 AT_OH = cvar.AT_OH
6476 AT_HH = cvar.AT_HH
6477 AT_HH11 = cvar.AT_HH11
6478 AT_HH21 = cvar.AT_HH21
6479 AT_HH2 = cvar.AT_HH2
6480 AT_HH12 = cvar.AT_HH12
6481 AT_HH22 = cvar.AT_HH22
6482 AT_HH13 = cvar.AT_HH13
6483 AT_HH23 = cvar.AT_HH23
6484 AT_HH33 = cvar.AT_HH33
6485 AT_P = cvar.AT_P
6486 AT_OP1 = cvar.AT_OP1
6487 AT_OP2 = cvar.AT_OP2
6488 AT_OP3 = cvar.AT_OP3
6489 AT_O5p = cvar.AT_O5p
6490 AT_C5p = cvar.AT_C5p
6491 AT_H5p = cvar.AT_H5p
6492 AT_H5pp = cvar.AT_H5pp
6493 AT_C4p = cvar.AT_C4p
6494 AT_H4p = cvar.AT_H4p
6495 AT_O4p = cvar.AT_O4p
6496 AT_C1p = cvar.AT_C1p
6497 AT_H1p = cvar.AT_H1p
6498 AT_C3p = cvar.AT_C3p
6499 AT_H3p = cvar.AT_H3p
6500 AT_O3p = cvar.AT_O3p
6501 AT_C2p = cvar.AT_C2p
6502 AT_H2p = cvar.AT_H2p
6503 AT_H2pp = cvar.AT_H2pp
6504 AT_O2p = cvar.AT_O2p
6505 AT_HO2p = cvar.AT_HO2p
6506 AT_N9 = cvar.AT_N9
6507 AT_C8 = cvar.AT_C8
6508 AT_H8 = cvar.AT_H8
6509 AT_N7 = cvar.AT_N7
6510 AT_C5 = cvar.AT_C5
6511 AT_C4 = cvar.AT_C4
6512 AT_N3 = cvar.AT_N3
6513 AT_C2 = cvar.AT_C2
6514 AT_N1 = cvar.AT_N1
6515 AT_C6 = cvar.AT_C6
6516 AT_N6 = cvar.AT_N6
6517 AT_H61 = cvar.AT_H61
6518 AT_H62 = cvar.AT_H62
6519 AT_O6 = cvar.AT_O6
6520 AT_N2 = cvar.AT_N2
6521 AT_NT = cvar.AT_NT
6522 AT_H21 = cvar.AT_H21
6523 AT_H22 = cvar.AT_H22
6524 AT_H6 = cvar.AT_H6
6525 AT_H5 = cvar.AT_H5
6526 AT_O2 = cvar.AT_O2
6527 AT_N4 = cvar.AT_N4
6528 AT_H41 = cvar.AT_H41
6529 AT_H42 = cvar.AT_H42
6530 AT_O4 = cvar.AT_O4
6531 AT_C7 = cvar.AT_C7
6532 AT_H71 = cvar.AT_H71
6533 AT_H72 = cvar.AT_H72
6534 AT_H73 = cvar.AT_H73
6535 AT_O1A = cvar.AT_O1A
6536 AT_O2A = cvar.AT_O2A
6537 AT_O3A = cvar.AT_O3A
6538 AT_O1B = cvar.AT_O1B
6539 AT_O2B = cvar.AT_O2B
6540 AT_O3B = cvar.AT_O3B
6541 
6542 def Atom_decorate_particle(*args):
6543  """Atom_decorate_particle(Particle p) -> Atom"""
6544  return _IMP_atom.Atom_decorate_particle(*args)
6545 
6546 def Atom_setup_particle(*args):
6547  """
6548  setup_particle(Model m, IMP::kernel::ParticleIndex pi, AtomType t) -> Atom
6549  setup_particle(Particle p, AtomType t) -> Atom
6550  Atom_setup_particle(Particle p, Atom o) -> Atom
6551  """
6552  return _IMP_atom.Atom_setup_particle(*args)
6553 
6554 def Atom_particle_is_instance(*args):
6555  """Atom_particle_is_instance(Particle p) -> bool"""
6556  return _IMP_atom.Atom_particle_is_instance(*args)
6557 
6558 def Atom_get_atom_type_key():
6559  """Atom_get_atom_type_key() -> IntKey"""
6560  return _IMP_atom.Atom_get_atom_type_key()
6561 
6562 def Atom_get_element_key():
6563  """Atom_get_element_key() -> IntKey"""
6564  return _IMP_atom.Atom_get_element_key()
6565 
6566 def Atom_get_input_index_key():
6567  """Atom_get_input_index_key() -> IntKey"""
6568  return _IMP_atom.Atom_get_input_index_key()
6569 
6570 def Atom_get_occupancy_key():
6571  """Atom_get_occupancy_key() -> FloatKey"""
6572  return _IMP_atom.Atom_get_occupancy_key()
6573 
6574 def Atom_get_temperature_factor_key():
6575  """Atom_get_temperature_factor_key() -> FloatKey"""
6576  return _IMP_atom.Atom_get_temperature_factor_key()
6577 
6578 
6579 def get_residue(*args):
6580  """
6581  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
6582  get_residue(Atom d, bool nothrow=False) -> Residue
6583  get_residue(Atom d) -> Residue
6584  """
6585  return _IMP_atom.get_residue(*args)
6586 
6587 def get_atom(*args):
6588  """get_atom(Residue rd, AtomType at) -> Atom"""
6589  return _IMP_atom.get_atom(*args)
6590 
6591 def add_atom_type(*args):
6592  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
6593  return _IMP_atom.add_atom_type(*args)
6594 
6595 def get_element_for_atom_type(*args):
6596  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
6597  return _IMP_atom.get_element_for_atom_type(*args)
6598 
6599 def get_atom_type_exists(*args):
6600  """get_atom_type_exists(std::string name) -> bool"""
6601  return _IMP_atom.get_atom_type_exists(*args)
6602 class Residue(Hierarchy):
6603  """Proxy of C++ IMP::atom::Residue class"""
6604  __swig_setmethods__ = {}
6605  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6606  __setattr__ = lambda self, name, value: _swig_setattr(self, Residue, name, value)
6607  __swig_getmethods__ = {}
6608  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6609  __getattr__ = lambda self, name: _swig_getattr(self, Residue, name)
6610  def __init__(self, *args):
6611  """
6612  __init__(IMP::atom::Residue self) -> Residue
6613  __init__(IMP::atom::Residue self, Model m, IMP::kernel::ParticleIndex id) -> Residue
6614  __init__(IMP::atom::Residue self, Particle p) -> Residue
6615  """
6616  this = _IMP_atom.new_Residue(*args)
6617  try: self.this.append(this)
6618  except: self.this = this
6619  def decorate_particle(*args):
6620  """decorate_particle(Particle p) -> Residue"""
6621  return _IMP_atom.Residue_decorate_particle(*args)
6622 
6623  if _newclass:decorate_particle = staticmethod(decorate_particle)
6624  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6625  def show(self, *args):
6626  """
6627  show(Residue self, _ostream out=std::cout)
6628  show(Residue self)
6629  """
6630  return _IMP_atom.Residue_show(self, *args)
6631 
6632  def setup_particle(*args):
6633  """
6634  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK, int index=-1, int insertion_code=32) -> Residue
6635  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK, int index=-1) -> Residue
6636  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK) -> Residue
6637  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Residue
6638  setup_particle(Particle p, ResidueType t=UNK, int index=-1, int insertion_code=32) -> Residue
6639  setup_particle(Particle p, ResidueType t=UNK, int index=-1) -> Residue
6640  setup_particle(Particle p, ResidueType t=UNK) -> Residue
6641  setup_particle(Particle p) -> Residue
6642  setup_particle(Particle p, Residue o) -> Residue
6643  """
6644  return _IMP_atom.Residue_setup_particle(*args)
6645 
6646  if _newclass:setup_particle = staticmethod(setup_particle)
6647  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6648  def particle_is_instance(*args):
6649  """particle_is_instance(Particle p) -> bool"""
6650  return _IMP_atom.Residue_particle_is_instance(*args)
6651 
6652  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
6653  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
6654  def get_residue_type(self):
6655  """get_residue_type(Residue self) -> ResidueType"""
6656  return _IMP_atom.Residue_get_residue_type(self)
6657 
6658  def set_residue_type(self, *args):
6659  """set_residue_type(Residue self, ResidueType t)"""
6660  return _IMP_atom.Residue_set_residue_type(self, *args)
6661 
6662  def get_is_protein(self):
6663  """get_is_protein(Residue self) -> bool"""
6664  return _IMP_atom.Residue_get_is_protein(self)
6665 
6666  def get_is_dna(self):
6667  """get_is_dna(Residue self) -> bool"""
6668  return _IMP_atom.Residue_get_is_dna(self)
6669 
6670  def get_is_rna(self):
6671  """get_is_rna(Residue self) -> bool"""
6672  return _IMP_atom.Residue_get_is_rna(self)
6673 
6674  def get_index(self):
6675  """get_index(Residue self) -> IMP::Int"""
6676  return _IMP_atom.Residue_get_index(self)
6677 
6678  def set_index(self, *args):
6679  """set_index(Residue self, IMP::Int t)"""
6680  return _IMP_atom.Residue_set_index(self, *args)
6681 
6682  def get_insertion_code(self):
6683  """get_insertion_code(Residue self) -> char"""
6684  return _IMP_atom.Residue_get_insertion_code(self)
6685 
6686  def set_insertion_code(self, *args):
6687  """set_insertion_code(Residue self, char insertion_code)"""
6688  return _IMP_atom.Residue_set_insertion_code(self, *args)
6689 
6690  def get_index_key():
6691  """get_index_key() -> IntKey"""
6692  return _IMP_atom.Residue_get_index_key()
6693 
6694  if _newclass:get_index_key = staticmethod(get_index_key)
6695  __swig_getmethods__["get_index_key"] = lambda x: get_index_key
6696  def get_residue_type_key():
6697  """get_residue_type_key() -> IntKey"""
6698  return _IMP_atom.Residue_get_residue_type_key()
6699 
6700  if _newclass:get_residue_type_key = staticmethod(get_residue_type_key)
6701  __swig_getmethods__["get_residue_type_key"] = lambda x: get_residue_type_key
6702  def get_insertion_code_key():
6703  """get_insertion_code_key() -> IntKey"""
6704  return _IMP_atom.Residue_get_insertion_code_key()
6705 
6706  if _newclass:get_insertion_code_key = staticmethod(get_insertion_code_key)
6707  __swig_getmethods__["get_insertion_code_key"] = lambda x: get_insertion_code_key
6708  def add_attribute(self, *args):
6709  """
6710  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
6711  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
6712  add_attribute(Residue self, IntKey a0, IMP::Int a1)
6713  add_attribute(Residue self, StringKey a0, IMP::String a1)
6714  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
6715  add_attribute(Residue self, ObjectKey a0, IMP::Object * a1)
6716  """
6717  return _IMP_atom.Residue_add_attribute(self, *args)
6718 
6719  def get_value(self, *args):
6720  """
6721  get_value(Residue self, FloatKey a0) -> IMP::Float
6722  get_value(Residue self, IntKey a0) -> IMP::Int
6723  get_value(Residue self, StringKey a0) -> IMP::String
6724  get_value(Residue self, ParticleIndexKey a0) -> Particle
6725  get_value(Residue self, ObjectKey a0) -> IMP::Object *
6726  """
6727  return _IMP_atom.Residue_get_value(self, *args)
6728 
6729  def set_value(self, *args):
6730  """
6731  set_value(Residue self, FloatKey a0, IMP::Float a1)
6732  set_value(Residue self, IntKey a0, IMP::Int a1)
6733  set_value(Residue self, StringKey a0, IMP::String a1)
6734  set_value(Residue self, ParticleIndexKey a0, Particle a1)
6735  set_value(Residue self, ObjectKey a0, IMP::Object * a1)
6736  """
6737  return _IMP_atom.Residue_set_value(self, *args)
6738 
6739  def remove_attribute(self, *args):
6740  """
6741  remove_attribute(Residue self, FloatKey a0)
6742  remove_attribute(Residue self, IntKey a0)
6743  remove_attribute(Residue self, StringKey a0)
6744  remove_attribute(Residue self, ParticleIndexKey a0)
6745  remove_attribute(Residue self, ObjectKey a0)
6746  """
6747  return _IMP_atom.Residue_remove_attribute(self, *args)
6748 
6749  def has_attribute(self, *args):
6750  """
6751  has_attribute(Residue self, FloatKey a0) -> bool
6752  has_attribute(Residue self, IntKey a0) -> bool
6753  has_attribute(Residue self, StringKey a0) -> bool
6754  has_attribute(Residue self, ParticleIndexKey a0) -> bool
6755  has_attribute(Residue self, ObjectKey a0) -> bool
6756  """
6757  return _IMP_atom.Residue_has_attribute(self, *args)
6758 
6759  def get_derivative(self, *args):
6760  """get_derivative(Residue self, FloatKey a0) -> double"""
6761  return _IMP_atom.Residue_get_derivative(self, *args)
6762 
6763  def get_name(self):
6764  """get_name(Residue self) -> std::string"""
6765  return _IMP_atom.Residue_get_name(self)
6766 
6767  def clear_caches(self):
6768  """clear_caches(Residue self)"""
6769  return _IMP_atom.Residue_clear_caches(self)
6770 
6771  def set_name(self, *args):
6772  """set_name(Residue self, std::string a0)"""
6773  return _IMP_atom.Residue_set_name(self, *args)
6774 
6775  def set_check_level(self, *args):
6776  """set_check_level(Residue self, IMP::base::CheckLevel a0)"""
6777  return _IMP_atom.Residue_set_check_level(self, *args)
6778 
6779  def add_to_derivative(self, *args):
6780  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6781  return _IMP_atom.Residue_add_to_derivative(self, *args)
6782 
6783  def set_is_optimized(self, *args):
6784  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
6785  return _IMP_atom.Residue_set_is_optimized(self, *args)
6786 
6787  def get_is_optimized(self, *args):
6788  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
6789  return _IMP_atom.Residue_get_is_optimized(self, *args)
6790 
6791  def get_check_level(self):
6792  """get_check_level(Residue self) -> IMP::base::CheckLevel"""
6793  return _IMP_atom.Residue_get_check_level(self)
6794 
6795  def __eq__(self, *args):
6796  """
6797  __eq__(Residue self, Residue o) -> bool
6798  __eq__(Residue self, Particle d) -> bool
6799  """
6800  return _IMP_atom.Residue___eq__(self, *args)
6801 
6802  def __ne__(self, *args):
6803  """
6804  __ne__(Residue self, Residue o) -> bool
6805  __ne__(Residue self, Particle d) -> bool
6806  """
6807  return _IMP_atom.Residue___ne__(self, *args)
6808 
6809  def __le__(self, *args):
6810  """
6811  __le__(Residue self, Residue o) -> bool
6812  __le__(Residue self, Particle d) -> bool
6813  """
6814  return _IMP_atom.Residue___le__(self, *args)
6815 
6816  def __lt__(self, *args):
6817  """
6818  __lt__(Residue self, Residue o) -> bool
6819  __lt__(Residue self, Particle d) -> bool
6820  """
6821  return _IMP_atom.Residue___lt__(self, *args)
6822 
6823  def __ge__(self, *args):
6824  """
6825  __ge__(Residue self, Residue o) -> bool
6826  __ge__(Residue self, Particle d) -> bool
6827  """
6828  return _IMP_atom.Residue___ge__(self, *args)
6829 
6830  def __gt__(self, *args):
6831  """
6832  __gt__(Residue self, Residue o) -> bool
6833  __gt__(Residue self, Particle d) -> bool
6834  """
6835  return _IMP_atom.Residue___gt__(self, *args)
6836 
6837  def __str__(self):
6838  """__str__(Residue self) -> std::string"""
6839  return _IMP_atom.Residue___str__(self)
6840 
6841  def __repr__(self):
6842  """__repr__(Residue self) -> std::string"""
6843  return _IMP_atom.Residue___repr__(self)
6844 
6845  __swig_destroy__ = _IMP_atom.delete_Residue
6846  __del__ = lambda self : None;
6847 Residue_swigregister = _IMP_atom.Residue_swigregister
6848 Residue_swigregister(Residue)
6849 UNK = cvar.UNK
6850 GLY = cvar.GLY
6851 ALA = cvar.ALA
6852 VAL = cvar.VAL
6853 LEU = cvar.LEU
6854 ILE = cvar.ILE
6855 SER = cvar.SER
6856 THR = cvar.THR
6857 CYS = cvar.CYS
6858 MET = cvar.MET
6859 PRO = cvar.PRO
6860 ASP = cvar.ASP
6861 ASN = cvar.ASN
6862 GLU = cvar.GLU
6863 GLN = cvar.GLN
6864 LYS = cvar.LYS
6865 ARG = cvar.ARG
6866 HIS = cvar.HIS
6867 PHE = cvar.PHE
6868 TYR = cvar.TYR
6869 TRP = cvar.TRP
6870 ACE = cvar.ACE
6871 NH2 = cvar.NH2
6872 ADE = cvar.ADE
6873 URA = cvar.URA
6874 CYT = cvar.CYT
6875 GUA = cvar.GUA
6876 THY = cvar.THY
6877 DADE = cvar.DADE
6878 DURA = cvar.DURA
6879 DCYT = cvar.DCYT
6880 DGUA = cvar.DGUA
6881 DTHY = cvar.DTHY
6882 HOH = cvar.HOH
6883 HEME = cvar.HEME
6884 
6885 def Residue_decorate_particle(*args):
6886  """Residue_decorate_particle(Particle p) -> Residue"""
6887  return _IMP_atom.Residue_decorate_particle(*args)
6888 
6889 def Residue_setup_particle(*args):
6890  """
6891  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK, int index=-1, int insertion_code=32) -> Residue
6892  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK, int index=-1) -> Residue
6893  setup_particle(Model m, IMP::kernel::ParticleIndex pi, ResidueType t=UNK) -> Residue
6894  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> Residue
6895  setup_particle(Particle p, ResidueType t=UNK, int index=-1, int insertion_code=32) -> Residue
6896  setup_particle(Particle p, ResidueType t=UNK, int index=-1) -> Residue
6897  setup_particle(Particle p, ResidueType t=UNK) -> Residue
6898  setup_particle(Particle p) -> Residue
6899  Residue_setup_particle(Particle p, Residue o) -> Residue
6900  """
6901  return _IMP_atom.Residue_setup_particle(*args)
6902 
6903 def Residue_particle_is_instance(*args):
6904  """Residue_particle_is_instance(Particle p) -> bool"""
6905  return _IMP_atom.Residue_particle_is_instance(*args)
6906 
6907 def Residue_get_index_key():
6908  """Residue_get_index_key() -> IntKey"""
6909  return _IMP_atom.Residue_get_index_key()
6910 
6911 def Residue_get_residue_type_key():
6912  """Residue_get_residue_type_key() -> IntKey"""
6913  return _IMP_atom.Residue_get_residue_type_key()
6914 
6915 def Residue_get_insertion_code_key():
6916  """Residue_get_insertion_code_key() -> IntKey"""
6917  return _IMP_atom.Residue_get_insertion_code_key()
6918 
6919 
6920 def get_next_residue(*args):
6921  """get_next_residue(Residue rd) -> Hierarchy"""
6922  return _IMP_atom.get_next_residue(*args)
6923 
6924 def get_previous_residue(*args):
6925  """get_previous_residue(Residue rd) -> Hierarchy"""
6926  return _IMP_atom.get_previous_residue(*args)
6927 
6928 def get_one_letter_code(*args):
6929  """get_one_letter_code(ResidueType c) -> char"""
6930  return _IMP_atom.get_one_letter_code(*args)
6931 
6932 def get_phi_dihedral_atoms(*args):
6933  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
6934  return _IMP_atom.get_phi_dihedral_atoms(*args)
6935 
6936 def get_psi_dihedral_atoms(*args):
6937  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
6938  return _IMP_atom.get_psi_dihedral_atoms(*args)
6939 class Molecule(Hierarchy):
6940  """Proxy of C++ IMP::atom::Molecule class"""
6941  __swig_setmethods__ = {}
6942  for _s in [Hierarchy]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
6943  __setattr__ = lambda self, name, value: _swig_setattr(self, Molecule, name, value)
6944  __swig_getmethods__ = {}
6945  for _s in [Hierarchy]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
6946  __getattr__ = lambda self, name: _swig_getattr(self, Molecule, name)
6947  def __init__(self, *args):
6948  """
6949  __init__(IMP::atom::Molecule self) -> Molecule
6950  __init__(IMP::atom::Molecule self, Model m, IMP::kernel::ParticleIndex id) -> Molecule
6951  __init__(IMP::atom::Molecule self, Particle p) -> Molecule
6952  """
6953  this = _IMP_atom.new_Molecule(*args)
6954  try: self.this.append(this)
6955  except: self.this = this
6956  def decorate_particle(*args):
6957  """decorate_particle(Particle p) -> Molecule"""
6958  return _IMP_atom.Molecule_decorate_particle(*args)
6959 
6960  if _newclass:decorate_particle = staticmethod(decorate_particle)
6961  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
6962  def show(self, *args):
6963  """
6964  show(Molecule self, _ostream out=std::cout)
6965  show(Molecule self)
6966  """
6967  return _IMP_atom.Molecule_show(self, *args)
6968 
6969  def setup_particle(*args):
6970  """
6971  setup_particle(Particle p) -> Molecule
6972  setup_particle(Particle p, Molecule arg2) -> Molecule
6973  """
6974  return _IMP_atom.Molecule_setup_particle(*args)
6975 
6976  if _newclass:setup_particle = staticmethod(setup_particle)
6977  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
6978  def particle_is_instance(*args):
6979  """particle_is_instance(Particle p) -> bool"""
6980  return _IMP_atom.Molecule_particle_is_instance(*args)
6981 
6982  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
6983  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
6984  def add_attribute(self, *args):
6985  """
6986  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
6987  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
6988  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
6989  add_attribute(Molecule self, StringKey a0, IMP::String a1)
6990  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
6991  add_attribute(Molecule self, ObjectKey a0, IMP::Object * a1)
6992  """
6993  return _IMP_atom.Molecule_add_attribute(self, *args)
6994 
6995  def get_value(self, *args):
6996  """
6997  get_value(Molecule self, FloatKey a0) -> IMP::Float
6998  get_value(Molecule self, IntKey a0) -> IMP::Int
6999  get_value(Molecule self, StringKey a0) -> IMP::String
7000  get_value(Molecule self, ParticleIndexKey a0) -> Particle
7001  get_value(Molecule self, ObjectKey a0) -> IMP::Object *
7002  """
7003  return _IMP_atom.Molecule_get_value(self, *args)
7004 
7005  def set_value(self, *args):
7006  """
7007  set_value(Molecule self, FloatKey a0, IMP::Float a1)
7008  set_value(Molecule self, IntKey a0, IMP::Int a1)
7009  set_value(Molecule self, StringKey a0, IMP::String a1)
7010  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
7011  set_value(Molecule self, ObjectKey a0, IMP::Object * a1)
7012  """
7013  return _IMP_atom.Molecule_set_value(self, *args)
7014 
7015  def remove_attribute(self, *args):
7016  """
7017  remove_attribute(Molecule self, FloatKey a0)
7018  remove_attribute(Molecule self, IntKey a0)
7019  remove_attribute(Molecule self, StringKey a0)
7020  remove_attribute(Molecule self, ParticleIndexKey a0)
7021  remove_attribute(Molecule self, ObjectKey a0)
7022  """
7023  return _IMP_atom.Molecule_remove_attribute(self, *args)
7024 
7025  def has_attribute(self, *args):
7026  """
7027  has_attribute(Molecule self, FloatKey a0) -> bool
7028  has_attribute(Molecule self, IntKey a0) -> bool
7029  has_attribute(Molecule self, StringKey a0) -> bool
7030  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
7031  has_attribute(Molecule self, ObjectKey a0) -> bool
7032  """
7033  return _IMP_atom.Molecule_has_attribute(self, *args)
7034 
7035  def get_derivative(self, *args):
7036  """get_derivative(Molecule self, FloatKey a0) -> double"""
7037  return _IMP_atom.Molecule_get_derivative(self, *args)
7038 
7039  def get_name(self):
7040  """get_name(Molecule self) -> std::string"""
7041  return _IMP_atom.Molecule_get_name(self)
7042 
7043  def clear_caches(self):
7044  """clear_caches(Molecule self)"""
7045  return _IMP_atom.Molecule_clear_caches(self)
7046 
7047  def set_name(self, *args):
7048  """set_name(Molecule self, std::string a0)"""
7049  return _IMP_atom.Molecule_set_name(self, *args)
7050 
7051  def set_check_level(self, *args):
7052  """set_check_level(Molecule self, IMP::base::CheckLevel a0)"""
7053  return _IMP_atom.Molecule_set_check_level(self, *args)
7054 
7055  def add_to_derivative(self, *args):
7056  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7057  return _IMP_atom.Molecule_add_to_derivative(self, *args)
7058 
7059  def set_is_optimized(self, *args):
7060  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
7061  return _IMP_atom.Molecule_set_is_optimized(self, *args)
7062 
7063  def get_is_optimized(self, *args):
7064  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
7065  return _IMP_atom.Molecule_get_is_optimized(self, *args)
7066 
7067  def get_check_level(self):
7068  """get_check_level(Molecule self) -> IMP::base::CheckLevel"""
7069  return _IMP_atom.Molecule_get_check_level(self)
7070 
7071  def __eq__(self, *args):
7072  """
7073  __eq__(Molecule self, Molecule o) -> bool
7074  __eq__(Molecule self, Particle d) -> bool
7075  """
7076  return _IMP_atom.Molecule___eq__(self, *args)
7077 
7078  def __ne__(self, *args):
7079  """
7080  __ne__(Molecule self, Molecule o) -> bool
7081  __ne__(Molecule self, Particle d) -> bool
7082  """
7083  return _IMP_atom.Molecule___ne__(self, *args)
7084 
7085  def __le__(self, *args):
7086  """
7087  __le__(Molecule self, Molecule o) -> bool
7088  __le__(Molecule self, Particle d) -> bool
7089  """
7090  return _IMP_atom.Molecule___le__(self, *args)
7091 
7092  def __lt__(self, *args):
7093  """
7094  __lt__(Molecule self, Molecule o) -> bool
7095  __lt__(Molecule self, Particle d) -> bool
7096  """
7097  return _IMP_atom.Molecule___lt__(self, *args)
7098 
7099  def __ge__(self, *args):
7100  """
7101  __ge__(Molecule self, Molecule o) -> bool
7102  __ge__(Molecule self, Particle d) -> bool
7103  """
7104  return _IMP_atom.Molecule___ge__(self, *args)
7105 
7106  def __gt__(self, *args):
7107  """
7108  __gt__(Molecule self, Molecule o) -> bool
7109  __gt__(Molecule self, Particle d) -> bool
7110  """
7111  return _IMP_atom.Molecule___gt__(self, *args)
7112 
7113  def __str__(self):
7114  """__str__(Molecule self) -> std::string"""
7115  return _IMP_atom.Molecule___str__(self)
7116 
7117  def __repr__(self):
7118  """__repr__(Molecule self) -> std::string"""
7119  return _IMP_atom.Molecule___repr__(self)
7120 
7121  __swig_destroy__ = _IMP_atom.delete_Molecule
7122  __del__ = lambda self : None;
7123 Molecule_swigregister = _IMP_atom.Molecule_swigregister
7124 Molecule_swigregister(Molecule)
7125 
7126 def Molecule_decorate_particle(*args):
7127  """Molecule_decorate_particle(Particle p) -> Molecule"""
7128  return _IMP_atom.Molecule_decorate_particle(*args)
7129 
7130 def Molecule_setup_particle(*args):
7131  """
7132  setup_particle(Particle p) -> Molecule
7133  Molecule_setup_particle(Particle p, Molecule arg2) -> Molecule
7134  """
7135  return _IMP_atom.Molecule_setup_particle(*args)
7136 
7137 def Molecule_particle_is_instance(*args):
7138  """Molecule_particle_is_instance(Particle p) -> bool"""
7139  return _IMP_atom.Molecule_particle_is_instance(*args)
7140 
7141 class Copy(Molecule):
7142  """Proxy of C++ IMP::atom::Copy class"""
7143  __swig_setmethods__ = {}
7144  for _s in [Molecule]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7145  __setattr__ = lambda self, name, value: _swig_setattr(self, Copy, name, value)
7146  __swig_getmethods__ = {}
7147  for _s in [Molecule]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7148  __getattr__ = lambda self, name: _swig_getattr(self, Copy, name)
7149  def get_copy_index_key():
7150  """get_copy_index_key() -> IntKey"""
7151  return _IMP_atom.Copy_get_copy_index_key()
7152 
7153  if _newclass:get_copy_index_key = staticmethod(get_copy_index_key)
7154  __swig_getmethods__["get_copy_index_key"] = lambda x: get_copy_index_key
7155  def __init__(self, *args):
7156  """
7157  __init__(IMP::atom::Copy self) -> Copy
7158  __init__(IMP::atom::Copy self, Model m, IMP::kernel::ParticleIndex id) -> Copy
7159  __init__(IMP::atom::Copy self, Particle p) -> Copy
7160  """
7161  this = _IMP_atom.new_Copy(*args)
7162  try: self.this.append(this)
7163  except: self.this = this
7164  def decorate_particle(*args):
7165  """decorate_particle(Particle p) -> Copy"""
7166  return _IMP_atom.Copy_decorate_particle(*args)
7167 
7168  if _newclass:decorate_particle = staticmethod(decorate_particle)
7169  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
7170  def show(self, *args):
7171  """
7172  show(Copy self, _ostream out=std::cout)
7173  show(Copy self)
7174  """
7175  return _IMP_atom.Copy_show(self, *args)
7176 
7177  def setup_particle(*args):
7178  """setup_particle(Particle p, int number) -> Copy"""
7179  return _IMP_atom.Copy_setup_particle(*args)
7180 
7181  if _newclass:setup_particle = staticmethod(setup_particle)
7182  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
7183  def particle_is_instance(*args):
7184  """particle_is_instance(Particle p) -> bool"""
7185  return _IMP_atom.Copy_particle_is_instance(*args)
7186 
7187  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
7188  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
7189  def get_copy_index(self):
7190  """get_copy_index(Copy self) -> int"""
7191  return _IMP_atom.Copy_get_copy_index(self)
7192 
7193  def add_attribute(self, *args):
7194  """
7195  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
7196  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
7197  add_attribute(Copy self, IntKey a0, IMP::Int a1)
7198  add_attribute(Copy self, StringKey a0, IMP::String a1)
7199  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
7200  add_attribute(Copy self, ObjectKey a0, IMP::Object * a1)
7201  """
7202  return _IMP_atom.Copy_add_attribute(self, *args)
7203 
7204  def get_value(self, *args):
7205  """
7206  get_value(Copy self, FloatKey a0) -> IMP::Float
7207  get_value(Copy self, IntKey a0) -> IMP::Int
7208  get_value(Copy self, StringKey a0) -> IMP::String
7209  get_value(Copy self, ParticleIndexKey a0) -> Particle
7210  get_value(Copy self, ObjectKey a0) -> IMP::Object *
7211  """
7212  return _IMP_atom.Copy_get_value(self, *args)
7213 
7214  def set_value(self, *args):
7215  """
7216  set_value(Copy self, FloatKey a0, IMP::Float a1)
7217  set_value(Copy self, IntKey a0, IMP::Int a1)
7218  set_value(Copy self, StringKey a0, IMP::String a1)
7219  set_value(Copy self, ParticleIndexKey a0, Particle a1)
7220  set_value(Copy self, ObjectKey a0, IMP::Object * a1)
7221  """
7222  return _IMP_atom.Copy_set_value(self, *args)
7223 
7224  def remove_attribute(self, *args):
7225  """
7226  remove_attribute(Copy self, FloatKey a0)
7227  remove_attribute(Copy self, IntKey a0)
7228  remove_attribute(Copy self, StringKey a0)
7229  remove_attribute(Copy self, ParticleIndexKey a0)
7230  remove_attribute(Copy self, ObjectKey a0)
7231  """
7232  return _IMP_atom.Copy_remove_attribute(self, *args)
7233 
7234  def has_attribute(self, *args):
7235  """
7236  has_attribute(Copy self, FloatKey a0) -> bool
7237  has_attribute(Copy self, IntKey a0) -> bool
7238  has_attribute(Copy self, StringKey a0) -> bool
7239  has_attribute(Copy self, ParticleIndexKey a0) -> bool
7240  has_attribute(Copy self, ObjectKey a0) -> bool
7241  """
7242  return _IMP_atom.Copy_has_attribute(self, *args)
7243 
7244  def get_derivative(self, *args):
7245  """get_derivative(Copy self, FloatKey a0) -> double"""
7246  return _IMP_atom.Copy_get_derivative(self, *args)
7247 
7248  def get_name(self):
7249  """get_name(Copy self) -> std::string"""
7250  return _IMP_atom.Copy_get_name(self)
7251 
7252  def clear_caches(self):
7253  """clear_caches(Copy self)"""
7254  return _IMP_atom.Copy_clear_caches(self)
7255 
7256  def set_name(self, *args):
7257  """set_name(Copy self, std::string a0)"""
7258  return _IMP_atom.Copy_set_name(self, *args)
7259 
7260  def set_check_level(self, *args):
7261  """set_check_level(Copy self, IMP::base::CheckLevel a0)"""
7262  return _IMP_atom.Copy_set_check_level(self, *args)
7263 
7264  def add_to_derivative(self, *args):
7265  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7266  return _IMP_atom.Copy_add_to_derivative(self, *args)
7267 
7268  def set_is_optimized(self, *args):
7269  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
7270  return _IMP_atom.Copy_set_is_optimized(self, *args)
7271 
7272  def get_is_optimized(self, *args):
7273  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
7274  return _IMP_atom.Copy_get_is_optimized(self, *args)
7275 
7276  def get_check_level(self):
7277  """get_check_level(Copy self) -> IMP::base::CheckLevel"""
7278  return _IMP_atom.Copy_get_check_level(self)
7279 
7280  def __eq__(self, *args):
7281  """
7282  __eq__(Copy self, Copy o) -> bool
7283  __eq__(Copy self, Particle d) -> bool
7284  """
7285  return _IMP_atom.Copy___eq__(self, *args)
7286 
7287  def __ne__(self, *args):
7288  """
7289  __ne__(Copy self, Copy o) -> bool
7290  __ne__(Copy self, Particle d) -> bool
7291  """
7292  return _IMP_atom.Copy___ne__(self, *args)
7293 
7294  def __le__(self, *args):
7295  """
7296  __le__(Copy self, Copy o) -> bool
7297  __le__(Copy self, Particle d) -> bool
7298  """
7299  return _IMP_atom.Copy___le__(self, *args)
7300 
7301  def __lt__(self, *args):
7302  """
7303  __lt__(Copy self, Copy o) -> bool
7304  __lt__(Copy self, Particle d) -> bool
7305  """
7306  return _IMP_atom.Copy___lt__(self, *args)
7307 
7308  def __ge__(self, *args):
7309  """
7310  __ge__(Copy self, Copy o) -> bool
7311  __ge__(Copy self, Particle d) -> bool
7312  """
7313  return _IMP_atom.Copy___ge__(self, *args)
7314 
7315  def __gt__(self, *args):
7316  """
7317  __gt__(Copy self, Copy o) -> bool
7318  __gt__(Copy self, Particle d) -> bool
7319  """
7320  return _IMP_atom.Copy___gt__(self, *args)
7321 
7322  def __str__(self):
7323  """__str__(Copy self) -> std::string"""
7324  return _IMP_atom.Copy___str__(self)
7325 
7326  def __repr__(self):
7327  """__repr__(Copy self) -> std::string"""
7328  return _IMP_atom.Copy___repr__(self)
7329 
7330  __swig_destroy__ = _IMP_atom.delete_Copy
7331  __del__ = lambda self : None;
7332 Copy_swigregister = _IMP_atom.Copy_swigregister
7333 Copy_swigregister(Copy)
7334 
7335 def Copy_get_copy_index_key():
7336  """Copy_get_copy_index_key() -> IntKey"""
7337  return _IMP_atom.Copy_get_copy_index_key()
7338 
7339 def Copy_decorate_particle(*args):
7340  """Copy_decorate_particle(Particle p) -> Copy"""
7341  return _IMP_atom.Copy_decorate_particle(*args)
7342 
7343 def Copy_setup_particle(*args):
7344  """Copy_setup_particle(Particle p, int number) -> Copy"""
7345  return _IMP_atom.Copy_setup_particle(*args)
7346 
7347 def Copy_particle_is_instance(*args):
7348  """Copy_particle_is_instance(Particle p) -> bool"""
7349  return _IMP_atom.Copy_particle_is_instance(*args)
7350 
7351 
7352 def __lshift__(*args):
7353  """
7354  __lshift__(_ostream out, Bonded n) -> _ostream
7355  __lshift__(_ostream out, Bond n) -> _ostream
7356  __lshift__(_ostream out, Hierarchy n) -> _ostream
7357  __lshift__(_ostream out, Angle n) -> _ostream
7358  __lshift__(_ostream out, Dihedral n) -> _ostream
7359  __lshift__(_ostream out, Diffusion n) -> _ostream
7360  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
7361  __lshift__(_ostream out, Chain n) -> _ostream
7362  __lshift__(_ostream out, Charged n) -> _ostream
7363  __lshift__(_ostream out, Domain n) -> _ostream
7364  __lshift__(_ostream out, LennardJones n) -> _ostream
7365  __lshift__(_ostream out, Fragment n) -> _ostream
7366  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
7367  __lshift__(_ostream out, Atom n) -> _ostream
7368  __lshift__(_ostream out, Residue n) -> _ostream
7369  __lshift__(_ostream out, Molecule n) -> _ostream
7370  __lshift__(_ostream out, Copy n) -> _ostream
7371  """
7372  return _IMP_atom.__lshift__(*args)
7373 class Selection(IMP.base._InputAdaptor):
7374  """Proxy of C++ IMP::atom::Selection class"""
7375  __swig_setmethods__ = {}
7376  for _s in [IMP.base._InputAdaptor]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7377  __setattr__ = lambda self, name, value: _swig_setattr(self, Selection, name, value)
7378  __swig_getmethods__ = {}
7379  for _s in [IMP.base._InputAdaptor]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7380  __getattr__ = lambda self, name: _swig_getattr(self, Selection, name)
7381  NONE = _IMP_atom.Selection_NONE
7382  C = _IMP_atom.Selection_C
7383  N = _IMP_atom.Selection_N
7384  def __init__(self, *args):
7385  """
7386  __init__(IMP::atom::Selection self) -> Selection
7387  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
7388  __init__(IMP::atom::Selection self, Particle h) -> Selection
7389  __init__(IMP::atom::Selection self, Model m, IMP::kernel::ParticleIndexes const & pis) -> Selection
7390  __init__(IMP::atom::Selection self, IMP::kernel::ParticlesTemp const & h) -> Selection
7391  """
7392  this = _IMP_atom.new_Selection(*args)
7393  try: self.this.append(this)
7394  except: self.this = this
7395  def get_hierarchies(self):
7396  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
7397  return _IMP_atom.Selection_get_hierarchies(self)
7398 
7399  def set_molecules(self, *args):
7400  """set_molecules(Selection self, IMP::Strings mols)"""
7401  return _IMP_atom.Selection_set_molecules(self, *args)
7402 
7403  def set_target_radius(self, *args):
7404  """set_target_radius(Selection self, double r)"""
7405  return _IMP_atom.Selection_set_target_radius(self, *args)
7406 
7407  def set_terminus(self, *args):
7408  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
7409  return _IMP_atom.Selection_set_terminus(self, *args)
7410 
7411  def set_chains(self, *args):
7412  """set_chains(Selection self, std::string chains)"""
7413  return _IMP_atom.Selection_set_chains(self, *args)
7414 
7415  def set_residue_indexes(self, *args):
7416  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
7417  return _IMP_atom.Selection_set_residue_indexes(self, *args)
7418 
7419  def set_atom_types(self, *args):
7420  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
7421  return _IMP_atom.Selection_set_atom_types(self, *args)
7422 
7423  def set_residue_types(self, *args):
7424  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
7425  return _IMP_atom.Selection_set_residue_types(self, *args)
7426 
7427  def set_domains(self, *args):
7428  """set_domains(Selection self, IMP::Strings names)"""
7429  return _IMP_atom.Selection_set_domains(self, *args)
7430 
7431  def set_molecule(self, *args):
7432  """set_molecule(Selection self, std::string mol)"""
7433  return _IMP_atom.Selection_set_molecule(self, *args)
7434 
7435  def set_chain(self, *args):
7436  """set_chain(Selection self, char c)"""
7437  return _IMP_atom.Selection_set_chain(self, *args)
7438 
7439  def set_residue_index(self, *args):
7440  """set_residue_index(Selection self, int i)"""
7441  return _IMP_atom.Selection_set_residue_index(self, *args)
7442 
7443  def set_atom_type(self, *args):
7444  """set_atom_type(Selection self, AtomType types)"""
7445  return _IMP_atom.Selection_set_atom_type(self, *args)
7446 
7447  def set_residue_type(self, *args):
7448  """set_residue_type(Selection self, ResidueType type)"""
7449  return _IMP_atom.Selection_set_residue_type(self, *args)
7450 
7451  def set_domain(self, *args):
7452  """set_domain(Selection self, std::string name)"""
7453  return _IMP_atom.Selection_set_domain(self, *args)
7454 
7455  def set_copy_index(self, *args):
7456  """set_copy_index(Selection self, unsigned int copy)"""
7457  return _IMP_atom.Selection_set_copy_index(self, *args)
7458 
7459  def set_copy_indexes(self, *args):
7460  """set_copy_indexes(Selection self, IMP::Ints const & copies)"""
7461  return _IMP_atom.Selection_set_copy_indexes(self, *args)
7462 
7463  def set_particle_type(self, *args):
7464  """set_particle_type(Selection self, ParticleType t)"""
7465  return _IMP_atom.Selection_set_particle_type(self, *args)
7466 
7467  def set_particle_types(self, *args):
7468  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
7469  return _IMP_atom.Selection_set_particle_types(self, *args)
7470 
7471  def set_hierarchy_types(self, *args):
7472  """set_hierarchy_types(Selection self, IMP::Ints const & types)"""
7473  return _IMP_atom.Selection_set_hierarchy_types(self, *args)
7474 
7475  def get_selected_particles(self):
7476  """get_selected_particles(Selection self) -> IMP::kernel::ParticlesTemp"""
7477  return _IMP_atom.Selection_get_selected_particles(self)
7478 
7479  def show(self, *args):
7480  """
7481  show(Selection self, _ostream out=std::cout)
7482  show(Selection self)
7483  """
7484  return _IMP_atom.Selection_show(self, *args)
7485 
7486  def __str__(self):
7487  """__str__(Selection self) -> std::string"""
7488  return _IMP_atom.Selection___str__(self)
7489 
7490  def __repr__(self):
7491  """__repr__(Selection self) -> std::string"""
7492  return _IMP_atom.Selection___repr__(self)
7493 
7494  def __init__(self, hierarchy=None,
7495  hierarchies=None,
7496  molecules=None,
7497  residue_indexes=None,
7498  chains=None,
7499  atom_types=None,
7500  residue_types=None,
7501  domains=None,
7502  target_radius=-1,
7503  molecule=None,
7504  residue_index=None,
7505  chain=None,
7506  atom_type=None,
7507  residue_type=None,
7508  terminus=None,
7509  domain=None,
7510  particle_type=None,
7511  particle_types=None,
7512  hierarchy_types=None,
7513  copy_index=-1,
7514  copy_indexes=None):
7515  if hierarchy:
7516  this = _IMP_atom.new_Selection(hierarchy)
7517  try: self.this.append(this)
7518  except: self.this = this
7519  else:
7520  this = _IMP_atom.new_Selection(hierarchies)
7521  try: self.this.append(this)
7522  except: self.this = this
7523  if not molecules:
7524  molecules=[]
7525  if not residue_indexes:
7526  residue_indexes=[]
7527  if not chains:
7528  chains=[]
7529  if not atom_types:
7530  atom_types=[]
7531  if not residue_types:
7532  residue_types=[]
7533  if not domains:
7534  domains=[]
7535  if molecule:
7536  molecules.append(molecule)
7537  if residue_index:
7538  residue_indexes.append(residue_index)
7539  if chain:
7540  chains.append(chain)
7541  if atom_type:
7542  atom_types.append(atom_type)
7543  if residue_type:
7544  residue_types.append(residue_type)
7545  if domain:
7546  domains.append(domain)
7547  if terminus:
7548  self.set_terminus(terminus)
7549  if not copy_indexes:
7550  copy_indexes=[]
7551  if copy_index !=-1:
7552  copy_indexes.append(copy_index)
7553  if not particle_types:
7554  particle_types=[]
7555  if particle_type:
7556  particle_types.append(particle_type)
7557  if not hierarchy_types:
7558  hierarchy_types=[]
7559  presidue_indexes=[]
7560  for ri in residue_indexes:
7561  if type(ri) == type(()):
7562  presidue_indexes= presidue_indexes+ range(ri[0], ri[1])
7563  else:
7564  presidue_indexes.append(ri)
7565  self.set_molecules(molecules);
7566  self.set_chains("".join(chains));
7567  self.set_residue_indexes(presidue_indexes);
7568  self.set_atom_types(atom_types);
7569  self.set_residue_types(residue_types);
7570  self.set_domains(domains);
7571  self.set_target_radius(target_radius);
7572  self.set_copy_indexes(copy_indexes)
7573  self.set_particle_types(particle_types)
7574  self.set_hierarchy_types(hierarchy_types)
7575 
7576  __swig_destroy__ = _IMP_atom.delete_Selection
7577  __del__ = lambda self : None;
7578 Selection_swigregister = _IMP_atom.Selection_swigregister
7579 Selection_swigregister(Selection)
7580 
7581 
7582 def create_distance_restraint(*args):
7583  """
7584  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint
7585  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
7586  """
7587  return _IMP_atom.create_distance_restraint(*args)
7588 
7590  """
7591  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
7592  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
7593  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
7594  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
7595  """
7596  return _IMP_atom.create_connectivity_restraint(*args)
7597 
7599  """
7600  create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
7601  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
7602  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
7603  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
7604  """
7605  return _IMP_atom.create_internal_connectivity_restraint(*args)
7606 
7607 def create_cover(*args):
7608  """
7609  create_cover(Selection s, std::string name=std::string()) -> XYZR
7610  create_cover(Selection s) -> XYZR
7611  """
7612  return _IMP_atom.create_cover(*args)
7613 
7614 def get_mass(*args):
7615  """get_mass(Selection s) -> double"""
7616  return _IMP_atom.get_mass(*args)
7617 
7618 def get_volume(*args):
7619  """get_volume(Selection s) -> double"""
7620  return _IMP_atom.get_volume(*args)
7621 
7622 def get_surface_area(*args):
7623  """get_surface_area(Selection s) -> double"""
7624  return _IMP_atom.get_surface_area(*args)
7625 
7626 def get_leaves(*args):
7627  """
7628  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
7629  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
7630  get_leaves(Selection h) -> IMP::atom::Hierarchies
7631  """
7632  return _IMP_atom.get_leaves(*args)
7633 class SelectionGeometry(IMP.display.Geometry):
7634  """Proxy of C++ IMP::atom::SelectionGeometry class"""
7635  __swig_setmethods__ = {}
7636  for _s in [IMP.display.Geometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7637  __setattr__ = lambda self, name, value: _swig_setattr(self, SelectionGeometry, name, value)
7638  __swig_getmethods__ = {}
7639  for _s in [IMP.display.Geometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7640  __getattr__ = lambda self, name: _swig_getattr(self, SelectionGeometry, name)
7641  def __init__(self, *args):
7642  """
7643  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry
7644  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
7645  """
7646  this = _IMP_atom.new_SelectionGeometry(*args)
7647  try: self.this.append(this)
7648  except: self.this = this
7649  def get_version_info(self):
7650  """get_version_info(SelectionGeometry self) -> VersionInfo"""
7651  return _IMP_atom.SelectionGeometry_get_version_info(self)
7652 
7653  __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
7654  __del__ = lambda self : None;
7655  def __str__(self):
7656  """__str__(SelectionGeometry self) -> std::string"""
7657  return _IMP_atom.SelectionGeometry___str__(self)
7658 
7659  def __repr__(self):
7660  """__repr__(SelectionGeometry self) -> std::string"""
7661  return _IMP_atom.SelectionGeometry___repr__(self)
7662 
7663  def get_from(o):
7664  return _object_cast_to_SelectionGeometry(o)
7665  get_from = staticmethod(get_from)
7666 
7667 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
7668 SelectionGeometry_swigregister(SelectionGeometry)
7669 
7670 
7671 def get_rmsd(*args):
7672  """
7673  get_rmsd(Selection s0, Selection s1, Transformation3D tr_for_second=IMP::algebra::get_identity_transformation_3d()) -> double
7674  get_rmsd(Selection s0, Selection s1) -> double
7675  """
7676  return _IMP_atom.get_rmsd(*args)
7677 
7678 def get_placement_score(*args):
7679  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
7680  return _IMP_atom.get_placement_score(*args)
7681 
7683  """
7684  get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
7685  IMP::core::XYZs const & mdl2) -> IMP::FloatPair
7686  """
7687  return _IMP_atom.get_component_placement_score(*args)
7688 
7689 def get_pairwise_rmsd_score(*args):
7690  """
7691  get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1,
7692  IMP::core::XYZs const & mdl2) -> double
7693  """
7694  return _IMP_atom.get_pairwise_rmsd_score(*args)
7695 
7696 def get_radius_of_gyration(*args):
7697  """
7698  get_radius_of_gyration(Selection s) -> double
7699  get_radius_of_gyration(IMP::kernel::ParticlesTemp const & ps) -> double
7700  """
7701  return _IMP_atom.get_radius_of_gyration(*args)
7702 class RMSDCalculator(_object):
7703  """Proxy of C++ IMP::atom::RMSDCalculator class"""
7704  __swig_setmethods__ = {}
7705  __setattr__ = lambda self, name, value: _swig_setattr(self, RMSDCalculator, name, value)
7706  __swig_getmethods__ = {}
7707  __getattr__ = lambda self, name: _swig_getattr(self, RMSDCalculator, name)
7708  def __init__(self, *args):
7709  """
7710  __init__(IMP::atom::RMSDCalculator self) -> RMSDCalculator
7711  __init__(IMP::atom::RMSDCalculator self, IMP::kernel::ParticlesTemp const & ps) -> RMSDCalculator
7712  """
7713  this = _IMP_atom.new_RMSDCalculator(*args)
7714  try: self.this.append(this)
7715  except: self.this = this
7716  def get_rmsd(self, *args):
7717  """get_rmsd(RMSDCalculator self, Transformation3D t1, Transformation3D t2) -> double"""
7718  return _IMP_atom.RMSDCalculator_get_rmsd(self, *args)
7719 
7720  def get_squared_rmsd(self, *args):
7721  """get_squared_rmsd(RMSDCalculator self, Transformation3D t1, Transformation3D t2) -> double"""
7722  return _IMP_atom.RMSDCalculator_get_squared_rmsd(self, *args)
7723 
7724  def show(self, *args):
7725  """
7726  show(RMSDCalculator self, _ostream out=std::cout)
7727  show(RMSDCalculator self)
7728  """
7729  return _IMP_atom.RMSDCalculator_show(self, *args)
7730 
7731  def __str__(self):
7732  """__str__(RMSDCalculator self) -> std::string"""
7733  return _IMP_atom.RMSDCalculator___str__(self)
7734 
7735  def __repr__(self):
7736  """__repr__(RMSDCalculator self) -> std::string"""
7737  return _IMP_atom.RMSDCalculator___repr__(self)
7738 
7739  __swig_destroy__ = _IMP_atom.delete_RMSDCalculator
7740  __del__ = lambda self : None;
7741 RMSDCalculator_swigregister = _IMP_atom.RMSDCalculator_swigregister
7742 RMSDCalculator_swigregister(RMSDCalculator)
7743 
7744 class ForceFieldParameters(IMP.base.Object):
7745  """Proxy of C++ IMP::atom::ForceFieldParameters class"""
7746  __swig_setmethods__ = {}
7747  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7748  __setattr__ = lambda self, name, value: _swig_setattr(self, ForceFieldParameters, name, value)
7749  __swig_getmethods__ = {}
7750  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7751  __getattr__ = lambda self, name: _swig_getattr(self, ForceFieldParameters, name)
7752  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
7753  def get_radius(self, *args):
7754  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
7755  return _IMP_atom.ForceFieldParameters_get_radius(self, *args)
7756 
7757  def get_epsilon(self, *args):
7758  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
7759  return _IMP_atom.ForceFieldParameters_get_epsilon(self, *args)
7760 
7761  def add_radii(self, *args):
7762  """
7763  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius"))
7764  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
7765  add_radii(ForceFieldParameters self, Hierarchy mhd)
7766  """
7767  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
7768 
7769  def add_well_depths(self, *args):
7770  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
7771  return _IMP_atom.ForceFieldParameters_add_well_depths(self, *args)
7772 
7773  def add_bonds(self, *args):
7774  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
7775  return _IMP_atom.ForceFieldParameters_add_bonds(self, *args)
7776 
7777  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
7778  __del__ = lambda self : None;
7779  def __str__(self):
7780  """__str__(ForceFieldParameters self) -> std::string"""
7781  return _IMP_atom.ForceFieldParameters___str__(self)
7782 
7783  def __repr__(self):
7784  """__repr__(ForceFieldParameters self) -> std::string"""
7785  return _IMP_atom.ForceFieldParameters___repr__(self)
7786 
7787  def get_from(o):
7788  return _object_cast_to_ForceFieldParameters(o)
7789  get_from = staticmethod(get_from)
7790 
7791 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
7792 ForceFieldParameters_swigregister(ForceFieldParameters)
7793 
7794 class CHARMMAtomTopology(_object):
7795  """Proxy of C++ IMP::atom::CHARMMAtomTopology class"""
7796  __swig_setmethods__ = {}
7797  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtomTopology, name, value)
7798  __swig_getmethods__ = {}
7799  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtomTopology, name)
7800  def __init__(self, *args):
7801  """
7802  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
7803  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
7804  """
7805  this = _IMP_atom.new_CHARMMAtomTopology(*args)
7806  try: self.this.append(this)
7807  except: self.this = this
7808  def get_name(self):
7809  """get_name(CHARMMAtomTopology self) -> std::string"""
7810  return _IMP_atom.CHARMMAtomTopology_get_name(self)
7811 
7812  def get_charmm_type(self):
7813  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
7814  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
7815 
7816  def get_charge(self):
7817  """get_charge(CHARMMAtomTopology self) -> double"""
7818  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
7819 
7820  def set_charmm_type(self, *args):
7821  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
7822  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, *args)
7823 
7824  def set_charge(self, *args):
7825  """set_charge(CHARMMAtomTopology self, double charge)"""
7826  return _IMP_atom.CHARMMAtomTopology_set_charge(self, *args)
7827 
7828  def show(self, *args):
7829  """
7830  show(CHARMMAtomTopology self, _ostream out=std::cout)
7831  show(CHARMMAtomTopology self)
7832  """
7833  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
7834 
7835  def __str__(self):
7836  """__str__(CHARMMAtomTopology self) -> std::string"""
7837  return _IMP_atom.CHARMMAtomTopology___str__(self)
7838 
7839  def __repr__(self):
7840  """__repr__(CHARMMAtomTopology self) -> std::string"""
7841  return _IMP_atom.CHARMMAtomTopology___repr__(self)
7842 
7843  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
7844  __del__ = lambda self : None;
7845 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
7846 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
7847 
7848 class CHARMMBondEndpoint(_object):
7849  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class"""
7850  __swig_setmethods__ = {}
7851  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondEndpoint, name, value)
7852  __swig_getmethods__ = {}
7853  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondEndpoint, name)
7854  def __init__(self, *args):
7855  """
7856  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=nullptr) -> CHARMMBondEndpoint
7857  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
7858  """
7859  this = _IMP_atom.new_CHARMMBondEndpoint(*args)
7860  try: self.this.append(this)
7861  except: self.this = this
7862  def get_atom_name(self):
7863  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
7864  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
7865 
7866  def get_atom(self, *args):
7867  """
7868  get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue,
7869  std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom
7870  """
7871  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, *args)
7872 
7873  def show(self, *args):
7874  """
7875  show(CHARMMBondEndpoint self, _ostream out=std::cout)
7876  show(CHARMMBondEndpoint self)
7877  """
7878  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
7879 
7880  def __str__(self):
7881  """__str__(CHARMMBondEndpoint self) -> std::string"""
7882  return _IMP_atom.CHARMMBondEndpoint___str__(self)
7883 
7884  def __repr__(self):
7885  """__repr__(CHARMMBondEndpoint self) -> std::string"""
7886  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
7887 
7888  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
7889  __del__ = lambda self : None;
7890 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
7891 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
7892 
7893 class CHARMMDihedral(_object):
7894  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class"""
7895  __swig_setmethods__ = {}
7896  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedral, name, value)
7897  __swig_getmethods__ = {}
7898  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedral, name)
7899  __repr__ = _swig_repr
7900  def __init__(self, *args):
7901  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
7902  this = _IMP_atom.new_CHARMMDihedral(*args)
7903  try: self.this.append(this)
7904  except: self.this = this
7905  def get_endpoint(self, *args):
7906  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
7907  return _IMP_atom.CHARMMDihedral_get_endpoint(self, *args)
7908 
7909  def get_contains_atom(self, *args):
7910  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
7911  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, *args)
7912 
7913  def show(self, *args):
7914  """
7915  show(CHARMMDihedral self, _ostream out=std::cout)
7916  show(CHARMMDihedral self)
7917  """
7918  return _IMP_atom.CHARMMDihedral_show(self, *args)
7919 
7920  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
7921  __del__ = lambda self : None;
7922 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
7923 CHARMMDihedral_swigregister(CHARMMDihedral)
7924 
7925 class CHARMMInternalCoordinate(CHARMMDihedral):
7926  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class"""
7927  __swig_setmethods__ = {}
7928  for _s in [CHARMMDihedral]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7929  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMInternalCoordinate, name, value)
7930  __swig_getmethods__ = {}
7931  for _s in [CHARMMDihedral]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7932  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMInternalCoordinate, name)
7933  def __init__(self, *args):
7934  """
7935  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral,
7936  float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
7937  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::base::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance,
7938  float first_angle, float dihedral, float second_angle, float second_distance,
7939  bool improper) -> CHARMMInternalCoordinate
7940  """
7941  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
7942  try: self.this.append(this)
7943  except: self.this = this
7944  def get_first_distance(self):
7945  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
7946  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
7947 
7948  def get_second_distance(self):
7949  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
7950  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
7951 
7952  def get_first_angle(self):
7953  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
7954  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
7955 
7956  def get_second_angle(self):
7957  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
7958  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
7959 
7960  def get_dihedral(self):
7961  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
7962  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
7963 
7964  def get_improper(self):
7965  """get_improper(CHARMMInternalCoordinate self) -> bool"""
7966  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
7967 
7968  def show(self, *args):
7969  """
7970  show(CHARMMInternalCoordinate self, _ostream out=std::cout)
7971  show(CHARMMInternalCoordinate self)
7972  """
7973  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
7974 
7975  def __str__(self):
7976  """__str__(CHARMMInternalCoordinate self) -> std::string"""
7977  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
7978 
7979  def __repr__(self):
7980  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
7981  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
7982 
7983  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
7984  __del__ = lambda self : None;
7985 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
7986 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
7987 
7988 class CHARMMResidueTopologyBase(IMP.base.Object):
7989  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class"""
7990  __swig_setmethods__ = {}
7991  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
7992  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopologyBase, name, value)
7993  __swig_getmethods__ = {}
7994  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
7995  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopologyBase, name)
7996  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
7997  def get_type(self):
7998  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
7999  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
8000 
8001  def get_number_of_atoms(self):
8002  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
8003  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
8004 
8005  def add_atom(self, *args):
8006  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
8007  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, *args)
8008 
8009  def get_atom(self, *args):
8010  """
8011  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
8012  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
8013  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
8014  """
8015  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
8016 
8017  def get_number_of_bonds(self):
8018  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
8019  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
8020 
8021  def add_bond(self, *args):
8022  """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
8023  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, *args)
8024 
8025  def get_number_of_angles(self):
8026  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
8027  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
8028 
8029  def add_angle(self, *args):
8030  """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
8031  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, *args)
8032 
8033  def get_number_of_dihedrals(self):
8034  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
8035  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
8036 
8037  def add_dihedral(self, *args):
8038  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8039  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, *args)
8040 
8041  def get_number_of_impropers(self):
8042  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
8043  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
8044 
8045  def add_improper(self, *args):
8046  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
8047  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, *args)
8048 
8049  def get_number_of_internal_coordinates(self):
8050  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
8051  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
8052 
8053  def add_internal_coordinate(self, *args):
8054  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
8055  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, *args)
8056 
8057  def get_internal_coordinate(self, *args):
8058  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
8059  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, *args)
8060 
8061  def get_bond(self, *args):
8062  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
8063  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, *args)
8064 
8065  def get_angle(self, *args):
8066  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
8067  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, *args)
8068 
8069  def get_dihedral(self, *args):
8070  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8071  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, *args)
8072 
8073  def get_improper(self, *args):
8074  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
8075  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, *args)
8076 
8077  def get_version_info(self):
8078  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
8079  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
8080 
8081  def do_show(self, *args):
8082  """do_show(CHARMMResidueTopologyBase self, _ostream out)"""
8083  return _IMP_atom.CHARMMResidueTopologyBase_do_show(self, *args)
8084 
8085  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
8086  __del__ = lambda self : None;
8087  def __str__(self):
8088  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
8089  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
8090 
8091  def __repr__(self):
8092  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
8093  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
8094 
8095  def get_from(o):
8096  return _object_cast_to_CHARMMResidueTopologyBase(o)
8097  get_from = staticmethod(get_from)
8098 
8099 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
8100 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
8101 
8102 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
8103  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class"""
8104  __swig_setmethods__ = {}
8105  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8106  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMIdealResidueTopology, name, value)
8107  __swig_getmethods__ = {}
8108  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8109  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMIdealResidueTopology, name)
8110  def __init__(self, *args):
8111  """
8112  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
8113  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
8114  """
8115  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
8116  try: self.this.append(this)
8117  except: self.this = this
8118  def remove_atom(self, *args):
8119  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
8120  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, *args)
8121 
8122  def set_default_first_patch(self, *args):
8123  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8124  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, *args)
8125 
8126  def set_default_last_patch(self, *args):
8127  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
8128  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, *args)
8129 
8130  def get_default_first_patch(self):
8131  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
8132  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
8133 
8134  def get_default_last_patch(self):
8135  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
8136  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
8137 
8138  __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
8139  __del__ = lambda self : None;
8140  def __str__(self):
8141  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
8142  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
8143 
8144  def __repr__(self):
8145  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
8146  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
8147 
8148  def get_from(o):
8149  return _object_cast_to_CHARMMIdealResidueTopology(o)
8150  get_from = staticmethod(get_from)
8151 
8152 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
8153 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
8154 
8155 class CHARMMPatch(CHARMMResidueTopologyBase):
8156  """Proxy of C++ IMP::atom::CHARMMPatch class"""
8157  __swig_setmethods__ = {}
8158  for _s in [CHARMMResidueTopologyBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8159  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMPatch, name, value)
8160  __swig_getmethods__ = {}
8161  for _s in [CHARMMResidueTopologyBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8162  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMPatch, name)
8163  def __init__(self, *args):
8164  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
8165  this = _IMP_atom.new_CHARMMPatch(*args)
8166  try: self.this.append(this)
8167  except: self.this = this
8168  def add_removed_atom(self, *args):
8169  """add_removed_atom(CHARMMPatch self, std::string name)"""
8170  return _IMP_atom.CHARMMPatch_add_removed_atom(self, *args)
8171 
8172  def get_number_of_removed_atoms(self):
8173  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
8174  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
8175 
8176  def get_removed_atom(self, *args):
8177  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
8178  return _IMP_atom.CHARMMPatch_get_removed_atom(self, *args)
8179 
8180  def apply(self, *args):
8181  """
8182  apply(CHARMMPatch self, CHARMMResidueTopology res)
8183  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
8184  """
8185  return _IMP_atom.CHARMMPatch_apply(self, *args)
8186 
8187  __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
8188  __del__ = lambda self : None;
8189  def __str__(self):
8190  """__str__(CHARMMPatch self) -> std::string"""
8191  return _IMP_atom.CHARMMPatch___str__(self)
8192 
8193  def __repr__(self):
8194  """__repr__(CHARMMPatch self) -> std::string"""
8195  return _IMP_atom.CHARMMPatch___repr__(self)
8196 
8197  def get_from(o):
8198  return _object_cast_to_CHARMMPatch(o)
8199  get_from = staticmethod(get_from)
8200 
8201 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
8202 CHARMMPatch_swigregister(CHARMMPatch)
8203 
8204 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
8205  """Proxy of C++ IMP::atom::CHARMMResidueTopology class"""
8206  __swig_setmethods__ = {}
8207  for _s in [CHARMMIdealResidueTopology]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8208  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMResidueTopology, name, value)
8209  __swig_getmethods__ = {}
8210  for _s in [CHARMMIdealResidueTopology]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8211  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMResidueTopology, name)
8212  def __init__(self, *args):
8213  """
8214  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
8215  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
8216  """
8217  this = _IMP_atom.new_CHARMMResidueTopology(*args)
8218  try: self.this.append(this)
8219  except: self.this = this
8220  def get_patched(self):
8221  """get_patched(CHARMMResidueTopology self) -> bool"""
8222  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
8223 
8224  def set_patched(self, *args):
8225  """set_patched(CHARMMResidueTopology self, bool patched)"""
8226  return _IMP_atom.CHARMMResidueTopology_set_patched(self, *args)
8227 
8228  __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
8229  __del__ = lambda self : None;
8230  def __str__(self):
8231  """__str__(CHARMMResidueTopology self) -> std::string"""
8232  return _IMP_atom.CHARMMResidueTopology___str__(self)
8233 
8234  def __repr__(self):
8235  """__repr__(CHARMMResidueTopology self) -> std::string"""
8236  return _IMP_atom.CHARMMResidueTopology___repr__(self)
8237 
8238  def get_from(o):
8239  return _object_cast_to_CHARMMResidueTopology(o)
8240  get_from = staticmethod(get_from)
8241 
8242 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
8243 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
8244 
8245 class CHARMMAtom(Atom):
8246  """Proxy of C++ IMP::atom::CHARMMAtom class"""
8247  __swig_setmethods__ = {}
8248  for _s in [Atom]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8249  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAtom, name, value)
8250  __swig_getmethods__ = {}
8251  for _s in [Atom]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8252  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAtom, name)
8253  def __init__(self, *args):
8254  """
8255  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
8256  __init__(IMP::atom::CHARMMAtom self, Model m, IMP::kernel::ParticleIndex id) -> CHARMMAtom
8257  __init__(IMP::atom::CHARMMAtom self, Particle p) -> CHARMMAtom
8258  """
8259  this = _IMP_atom.new_CHARMMAtom(*args)
8260  try: self.this.append(this)
8261  except: self.this = this
8262  def decorate_particle(*args):
8263  """decorate_particle(Particle p) -> CHARMMAtom"""
8264  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
8265 
8266  if _newclass:decorate_particle = staticmethod(decorate_particle)
8267  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
8268  def show(self, *args):
8269  """
8270  show(CHARMMAtom self, _ostream out=std::cout)
8271  show(CHARMMAtom self)
8272  """
8273  return _IMP_atom.CHARMMAtom_show(self, *args)
8274 
8275  def setup_particle(*args):
8276  """setup_particle(Particle p, IMP::String charmm_type) -> CHARMMAtom"""
8277  return _IMP_atom.CHARMMAtom_setup_particle(*args)
8278 
8279  if _newclass:setup_particle = staticmethod(setup_particle)
8280  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
8281  def get_charmm_type(self):
8282  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
8283  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
8284 
8285  def set_charmm_type(self, *args):
8286  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
8287  return _IMP_atom.CHARMMAtom_set_charmm_type(self, *args)
8288 
8289  def particle_is_instance(*args):
8290  """particle_is_instance(Particle p) -> bool"""
8291  return _IMP_atom.CHARMMAtom_particle_is_instance(*args)
8292 
8293  if _newclass:particle_is_instance = staticmethod(particle_is_instance)
8294  __swig_getmethods__["particle_is_instance"] = lambda x: particle_is_instance
8295  def get_charmm_type_key():
8296  """get_charmm_type_key() -> StringKey"""
8297  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
8298 
8299  if _newclass:get_charmm_type_key = staticmethod(get_charmm_type_key)
8300  __swig_getmethods__["get_charmm_type_key"] = lambda x: get_charmm_type_key
8301  def add_attribute(self, *args):
8302  """
8303  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
8304  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8305  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
8306  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
8307  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8308  add_attribute(CHARMMAtom self, ObjectKey a0, IMP::Object * a1)
8309  """
8310  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
8311 
8312  def get_value(self, *args):
8313  """
8314  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
8315  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
8316  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
8317  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
8318  get_value(CHARMMAtom self, ObjectKey a0) -> IMP::Object *
8319  """
8320  return _IMP_atom.CHARMMAtom_get_value(self, *args)
8321 
8322  def set_value(self, *args):
8323  """
8324  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
8325  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
8326  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
8327  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
8328  set_value(CHARMMAtom self, ObjectKey a0, IMP::Object * a1)
8329  """
8330  return _IMP_atom.CHARMMAtom_set_value(self, *args)
8331 
8332  def remove_attribute(self, *args):
8333  """
8334  remove_attribute(CHARMMAtom self, FloatKey a0)
8335  remove_attribute(CHARMMAtom self, IntKey a0)
8336  remove_attribute(CHARMMAtom self, StringKey a0)
8337  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
8338  remove_attribute(CHARMMAtom self, ObjectKey a0)
8339  """
8340  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
8341 
8342  def has_attribute(self, *args):
8343  """
8344  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
8345  has_attribute(CHARMMAtom self, IntKey a0) -> bool
8346  has_attribute(CHARMMAtom self, StringKey a0) -> bool
8347  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
8348  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
8349  """
8350  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
8351 
8352  def get_derivative(self, *args):
8353  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
8354  return _IMP_atom.CHARMMAtom_get_derivative(self, *args)
8355 
8356  def get_name(self):
8357  """get_name(CHARMMAtom self) -> std::string"""
8358  return _IMP_atom.CHARMMAtom_get_name(self)
8359 
8360  def clear_caches(self):
8361  """clear_caches(CHARMMAtom self)"""
8362  return _IMP_atom.CHARMMAtom_clear_caches(self)
8363 
8364  def set_name(self, *args):
8365  """set_name(CHARMMAtom self, std::string a0)"""
8366  return _IMP_atom.CHARMMAtom_set_name(self, *args)
8367 
8368  def set_check_level(self, *args):
8369  """set_check_level(CHARMMAtom self, IMP::base::CheckLevel a0)"""
8370  return _IMP_atom.CHARMMAtom_set_check_level(self, *args)
8371 
8372  def add_to_derivative(self, *args):
8373  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8374  return _IMP_atom.CHARMMAtom_add_to_derivative(self, *args)
8375 
8376  def set_is_optimized(self, *args):
8377  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
8378  return _IMP_atom.CHARMMAtom_set_is_optimized(self, *args)
8379 
8380  def get_is_optimized(self, *args):
8381  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
8382  return _IMP_atom.CHARMMAtom_get_is_optimized(self, *args)
8383 
8384  def get_check_level(self):
8385  """get_check_level(CHARMMAtom self) -> IMP::base::CheckLevel"""
8386  return _IMP_atom.CHARMMAtom_get_check_level(self)
8387 
8388  def __eq__(self, *args):
8389  """
8390  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
8391  __eq__(CHARMMAtom self, Particle d) -> bool
8392  """
8393  return _IMP_atom.CHARMMAtom___eq__(self, *args)
8394 
8395  def __ne__(self, *args):
8396  """
8397  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
8398  __ne__(CHARMMAtom self, Particle d) -> bool
8399  """
8400  return _IMP_atom.CHARMMAtom___ne__(self, *args)
8401 
8402  def __le__(self, *args):
8403  """
8404  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
8405  __le__(CHARMMAtom self, Particle d) -> bool
8406  """
8407  return _IMP_atom.CHARMMAtom___le__(self, *args)
8408 
8409  def __lt__(self, *args):
8410  """
8411  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
8412  __lt__(CHARMMAtom self, Particle d) -> bool
8413  """
8414  return _IMP_atom.CHARMMAtom___lt__(self, *args)
8415 
8416  def __ge__(self, *args):
8417  """
8418  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
8419  __ge__(CHARMMAtom self, Particle d) -> bool
8420  """
8421  return _IMP_atom.CHARMMAtom___ge__(self, *args)
8422 
8423  def __gt__(self, *args):
8424  """
8425  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
8426  __gt__(CHARMMAtom self, Particle d) -> bool
8427  """
8428  return _IMP_atom.CHARMMAtom___gt__(self, *args)
8429 
8430  def __str__(self):
8431  """__str__(CHARMMAtom self) -> std::string"""
8432  return _IMP_atom.CHARMMAtom___str__(self)
8433 
8434  def __repr__(self):
8435  """__repr__(CHARMMAtom self) -> std::string"""
8436  return _IMP_atom.CHARMMAtom___repr__(self)
8437 
8438  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
8439  __del__ = lambda self : None;
8440 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
8441 CHARMMAtom_swigregister(CHARMMAtom)
8442 
8443 def CHARMMAtom_decorate_particle(*args):
8444  """CHARMMAtom_decorate_particle(Particle p) -> CHARMMAtom"""
8445  return _IMP_atom.CHARMMAtom_decorate_particle(*args)
8446 
8447 def CHARMMAtom_setup_particle(*args):
8448  """CHARMMAtom_setup_particle(Particle p, IMP::String charmm_type) -> CHARMMAtom"""
8449  return _IMP_atom.CHARMMAtom_setup_particle(*args)
8450 
8451 def CHARMMAtom_particle_is_instance(*args):
8452  """CHARMMAtom_particle_is_instance(Particle p) -> bool"""
8453  return _IMP_atom.CHARMMAtom_particle_is_instance(*args)
8454 
8455 def CHARMMAtom_get_charmm_type_key():
8456  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
8457  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
8458 
8459 
8460 def get_charmm_untyped_atoms(*args):
8461  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
8462  return _IMP_atom.get_charmm_untyped_atoms(*args)
8463 
8464 def remove_charmm_untyped_atoms(*args):
8465  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
8466  return _IMP_atom.remove_charmm_untyped_atoms(*args)
8467 class CHARMMBondParameters(_object):
8468  """Proxy of C++ IMP::atom::CHARMMBondParameters class"""
8469  __swig_setmethods__ = {}
8470  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBondParameters, name, value)
8471  __swig_getmethods__ = {}
8472  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBondParameters, name)
8473  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_set
8474  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMBondParameters_force_constant_get
8475  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
8476  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_set
8477  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMBondParameters_ideal_get
8478  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
8479  def __init__(self):
8480  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
8481  this = _IMP_atom.new_CHARMMBondParameters()
8482  try: self.this.append(this)
8483  except: self.this = this
8484  def show(self, *args):
8485  """
8486  show(CHARMMBondParameters self, _ostream out=std::cout)
8487  show(CHARMMBondParameters self)
8488  """
8489  return _IMP_atom.CHARMMBondParameters_show(self, *args)
8490 
8491  def __str__(self):
8492  """__str__(CHARMMBondParameters self) -> std::string"""
8493  return _IMP_atom.CHARMMBondParameters___str__(self)
8494 
8495  def __repr__(self):
8496  """__repr__(CHARMMBondParameters self) -> std::string"""
8497  return _IMP_atom.CHARMMBondParameters___repr__(self)
8498 
8499  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
8500  __del__ = lambda self : None;
8501 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
8502 CHARMMBondParameters_swigregister(CHARMMBondParameters)
8503 
8504 class CHARMMDihedralParameters(_object):
8505  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class"""
8506  __swig_setmethods__ = {}
8507  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMDihedralParameters, name, value)
8508  __swig_getmethods__ = {}
8509  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMDihedralParameters, name)
8510  __swig_setmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_set
8511  __swig_getmethods__["force_constant"] = _IMP_atom.CHARMMDihedralParameters_force_constant_get
8512  if _newclass:force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
8513  __swig_setmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_set
8514  __swig_getmethods__["multiplicity"] = _IMP_atom.CHARMMDihedralParameters_multiplicity_get
8515  if _newclass:multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
8516  __swig_setmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_set
8517  __swig_getmethods__["ideal"] = _IMP_atom.CHARMMDihedralParameters_ideal_get
8518  if _newclass:ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
8519  def __init__(self):
8520  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
8521  this = _IMP_atom.new_CHARMMDihedralParameters()
8522  try: self.this.append(this)
8523  except: self.this = this
8524  def show(self, *args):
8525  """
8526  show(CHARMMDihedralParameters self, _ostream out=std::cout)
8527  show(CHARMMDihedralParameters self)
8528  """
8529  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
8530 
8531  def __str__(self):
8532  """__str__(CHARMMDihedralParameters self) -> std::string"""
8533  return _IMP_atom.CHARMMDihedralParameters___str__(self)
8534 
8535  def __repr__(self):
8536  """__repr__(CHARMMDihedralParameters self) -> std::string"""
8537  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
8538 
8539  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
8540  __del__ = lambda self : None;
8541 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
8542 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
8543 
8544 class CHARMMParameters(ForceFieldParameters):
8545  """Proxy of C++ IMP::atom::CHARMMParameters class"""
8546  __swig_setmethods__ = {}
8547  for _s in [ForceFieldParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8548  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMParameters, name, value)
8549  __swig_getmethods__ = {}
8550  for _s in [ForceFieldParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8551  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMParameters, name)
8552  def __init__(self, *args):
8553  """
8554  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters
8555  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::base::TextInput()) -> CHARMMParameters
8556  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
8557  """
8558  this = _IMP_atom.new_CHARMMParameters(*args)
8559  try: self.this.append(this)
8560  except: self.this = this
8561  def add_residue_topology(self, *args):
8562  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
8563  return _IMP_atom.CHARMMParameters_add_residue_topology(self, *args)
8564 
8565  def get_residue_topology(self, *args):
8566  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
8567  return _IMP_atom.CHARMMParameters_get_residue_topology(self, *args)
8568 
8569  def add_patch(self, *args):
8570  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
8571  return _IMP_atom.CHARMMParameters_add_patch(self, *args)
8572 
8573  def get_patch(self, *args):
8574  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
8575  return _IMP_atom.CHARMMParameters_get_patch(self, *args)
8576 
8577  def create_topology(self, *args):
8578  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
8579  return _IMP_atom.CHARMMParameters_create_topology(self, *args)
8580 
8581  def get_bond_parameters(self, *args):
8582  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
8583  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, *args)
8584 
8585  def get_angle_parameters(self, *args):
8586  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
8587  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, *args)
8588 
8589  def get_dihedral_parameters(self, *args):
8590  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
8591  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, *args)
8592 
8593  def get_improper_parameters(self, *args):
8594  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
8595  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, *args)
8596 
8597  def create_angles(self, *args):
8598  """create_angles(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
8599  return _IMP_atom.CHARMMParameters_create_angles(self, *args)
8600 
8601  def create_dihedrals(self, *args):
8602  """create_dihedrals(CHARMMParameters self, IMP::kernel::Particles bonds) -> IMP::kernel::Particles"""
8603  return _IMP_atom.CHARMMParameters_create_dihedrals(self, *args)
8604 
8605  def get_version_info(self):
8606  """get_version_info(CHARMMParameters self) -> VersionInfo"""
8607  return _IMP_atom.CHARMMParameters_get_version_info(self)
8608 
8609  def do_show(self, *args):
8610  """do_show(CHARMMParameters self, _ostream out)"""
8611  return _IMP_atom.CHARMMParameters_do_show(self, *args)
8612 
8613  __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
8614  __del__ = lambda self : None;
8615  def __str__(self):
8616  """__str__(CHARMMParameters self) -> std::string"""
8617  return _IMP_atom.CHARMMParameters___str__(self)
8618 
8619  def __repr__(self):
8620  """__repr__(CHARMMParameters self) -> std::string"""
8621  return _IMP_atom.CHARMMParameters___repr__(self)
8622 
8623  def get_from(o):
8624  return _object_cast_to_CHARMMParameters(o)
8625  get_from = staticmethod(get_from)
8626 
8627 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
8628 CHARMMParameters_swigregister(CHARMMParameters)
8629 
8630 
8632  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
8633  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
8634 
8636  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
8637  return _IMP_atom.get_all_atom_CHARMM_parameters()
8638 class CHARMMSegmentTopology(IMP.base.Object):
8639  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class"""
8640  __swig_setmethods__ = {}
8641  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8642  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMSegmentTopology, name, value)
8643  __swig_getmethods__ = {}
8644  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8645  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMSegmentTopology, name)
8646  def remove_residue(self, *args):
8647  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
8648  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, *args)
8649 
8650  def remove_residues(self, *args):
8651  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
8652  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, *args)
8653 
8654  def set_residues(self, *args):
8655  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
8656  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, *args)
8657 
8658  def set_residues_order(self, *args):
8659  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
8660  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, *args)
8661 
8662  def add_residue(self, *args):
8663  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
8664  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, *args)
8665 
8666  def add_residues(self, *args):
8667  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
8668  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, *args)
8669 
8670  def clear_residues(self):
8671  """clear_residues(CHARMMSegmentTopology self)"""
8672  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
8673 
8674  def get_number_of_residues(self):
8675  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
8676  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
8677 
8678  def get_has_residues(self):
8679  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
8680  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
8681 
8682  def get_residue(self, *args):
8683  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
8684  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, *args)
8685 
8686  def get_residues(self):
8687  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
8688  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
8689 
8690  def reserve_residues(self, *args):
8691  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
8692  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, *args)
8693 
8694  def get_version_info(self):
8695  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
8696  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
8697 
8698  def do_show(self, *args):
8699  """do_show(CHARMMSegmentTopology self, _ostream out)"""
8700  return _IMP_atom.CHARMMSegmentTopology_do_show(self, *args)
8701 
8702  __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
8703  __del__ = lambda self : None;
8704  def __init__(self, name="CHARMM segment topology %1%"):
8705  """
8706  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology
8707  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
8708  """
8709  this = _IMP_atom.new_CHARMMSegmentTopology(name)
8710  try: self.this.append(this)
8711  except: self.this = this
8712  def apply_default_patches(self, *args):
8713  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
8714  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, *args)
8715 
8716  def __str__(self):
8717  """__str__(CHARMMSegmentTopology self) -> std::string"""
8718  return _IMP_atom.CHARMMSegmentTopology___str__(self)
8719 
8720  def __repr__(self):
8721  """__repr__(CHARMMSegmentTopology self) -> std::string"""
8722  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
8723 
8724  def get_from(o):
8725  return _object_cast_to_CHARMMSegmentTopology(o)
8726  get_from = staticmethod(get_from)
8727 
8728 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
8729 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
8730 
8731 class CHARMMTopology(IMP.base.Object):
8732  """Proxy of C++ IMP::atom::CHARMMTopology class"""
8733  __swig_setmethods__ = {}
8734  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8735  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMTopology, name, value)
8736  __swig_getmethods__ = {}
8737  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8738  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMTopology, name)
8739  def __init__(self, *args):
8740  """
8741  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology
8742  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
8743  """
8744  this = _IMP_atom.new_CHARMMTopology(*args)
8745  try: self.this.append(this)
8746  except: self.this = this
8747  def get_parameters(self):
8748  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
8749  return _IMP_atom.CHARMMTopology_get_parameters(self)
8750 
8751  def add_sequence(self, *args):
8752  """add_sequence(CHARMMTopology self, std::string sequence)"""
8753  return _IMP_atom.CHARMMTopology_add_sequence(self, *args)
8754 
8755  def apply_default_patches(self):
8756  """apply_default_patches(CHARMMTopology self)"""
8757  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
8758 
8759  def create_hierarchy(self, *args):
8760  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
8761  return _IMP_atom.CHARMMTopology_create_hierarchy(self, *args)
8762 
8763  def add_atom_types(self, *args):
8764  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
8765  return _IMP_atom.CHARMMTopology_add_atom_types(self, *args)
8766 
8767  def add_coordinates(self, *args):
8768  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
8769  return _IMP_atom.CHARMMTopology_add_coordinates(self, *args)
8770 
8771  def add_missing_atoms(self, *args):
8772  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
8773  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, *args)
8774 
8775  def setup_hierarchy(self, *args):
8776  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
8777  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, *args)
8778 
8779  def add_charges(self, *args):
8780  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
8781  return _IMP_atom.CHARMMTopology_add_charges(self, *args)
8782 
8783  def add_bonds(self, *args):
8784  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
8785  return _IMP_atom.CHARMMTopology_add_bonds(self, *args)
8786 
8787  def add_dihedrals(self, *args):
8788  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
8789  return _IMP_atom.CHARMMTopology_add_dihedrals(self, *args)
8790 
8791  def add_impropers(self, *args):
8792  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::kernel::Particles"""
8793  return _IMP_atom.CHARMMTopology_add_impropers(self, *args)
8794 
8795  def remove_segment(self, *args):
8796  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
8797  return _IMP_atom.CHARMMTopology_remove_segment(self, *args)
8798 
8799  def remove_segments(self, *args):
8800  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
8801  return _IMP_atom.CHARMMTopology_remove_segments(self, *args)
8802 
8803  def set_segments(self, *args):
8804  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
8805  return _IMP_atom.CHARMMTopology_set_segments(self, *args)
8806 
8807  def set_segments_order(self, *args):
8808  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
8809  return _IMP_atom.CHARMMTopology_set_segments_order(self, *args)
8810 
8811  def add_segment(self, *args):
8812  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
8813  return _IMP_atom.CHARMMTopology_add_segment(self, *args)
8814 
8815  def add_segments(self, *args):
8816  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
8817  return _IMP_atom.CHARMMTopology_add_segments(self, *args)
8818 
8819  def clear_segments(self):
8820  """clear_segments(CHARMMTopology self)"""
8821  return _IMP_atom.CHARMMTopology_clear_segments(self)
8822 
8823  def get_number_of_segments(self):
8824  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
8825  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
8826 
8827  def get_has_segments(self):
8828  """get_has_segments(CHARMMTopology self) -> bool"""
8829  return _IMP_atom.CHARMMTopology_get_has_segments(self)
8830 
8831  def get_segment(self, *args):
8832  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
8833  return _IMP_atom.CHARMMTopology_get_segment(self, *args)
8834 
8835  def get_segments(self):
8836  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
8837  return _IMP_atom.CHARMMTopology_get_segments(self)
8838 
8839  def reserve_segments(self, *args):
8840  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
8841  return _IMP_atom.CHARMMTopology_reserve_segments(self, *args)
8842 
8843  def get_version_info(self):
8844  """get_version_info(CHARMMTopology self) -> VersionInfo"""
8845  return _IMP_atom.CHARMMTopology_get_version_info(self)
8846 
8847  def do_show(self, *args):
8848  """do_show(CHARMMTopology self, _ostream out)"""
8849  return _IMP_atom.CHARMMTopology_do_show(self, *args)
8850 
8851  __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
8852  __del__ = lambda self : None;
8853  def __str__(self):
8854  """__str__(CHARMMTopology self) -> std::string"""
8855  return _IMP_atom.CHARMMTopology___str__(self)
8856 
8857  def __repr__(self):
8858  """__repr__(CHARMMTopology self) -> std::string"""
8859  return _IMP_atom.CHARMMTopology___repr__(self)
8860 
8861  def get_from(o):
8862  return _object_cast_to_CHARMMTopology(o)
8863  get_from = staticmethod(get_from)
8864 
8865 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
8866 CHARMMTopology_swigregister(CHARMMTopology)
8867 
8868 class CHARMMStereochemistryRestraint(IMP.kernel.Restraint):
8869  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class"""
8870  __swig_setmethods__ = {}
8871  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
8872  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMStereochemistryRestraint, name, value)
8873  __swig_getmethods__ = {}
8874  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
8875  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMStereochemistryRestraint, name)
8876  def __init__(self, *args):
8877  """__init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint"""
8878  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
8879  try: self.this.append(this)
8880  except: self.this = this
8881  def get_pair_filter(self):
8882  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
8883  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
8884 
8885  def get_input_particles(self):
8886  """get_input_particles(CHARMMStereochemistryRestraint self) -> IMP::kernel::ParticlesTemp"""
8887  return _IMP_atom.CHARMMStereochemistryRestraint_get_input_particles(self)
8888 
8889  def get_input_containers(self):
8890  """get_input_containers(CHARMMStereochemistryRestraint self) -> IMP::kernel::ContainersTemp"""
8891  return _IMP_atom.CHARMMStereochemistryRestraint_get_input_containers(self)
8892 
8893  def do_get_inputs(self):
8894  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::kernel::ModelObjectsTemp"""
8895  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
8896 
8897  def get_version_info(self):
8898  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
8899  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
8900 
8901  def do_show(self, *args):
8902  """do_show(CHARMMStereochemistryRestraint self, _ostream out)"""
8903  return _IMP_atom.CHARMMStereochemistryRestraint_do_show(self, *args)
8904 
8905  __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
8906  __del__ = lambda self : None;
8907  def __str__(self):
8908  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
8909  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
8910 
8911  def __repr__(self):
8912  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
8913  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
8914 
8915  def get_from(o):
8916  return _object_cast_to_CHARMMStereochemistryRestraint(o)
8917  get_from = staticmethod(get_from)
8918 
8919 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
8920 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
8921 
8922 
8923 def add_bonds(*args):
8924  """
8925  add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
8926  add_bonds(Hierarchy d)
8927  """
8928  return _IMP_atom.add_bonds(*args)
8929 
8930 def add_radii(*args):
8931  """
8932  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(),
8933  FloatKey radius_key=FloatKey("radius"))
8934  add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())
8935  add_radii(Hierarchy d)
8936  """
8937  return _IMP_atom.add_radii(*args)
8938 ALBER = _IMP_atom.ALBER
8939 HARPAZ = _IMP_atom.HARPAZ
8940 ANDERSSON = _IMP_atom.ANDERSSON
8941 TSAI = _IMP_atom.TSAI
8942 QUILLIN = _IMP_atom.QUILLIN
8943 SQUIRE = _IMP_atom.SQUIRE
8944 
8946  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
8947  return _IMP_atom.get_protein_density_from_reference(*args)
8948 
8949 def get_volume_from_mass(*args):
8950  """
8951  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double
8952  get_volume_from_mass(double m) -> double
8953  """
8954  return _IMP_atom.get_volume_from_mass(*args)
8955 
8956 def get_mass_from_volume(*args):
8957  """
8958  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double
8959  get_mass_from_volume(double v) -> double
8960  """
8961  return _IMP_atom.get_mass_from_volume(*args)
8962 
8964  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
8965  return _IMP_atom.get_mass_from_number_of_residues(*args)
8966 
8967 def get_volume_from_residue_type(*args):
8968  """get_volume_from_residue_type(ResidueType rt) -> double"""
8969  return _IMP_atom.get_volume_from_residue_type(*args)
8970 
8971 def get_molarity(*args):
8972  """get_molarity(double n, double volume) -> double"""
8973  return _IMP_atom.get_molarity(*args)
8974 
8975 def get_kd(*args):
8976  """get_kd(double na, double nb, double nab, double volume) -> double"""
8977  return _IMP_atom.get_kd(*args)
8978 
8980  """get_einstein_diffusion_coefficient(double r) -> double"""
8981  return _IMP_atom.get_einstein_diffusion_coefficient(*args)
8982 
8984  """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
8985  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(*args)
8986 
8987 def get_diffusion_length(*args):
8988  """
8989  get_diffusion_length(double D, double t) -> double
8990  get_diffusion_length(double D, double force, double t, double temp=273) -> double
8991  get_diffusion_length(double D, double force, double t) -> double
8992  """
8993  return _IMP_atom.get_diffusion_length(*args)
8994 
8995 def get_diffusion_angle(*args):
8996  """get_diffusion_angle(double D, double dtfs) -> double"""
8997  return _IMP_atom.get_diffusion_angle(*args)
8998 
8999 def get_diffusion_coefficient(*args):
9000  """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
9001  return _IMP_atom.get_diffusion_coefficient(*args)
9002 
9004  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
9005  return _IMP_atom.get_rotational_diffusion_coefficient(*args)
9006 
9007 def create_protein(*args):
9008  """
9009  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0,
9010  double volume=-1, bool ismol=True) -> Hierarchy
9011  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0,
9012  double volume=-1) -> Hierarchy
9013  create_protein(Model m, std::string name, double resolution, int number_of_residues, int first_residue_index=0) -> Hierarchy
9014  create_protein(Model m, std::string name, double resolution, int number_of_residues) -> Hierarchy
9015  create_protein(Model m, std::string name, double resolution, IMP::Ints const domain_boundaries) -> Hierarchy
9016  """
9017  return _IMP_atom.create_protein(*args)
9018 
9020  """
9021  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
9022  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
9023  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
9024  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
9025  """
9026  return _IMP_atom.create_simplified_along_backbone(*args)
9027 
9028 def get_molecule_name(*args):
9029  """get_molecule_name(Hierarchy h) -> std::string"""
9030  return _IMP_atom.get_molecule_name(*args)
9031 
9032 def get_residue_indexes(*args):
9033  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
9034  return _IMP_atom.get_residue_indexes(*args)
9035 
9036 def get_residue_type(*args):
9037  """
9038  get_residue_type(char c) -> ResidueType
9039  get_residue_type(Hierarchy h) -> ResidueType
9040  """
9041  return _IMP_atom.get_residue_type(*args)
9042 
9043 def get_chain_id(*args):
9044  """get_chain_id(Hierarchy h) -> int"""
9045  return _IMP_atom.get_chain_id(*args)
9046 
9047 def get_atom_type(*args):
9048  """get_atom_type(Hierarchy h) -> AtomType"""
9049  return _IMP_atom.get_atom_type(*args)
9050 
9051 def get_domain_name(*args):
9052  """get_domain_name(Hierarchy h) -> std::string"""
9053  return _IMP_atom.get_domain_name(*args)
9054 
9055 def get_copy_index(*args):
9056  """get_copy_index(Hierarchy h) -> int"""
9057  return _IMP_atom.get_copy_index(*args)
9058 
9060  """
9061  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
9062  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
9063  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
9064  """
9065  return _IMP_atom.create_excluded_volume_restraint(*args)
9066 
9067 def setup_as_approximation(*args):
9068  """
9069  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other, double resolution=-1)
9070  setup_as_approximation(Particle h, IMP::kernel::ParticlesTemp const & other)
9071  setup_as_approximation(Hierarchy h, double resolution=-1)
9072  setup_as_approximation(Hierarchy h)
9073  """
9074  return _IMP_atom.setup_as_approximation(*args)
9075 
9076 def transform(*args):
9077  """transform(Hierarchy h, Transformation3D tr)"""
9078  return _IMP_atom.transform(*args)
9079 class _HierarchyTreeVertexIndex(_object):
9080  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class"""
9081  __swig_setmethods__ = {}
9082  __setattr__ = lambda self, name, value: _swig_setattr(self, _HierarchyTreeVertexIndex, name, value)
9083  __swig_getmethods__ = {}
9084  __getattr__ = lambda self, name: _swig_getattr(self, _HierarchyTreeVertexIndex, name)
9085  __repr__ = _swig_repr
9086  def __init__(self):
9087  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
9088  this = _IMP_atom.new__HierarchyTreeVertexIndex()
9089  try: self.this.append(this)
9090  except: self.this = this
9091  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
9092  __del__ = lambda self : None;
9093 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
9094 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
9095 
9096 
9097 def get_vertex_index(*args):
9098  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
9099  return _IMP_atom.get_vertex_index(*args)
9100 
9101 def get_hierarchy_tree(*args):
9102  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
9103  return _IMP_atom.get_hierarchy_tree(*args)
9104 class HierarchyGeometry(IMP.display.SingletonGeometry):
9105  """Proxy of C++ IMP::atom::HierarchyGeometry class"""
9106  __swig_setmethods__ = {}
9107  for _s in [IMP.display.SingletonGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9108  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchyGeometry, name, value)
9109  __swig_getmethods__ = {}
9110  for _s in [IMP.display.SingletonGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9111  __getattr__ = lambda self, name: _swig_getattr(self, HierarchyGeometry, name)
9112  def __init__(self, *args):
9113  """
9114  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=-1) -> HierarchyGeometry
9115  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
9116  """
9117  this = _IMP_atom.new_HierarchyGeometry(*args)
9118  try: self.this.append(this)
9119  except: self.this = this
9120  def get_version_info(self):
9121  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
9122  return _IMP_atom.HierarchyGeometry_get_version_info(self)
9123 
9124  __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
9125  __del__ = lambda self : None;
9126  def __str__(self):
9127  """__str__(HierarchyGeometry self) -> std::string"""
9128  return _IMP_atom.HierarchyGeometry___str__(self)
9129 
9130  def __repr__(self):
9131  """__repr__(HierarchyGeometry self) -> std::string"""
9132  return _IMP_atom.HierarchyGeometry___repr__(self)
9133 
9134  def get_from(o):
9135  return _object_cast_to_HierarchyGeometry(o)
9136  get_from = staticmethod(get_from)
9137 
9138 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
9139 HierarchyGeometry_swigregister(HierarchyGeometry)
9140 
9141 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
9142  """Proxy of C++ IMP::atom::HierarchiesGeometry class"""
9143  __swig_setmethods__ = {}
9144  for _s in [IMP.display.SingletonsGeometry]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9145  __setattr__ = lambda self, name, value: _swig_setattr(self, HierarchiesGeometry, name, value)
9146  __swig_getmethods__ = {}
9147  for _s in [IMP.display.SingletonsGeometry]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9148  __getattr__ = lambda self, name: _swig_getattr(self, HierarchiesGeometry, name)
9149  def __init__(self, *args):
9150  """
9151  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
9152  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
9153  """
9154  this = _IMP_atom.new_HierarchiesGeometry(*args)
9155  try: self.this.append(this)
9156  except: self.this = this
9157  def get_version_info(self):
9158  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
9159  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
9160 
9161  __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
9162  __del__ = lambda self : None;
9163  def __str__(self):
9164  """__str__(HierarchiesGeometry self) -> std::string"""
9165  return _IMP_atom.HierarchiesGeometry___str__(self)
9166 
9167  def __repr__(self):
9168  """__repr__(HierarchiesGeometry self) -> std::string"""
9169  return _IMP_atom.HierarchiesGeometry___repr__(self)
9170 
9171  def get_from(o):
9172  return _object_cast_to_HierarchiesGeometry(o)
9173  get_from = staticmethod(get_from)
9174 
9175 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
9176 HierarchiesGeometry_swigregister(HierarchiesGeometry)
9177 
9178 class DopePairScore(_ADopeBase):
9179  """Proxy of C++ IMP::atom::DopePairScore class"""
9180  __swig_setmethods__ = {}
9181  for _s in [_ADopeBase]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9182  __setattr__ = lambda self, name, value: _swig_setattr(self, DopePairScore, name, value)
9183  __swig_getmethods__ = {}
9184  for _s in [_ADopeBase]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9185  __getattr__ = lambda self, name: _swig_getattr(self, DopePairScore, name)
9186  def __init__(self, *args):
9187  """
9188  __init__(IMP::atom::DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
9189  __init__(IMP::atom::DopePairScore self) -> DopePairScore
9190  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
9191  """
9192  this = _IMP_atom.new_DopePairScore(*args)
9193  try: self.this.append(this)
9194  except: self.this = this
9195  def __str__(self):
9196  """__str__(DopePairScore self) -> std::string"""
9197  return _IMP_atom.DopePairScore___str__(self)
9198 
9199  def __repr__(self):
9200  """__repr__(DopePairScore self) -> std::string"""
9201  return _IMP_atom.DopePairScore___repr__(self)
9202 
9203  def get_from(o):
9204  return _object_cast_to_DopePairScore(o)
9205  get_from = staticmethod(get_from)
9206 
9207  __swig_destroy__ = _IMP_atom.delete_DopePairScore
9208  __del__ = lambda self : None;
9209 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
9210 DopePairScore_swigregister(DopePairScore)
9211 
9212 
9213 def add_dope_score_data(*args):
9214  """add_dope_score_data(Hierarchy h)"""
9215  return _IMP_atom.add_dope_score_data(*args)
9216 class SameResiduePairFilter(IMP.kernel.PairPredicate):
9217  """Proxy of C++ IMP::atom::SameResiduePairFilter class"""
9218  __swig_setmethods__ = {}
9219  for _s in [IMP.kernel.PairPredicate]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9220  __setattr__ = lambda self, name, value: _swig_setattr(self, SameResiduePairFilter, name, value)
9221  __swig_getmethods__ = {}
9222  for _s in [IMP.kernel.PairPredicate]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9223  __getattr__ = lambda self, name: _swig_getattr(self, SameResiduePairFilter, name)
9224  def __init__(self):
9225  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
9226  this = _IMP_atom.new_SameResiduePairFilter()
9227  try: self.this.append(this)
9228  except: self.this = this
9229  def get_value(self, *args):
9230  """
9231  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePair const & a) -> int
9232  get_value(SameResiduePairFilter self, IMP::kernel::ParticlePairsTemp const & o) -> IMP::Ints
9233  """
9234  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
9235 
9236  def get_value_index(self, *args):
9237  """
9238  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPair const & vt) -> int
9239  get_value_index(SameResiduePairFilter self, Model m, IMP::kernel::ParticleIndexPairs const & o) -> IMP::Ints
9240  """
9241  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
9242 
9243  def get_input_particles(self, *args):
9244  """get_input_particles(SameResiduePairFilter self, Particle arg2) -> IMP::kernel::ParticlesTemp"""
9245  return _IMP_atom.SameResiduePairFilter_get_input_particles(self, *args)
9246 
9247  def get_input_containers(self, *args):
9248  """get_input_containers(SameResiduePairFilter self, Particle arg2) -> IMP::kernel::ContainersTemp"""
9249  return _IMP_atom.SameResiduePairFilter_get_input_containers(self, *args)
9250 
9251  def get_version_info(self):
9252  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
9253  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
9254 
9255  def do_show(self, *args):
9256  """do_show(SameResiduePairFilter self, _ostream out)"""
9257  return _IMP_atom.SameResiduePairFilter_do_show(self, *args)
9258 
9259  __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
9260  __del__ = lambda self : None;
9261  def __str__(self):
9262  """__str__(SameResiduePairFilter self) -> std::string"""
9263  return _IMP_atom.SameResiduePairFilter___str__(self)
9264 
9265  def __repr__(self):
9266  """__repr__(SameResiduePairFilter self) -> std::string"""
9267  return _IMP_atom.SameResiduePairFilter___repr__(self)
9268 
9269  def get_from(o):
9270  return _object_cast_to_SameResiduePairFilter(o)
9271  get_from = staticmethod(get_from)
9272 
9273 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
9274 SameResiduePairFilter_swigregister(SameResiduePairFilter)
9275 
9276 class RemoveRigidMotionOptimizerState(IMP.kernel.OptimizerState):
9277  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class"""
9278  __swig_setmethods__ = {}
9279  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9280  __setattr__ = lambda self, name, value: _swig_setattr(self, RemoveRigidMotionOptimizerState, name, value)
9281  __swig_getmethods__ = {}
9282  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9283  __getattr__ = lambda self, name: _swig_getattr(self, RemoveRigidMotionOptimizerState, name)
9284  def __init__(self, *args):
9285  """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, IMP::kernel::ParticlesTemp const & pis, unsigned int skip_steps) -> RemoveRigidMotionOptimizerState"""
9286  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(*args)
9287  try: self.this.append(this)
9288  except: self.this = this
9289  def set_skip_steps(self, *args):
9290  """set_skip_steps(RemoveRigidMotionOptimizerState self, unsigned int skip_steps)"""
9291  return _IMP_atom.RemoveRigidMotionOptimizerState_set_skip_steps(self, *args)
9292 
9293  def get_skip_steps(self):
9294  """get_skip_steps(RemoveRigidMotionOptimizerState self) -> unsigned int"""
9295  return _IMP_atom.RemoveRigidMotionOptimizerState_get_skip_steps(self)
9296 
9297  def set_particles(self, *args):
9298  """set_particles(RemoveRigidMotionOptimizerState self, IMP::kernel::Particles const & pis)"""
9299  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, *args)
9300 
9301  def remove_rigid_motion(self):
9302  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
9303  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
9304 
9305  def get_version_info(self):
9306  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
9307  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
9308 
9309  def do_show(self, *args):
9310  """do_show(RemoveRigidMotionOptimizerState self, _ostream out)"""
9311  return _IMP_atom.RemoveRigidMotionOptimizerState_do_show(self, *args)
9312 
9313  __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
9314  __del__ = lambda self : None;
9315  def __str__(self):
9316  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
9317  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
9318 
9319  def __repr__(self):
9320  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
9321  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
9322 
9323  def get_from(o):
9324  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
9325  get_from = staticmethod(get_from)
9326 
9327 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
9328 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
9329 
9330 class BerendsenThermostatOptimizerState(IMP.kernel.OptimizerState):
9331  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class"""
9332  __swig_setmethods__ = {}
9333  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9334  __setattr__ = lambda self, name, value: _swig_setattr(self, BerendsenThermostatOptimizerState, name, value)
9335  __swig_getmethods__ = {}
9336  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9337  __getattr__ = lambda self, name: _swig_getattr(self, BerendsenThermostatOptimizerState, name)
9338  def __init__(self, *args):
9339  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
9340  this = _IMP_atom.new_BerendsenThermostatOptimizerState(*args)
9341  try: self.this.append(this)
9342  except: self.this = this
9343  def set_particles(self, *args):
9344  """set_particles(BerendsenThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9345  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, *args)
9346 
9347  def get_temperature(self):
9348  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
9349  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
9350 
9351  def get_tau(self):
9352  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
9353  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
9354 
9355  def set_temperature(self, *args):
9356  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
9357  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, *args)
9358 
9359  def set_tau(self, *args):
9360  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
9361  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, *args)
9362 
9363  def rescale_velocities(self):
9364  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
9365  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
9366 
9367  def get_version_info(self):
9368  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
9369  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
9370 
9371  def do_show(self, *args):
9372  """do_show(BerendsenThermostatOptimizerState self, _ostream out)"""
9373  return _IMP_atom.BerendsenThermostatOptimizerState_do_show(self, *args)
9374 
9375  __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
9376  __del__ = lambda self : None;
9377  def __str__(self):
9378  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
9379  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
9380 
9381  def __repr__(self):
9382  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
9383  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
9384 
9385  def get_from(o):
9386  return _object_cast_to_BerendsenThermostatOptimizerState(o)
9387  get_from = staticmethod(get_from)
9388 
9389 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
9390 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
9391 
9392 class LangevinThermostatOptimizerState(IMP.kernel.OptimizerState):
9393  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class"""
9394  __swig_setmethods__ = {}
9395  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9396  __setattr__ = lambda self, name, value: _swig_setattr(self, LangevinThermostatOptimizerState, name, value)
9397  __swig_getmethods__ = {}
9398  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9399  __getattr__ = lambda self, name: _swig_getattr(self, LangevinThermostatOptimizerState, name)
9400  def __init__(self, *args):
9401  """__init__(IMP::atom::LangevinThermostatOptimizerState self, IMP::kernel::ParticlesTemp const & pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
9402  this = _IMP_atom.new_LangevinThermostatOptimizerState(*args)
9403  try: self.this.append(this)
9404  except: self.this = this
9405  def set_particles(self, *args):
9406  """set_particles(LangevinThermostatOptimizerState self, IMP::kernel::Particles const & pis)"""
9407  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, *args)
9408 
9409  def get_temperature(self):
9410  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
9411  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
9412 
9413  def get_gamma(self):
9414  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
9415  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
9416 
9417  def set_temperature(self, *args):
9418  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
9419  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, *args)
9420 
9421  def set_gamma(self, *args):
9422  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
9423  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, *args)
9424 
9425  def rescale_velocities(self):
9426  """rescale_velocities(LangevinThermostatOptimizerState self)"""
9427  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
9428 
9429  def get_version_info(self):
9430  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
9431  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
9432 
9433  def do_show(self, *args):
9434  """do_show(LangevinThermostatOptimizerState self, _ostream out)"""
9435  return _IMP_atom.LangevinThermostatOptimizerState_do_show(self, *args)
9436 
9437  __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
9438  __del__ = lambda self : None;
9439  def __str__(self):
9440  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
9441  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
9442 
9443  def __repr__(self):
9444  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
9445  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
9446 
9447  def get_from(o):
9448  return _object_cast_to_LangevinThermostatOptimizerState(o)
9449  get_from = staticmethod(get_from)
9450 
9451 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
9452 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
9453 
9454 class PDBSelector(IMP.base.Object):
9455  """Proxy of C++ IMP::atom::PDBSelector class"""
9456  __swig_setmethods__ = {}
9457  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9458  __setattr__ = lambda self, name, value: _swig_setattr(self, PDBSelector, name, value)
9459  __swig_getmethods__ = {}
9460  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9461  __getattr__ = lambda self, name: _swig_getattr(self, PDBSelector, name)
9462  def __init__(self, *args):
9463  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
9464  if self.__class__ == PDBSelector:
9465  _self = None
9466  else:
9467  _self = self
9468  this = _IMP_atom.new_PDBSelector(_self, *args)
9469  try: self.this.append(this)
9470  except: self.this = this
9471  if self.__class__ != PDBSelector:
9472  import IMP.base
9473  IMP.base._director_objects.register(self)
9474 
9475 
9476 
9477  def get_is_selected(self, *args):
9478  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
9479  return _IMP_atom.PDBSelector_get_is_selected(self, *args)
9480 
9481  __swig_destroy__ = _IMP_atom.delete_PDBSelector
9482  __del__ = lambda self : None;
9483  def __str__(self):
9484  """__str__(PDBSelector self) -> std::string"""
9485  return _IMP_atom.PDBSelector___str__(self)
9486 
9487  def __repr__(self):
9488  """__repr__(PDBSelector self) -> std::string"""
9489  return _IMP_atom.PDBSelector___repr__(self)
9490 
9491  def get_from(o):
9492  return _object_cast_to_PDBSelector(o)
9493  get_from = staticmethod(get_from)
9494 
9495  def get_type_name(self):
9496  return self.__class__.__name__
9497  def do_show(self, out):
9498  pass
9499  def get_version_info(self):
9500  if"IMP::atom" == "IMP":
9501  return VersionInfo("python", "0")
9502  else:
9503  return IMP.VersionInfo("python", "0")
9504  def get_from(o):
9505  return _object_cast_to_PDBSelector(o)
9506  get_from = staticmethod(get_from)
9507 
9508  def __disown__(self):
9509  self.this.disown()
9510  _IMP_atom.disown_PDBSelector(self)
9511  return weakref_proxy(self)
9512 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
9513 PDBSelector_swigregister(PDBSelector)
9514 
9515 class NonAlternativePDBSelector(PDBSelector):
9516  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class"""
9517  __swig_setmethods__ = {}
9518  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9519  __setattr__ = lambda self, name, value: _swig_setattr(self, NonAlternativePDBSelector, name, value)
9520  __swig_getmethods__ = {}
9521  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9522  __getattr__ = lambda self, name: _swig_getattr(self, NonAlternativePDBSelector, name)
9523  def __init__(self, *args):
9524  """
9525  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
9526  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
9527  """
9528  this = _IMP_atom.new_NonAlternativePDBSelector(*args)
9529  try: self.this.append(this)
9530  except: self.this = this
9531  def get_version_info(self):
9532  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
9533  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
9534 
9535  __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
9536  __del__ = lambda self : None;
9537  def __str__(self):
9538  """__str__(NonAlternativePDBSelector self) -> std::string"""
9539  return _IMP_atom.NonAlternativePDBSelector___str__(self)
9540 
9541  def __repr__(self):
9542  """__repr__(NonAlternativePDBSelector self) -> std::string"""
9543  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
9544 
9545  def get_from(o):
9546  return _object_cast_to_NonAlternativePDBSelector(o)
9547  get_from = staticmethod(get_from)
9548 
9549 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
9550 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
9551 
9552 class ATOMPDBSelector(NonAlternativePDBSelector):
9553  """Proxy of C++ IMP::atom::ATOMPDBSelector class"""
9554  __swig_setmethods__ = {}
9555  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9556  __setattr__ = lambda self, name, value: _swig_setattr(self, ATOMPDBSelector, name, value)
9557  __swig_getmethods__ = {}
9558  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9559  __getattr__ = lambda self, name: _swig_getattr(self, ATOMPDBSelector, name)
9560  def __init__(self, *args):
9561  """
9562  __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
9563  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
9564  """
9565  this = _IMP_atom.new_ATOMPDBSelector(*args)
9566  try: self.this.append(this)
9567  except: self.this = this
9568  __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
9569  __del__ = lambda self : None;
9570  def __str__(self):
9571  """__str__(ATOMPDBSelector self) -> std::string"""
9572  return _IMP_atom.ATOMPDBSelector___str__(self)
9573 
9574  def __repr__(self):
9575  """__repr__(ATOMPDBSelector self) -> std::string"""
9576  return _IMP_atom.ATOMPDBSelector___repr__(self)
9577 
9578  def get_from(o):
9579  return _object_cast_to_ATOMPDBSelector(o)
9580  get_from = staticmethod(get_from)
9581 
9582 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
9583 ATOMPDBSelector_swigregister(ATOMPDBSelector)
9584 
9585 class CAlphaPDBSelector(NonAlternativePDBSelector):
9586  """Proxy of C++ IMP::atom::CAlphaPDBSelector class"""
9587  __swig_setmethods__ = {}
9588  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9589  __setattr__ = lambda self, name, value: _swig_setattr(self, CAlphaPDBSelector, name, value)
9590  __swig_getmethods__ = {}
9591  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9592  __getattr__ = lambda self, name: _swig_getattr(self, CAlphaPDBSelector, name)
9593  def __init__(self, *args):
9594  """
9595  __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
9596  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
9597  """
9598  this = _IMP_atom.new_CAlphaPDBSelector(*args)
9599  try: self.this.append(this)
9600  except: self.this = this
9601  __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
9602  __del__ = lambda self : None;
9603  def __str__(self):
9604  """__str__(CAlphaPDBSelector self) -> std::string"""
9605  return _IMP_atom.CAlphaPDBSelector___str__(self)
9606 
9607  def __repr__(self):
9608  """__repr__(CAlphaPDBSelector self) -> std::string"""
9609  return _IMP_atom.CAlphaPDBSelector___repr__(self)
9610 
9611  def get_from(o):
9612  return _object_cast_to_CAlphaPDBSelector(o)
9613  get_from = staticmethod(get_from)
9614 
9615 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
9616 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
9617 
9618 class CBetaPDBSelector(NonAlternativePDBSelector):
9619  """Proxy of C++ IMP::atom::CBetaPDBSelector class"""
9620  __swig_setmethods__ = {}
9621  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9622  __setattr__ = lambda self, name, value: _swig_setattr(self, CBetaPDBSelector, name, value)
9623  __swig_getmethods__ = {}
9624  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9625  __getattr__ = lambda self, name: _swig_getattr(self, CBetaPDBSelector, name)
9626  def __init__(self, *args):
9627  """
9628  __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
9629  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
9630  """
9631  this = _IMP_atom.new_CBetaPDBSelector(*args)
9632  try: self.this.append(this)
9633  except: self.this = this
9634  __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
9635  __del__ = lambda self : None;
9636  def __str__(self):
9637  """__str__(CBetaPDBSelector self) -> std::string"""
9638  return _IMP_atom.CBetaPDBSelector___str__(self)
9639 
9640  def __repr__(self):
9641  """__repr__(CBetaPDBSelector self) -> std::string"""
9642  return _IMP_atom.CBetaPDBSelector___repr__(self)
9643 
9644  def get_from(o):
9645  return _object_cast_to_CBetaPDBSelector(o)
9646  get_from = staticmethod(get_from)
9647 
9648 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
9649 CBetaPDBSelector_swigregister(CBetaPDBSelector)
9650 
9651 class CPDBSelector(NonAlternativePDBSelector):
9652  """Proxy of C++ IMP::atom::CPDBSelector class"""
9653  __swig_setmethods__ = {}
9654  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9655  __setattr__ = lambda self, name, value: _swig_setattr(self, CPDBSelector, name, value)
9656  __swig_getmethods__ = {}
9657  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9658  __getattr__ = lambda self, name: _swig_getattr(self, CPDBSelector, name)
9659  def __init__(self, *args):
9660  """
9661  __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
9662  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
9663  """
9664  this = _IMP_atom.new_CPDBSelector(*args)
9665  try: self.this.append(this)
9666  except: self.this = this
9667  __swig_destroy__ = _IMP_atom.delete_CPDBSelector
9668  __del__ = lambda self : None;
9669  def __str__(self):
9670  """__str__(CPDBSelector self) -> std::string"""
9671  return _IMP_atom.CPDBSelector___str__(self)
9672 
9673  def __repr__(self):
9674  """__repr__(CPDBSelector self) -> std::string"""
9675  return _IMP_atom.CPDBSelector___repr__(self)
9676 
9677  def get_from(o):
9678  return _object_cast_to_CPDBSelector(o)
9679  get_from = staticmethod(get_from)
9680 
9681 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
9682 CPDBSelector_swigregister(CPDBSelector)
9683 
9684 class NPDBSelector(NonAlternativePDBSelector):
9685  """Proxy of C++ IMP::atom::NPDBSelector class"""
9686  __swig_setmethods__ = {}
9687  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9688  __setattr__ = lambda self, name, value: _swig_setattr(self, NPDBSelector, name, value)
9689  __swig_getmethods__ = {}
9690  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9691  __getattr__ = lambda self, name: _swig_getattr(self, NPDBSelector, name)
9692  def __init__(self, *args):
9693  """
9694  __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
9695  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
9696  """
9697  this = _IMP_atom.new_NPDBSelector(*args)
9698  try: self.this.append(this)
9699  except: self.this = this
9700  __swig_destroy__ = _IMP_atom.delete_NPDBSelector
9701  __del__ = lambda self : None;
9702  def __str__(self):
9703  """__str__(NPDBSelector self) -> std::string"""
9704  return _IMP_atom.NPDBSelector___str__(self)
9705 
9706  def __repr__(self):
9707  """__repr__(NPDBSelector self) -> std::string"""
9708  return _IMP_atom.NPDBSelector___repr__(self)
9709 
9710  def get_from(o):
9711  return _object_cast_to_NPDBSelector(o)
9712  get_from = staticmethod(get_from)
9713 
9714 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
9715 NPDBSelector_swigregister(NPDBSelector)
9716 
9717 class AllPDBSelector(PDBSelector):
9718  """Proxy of C++ IMP::atom::AllPDBSelector class"""
9719  __swig_setmethods__ = {}
9720  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9721  __setattr__ = lambda self, name, value: _swig_setattr(self, AllPDBSelector, name, value)
9722  __swig_getmethods__ = {}
9723  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9724  __getattr__ = lambda self, name: _swig_getattr(self, AllPDBSelector, name)
9725  def __init__(self, *args):
9726  """
9727  __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
9728  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
9729  """
9730  this = _IMP_atom.new_AllPDBSelector(*args)
9731  try: self.this.append(this)
9732  except: self.this = this
9733  def get_version_info(self):
9734  """get_version_info(AllPDBSelector self) -> VersionInfo"""
9735  return _IMP_atom.AllPDBSelector_get_version_info(self)
9736 
9737  __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
9738  __del__ = lambda self : None;
9739  def __str__(self):
9740  """__str__(AllPDBSelector self) -> std::string"""
9741  return _IMP_atom.AllPDBSelector___str__(self)
9742 
9743  def __repr__(self):
9744  """__repr__(AllPDBSelector self) -> std::string"""
9745  return _IMP_atom.AllPDBSelector___repr__(self)
9746 
9747  def get_from(o):
9748  return _object_cast_to_AllPDBSelector(o)
9749  get_from = staticmethod(get_from)
9750 
9751 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
9752 AllPDBSelector_swigregister(AllPDBSelector)
9753 
9754 class ChainPDBSelector(NonAlternativePDBSelector):
9755  """Proxy of C++ IMP::atom::ChainPDBSelector class"""
9756  __swig_setmethods__ = {}
9757  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9758  __setattr__ = lambda self, name, value: _swig_setattr(self, ChainPDBSelector, name, value)
9759  __swig_getmethods__ = {}
9760  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9761  __getattr__ = lambda self, name: _swig_getattr(self, ChainPDBSelector, name)
9762  __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
9763  __del__ = lambda self : None;
9764  def __init__(self, *args):
9765  """
9766  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
9767  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
9768  """
9769  this = _IMP_atom.new_ChainPDBSelector(*args)
9770  try: self.this.append(this)
9771  except: self.this = this
9772  def __str__(self):
9773  """__str__(ChainPDBSelector self) -> std::string"""
9774  return _IMP_atom.ChainPDBSelector___str__(self)
9775 
9776  def __repr__(self):
9777  """__repr__(ChainPDBSelector self) -> std::string"""
9778  return _IMP_atom.ChainPDBSelector___repr__(self)
9779 
9780  def get_from(o):
9781  return _object_cast_to_ChainPDBSelector(o)
9782  get_from = staticmethod(get_from)
9783 
9784 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
9785 ChainPDBSelector_swigregister(ChainPDBSelector)
9786 
9787 class WaterPDBSelector(NonAlternativePDBSelector):
9788  """Proxy of C++ IMP::atom::WaterPDBSelector class"""
9789  __swig_setmethods__ = {}
9790  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9791  __setattr__ = lambda self, name, value: _swig_setattr(self, WaterPDBSelector, name, value)
9792  __swig_getmethods__ = {}
9793  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9794  __getattr__ = lambda self, name: _swig_getattr(self, WaterPDBSelector, name)
9795  def __init__(self, *args):
9796  """
9797  __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
9798  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
9799  """
9800  this = _IMP_atom.new_WaterPDBSelector(*args)
9801  try: self.this.append(this)
9802  except: self.this = this
9803  __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
9804  __del__ = lambda self : None;
9805  def __str__(self):
9806  """__str__(WaterPDBSelector self) -> std::string"""
9807  return _IMP_atom.WaterPDBSelector___str__(self)
9808 
9809  def __repr__(self):
9810  """__repr__(WaterPDBSelector self) -> std::string"""
9811  return _IMP_atom.WaterPDBSelector___repr__(self)
9812 
9813  def get_from(o):
9814  return _object_cast_to_WaterPDBSelector(o)
9815  get_from = staticmethod(get_from)
9816 
9817 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
9818 WaterPDBSelector_swigregister(WaterPDBSelector)
9819 
9820 class HydrogenPDBSelector(NonAlternativePDBSelector):
9821  """Proxy of C++ IMP::atom::HydrogenPDBSelector class"""
9822  __swig_setmethods__ = {}
9823  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9824  __setattr__ = lambda self, name, value: _swig_setattr(self, HydrogenPDBSelector, name, value)
9825  __swig_getmethods__ = {}
9826  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9827  __getattr__ = lambda self, name: _swig_getattr(self, HydrogenPDBSelector, name)
9828  def __init__(self, *args):
9829  """
9830  __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
9831  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
9832  """
9833  this = _IMP_atom.new_HydrogenPDBSelector(*args)
9834  try: self.this.append(this)
9835  except: self.this = this
9836  __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
9837  __del__ = lambda self : None;
9838  def __str__(self):
9839  """__str__(HydrogenPDBSelector self) -> std::string"""
9840  return _IMP_atom.HydrogenPDBSelector___str__(self)
9841 
9842  def __repr__(self):
9843  """__repr__(HydrogenPDBSelector self) -> std::string"""
9844  return _IMP_atom.HydrogenPDBSelector___repr__(self)
9845 
9846  def get_from(o):
9847  return _object_cast_to_HydrogenPDBSelector(o)
9848  get_from = staticmethod(get_from)
9849 
9850 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
9851 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
9852 
9853 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
9854  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class"""
9855  __swig_setmethods__ = {}
9856  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9857  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterNonHydrogenPDBSelector, name, value)
9858  __swig_getmethods__ = {}
9859  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9860  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterNonHydrogenPDBSelector, name)
9861  __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
9862  __del__ = lambda self : None;
9863  def __init__(self, *args):
9864  """
9865  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
9866  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
9867  """
9868  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
9869  try: self.this.append(this)
9870  except: self.this = this
9871  def __str__(self):
9872  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
9873  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
9874 
9875  def __repr__(self):
9876  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
9877  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
9878 
9879  def get_from(o):
9880  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
9881  get_from = staticmethod(get_from)
9882 
9883 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
9884 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
9885 
9886 class NonWaterPDBSelector(NonAlternativePDBSelector):
9887  """Proxy of C++ IMP::atom::NonWaterPDBSelector class"""
9888  __swig_setmethods__ = {}
9889  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9890  __setattr__ = lambda self, name, value: _swig_setattr(self, NonWaterPDBSelector, name, value)
9891  __swig_getmethods__ = {}
9892  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9893  __getattr__ = lambda self, name: _swig_getattr(self, NonWaterPDBSelector, name)
9894  __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
9895  __del__ = lambda self : None;
9896  def __init__(self, *args):
9897  """
9898  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
9899  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
9900  """
9901  this = _IMP_atom.new_NonWaterPDBSelector(*args)
9902  try: self.this.append(this)
9903  except: self.this = this
9904  def __str__(self):
9905  """__str__(NonWaterPDBSelector self) -> std::string"""
9906  return _IMP_atom.NonWaterPDBSelector___str__(self)
9907 
9908  def __repr__(self):
9909  """__repr__(NonWaterPDBSelector self) -> std::string"""
9910  return _IMP_atom.NonWaterPDBSelector___repr__(self)
9911 
9912  def get_from(o):
9913  return _object_cast_to_NonWaterPDBSelector(o)
9914  get_from = staticmethod(get_from)
9915 
9916 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
9917 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
9918 
9919 class PPDBSelector(NonAlternativePDBSelector):
9920  """Proxy of C++ IMP::atom::PPDBSelector class"""
9921  __swig_setmethods__ = {}
9922  for _s in [NonAlternativePDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9923  __setattr__ = lambda self, name, value: _swig_setattr(self, PPDBSelector, name, value)
9924  __swig_getmethods__ = {}
9925  for _s in [NonAlternativePDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9926  __getattr__ = lambda self, name: _swig_getattr(self, PPDBSelector, name)
9927  def __init__(self, *args):
9928  """
9929  __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
9930  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
9931  """
9932  this = _IMP_atom.new_PPDBSelector(*args)
9933  try: self.this.append(this)
9934  except: self.this = this
9935  __swig_destroy__ = _IMP_atom.delete_PPDBSelector
9936  __del__ = lambda self : None;
9937  def __str__(self):
9938  """__str__(PPDBSelector self) -> std::string"""
9939  return _IMP_atom.PPDBSelector___str__(self)
9940 
9941  def __repr__(self):
9942  """__repr__(PPDBSelector self) -> std::string"""
9943  return _IMP_atom.PPDBSelector___repr__(self)
9944 
9945  def get_from(o):
9946  return _object_cast_to_PPDBSelector(o)
9947  get_from = staticmethod(get_from)
9948 
9949 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
9950 PPDBSelector_swigregister(PPDBSelector)
9951 
9952 class AndPDBSelector(PDBSelector):
9953  """Proxy of C++ IMP::atom::AndPDBSelector class"""
9954  __swig_setmethods__ = {}
9955  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9956  __setattr__ = lambda self, name, value: _swig_setattr(self, AndPDBSelector, name, value)
9957  __swig_getmethods__ = {}
9958  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9959  __getattr__ = lambda self, name: _swig_getattr(self, AndPDBSelector, name)
9960  def get_version_info(self):
9961  """get_version_info(AndPDBSelector self) -> VersionInfo"""
9962  return _IMP_atom.AndPDBSelector_get_version_info(self)
9963 
9964  __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
9965  __del__ = lambda self : None;
9966  def __init__(self, *args):
9967  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
9968  this = _IMP_atom.new_AndPDBSelector(*args)
9969  try: self.this.append(this)
9970  except: self.this = this
9971  def __str__(self):
9972  """__str__(AndPDBSelector self) -> std::string"""
9973  return _IMP_atom.AndPDBSelector___str__(self)
9974 
9975  def __repr__(self):
9976  """__repr__(AndPDBSelector self) -> std::string"""
9977  return _IMP_atom.AndPDBSelector___repr__(self)
9978 
9979  def get_from(o):
9980  return _object_cast_to_AndPDBSelector(o)
9981  get_from = staticmethod(get_from)
9982 
9983 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
9984 AndPDBSelector_swigregister(AndPDBSelector)
9985 
9986 class OrPDBSelector(PDBSelector):
9987  """Proxy of C++ IMP::atom::OrPDBSelector class"""
9988  __swig_setmethods__ = {}
9989  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
9990  __setattr__ = lambda self, name, value: _swig_setattr(self, OrPDBSelector, name, value)
9991  __swig_getmethods__ = {}
9992  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
9993  __getattr__ = lambda self, name: _swig_getattr(self, OrPDBSelector, name)
9994  def get_version_info(self):
9995  """get_version_info(OrPDBSelector self) -> VersionInfo"""
9996  return _IMP_atom.OrPDBSelector_get_version_info(self)
9997 
9998  __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
9999  __del__ = lambda self : None;
10000  def __init__(self, *args):
10001  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
10002  this = _IMP_atom.new_OrPDBSelector(*args)
10003  try: self.this.append(this)
10004  except: self.this = this
10005  def __str__(self):
10006  """__str__(OrPDBSelector self) -> std::string"""
10007  return _IMP_atom.OrPDBSelector___str__(self)
10008 
10009  def __repr__(self):
10010  """__repr__(OrPDBSelector self) -> std::string"""
10011  return _IMP_atom.OrPDBSelector___repr__(self)
10012 
10013  def get_from(o):
10014  return _object_cast_to_OrPDBSelector(o)
10015  get_from = staticmethod(get_from)
10016 
10017 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
10018 OrPDBSelector_swigregister(OrPDBSelector)
10019 
10020 class NotPDBSelector(PDBSelector):
10021  """Proxy of C++ IMP::atom::NotPDBSelector class"""
10022  __swig_setmethods__ = {}
10023  for _s in [PDBSelector]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10024  __setattr__ = lambda self, name, value: _swig_setattr(self, NotPDBSelector, name, value)
10025  __swig_getmethods__ = {}
10026  for _s in [PDBSelector]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10027  __getattr__ = lambda self, name: _swig_getattr(self, NotPDBSelector, name)
10028  def get_version_info(self):
10029  """get_version_info(NotPDBSelector self) -> VersionInfo"""
10030  return _IMP_atom.NotPDBSelector_get_version_info(self)
10031 
10032  __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
10033  __del__ = lambda self : None;
10034  def __init__(self, *args):
10035  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
10036  this = _IMP_atom.new_NotPDBSelector(*args)
10037  try: self.this.append(this)
10038  except: self.this = this
10039  def __str__(self):
10040  """__str__(NotPDBSelector self) -> std::string"""
10041  return _IMP_atom.NotPDBSelector___str__(self)
10042 
10043  def __repr__(self):
10044  """__repr__(NotPDBSelector self) -> std::string"""
10045  return _IMP_atom.NotPDBSelector___repr__(self)
10046 
10047  def get_from(o):
10048  return _object_cast_to_NotPDBSelector(o)
10049  get_from = staticmethod(get_from)
10050 
10051 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
10052 NotPDBSelector_swigregister(NotPDBSelector)
10053 
10054 
10055 def read_pdb(*args):
10056  """
10057  read_pdb(TextInput input, Model model) -> Hierarchy
10058  read_pdb(TextInput input, int model, Hierarchy h)
10059  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True,
10060  bool no_radii=False) -> Hierarchy
10061  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
10062  read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
10063  """
10064  return _IMP_atom.read_pdb(*args)
10065 
10066 def read_multimodel_pdb(*args):
10067  """
10068  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
10069  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
10070  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
10071  """
10072  return _IMP_atom.read_multimodel_pdb(*args)
10073 
10074 def write_pdb(*args):
10075  """
10076  write_pdb(Selection mhd, TextOutput out, unsigned int model=0)
10077  write_pdb(Selection mhd, TextOutput out)
10078  """
10079  return _IMP_atom.write_pdb(*args)
10080 
10081 def write_pdb_of_c_alphas(*args):
10082  """
10083  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=0)
10084  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
10085  """
10086  return _IMP_atom.write_pdb_of_c_alphas(*args)
10087 
10088 def write_multimodel_pdb(*args):
10089  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
10090  return _IMP_atom.write_multimodel_pdb(*args)
10091 
10092 def get_pdb_string(*args):
10093  """
10094  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10095  char res_icode=' ', double occpancy=1.00, double tempFactor=0.00,
10096  IMP::atom::Element e=C) -> std::string
10097  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10098  char res_icode=' ', double occpancy=1.00, double tempFactor=0.00) -> std::string
10099  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10100  char res_icode=' ', double occpancy=1.00) -> std::string
10101  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1,
10102  char res_icode=' ') -> std::string
10103  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ', int res_index=1) -> std::string
10104  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA, char chain=' ') -> std::string
10105  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C, ResidueType rt=ALA) -> std::string
10106  get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_C) -> std::string
10107  get_pdb_string(Vector3D v, int index=-1) -> std::string
10108  get_pdb_string(Vector3D v) -> std::string
10109  """
10110  return _IMP_atom.get_pdb_string(*args)
10111 
10112 def get_pdb_conect_record_string(*args):
10113  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
10114  return _IMP_atom.get_pdb_conect_record_string(*args)
10115 class WritePDBOptimizerState(IMP.kernel.OptimizerState):
10116  """Proxy of C++ IMP::atom::WritePDBOptimizerState class"""
10117  __swig_setmethods__ = {}
10118  for _s in [IMP.kernel.OptimizerState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
10119  __setattr__ = lambda self, name, value: _swig_setattr(self, WritePDBOptimizerState, name, value)
10120  __swig_getmethods__ = {}
10121  for _s in [IMP.kernel.OptimizerState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
10122  __getattr__ = lambda self, name: _swig_getattr(self, WritePDBOptimizerState, name)
10123  def __init__(self, *args):
10124  """__init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const & mh, std::string file_name) -> WritePDBOptimizerState"""
10125  this = _IMP_atom.new_WritePDBOptimizerState(*args)
10126  try: self.this.append(this)
10127  except: self.this = this
10128  def set_skip_steps(self, *args):
10129  """set_skip_steps(WritePDBOptimizerState self, unsigned int k)"""
10130  return _IMP_atom.WritePDBOptimizerState_set_skip_steps(self, *args)
10131 
10132  def set_period(self, *args):
10133  """set_period(WritePDBOptimizerState self, unsigned int p)"""
10134  return _IMP_atom.WritePDBOptimizerState_set_period(self, *args)
10135 
10136  def write(self, *args):
10137  """
10138  write(WritePDBOptimizerState self, std::string file_name, unsigned int call=0, bool append=False)
10139  write(WritePDBOptimizerState self, std::string file_name, unsigned int call=0)
10140  write(WritePDBOptimizerState self, std::string file_name)
10141  """
10142  return _IMP_atom.WritePDBOptimizerState_write(self, *args)
10143 
10144  def get_version_info(self):
10145  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
10146  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
10147 
10148  __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
10149  __del__ = lambda self : None;
10150  def __str__(self):
10151  """__str__(WritePDBOptimizerState self) -> std::string"""
10152  return _IMP_atom.WritePDBOptimizerState___str__(self)
10153 
10154  def __repr__(self):
10155  """__repr__(WritePDBOptimizerState self) -> std::string"""
10156  return _IMP_atom.WritePDBOptimizerState___repr__(self)
10157 
10158  def get_from(o):
10159  return _object_cast_to_WritePDBOptimizerState(o)
10160  get_from = staticmethod(get_from)
10161 
10162 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
10163 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
10164 
10165 
10166 def get_kt(*args):
10167  """get_kt(double T) -> double"""
10168  return _IMP_atom.get_kt(*args)
10169 
10170 def show_molecular_hierarchy(*args):
10171  """
10172  show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream
10173  show_molecular_hierarchy(Hierarchy h) -> _ostream
10174  """
10175  return _IMP_atom.show_molecular_hierarchy(*args)
10176 class CHARMMBond(_object):
10177  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class"""
10178  __swig_setmethods__ = {}
10179  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMBond, name, value)
10180  __swig_getmethods__ = {}
10181  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMBond, name)
10182  __repr__ = _swig_repr
10183  def __init__(self, *args):
10184  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
10185  this = _IMP_atom.new_CHARMMBond(*args)
10186  try: self.this.append(this)
10187  except: self.this = this
10188  def get_endpoint(self, *args):
10189  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
10190  return _IMP_atom.CHARMMBond_get_endpoint(self, *args)
10191 
10192  def get_contains_atom(self, *args):
10193  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
10194  return _IMP_atom.CHARMMBond_get_contains_atom(self, *args)
10195 
10196  def show(self, *args):
10197  """
10198  show(CHARMMBond self, _ostream out=std::cout)
10199  show(CHARMMBond self)
10200  """
10201  return _IMP_atom.CHARMMBond_show(self, *args)
10202 
10203  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
10204  __del__ = lambda self : None;
10205 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
10206 CHARMMBond_swigregister(CHARMMBond)
10207 
10208 class CHARMMAngle(_object):
10209  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class"""
10210  __swig_setmethods__ = {}
10211  __setattr__ = lambda self, name, value: _swig_setattr(self, CHARMMAngle, name, value)
10212  __swig_getmethods__ = {}
10213  __getattr__ = lambda self, name: _swig_getattr(self, CHARMMAngle, name)
10214  __repr__ = _swig_repr
10215  def __init__(self, *args):
10216  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
10217  this = _IMP_atom.new_CHARMMAngle(*args)
10218  try: self.this.append(this)
10219  except: self.this = this
10220  def get_endpoint(self, *args):
10221  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
10222  return _IMP_atom.CHARMMAngle_get_endpoint(self, *args)
10223 
10224  def get_contains_atom(self, *args):
10225  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
10226  return _IMP_atom.CHARMMAngle_get_contains_atom(self, *args)
10227 
10228  def show(self, *args):
10229  """
10230  show(CHARMMAngle self, _ostream out=std::cout)
10231  show(CHARMMAngle self)
10232  """
10233  return _IMP_atom.CHARMMAngle_show(self, *args)
10234 
10235  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
10236  __del__ = lambda self : None;
10237 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
10238 CHARMMAngle_swigregister(CHARMMAngle)
10239 
10240 
10241 def _get_rmsd_cpp(*args):
10242  """
10243  _get_rmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10244  Transformation3D tr_for_second=IMP::algebra::get_identity_transformation_3d()) -> double
10245  _get_rmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double
10246  """
10247  return _IMP_atom._get_rmsd_cpp(*args)
10248 
10249 def _get_native_overlap_cpp(*args):
10250  """
10251  _get_native_overlap_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10252  double threshold) -> double
10253  """
10254  return _IMP_atom._get_native_overlap_cpp(*args)
10255 
10256 def _get_drmsd_cpp(*args):
10257  """_get_drmsd_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
10258  return _IMP_atom._get_drmsd_cpp(*args)
10259 
10260 def _get_drms_cpp(*args):
10261  """_get_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
10262  return _IMP_atom._get_drms_cpp(*args)
10263 
10264 def _get_rigid_bodies_drms_cpp(*args):
10265  """
10266  _get_rigid_bodies_drms_cpp(IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::base::Vector< IMP::algebra::VectorD< 3 > > const & m2,
10267  IMP::IntRanges const & ranges) -> double
10268  """
10269  return _IMP_atom._get_rigid_bodies_drms_cpp(*args)
10270 def get_rmsd(a, b):
10271  va= [IMP.algebra.get_vector(x) for x in a]
10272  vb= [IMP.algebra.get_vector(x) for x in b]
10273  return _get_rmsd_cpp(va, vb)
10274 def get_native_overlap(a, b, d):
10275  va= [IMP.algebra.get_vector(x) for x in a]
10276  vb= [IMP.algebra.get_vector(x) for x in b]
10277  return _get_native_overlap_cpp(va, vb, d)
10278 
10279 def get_drmsd(a, b):
10280  va= [IMP.algebra.get_vector(x) for x in a]
10281  vb= [IMP.algebra.get_vector(x) for x in b]
10282  return _get_drmsd_cpp(va, vb)
10283 
10284 def get_drms(a, b):
10285  va= [IMP.algebra.get_vector(x) for x in a]
10286  vb= [IMP.algebra.get_vector(x) for x in b]
10287  return _get_drms_cpp(va, vb)
10288 
10289 def get_rigid_bodies_drms(a, b, ranges):
10290  va= [IMP.algebra.get_vector(x) for x in a]
10291  vb= [IMP.algebra.get_vector(x) for x in b]
10292  #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
10293  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
10294 
10295 
10296 
10297 def get_module_version():
10298  """get_module_version() -> std::string const"""
10299  return _IMP_atom.get_module_version()
10300 
10301 def get_example_path(*args):
10302  """get_example_path(std::string fname) -> std::string"""
10303  return _IMP_atom.get_example_path(*args)
10304 
10305 def get_data_path(*args):
10306  """get_data_path(std::string fname) -> std::string"""
10307  return _IMP_atom.get_data_path(*args)
10308 import _version_check
10309 _version_check.check_version(get_module_version())
10310 
10311 # This file is compatible with both classic and new-style classes.
10312 
10313