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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
atom/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.7
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2016 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info
16 if version_info >= (2, 6, 0):
17  def swig_import_helper():
18  from os.path import dirname
19  import imp
20  fp = None
21  try:
22  fp, pathname, description = imp.find_module('_IMP_atom', [dirname(__file__)])
23  except ImportError:
24  import _IMP_atom
25  return _IMP_atom
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_atom', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_atom = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_atom
36 del version_info
37 try:
38  _swig_property = property
39 except NameError:
40  pass # Python < 2.2 doesn't have 'property'.
41 
42 
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44  if (name == "thisown"):
45  return self.this.own(value)
46  if (name == "this"):
47  if type(value).__name__ == 'SwigPyObject':
48  self.__dict__[name] = value
49  return
50  method = class_type.__swig_setmethods__.get(name, None)
51  if method:
52  return method(self, value)
53  if (not static):
54  object.__setattr__(self, name, value)
55  else:
56  raise AttributeError("You cannot add attributes to %s" % self)
57 
58 
59 def _swig_setattr(self, class_type, name, value):
60  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
61 
62 
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64  if (name == "thisown"):
65  return self.this.own()
66  method = class_type.__swig_getmethods__.get(name, None)
67  if method:
68  return method(self)
69  if (not static):
70  return object.__getattr__(self, name)
71  else:
72  raise AttributeError(name)
73 
74 def _swig_getattr(self, class_type, name):
75  return _swig_getattr_nondynamic(self, class_type, name, 0)
76 
77 
78 def _swig_repr(self):
79  try:
80  strthis = "proxy of " + self.this.__repr__()
81  except:
82  strthis = ""
83  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
84 
85 try:
86  _object = object
87  _newclass = 1
88 except AttributeError:
89  class _object:
90  pass
91  _newclass = 0
92 
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_ATOM_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class"""
115  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
116 
117  def __init__(self, *args, **kwargs):
118  raise AttributeError("No constructor defined - class is abstract")
119  __repr__ = _swig_repr
120  __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
121  __del__ = lambda self: None
122 
123  def value(self):
124  """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
125  return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
131  incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
132  """
133  return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
139  decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
140  """
141  return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
142 
143 
144  def distance(self, x):
145  """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
146  return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
147 
148 
149  def equal(self, x):
150  """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
151  return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
156  return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
161  return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
166  return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
171  return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
172 
173 
174  def advance(self, n):
175  """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
176  return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
181  return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
186  return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
187 
188 
189  def __iadd__(self, n):
190  """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
191  return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
192 
193 
194  def __isub__(self, n):
195  """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
196  return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
197 
198 
199  def __add__(self, n):
200  """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
201  return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
207  __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
214 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
215 
216 
217 _value_types=[]
218 _object_types=[]
219 _raii_types=[]
220 _plural_types=[]
221 
222 
223 _IMP_atom.IMP_DEBUG_swigconstant(_IMP_atom)
224 IMP_DEBUG = _IMP_atom.IMP_DEBUG
225 
226 _IMP_atom.IMP_RELEASE_swigconstant(_IMP_atom)
227 IMP_RELEASE = _IMP_atom.IMP_RELEASE
228 
229 _IMP_atom.IMP_SILENT_swigconstant(_IMP_atom)
230 IMP_SILENT = _IMP_atom.IMP_SILENT
231 
232 _IMP_atom.IMP_PROGRESS_swigconstant(_IMP_atom)
233 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
234 
235 _IMP_atom.IMP_TERSE_swigconstant(_IMP_atom)
236 IMP_TERSE = _IMP_atom.IMP_TERSE
237 
238 _IMP_atom.IMP_VERBOSE_swigconstant(_IMP_atom)
239 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
240 
241 _IMP_atom.IMP_MEMORY_swigconstant(_IMP_atom)
242 IMP_MEMORY = _IMP_atom.IMP_MEMORY
243 
244 _IMP_atom.IMP_NONE_swigconstant(_IMP_atom)
245 IMP_NONE = _IMP_atom.IMP_NONE
246 
247 _IMP_atom.IMP_USAGE_swigconstant(_IMP_atom)
248 IMP_USAGE = _IMP_atom.IMP_USAGE
249 
250 _IMP_atom.IMP_INTERNAL_swigconstant(_IMP_atom)
251 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
252 
253 _IMP_atom.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_atom)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
255 
256 _IMP_atom.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_atom)
257 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
258 
259 _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_atom)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
261 
262 _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_atom)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR
264 
265 _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
267 
268 _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_atom)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
270 
271 _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_atom)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
273 
274 _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_atom)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
276 
277 _IMP_atom.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_atom)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
279 
280 import sys
281 class _DirectorObjects(object):
282  """@internal Simple class to keep references to director objects
283  to prevent premature deletion."""
284  def __init__(self):
285  self._objects = []
286  def register(self, obj):
287  """Take a reference to a director object; will only work for
288  refcounted C++ classes"""
289  if hasattr(obj, 'get_ref_count'):
290  self._objects.append(obj)
291  def cleanup(self):
292  """Only drop our reference and allow cleanup by Python if no other
293  Python references exist (we hold 3 references: one in self._objects,
294  one in x, and one in the argument list for getrefcount) *and* no
295  other C++ references exist (the Python object always holds one)"""
296  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
297  or x.get_ref_count() > 1]
298 # Do in two steps so the references are kept until the end of the
299 # function (deleting references may trigger a fresh call to this method)
300  self._objects = objs
301  def get_object_count(self):
302  """Get number of director objects (useful for testing only)"""
303  return len(self._objects)
304 _director_objects = _DirectorObjects()
305 
306 class _ostream(object):
307  """Proxy of C++ std::ostream class"""
308  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
309 
310  def __init__(self, *args, **kwargs):
311  raise AttributeError("No constructor defined")
312  __repr__ = _swig_repr
313 
314  def write(self, osa_buf):
315  """write(_ostream self, char const * osa_buf)"""
316  return _IMP_atom._ostream_write(self, osa_buf)
317 
318 _ostream_swigregister = _IMP_atom._ostream_swigregister
319 _ostream_swigregister(_ostream)
320 
321 
322 _IMP_atom.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_atom)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
324 
325 _IMP_atom.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_atom)
326 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
327 
328 _IMP_atom.IMP_HAS_NOEXCEPT_swigconstant(_IMP_atom)
329 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
330 import IMP
331 
332 _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
333 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
334 
335 _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
336 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
337 
338 _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
339 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
340 
341 _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
342 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
343 
344 _IMP_atom.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_atom)
345 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
346 import IMP.cgal
347 
348 _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_atom)
349 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
350 
351 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
352 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
353 
354 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
355 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
356 
357 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
358 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
359 
360 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
361 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
362 
363 _IMP_atom.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_atom)
364 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
365 
366 _IMP_atom.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_atom)
367 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
368 
369 _IMP_atom.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_atom)
370 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
371 import IMP.algebra
372 
373 _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_atom)
374 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
375 
376 _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
377 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
378 
379 _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
380 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
381 
382 _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
383 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
384 
385 _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
386 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
387 
388 _IMP_atom.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_atom)
389 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
390 
391 _IMP_atom.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_atom)
392 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
393 import IMP.display
394 
395 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_atom)
396 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
397 
398 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
399 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
400 
401 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
402 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
403 
404 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
405 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
406 
407 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
408 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
409 
410 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_atom)
411 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
412 
413 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_atom)
414 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
415 
416 _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_atom)
417 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
418 import IMP.score_functor
419 
420 _IMP_atom.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_atom)
421 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
422 
423 _IMP_atom.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
424 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
425 
426 _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
427 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
428 
429 _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
430 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
431 
432 _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
433 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
434 
435 _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
436 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
437 
438 _IMP_atom.IMP_CORE_HAS_CGAL_swigconstant(_IMP_atom)
439 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
440 
441 _IMP_atom.IMP_CORE_HAS_HDF5_swigconstant(_IMP_atom)
442 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
443 
444 _IMP_atom.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_atom)
445 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
446 import IMP.core
447 
448 _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_atom)
449 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
450 
451 _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_atom)
452 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
453 
454 _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_atom)
455 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
456 
457 _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
458 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
459 
460 _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_atom)
461 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
462 
463 _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
464 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
465 
466 _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
467 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
468 
469 _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
470 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
471 
472 _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
473 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
474 
475 _IMP_atom.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_atom)
476 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
477 
478 _IMP_atom.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_atom)
479 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
480 
481 _IMP_atom.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_atom)
482 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
483 import IMP.container
484 
485 _IMP_atom.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_atom)
486 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
487 
488 _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
489 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
490 
491 _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_atom)
492 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
493 
494 _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
495 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
496 
497 _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
498 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
499 
500 _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_atom)
501 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
502 
503 _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
504 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
505 
506 _IMP_atom.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_atom)
507 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
508 
509 _IMP_atom.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_atom)
510 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
511 
512 _IMP_atom.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_atom)
513 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
514 
515 _IMP_atom.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_atom)
516 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
517 
518 _IMP_atom.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_atom)
519 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
520 
521 _IMP_atom.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_atom)
522 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
524  """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class"""
525  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
526  __repr__ = _swig_repr
527 
528  def __init__(self):
529  """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
530  this = _IMP_atom.new_HierarchyTree()
531  try:
532  self.this.append(this)
533  except:
534  self.this = this
535 
536  def get_graph(self):
537  """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
538  return _IMP_atom.HierarchyTree_get_graph(self)
539 
540 
541  def get_vertices(self):
542  """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
543  return _IMP_atom.HierarchyTree_get_vertices(self)
544 
545 
546  def get_vertex_name(self, i):
547  """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
548  return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
549 
550 
551  def get_in_neighbors(self, v):
552  """get_in_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
553  return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
554 
555 
556  def get_out_neighbors(self, v):
557  """get_out_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
558  return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
559 
560 
561  def show_graphviz(self, *args):
562  """
563  show_graphviz(HierarchyTree self, _ostream out)
564  show_graphviz(HierarchyTree self)
565  """
566  return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
567 
568 
569  def get_graphviz_string(self):
570  """get_graphviz_string(HierarchyTree self) -> std::string"""
571  return _IMP_atom.HierarchyTree_get_graphviz_string(self)
572 
573 
574  def add_edge(self, v0, v1):
575  """add_edge(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)"""
576  return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
577 
578 
579  def add_vertex(self, l):
580  """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
581  return _IMP_atom.HierarchyTree_add_vertex(self, l)
582 
583 
584  def remove_vertex(self, l):
585  """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
586  return _IMP_atom.HierarchyTree_remove_vertex(self, l)
587 
588  __swig_destroy__ = _IMP_atom.delete_HierarchyTree
589  __del__ = lambda self: None
590 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
591 HierarchyTree_swigregister(HierarchyTree)
592 
593 
594 _value_types.append("HierarchyTree")
595 
596 
597 _object_types.append("PDBSelector")
598 
599 
600 def _object_cast_to_PDBSelector(o):
601  """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
602  return _IMP_atom._object_cast_to_PDBSelector(o)
603 
604 def Angles(l=[]):
605  return [Angle(x) for x in l]
606 _plural_types.append("Angles")
607 
608 
609 _value_types.append("Angle")
610 
611 
612 def Atoms(l=[]):
613  return [Atom(x) for x in l]
614 _plural_types.append("Atoms")
615 
616 
617 _value_types.append("Atom")
618 
619 
620 def Bonds(l=[]):
621  return [Bond(x) for x in l]
622 _plural_types.append("Bonds")
623 
624 
625 _value_types.append("Bond")
626 
627 
628 def Bondeds(l=[]):
629  return [Bonded(x) for x in l]
630 _plural_types.append("Bondeds")
631 
632 
633 _value_types.append("Bonded")
634 
635 
636 def CHARMMAtomList(l=[]):
637  return [CHARMMAtom(x) for x in l]
638 _plural_types.append("CHARMMAtomList")
639 
640 
641 _value_types.append("CHARMMAtom")
642 
643 
644 def Chains(l=[]):
645  return [Chain(x) for x in l]
646 _plural_types.append("Chains")
647 
648 
649 _value_types.append("Chain")
650 
651 
652 def CenterOfMasses(l=[]):
653  return [CenterOfMass(x) for x in l]
654 _plural_types.append("CenterOfMasses")
655 
656 
657 _value_types.append("CenterOfMass")
658 
659 
660 def Chargeds(l=[]):
661  return [Charged(x) for x in l]
662 _plural_types.append("Chargeds")
663 
664 
665 _value_types.append("Charged")
666 
667 
668 def Diffusions(l=[]):
669  return [Diffusion(x) for x in l]
670 _plural_types.append("Diffusions")
671 
672 
673 _value_types.append("Diffusion")
674 
675 
676 def RigidBodyDiffusions(l=[]):
677  return [RigidBodyDiffusion(x) for x in l]
678 _plural_types.append("RigidBodyDiffusions")
679 
680 
681 _value_types.append("RigidBodyDiffusion")
682 
683 
684 def TAMDParticles(l=[]):
685  return [TAMDParticle(x) for x in l]
686 _plural_types.append("TAMDParticles")
687 
688 
689 _value_types.append("TAMDParticle")
690 
691 
692 def TAMDCentroids(l=[]):
693  return [TAMDCentroid(x) for x in l]
694 _plural_types.append("TAMDCentroids")
695 
696 
697 _value_types.append("TAMDCentroid")
698 
699 
700 def Dihedrals(l=[]):
701  return [Dihedral(x) for x in l]
702 _plural_types.append("Dihedrals")
703 
704 
705 _value_types.append("Dihedral")
706 
707 
708 def Domains(l=[]):
709  return [Domain(x) for x in l]
710 _plural_types.append("Domains")
711 
712 
713 _value_types.append("Domain")
714 
715 
716 def Fragments(l=[]):
717  return [Fragment(x) for x in l]
718 _plural_types.append("Fragments")
719 
720 
721 _value_types.append("Fragment")
722 
723 
724 def Hierarchies(l=[]):
725  return [Hierarchy(x) for x in l]
726 _plural_types.append("Hierarchies")
727 
728 
729 _value_types.append("Hierarchy")
730 
731 
732 def LennardJonesList(l=[]):
733  return [LennardJones(x) for x in l]
734 _plural_types.append("LennardJonesList")
735 
736 
737 _value_types.append("LennardJones")
738 
739 
740 def Masses(l=[]):
741  return [Mass(x) for x in l]
742 _plural_types.append("Masses")
743 
744 
745 _value_types.append("Mass")
746 
747 
748 def LinearVelocities(l=[]):
749  return [LinearVelocity(x) for x in l]
750 _plural_types.append("LinearVelocities")
751 
752 
753 _value_types.append("LinearVelocity")
754 
755 
756 def AngularVelocities(l=[]):
757  return [AngularVelocity(x) for x in l]
758 _plural_types.append("AngularVelocities")
759 
760 
761 _value_types.append("AngularVelocity")
762 
763 
764 def Molecules(l=[]):
765  return [Molecule(x) for x in l]
766 _plural_types.append("Molecules")
767 
768 
769 _value_types.append("Molecule")
770 
771 
772 def Residues(l=[]):
773  return [Residue(x) for x in l]
774 _plural_types.append("Residues")
775 
776 
777 _value_types.append("Residue")
778 
779 
780 def Representations(l=[]):
781  return [Representation(x) for x in l]
782 _plural_types.append("Representations")
783 
784 
785 _value_types.append("Representation")
786 
787 
788 def States(l=[]):
789  return [State(x) for x in l]
790 _plural_types.append("States")
791 
792 
793 _value_types.append("State")
794 
795 
796 def Copies(l=[]):
797  return [Copy(x) for x in l]
798 _plural_types.append("Copies")
799 
800 
801 _value_types.append("Copy")
802 
803 
804 def SecondaryStructureResidues(l=[]):
805  return [SecondaryStructureResidue(x) for x in l]
806 _plural_types.append("SecondaryStructureResidues")
807 
808 
809 _value_types.append("SecondaryStructureResidue")
810 
811 
812 def StructureSources(l=[]):
813  return [StructureSource(x) for x in l]
814 _plural_types.append("StructureSources")
815 
816 
817 _value_types.append("StructureSource")
818 
819 
820 _object_types.append("Simulator")
821 
822 
823 def _object_cast_to_Simulator(o):
824  """_object_cast_to_Simulator(Object o) -> Simulator"""
825  return _IMP_atom._object_cast_to_Simulator(o)
826 
827 _object_types.append("ATOMPDBSelector")
828 
829 
830 def _object_cast_to_ATOMPDBSelector(o):
831  """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
832  return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
833 
834 _object_types.append("AllMol2Selector")
835 
836 
837 def _object_cast_to_AllMol2Selector(o):
838  """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
839  return _IMP_atom._object_cast_to_AllMol2Selector(o)
840 
841 _object_types.append("AllPDBSelector")
842 
843 
844 def _object_cast_to_AllPDBSelector(o):
845  """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
846  return _IMP_atom._object_cast_to_AllPDBSelector(o)
847 
848 _object_types.append("AndPDBSelector")
849 
850 
851 def _object_cast_to_AndPDBSelector(o):
852  """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
853  return _IMP_atom._object_cast_to_AndPDBSelector(o)
854 
855 _object_types.append("XorPDBSelector")
856 
857 
858 def _object_cast_to_XorPDBSelector(o):
859  """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
860  return _IMP_atom._object_cast_to_XorPDBSelector(o)
861 
862 _object_types.append("ResidueTypePDBSelector")
863 
864 
865 def _object_cast_to_ResidueTypePDBSelector(o):
866  """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
867  return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
868 
869 _object_types.append("AtomTypePDBSelector")
870 
871 
872 def _object_cast_to_AtomTypePDBSelector(o):
873  """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
874  return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
875 
876 _object_types.append("AngleSingletonScore")
877 
878 
879 def _object_cast_to_AngleSingletonScore(o):
880  """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
881  return _IMP_atom._object_cast_to_AngleSingletonScore(o)
882 
883 _object_types.append("BondEndpointsRefiner")
884 
885 
886 def _object_cast_to_BondEndpointsRefiner(o):
887  """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
888  return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
889 
890 _object_types.append("BondPairContainer")
891 
892 
893 def _object_cast_to_BondPairContainer(o):
894  """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
895  return _IMP_atom._object_cast_to_BondPairContainer(o)
896 
897 _object_types.append("BondSingletonScore")
898 
899 
900 def _object_cast_to_BondSingletonScore(o):
901  """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
902  return _IMP_atom._object_cast_to_BondSingletonScore(o)
903 
904 _object_types.append("BondedPairFilter")
905 
906 
907 def _object_cast_to_BondedPairFilter(o):
908  """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
909  return _IMP_atom._object_cast_to_BondedPairFilter(o)
910 
911 _object_types.append("BrownianDynamics")
912 
913 
914 def _object_cast_to_BrownianDynamics(o):
915  """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
916  return _IMP_atom._object_cast_to_BrownianDynamics(o)
917 
918 _object_types.append("BrownianDynamicsTAMD")
919 
920 
921 def _object_cast_to_BrownianDynamicsTAMD(o):
922  """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
923  return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
924 
925 _object_types.append("CAlphaPDBSelector")
926 
927 
928 def _object_cast_to_CAlphaPDBSelector(o):
929  """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
930  return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
931 
932 _object_types.append("CBetaPDBSelector")
933 
934 
935 def _object_cast_to_CBetaPDBSelector(o):
936  """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
937  return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
938 
939 _object_types.append("BackbonePDBSelector")
940 
941 
942 def _object_cast_to_BackbonePDBSelector(o):
943  """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
944  return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
945 
946 _object_types.append("CHARMMParameters")
947 
948 
949 def _object_cast_to_CHARMMParameters(o):
950  """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
951  return _IMP_atom._object_cast_to_CHARMMParameters(o)
952 
953 _object_types.append("CHARMMResidueTopology")
954 
955 
956 def _object_cast_to_CHARMMResidueTopology(o):
957  """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
958  return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
959 
960 _object_types.append("CHARMMSegmentTopology")
961 
962 
963 def _object_cast_to_CHARMMSegmentTopology(o):
964  """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
965  return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
966 
967 _object_types.append("CHARMMStereochemistryRestraint")
968 
969 
970 def _object_cast_to_CHARMMStereochemistryRestraint(o):
971  """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
972  return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
973 
974 _object_types.append("CHARMMTopology")
975 
976 
977 def _object_cast_to_CHARMMTopology(o):
978  """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
979  return _IMP_atom._object_cast_to_CHARMMTopology(o)
980 
981 _object_types.append("CPDBSelector")
982 
983 
984 def _object_cast_to_CPDBSelector(o):
985  """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
986  return _IMP_atom._object_cast_to_CPDBSelector(o)
987 
988 _object_types.append("ChainPDBSelector")
989 
990 
991 def _object_cast_to_ChainPDBSelector(o):
992  """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
993  return _IMP_atom._object_cast_to_ChainPDBSelector(o)
994 
995 _object_types.append("CoulombPairScore")
996 
997 
998 def _object_cast_to_CoulombPairScore(o):
999  """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
1000  return _IMP_atom._object_cast_to_CoulombPairScore(o)
1001 
1002 _object_types.append("CoverBond")
1003 
1004 
1005 def _object_cast_to_CoverBond(o):
1006  """_object_cast_to_CoverBond(Object o) -> CoverBond"""
1007  return _IMP_atom._object_cast_to_CoverBond(o)
1008 
1009 _object_types.append("DihedralSingletonScore")
1010 
1011 
1012 def _object_cast_to_DihedralSingletonScore(o):
1013  """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
1014  return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
1015 
1016 _object_types.append("DopePairScore")
1017 
1018 
1019 def _object_cast_to_DopePairScore(o):
1020  """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
1021  return _IMP_atom._object_cast_to_DopePairScore(o)
1022 
1023 _object_types.append("OrientedSoapPairScore")
1024 
1025 
1026 def _object_cast_to_OrientedSoapPairScore(o):
1027  """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
1028  return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
1029 
1030 _object_types.append("EzRestraint")
1031 
1032 
1033 def _object_cast_to_EzRestraint(o):
1034  """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
1035  return _IMP_atom._object_cast_to_EzRestraint(o)
1036 
1037 _object_types.append("ForceFieldParameters")
1038 
1039 
1040 def _object_cast_to_ForceFieldParameters(o):
1041  """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
1042  return _IMP_atom._object_cast_to_ForceFieldParameters(o)
1043 
1044 _object_types.append("ForceSwitch")
1045 
1046 
1047 def _object_cast_to_ForceSwitch(o):
1048  """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
1049  return _IMP_atom._object_cast_to_ForceSwitch(o)
1050 
1051 _object_types.append("HydrogenPDBSelector")
1052 
1053 
1054 def _object_cast_to_HydrogenPDBSelector(o):
1055  """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
1056  return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
1057 
1058 _object_types.append("ImproperSingletonScore")
1059 
1060 
1061 def _object_cast_to_ImproperSingletonScore(o):
1062  """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
1063  return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
1064 
1065 _object_types.append("LennardJonesPairScore")
1066 
1067 
1068 def _object_cast_to_LennardJonesPairScore(o):
1069  """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
1070  return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
1071 
1072 _object_types.append("Mol2Selector")
1073 
1074 
1075 def _object_cast_to_Mol2Selector(o):
1076  """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
1077  return _IMP_atom._object_cast_to_Mol2Selector(o)
1078 
1079 _object_types.append("MolecularDynamics")
1080 
1081 
1082 def _object_cast_to_MolecularDynamics(o):
1083  """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
1084  return _IMP_atom._object_cast_to_MolecularDynamics(o)
1085 
1086 _object_types.append("NPDBSelector")
1087 
1088 
1089 def _object_cast_to_NPDBSelector(o):
1090  """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
1091  return _IMP_atom._object_cast_to_NPDBSelector(o)
1092 
1093 _object_types.append("NonAlternativePDBSelector")
1094 
1095 
1096 def _object_cast_to_NonAlternativePDBSelector(o):
1097  """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
1098  return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
1099 
1100 _object_types.append("NonHydrogenMol2Selector")
1101 
1102 
1103 def _object_cast_to_NonHydrogenMol2Selector(o):
1104  """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
1105  return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
1106 
1107 _object_types.append("NonWaterNonHydrogenPDBSelector")
1108 
1109 
1110 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
1111  """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
1112  return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
1113 
1114 _object_types.append("NonWaterPDBSelector")
1115 
1116 
1117 def _object_cast_to_NonWaterPDBSelector(o):
1118  """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
1119  return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
1120 
1121 _object_types.append("NotPDBSelector")
1122 
1123 
1124 def _object_cast_to_NotPDBSelector(o):
1125  """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1126  return _IMP_atom._object_cast_to_NotPDBSelector(o)
1127 
1128 _object_types.append("OrPDBSelector")
1129 
1130 
1131 def _object_cast_to_OrPDBSelector(o):
1132  """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1133  return _IMP_atom._object_cast_to_OrPDBSelector(o)
1134 
1135 _object_types.append("PPDBSelector")
1136 
1137 
1138 def _object_cast_to_PPDBSelector(o):
1139  """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1140  return _IMP_atom._object_cast_to_PPDBSelector(o)
1141 
1142 _object_types.append("ProteinLigandAtomPairScore")
1143 
1144 
1145 def _object_cast_to_ProteinLigandAtomPairScore(o):
1146  """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1147  return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1148 
1149 _object_types.append("ProteinLigandRestraint")
1150 
1151 
1152 def _object_cast_to_ProteinLigandRestraint(o):
1153  """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1154  return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1155 
1156 _object_types.append("SameResiduePairFilter")
1157 
1158 
1159 def _object_cast_to_SameResiduePairFilter(o):
1160  """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1161  return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1162 
1163 _object_types.append("SoapPairFilter")
1164 
1165 
1166 def _object_cast_to_SoapPairFilter(o):
1167  """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1168  return _IMP_atom._object_cast_to_SoapPairFilter(o)
1169 
1170 _object_types.append("SmoothingFunction")
1171 
1172 
1173 def _object_cast_to_SmoothingFunction(o):
1174  """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1175  return _IMP_atom._object_cast_to_SmoothingFunction(o)
1176 
1177 _object_types.append("StereochemistryPairFilter")
1178 
1179 
1180 def _object_cast_to_StereochemistryPairFilter(o):
1181  """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1182  return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1183 
1184 _object_types.append("VelocityScalingOptimizerState")
1185 
1186 
1187 def _object_cast_to_VelocityScalingOptimizerState(o):
1188  """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1189  return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1190 
1191 _object_types.append("WaterPDBSelector")
1192 
1193 
1194 def _object_cast_to_WaterPDBSelector(o):
1195  """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1196  return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1197 
1198 _object_types.append("WritePDBOptimizerState")
1199 
1200 
1201 def _object_cast_to_WritePDBOptimizerState(o):
1202  """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1203  return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1204 
1205 AtomTypes=list
1206 _plural_types.append("AtomTypes")
1207 _value_types.append("AtomType")
1208 
1209 
1210 CHARMMAtomTopologies=list
1211 _plural_types.append("CHARMMAtomTopologies")
1212 _value_types.append("CHARMMAtomTopology")
1213 
1214 
1215 CHARMMBondEndpoints=list
1216 _plural_types.append("CHARMMBondEndpoints")
1217 _value_types.append("CHARMMBondEndpoint")
1218 
1219 
1220 CHARMMBondParametersList=list
1221 _plural_types.append("CHARMMBondParametersList")
1222 _value_types.append("CHARMMBondParameters")
1223 
1224 
1225 CHARMMDihedralParametersList=list
1226 _plural_types.append("CHARMMDihedralParametersList")
1227 _value_types.append("CHARMMDihedralParameters")
1228 
1229 
1230 _object_types.append("CHARMMIdealResidueTopology")
1231 
1232 
1233 def _object_cast_to_CHARMMIdealResidueTopology(o):
1234  """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1235  return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1236 
1237 CHARMMInternalCoordinates=list
1238 _plural_types.append("CHARMMInternalCoordinates")
1239 _value_types.append("CHARMMInternalCoordinate")
1240 
1241 
1242 _object_types.append("CHARMMPatch")
1243 
1244 
1245 def _object_cast_to_CHARMMPatch(o):
1246  """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1247  return _IMP_atom._object_cast_to_CHARMMPatch(o)
1248 
1249 _object_types.append("CHARMMResidueTopologyBase")
1250 
1251 
1252 def _object_cast_to_CHARMMResidueTopologyBase(o):
1253  """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1254  return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1255 
1256 ResidueTypes=list
1257 _plural_types.append("ResidueTypes")
1258 _value_types.append("ResidueType")
1259 
1260 
1261 Selections=list
1262 _plural_types.append("Selections")
1263 _value_types.append("Selection")
1264 
1265 
1266 _object_types.append("RemoveRigidMotionOptimizerState")
1267 
1268 
1269 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1270  """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1271  return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1272 
1273 _object_types.append("BerendsenThermostatOptimizerState")
1274 
1275 
1276 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1277  """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1278  return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1279 
1280 _object_types.append("LangevinThermostatOptimizerState")
1281 
1282 
1283 def _object_cast_to_LangevinThermostatOptimizerState(o):
1284  """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1285  return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1286 
1287 _object_types.append("SelectionGeometry")
1288 
1289 
1290 def _object_cast_to_SelectionGeometry(o):
1291  """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1292  return _IMP_atom._object_cast_to_SelectionGeometry(o)
1293 
1294 _object_types.append("HierarchyGeometry")
1295 
1296 
1297 def _object_cast_to_HierarchyGeometry(o):
1298  """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1299  return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1300 
1301 _object_types.append("HierarchiesGeometry")
1302 
1303 
1304 def _object_cast_to_HierarchiesGeometry(o):
1305  """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1306  return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1307 
1308 _object_types.append("BondGeometry")
1309 
1310 
1311 def _object_cast_to_BondGeometry(o):
1312  """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1313  return _IMP_atom._object_cast_to_BondGeometry(o)
1314 
1315 _object_types.append("BondsGeometry")
1316 
1317 
1318 def _object_cast_to_BondsGeometry(o):
1319  """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1320  return _IMP_atom._object_cast_to_BondsGeometry(o)
1321 
1322 _object_types.append("CAAngleRestraint")
1323 
1324 
1325 def _object_cast_to_CAAngleRestraint(o):
1326  """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1327  return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1328 
1329 _object_types.append("CADihedralRestraint")
1330 
1331 
1332 def _object_cast_to_CADihedralRestraint(o):
1333  """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1334  return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1335 
1336 CHARMMDihedrals=list
1337 _plural_types.append("CHARMMDihedrals")
1338 _value_types.append("CHARMMDihedral")
1339 
1340 
1341 CHARMMBonds=list
1342 _plural_types.append("CHARMMBonds")
1343 _value_types.append("CHARMMBond")
1344 
1345 
1346 CHARMMAngles=list
1347 _plural_types.append("CHARMMAngles")
1348 _value_types.append("CHARMMAngle")
1349 
1350 class Bond(IMP.Decorator):
1351  """Proxy of C++ IMP::atom::Bond class"""
1352  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1353 
1354  def __init__(self, *args):
1355  """
1356  __init__(IMP::atom::Bond self) -> Bond
1357  __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1358  __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1359  """
1360  this = _IMP_atom.new_Bond(*args)
1361  try:
1362  self.this.append(this)
1363  except:
1364  self.this = this
1365 
1366  def show(self, *args):
1367  """
1368  show(Bond self, _ostream out)
1369  show(Bond self)
1370  """
1371  return _IMP_atom.Bond_show(self, *args)
1372 
1373 
1374  def get_is_setup(*args):
1375  """
1376  get_is_setup(_ParticleAdaptor p) -> bool
1377  get_is_setup(Model m, ParticleIndex pi) -> bool
1378  """
1379  return _IMP_atom.Bond_get_is_setup(*args)
1380 
1381  get_is_setup = staticmethod(get_is_setup)
1382  UNKNOWN = _IMP_atom.Bond_UNKNOWN
1383  NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1384  SINGLE = _IMP_atom.Bond_SINGLE
1385  DOUBLE = _IMP_atom.Bond_DOUBLE
1386  TRIPLE = _IMP_atom.Bond_TRIPLE
1387  HYDROGEN = _IMP_atom.Bond_HYDROGEN
1388  SALT = _IMP_atom.Bond_SALT
1389  PEPTIDE = _IMP_atom.Bond_PEPTIDE
1390  AMIDE = _IMP_atom.Bond_AMIDE
1391  AROMATIC = _IMP_atom.Bond_AROMATIC
1392 
1393  def get_bonded(self, i):
1394  """get_bonded(Bond self, unsigned int i) -> Bonded"""
1395  return _IMP_atom.Bond_get_bonded(self, i)
1396 
1397 
1398  def get_type(self):
1399  """get_type(Bond self) -> IMP::Int"""
1400  return _IMP_atom.Bond_get_type(self)
1401 
1402 
1403  def set_type(self, t):
1404  """set_type(Bond self, IMP::Int t)"""
1405  return _IMP_atom.Bond_set_type(self, t)
1406 
1407 
1408  def get_order(self):
1409  """get_order(Bond self) -> IMP::Int"""
1410  return _IMP_atom.Bond_get_order(self)
1411 
1412 
1413  def set_order(self, t):
1414  """set_order(Bond self, IMP::Int t)"""
1415  return _IMP_atom.Bond_set_order(self, t)
1416 
1417 
1418  def get_length(self):
1419  """get_length(Bond self) -> IMP::Float"""
1420  return _IMP_atom.Bond_get_length(self)
1421 
1422 
1423  def set_length(self, t):
1424  """set_length(Bond self, IMP::Float t)"""
1425  return _IMP_atom.Bond_set_length(self, t)
1426 
1427 
1428  def get_stiffness(self):
1429  """get_stiffness(Bond self) -> IMP::Float"""
1430  return _IMP_atom.Bond_get_stiffness(self)
1431 
1432 
1433  def set_stiffness(self, t):
1434  """set_stiffness(Bond self, IMP::Float t)"""
1435  return _IMP_atom.Bond_set_stiffness(self, t)
1436 
1437 
1438  def get_length_key():
1439  """get_length_key() -> FloatKey"""
1440  return _IMP_atom.Bond_get_length_key()
1441 
1442  get_length_key = staticmethod(get_length_key)
1443 
1444  def add_attribute(self, *args):
1445  """
1446  add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1447  add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1448  add_attribute(Bond self, IntKey a0, IMP::Int a1)
1449  add_attribute(Bond self, StringKey a0, IMP::String a1)
1450  add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1451  add_attribute(Bond self, ObjectKey a0, Object a1)
1452  """
1453  return _IMP_atom.Bond_add_attribute(self, *args)
1454 
1455 
1456  def get_value(self, *args):
1457  """
1458  get_value(Bond self, FloatKey a0) -> IMP::Float
1459  get_value(Bond self, IntKey a0) -> IMP::Int
1460  get_value(Bond self, StringKey a0) -> IMP::String
1461  get_value(Bond self, ParticleIndexKey a0) -> Particle
1462  get_value(Bond self, ObjectKey a0) -> Object
1463  """
1464  return _IMP_atom.Bond_get_value(self, *args)
1465 
1466 
1467  def set_value(self, *args):
1468  """
1469  set_value(Bond self, FloatKey a0, IMP::Float a1)
1470  set_value(Bond self, IntKey a0, IMP::Int a1)
1471  set_value(Bond self, StringKey a0, IMP::String a1)
1472  set_value(Bond self, ParticleIndexKey a0, Particle a1)
1473  set_value(Bond self, ObjectKey a0, Object a1)
1474  """
1475  return _IMP_atom.Bond_set_value(self, *args)
1476 
1477 
1478  def remove_attribute(self, *args):
1479  """
1480  remove_attribute(Bond self, FloatKey a0)
1481  remove_attribute(Bond self, IntKey a0)
1482  remove_attribute(Bond self, StringKey a0)
1483  remove_attribute(Bond self, ParticleIndexKey a0)
1484  remove_attribute(Bond self, ObjectKey a0)
1485  """
1486  return _IMP_atom.Bond_remove_attribute(self, *args)
1487 
1488 
1489  def has_attribute(self, *args):
1490  """
1491  has_attribute(Bond self, FloatKey a0) -> bool
1492  has_attribute(Bond self, IntKey a0) -> bool
1493  has_attribute(Bond self, StringKey a0) -> bool
1494  has_attribute(Bond self, ParticleIndexKey a0) -> bool
1495  has_attribute(Bond self, ObjectKey a0) -> bool
1496  """
1497  return _IMP_atom.Bond_has_attribute(self, *args)
1498 
1499 
1500  def get_derivative(self, a0):
1501  """get_derivative(Bond self, FloatKey a0) -> double"""
1502  return _IMP_atom.Bond_get_derivative(self, a0)
1503 
1504 
1505  def get_name(self):
1506  """get_name(Bond self) -> std::string"""
1507  return _IMP_atom.Bond_get_name(self)
1508 
1509 
1510  def clear_caches(self):
1511  """clear_caches(Bond self)"""
1512  return _IMP_atom.Bond_clear_caches(self)
1513 
1514 
1515  def set_name(self, a0):
1516  """set_name(Bond self, std::string a0)"""
1517  return _IMP_atom.Bond_set_name(self, a0)
1518 
1519 
1520  def set_check_level(self, a0):
1521  """set_check_level(Bond self, IMP::CheckLevel a0)"""
1522  return _IMP_atom.Bond_set_check_level(self, a0)
1523 
1524 
1525  def add_to_derivative(self, a0, a1, a2):
1526  """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1527  return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1528 
1529 
1530  def set_is_optimized(self, a0, a1):
1531  """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1532  return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1533 
1534 
1535  def get_is_optimized(self, a0):
1536  """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1537  return _IMP_atom.Bond_get_is_optimized(self, a0)
1538 
1539 
1540  def get_check_level(self):
1541  """get_check_level(Bond self) -> IMP::CheckLevel"""
1542  return _IMP_atom.Bond_get_check_level(self)
1543 
1544 
1545  def __eq__(self, *args):
1546  """
1547  __eq__(Bond self, Bond o) -> bool
1548  __eq__(Bond self, Particle d) -> bool
1549  """
1550  return _IMP_atom.Bond___eq__(self, *args)
1551 
1552 
1553  def __ne__(self, *args):
1554  """
1555  __ne__(Bond self, Bond o) -> bool
1556  __ne__(Bond self, Particle d) -> bool
1557  """
1558  return _IMP_atom.Bond___ne__(self, *args)
1559 
1560 
1561  def __le__(self, *args):
1562  """
1563  __le__(Bond self, Bond o) -> bool
1564  __le__(Bond self, Particle d) -> bool
1565  """
1566  return _IMP_atom.Bond___le__(self, *args)
1567 
1568 
1569  def __lt__(self, *args):
1570  """
1571  __lt__(Bond self, Bond o) -> bool
1572  __lt__(Bond self, Particle d) -> bool
1573  """
1574  return _IMP_atom.Bond___lt__(self, *args)
1575 
1576 
1577  def __ge__(self, *args):
1578  """
1579  __ge__(Bond self, Bond o) -> bool
1580  __ge__(Bond self, Particle d) -> bool
1581  """
1582  return _IMP_atom.Bond___ge__(self, *args)
1583 
1584 
1585  def __gt__(self, *args):
1586  """
1587  __gt__(Bond self, Bond o) -> bool
1588  __gt__(Bond self, Particle d) -> bool
1589  """
1590  return _IMP_atom.Bond___gt__(self, *args)
1591 
1592 
1593  def __hash__(self):
1594  """__hash__(Bond self) -> std::size_t"""
1595  return _IMP_atom.Bond___hash__(self)
1596 
1597 
1598  def __str__(self):
1599  """__str__(Bond self) -> std::string"""
1600  return _IMP_atom.Bond___str__(self)
1601 
1602 
1603  def __repr__(self):
1604  """__repr__(Bond self) -> std::string"""
1605  return _IMP_atom.Bond___repr__(self)
1606 
1607  __swig_destroy__ = _IMP_atom.delete_Bond
1608  __del__ = lambda self: None
1609 Bond_swigregister = _IMP_atom.Bond_swigregister
1610 Bond_swigregister(Bond)
1611 
1612 def Bond_get_is_setup(*args):
1613  """
1614  get_is_setup(_ParticleAdaptor p) -> bool
1615  Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1616  """
1617  return _IMP_atom.Bond_get_is_setup(*args)
1618 
1619 def Bond_get_length_key():
1620  """Bond_get_length_key() -> FloatKey"""
1621  return _IMP_atom.Bond_get_length_key()
1622 
1623 class Bonded(IMP.Decorator):
1624  """Proxy of C++ IMP::atom::Bonded class"""
1625  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1626 
1627  def __init__(self, *args):
1628  """
1629  __init__(IMP::atom::Bonded self) -> Bonded
1630  __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1631  __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1632  """
1633  this = _IMP_atom.new_Bonded(*args)
1634  try:
1635  self.this.append(this)
1636  except:
1637  self.this = this
1638 
1639  def show(self, *args):
1640  """
1641  show(Bonded self, _ostream out)
1642  show(Bonded self)
1643  """
1644  return _IMP_atom.Bonded_show(self, *args)
1645 
1646 
1647  def setup_particle(*args):
1648  """
1649  setup_particle(Model m, ParticleIndex pi) -> Bonded
1650  setup_particle(_ParticleAdaptor decorator) -> Bonded
1651  """
1652  return _IMP_atom.Bonded_setup_particle(*args)
1653 
1654  setup_particle = staticmethod(setup_particle)
1655 
1656  def get_is_setup(*args):
1657  """
1658  get_is_setup(_ParticleAdaptor p) -> bool
1659  get_is_setup(Model m, ParticleIndex pi) -> bool
1660  """
1661  return _IMP_atom.Bonded_get_is_setup(*args)
1662 
1663  get_is_setup = staticmethod(get_is_setup)
1664 
1665  def get_number_of_bonds(self):
1666  """get_number_of_bonds(Bonded self) -> unsigned int"""
1667  return _IMP_atom.Bonded_get_number_of_bonds(self)
1668 
1669 
1670  def get_bond_indexes(self):
1671  """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1672  return _IMP_atom.Bonded_get_bond_indexes(self)
1673 
1674 
1675  def get_bond(self, i):
1676  """get_bond(Bonded self, unsigned int i) -> Bond"""
1677  return _IMP_atom.Bonded_get_bond(self, i)
1678 
1679 
1680  def get_bonded(self, i):
1681  """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1682  return _IMP_atom.Bonded_get_bonded(self, i)
1683 
1684 
1685  def add_attribute(self, *args):
1686  """
1687  add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1688  add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1689  add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1690  add_attribute(Bonded self, StringKey a0, IMP::String a1)
1691  add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1692  add_attribute(Bonded self, ObjectKey a0, Object a1)
1693  """
1694  return _IMP_atom.Bonded_add_attribute(self, *args)
1695 
1696 
1697  def get_value(self, *args):
1698  """
1699  get_value(Bonded self, FloatKey a0) -> IMP::Float
1700  get_value(Bonded self, IntKey a0) -> IMP::Int
1701  get_value(Bonded self, StringKey a0) -> IMP::String
1702  get_value(Bonded self, ParticleIndexKey a0) -> Particle
1703  get_value(Bonded self, ObjectKey a0) -> Object
1704  """
1705  return _IMP_atom.Bonded_get_value(self, *args)
1706 
1707 
1708  def set_value(self, *args):
1709  """
1710  set_value(Bonded self, FloatKey a0, IMP::Float a1)
1711  set_value(Bonded self, IntKey a0, IMP::Int a1)
1712  set_value(Bonded self, StringKey a0, IMP::String a1)
1713  set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1714  set_value(Bonded self, ObjectKey a0, Object a1)
1715  """
1716  return _IMP_atom.Bonded_set_value(self, *args)
1717 
1718 
1719  def remove_attribute(self, *args):
1720  """
1721  remove_attribute(Bonded self, FloatKey a0)
1722  remove_attribute(Bonded self, IntKey a0)
1723  remove_attribute(Bonded self, StringKey a0)
1724  remove_attribute(Bonded self, ParticleIndexKey a0)
1725  remove_attribute(Bonded self, ObjectKey a0)
1726  """
1727  return _IMP_atom.Bonded_remove_attribute(self, *args)
1728 
1729 
1730  def has_attribute(self, *args):
1731  """
1732  has_attribute(Bonded self, FloatKey a0) -> bool
1733  has_attribute(Bonded self, IntKey a0) -> bool
1734  has_attribute(Bonded self, StringKey a0) -> bool
1735  has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1736  has_attribute(Bonded self, ObjectKey a0) -> bool
1737  """
1738  return _IMP_atom.Bonded_has_attribute(self, *args)
1739 
1740 
1741  def get_derivative(self, a0):
1742  """get_derivative(Bonded self, FloatKey a0) -> double"""
1743  return _IMP_atom.Bonded_get_derivative(self, a0)
1744 
1745 
1746  def get_name(self):
1747  """get_name(Bonded self) -> std::string"""
1748  return _IMP_atom.Bonded_get_name(self)
1749 
1750 
1751  def clear_caches(self):
1752  """clear_caches(Bonded self)"""
1753  return _IMP_atom.Bonded_clear_caches(self)
1754 
1755 
1756  def set_name(self, a0):
1757  """set_name(Bonded self, std::string a0)"""
1758  return _IMP_atom.Bonded_set_name(self, a0)
1759 
1760 
1761  def set_check_level(self, a0):
1762  """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1763  return _IMP_atom.Bonded_set_check_level(self, a0)
1764 
1765 
1766  def add_to_derivative(self, a0, a1, a2):
1767  """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1768  return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1769 
1770 
1771  def set_is_optimized(self, a0, a1):
1772  """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1773  return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1774 
1775 
1776  def get_is_optimized(self, a0):
1777  """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1778  return _IMP_atom.Bonded_get_is_optimized(self, a0)
1779 
1780 
1781  def get_check_level(self):
1782  """get_check_level(Bonded self) -> IMP::CheckLevel"""
1783  return _IMP_atom.Bonded_get_check_level(self)
1784 
1785 
1786  def __eq__(self, *args):
1787  """
1788  __eq__(Bonded self, Bonded o) -> bool
1789  __eq__(Bonded self, Particle d) -> bool
1790  """
1791  return _IMP_atom.Bonded___eq__(self, *args)
1792 
1793 
1794  def __ne__(self, *args):
1795  """
1796  __ne__(Bonded self, Bonded o) -> bool
1797  __ne__(Bonded self, Particle d) -> bool
1798  """
1799  return _IMP_atom.Bonded___ne__(self, *args)
1800 
1801 
1802  def __le__(self, *args):
1803  """
1804  __le__(Bonded self, Bonded o) -> bool
1805  __le__(Bonded self, Particle d) -> bool
1806  """
1807  return _IMP_atom.Bonded___le__(self, *args)
1808 
1809 
1810  def __lt__(self, *args):
1811  """
1812  __lt__(Bonded self, Bonded o) -> bool
1813  __lt__(Bonded self, Particle d) -> bool
1814  """
1815  return _IMP_atom.Bonded___lt__(self, *args)
1816 
1817 
1818  def __ge__(self, *args):
1819  """
1820  __ge__(Bonded self, Bonded o) -> bool
1821  __ge__(Bonded self, Particle d) -> bool
1822  """
1823  return _IMP_atom.Bonded___ge__(self, *args)
1824 
1825 
1826  def __gt__(self, *args):
1827  """
1828  __gt__(Bonded self, Bonded o) -> bool
1829  __gt__(Bonded self, Particle d) -> bool
1830  """
1831  return _IMP_atom.Bonded___gt__(self, *args)
1832 
1833 
1834  def __hash__(self):
1835  """__hash__(Bonded self) -> std::size_t"""
1836  return _IMP_atom.Bonded___hash__(self)
1837 
1838 
1839  def __str__(self):
1840  """__str__(Bonded self) -> std::string"""
1841  return _IMP_atom.Bonded___str__(self)
1842 
1843 
1844  def __repr__(self):
1845  """__repr__(Bonded self) -> std::string"""
1846  return _IMP_atom.Bonded___repr__(self)
1847 
1848  __swig_destroy__ = _IMP_atom.delete_Bonded
1849  __del__ = lambda self: None
1850 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1851 Bonded_swigregister(Bonded)
1852 
1853 def Bonded_setup_particle(*args):
1854  """
1855  setup_particle(Model m, ParticleIndex pi) -> Bonded
1856  Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1857  """
1858  return _IMP_atom.Bonded_setup_particle(*args)
1859 
1860 def Bonded_get_is_setup(*args):
1861  """
1862  get_is_setup(_ParticleAdaptor p) -> bool
1863  Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1864  """
1865  return _IMP_atom.Bonded_get_is_setup(*args)
1866 
1867 
1868 def create_custom_bond(a, b, length, stiffness=-1):
1869  """
1870  create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1871  create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1872  """
1873  return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1874 
1875 def create_bond(*args):
1876  """
1877  create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1878  create_bond(Bonded a, Bonded b, Bond o) -> Bond
1879  """
1880  return _IMP_atom.create_bond(*args)
1881 
1882 def destroy_bond(b):
1883  """destroy_bond(Bond b)"""
1884  return _IMP_atom.destroy_bond(b)
1885 
1886 def get_bond(a, b):
1887  """get_bond(Bonded a, Bonded b) -> Bond"""
1888  return _IMP_atom.get_bond(a, b)
1889 class BondGeometry(IMP.display.SingletonGeometry):
1890  """Proxy of C++ IMP::atom::BondGeometry class"""
1891  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1892 
1893  def __init__(self, *args):
1894  """
1895  __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1896  __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1897  """
1898  this = _IMP_atom.new_BondGeometry(*args)
1899  try:
1900  self.this.append(this)
1901  except:
1902  self.this = this
1903 
1904  def get_version_info(self):
1905  """get_version_info(BondGeometry self) -> VersionInfo"""
1906  return _IMP_atom.BondGeometry_get_version_info(self)
1907 
1908 
1909  def __str__(self):
1910  """__str__(BondGeometry self) -> std::string"""
1911  return _IMP_atom.BondGeometry___str__(self)
1912 
1913 
1914  def __repr__(self):
1915  """__repr__(BondGeometry self) -> std::string"""
1916  return _IMP_atom.BondGeometry___repr__(self)
1917 
1918 
1919  @staticmethod
1920  def get_from(o):
1921  return _object_cast_to_BondGeometry(o)
1922 
1923 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1924 BondGeometry_swigregister(BondGeometry)
1925 
1926 class BondsGeometry(IMP.display.SingletonsGeometry):
1927  """Proxy of C++ IMP::atom::BondsGeometry class"""
1928  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1929 
1930  def __init__(self, sc):
1931  """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1932  this = _IMP_atom.new_BondsGeometry(sc)
1933  try:
1934  self.this.append(this)
1935  except:
1936  self.this = this
1937 
1938  def get_version_info(self):
1939  """get_version_info(BondsGeometry self) -> VersionInfo"""
1940  return _IMP_atom.BondsGeometry_get_version_info(self)
1941 
1942 
1943  def __str__(self):
1944  """__str__(BondsGeometry self) -> std::string"""
1945  return _IMP_atom.BondsGeometry___str__(self)
1946 
1947 
1948  def __repr__(self):
1949  """__repr__(BondsGeometry self) -> std::string"""
1950  return _IMP_atom.BondsGeometry___repr__(self)
1951 
1952 
1953  @staticmethod
1954  def get_from(o):
1955  return _object_cast_to_BondsGeometry(o)
1956 
1957 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1958 BondsGeometry_swigregister(BondsGeometry)
1959 
1960 class Hierarchy(IMP.core.Hierarchy):
1961  """Proxy of C++ IMP::atom::Hierarchy class"""
1962  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1963 
1964  def __init__(self, *args):
1965  """
1966  __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1967  __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1968  __init__(IMP::atom::Hierarchy self) -> Hierarchy
1969  __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1970  """
1971  this = _IMP_atom.new_Hierarchy(*args)
1972  try:
1973  self.this.append(this)
1974  except:
1975  self.this = this
1976 
1977  def setup_particle(*args):
1978  """
1979  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1980  setup_particle(Particle p) -> Hierarchy
1981  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1982  setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1983  """
1984  return _IMP_atom.Hierarchy_setup_particle(*args)
1985 
1986  setup_particle = staticmethod(setup_particle)
1987 
1988  def get_is_setup(*args):
1989  """
1990  get_is_setup(Particle p) -> bool
1991  get_is_setup(Model m, ParticleIndex p) -> bool
1992  """
1993  return _IMP_atom.Hierarchy_get_is_setup(*args)
1994 
1995  get_is_setup = staticmethod(get_is_setup)
1996 
1997  def get_is_valid(self, print_info=False):
1998  """
1999  get_is_valid(Hierarchy self, bool print_info=False) -> bool
2000  get_is_valid(Hierarchy self) -> bool
2001  """
2002  return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
2003 
2004 
2005  def add_child(self, o):
2006  """add_child(Hierarchy self, Hierarchy o)"""
2007  return _IMP_atom.Hierarchy_add_child(self, o)
2008 
2009 
2010  def get_child(self, i):
2011  """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
2012  return _IMP_atom.Hierarchy_get_child(self, i)
2013 
2014 
2015  def get_children(self):
2016  """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
2017  return _IMP_atom.Hierarchy_get_children(self)
2018 
2019 
2020  def get_parent(self):
2021  """get_parent(Hierarchy self) -> Hierarchy"""
2022  return _IMP_atom.Hierarchy_get_parent(self)
2023 
2024 
2025  def get_as_atom(self):
2026  """get_as_atom(Hierarchy self) -> Atom"""
2027  return _IMP_atom.Hierarchy_get_as_atom(self)
2028 
2029 
2030  def get_as_residue(self):
2031  """get_as_residue(Hierarchy self) -> Residue"""
2032  return _IMP_atom.Hierarchy_get_as_residue(self)
2033 
2034 
2035  def get_as_chain(self):
2036  """get_as_chain(Hierarchy self) -> Chain"""
2037  return _IMP_atom.Hierarchy_get_as_chain(self)
2038 
2039 
2040  def get_as_molecule(self):
2041  """get_as_molecule(Hierarchy self) -> Molecule"""
2042  return _IMP_atom.Hierarchy_get_as_molecule(self)
2043 
2044 
2045  def get_as_domain(self):
2046  """get_as_domain(Hierarchy self) -> Domain"""
2047  return _IMP_atom.Hierarchy_get_as_domain(self)
2048 
2049 
2050  def get_as_fragment(self):
2051  """get_as_fragment(Hierarchy self) -> Fragment"""
2052  return _IMP_atom.Hierarchy_get_as_fragment(self)
2053 
2054 
2055  def get_as_xyz(self):
2056  """get_as_xyz(Hierarchy self) -> XYZ"""
2057  return _IMP_atom.Hierarchy_get_as_xyz(self)
2058 
2059 
2060  def get_as_xyzr(self):
2061  """get_as_xyzr(Hierarchy self) -> XYZR"""
2062  return _IMP_atom.Hierarchy_get_as_xyzr(self)
2063 
2064 
2065  def get_as_mass(self):
2066  """get_as_mass(Hierarchy self) -> Mass"""
2067  return _IMP_atom.Hierarchy_get_as_mass(self)
2068 
2069 
2070  def get_as_state(self):
2071  """get_as_state(Hierarchy self) -> State"""
2072  return _IMP_atom.Hierarchy_get_as_state(self)
2073 
2074 
2075  def get_traits():
2076  """get_traits() -> HierarchyTraits"""
2077  return _IMP_atom.Hierarchy_get_traits()
2078 
2079  get_traits = staticmethod(get_traits)
2080 
2081  def show(self, *args):
2082  """
2083  show(Hierarchy self, _ostream out, std::string delimiter)
2084  show(Hierarchy self, _ostream out)
2085  show(Hierarchy self)
2086  """
2087  return _IMP_atom.Hierarchy_show(self, *args)
2088 
2089 
2090  def add_attribute(self, *args):
2091  """
2092  add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
2093  add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
2094  add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
2095  add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
2096  add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
2097  add_attribute(Hierarchy self, ObjectKey a0, Object a1)
2098  """
2099  return _IMP_atom.Hierarchy_add_attribute(self, *args)
2100 
2101 
2102  def get_value(self, *args):
2103  """
2104  get_value(Hierarchy self, FloatKey a0) -> IMP::Float
2105  get_value(Hierarchy self, IntKey a0) -> IMP::Int
2106  get_value(Hierarchy self, StringKey a0) -> IMP::String
2107  get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
2108  get_value(Hierarchy self, ObjectKey a0) -> Object
2109  """
2110  return _IMP_atom.Hierarchy_get_value(self, *args)
2111 
2112 
2113  def set_value(self, *args):
2114  """
2115  set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
2116  set_value(Hierarchy self, IntKey a0, IMP::Int a1)
2117  set_value(Hierarchy self, StringKey a0, IMP::String a1)
2118  set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
2119  set_value(Hierarchy self, ObjectKey a0, Object a1)
2120  """
2121  return _IMP_atom.Hierarchy_set_value(self, *args)
2122 
2123 
2124  def remove_attribute(self, *args):
2125  """
2126  remove_attribute(Hierarchy self, FloatKey a0)
2127  remove_attribute(Hierarchy self, IntKey a0)
2128  remove_attribute(Hierarchy self, StringKey a0)
2129  remove_attribute(Hierarchy self, ParticleIndexKey a0)
2130  remove_attribute(Hierarchy self, ObjectKey a0)
2131  """
2132  return _IMP_atom.Hierarchy_remove_attribute(self, *args)
2133 
2134 
2135  def has_attribute(self, *args):
2136  """
2137  has_attribute(Hierarchy self, FloatKey a0) -> bool
2138  has_attribute(Hierarchy self, IntKey a0) -> bool
2139  has_attribute(Hierarchy self, StringKey a0) -> bool
2140  has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2141  has_attribute(Hierarchy self, ObjectKey a0) -> bool
2142  """
2143  return _IMP_atom.Hierarchy_has_attribute(self, *args)
2144 
2145 
2146  def get_derivative(self, a0):
2147  """get_derivative(Hierarchy self, FloatKey a0) -> double"""
2148  return _IMP_atom.Hierarchy_get_derivative(self, a0)
2149 
2150 
2151  def get_name(self):
2152  """get_name(Hierarchy self) -> std::string"""
2153  return _IMP_atom.Hierarchy_get_name(self)
2154 
2155 
2156  def clear_caches(self):
2157  """clear_caches(Hierarchy self)"""
2158  return _IMP_atom.Hierarchy_clear_caches(self)
2159 
2160 
2161  def set_name(self, a0):
2162  """set_name(Hierarchy self, std::string a0)"""
2163  return _IMP_atom.Hierarchy_set_name(self, a0)
2164 
2165 
2166  def set_check_level(self, a0):
2167  """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2168  return _IMP_atom.Hierarchy_set_check_level(self, a0)
2169 
2170 
2171  def add_to_derivative(self, a0, a1, a2):
2172  """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2173  return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2174 
2175 
2176  def set_is_optimized(self, a0, a1):
2177  """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2178  return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2179 
2180 
2181  def get_is_optimized(self, a0):
2182  """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2183  return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2184 
2185 
2186  def get_check_level(self):
2187  """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2188  return _IMP_atom.Hierarchy_get_check_level(self)
2189 
2190 
2191  def __eq__(self, *args):
2192  """
2193  __eq__(Hierarchy self, Hierarchy o) -> bool
2194  __eq__(Hierarchy self, Particle d) -> bool
2195  """
2196  return _IMP_atom.Hierarchy___eq__(self, *args)
2197 
2198 
2199  def __ne__(self, *args):
2200  """
2201  __ne__(Hierarchy self, Hierarchy o) -> bool
2202  __ne__(Hierarchy self, Particle d) -> bool
2203  """
2204  return _IMP_atom.Hierarchy___ne__(self, *args)
2205 
2206 
2207  def __le__(self, *args):
2208  """
2209  __le__(Hierarchy self, Hierarchy o) -> bool
2210  __le__(Hierarchy self, Particle d) -> bool
2211  """
2212  return _IMP_atom.Hierarchy___le__(self, *args)
2213 
2214 
2215  def __lt__(self, *args):
2216  """
2217  __lt__(Hierarchy self, Hierarchy o) -> bool
2218  __lt__(Hierarchy self, Particle d) -> bool
2219  """
2220  return _IMP_atom.Hierarchy___lt__(self, *args)
2221 
2222 
2223  def __ge__(self, *args):
2224  """
2225  __ge__(Hierarchy self, Hierarchy o) -> bool
2226  __ge__(Hierarchy self, Particle d) -> bool
2227  """
2228  return _IMP_atom.Hierarchy___ge__(self, *args)
2229 
2230 
2231  def __gt__(self, *args):
2232  """
2233  __gt__(Hierarchy self, Hierarchy o) -> bool
2234  __gt__(Hierarchy self, Particle d) -> bool
2235  """
2236  return _IMP_atom.Hierarchy___gt__(self, *args)
2237 
2238 
2239  def __hash__(self):
2240  """__hash__(Hierarchy self) -> std::size_t"""
2241  return _IMP_atom.Hierarchy___hash__(self)
2242 
2243 
2244  def __str__(self):
2245  """__str__(Hierarchy self) -> std::string"""
2246  return _IMP_atom.Hierarchy___str__(self)
2247 
2248 
2249  def __repr__(self):
2250  """__repr__(Hierarchy self) -> std::string"""
2251  return _IMP_atom.Hierarchy___repr__(self)
2252 
2253  __swig_destroy__ = _IMP_atom.delete_Hierarchy
2254  __del__ = lambda self: None
2255 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2256 Hierarchy_swigregister(Hierarchy)
2257 
2258 def Hierarchy_setup_particle(*args):
2259  """
2260  setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2261  setup_particle(Particle p) -> Hierarchy
2262  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2263  Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2264  """
2265  return _IMP_atom.Hierarchy_setup_particle(*args)
2266 
2267 def Hierarchy_get_is_setup(*args):
2268  """
2269  get_is_setup(Particle p) -> bool
2270  Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2271  """
2272  return _IMP_atom.Hierarchy_get_is_setup(*args)
2273 
2274 def Hierarchy_get_traits():
2275  """Hierarchy_get_traits() -> HierarchyTraits"""
2276  return _IMP_atom.Hierarchy_get_traits()
2277 
2278 
2279 _IMP_atom.ATOM_TYPE_swigconstant(_IMP_atom)
2280 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2281 
2282 _IMP_atom.RESIDUE_TYPE_swigconstant(_IMP_atom)
2283 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2284 
2285 _IMP_atom.CHAIN_TYPE_swigconstant(_IMP_atom)
2286 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2287 
2288 _IMP_atom.MOLECULE_TYPE_swigconstant(_IMP_atom)
2289 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2290 
2291 _IMP_atom.DOMAIN_TYPE_swigconstant(_IMP_atom)
2292 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2293 
2294 _IMP_atom.FRAGMENT_TYPE_swigconstant(_IMP_atom)
2295 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2296 
2297 _IMP_atom.XYZ_TYPE_swigconstant(_IMP_atom)
2298 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2299 
2300 _IMP_atom.XYZR_TYPE_swigconstant(_IMP_atom)
2301 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2302 
2303 _IMP_atom.MASS_TYPE_swigconstant(_IMP_atom)
2304 MASS_TYPE = _IMP_atom.MASS_TYPE
2305 
2306 _IMP_atom.STATE_TYPE_swigconstant(_IMP_atom)
2307 STATE_TYPE = _IMP_atom.STATE_TYPE
2308 
2309 def get_by_type(mhd, t):
2310  """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2311  return _IMP_atom.get_by_type(mhd, t)
2312 
2313 def create_fragment(ps):
2314  """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2315  return _IMP_atom.create_fragment(ps)
2316 
2317 def get_internal_bonds(mhd):
2318  """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2319  return _IMP_atom.get_internal_bonds(mhd)
2320 
2321 def get_root(h):
2322  """get_root(Hierarchy h) -> Hierarchy"""
2323  return _IMP_atom.get_root(h)
2324 
2325 def show(*args):
2326  """
2327  show(Hierarchy h, _ostream out)
2328  show(Hierarchy h)
2329  """
2330  return _IMP_atom.show(*args)
2331 
2332 def create_rigid_body(*args):
2333  """
2334  create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2335  create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2336  create_rigid_body(Hierarchy h) -> RigidBody
2337  """
2338  return _IMP_atom.create_rigid_body(*args)
2339 
2340 def create_compatible_rigid_body(h, reference):
2341  """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2342  return _IMP_atom.create_compatible_rigid_body(h, reference)
2343 
2344 def setup_as_rigid_body(h):
2345  """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
2346  return _IMP_atom.setup_as_rigid_body(h)
2347 
2348 def get_is_heterogen(h):
2349  """get_is_heterogen(Hierarchy h) -> bool"""
2350  return _IMP_atom.get_is_heterogen(h)
2351 
2352 def create_clone(d):
2353  """create_clone(Hierarchy d) -> Hierarchy"""
2354  return _IMP_atom.create_clone(d)
2355 
2356 def create_clone_one(d):
2357  """create_clone_one(Hierarchy d) -> Hierarchy"""
2358  return _IMP_atom.create_clone_one(d)
2359 
2360 def destroy(d):
2361  """destroy(Hierarchy d)"""
2362  return _IMP_atom.destroy(d)
2363 
2364 def get_bounding_box(h):
2365  """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2366  return _IMP_atom.get_bounding_box(h)
2367 
2368 def get_bounding_sphere(h):
2369  """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2370  return _IMP_atom.get_bounding_sphere(h)
2371 class Angle(IMP.Decorator):
2372  """Proxy of C++ IMP::atom::Angle class"""
2373  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2374 
2375  def __init__(self, *args):
2376  """
2377  __init__(IMP::atom::Angle self) -> Angle
2378  __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2379  __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2380  """
2381  this = _IMP_atom.new_Angle(*args)
2382  try:
2383  self.this.append(this)
2384  except:
2385  self.this = this
2386 
2387  def show(self, *args):
2388  """
2389  show(Angle self, _ostream out)
2390  show(Angle self)
2391  """
2392  return _IMP_atom.Angle_show(self, *args)
2393 
2394 
2395  def setup_particle(*args):
2396  """
2397  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2398  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2399  """
2400  return _IMP_atom.Angle_setup_particle(*args)
2401 
2402  setup_particle = staticmethod(setup_particle)
2403 
2404  def get_is_setup(*args):
2405  """
2406  get_is_setup(_ParticleAdaptor p) -> bool
2407  get_is_setup(Model m, ParticleIndex pi) -> bool
2408  """
2409  return _IMP_atom.Angle_get_is_setup(*args)
2410 
2411  get_is_setup = staticmethod(get_is_setup)
2412 
2413  def get_particle(self, *args):
2414  """
2415  get_particle(Angle self) -> Particle
2416  get_particle(Angle self, unsigned int i) -> Particle
2417  """
2418  return _IMP_atom.Angle_get_particle(self, *args)
2419 
2420 
2421  def get_ideal(self):
2422  """get_ideal(Angle self) -> IMP::Float"""
2423  return _IMP_atom.Angle_get_ideal(self)
2424 
2425 
2426  def set_ideal(self, t):
2427  """set_ideal(Angle self, IMP::Float t)"""
2428  return _IMP_atom.Angle_set_ideal(self, t)
2429 
2430 
2431  def get_stiffness(self):
2432  """get_stiffness(Angle self) -> IMP::Float"""
2433  return _IMP_atom.Angle_get_stiffness(self)
2434 
2435 
2436  def set_stiffness(self, t):
2437  """set_stiffness(Angle self, IMP::Float t)"""
2438  return _IMP_atom.Angle_set_stiffness(self, t)
2439 
2440 
2441  def get_particle_key(i):
2442  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2443  return _IMP_atom.Angle_get_particle_key(i)
2444 
2445  get_particle_key = staticmethod(get_particle_key)
2446 
2447  def get_ideal_key():
2448  """get_ideal_key() -> FloatKey"""
2449  return _IMP_atom.Angle_get_ideal_key()
2450 
2451  get_ideal_key = staticmethod(get_ideal_key)
2452 
2453  def get_stiffness_key():
2454  """get_stiffness_key() -> FloatKey"""
2455  return _IMP_atom.Angle_get_stiffness_key()
2456 
2457  get_stiffness_key = staticmethod(get_stiffness_key)
2458 
2459  def add_attribute(self, *args):
2460  """
2461  add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2462  add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2463  add_attribute(Angle self, IntKey a0, IMP::Int a1)
2464  add_attribute(Angle self, StringKey a0, IMP::String a1)
2465  add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2466  add_attribute(Angle self, ObjectKey a0, Object a1)
2467  """
2468  return _IMP_atom.Angle_add_attribute(self, *args)
2469 
2470 
2471  def get_value(self, *args):
2472  """
2473  get_value(Angle self, FloatKey a0) -> IMP::Float
2474  get_value(Angle self, IntKey a0) -> IMP::Int
2475  get_value(Angle self, StringKey a0) -> IMP::String
2476  get_value(Angle self, ParticleIndexKey a0) -> Particle
2477  get_value(Angle self, ObjectKey a0) -> Object
2478  """
2479  return _IMP_atom.Angle_get_value(self, *args)
2480 
2481 
2482  def set_value(self, *args):
2483  """
2484  set_value(Angle self, FloatKey a0, IMP::Float a1)
2485  set_value(Angle self, IntKey a0, IMP::Int a1)
2486  set_value(Angle self, StringKey a0, IMP::String a1)
2487  set_value(Angle self, ParticleIndexKey a0, Particle a1)
2488  set_value(Angle self, ObjectKey a0, Object a1)
2489  """
2490  return _IMP_atom.Angle_set_value(self, *args)
2491 
2492 
2493  def remove_attribute(self, *args):
2494  """
2495  remove_attribute(Angle self, FloatKey a0)
2496  remove_attribute(Angle self, IntKey a0)
2497  remove_attribute(Angle self, StringKey a0)
2498  remove_attribute(Angle self, ParticleIndexKey a0)
2499  remove_attribute(Angle self, ObjectKey a0)
2500  """
2501  return _IMP_atom.Angle_remove_attribute(self, *args)
2502 
2503 
2504  def has_attribute(self, *args):
2505  """
2506  has_attribute(Angle self, FloatKey a0) -> bool
2507  has_attribute(Angle self, IntKey a0) -> bool
2508  has_attribute(Angle self, StringKey a0) -> bool
2509  has_attribute(Angle self, ParticleIndexKey a0) -> bool
2510  has_attribute(Angle self, ObjectKey a0) -> bool
2511  """
2512  return _IMP_atom.Angle_has_attribute(self, *args)
2513 
2514 
2515  def get_derivative(self, a0):
2516  """get_derivative(Angle self, FloatKey a0) -> double"""
2517  return _IMP_atom.Angle_get_derivative(self, a0)
2518 
2519 
2520  def get_name(self):
2521  """get_name(Angle self) -> std::string"""
2522  return _IMP_atom.Angle_get_name(self)
2523 
2524 
2525  def clear_caches(self):
2526  """clear_caches(Angle self)"""
2527  return _IMP_atom.Angle_clear_caches(self)
2528 
2529 
2530  def set_name(self, a0):
2531  """set_name(Angle self, std::string a0)"""
2532  return _IMP_atom.Angle_set_name(self, a0)
2533 
2534 
2535  def set_check_level(self, a0):
2536  """set_check_level(Angle self, IMP::CheckLevel a0)"""
2537  return _IMP_atom.Angle_set_check_level(self, a0)
2538 
2539 
2540  def add_to_derivative(self, a0, a1, a2):
2541  """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2542  return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2543 
2544 
2545  def set_is_optimized(self, a0, a1):
2546  """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2547  return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2548 
2549 
2550  def get_is_optimized(self, a0):
2551  """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2552  return _IMP_atom.Angle_get_is_optimized(self, a0)
2553 
2554 
2555  def get_check_level(self):
2556  """get_check_level(Angle self) -> IMP::CheckLevel"""
2557  return _IMP_atom.Angle_get_check_level(self)
2558 
2559 
2560  def __eq__(self, *args):
2561  """
2562  __eq__(Angle self, Angle o) -> bool
2563  __eq__(Angle self, Particle d) -> bool
2564  """
2565  return _IMP_atom.Angle___eq__(self, *args)
2566 
2567 
2568  def __ne__(self, *args):
2569  """
2570  __ne__(Angle self, Angle o) -> bool
2571  __ne__(Angle self, Particle d) -> bool
2572  """
2573  return _IMP_atom.Angle___ne__(self, *args)
2574 
2575 
2576  def __le__(self, *args):
2577  """
2578  __le__(Angle self, Angle o) -> bool
2579  __le__(Angle self, Particle d) -> bool
2580  """
2581  return _IMP_atom.Angle___le__(self, *args)
2582 
2583 
2584  def __lt__(self, *args):
2585  """
2586  __lt__(Angle self, Angle o) -> bool
2587  __lt__(Angle self, Particle d) -> bool
2588  """
2589  return _IMP_atom.Angle___lt__(self, *args)
2590 
2591 
2592  def __ge__(self, *args):
2593  """
2594  __ge__(Angle self, Angle o) -> bool
2595  __ge__(Angle self, Particle d) -> bool
2596  """
2597  return _IMP_atom.Angle___ge__(self, *args)
2598 
2599 
2600  def __gt__(self, *args):
2601  """
2602  __gt__(Angle self, Angle o) -> bool
2603  __gt__(Angle self, Particle d) -> bool
2604  """
2605  return _IMP_atom.Angle___gt__(self, *args)
2606 
2607 
2608  def __hash__(self):
2609  """__hash__(Angle self) -> std::size_t"""
2610  return _IMP_atom.Angle___hash__(self)
2611 
2612 
2613  def __str__(self):
2614  """__str__(Angle self) -> std::string"""
2615  return _IMP_atom.Angle___str__(self)
2616 
2617 
2618  def __repr__(self):
2619  """__repr__(Angle self) -> std::string"""
2620  return _IMP_atom.Angle___repr__(self)
2621 
2622  __swig_destroy__ = _IMP_atom.delete_Angle
2623  __del__ = lambda self: None
2624 Angle_swigregister = _IMP_atom.Angle_swigregister
2625 Angle_swigregister(Angle)
2626 
2627 def Angle_setup_particle(*args):
2628  """
2629  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2630  Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2631  """
2632  return _IMP_atom.Angle_setup_particle(*args)
2633 
2634 def Angle_get_is_setup(*args):
2635  """
2636  get_is_setup(_ParticleAdaptor p) -> bool
2637  Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2638  """
2639  return _IMP_atom.Angle_get_is_setup(*args)
2640 
2641 def Angle_get_particle_key(i):
2642  """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2643  return _IMP_atom.Angle_get_particle_key(i)
2644 
2645 def Angle_get_ideal_key():
2646  """Angle_get_ideal_key() -> FloatKey"""
2647  return _IMP_atom.Angle_get_ideal_key()
2648 
2649 def Angle_get_stiffness_key():
2650  """Angle_get_stiffness_key() -> FloatKey"""
2651  return _IMP_atom.Angle_get_stiffness_key()
2652 
2653 class Dihedral(IMP.Decorator):
2654  """Proxy of C++ IMP::atom::Dihedral class"""
2655  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2656 
2657  def __init__(self, *args):
2658  """
2659  __init__(IMP::atom::Dihedral self) -> Dihedral
2660  __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2661  __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2662  """
2663  this = _IMP_atom.new_Dihedral(*args)
2664  try:
2665  self.this.append(this)
2666  except:
2667  self.this = this
2668 
2669  def show(self, *args):
2670  """
2671  show(Dihedral self, _ostream out)
2672  show(Dihedral self)
2673  """
2674  return _IMP_atom.Dihedral_show(self, *args)
2675 
2676 
2677  def setup_particle(*args):
2678  """
2679  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2680  setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2681  """
2682  return _IMP_atom.Dihedral_setup_particle(*args)
2683 
2684  setup_particle = staticmethod(setup_particle)
2685 
2686  def get_is_setup(*args):
2687  """
2688  get_is_setup(_ParticleAdaptor p) -> bool
2689  get_is_setup(Model m, ParticleIndex pi) -> bool
2690  """
2691  return _IMP_atom.Dihedral_get_is_setup(*args)
2692 
2693  get_is_setup = staticmethod(get_is_setup)
2694 
2695  def get_particle(self, *args):
2696  """
2697  get_particle(Dihedral self) -> Particle
2698  get_particle(Dihedral self, unsigned int i) -> Particle
2699  """
2700  return _IMP_atom.Dihedral_get_particle(self, *args)
2701 
2702 
2703  def get_ideal(self):
2704  """get_ideal(Dihedral self) -> IMP::Float"""
2705  return _IMP_atom.Dihedral_get_ideal(self)
2706 
2707 
2708  def set_ideal(self, t):
2709  """set_ideal(Dihedral self, IMP::Float t)"""
2710  return _IMP_atom.Dihedral_set_ideal(self, t)
2711 
2712 
2713  def get_multiplicity(self):
2714  """get_multiplicity(Dihedral self) -> IMP::Int"""
2715  return _IMP_atom.Dihedral_get_multiplicity(self)
2716 
2717 
2718  def set_multiplicity(self, t):
2719  """set_multiplicity(Dihedral self, IMP::Int t)"""
2720  return _IMP_atom.Dihedral_set_multiplicity(self, t)
2721 
2722 
2723  def get_stiffness(self):
2724  """get_stiffness(Dihedral self) -> IMP::Float"""
2725  return _IMP_atom.Dihedral_get_stiffness(self)
2726 
2727 
2728  def set_stiffness(self, t):
2729  """set_stiffness(Dihedral self, IMP::Float t)"""
2730  return _IMP_atom.Dihedral_set_stiffness(self, t)
2731 
2732 
2733  def get_particle_key(i):
2734  """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2735  return _IMP_atom.Dihedral_get_particle_key(i)
2736 
2737  get_particle_key = staticmethod(get_particle_key)
2738 
2739  def get_ideal_key():
2740  """get_ideal_key() -> FloatKey"""
2741  return _IMP_atom.Dihedral_get_ideal_key()
2742 
2743  get_ideal_key = staticmethod(get_ideal_key)
2744 
2745  def get_multiplicity_key():
2746  """get_multiplicity_key() -> IntKey"""
2747  return _IMP_atom.Dihedral_get_multiplicity_key()
2748 
2749  get_multiplicity_key = staticmethod(get_multiplicity_key)
2750 
2751  def get_stiffness_key():
2752  """get_stiffness_key() -> FloatKey"""
2753  return _IMP_atom.Dihedral_get_stiffness_key()
2754 
2755  get_stiffness_key = staticmethod(get_stiffness_key)
2756 
2757  def add_attribute(self, *args):
2758  """
2759  add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2760  add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2761  add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2762  add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2763  add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2764  add_attribute(Dihedral self, ObjectKey a0, Object a1)
2765  """
2766  return _IMP_atom.Dihedral_add_attribute(self, *args)
2767 
2768 
2769  def get_value(self, *args):
2770  """
2771  get_value(Dihedral self, FloatKey a0) -> IMP::Float
2772  get_value(Dihedral self, IntKey a0) -> IMP::Int
2773  get_value(Dihedral self, StringKey a0) -> IMP::String
2774  get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2775  get_value(Dihedral self, ObjectKey a0) -> Object
2776  """
2777  return _IMP_atom.Dihedral_get_value(self, *args)
2778 
2779 
2780  def set_value(self, *args):
2781  """
2782  set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2783  set_value(Dihedral self, IntKey a0, IMP::Int a1)
2784  set_value(Dihedral self, StringKey a0, IMP::String a1)
2785  set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2786  set_value(Dihedral self, ObjectKey a0, Object a1)
2787  """
2788  return _IMP_atom.Dihedral_set_value(self, *args)
2789 
2790 
2791  def remove_attribute(self, *args):
2792  """
2793  remove_attribute(Dihedral self, FloatKey a0)
2794  remove_attribute(Dihedral self, IntKey a0)
2795  remove_attribute(Dihedral self, StringKey a0)
2796  remove_attribute(Dihedral self, ParticleIndexKey a0)
2797  remove_attribute(Dihedral self, ObjectKey a0)
2798  """
2799  return _IMP_atom.Dihedral_remove_attribute(self, *args)
2800 
2801 
2802  def has_attribute(self, *args):
2803  """
2804  has_attribute(Dihedral self, FloatKey a0) -> bool
2805  has_attribute(Dihedral self, IntKey a0) -> bool
2806  has_attribute(Dihedral self, StringKey a0) -> bool
2807  has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2808  has_attribute(Dihedral self, ObjectKey a0) -> bool
2809  """
2810  return _IMP_atom.Dihedral_has_attribute(self, *args)
2811 
2812 
2813  def get_derivative(self, a0):
2814  """get_derivative(Dihedral self, FloatKey a0) -> double"""
2815  return _IMP_atom.Dihedral_get_derivative(self, a0)
2816 
2817 
2818  def get_name(self):
2819  """get_name(Dihedral self) -> std::string"""
2820  return _IMP_atom.Dihedral_get_name(self)
2821 
2822 
2823  def clear_caches(self):
2824  """clear_caches(Dihedral self)"""
2825  return _IMP_atom.Dihedral_clear_caches(self)
2826 
2827 
2828  def set_name(self, a0):
2829  """set_name(Dihedral self, std::string a0)"""
2830  return _IMP_atom.Dihedral_set_name(self, a0)
2831 
2832 
2833  def set_check_level(self, a0):
2834  """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2835  return _IMP_atom.Dihedral_set_check_level(self, a0)
2836 
2837 
2838  def add_to_derivative(self, a0, a1, a2):
2839  """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2840  return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2841 
2842 
2843  def set_is_optimized(self, a0, a1):
2844  """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2845  return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2846 
2847 
2848  def get_is_optimized(self, a0):
2849  """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2850  return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2851 
2852 
2853  def get_check_level(self):
2854  """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2855  return _IMP_atom.Dihedral_get_check_level(self)
2856 
2857 
2858  def __eq__(self, *args):
2859  """
2860  __eq__(Dihedral self, Dihedral o) -> bool
2861  __eq__(Dihedral self, Particle d) -> bool
2862  """
2863  return _IMP_atom.Dihedral___eq__(self, *args)
2864 
2865 
2866  def __ne__(self, *args):
2867  """
2868  __ne__(Dihedral self, Dihedral o) -> bool
2869  __ne__(Dihedral self, Particle d) -> bool
2870  """
2871  return _IMP_atom.Dihedral___ne__(self, *args)
2872 
2873 
2874  def __le__(self, *args):
2875  """
2876  __le__(Dihedral self, Dihedral o) -> bool
2877  __le__(Dihedral self, Particle d) -> bool
2878  """
2879  return _IMP_atom.Dihedral___le__(self, *args)
2880 
2881 
2882  def __lt__(self, *args):
2883  """
2884  __lt__(Dihedral self, Dihedral o) -> bool
2885  __lt__(Dihedral self, Particle d) -> bool
2886  """
2887  return _IMP_atom.Dihedral___lt__(self, *args)
2888 
2889 
2890  def __ge__(self, *args):
2891  """
2892  __ge__(Dihedral self, Dihedral o) -> bool
2893  __ge__(Dihedral self, Particle d) -> bool
2894  """
2895  return _IMP_atom.Dihedral___ge__(self, *args)
2896 
2897 
2898  def __gt__(self, *args):
2899  """
2900  __gt__(Dihedral self, Dihedral o) -> bool
2901  __gt__(Dihedral self, Particle d) -> bool
2902  """
2903  return _IMP_atom.Dihedral___gt__(self, *args)
2904 
2905 
2906  def __hash__(self):
2907  """__hash__(Dihedral self) -> std::size_t"""
2908  return _IMP_atom.Dihedral___hash__(self)
2909 
2910 
2911  def __str__(self):
2912  """__str__(Dihedral self) -> std::string"""
2913  return _IMP_atom.Dihedral___str__(self)
2914 
2915 
2916  def __repr__(self):
2917  """__repr__(Dihedral self) -> std::string"""
2918  return _IMP_atom.Dihedral___repr__(self)
2919 
2920  __swig_destroy__ = _IMP_atom.delete_Dihedral
2921  __del__ = lambda self: None
2922 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2923 Dihedral_swigregister(Dihedral)
2924 
2925 def Dihedral_setup_particle(*args):
2926  """
2927  setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2928  Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2929  """
2930  return _IMP_atom.Dihedral_setup_particle(*args)
2931 
2932 def Dihedral_get_is_setup(*args):
2933  """
2934  get_is_setup(_ParticleAdaptor p) -> bool
2935  Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2936  """
2937  return _IMP_atom.Dihedral_get_is_setup(*args)
2938 
2939 def Dihedral_get_particle_key(i):
2940  """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2941  return _IMP_atom.Dihedral_get_particle_key(i)
2942 
2943 def Dihedral_get_ideal_key():
2944  """Dihedral_get_ideal_key() -> FloatKey"""
2945  return _IMP_atom.Dihedral_get_ideal_key()
2946 
2947 def Dihedral_get_multiplicity_key():
2948  """Dihedral_get_multiplicity_key() -> IntKey"""
2949  return _IMP_atom.Dihedral_get_multiplicity_key()
2950 
2951 def Dihedral_get_stiffness_key():
2952  """Dihedral_get_stiffness_key() -> FloatKey"""
2953  return _IMP_atom.Dihedral_get_stiffness_key()
2954 
2955 class SmoothingFunction(IMP.Object):
2956  """Proxy of C++ IMP::atom::SmoothingFunction class"""
2957  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2958 
2959  def __init__(self, *args, **kwargs):
2960  raise AttributeError("No constructor defined - class is abstract")
2961 
2962  def __call__(self, *args):
2963  """
2964  __call__(SmoothingFunction self, double score, double distance) -> double
2965  __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2966  """
2967  return _IMP_atom.SmoothingFunction___call__(self, *args)
2968 
2969  __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2970  __del__ = lambda self: None
2971 
2972  def __str__(self):
2973  """__str__(SmoothingFunction self) -> std::string"""
2974  return _IMP_atom.SmoothingFunction___str__(self)
2975 
2976 
2977  def __repr__(self):
2978  """__repr__(SmoothingFunction self) -> std::string"""
2979  return _IMP_atom.SmoothingFunction___repr__(self)
2980 
2981 
2982  @staticmethod
2983  def get_from(o):
2984  return _object_cast_to_SmoothingFunction(o)
2985 
2986 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2987 SmoothingFunction_swigregister(SmoothingFunction)
2988 
2989 class ForceSwitch(SmoothingFunction):
2990  """Proxy of C++ IMP::atom::ForceSwitch class"""
2991  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2992 
2993  def __init__(self, min_distance, max_distance):
2994  """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2995  this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2996  try:
2997  self.this.append(this)
2998  except:
2999  self.this = this
3000 
3001  def __call__(self, *args):
3002  """
3003  __call__(ForceSwitch self, double score, double distance) -> double
3004  __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
3005  """
3006  return _IMP_atom.ForceSwitch___call__(self, *args)
3007 
3008 
3009  def get_version_info(self):
3010  """get_version_info(ForceSwitch self) -> VersionInfo"""
3011  return _IMP_atom.ForceSwitch_get_version_info(self)
3012 
3013 
3014  def __str__(self):
3015  """__str__(ForceSwitch self) -> std::string"""
3016  return _IMP_atom.ForceSwitch___str__(self)
3017 
3018 
3019  def __repr__(self):
3020  """__repr__(ForceSwitch self) -> std::string"""
3021  return _IMP_atom.ForceSwitch___repr__(self)
3022 
3023 
3024  @staticmethod
3025  def get_from(o):
3026  return _object_cast_to_ForceSwitch(o)
3027 
3028 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
3029 ForceSwitch_swigregister(ForceSwitch)
3030 
3031 class AngleSingletonScore(IMP.SingletonScore):
3032  """Proxy of C++ IMP::atom::AngleSingletonScore class"""
3033  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3034 
3035  def __init__(self, f):
3036  """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
3037  this = _IMP_atom.new_AngleSingletonScore(f)
3038  try:
3039  self.this.append(this)
3040  except:
3041  self.this = this
3042 
3043  def do_get_inputs(self, m, pis):
3044  """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3045  return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
3046 
3047 
3048  def get_version_info(self):
3049  """get_version_info(AngleSingletonScore self) -> VersionInfo"""
3050  return _IMP_atom.AngleSingletonScore_get_version_info(self)
3051 
3052 
3053  def __str__(self):
3054  """__str__(AngleSingletonScore self) -> std::string"""
3055  return _IMP_atom.AngleSingletonScore___str__(self)
3056 
3057 
3058  def __repr__(self):
3059  """__repr__(AngleSingletonScore self) -> std::string"""
3060  return _IMP_atom.AngleSingletonScore___repr__(self)
3061 
3062 
3063  @staticmethod
3064  def get_from(o):
3065  return _object_cast_to_AngleSingletonScore(o)
3066 
3067 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
3068 AngleSingletonScore_swigregister(AngleSingletonScore)
3069 
3070 class BondEndpointsRefiner(IMP.Refiner):
3071  """Proxy of C++ IMP::atom::BondEndpointsRefiner class"""
3072  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3073 
3074  def __init__(self):
3075  """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
3076  this = _IMP_atom.new_BondEndpointsRefiner()
3077  try:
3078  self.this.append(this)
3079  except:
3080  self.this = this
3081 
3082  def do_get_inputs(self, m, pis):
3083  """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3084  return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
3085 
3086 
3087  def get_version_info(self):
3088  """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
3089  return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
3090 
3091 
3092  def __str__(self):
3093  """__str__(BondEndpointsRefiner self) -> std::string"""
3094  return _IMP_atom.BondEndpointsRefiner___str__(self)
3095 
3096 
3097  def __repr__(self):
3098  """__repr__(BondEndpointsRefiner self) -> std::string"""
3099  return _IMP_atom.BondEndpointsRefiner___repr__(self)
3100 
3101 
3102  @staticmethod
3103  def get_from(o):
3104  return _object_cast_to_BondEndpointsRefiner(o)
3105 
3106 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
3107 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
3108 
3109 class BondPairContainer(IMP.PairContainer):
3110  """Proxy of C++ IMP::atom::BondPairContainer class"""
3111  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3112 
3113  def __init__(self, sc):
3114  """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
3115  this = _IMP_atom.new_BondPairContainer(sc)
3116  try:
3117  self.this.append(this)
3118  except:
3119  self.this = this
3120 
3121  def do_get_inputs(self):
3122  """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
3123  return _IMP_atom.BondPairContainer_do_get_inputs(self)
3124 
3125 
3126  def do_apply(self, sm):
3127  """do_apply(BondPairContainer self, PairModifier sm)"""
3128  return _IMP_atom.BondPairContainer_do_apply(self, sm)
3129 
3130 
3131  def get_version_info(self):
3132  """get_version_info(BondPairContainer self) -> VersionInfo"""
3133  return _IMP_atom.BondPairContainer_get_version_info(self)
3134 
3135 
3136  def __str__(self):
3137  """__str__(BondPairContainer self) -> std::string"""
3138  return _IMP_atom.BondPairContainer___str__(self)
3139 
3140 
3141  def __repr__(self):
3142  """__repr__(BondPairContainer self) -> std::string"""
3143  return _IMP_atom.BondPairContainer___repr__(self)
3144 
3145 
3146  @staticmethod
3147  def get_from(o):
3148  return _object_cast_to_BondPairContainer(o)
3149 
3150 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
3151 BondPairContainer_swigregister(BondPairContainer)
3152 
3153 class BondSingletonScore(IMP.SingletonScore):
3154  """Proxy of C++ IMP::atom::BondSingletonScore class"""
3155  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3156 
3157  def __init__(self, f):
3158  """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
3159  this = _IMP_atom.new_BondSingletonScore(f)
3160  try:
3161  self.this.append(this)
3162  except:
3163  self.this = this
3164 
3165  def get_unary_function(self):
3166  """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
3167  return _IMP_atom.BondSingletonScore_get_unary_function(self)
3168 
3169 
3170  def do_get_inputs(self, m, pis):
3171  """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3172  return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
3173 
3174 
3175  def get_version_info(self):
3176  """get_version_info(BondSingletonScore self) -> VersionInfo"""
3177  return _IMP_atom.BondSingletonScore_get_version_info(self)
3178 
3179 
3180  def __str__(self):
3181  """__str__(BondSingletonScore self) -> std::string"""
3182  return _IMP_atom.BondSingletonScore___str__(self)
3183 
3184 
3185  def __repr__(self):
3186  """__repr__(BondSingletonScore self) -> std::string"""
3187  return _IMP_atom.BondSingletonScore___repr__(self)
3188 
3189 
3190  @staticmethod
3191  def get_from(o):
3192  return _object_cast_to_BondSingletonScore(o)
3193 
3194 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
3195 BondSingletonScore_swigregister(BondSingletonScore)
3196 
3197 class DihedralSingletonScore(IMP.SingletonScore):
3198  """Proxy of C++ IMP::atom::DihedralSingletonScore class"""
3199  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3200 
3201  def __init__(self):
3202  """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
3203  this = _IMP_atom.new_DihedralSingletonScore()
3204  try:
3205  self.this.append(this)
3206  except:
3207  self.this = this
3208 
3209  def do_get_inputs(self, m, pis):
3210  """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3211  return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3212 
3213 
3214  def get_version_info(self):
3215  """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3216  return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3217 
3218 
3219  def __str__(self):
3220  """__str__(DihedralSingletonScore self) -> std::string"""
3221  return _IMP_atom.DihedralSingletonScore___str__(self)
3222 
3223 
3224  def __repr__(self):
3225  """__repr__(DihedralSingletonScore self) -> std::string"""
3226  return _IMP_atom.DihedralSingletonScore___repr__(self)
3227 
3228 
3229  @staticmethod
3230  def get_from(o):
3231  return _object_cast_to_DihedralSingletonScore(o)
3232 
3233 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3234 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3235 
3236 class ImproperSingletonScore(IMP.SingletonScore):
3237  """Proxy of C++ IMP::atom::ImproperSingletonScore class"""
3238  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3239 
3240  def __init__(self, f):
3241  """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3242  this = _IMP_atom.new_ImproperSingletonScore(f)
3243  try:
3244  self.this.append(this)
3245  except:
3246  self.this = this
3247 
3248  def do_get_inputs(self, m, pis):
3249  """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3250  return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3251 
3252 
3253  def get_version_info(self):
3254  """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3255  return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3256 
3257 
3258  def __str__(self):
3259  """__str__(ImproperSingletonScore self) -> std::string"""
3260  return _IMP_atom.ImproperSingletonScore___str__(self)
3261 
3262 
3263  def __repr__(self):
3264  """__repr__(ImproperSingletonScore self) -> std::string"""
3265  return _IMP_atom.ImproperSingletonScore___repr__(self)
3266 
3267 
3268  @staticmethod
3269  def get_from(o):
3270  return _object_cast_to_ImproperSingletonScore(o)
3271 
3272 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3273 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3274 
3275 class CenterOfMass(IMP.Decorator):
3276  """Proxy of C++ IMP::atom::CenterOfMass class"""
3277  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3278 
3279  def get_constraint(self):
3280  """get_constraint(CenterOfMass self) -> Constraint"""
3281  return _IMP_atom.CenterOfMass_get_constraint(self)
3282 
3283 
3284  def get_mass(self):
3285  """get_mass(CenterOfMass self) -> IMP::Float"""
3286  return _IMP_atom.CenterOfMass_get_mass(self)
3287 
3288 
3289  def get_coordinate(self, i):
3290  """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3291  return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3292 
3293 
3294  def get_coordinates(self):
3295  """get_coordinates(CenterOfMass self) -> Vector3D"""
3296  return _IMP_atom.CenterOfMass_get_coordinates(self)
3297 
3298 
3299  def __init__(self, *args):
3300  """
3301  __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3302  __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3303  __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3304  """
3305  this = _IMP_atom.new_CenterOfMass(*args)
3306  try:
3307  self.this.append(this)
3308  except:
3309  self.this = this
3310 
3311  def show(self, *args):
3312  """
3313  show(CenterOfMass self, _ostream out)
3314  show(CenterOfMass self)
3315  """
3316  return _IMP_atom.CenterOfMass_show(self, *args)
3317 
3318 
3319  def setup_particle(*args):
3320  """
3321  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3322  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3323  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3324  setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3325  """
3326  return _IMP_atom.CenterOfMass_setup_particle(*args)
3327 
3328  setup_particle = staticmethod(setup_particle)
3329 
3330  def get_is_setup(*args):
3331  """
3332  get_is_setup(_ParticleAdaptor p) -> bool
3333  get_is_setup(Model m, ParticleIndex pi) -> bool
3334  """
3335  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3336 
3337  get_is_setup = staticmethod(get_is_setup)
3338 
3339  def add_attribute(self, *args):
3340  """
3341  add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3342  add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3343  add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3344  add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3345  add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3346  add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3347  """
3348  return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3349 
3350 
3351  def get_value(self, *args):
3352  """
3353  get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3354  get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3355  get_value(CenterOfMass self, StringKey a0) -> IMP::String
3356  get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3357  get_value(CenterOfMass self, ObjectKey a0) -> Object
3358  """
3359  return _IMP_atom.CenterOfMass_get_value(self, *args)
3360 
3361 
3362  def set_value(self, *args):
3363  """
3364  set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3365  set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3366  set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3367  set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3368  set_value(CenterOfMass self, ObjectKey a0, Object a1)
3369  """
3370  return _IMP_atom.CenterOfMass_set_value(self, *args)
3371 
3372 
3373  def remove_attribute(self, *args):
3374  """
3375  remove_attribute(CenterOfMass self, FloatKey a0)
3376  remove_attribute(CenterOfMass self, IntKey a0)
3377  remove_attribute(CenterOfMass self, StringKey a0)
3378  remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3379  remove_attribute(CenterOfMass self, ObjectKey a0)
3380  """
3381  return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3382 
3383 
3384  def has_attribute(self, *args):
3385  """
3386  has_attribute(CenterOfMass self, FloatKey a0) -> bool
3387  has_attribute(CenterOfMass self, IntKey a0) -> bool
3388  has_attribute(CenterOfMass self, StringKey a0) -> bool
3389  has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3390  has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3391  """
3392  return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3393 
3394 
3395  def get_derivative(self, a0):
3396  """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3397  return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3398 
3399 
3400  def get_name(self):
3401  """get_name(CenterOfMass self) -> std::string"""
3402  return _IMP_atom.CenterOfMass_get_name(self)
3403 
3404 
3405  def clear_caches(self):
3406  """clear_caches(CenterOfMass self)"""
3407  return _IMP_atom.CenterOfMass_clear_caches(self)
3408 
3409 
3410  def set_name(self, a0):
3411  """set_name(CenterOfMass self, std::string a0)"""
3412  return _IMP_atom.CenterOfMass_set_name(self, a0)
3413 
3414 
3415  def set_check_level(self, a0):
3416  """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3417  return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3418 
3419 
3420  def add_to_derivative(self, a0, a1, a2):
3421  """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3422  return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3423 
3424 
3425  def set_is_optimized(self, a0, a1):
3426  """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3427  return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3428 
3429 
3430  def get_is_optimized(self, a0):
3431  """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3432  return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3433 
3434 
3435  def get_check_level(self):
3436  """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3437  return _IMP_atom.CenterOfMass_get_check_level(self)
3438 
3439 
3440  def __eq__(self, *args):
3441  """
3442  __eq__(CenterOfMass self, CenterOfMass o) -> bool
3443  __eq__(CenterOfMass self, Particle d) -> bool
3444  """
3445  return _IMP_atom.CenterOfMass___eq__(self, *args)
3446 
3447 
3448  def __ne__(self, *args):
3449  """
3450  __ne__(CenterOfMass self, CenterOfMass o) -> bool
3451  __ne__(CenterOfMass self, Particle d) -> bool
3452  """
3453  return _IMP_atom.CenterOfMass___ne__(self, *args)
3454 
3455 
3456  def __le__(self, *args):
3457  """
3458  __le__(CenterOfMass self, CenterOfMass o) -> bool
3459  __le__(CenterOfMass self, Particle d) -> bool
3460  """
3461  return _IMP_atom.CenterOfMass___le__(self, *args)
3462 
3463 
3464  def __lt__(self, *args):
3465  """
3466  __lt__(CenterOfMass self, CenterOfMass o) -> bool
3467  __lt__(CenterOfMass self, Particle d) -> bool
3468  """
3469  return _IMP_atom.CenterOfMass___lt__(self, *args)
3470 
3471 
3472  def __ge__(self, *args):
3473  """
3474  __ge__(CenterOfMass self, CenterOfMass o) -> bool
3475  __ge__(CenterOfMass self, Particle d) -> bool
3476  """
3477  return _IMP_atom.CenterOfMass___ge__(self, *args)
3478 
3479 
3480  def __gt__(self, *args):
3481  """
3482  __gt__(CenterOfMass self, CenterOfMass o) -> bool
3483  __gt__(CenterOfMass self, Particle d) -> bool
3484  """
3485  return _IMP_atom.CenterOfMass___gt__(self, *args)
3486 
3487 
3488  def __hash__(self):
3489  """__hash__(CenterOfMass self) -> std::size_t"""
3490  return _IMP_atom.CenterOfMass___hash__(self)
3491 
3492 
3493  def __str__(self):
3494  """__str__(CenterOfMass self) -> std::string"""
3495  return _IMP_atom.CenterOfMass___str__(self)
3496 
3497 
3498  def __repr__(self):
3499  """__repr__(CenterOfMass self) -> std::string"""
3500  return _IMP_atom.CenterOfMass___repr__(self)
3501 
3502  __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3503  __del__ = lambda self: None
3504 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3505 CenterOfMass_swigregister(CenterOfMass)
3506 
3507 def CenterOfMass_setup_particle(*args):
3508  """
3509  setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3510  setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3511  setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3512  CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3513  """
3514  return _IMP_atom.CenterOfMass_setup_particle(*args)
3515 
3516 def CenterOfMass_get_is_setup(*args):
3517  """
3518  get_is_setup(_ParticleAdaptor p) -> bool
3519  CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3520  """
3521  return _IMP_atom.CenterOfMass_get_is_setup(*args)
3522 
3523 class CoverBond(IMP.SingletonModifier):
3524  """Proxy of C++ IMP::atom::CoverBond class"""
3525  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3526 
3527  def __init__(self):
3528  """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3529  this = _IMP_atom.new_CoverBond()
3530  try:
3531  self.this.append(this)
3532  except:
3533  self.this = this
3534 
3535  def do_get_inputs(self, m, pis):
3536  """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3537  return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3538 
3539 
3540  def do_get_outputs(self, m, pis):
3541  """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3542  return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3543 
3544 
3545  def get_version_info(self):
3546  """get_version_info(CoverBond self) -> VersionInfo"""
3547  return _IMP_atom.CoverBond_get_version_info(self)
3548 
3549 
3550  def __str__(self):
3551  """__str__(CoverBond self) -> std::string"""
3552  return _IMP_atom.CoverBond___str__(self)
3553 
3554 
3555  def __repr__(self):
3556  """__repr__(CoverBond self) -> std::string"""
3557  return _IMP_atom.CoverBond___repr__(self)
3558 
3559 
3560  @staticmethod
3561  def get_from(o):
3562  return _object_cast_to_CoverBond(o)
3563 
3564 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3565 CoverBond_swigregister(CoverBond)
3566 
3567 class Simulator(IMP.Optimizer):
3568  """Proxy of C++ IMP::atom::Simulator class"""
3569  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3570 
3571  def __init__(self, *args):
3572  """
3573  __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3574  __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3575  __init__(IMP::atom::Simulator self, Model m) -> Simulator
3576  """
3577  if self.__class__ == Simulator:
3578  _self = None
3579  else:
3580  _self = self
3581  this = _IMP_atom.new_Simulator(_self, *args)
3582  try:
3583  self.this.append(this)
3584  except:
3585  self.this = this
3586 
3587  if self.__class__ != Simulator:
3588  _director_objects.register(self)
3589 
3590 
3591 
3592 
3593  def simulate(self, time_in_fs):
3594  """simulate(Simulator self, double time_in_fs) -> double"""
3595  return _IMP_atom.Simulator_simulate(self, time_in_fs)
3596 
3597 
3598  def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3599  """
3600  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3601  simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3602  simulate_wave(Simulator self, double time_in_fs) -> double
3603  """
3604  return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3605 
3606 
3607  def get_temperature(self):
3608  """get_temperature(Simulator self) -> double"""
3609  return _IMP_atom.Simulator_get_temperature(self)
3610 
3611 
3612  def set_temperature(self, d):
3613  """set_temperature(Simulator self, double d)"""
3614  return _IMP_atom.Simulator_set_temperature(self, d)
3615 
3616 
3617  def set_maximum_time_step(self, ts):
3618  """set_maximum_time_step(Simulator self, double ts)"""
3619  return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3620 
3621 
3622  def get_maximum_time_step(self):
3623  """get_maximum_time_step(Simulator self) -> double"""
3624  return _IMP_atom.Simulator_get_maximum_time_step(self)
3625 
3626 
3627  def get_last_time_step(self):
3628  """get_last_time_step(Simulator self) -> double"""
3629  return _IMP_atom.Simulator_get_last_time_step(self)
3630 
3631 
3632  def set_time_step(self, ts):
3633  """set_time_step(Simulator self, double ts)"""
3634  return _IMP_atom.Simulator_set_time_step(self, ts)
3635 
3636 
3637  def get_kt(self):
3638  """get_kt(Simulator self) -> double"""
3639  return _IMP_atom.Simulator_get_kt(self)
3640 
3641 
3642  def get_current_time(self):
3643  """get_current_time(Simulator self) -> double"""
3644  return _IMP_atom.Simulator_get_current_time(self)
3645 
3646 
3647  def set_current_time(self, ct):
3648  """set_current_time(Simulator self, double ct)"""
3649  return _IMP_atom.Simulator_set_current_time(self, ct)
3650 
3651 
3652  def get_simulation_particles(self):
3653  """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3654  return _IMP_atom.Simulator_get_simulation_particles(self)
3655 
3656 
3657  def get_simulation_particle_indexes(self):
3658  """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3659  return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3660 
3661 
3662  def remove_particle(self, d):
3663  """remove_particle(Simulator self, Particle d)"""
3664  return _IMP_atom.Simulator_remove_particle(self, d)
3665 
3666 
3667  def remove_particles(self, d):
3668  """remove_particles(Simulator self, IMP::Particles const & d)"""
3669  return _IMP_atom.Simulator_remove_particles(self, d)
3670 
3671 
3672  def set_particles(self, ps):
3673  """set_particles(Simulator self, IMP::Particles const & ps)"""
3674  return _IMP_atom.Simulator_set_particles(self, ps)
3675 
3676 
3677  def set_particles_order(self, objs):
3678  """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3679  return _IMP_atom.Simulator_set_particles_order(self, objs)
3680 
3681 
3682  def add_particle(self, obj):
3683  """add_particle(Simulator self, Particle obj) -> unsigned int"""
3684  return _IMP_atom.Simulator_add_particle(self, obj)
3685 
3686 
3687  def add_particles(self, objs):
3688  """add_particles(Simulator self, IMP::Particles const & objs)"""
3689  return _IMP_atom.Simulator_add_particles(self, objs)
3690 
3691 
3692  def clear_particles(self):
3693  """clear_particles(Simulator self)"""
3694  return _IMP_atom.Simulator_clear_particles(self)
3695 
3696 
3697  def get_number_of_particles(self):
3698  """get_number_of_particles(Simulator self) -> unsigned int"""
3699  return _IMP_atom.Simulator_get_number_of_particles(self)
3700 
3701 
3702  def get_has_particles(self):
3703  """get_has_particles(Simulator self) -> bool"""
3704  return _IMP_atom.Simulator_get_has_particles(self)
3705 
3706 
3707  def get_particle(self, i):
3708  """get_particle(Simulator self, unsigned int i) -> Particle"""
3709  return _IMP_atom.Simulator_get_particle(self, i)
3710 
3711 
3712  def get_particles(self):
3713  """get_particles(Simulator self) -> IMP::Particles"""
3714  return _IMP_atom.Simulator_get_particles(self)
3715 
3716 
3717  def reserve_particles(self, sz):
3718  """reserve_particles(Simulator self, unsigned int sz)"""
3719  return _IMP_atom.Simulator_reserve_particles(self, sz)
3720 
3721 
3722  def do_optimize(self, max_steps):
3723  """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3724  return _IMP_atom.Simulator_do_optimize(self, max_steps)
3725 
3726 
3727  def setup(self, arg0):
3728  """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3729  return _IMP_atom.Simulator_setup(self, arg0)
3730 
3731 
3732  def do_step(self, sc, dt):
3733  """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3734  return _IMP_atom.Simulator_do_step(self, sc, dt)
3735 
3736 
3737  def get_is_simulation_particle(self, p):
3738  """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3739  return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3740 
3741 
3742  def do_simulate(self, time):
3743  """do_simulate(Simulator self, double time) -> double"""
3744  return _IMP_atom.Simulator_do_simulate(self, time)
3745 
3746 
3747  def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3748  """
3749  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3750  do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3751  do_simulate_wave(Simulator self, double time_in_fs) -> double
3752  """
3753  return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3754 
3755 
3756  def __str__(self):
3757  """__str__(Simulator self) -> std::string"""
3758  return _IMP_atom.Simulator___str__(self)
3759 
3760 
3761  def __repr__(self):
3762  """__repr__(Simulator self) -> std::string"""
3763  return _IMP_atom.Simulator___repr__(self)
3764 
3765 
3766  @staticmethod
3767  def get_from(o):
3768  return _object_cast_to_Simulator(o)
3769 
3770 
3771  def get_type_name(self):
3772  return self.__class__.__name__
3773  def do_show(self, out):
3774  pass
3775  def get_version_info(self):
3776  if"IMP::atom" == "IMP":
3777  return VersionInfo(self.__module__,
3778  __import__(self.__module__).get_module_version())
3779  else:
3780  return IMP.VersionInfo(self.__module__,
3781  __import__(self.__module__).get_module_version())
3782  @staticmethod
3783  def get_from(o):
3784  return _object_cast_to_Simulator(o)
3785 
3786  __swig_destroy__ = _IMP_atom.delete_Simulator
3787  __del__ = lambda self: None
3788  def __disown__(self):
3789  self.this.disown()
3790  _IMP_atom.disown_Simulator(self)
3791  return weakref_proxy(self)
3792 
3793  def do_destroy(self):
3794  """do_destroy(Simulator self)"""
3795  return _IMP_atom.Simulator_do_destroy(self)
3796 
3797 
3798  def handle_set_has_required_score_states(self, arg0):
3799  """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3800  return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3801 
3802 
3803  def do_get_inputs(self):
3804  """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3805  return _IMP_atom.Simulator_do_get_inputs(self)
3806 
3807 
3808  def do_get_outputs(self):
3809  """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3810  return _IMP_atom.Simulator_do_get_outputs(self)
3811 
3812 
3813  def do_get_interactions(self):
3814  """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3815  return _IMP_atom.Simulator_do_get_interactions(self)
3816 
3817 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3818 Simulator_swigregister(Simulator)
3819 
3820 
3821 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
3822  """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
3823  return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
3824 
3825 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
3826  """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
3827  return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
3828 
3829 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
3830  """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
3831  return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
3832 
3833 _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE_swigconstant(_IMP_atom)
3834 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3835 class BrownianDynamics(Simulator):
3836  """Proxy of C++ IMP::atom::BrownianDynamics class"""
3837  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3838 
3839  def __init__(self, *args):
3840  """
3841  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=500) -> BrownianDynamics
3842  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3843  __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3844  __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3845  """
3846  this = _IMP_atom.new_BrownianDynamics(*args)
3847  try:
3848  self.this.append(this)
3849  except:
3850  self.this = this
3851 
3852  def set_maximum_move(self, ms):
3853  """set_maximum_move(BrownianDynamics self, double ms)"""
3854  return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms)
3855 
3856 
3857  def set_use_stochastic_runge_kutta(self, tf):
3858  """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3859  return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3860 
3861 
3862  def get_version_info(self):
3863  """get_version_info(BrownianDynamics self) -> VersionInfo"""
3864  return _IMP_atom.BrownianDynamics_get_version_info(self)
3865 
3866 
3867  def __str__(self):
3868  """__str__(BrownianDynamics self) -> std::string"""
3869  return _IMP_atom.BrownianDynamics___str__(self)
3870 
3871 
3872  def __repr__(self):
3873  """__repr__(BrownianDynamics self) -> std::string"""
3874  return _IMP_atom.BrownianDynamics___repr__(self)
3875 
3876 
3877  @staticmethod
3878  def get_from(o):
3879  return _object_cast_to_BrownianDynamics(o)
3880 
3881 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3882 BrownianDynamics_swigregister(BrownianDynamics)
3883 
3884 
3886  """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3887  return _IMP_atom.get_maximum_time_step_estimate(bd)
3888 
3889 def get_harmonic_sigma(D, f):
3890  """get_harmonic_sigma(double D, double f) -> double"""
3891  return _IMP_atom.get_harmonic_sigma(D, f)
3892 class BrownianDynamicsTAMD(BrownianDynamics):
3893  """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class"""
3894  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3895 
3896  def __init__(self, *args):
3897  """
3898  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3899  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3900  __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3901  """
3902  this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3903  try:
3904  self.this.append(this)
3905  except:
3906  self.this = this
3907 
3908  def __str__(self):
3909  """__str__(BrownianDynamicsTAMD self) -> std::string"""
3910  return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3911 
3912 
3913  def __repr__(self):
3914  """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3915  return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3916 
3917 
3918  @staticmethod
3919  def get_from(o):
3920  return _object_cast_to_BrownianDynamicsTAMD(o)
3921 
3922  __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3923  __del__ = lambda self: None
3924 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3925 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3926 
3927 class Diffusion(IMP.core.XYZ):
3928  """Proxy of C++ IMP::atom::Diffusion class"""
3929  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3930 
3931  def __init__(self, *args):
3932  """
3933  __init__(IMP::atom::Diffusion self) -> Diffusion
3934  __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3935  __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3936  """
3937  this = _IMP_atom.new_Diffusion(*args)
3938  try:
3939  self.this.append(this)
3940  except:
3941  self.this = this
3942 
3943  def show(self, *args):
3944  """
3945  show(Diffusion self, _ostream out)
3946  show(Diffusion self)
3947  """
3948  return _IMP_atom.Diffusion_show(self, *args)
3949 
3950 
3951  def setup_particle(*args):
3952  """
3953  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3954  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3955  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3956  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3957  setup_particle(Model m, ParticleIndex pi) -> Diffusion
3958  setup_particle(_ParticleAdaptor decorator) -> Diffusion
3959  """
3960  return _IMP_atom.Diffusion_setup_particle(*args)
3961 
3962  setup_particle = staticmethod(setup_particle)
3963 
3964  def get_is_setup(*args):
3965  """
3966  get_is_setup(_ParticleAdaptor p) -> bool
3967  get_is_setup(Model m, ParticleIndex p) -> bool
3968  """
3969  return _IMP_atom.Diffusion_get_is_setup(*args)
3970 
3971  get_is_setup = staticmethod(get_is_setup)
3972 
3973  def set_diffusion_coefficient(self, d):
3974  """set_diffusion_coefficient(Diffusion self, double d)"""
3975  return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3976 
3977 
3978  def get_diffusion_coefficient(self):
3979  """get_diffusion_coefficient(Diffusion self) -> double"""
3980  return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3981 
3982 
3983  def get_diffusion_coefficient_key():
3984  """get_diffusion_coefficient_key() -> FloatKey"""
3985  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3986 
3987  get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3988 
3989  def add_attribute(self, *args):
3990  """
3991  add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3992  add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3993  add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3994  add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3995  add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3996  add_attribute(Diffusion self, ObjectKey a0, Object a1)
3997  """
3998  return _IMP_atom.Diffusion_add_attribute(self, *args)
3999 
4000 
4001  def get_value(self, *args):
4002  """
4003  get_value(Diffusion self, FloatKey a0) -> IMP::Float
4004  get_value(Diffusion self, IntKey a0) -> IMP::Int
4005  get_value(Diffusion self, StringKey a0) -> IMP::String
4006  get_value(Diffusion self, ParticleIndexKey a0) -> Particle
4007  get_value(Diffusion self, ObjectKey a0) -> Object
4008  """
4009  return _IMP_atom.Diffusion_get_value(self, *args)
4010 
4011 
4012  def set_value(self, *args):
4013  """
4014  set_value(Diffusion self, FloatKey a0, IMP::Float a1)
4015  set_value(Diffusion self, IntKey a0, IMP::Int a1)
4016  set_value(Diffusion self, StringKey a0, IMP::String a1)
4017  set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
4018  set_value(Diffusion self, ObjectKey a0, Object a1)
4019  """
4020  return _IMP_atom.Diffusion_set_value(self, *args)
4021 
4022 
4023  def remove_attribute(self, *args):
4024  """
4025  remove_attribute(Diffusion self, FloatKey a0)
4026  remove_attribute(Diffusion self, IntKey a0)
4027  remove_attribute(Diffusion self, StringKey a0)
4028  remove_attribute(Diffusion self, ParticleIndexKey a0)
4029  remove_attribute(Diffusion self, ObjectKey a0)
4030  """
4031  return _IMP_atom.Diffusion_remove_attribute(self, *args)
4032 
4033 
4034  def has_attribute(self, *args):
4035  """
4036  has_attribute(Diffusion self, FloatKey a0) -> bool
4037  has_attribute(Diffusion self, IntKey a0) -> bool
4038  has_attribute(Diffusion self, StringKey a0) -> bool
4039  has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
4040  has_attribute(Diffusion self, ObjectKey a0) -> bool
4041  """
4042  return _IMP_atom.Diffusion_has_attribute(self, *args)
4043 
4044 
4045  def get_derivative(self, a0):
4046  """get_derivative(Diffusion self, FloatKey a0) -> double"""
4047  return _IMP_atom.Diffusion_get_derivative(self, a0)
4048 
4049 
4050  def get_name(self):
4051  """get_name(Diffusion self) -> std::string"""
4052  return _IMP_atom.Diffusion_get_name(self)
4053 
4054 
4055  def clear_caches(self):
4056  """clear_caches(Diffusion self)"""
4057  return _IMP_atom.Diffusion_clear_caches(self)
4058 
4059 
4060  def set_name(self, a0):
4061  """set_name(Diffusion self, std::string a0)"""
4062  return _IMP_atom.Diffusion_set_name(self, a0)
4063 
4064 
4065  def set_check_level(self, a0):
4066  """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
4067  return _IMP_atom.Diffusion_set_check_level(self, a0)
4068 
4069 
4070  def add_to_derivative(self, a0, a1, a2):
4071  """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4072  return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
4073 
4074 
4075  def set_is_optimized(self, a0, a1):
4076  """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
4077  return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
4078 
4079 
4080  def get_is_optimized(self, a0):
4081  """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
4082  return _IMP_atom.Diffusion_get_is_optimized(self, a0)
4083 
4084 
4085  def get_check_level(self):
4086  """get_check_level(Diffusion self) -> IMP::CheckLevel"""
4087  return _IMP_atom.Diffusion_get_check_level(self)
4088 
4089 
4090  def __eq__(self, *args):
4091  """
4092  __eq__(Diffusion self, Diffusion o) -> bool
4093  __eq__(Diffusion self, Particle d) -> bool
4094  """
4095  return _IMP_atom.Diffusion___eq__(self, *args)
4096 
4097 
4098  def __ne__(self, *args):
4099  """
4100  __ne__(Diffusion self, Diffusion o) -> bool
4101  __ne__(Diffusion self, Particle d) -> bool
4102  """
4103  return _IMP_atom.Diffusion___ne__(self, *args)
4104 
4105 
4106  def __le__(self, *args):
4107  """
4108  __le__(Diffusion self, Diffusion o) -> bool
4109  __le__(Diffusion self, Particle d) -> bool
4110  """
4111  return _IMP_atom.Diffusion___le__(self, *args)
4112 
4113 
4114  def __lt__(self, *args):
4115  """
4116  __lt__(Diffusion self, Diffusion o) -> bool
4117  __lt__(Diffusion self, Particle d) -> bool
4118  """
4119  return _IMP_atom.Diffusion___lt__(self, *args)
4120 
4121 
4122  def __ge__(self, *args):
4123  """
4124  __ge__(Diffusion self, Diffusion o) -> bool
4125  __ge__(Diffusion self, Particle d) -> bool
4126  """
4127  return _IMP_atom.Diffusion___ge__(self, *args)
4128 
4129 
4130  def __gt__(self, *args):
4131  """
4132  __gt__(Diffusion self, Diffusion o) -> bool
4133  __gt__(Diffusion self, Particle d) -> bool
4134  """
4135  return _IMP_atom.Diffusion___gt__(self, *args)
4136 
4137 
4138  def __hash__(self):
4139  """__hash__(Diffusion self) -> std::size_t"""
4140  return _IMP_atom.Diffusion___hash__(self)
4141 
4142 
4143  def __str__(self):
4144  """__str__(Diffusion self) -> std::string"""
4145  return _IMP_atom.Diffusion___str__(self)
4146 
4147 
4148  def __repr__(self):
4149  """__repr__(Diffusion self) -> std::string"""
4150  return _IMP_atom.Diffusion___repr__(self)
4151 
4152  __swig_destroy__ = _IMP_atom.delete_Diffusion
4153  __del__ = lambda self: None
4154 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
4155 Diffusion_swigregister(Diffusion)
4156 
4157 def Diffusion_setup_particle(*args):
4158  """
4159  setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
4160  setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
4161  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
4162  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
4163  setup_particle(Model m, ParticleIndex pi) -> Diffusion
4164  Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
4165  """
4166  return _IMP_atom.Diffusion_setup_particle(*args)
4167 
4168 def Diffusion_get_is_setup(*args):
4169  """
4170  get_is_setup(_ParticleAdaptor p) -> bool
4171  Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4172  """
4173  return _IMP_atom.Diffusion_get_is_setup(*args)
4174 
4175 def Diffusion_get_diffusion_coefficient_key():
4176  """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
4177  return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
4178 
4179 
4180 def get_diffusion_coefficient_from_cm2_per_second(din):
4181  """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
4182  return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
4183 class RigidBodyDiffusion(Diffusion):
4184  """Proxy of C++ IMP::atom::RigidBodyDiffusion class"""
4185  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4186 
4187  def __init__(self, *args):
4188  """
4189  __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
4190  __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
4191  __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
4192  """
4193  this = _IMP_atom.new_RigidBodyDiffusion(*args)
4194  try:
4195  self.this.append(this)
4196  except:
4197  self.this = this
4198 
4199  def show(self, *args):
4200  """
4201  show(RigidBodyDiffusion self, _ostream out)
4202  show(RigidBodyDiffusion self)
4203  """
4204  return _IMP_atom.RigidBodyDiffusion_show(self, *args)
4205 
4206 
4207  def setup_particle(*args):
4208  """
4209  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4210  setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4211  """
4212  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4213 
4214  setup_particle = staticmethod(setup_particle)
4215 
4217  """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4218  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4219 
4220 
4221  def set_rotational_diffusion_coefficient(self, d):
4222  """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4223  return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4224 
4225 
4226  def get_is_setup(*args):
4227  """
4228  get_is_setup(_ParticleAdaptor p) -> bool
4229  get_is_setup(Model m, ParticleIndex p) -> bool
4230  """
4231  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4232 
4233  get_is_setup = staticmethod(get_is_setup)
4234 
4235  def get_rotational_diffusion_coefficient_key():
4236  """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4237  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4238 
4239  get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4240 
4241  def add_attribute(self, *args):
4242  """
4243  add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4244  add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4245  add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4246  add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4247  add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4248  add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4249  """
4250  return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4251 
4252 
4253  def get_value(self, *args):
4254  """
4255  get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4256  get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4257  get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4258  get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4259  get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4260  """
4261  return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4262 
4263 
4264  def set_value(self, *args):
4265  """
4266  set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4267  set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4268  set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4269  set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4270  set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4271  """
4272  return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4273 
4274 
4275  def remove_attribute(self, *args):
4276  """
4277  remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4278  remove_attribute(RigidBodyDiffusion self, IntKey a0)
4279  remove_attribute(RigidBodyDiffusion self, StringKey a0)
4280  remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4281  remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4282  """
4283  return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4284 
4285 
4286  def has_attribute(self, *args):
4287  """
4288  has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4289  has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4290  has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4291  has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4292  has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4293  """
4294  return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4295 
4296 
4297  def get_derivative(self, a0):
4298  """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4299  return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4300 
4301 
4302  def get_name(self):
4303  """get_name(RigidBodyDiffusion self) -> std::string"""
4304  return _IMP_atom.RigidBodyDiffusion_get_name(self)
4305 
4306 
4307  def clear_caches(self):
4308  """clear_caches(RigidBodyDiffusion self)"""
4309  return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4310 
4311 
4312  def set_name(self, a0):
4313  """set_name(RigidBodyDiffusion self, std::string a0)"""
4314  return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4315 
4316 
4317  def set_check_level(self, a0):
4318  """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4319  return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4320 
4321 
4322  def add_to_derivative(self, a0, a1, a2):
4323  """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4324  return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4325 
4326 
4327  def set_is_optimized(self, a0, a1):
4328  """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4329  return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4330 
4331 
4332  def get_is_optimized(self, a0):
4333  """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4334  return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4335 
4336 
4337  def get_check_level(self):
4338  """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4339  return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4340 
4341 
4342  def __eq__(self, *args):
4343  """
4344  __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4345  __eq__(RigidBodyDiffusion self, Particle d) -> bool
4346  """
4347  return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4348 
4349 
4350  def __ne__(self, *args):
4351  """
4352  __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4353  __ne__(RigidBodyDiffusion self, Particle d) -> bool
4354  """
4355  return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4356 
4357 
4358  def __le__(self, *args):
4359  """
4360  __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4361  __le__(RigidBodyDiffusion self, Particle d) -> bool
4362  """
4363  return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4364 
4365 
4366  def __lt__(self, *args):
4367  """
4368  __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4369  __lt__(RigidBodyDiffusion self, Particle d) -> bool
4370  """
4371  return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4372 
4373 
4374  def __ge__(self, *args):
4375  """
4376  __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4377  __ge__(RigidBodyDiffusion self, Particle d) -> bool
4378  """
4379  return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4380 
4381 
4382  def __gt__(self, *args):
4383  """
4384  __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4385  __gt__(RigidBodyDiffusion self, Particle d) -> bool
4386  """
4387  return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4388 
4389 
4390  def __hash__(self):
4391  """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4392  return _IMP_atom.RigidBodyDiffusion___hash__(self)
4393 
4394 
4395  def __str__(self):
4396  """__str__(RigidBodyDiffusion self) -> std::string"""
4397  return _IMP_atom.RigidBodyDiffusion___str__(self)
4398 
4399 
4400  def __repr__(self):
4401  """__repr__(RigidBodyDiffusion self) -> std::string"""
4402  return _IMP_atom.RigidBodyDiffusion___repr__(self)
4403 
4404  __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4405  __del__ = lambda self: None
4406 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4407 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4408 
4409 def RigidBodyDiffusion_setup_particle(*args):
4410  """
4411  setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4412  RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4413  """
4414  return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4415 
4416 def RigidBodyDiffusion_get_is_setup(*args):
4417  """
4418  get_is_setup(_ParticleAdaptor p) -> bool
4419  RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4420  """
4421  return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4422 
4423 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4424  """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4425  return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4426 
4427 class TAMDParticle(IMP.Decorator):
4428  """Proxy of C++ IMP::atom::TAMDParticle class"""
4429  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4430 
4431  def __init__(self, *args):
4432  """
4433  __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4434  __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4435  __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4436  """
4437  this = _IMP_atom.new_TAMDParticle(*args)
4438  try:
4439  self.this.append(this)
4440  except:
4441  self.this = this
4442 
4443  def show(self, *args):
4444  """
4445  show(TAMDParticle self, _ostream out)
4446  show(TAMDParticle self)
4447  """
4448  return _IMP_atom.TAMDParticle_show(self, *args)
4449 
4450 
4451  def setup_particle(*args):
4452  """
4453  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4454  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4455  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4456  setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4457  """
4458  return _IMP_atom.TAMDParticle_setup_particle(*args)
4459 
4460  setup_particle = staticmethod(setup_particle)
4461 
4462  def get_is_setup(*args):
4463  """
4464  get_is_setup(_ParticleAdaptor p) -> bool
4465  get_is_setup(Model m, ParticleIndex p) -> bool
4466  """
4467  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4468 
4469  get_is_setup = staticmethod(get_is_setup)
4470 
4471  def get_reference_particle_index(self):
4472  """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4473  return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4474 
4475 
4476  def set_temperature_scale_factor(self, tsf):
4477  """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4478  return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4479 
4480 
4481  def get_temperature_scale_factor(self):
4482  """get_temperature_scale_factor(TAMDParticle self) -> double"""
4483  return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4484 
4485 
4486  def set_friction_scale_factor(self, tsf):
4487  """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4488  return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4489 
4490 
4491  def get_friction_scale_factor(self):
4492  """get_friction_scale_factor(TAMDParticle self) -> double"""
4493  return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4494 
4495 
4496  def update_coordinates_from_ref(self):
4497  """update_coordinates_from_ref(TAMDParticle self)"""
4498  return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4499 
4500 
4501  def get_temperature_scale_factor_key():
4502  """get_temperature_scale_factor_key() -> FloatKey"""
4503  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4504 
4505  get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4506 
4507  def get_friction_scale_factor_key():
4508  """get_friction_scale_factor_key() -> FloatKey"""
4509  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4510 
4511  get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4512 
4513  def get_reference_particle_index_key():
4514  """get_reference_particle_index_key() -> ParticleIndexKey"""
4515  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4516 
4517  get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4518 
4519  def add_attribute(self, *args):
4520  """
4521  add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4522  add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4523  add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4524  add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4525  add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4526  add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4527  """
4528  return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4529 
4530 
4531  def get_value(self, *args):
4532  """
4533  get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4534  get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4535  get_value(TAMDParticle self, StringKey a0) -> IMP::String
4536  get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4537  get_value(TAMDParticle self, ObjectKey a0) -> Object
4538  """
4539  return _IMP_atom.TAMDParticle_get_value(self, *args)
4540 
4541 
4542  def set_value(self, *args):
4543  """
4544  set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4545  set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4546  set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4547  set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4548  set_value(TAMDParticle self, ObjectKey a0, Object a1)
4549  """
4550  return _IMP_atom.TAMDParticle_set_value(self, *args)
4551 
4552 
4553  def remove_attribute(self, *args):
4554  """
4555  remove_attribute(TAMDParticle self, FloatKey a0)
4556  remove_attribute(TAMDParticle self, IntKey a0)
4557  remove_attribute(TAMDParticle self, StringKey a0)
4558  remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4559  remove_attribute(TAMDParticle self, ObjectKey a0)
4560  """
4561  return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4562 
4563 
4564  def has_attribute(self, *args):
4565  """
4566  has_attribute(TAMDParticle self, FloatKey a0) -> bool
4567  has_attribute(TAMDParticle self, IntKey a0) -> bool
4568  has_attribute(TAMDParticle self, StringKey a0) -> bool
4569  has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4570  has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4571  """
4572  return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4573 
4574 
4575  def get_derivative(self, a0):
4576  """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4577  return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4578 
4579 
4580  def get_name(self):
4581  """get_name(TAMDParticle self) -> std::string"""
4582  return _IMP_atom.TAMDParticle_get_name(self)
4583 
4584 
4585  def clear_caches(self):
4586  """clear_caches(TAMDParticle self)"""
4587  return _IMP_atom.TAMDParticle_clear_caches(self)
4588 
4589 
4590  def set_name(self, a0):
4591  """set_name(TAMDParticle self, std::string a0)"""
4592  return _IMP_atom.TAMDParticle_set_name(self, a0)
4593 
4594 
4595  def set_check_level(self, a0):
4596  """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4597  return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4598 
4599 
4600  def add_to_derivative(self, a0, a1, a2):
4601  """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4602  return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4603 
4604 
4605  def set_is_optimized(self, a0, a1):
4606  """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4607  return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4608 
4609 
4610  def get_is_optimized(self, a0):
4611  """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4612  return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4613 
4614 
4615  def get_check_level(self):
4616  """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4617  return _IMP_atom.TAMDParticle_get_check_level(self)
4618 
4619 
4620  def __eq__(self, *args):
4621  """
4622  __eq__(TAMDParticle self, TAMDParticle o) -> bool
4623  __eq__(TAMDParticle self, Particle d) -> bool
4624  """
4625  return _IMP_atom.TAMDParticle___eq__(self, *args)
4626 
4627 
4628  def __ne__(self, *args):
4629  """
4630  __ne__(TAMDParticle self, TAMDParticle o) -> bool
4631  __ne__(TAMDParticle self, Particle d) -> bool
4632  """
4633  return _IMP_atom.TAMDParticle___ne__(self, *args)
4634 
4635 
4636  def __le__(self, *args):
4637  """
4638  __le__(TAMDParticle self, TAMDParticle o) -> bool
4639  __le__(TAMDParticle self, Particle d) -> bool
4640  """
4641  return _IMP_atom.TAMDParticle___le__(self, *args)
4642 
4643 
4644  def __lt__(self, *args):
4645  """
4646  __lt__(TAMDParticle self, TAMDParticle o) -> bool
4647  __lt__(TAMDParticle self, Particle d) -> bool
4648  """
4649  return _IMP_atom.TAMDParticle___lt__(self, *args)
4650 
4651 
4652  def __ge__(self, *args):
4653  """
4654  __ge__(TAMDParticle self, TAMDParticle o) -> bool
4655  __ge__(TAMDParticle self, Particle d) -> bool
4656  """
4657  return _IMP_atom.TAMDParticle___ge__(self, *args)
4658 
4659 
4660  def __gt__(self, *args):
4661  """
4662  __gt__(TAMDParticle self, TAMDParticle o) -> bool
4663  __gt__(TAMDParticle self, Particle d) -> bool
4664  """
4665  return _IMP_atom.TAMDParticle___gt__(self, *args)
4666 
4667 
4668  def __hash__(self):
4669  """__hash__(TAMDParticle self) -> std::size_t"""
4670  return _IMP_atom.TAMDParticle___hash__(self)
4671 
4672 
4673  def __str__(self):
4674  """__str__(TAMDParticle self) -> std::string"""
4675  return _IMP_atom.TAMDParticle___str__(self)
4676 
4677 
4678  def __repr__(self):
4679  """__repr__(TAMDParticle self) -> std::string"""
4680  return _IMP_atom.TAMDParticle___repr__(self)
4681 
4682  __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4683  __del__ = lambda self: None
4684 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4685 TAMDParticle_swigregister(TAMDParticle)
4686 
4687 def TAMDParticle_setup_particle(*args):
4688  """
4689  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4690  setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4691  setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4692  TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4693  """
4694  return _IMP_atom.TAMDParticle_setup_particle(*args)
4695 
4696 def TAMDParticle_get_is_setup(*args):
4697  """
4698  get_is_setup(_ParticleAdaptor p) -> bool
4699  TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4700  """
4701  return _IMP_atom.TAMDParticle_get_is_setup(*args)
4702 
4703 def TAMDParticle_get_temperature_scale_factor_key():
4704  """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4705  return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4706 
4707 def TAMDParticle_get_friction_scale_factor_key():
4708  """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4709  return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4710 
4711 def TAMDParticle_get_reference_particle_index_key():
4712  """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4713  return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4714 
4715 class Chain(Hierarchy):
4716  """Proxy of C++ IMP::atom::Chain class"""
4717  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4718 
4719  def __init__(self, *args):
4720  """
4721  __init__(IMP::atom::Chain self) -> Chain
4722  __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4723  __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4724  """
4725  this = _IMP_atom.new_Chain(*args)
4726  try:
4727  self.this.append(this)
4728  except:
4729  self.this = this
4730 
4731  def show(self, *args):
4732  """
4733  show(Chain self, _ostream out)
4734  show(Chain self)
4735  """
4736  return _IMP_atom.Chain_show(self, *args)
4737 
4738 
4739  def setup_particle(*args):
4740  """
4741  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4742  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4743  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4744  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4745  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4746  setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4747  """
4748  return _IMP_atom.Chain_setup_particle(*args)
4749 
4750  setup_particle = staticmethod(setup_particle)
4751 
4752  def get_is_setup(*args):
4753  """
4754  get_is_setup(_ParticleAdaptor p) -> bool
4755  get_is_setup(Model m, ParticleIndex pi) -> bool
4756  """
4757  return _IMP_atom.Chain_get_is_setup(*args)
4758 
4759  get_is_setup = staticmethod(get_is_setup)
4760 
4761  def get_id(self):
4762  """get_id(Chain self) -> std::string"""
4763  return _IMP_atom.Chain_get_id(self)
4764 
4765 
4766  def set_id(self, c):
4767  """set_id(Chain self, std::string c)"""
4768  return _IMP_atom.Chain_set_id(self, c)
4769 
4770 
4771  def get_id_key():
4772  """get_id_key() -> StringKey"""
4773  return _IMP_atom.Chain_get_id_key()
4774 
4775  get_id_key = staticmethod(get_id_key)
4776 
4777  def add_attribute(self, *args):
4778  """
4779  add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4780  add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4781  add_attribute(Chain self, IntKey a0, IMP::Int a1)
4782  add_attribute(Chain self, StringKey a0, IMP::String a1)
4783  add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4784  add_attribute(Chain self, ObjectKey a0, Object a1)
4785  """
4786  return _IMP_atom.Chain_add_attribute(self, *args)
4787 
4788 
4789  def get_value(self, *args):
4790  """
4791  get_value(Chain self, FloatKey a0) -> IMP::Float
4792  get_value(Chain self, IntKey a0) -> IMP::Int
4793  get_value(Chain self, StringKey a0) -> IMP::String
4794  get_value(Chain self, ParticleIndexKey a0) -> Particle
4795  get_value(Chain self, ObjectKey a0) -> Object
4796  """
4797  return _IMP_atom.Chain_get_value(self, *args)
4798 
4799 
4800  def set_value(self, *args):
4801  """
4802  set_value(Chain self, FloatKey a0, IMP::Float a1)
4803  set_value(Chain self, IntKey a0, IMP::Int a1)
4804  set_value(Chain self, StringKey a0, IMP::String a1)
4805  set_value(Chain self, ParticleIndexKey a0, Particle a1)
4806  set_value(Chain self, ObjectKey a0, Object a1)
4807  """
4808  return _IMP_atom.Chain_set_value(self, *args)
4809 
4810 
4811  def remove_attribute(self, *args):
4812  """
4813  remove_attribute(Chain self, FloatKey a0)
4814  remove_attribute(Chain self, IntKey a0)
4815  remove_attribute(Chain self, StringKey a0)
4816  remove_attribute(Chain self, ParticleIndexKey a0)
4817  remove_attribute(Chain self, ObjectKey a0)
4818  """
4819  return _IMP_atom.Chain_remove_attribute(self, *args)
4820 
4821 
4822  def has_attribute(self, *args):
4823  """
4824  has_attribute(Chain self, FloatKey a0) -> bool
4825  has_attribute(Chain self, IntKey a0) -> bool
4826  has_attribute(Chain self, StringKey a0) -> bool
4827  has_attribute(Chain self, ParticleIndexKey a0) -> bool
4828  has_attribute(Chain self, ObjectKey a0) -> bool
4829  """
4830  return _IMP_atom.Chain_has_attribute(self, *args)
4831 
4832 
4833  def get_derivative(self, a0):
4834  """get_derivative(Chain self, FloatKey a0) -> double"""
4835  return _IMP_atom.Chain_get_derivative(self, a0)
4836 
4837 
4838  def get_name(self):
4839  """get_name(Chain self) -> std::string"""
4840  return _IMP_atom.Chain_get_name(self)
4841 
4842 
4843  def clear_caches(self):
4844  """clear_caches(Chain self)"""
4845  return _IMP_atom.Chain_clear_caches(self)
4846 
4847 
4848  def set_name(self, a0):
4849  """set_name(Chain self, std::string a0)"""
4850  return _IMP_atom.Chain_set_name(self, a0)
4851 
4852 
4853  def set_check_level(self, a0):
4854  """set_check_level(Chain self, IMP::CheckLevel a0)"""
4855  return _IMP_atom.Chain_set_check_level(self, a0)
4856 
4857 
4858  def add_to_derivative(self, a0, a1, a2):
4859  """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4860  return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4861 
4862 
4863  def set_is_optimized(self, a0, a1):
4864  """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4865  return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4866 
4867 
4868  def get_is_optimized(self, a0):
4869  """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4870  return _IMP_atom.Chain_get_is_optimized(self, a0)
4871 
4872 
4873  def get_check_level(self):
4874  """get_check_level(Chain self) -> IMP::CheckLevel"""
4875  return _IMP_atom.Chain_get_check_level(self)
4876 
4877 
4878  def __eq__(self, *args):
4879  """
4880  __eq__(Chain self, Chain o) -> bool
4881  __eq__(Chain self, Particle d) -> bool
4882  """
4883  return _IMP_atom.Chain___eq__(self, *args)
4884 
4885 
4886  def __ne__(self, *args):
4887  """
4888  __ne__(Chain self, Chain o) -> bool
4889  __ne__(Chain self, Particle d) -> bool
4890  """
4891  return _IMP_atom.Chain___ne__(self, *args)
4892 
4893 
4894  def __le__(self, *args):
4895  """
4896  __le__(Chain self, Chain o) -> bool
4897  __le__(Chain self, Particle d) -> bool
4898  """
4899  return _IMP_atom.Chain___le__(self, *args)
4900 
4901 
4902  def __lt__(self, *args):
4903  """
4904  __lt__(Chain self, Chain o) -> bool
4905  __lt__(Chain self, Particle d) -> bool
4906  """
4907  return _IMP_atom.Chain___lt__(self, *args)
4908 
4909 
4910  def __ge__(self, *args):
4911  """
4912  __ge__(Chain self, Chain o) -> bool
4913  __ge__(Chain self, Particle d) -> bool
4914  """
4915  return _IMP_atom.Chain___ge__(self, *args)
4916 
4917 
4918  def __gt__(self, *args):
4919  """
4920  __gt__(Chain self, Chain o) -> bool
4921  __gt__(Chain self, Particle d) -> bool
4922  """
4923  return _IMP_atom.Chain___gt__(self, *args)
4924 
4925 
4926  def __hash__(self):
4927  """__hash__(Chain self) -> std::size_t"""
4928  return _IMP_atom.Chain___hash__(self)
4929 
4930 
4931  def __str__(self):
4932  """__str__(Chain self) -> std::string"""
4933  return _IMP_atom.Chain___str__(self)
4934 
4935 
4936  def __repr__(self):
4937  """__repr__(Chain self) -> std::string"""
4938  return _IMP_atom.Chain___repr__(self)
4939 
4940  __swig_destroy__ = _IMP_atom.delete_Chain
4941  __del__ = lambda self: None
4942 Chain_swigregister = _IMP_atom.Chain_swigregister
4943 Chain_swigregister(Chain)
4944 
4945 def Chain_setup_particle(*args):
4946  """
4947  setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4948  setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4949  setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4950  setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4951  setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4952  Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4953  """
4954  return _IMP_atom.Chain_setup_particle(*args)
4955 
4956 def Chain_get_is_setup(*args):
4957  """
4958  get_is_setup(_ParticleAdaptor p) -> bool
4959  Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4960  """
4961  return _IMP_atom.Chain_get_is_setup(*args)
4962 
4963 def Chain_get_id_key():
4964  """Chain_get_id_key() -> StringKey"""
4965  return _IMP_atom.Chain_get_id_key()
4966 
4967 
4968 def get_chain(h):
4969  """get_chain(Hierarchy h) -> Chain"""
4970  return _IMP_atom.get_chain(h)
4971 
4972 def get_chain_id(h):
4973  """get_chain_id(Hierarchy h) -> std::string"""
4974  return _IMP_atom.get_chain_id(h)
4975 class Charged(IMP.core.XYZ):
4976  """Proxy of C++ IMP::atom::Charged class"""
4977  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4978 
4979  def __init__(self, *args):
4980  """
4981  __init__(IMP::atom::Charged self) -> Charged
4982  __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4983  __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4984  """
4985  this = _IMP_atom.new_Charged(*args)
4986  try:
4987  self.this.append(this)
4988  except:
4989  self.this = this
4990 
4991  def show(self, *args):
4992  """
4993  show(Charged self, _ostream out)
4994  show(Charged self)
4995  """
4996  return _IMP_atom.Charged_show(self, *args)
4997 
4998 
4999  def setup_particle(*args):
5000  """
5001  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5002  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5003  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5004  setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5005  """
5006  return _IMP_atom.Charged_setup_particle(*args)
5007 
5008  setup_particle = staticmethod(setup_particle)
5009 
5010  def get_charge(self):
5011  """get_charge(Charged self) -> IMP::Float"""
5012  return _IMP_atom.Charged_get_charge(self)
5013 
5014 
5015  def set_charge(self, t):
5016  """set_charge(Charged self, IMP::Float t)"""
5017  return _IMP_atom.Charged_set_charge(self, t)
5018 
5019 
5020  def get_is_setup(*args):
5021  """
5022  get_is_setup(_ParticleAdaptor p) -> bool
5023  get_is_setup(Model m, ParticleIndex pi) -> bool
5024  """
5025  return _IMP_atom.Charged_get_is_setup(*args)
5026 
5027  get_is_setup = staticmethod(get_is_setup)
5028 
5029  def get_charge_key():
5030  """get_charge_key() -> FloatKey"""
5031  return _IMP_atom.Charged_get_charge_key()
5032 
5033  get_charge_key = staticmethod(get_charge_key)
5034 
5035  def add_attribute(self, *args):
5036  """
5037  add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
5038  add_attribute(Charged self, FloatKey a0, IMP::Float a1)
5039  add_attribute(Charged self, IntKey a0, IMP::Int a1)
5040  add_attribute(Charged self, StringKey a0, IMP::String a1)
5041  add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
5042  add_attribute(Charged self, ObjectKey a0, Object a1)
5043  """
5044  return _IMP_atom.Charged_add_attribute(self, *args)
5045 
5046 
5047  def get_value(self, *args):
5048  """
5049  get_value(Charged self, FloatKey a0) -> IMP::Float
5050  get_value(Charged self, IntKey a0) -> IMP::Int
5051  get_value(Charged self, StringKey a0) -> IMP::String
5052  get_value(Charged self, ParticleIndexKey a0) -> Particle
5053  get_value(Charged self, ObjectKey a0) -> Object
5054  """
5055  return _IMP_atom.Charged_get_value(self, *args)
5056 
5057 
5058  def set_value(self, *args):
5059  """
5060  set_value(Charged self, FloatKey a0, IMP::Float a1)
5061  set_value(Charged self, IntKey a0, IMP::Int a1)
5062  set_value(Charged self, StringKey a0, IMP::String a1)
5063  set_value(Charged self, ParticleIndexKey a0, Particle a1)
5064  set_value(Charged self, ObjectKey a0, Object a1)
5065  """
5066  return _IMP_atom.Charged_set_value(self, *args)
5067 
5068 
5069  def remove_attribute(self, *args):
5070  """
5071  remove_attribute(Charged self, FloatKey a0)
5072  remove_attribute(Charged self, IntKey a0)
5073  remove_attribute(Charged self, StringKey a0)
5074  remove_attribute(Charged self, ParticleIndexKey a0)
5075  remove_attribute(Charged self, ObjectKey a0)
5076  """
5077  return _IMP_atom.Charged_remove_attribute(self, *args)
5078 
5079 
5080  def has_attribute(self, *args):
5081  """
5082  has_attribute(Charged self, FloatKey a0) -> bool
5083  has_attribute(Charged self, IntKey a0) -> bool
5084  has_attribute(Charged self, StringKey a0) -> bool
5085  has_attribute(Charged self, ParticleIndexKey a0) -> bool
5086  has_attribute(Charged self, ObjectKey a0) -> bool
5087  """
5088  return _IMP_atom.Charged_has_attribute(self, *args)
5089 
5090 
5091  def get_derivative(self, a0):
5092  """get_derivative(Charged self, FloatKey a0) -> double"""
5093  return _IMP_atom.Charged_get_derivative(self, a0)
5094 
5095 
5096  def get_name(self):
5097  """get_name(Charged self) -> std::string"""
5098  return _IMP_atom.Charged_get_name(self)
5099 
5100 
5101  def clear_caches(self):
5102  """clear_caches(Charged self)"""
5103  return _IMP_atom.Charged_clear_caches(self)
5104 
5105 
5106  def set_name(self, a0):
5107  """set_name(Charged self, std::string a0)"""
5108  return _IMP_atom.Charged_set_name(self, a0)
5109 
5110 
5111  def set_check_level(self, a0):
5112  """set_check_level(Charged self, IMP::CheckLevel a0)"""
5113  return _IMP_atom.Charged_set_check_level(self, a0)
5114 
5115 
5116  def add_to_derivative(self, a0, a1, a2):
5117  """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5118  return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
5119 
5120 
5121  def set_is_optimized(self, a0, a1):
5122  """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
5123  return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
5124 
5125 
5126  def get_is_optimized(self, a0):
5127  """get_is_optimized(Charged self, FloatKey a0) -> bool"""
5128  return _IMP_atom.Charged_get_is_optimized(self, a0)
5129 
5130 
5131  def get_check_level(self):
5132  """get_check_level(Charged self) -> IMP::CheckLevel"""
5133  return _IMP_atom.Charged_get_check_level(self)
5134 
5135 
5136  def __eq__(self, *args):
5137  """
5138  __eq__(Charged self, Charged o) -> bool
5139  __eq__(Charged self, Particle d) -> bool
5140  """
5141  return _IMP_atom.Charged___eq__(self, *args)
5142 
5143 
5144  def __ne__(self, *args):
5145  """
5146  __ne__(Charged self, Charged o) -> bool
5147  __ne__(Charged self, Particle d) -> bool
5148  """
5149  return _IMP_atom.Charged___ne__(self, *args)
5150 
5151 
5152  def __le__(self, *args):
5153  """
5154  __le__(Charged self, Charged o) -> bool
5155  __le__(Charged self, Particle d) -> bool
5156  """
5157  return _IMP_atom.Charged___le__(self, *args)
5158 
5159 
5160  def __lt__(self, *args):
5161  """
5162  __lt__(Charged self, Charged o) -> bool
5163  __lt__(Charged self, Particle d) -> bool
5164  """
5165  return _IMP_atom.Charged___lt__(self, *args)
5166 
5167 
5168  def __ge__(self, *args):
5169  """
5170  __ge__(Charged self, Charged o) -> bool
5171  __ge__(Charged self, Particle d) -> bool
5172  """
5173  return _IMP_atom.Charged___ge__(self, *args)
5174 
5175 
5176  def __gt__(self, *args):
5177  """
5178  __gt__(Charged self, Charged o) -> bool
5179  __gt__(Charged self, Particle d) -> bool
5180  """
5181  return _IMP_atom.Charged___gt__(self, *args)
5182 
5183 
5184  def __hash__(self):
5185  """__hash__(Charged self) -> std::size_t"""
5186  return _IMP_atom.Charged___hash__(self)
5187 
5188 
5189  def __str__(self):
5190  """__str__(Charged self) -> std::string"""
5191  return _IMP_atom.Charged___str__(self)
5192 
5193 
5194  def __repr__(self):
5195  """__repr__(Charged self) -> std::string"""
5196  return _IMP_atom.Charged___repr__(self)
5197 
5198  __swig_destroy__ = _IMP_atom.delete_Charged
5199  __del__ = lambda self: None
5200 Charged_swigregister = _IMP_atom.Charged_swigregister
5201 Charged_swigregister(Charged)
5202 
5203 def Charged_setup_particle(*args):
5204  """
5205  setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5206  setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5207  setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5208  Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5209  """
5210  return _IMP_atom.Charged_setup_particle(*args)
5211 
5212 def Charged_get_is_setup(*args):
5213  """
5214  get_is_setup(_ParticleAdaptor p) -> bool
5215  Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5216  """
5217  return _IMP_atom.Charged_get_is_setup(*args)
5218 
5219 def Charged_get_charge_key():
5220  """Charged_get_charge_key() -> FloatKey"""
5221  return _IMP_atom.Charged_get_charge_key()
5222 
5223 class CoulombPairScore(IMP.PairScore):
5224  """Proxy of C++ IMP::atom::CoulombPairScore class"""
5225  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5226 
5227  def __init__(self, f):
5228  """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5229  this = _IMP_atom.new_CoulombPairScore(f)
5230  try:
5231  self.this.append(this)
5232  except:
5233  self.this = this
5234 
5235  def set_relative_dielectric(self, relative_dielectric):
5236  """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5237  return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5238 
5239 
5240  def get_relative_dielectric(self):
5241  """get_relative_dielectric(CoulombPairScore self) -> double"""
5242  return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5243 
5244 
5245  def do_get_inputs(self, m, pis):
5246  """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5247  return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5248 
5249 
5250  def get_version_info(self):
5251  """get_version_info(CoulombPairScore self) -> VersionInfo"""
5252  return _IMP_atom.CoulombPairScore_get_version_info(self)
5253 
5254 
5255  def __str__(self):
5256  """__str__(CoulombPairScore self) -> std::string"""
5257  return _IMP_atom.CoulombPairScore___str__(self)
5258 
5259 
5260  def __repr__(self):
5261  """__repr__(CoulombPairScore self) -> std::string"""
5262  return _IMP_atom.CoulombPairScore___repr__(self)
5263 
5264 
5265  @staticmethod
5266  def get_from(o):
5267  return _object_cast_to_CoulombPairScore(o)
5268 
5269 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5270 CoulombPairScore_swigregister(CoulombPairScore)
5271 
5272 class Domain(Hierarchy):
5273  """Proxy of C++ IMP::atom::Domain class"""
5274  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5275 
5276  def set_index_range(self, ir):
5277  """set_index_range(Domain self, IMP::IntRange ir)"""
5278  return _IMP_atom.Domain_set_index_range(self, ir)
5279 
5280 
5281  def get_index_range(self):
5282  """get_index_range(Domain self) -> IMP::IntRange"""
5283  return _IMP_atom.Domain_get_index_range(self)
5284 
5285 
5286  def __init__(self, *args):
5287  """
5288  __init__(IMP::atom::Domain self) -> Domain
5289  __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5290  __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5291  """
5292  this = _IMP_atom.new_Domain(*args)
5293  try:
5294  self.this.append(this)
5295  except:
5296  self.this = this
5297 
5298  def get_is_setup(*args):
5299  """
5300  get_is_setup(Model m, ParticleIndex pi) -> bool
5301  get_is_setup(_ParticleAdaptor p) -> bool
5302  """
5303  return _IMP_atom.Domain_get_is_setup(*args)
5304 
5305  get_is_setup = staticmethod(get_is_setup)
5306 
5307  def show(self, *args):
5308  """
5309  show(Domain self, _ostream out)
5310  show(Domain self)
5311  """
5312  return _IMP_atom.Domain_show(self, *args)
5313 
5314 
5315  def setup_particle(*args):
5316  """
5317  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5318  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5319  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5320  setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5321  """
5322  return _IMP_atom.Domain_setup_particle(*args)
5323 
5324  setup_particle = staticmethod(setup_particle)
5325 
5326  def add_attribute(self, *args):
5327  """
5328  add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5329  add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5330  add_attribute(Domain self, IntKey a0, IMP::Int a1)
5331  add_attribute(Domain self, StringKey a0, IMP::String a1)
5332  add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5333  add_attribute(Domain self, ObjectKey a0, Object a1)
5334  """
5335  return _IMP_atom.Domain_add_attribute(self, *args)
5336 
5337 
5338  def get_value(self, *args):
5339  """
5340  get_value(Domain self, FloatKey a0) -> IMP::Float
5341  get_value(Domain self, IntKey a0) -> IMP::Int
5342  get_value(Domain self, StringKey a0) -> IMP::String
5343  get_value(Domain self, ParticleIndexKey a0) -> Particle
5344  get_value(Domain self, ObjectKey a0) -> Object
5345  """
5346  return _IMP_atom.Domain_get_value(self, *args)
5347 
5348 
5349  def set_value(self, *args):
5350  """
5351  set_value(Domain self, FloatKey a0, IMP::Float a1)
5352  set_value(Domain self, IntKey a0, IMP::Int a1)
5353  set_value(Domain self, StringKey a0, IMP::String a1)
5354  set_value(Domain self, ParticleIndexKey a0, Particle a1)
5355  set_value(Domain self, ObjectKey a0, Object a1)
5356  """
5357  return _IMP_atom.Domain_set_value(self, *args)
5358 
5359 
5360  def remove_attribute(self, *args):
5361  """
5362  remove_attribute(Domain self, FloatKey a0)
5363  remove_attribute(Domain self, IntKey a0)
5364  remove_attribute(Domain self, StringKey a0)
5365  remove_attribute(Domain self, ParticleIndexKey a0)
5366  remove_attribute(Domain self, ObjectKey a0)
5367  """
5368  return _IMP_atom.Domain_remove_attribute(self, *args)
5369 
5370 
5371  def has_attribute(self, *args):
5372  """
5373  has_attribute(Domain self, FloatKey a0) -> bool
5374  has_attribute(Domain self, IntKey a0) -> bool
5375  has_attribute(Domain self, StringKey a0) -> bool
5376  has_attribute(Domain self, ParticleIndexKey a0) -> bool
5377  has_attribute(Domain self, ObjectKey a0) -> bool
5378  """
5379  return _IMP_atom.Domain_has_attribute(self, *args)
5380 
5381 
5382  def get_derivative(self, a0):
5383  """get_derivative(Domain self, FloatKey a0) -> double"""
5384  return _IMP_atom.Domain_get_derivative(self, a0)
5385 
5386 
5387  def get_name(self):
5388  """get_name(Domain self) -> std::string"""
5389  return _IMP_atom.Domain_get_name(self)
5390 
5391 
5392  def clear_caches(self):
5393  """clear_caches(Domain self)"""
5394  return _IMP_atom.Domain_clear_caches(self)
5395 
5396 
5397  def set_name(self, a0):
5398  """set_name(Domain self, std::string a0)"""
5399  return _IMP_atom.Domain_set_name(self, a0)
5400 
5401 
5402  def set_check_level(self, a0):
5403  """set_check_level(Domain self, IMP::CheckLevel a0)"""
5404  return _IMP_atom.Domain_set_check_level(self, a0)
5405 
5406 
5407  def add_to_derivative(self, a0, a1, a2):
5408  """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5409  return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5410 
5411 
5412  def set_is_optimized(self, a0, a1):
5413  """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5414  return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5415 
5416 
5417  def get_is_optimized(self, a0):
5418  """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5419  return _IMP_atom.Domain_get_is_optimized(self, a0)
5420 
5421 
5422  def get_check_level(self):
5423  """get_check_level(Domain self) -> IMP::CheckLevel"""
5424  return _IMP_atom.Domain_get_check_level(self)
5425 
5426 
5427  def __eq__(self, *args):
5428  """
5429  __eq__(Domain self, Domain o) -> bool
5430  __eq__(Domain self, Particle d) -> bool
5431  """
5432  return _IMP_atom.Domain___eq__(self, *args)
5433 
5434 
5435  def __ne__(self, *args):
5436  """
5437  __ne__(Domain self, Domain o) -> bool
5438  __ne__(Domain self, Particle d) -> bool
5439  """
5440  return _IMP_atom.Domain___ne__(self, *args)
5441 
5442 
5443  def __le__(self, *args):
5444  """
5445  __le__(Domain self, Domain o) -> bool
5446  __le__(Domain self, Particle d) -> bool
5447  """
5448  return _IMP_atom.Domain___le__(self, *args)
5449 
5450 
5451  def __lt__(self, *args):
5452  """
5453  __lt__(Domain self, Domain o) -> bool
5454  __lt__(Domain self, Particle d) -> bool
5455  """
5456  return _IMP_atom.Domain___lt__(self, *args)
5457 
5458 
5459  def __ge__(self, *args):
5460  """
5461  __ge__(Domain self, Domain o) -> bool
5462  __ge__(Domain self, Particle d) -> bool
5463  """
5464  return _IMP_atom.Domain___ge__(self, *args)
5465 
5466 
5467  def __gt__(self, *args):
5468  """
5469  __gt__(Domain self, Domain o) -> bool
5470  __gt__(Domain self, Particle d) -> bool
5471  """
5472  return _IMP_atom.Domain___gt__(self, *args)
5473 
5474 
5475  def __hash__(self):
5476  """__hash__(Domain self) -> std::size_t"""
5477  return _IMP_atom.Domain___hash__(self)
5478 
5479 
5480  def __str__(self):
5481  """__str__(Domain self) -> std::string"""
5482  return _IMP_atom.Domain___str__(self)
5483 
5484 
5485  def __repr__(self):
5486  """__repr__(Domain self) -> std::string"""
5487  return _IMP_atom.Domain___repr__(self)
5488 
5489  __swig_destroy__ = _IMP_atom.delete_Domain
5490  __del__ = lambda self: None
5491 Domain_swigregister = _IMP_atom.Domain_swigregister
5492 Domain_swigregister(Domain)
5493 
5494 def Domain_get_is_setup(*args):
5495  """
5496  get_is_setup(Model m, ParticleIndex pi) -> bool
5497  Domain_get_is_setup(_ParticleAdaptor p) -> bool
5498  """
5499  return _IMP_atom.Domain_get_is_setup(*args)
5500 
5501 def Domain_setup_particle(*args):
5502  """
5503  setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5504  setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5505  setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5506  Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5507  """
5508  return _IMP_atom.Domain_setup_particle(*args)
5509 
5510 class LennardJones(IMP.core.XYZR):
5511  """Proxy of C++ IMP::atom::LennardJones class"""
5512  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5513 
5514  def __init__(self, *args):
5515  """
5516  __init__(IMP::atom::LennardJones self) -> LennardJones
5517  __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5518  __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5519  """
5520  this = _IMP_atom.new_LennardJones(*args)
5521  try:
5522  self.this.append(this)
5523  except:
5524  self.this = this
5525 
5526  def show(self, *args):
5527  """
5528  show(LennardJones self, _ostream out)
5529  show(LennardJones self)
5530  """
5531  return _IMP_atom.LennardJones_show(self, *args)
5532 
5533 
5534  def setup_particle(*args):
5535  """
5536  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5537  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5538  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5539  setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5540  """
5541  return _IMP_atom.LennardJones_setup_particle(*args)
5542 
5543  setup_particle = staticmethod(setup_particle)
5544 
5545  def get_well_depth(self):
5546  """get_well_depth(LennardJones self) -> IMP::Float"""
5547  return _IMP_atom.LennardJones_get_well_depth(self)
5548 
5549 
5550  def set_well_depth(self, well_depth):
5551  """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5552  return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5553 
5554 
5555  def get_is_setup(*args):
5556  """
5557  get_is_setup(_ParticleAdaptor p) -> bool
5558  get_is_setup(Model m, ParticleIndex pi) -> bool
5559  """
5560  return _IMP_atom.LennardJones_get_is_setup(*args)
5561 
5562  get_is_setup = staticmethod(get_is_setup)
5563 
5564  def get_well_depth_key():
5565  """get_well_depth_key() -> FloatKey"""
5566  return _IMP_atom.LennardJones_get_well_depth_key()
5567 
5568  get_well_depth_key = staticmethod(get_well_depth_key)
5569 
5570  def add_attribute(self, *args):
5571  """
5572  add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5573  add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5574  add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5575  add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5576  add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5577  add_attribute(LennardJones self, ObjectKey a0, Object a1)
5578  """
5579  return _IMP_atom.LennardJones_add_attribute(self, *args)
5580 
5581 
5582  def get_value(self, *args):
5583  """
5584  get_value(LennardJones self, FloatKey a0) -> IMP::Float
5585  get_value(LennardJones self, IntKey a0) -> IMP::Int
5586  get_value(LennardJones self, StringKey a0) -> IMP::String
5587  get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5588  get_value(LennardJones self, ObjectKey a0) -> Object
5589  """
5590  return _IMP_atom.LennardJones_get_value(self, *args)
5591 
5592 
5593  def set_value(self, *args):
5594  """
5595  set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5596  set_value(LennardJones self, IntKey a0, IMP::Int a1)
5597  set_value(LennardJones self, StringKey a0, IMP::String a1)
5598  set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5599  set_value(LennardJones self, ObjectKey a0, Object a1)
5600  """
5601  return _IMP_atom.LennardJones_set_value(self, *args)
5602 
5603 
5604  def remove_attribute(self, *args):
5605  """
5606  remove_attribute(LennardJones self, FloatKey a0)
5607  remove_attribute(LennardJones self, IntKey a0)
5608  remove_attribute(LennardJones self, StringKey a0)
5609  remove_attribute(LennardJones self, ParticleIndexKey a0)
5610  remove_attribute(LennardJones self, ObjectKey a0)
5611  """
5612  return _IMP_atom.LennardJones_remove_attribute(self, *args)
5613 
5614 
5615  def has_attribute(self, *args):
5616  """
5617  has_attribute(LennardJones self, FloatKey a0) -> bool
5618  has_attribute(LennardJones self, IntKey a0) -> bool
5619  has_attribute(LennardJones self, StringKey a0) -> bool
5620  has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5621  has_attribute(LennardJones self, ObjectKey a0) -> bool
5622  """
5623  return _IMP_atom.LennardJones_has_attribute(self, *args)
5624 
5625 
5626  def get_derivative(self, a0):
5627  """get_derivative(LennardJones self, FloatKey a0) -> double"""
5628  return _IMP_atom.LennardJones_get_derivative(self, a0)
5629 
5630 
5631  def get_name(self):
5632  """get_name(LennardJones self) -> std::string"""
5633  return _IMP_atom.LennardJones_get_name(self)
5634 
5635 
5636  def clear_caches(self):
5637  """clear_caches(LennardJones self)"""
5638  return _IMP_atom.LennardJones_clear_caches(self)
5639 
5640 
5641  def set_name(self, a0):
5642  """set_name(LennardJones self, std::string a0)"""
5643  return _IMP_atom.LennardJones_set_name(self, a0)
5644 
5645 
5646  def set_check_level(self, a0):
5647  """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5648  return _IMP_atom.LennardJones_set_check_level(self, a0)
5649 
5650 
5651  def add_to_derivative(self, a0, a1, a2):
5652  """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5653  return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5654 
5655 
5656  def set_is_optimized(self, a0, a1):
5657  """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5658  return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5659 
5660 
5661  def get_is_optimized(self, a0):
5662  """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5663  return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5664 
5665 
5666  def get_check_level(self):
5667  """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5668  return _IMP_atom.LennardJones_get_check_level(self)
5669 
5670 
5671  def __eq__(self, *args):
5672  """
5673  __eq__(LennardJones self, LennardJones o) -> bool
5674  __eq__(LennardJones self, Particle d) -> bool
5675  """
5676  return _IMP_atom.LennardJones___eq__(self, *args)
5677 
5678 
5679  def __ne__(self, *args):
5680  """
5681  __ne__(LennardJones self, LennardJones o) -> bool
5682  __ne__(LennardJones self, Particle d) -> bool
5683  """
5684  return _IMP_atom.LennardJones___ne__(self, *args)
5685 
5686 
5687  def __le__(self, *args):
5688  """
5689  __le__(LennardJones self, LennardJones o) -> bool
5690  __le__(LennardJones self, Particle d) -> bool
5691  """
5692  return _IMP_atom.LennardJones___le__(self, *args)
5693 
5694 
5695  def __lt__(self, *args):
5696  """
5697  __lt__(LennardJones self, LennardJones o) -> bool
5698  __lt__(LennardJones self, Particle d) -> bool
5699  """
5700  return _IMP_atom.LennardJones___lt__(self, *args)
5701 
5702 
5703  def __ge__(self, *args):
5704  """
5705  __ge__(LennardJones self, LennardJones o) -> bool
5706  __ge__(LennardJones self, Particle d) -> bool
5707  """
5708  return _IMP_atom.LennardJones___ge__(self, *args)
5709 
5710 
5711  def __gt__(self, *args):
5712  """
5713  __gt__(LennardJones self, LennardJones o) -> bool
5714  __gt__(LennardJones self, Particle d) -> bool
5715  """
5716  return _IMP_atom.LennardJones___gt__(self, *args)
5717 
5718 
5719  def __hash__(self):
5720  """__hash__(LennardJones self) -> std::size_t"""
5721  return _IMP_atom.LennardJones___hash__(self)
5722 
5723 
5724  def __str__(self):
5725  """__str__(LennardJones self) -> std::string"""
5726  return _IMP_atom.LennardJones___str__(self)
5727 
5728 
5729  def __repr__(self):
5730  """__repr__(LennardJones self) -> std::string"""
5731  return _IMP_atom.LennardJones___repr__(self)
5732 
5733  __swig_destroy__ = _IMP_atom.delete_LennardJones
5734  __del__ = lambda self: None
5735 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5736 LennardJones_swigregister(LennardJones)
5737 
5738 def LennardJones_setup_particle(*args):
5739  """
5740  setup_particle(Model m, ParticleIndex pi) -> LennardJones
5741  setup_particle(_ParticleAdaptor decorator) -> LennardJones
5742  setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5743  LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5744  """
5745  return _IMP_atom.LennardJones_setup_particle(*args)
5746 
5747 def LennardJones_get_is_setup(*args):
5748  """
5749  get_is_setup(_ParticleAdaptor p) -> bool
5750  LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5751  """
5752  return _IMP_atom.LennardJones_get_is_setup(*args)
5753 
5754 def LennardJones_get_well_depth_key():
5755  """LennardJones_get_well_depth_key() -> FloatKey"""
5756  return _IMP_atom.LennardJones_get_well_depth_key()
5757 
5758 class LennardJonesPairScore(IMP.PairScore):
5759  """Proxy of C++ IMP::atom::LennardJonesPairScore class"""
5760  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5761 
5762  def __init__(self, f):
5763  """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5764  this = _IMP_atom.new_LennardJonesPairScore(f)
5765  try:
5766  self.this.append(this)
5767  except:
5768  self.this = this
5769 
5770  def set_repulsive_weight(self, repulsive_weight):
5771  """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5772  return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5773 
5774 
5775  def get_repulsive_weight(self):
5776  """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5777  return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5778 
5779 
5780  def set_attractive_weight(self, attractive_weight):
5781  """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5782  return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5783 
5784 
5785  def get_attractive_weight(self):
5786  """get_attractive_weight(LennardJonesPairScore self) -> double"""
5787  return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5788 
5789 
5790  def do_get_inputs(self, m, pis):
5791  """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5792  return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5793 
5794 
5795  def get_version_info(self):
5796  """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5797  return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5798 
5799 
5800  def __str__(self):
5801  """__str__(LennardJonesPairScore self) -> std::string"""
5802  return _IMP_atom.LennardJonesPairScore___str__(self)
5803 
5804 
5805  def __repr__(self):
5806  """__repr__(LennardJonesPairScore self) -> std::string"""
5807  return _IMP_atom.LennardJonesPairScore___repr__(self)
5808 
5809 
5810  @staticmethod
5811  def get_from(o):
5812  return _object_cast_to_LennardJonesPairScore(o)
5813 
5814 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5815 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5816 
5817 class LinearVelocity(IMP.Decorator):
5818  """Proxy of C++ IMP::atom::LinearVelocity class"""
5819  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5820 
5821  def get_velocity_key(i):
5822  """get_velocity_key(unsigned int i) -> FloatKey"""
5823  return _IMP_atom.LinearVelocity_get_velocity_key(i)
5824 
5825  get_velocity_key = staticmethod(get_velocity_key)
5826 
5827  def __init__(self, *args):
5828  """
5829  __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5830  __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5831  __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5832  """
5833  this = _IMP_atom.new_LinearVelocity(*args)
5834  try:
5835  self.this.append(this)
5836  except:
5837  self.this = this
5838 
5839  def get_is_setup(*args):
5840  """
5841  get_is_setup(Model m, ParticleIndex pi) -> bool
5842  get_is_setup(_ParticleAdaptor p) -> bool
5843  """
5844  return _IMP_atom.LinearVelocity_get_is_setup(*args)
5845 
5846  get_is_setup = staticmethod(get_is_setup)
5847 
5848  def show(self, *args):
5849  """
5850  show(LinearVelocity self, _ostream out)
5851  show(LinearVelocity self)
5852  """
5853  return _IMP_atom.LinearVelocity_show(self, *args)
5854 
5855 
5856  def setup_particle(*args):
5857  """
5858  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5859  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5860  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5861  setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5862  """
5863  return _IMP_atom.LinearVelocity_setup_particle(*args)
5864 
5865  setup_particle = staticmethod(setup_particle)
5866 
5867  def set_velocity(self, v):
5868  """set_velocity(LinearVelocity self, Vector3D v)"""
5869  return _IMP_atom.LinearVelocity_set_velocity(self, v)
5870 
5871 
5872  def get_velocity(self):
5873  """get_velocity(LinearVelocity self) -> Vector3D"""
5874  return _IMP_atom.LinearVelocity_get_velocity(self)
5875 
5876 
5877  def add_attribute(self, *args):
5878  """
5879  add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5880  add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5881  add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5882  add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5883  add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5884  add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5885  """
5886  return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5887 
5888 
5889  def get_value(self, *args):
5890  """
5891  get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5892  get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5893  get_value(LinearVelocity self, StringKey a0) -> IMP::String
5894  get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5895  get_value(LinearVelocity self, ObjectKey a0) -> Object
5896  """
5897  return _IMP_atom.LinearVelocity_get_value(self, *args)
5898 
5899 
5900  def set_value(self, *args):
5901  """
5902  set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5903  set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5904  set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5905  set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5906  set_value(LinearVelocity self, ObjectKey a0, Object a1)
5907  """
5908  return _IMP_atom.LinearVelocity_set_value(self, *args)
5909 
5910 
5911  def remove_attribute(self, *args):
5912  """
5913  remove_attribute(LinearVelocity self, FloatKey a0)
5914  remove_attribute(LinearVelocity self, IntKey a0)
5915  remove_attribute(LinearVelocity self, StringKey a0)
5916  remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5917  remove_attribute(LinearVelocity self, ObjectKey a0)
5918  """
5919  return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5920 
5921 
5922  def has_attribute(self, *args):
5923  """
5924  has_attribute(LinearVelocity self, FloatKey a0) -> bool
5925  has_attribute(LinearVelocity self, IntKey a0) -> bool
5926  has_attribute(LinearVelocity self, StringKey a0) -> bool
5927  has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5928  has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5929  """
5930  return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5931 
5932 
5933  def get_derivative(self, a0):
5934  """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5935  return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5936 
5937 
5938  def get_name(self):
5939  """get_name(LinearVelocity self) -> std::string"""
5940  return _IMP_atom.LinearVelocity_get_name(self)
5941 
5942 
5943  def clear_caches(self):
5944  """clear_caches(LinearVelocity self)"""
5945  return _IMP_atom.LinearVelocity_clear_caches(self)
5946 
5947 
5948  def set_name(self, a0):
5949  """set_name(LinearVelocity self, std::string a0)"""
5950  return _IMP_atom.LinearVelocity_set_name(self, a0)
5951 
5952 
5953  def set_check_level(self, a0):
5954  """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5955  return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5956 
5957 
5958  def add_to_derivative(self, a0, a1, a2):
5959  """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5960  return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5961 
5962 
5963  def set_is_optimized(self, a0, a1):
5964  """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5965  return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5966 
5967 
5968  def get_is_optimized(self, a0):
5969  """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5970  return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5971 
5972 
5973  def get_check_level(self):
5974  """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5975  return _IMP_atom.LinearVelocity_get_check_level(self)
5976 
5977 
5978  def __eq__(self, *args):
5979  """
5980  __eq__(LinearVelocity self, LinearVelocity o) -> bool
5981  __eq__(LinearVelocity self, Particle d) -> bool
5982  """
5983  return _IMP_atom.LinearVelocity___eq__(self, *args)
5984 
5985 
5986  def __ne__(self, *args):
5987  """
5988  __ne__(LinearVelocity self, LinearVelocity o) -> bool
5989  __ne__(LinearVelocity self, Particle d) -> bool
5990  """
5991  return _IMP_atom.LinearVelocity___ne__(self, *args)
5992 
5993 
5994  def __le__(self, *args):
5995  """
5996  __le__(LinearVelocity self, LinearVelocity o) -> bool
5997  __le__(LinearVelocity self, Particle d) -> bool
5998  """
5999  return _IMP_atom.LinearVelocity___le__(self, *args)
6000 
6001 
6002  def __lt__(self, *args):
6003  """
6004  __lt__(LinearVelocity self, LinearVelocity o) -> bool
6005  __lt__(LinearVelocity self, Particle d) -> bool
6006  """
6007  return _IMP_atom.LinearVelocity___lt__(self, *args)
6008 
6009 
6010  def __ge__(self, *args):
6011  """
6012  __ge__(LinearVelocity self, LinearVelocity o) -> bool
6013  __ge__(LinearVelocity self, Particle d) -> bool
6014  """
6015  return _IMP_atom.LinearVelocity___ge__(self, *args)
6016 
6017 
6018  def __gt__(self, *args):
6019  """
6020  __gt__(LinearVelocity self, LinearVelocity o) -> bool
6021  __gt__(LinearVelocity self, Particle d) -> bool
6022  """
6023  return _IMP_atom.LinearVelocity___gt__(self, *args)
6024 
6025 
6026  def __hash__(self):
6027  """__hash__(LinearVelocity self) -> std::size_t"""
6028  return _IMP_atom.LinearVelocity___hash__(self)
6029 
6030 
6031  def __str__(self):
6032  """__str__(LinearVelocity self) -> std::string"""
6033  return _IMP_atom.LinearVelocity___str__(self)
6034 
6035 
6036  def __repr__(self):
6037  """__repr__(LinearVelocity self) -> std::string"""
6038  return _IMP_atom.LinearVelocity___repr__(self)
6039 
6040  __swig_destroy__ = _IMP_atom.delete_LinearVelocity
6041  __del__ = lambda self: None
6042 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
6043 LinearVelocity_swigregister(LinearVelocity)
6044 
6045 def LinearVelocity_get_velocity_key(i):
6046  """LinearVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6047  return _IMP_atom.LinearVelocity_get_velocity_key(i)
6048 
6049 def LinearVelocity_get_is_setup(*args):
6050  """
6051  get_is_setup(Model m, ParticleIndex pi) -> bool
6052  LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6053  """
6054  return _IMP_atom.LinearVelocity_get_is_setup(*args)
6055 
6056 def LinearVelocity_setup_particle(*args):
6057  """
6058  setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
6059  setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
6060  setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
6061  LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
6062  """
6063  return _IMP_atom.LinearVelocity_setup_particle(*args)
6064 
6065 class AngularVelocity(IMP.Decorator):
6066  """Proxy of C++ IMP::atom::AngularVelocity class"""
6067  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6068 
6069  def get_velocity_key(i):
6070  """get_velocity_key(unsigned int i) -> FloatKey"""
6071  return _IMP_atom.AngularVelocity_get_velocity_key(i)
6072 
6073  get_velocity_key = staticmethod(get_velocity_key)
6074 
6075  def __init__(self, *args):
6076  """
6077  __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
6078  __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
6079  __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
6080  """
6081  this = _IMP_atom.new_AngularVelocity(*args)
6082  try:
6083  self.this.append(this)
6084  except:
6085  self.this = this
6086 
6087  def get_is_setup(*args):
6088  """
6089  get_is_setup(Model m, ParticleIndex pi) -> bool
6090  get_is_setup(_ParticleAdaptor p) -> bool
6091  """
6092  return _IMP_atom.AngularVelocity_get_is_setup(*args)
6093 
6094  get_is_setup = staticmethod(get_is_setup)
6095 
6096  def show(self, *args):
6097  """
6098  show(AngularVelocity self, _ostream out)
6099  show(AngularVelocity self)
6100  """
6101  return _IMP_atom.AngularVelocity_show(self, *args)
6102 
6103 
6104  def setup_particle(*args):
6105  """
6106  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6107  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6108  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6109  setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6110  """
6111  return _IMP_atom.AngularVelocity_setup_particle(*args)
6112 
6113  setup_particle = staticmethod(setup_particle)
6114 
6115  def set_velocity(self, v):
6116  """set_velocity(AngularVelocity self, Vector4D v)"""
6117  return _IMP_atom.AngularVelocity_set_velocity(self, v)
6118 
6119 
6120  def get_velocity(self):
6121  """get_velocity(AngularVelocity self) -> Vector4D"""
6122  return _IMP_atom.AngularVelocity_get_velocity(self)
6123 
6124 
6125  def add_attribute(self, *args):
6126  """
6127  add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
6128  add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
6129  add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
6130  add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
6131  add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6132  add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
6133  """
6134  return _IMP_atom.AngularVelocity_add_attribute(self, *args)
6135 
6136 
6137  def get_value(self, *args):
6138  """
6139  get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
6140  get_value(AngularVelocity self, IntKey a0) -> IMP::Int
6141  get_value(AngularVelocity self, StringKey a0) -> IMP::String
6142  get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
6143  get_value(AngularVelocity self, ObjectKey a0) -> Object
6144  """
6145  return _IMP_atom.AngularVelocity_get_value(self, *args)
6146 
6147 
6148  def set_value(self, *args):
6149  """
6150  set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
6151  set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
6152  set_value(AngularVelocity self, StringKey a0, IMP::String a1)
6153  set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6154  set_value(AngularVelocity self, ObjectKey a0, Object a1)
6155  """
6156  return _IMP_atom.AngularVelocity_set_value(self, *args)
6157 
6158 
6159  def remove_attribute(self, *args):
6160  """
6161  remove_attribute(AngularVelocity self, FloatKey a0)
6162  remove_attribute(AngularVelocity self, IntKey a0)
6163  remove_attribute(AngularVelocity self, StringKey a0)
6164  remove_attribute(AngularVelocity self, ParticleIndexKey a0)
6165  remove_attribute(AngularVelocity self, ObjectKey a0)
6166  """
6167  return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
6168 
6169 
6170  def has_attribute(self, *args):
6171  """
6172  has_attribute(AngularVelocity self, FloatKey a0) -> bool
6173  has_attribute(AngularVelocity self, IntKey a0) -> bool
6174  has_attribute(AngularVelocity self, StringKey a0) -> bool
6175  has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6176  has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6177  """
6178  return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6179 
6180 
6181  def get_derivative(self, a0):
6182  """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6183  return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6184 
6185 
6186  def get_name(self):
6187  """get_name(AngularVelocity self) -> std::string"""
6188  return _IMP_atom.AngularVelocity_get_name(self)
6189 
6190 
6191  def clear_caches(self):
6192  """clear_caches(AngularVelocity self)"""
6193  return _IMP_atom.AngularVelocity_clear_caches(self)
6194 
6195 
6196  def set_name(self, a0):
6197  """set_name(AngularVelocity self, std::string a0)"""
6198  return _IMP_atom.AngularVelocity_set_name(self, a0)
6199 
6200 
6201  def set_check_level(self, a0):
6202  """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6203  return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6204 
6205 
6206  def add_to_derivative(self, a0, a1, a2):
6207  """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6208  return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6209 
6210 
6211  def set_is_optimized(self, a0, a1):
6212  """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6213  return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6214 
6215 
6216  def get_is_optimized(self, a0):
6217  """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6218  return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6219 
6220 
6221  def get_check_level(self):
6222  """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6223  return _IMP_atom.AngularVelocity_get_check_level(self)
6224 
6225 
6226  def __eq__(self, *args):
6227  """
6228  __eq__(AngularVelocity self, AngularVelocity o) -> bool
6229  __eq__(AngularVelocity self, Particle d) -> bool
6230  """
6231  return _IMP_atom.AngularVelocity___eq__(self, *args)
6232 
6233 
6234  def __ne__(self, *args):
6235  """
6236  __ne__(AngularVelocity self, AngularVelocity o) -> bool
6237  __ne__(AngularVelocity self, Particle d) -> bool
6238  """
6239  return _IMP_atom.AngularVelocity___ne__(self, *args)
6240 
6241 
6242  def __le__(self, *args):
6243  """
6244  __le__(AngularVelocity self, AngularVelocity o) -> bool
6245  __le__(AngularVelocity self, Particle d) -> bool
6246  """
6247  return _IMP_atom.AngularVelocity___le__(self, *args)
6248 
6249 
6250  def __lt__(self, *args):
6251  """
6252  __lt__(AngularVelocity self, AngularVelocity o) -> bool
6253  __lt__(AngularVelocity self, Particle d) -> bool
6254  """
6255  return _IMP_atom.AngularVelocity___lt__(self, *args)
6256 
6257 
6258  def __ge__(self, *args):
6259  """
6260  __ge__(AngularVelocity self, AngularVelocity o) -> bool
6261  __ge__(AngularVelocity self, Particle d) -> bool
6262  """
6263  return _IMP_atom.AngularVelocity___ge__(self, *args)
6264 
6265 
6266  def __gt__(self, *args):
6267  """
6268  __gt__(AngularVelocity self, AngularVelocity o) -> bool
6269  __gt__(AngularVelocity self, Particle d) -> bool
6270  """
6271  return _IMP_atom.AngularVelocity___gt__(self, *args)
6272 
6273 
6274  def __hash__(self):
6275  """__hash__(AngularVelocity self) -> std::size_t"""
6276  return _IMP_atom.AngularVelocity___hash__(self)
6277 
6278 
6279  def __str__(self):
6280  """__str__(AngularVelocity self) -> std::string"""
6281  return _IMP_atom.AngularVelocity___str__(self)
6282 
6283 
6284  def __repr__(self):
6285  """__repr__(AngularVelocity self) -> std::string"""
6286  return _IMP_atom.AngularVelocity___repr__(self)
6287 
6288  __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6289  __del__ = lambda self: None
6290 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6291 AngularVelocity_swigregister(AngularVelocity)
6292 
6293 def AngularVelocity_get_velocity_key(i):
6294  """AngularVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6295  return _IMP_atom.AngularVelocity_get_velocity_key(i)
6296 
6297 def AngularVelocity_get_is_setup(*args):
6298  """
6299  get_is_setup(Model m, ParticleIndex pi) -> bool
6300  AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6301  """
6302  return _IMP_atom.AngularVelocity_get_is_setup(*args)
6303 
6304 def AngularVelocity_setup_particle(*args):
6305  """
6306  setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6307  setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6308  setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6309  AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6310  """
6311  return _IMP_atom.AngularVelocity_setup_particle(*args)
6312 
6313 class MolecularDynamics(Simulator):
6314  """Proxy of C++ IMP::atom::MolecularDynamics class"""
6315  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6316 
6317  def __init__(self, m):
6318  """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6319  this = _IMP_atom.new_MolecularDynamics(m)
6320  try:
6321  self.this.append(this)
6322  except:
6323  self.this = this
6324 
6325  def get_kinetic_energy(self):
6326  """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6327  return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6328 
6329 
6330  def get_kinetic_temperature(self, ekinetic):
6331  """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6332  return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6333 
6334 
6335  def set_velocity_cap(self, velocity_cap):
6336  """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6337  return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6338 
6339 
6340  def assign_velocities(self, temperature):
6341  """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6342  return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6343 
6344 
6345  def setup(self, ps):
6346  """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6347  return _IMP_atom.MolecularDynamics_setup(self, ps)
6348 
6349 
6350  def do_step(self, sc, dt):
6351  """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6352  return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6353 
6354 
6355  def get_is_simulation_particle(self, p):
6356  """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6357  return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6358 
6359 
6360  def get_version_info(self):
6361  """get_version_info(MolecularDynamics self) -> VersionInfo"""
6362  return _IMP_atom.MolecularDynamics_get_version_info(self)
6363 
6364 
6365  def __str__(self):
6366  """__str__(MolecularDynamics self) -> std::string"""
6367  return _IMP_atom.MolecularDynamics___str__(self)
6368 
6369 
6370  def __repr__(self):
6371  """__repr__(MolecularDynamics self) -> std::string"""
6372  return _IMP_atom.MolecularDynamics___repr__(self)
6373 
6374 
6375  @staticmethod
6376  def get_from(o):
6377  return _object_cast_to_MolecularDynamics(o)
6378 
6379 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6380 MolecularDynamics_swigregister(MolecularDynamics)
6381 
6382 class VelocityScalingOptimizerState(IMP.OptimizerState):
6383  """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class"""
6384  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6385 
6386  def __init__(self, m, pis, temperature):
6387  """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6388  this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6389  try:
6390  self.this.append(this)
6391  except:
6392  self.this = this
6393 
6394  def set_particles(self, pis):
6395  """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6396  return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6397 
6398 
6399  def set_temperature(self, temperature):
6400  """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6401  return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6402 
6403 
6404  def rescale_velocities(self):
6405  """rescale_velocities(VelocityScalingOptimizerState self)"""
6406  return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6407 
6408 
6409  def get_version_info(self):
6410  """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6411  return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6412 
6413 
6414  def __str__(self):
6415  """__str__(VelocityScalingOptimizerState self) -> std::string"""
6416  return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6417 
6418 
6419  def __repr__(self):
6420  """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6421  return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6422 
6423 
6424  @staticmethod
6425  def get_from(o):
6426  return _object_cast_to_VelocityScalingOptimizerState(o)
6427 
6428 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6429 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6430 
6431 class Fragment(Hierarchy):
6432  """Proxy of C++ IMP::atom::Fragment class"""
6433  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6434 
6435  def set_residue_indexes(self, o):
6436  """set_residue_indexes(Fragment self, IMP::Ints o)"""
6437  return _IMP_atom.Fragment_set_residue_indexes(self, o)
6438 
6439 
6440  def get_residue_indexes(self):
6441  """get_residue_indexes(Fragment self) -> IMP::Ints"""
6442  return _IMP_atom.Fragment_get_residue_indexes(self)
6443 
6444 
6445  def get_contains_residue(self, rindex):
6446  """get_contains_residue(Fragment self, int rindex) -> bool"""
6447  return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6448 
6449 
6450  def __init__(self, *args):
6451  """
6452  __init__(IMP::atom::Fragment self) -> Fragment
6453  __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6454  __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6455  """
6456  this = _IMP_atom.new_Fragment(*args)
6457  try:
6458  self.this.append(this)
6459  except:
6460  self.this = this
6461 
6462  def get_is_setup(*args):
6463  """
6464  get_is_setup(Model m, ParticleIndex pi) -> bool
6465  get_is_setup(_ParticleAdaptor p) -> bool
6466  """
6467  return _IMP_atom.Fragment_get_is_setup(*args)
6468 
6469  get_is_setup = staticmethod(get_is_setup)
6470 
6471  def show(self, *args):
6472  """
6473  show(Fragment self, _ostream out)
6474  show(Fragment self)
6475  """
6476  return _IMP_atom.Fragment_show(self, *args)
6477 
6478 
6479  def setup_particle(*args):
6480  """
6481  setup_particle(Model m, ParticleIndex pi) -> Fragment
6482  setup_particle(_ParticleAdaptor decorator) -> Fragment
6483  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6484  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6485  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6486  setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6487  """
6488  return _IMP_atom.Fragment_setup_particle(*args)
6489 
6490  setup_particle = staticmethod(setup_particle)
6491 
6492  def add_attribute(self, *args):
6493  """
6494  add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6495  add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6496  add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6497  add_attribute(Fragment self, StringKey a0, IMP::String a1)
6498  add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6499  add_attribute(Fragment self, ObjectKey a0, Object a1)
6500  """
6501  return _IMP_atom.Fragment_add_attribute(self, *args)
6502 
6503 
6504  def get_value(self, *args):
6505  """
6506  get_value(Fragment self, FloatKey a0) -> IMP::Float
6507  get_value(Fragment self, IntKey a0) -> IMP::Int
6508  get_value(Fragment self, StringKey a0) -> IMP::String
6509  get_value(Fragment self, ParticleIndexKey a0) -> Particle
6510  get_value(Fragment self, ObjectKey a0) -> Object
6511  """
6512  return _IMP_atom.Fragment_get_value(self, *args)
6513 
6514 
6515  def set_value(self, *args):
6516  """
6517  set_value(Fragment self, FloatKey a0, IMP::Float a1)
6518  set_value(Fragment self, IntKey a0, IMP::Int a1)
6519  set_value(Fragment self, StringKey a0, IMP::String a1)
6520  set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6521  set_value(Fragment self, ObjectKey a0, Object a1)
6522  """
6523  return _IMP_atom.Fragment_set_value(self, *args)
6524 
6525 
6526  def remove_attribute(self, *args):
6527  """
6528  remove_attribute(Fragment self, FloatKey a0)
6529  remove_attribute(Fragment self, IntKey a0)
6530  remove_attribute(Fragment self, StringKey a0)
6531  remove_attribute(Fragment self, ParticleIndexKey a0)
6532  remove_attribute(Fragment self, ObjectKey a0)
6533  """
6534  return _IMP_atom.Fragment_remove_attribute(self, *args)
6535 
6536 
6537  def has_attribute(self, *args):
6538  """
6539  has_attribute(Fragment self, FloatKey a0) -> bool
6540  has_attribute(Fragment self, IntKey a0) -> bool
6541  has_attribute(Fragment self, StringKey a0) -> bool
6542  has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6543  has_attribute(Fragment self, ObjectKey a0) -> bool
6544  """
6545  return _IMP_atom.Fragment_has_attribute(self, *args)
6546 
6547 
6548  def get_derivative(self, a0):
6549  """get_derivative(Fragment self, FloatKey a0) -> double"""
6550  return _IMP_atom.Fragment_get_derivative(self, a0)
6551 
6552 
6553  def get_name(self):
6554  """get_name(Fragment self) -> std::string"""
6555  return _IMP_atom.Fragment_get_name(self)
6556 
6557 
6558  def clear_caches(self):
6559  """clear_caches(Fragment self)"""
6560  return _IMP_atom.Fragment_clear_caches(self)
6561 
6562 
6563  def set_name(self, a0):
6564  """set_name(Fragment self, std::string a0)"""
6565  return _IMP_atom.Fragment_set_name(self, a0)
6566 
6567 
6568  def set_check_level(self, a0):
6569  """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6570  return _IMP_atom.Fragment_set_check_level(self, a0)
6571 
6572 
6573  def add_to_derivative(self, a0, a1, a2):
6574  """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6575  return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6576 
6577 
6578  def set_is_optimized(self, a0, a1):
6579  """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6580  return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6581 
6582 
6583  def get_is_optimized(self, a0):
6584  """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6585  return _IMP_atom.Fragment_get_is_optimized(self, a0)
6586 
6587 
6588  def get_check_level(self):
6589  """get_check_level(Fragment self) -> IMP::CheckLevel"""
6590  return _IMP_atom.Fragment_get_check_level(self)
6591 
6592 
6593  def __eq__(self, *args):
6594  """
6595  __eq__(Fragment self, Fragment o) -> bool
6596  __eq__(Fragment self, Particle d) -> bool
6597  """
6598  return _IMP_atom.Fragment___eq__(self, *args)
6599 
6600 
6601  def __ne__(self, *args):
6602  """
6603  __ne__(Fragment self, Fragment o) -> bool
6604  __ne__(Fragment self, Particle d) -> bool
6605  """
6606  return _IMP_atom.Fragment___ne__(self, *args)
6607 
6608 
6609  def __le__(self, *args):
6610  """
6611  __le__(Fragment self, Fragment o) -> bool
6612  __le__(Fragment self, Particle d) -> bool
6613  """
6614  return _IMP_atom.Fragment___le__(self, *args)
6615 
6616 
6617  def __lt__(self, *args):
6618  """
6619  __lt__(Fragment self, Fragment o) -> bool
6620  __lt__(Fragment self, Particle d) -> bool
6621  """
6622  return _IMP_atom.Fragment___lt__(self, *args)
6623 
6624 
6625  def __ge__(self, *args):
6626  """
6627  __ge__(Fragment self, Fragment o) -> bool
6628  __ge__(Fragment self, Particle d) -> bool
6629  """
6630  return _IMP_atom.Fragment___ge__(self, *args)
6631 
6632 
6633  def __gt__(self, *args):
6634  """
6635  __gt__(Fragment self, Fragment o) -> bool
6636  __gt__(Fragment self, Particle d) -> bool
6637  """
6638  return _IMP_atom.Fragment___gt__(self, *args)
6639 
6640 
6641  def __hash__(self):
6642  """__hash__(Fragment self) -> std::size_t"""
6643  return _IMP_atom.Fragment___hash__(self)
6644 
6645 
6646  def __str__(self):
6647  """__str__(Fragment self) -> std::string"""
6648  return _IMP_atom.Fragment___str__(self)
6649 
6650 
6651  def __repr__(self):
6652  """__repr__(Fragment self) -> std::string"""
6653  return _IMP_atom.Fragment___repr__(self)
6654 
6655  __swig_destroy__ = _IMP_atom.delete_Fragment
6656  __del__ = lambda self: None
6657 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6658 Fragment_swigregister(Fragment)
6659 
6660 def Fragment_get_is_setup(*args):
6661  """
6662  get_is_setup(Model m, ParticleIndex pi) -> bool
6663  Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6664  """
6665  return _IMP_atom.Fragment_get_is_setup(*args)
6666 
6667 def Fragment_setup_particle(*args):
6668  """
6669  setup_particle(Model m, ParticleIndex pi) -> Fragment
6670  setup_particle(_ParticleAdaptor decorator) -> Fragment
6671  setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6672  setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6673  setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6674  Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6675  """
6676  return _IMP_atom.Fragment_setup_particle(*args)
6677 
6678 class StereochemistryPairFilter(IMP.PairPredicate):
6679  """Proxy of C++ IMP::atom::StereochemistryPairFilter class"""
6680  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6681 
6682  def __init__(self):
6683  """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6684  this = _IMP_atom.new_StereochemistryPairFilter()
6685  try:
6686  self.this.append(this)
6687  except:
6688  self.this = this
6689 
6690  def set_bonds(self, bonds):
6691  """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6692  return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6693 
6694 
6695  def set_angles(self, angles):
6696  """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6697  return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6698 
6699 
6700  def set_dihedrals(self, dihedrals):
6701  """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6702  return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6703 
6704 
6705  def do_get_inputs(self, m, pis):
6706  """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6707  return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6708 
6709 
6710  def get_value(self, *args):
6711  """
6712  get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6713  get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6714  """
6715  return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6716 
6717 
6718  def get_value_index(self, *args):
6719  """
6720  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6721  get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6722  """
6723  return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6724 
6725 
6726  def get_version_info(self):
6727  """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6728  return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6729 
6730 
6731  def __str__(self):
6732  """__str__(StereochemistryPairFilter self) -> std::string"""
6733  return _IMP_atom.StereochemistryPairFilter___str__(self)
6734 
6735 
6736  def __repr__(self):
6737  """__repr__(StereochemistryPairFilter self) -> std::string"""
6738  return _IMP_atom.StereochemistryPairFilter___repr__(self)
6739 
6740 
6741  @staticmethod
6742  def get_from(o):
6743  return _object_cast_to_StereochemistryPairFilter(o)
6744 
6745 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6746 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6747 
6748 class SoapPairFilter(IMP.PairPredicate):
6749  """Proxy of C++ IMP::atom::SoapPairFilter class"""
6750  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6751 
6752  def __init__(self, library):
6753  """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6754  this = _IMP_atom.new_SoapPairFilter(library)
6755  try:
6756  self.this.append(this)
6757  except:
6758  self.this = this
6759 
6760  def do_get_inputs(self, m, pis):
6761  """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6762  return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6763 
6764 
6765  def get_value(self, *args):
6766  """
6767  get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6768  get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6769  """
6770  return _IMP_atom.SoapPairFilter_get_value(self, *args)
6771 
6772 
6773  def get_value_index(self, *args):
6774  """
6775  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6776  get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6777  """
6778  return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6779 
6780 
6781  def get_version_info(self):
6782  """get_version_info(SoapPairFilter self) -> VersionInfo"""
6783  return _IMP_atom.SoapPairFilter_get_version_info(self)
6784 
6785 
6786  def __str__(self):
6787  """__str__(SoapPairFilter self) -> std::string"""
6788  return _IMP_atom.SoapPairFilter___str__(self)
6789 
6790 
6791  def __repr__(self):
6792  """__repr__(SoapPairFilter self) -> std::string"""
6793  return _IMP_atom.SoapPairFilter___repr__(self)
6794 
6795 
6796  @staticmethod
6797  def get_from(o):
6798  return _object_cast_to_SoapPairFilter(o)
6799 
6800 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6801 SoapPairFilter_swigregister(SoapPairFilter)
6802 
6803 class Mass(IMP.Decorator):
6804  """Proxy of C++ IMP::atom::Mass class"""
6805  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
6806 
6807  def get_mass(self):
6808  """get_mass(Mass self) -> IMP::Float"""
6809  return _IMP_atom.Mass_get_mass(self)
6810 
6811 
6812  def set_mass(self, d):
6813  """set_mass(Mass self, IMP::Float d)"""
6814  return _IMP_atom.Mass_set_mass(self, d)
6815 
6816 
6817  def __init__(self, *args):
6818  """
6819  __init__(IMP::atom::Mass self) -> Mass
6820  __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6821  __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6822  """
6823  this = _IMP_atom.new_Mass(*args)
6824  try:
6825  self.this.append(this)
6826  except:
6827  self.this = this
6828 
6829  def get_is_setup(*args):
6830  """
6831  get_is_setup(Model m, ParticleIndex pi) -> bool
6832  get_is_setup(_ParticleAdaptor p) -> bool
6833  """
6834  return _IMP_atom.Mass_get_is_setup(*args)
6835 
6836  get_is_setup = staticmethod(get_is_setup)
6837 
6838  def show(self, *args):
6839  """
6840  show(Mass self, _ostream out)
6841  show(Mass self)
6842  """
6843  return _IMP_atom.Mass_show(self, *args)
6844 
6845 
6846  def setup_particle(*args):
6847  """
6848  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6849  setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6850  """
6851  return _IMP_atom.Mass_setup_particle(*args)
6852 
6853  setup_particle = staticmethod(setup_particle)
6854 
6855  def get_mass_key():
6856  """get_mass_key() -> FloatKey"""
6857  return _IMP_atom.Mass_get_mass_key()
6858 
6859  get_mass_key = staticmethod(get_mass_key)
6860 
6861  def add_attribute(self, *args):
6862  """
6863  add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6864  add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6865  add_attribute(Mass self, IntKey a0, IMP::Int a1)
6866  add_attribute(Mass self, StringKey a0, IMP::String a1)
6867  add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6868  add_attribute(Mass self, ObjectKey a0, Object a1)
6869  """
6870  return _IMP_atom.Mass_add_attribute(self, *args)
6871 
6872 
6873  def get_value(self, *args):
6874  """
6875  get_value(Mass self, FloatKey a0) -> IMP::Float
6876  get_value(Mass self, IntKey a0) -> IMP::Int
6877  get_value(Mass self, StringKey a0) -> IMP::String
6878  get_value(Mass self, ParticleIndexKey a0) -> Particle
6879  get_value(Mass self, ObjectKey a0) -> Object
6880  """
6881  return _IMP_atom.Mass_get_value(self, *args)
6882 
6883 
6884  def set_value(self, *args):
6885  """
6886  set_value(Mass self, FloatKey a0, IMP::Float a1)
6887  set_value(Mass self, IntKey a0, IMP::Int a1)
6888  set_value(Mass self, StringKey a0, IMP::String a1)
6889  set_value(Mass self, ParticleIndexKey a0, Particle a1)
6890  set_value(Mass self, ObjectKey a0, Object a1)
6891  """
6892  return _IMP_atom.Mass_set_value(self, *args)
6893 
6894 
6895  def remove_attribute(self, *args):
6896  """
6897  remove_attribute(Mass self, FloatKey a0)
6898  remove_attribute(Mass self, IntKey a0)
6899  remove_attribute(Mass self, StringKey a0)
6900  remove_attribute(Mass self, ParticleIndexKey a0)
6901  remove_attribute(Mass self, ObjectKey a0)
6902  """
6903  return _IMP_atom.Mass_remove_attribute(self, *args)
6904 
6905 
6906  def has_attribute(self, *args):
6907  """
6908  has_attribute(Mass self, FloatKey a0) -> bool
6909  has_attribute(Mass self, IntKey a0) -> bool
6910  has_attribute(Mass self, StringKey a0) -> bool
6911  has_attribute(Mass self, ParticleIndexKey a0) -> bool
6912  has_attribute(Mass self, ObjectKey a0) -> bool
6913  """
6914  return _IMP_atom.Mass_has_attribute(self, *args)
6915 
6916 
6917  def get_derivative(self, a0):
6918  """get_derivative(Mass self, FloatKey a0) -> double"""
6919  return _IMP_atom.Mass_get_derivative(self, a0)
6920 
6921 
6922  def get_name(self):
6923  """get_name(Mass self) -> std::string"""
6924  return _IMP_atom.Mass_get_name(self)
6925 
6926 
6927  def clear_caches(self):
6928  """clear_caches(Mass self)"""
6929  return _IMP_atom.Mass_clear_caches(self)
6930 
6931 
6932  def set_name(self, a0):
6933  """set_name(Mass self, std::string a0)"""
6934  return _IMP_atom.Mass_set_name(self, a0)
6935 
6936 
6937  def set_check_level(self, a0):
6938  """set_check_level(Mass self, IMP::CheckLevel a0)"""
6939  return _IMP_atom.Mass_set_check_level(self, a0)
6940 
6941 
6942  def add_to_derivative(self, a0, a1, a2):
6943  """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6944  return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6945 
6946 
6947  def set_is_optimized(self, a0, a1):
6948  """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6949  return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6950 
6951 
6952  def get_is_optimized(self, a0):
6953  """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6954  return _IMP_atom.Mass_get_is_optimized(self, a0)
6955 
6956 
6957  def get_check_level(self):
6958  """get_check_level(Mass self) -> IMP::CheckLevel"""
6959  return _IMP_atom.Mass_get_check_level(self)
6960 
6961 
6962  def __eq__(self, *args):
6963  """
6964  __eq__(Mass self, Mass o) -> bool
6965  __eq__(Mass self, Particle d) -> bool
6966  """
6967  return _IMP_atom.Mass___eq__(self, *args)
6968 
6969 
6970  def __ne__(self, *args):
6971  """
6972  __ne__(Mass self, Mass o) -> bool
6973  __ne__(Mass self, Particle d) -> bool
6974  """
6975  return _IMP_atom.Mass___ne__(self, *args)
6976 
6977 
6978  def __le__(self, *args):
6979  """
6980  __le__(Mass self, Mass o) -> bool
6981  __le__(Mass self, Particle d) -> bool
6982  """
6983  return _IMP_atom.Mass___le__(self, *args)
6984 
6985 
6986  def __lt__(self, *args):
6987  """
6988  __lt__(Mass self, Mass o) -> bool
6989  __lt__(Mass self, Particle d) -> bool
6990  """
6991  return _IMP_atom.Mass___lt__(self, *args)
6992 
6993 
6994  def __ge__(self, *args):
6995  """
6996  __ge__(Mass self, Mass o) -> bool
6997  __ge__(Mass self, Particle d) -> bool
6998  """
6999  return _IMP_atom.Mass___ge__(self, *args)
7000 
7001 
7002  def __gt__(self, *args):
7003  """
7004  __gt__(Mass self, Mass o) -> bool
7005  __gt__(Mass self, Particle d) -> bool
7006  """
7007  return _IMP_atom.Mass___gt__(self, *args)
7008 
7009 
7010  def __hash__(self):
7011  """__hash__(Mass self) -> std::size_t"""
7012  return _IMP_atom.Mass___hash__(self)
7013 
7014 
7015  def __str__(self):
7016  """__str__(Mass self) -> std::string"""
7017  return _IMP_atom.Mass___str__(self)
7018 
7019 
7020  def __repr__(self):
7021  """__repr__(Mass self) -> std::string"""
7022  return _IMP_atom.Mass___repr__(self)
7023 
7024  __swig_destroy__ = _IMP_atom.delete_Mass
7025  __del__ = lambda self: None
7026 Mass_swigregister = _IMP_atom.Mass_swigregister
7027 Mass_swigregister(Mass)
7028 
7029 def Mass_get_is_setup(*args):
7030  """
7031  get_is_setup(Model m, ParticleIndex pi) -> bool
7032  Mass_get_is_setup(_ParticleAdaptor p) -> bool
7033  """
7034  return _IMP_atom.Mass_get_is_setup(*args)
7035 
7036 def Mass_setup_particle(*args):
7037  """
7038  setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
7039  Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
7040  """
7041  return _IMP_atom.Mass_setup_particle(*args)
7042 
7043 def Mass_get_mass_key():
7044  """Mass_get_mass_key() -> FloatKey"""
7045  return _IMP_atom.Mass_get_mass_key()
7046 
7047 class BondedPairFilter(IMP.PairPredicate):
7048  """Proxy of C++ IMP::atom::BondedPairFilter class"""
7049  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7050 
7051  def __init__(self):
7052  """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
7053  this = _IMP_atom.new_BondedPairFilter()
7054  try:
7055  self.this.append(this)
7056  except:
7057  self.this = this
7058 
7059  def do_get_inputs(self, m, pis):
7060  """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7061  return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
7062 
7063 
7064  def get_value(self, *args):
7065  """
7066  get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
7067  get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
7068  """
7069  return _IMP_atom.BondedPairFilter_get_value(self, *args)
7070 
7071 
7072  def get_value_index(self, *args):
7073  """
7074  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
7075  get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
7076  """
7077  return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
7078 
7079 
7080  def get_version_info(self):
7081  """get_version_info(BondedPairFilter self) -> VersionInfo"""
7082  return _IMP_atom.BondedPairFilter_get_version_info(self)
7083 
7084 
7085  def __str__(self):
7086  """__str__(BondedPairFilter self) -> std::string"""
7087  return _IMP_atom.BondedPairFilter___str__(self)
7088 
7089 
7090  def __repr__(self):
7091  """__repr__(BondedPairFilter self) -> std::string"""
7092  return _IMP_atom.BondedPairFilter___repr__(self)
7093 
7094 
7095  @staticmethod
7096  def get_from(o):
7097  return _object_cast_to_BondedPairFilter(o)
7098 
7099 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
7100 BondedPairFilter_swigregister(BondedPairFilter)
7101 
7102 class Mol2Selector(IMP.Object):
7103  """Proxy of C++ IMP::atom::Mol2Selector class"""
7104  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7105 
7106  def __init__(self, *args, **kwargs):
7107  raise AttributeError("No constructor defined - class is abstract")
7108 
7109  def get_is_selected(self, atom_line):
7110  """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
7111  return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
7112 
7113  __swig_destroy__ = _IMP_atom.delete_Mol2Selector
7114  __del__ = lambda self: None
7115 
7116  def __str__(self):
7117  """__str__(Mol2Selector self) -> std::string"""
7118  return _IMP_atom.Mol2Selector___str__(self)
7119 
7120 
7121  def __repr__(self):
7122  """__repr__(Mol2Selector self) -> std::string"""
7123  return _IMP_atom.Mol2Selector___repr__(self)
7124 
7125 
7126  @staticmethod
7127  def get_from(o):
7128  return _object_cast_to_Mol2Selector(o)
7129 
7130 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
7131 Mol2Selector_swigregister(Mol2Selector)
7132 
7133 class AllMol2Selector(Mol2Selector):
7134  """Proxy of C++ IMP::atom::AllMol2Selector class"""
7135  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7136 
7137  def __str__(self):
7138  """__str__(AllMol2Selector self) -> std::string"""
7139  return _IMP_atom.AllMol2Selector___str__(self)
7140 
7141 
7142  def __repr__(self):
7143  """__repr__(AllMol2Selector self) -> std::string"""
7144  return _IMP_atom.AllMol2Selector___repr__(self)
7145 
7146 
7147  @staticmethod
7148  def get_from(o):
7149  return _object_cast_to_AllMol2Selector(o)
7150 
7151 
7152  def __init__(self):
7153  """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
7154  this = _IMP_atom.new_AllMol2Selector()
7155  try:
7156  self.this.append(this)
7157  except:
7158  self.this = this
7159  __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
7160  __del__ = lambda self: None
7161 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
7162 AllMol2Selector_swigregister(AllMol2Selector)
7163 
7164 class NonHydrogenMol2Selector(Mol2Selector):
7165  """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class"""
7166  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7167 
7168  def __str__(self):
7169  """__str__(NonHydrogenMol2Selector self) -> std::string"""
7170  return _IMP_atom.NonHydrogenMol2Selector___str__(self)
7171 
7172 
7173  def __repr__(self):
7174  """__repr__(NonHydrogenMol2Selector self) -> std::string"""
7175  return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
7176 
7177 
7178  @staticmethod
7179  def get_from(o):
7180  return _object_cast_to_NonHydrogenMol2Selector(o)
7181 
7182 
7183  def __init__(self):
7184  """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
7185  this = _IMP_atom.new_NonHydrogenMol2Selector()
7186  try:
7187  self.this.append(this)
7188  except:
7189  self.this = this
7190  __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
7191  __del__ = lambda self: None
7192 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
7193 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7194 
7195 
7196 def read_mol2(mol2_file, model, mol2sel=None):
7197  """
7198  read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7199  read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7200  """
7201  return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7202 
7203 def write_mol2(rhd, file_name):
7204  """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7205  return _IMP_atom.write_mol2(rhd, file_name)
7206 class SecondaryStructureResidue(IMP.Decorator):
7207  """Proxy of C++ IMP::atom::SecondaryStructureResidue class"""
7208  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7209 
7210  def __init__(self, *args):
7211  """
7212  __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7213  __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7214  __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7215  """
7216  this = _IMP_atom.new_SecondaryStructureResidue(*args)
7217  try:
7218  self.this.append(this)
7219  except:
7220  self.this = this
7221 
7222  def show(self, *args):
7223  """
7224  show(SecondaryStructureResidue self, _ostream out)
7225  show(SecondaryStructureResidue self)
7226  """
7227  return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7228 
7229 
7230  def setup_particle(*args):
7231  """
7232  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7233  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7234  setup_particle(Particle res_p) -> SecondaryStructureResidue
7235  """
7236  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7237 
7238  setup_particle = staticmethod(setup_particle)
7239 
7240  def get_is_setup(*args):
7241  """
7242  get_is_setup(_ParticleAdaptor p) -> bool
7243  get_is_setup(Model m, ParticleIndex pi) -> bool
7244  """
7245  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7246 
7247  get_is_setup = staticmethod(get_is_setup)
7248 
7249  def get_particle(self):
7250  """get_particle(SecondaryStructureResidue self) -> Particle"""
7251  return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7252 
7253 
7254  def get_all_probabilities(self):
7255  """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7256  return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7257 
7258 
7259  def get_prob_helix(self):
7260  """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7261  return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7262 
7263 
7264  def set_prob_helix(self, t):
7265  """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7266  return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7267 
7268 
7269  def get_prob_strand(self):
7270  """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7271  return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7272 
7273 
7274  def set_prob_strand(self, t):
7275  """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7276  return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7277 
7278 
7279  def get_prob_coil(self):
7280  """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7281  return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7282 
7283 
7284  def set_prob_coil(self, t):
7285  """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7286  return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7287 
7288 
7289  def get_prob_helix_key():
7290  """get_prob_helix_key() -> FloatKey"""
7291  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7292 
7293  get_prob_helix_key = staticmethod(get_prob_helix_key)
7294 
7295  def get_prob_strand_key():
7296  """get_prob_strand_key() -> FloatKey"""
7297  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7298 
7299  get_prob_strand_key = staticmethod(get_prob_strand_key)
7300 
7301  def get_prob_coil_key():
7302  """get_prob_coil_key() -> FloatKey"""
7303  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7304 
7305  get_prob_coil_key = staticmethod(get_prob_coil_key)
7306 
7307  def add_attribute(self, *args):
7308  """
7309  add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7310  add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7311  add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7312  add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7313  add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7314  add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7315  """
7316  return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7317 
7318 
7319  def get_value(self, *args):
7320  """
7321  get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7322  get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7323  get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7324  get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7325  get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7326  """
7327  return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7328 
7329 
7330  def set_value(self, *args):
7331  """
7332  set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7333  set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7334  set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7335  set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7336  set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7337  """
7338  return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7339 
7340 
7341  def remove_attribute(self, *args):
7342  """
7343  remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7344  remove_attribute(SecondaryStructureResidue self, IntKey a0)
7345  remove_attribute(SecondaryStructureResidue self, StringKey a0)
7346  remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7347  remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7348  """
7349  return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7350 
7351 
7352  def has_attribute(self, *args):
7353  """
7354  has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7355  has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7356  has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7357  has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7358  has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7359  """
7360  return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7361 
7362 
7363  def get_derivative(self, a0):
7364  """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7365  return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7366 
7367 
7368  def get_name(self):
7369  """get_name(SecondaryStructureResidue self) -> std::string"""
7370  return _IMP_atom.SecondaryStructureResidue_get_name(self)
7371 
7372 
7373  def clear_caches(self):
7374  """clear_caches(SecondaryStructureResidue self)"""
7375  return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7376 
7377 
7378  def set_name(self, a0):
7379  """set_name(SecondaryStructureResidue self, std::string a0)"""
7380  return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7381 
7382 
7383  def set_check_level(self, a0):
7384  """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7385  return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7386 
7387 
7388  def add_to_derivative(self, a0, a1, a2):
7389  """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7390  return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7391 
7392 
7393  def set_is_optimized(self, a0, a1):
7394  """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7395  return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7396 
7397 
7398  def get_is_optimized(self, a0):
7399  """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7400  return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7401 
7402 
7403  def get_check_level(self):
7404  """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7405  return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7406 
7407 
7408  def __eq__(self, *args):
7409  """
7410  __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7411  __eq__(SecondaryStructureResidue self, Particle d) -> bool
7412  """
7413  return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7414 
7415 
7416  def __ne__(self, *args):
7417  """
7418  __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7419  __ne__(SecondaryStructureResidue self, Particle d) -> bool
7420  """
7421  return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7422 
7423 
7424  def __le__(self, *args):
7425  """
7426  __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7427  __le__(SecondaryStructureResidue self, Particle d) -> bool
7428  """
7429  return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7430 
7431 
7432  def __lt__(self, *args):
7433  """
7434  __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7435  __lt__(SecondaryStructureResidue self, Particle d) -> bool
7436  """
7437  return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7438 
7439 
7440  def __ge__(self, *args):
7441  """
7442  __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7443  __ge__(SecondaryStructureResidue self, Particle d) -> bool
7444  """
7445  return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7446 
7447 
7448  def __gt__(self, *args):
7449  """
7450  __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7451  __gt__(SecondaryStructureResidue self, Particle d) -> bool
7452  """
7453  return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7454 
7455 
7456  def __hash__(self):
7457  """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7458  return _IMP_atom.SecondaryStructureResidue___hash__(self)
7459 
7460 
7461  def __str__(self):
7462  """__str__(SecondaryStructureResidue self) -> std::string"""
7463  return _IMP_atom.SecondaryStructureResidue___str__(self)
7464 
7465 
7466  def __repr__(self):
7467  """__repr__(SecondaryStructureResidue self) -> std::string"""
7468  return _IMP_atom.SecondaryStructureResidue___repr__(self)
7469 
7470  __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7471  __del__ = lambda self: None
7472 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7473 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7474 
7475 def SecondaryStructureResidue_setup_particle(*args):
7476  """
7477  setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7478  setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7479  SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7480  """
7481  return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7482 
7483 def SecondaryStructureResidue_get_is_setup(*args):
7484  """
7485  get_is_setup(_ParticleAdaptor p) -> bool
7486  SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7487  """
7488  return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7489 
7490 def SecondaryStructureResidue_get_prob_helix_key():
7491  """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7492  return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7493 
7494 def SecondaryStructureResidue_get_prob_strand_key():
7495  """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7496  return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7497 
7498 def SecondaryStructureResidue_get_prob_coil_key():
7499  """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7500  return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7501 
7502 
7503 def setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res=False):
7504  """
7505  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7506  setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7507  """
7508  return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7509 
7510 def setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res=False):
7511  """
7512  setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues
7513  setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7514  """
7515  return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7516 
7517 def get_secondary_structure_match_score(ssr1, ssr2):
7518  """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7519  return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7520 
7521 def read_psipred(*args):
7522  """
7523  read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7524  read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7525  """
7526  return _IMP_atom.read_psipred(*args)
7527 class _ADopeBase(IMP.PairScore):
7528  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class"""
7529  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7530  __repr__ = _swig_repr
7531 
7532  def __init__(self, *args):
7533  """
7534  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7535  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7536  """
7537  this = _IMP_atom.new__ADopeBase(*args)
7538  try:
7539  self.this.append(this)
7540  except:
7541  self.this = this
7542 
7543  def do_get_inputs(self, m, pis):
7544  """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7545  return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7546 
7547 
7548  def get_score_functor(self):
7549  """get_score_functor(_ADopeBase self) -> Dope"""
7550  return _IMP_atom._ADopeBase_get_score_functor(self)
7551 
7552 
7553  def get_version_info(self):
7554  """get_version_info(_ADopeBase self) -> VersionInfo"""
7555  return _IMP_atom._ADopeBase_get_version_info(self)
7556 
7557 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7558 _ADopeBase_swigregister(_ADopeBase)
7559 
7560 class _BDopeBase(IMP.PairScore):
7561  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class"""
7562  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7563  __repr__ = _swig_repr
7564 
7565  def __init__(self, *args):
7566  """
7567  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BDopeBase
7568  __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
7569  """
7570  this = _IMP_atom.new__BDopeBase(*args)
7571  try:
7572  self.this.append(this)
7573  except:
7574  self.this = this
7575 
7576  def do_get_inputs(self, m, pis):
7577  """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7578  return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7579 
7580 
7581  def get_score_functor(self):
7582  """get_score_functor(_BDopeBase self) -> _DopeBase"""
7583  return _IMP_atom._BDopeBase_get_score_functor(self)
7584 
7585 
7586  def get_version_info(self):
7587  """get_version_info(_BDopeBase self) -> VersionInfo"""
7588  return _IMP_atom._BDopeBase_get_version_info(self)
7589 
7590 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7591 _BDopeBase_swigregister(_BDopeBase)
7592 
7593 class _OrientedSoapBase(IMP.PairScore):
7594  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class"""
7595  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7596  __repr__ = _swig_repr
7597 
7598  def __init__(self, *args):
7599  """
7600  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name) -> _OrientedSoapBase
7601  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7602  """
7603  this = _IMP_atom.new__OrientedSoapBase(*args)
7604  try:
7605  self.this.append(this)
7606  except:
7607  self.this = this
7608 
7609  def do_get_inputs(self, m, pis):
7610  """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7611  return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7612 
7613 
7614  def get_score_functor(self):
7615  """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7616  return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7617 
7618 
7619  def get_version_info(self):
7620  """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7621  return _IMP_atom._OrientedSoapBase_get_version_info(self)
7622 
7623 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7624 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7625 
7626 class _SPSFTB(IMP.PairScore):
7627  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class"""
7628  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7629  __repr__ = _swig_repr
7630 
7631  def __init__(self, *args):
7632  """
7633  __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name) -> _SPSFTB
7634  __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
7635  """
7636  this = _IMP_atom.new__SPSFTB(*args)
7637  try:
7638  self.this.append(this)
7639  except:
7640  self.this = this
7641 
7642  def do_get_inputs(self, m, pis):
7643  """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7644  return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7645 
7646 
7647  def get_score_functor(self):
7648  """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7649  return _IMP_atom._SPSFTB_get_score_functor(self)
7650 
7651 
7652  def get_version_info(self):
7653  """get_version_info(_SPSFTB self) -> VersionInfo"""
7654  return _IMP_atom._SPSFTB_get_version_info(self)
7655 
7656 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7657 _SPSFTB_swigregister(_SPSFTB)
7658 
7659 class _SPSTF(_SPSFTB):
7660  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class"""
7661  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7662  __repr__ = _swig_repr
7663 
7664  def __init__(self, *args):
7665  """
7666  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7667  __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7668  """
7669  this = _IMP_atom.new__SPSTF(*args)
7670  try:
7671  self.this.append(this)
7672  except:
7673  self.this = this
7674  __swig_destroy__ = _IMP_atom.delete__SPSTF
7675  __del__ = lambda self: None
7676 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7677 _SPSTF_swigregister(_SPSTF)
7678 
7679 class _SPSFT(_BDopeBase):
7680  """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class"""
7681  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7682  __repr__ = _swig_repr
7683 
7684  def __init__(self, *args):
7685  """
7686  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7687  __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7688  """
7689  this = _IMP_atom.new__SPSFT(*args)
7690  try:
7691  self.this.append(this)
7692  except:
7693  self.this = this
7694  __swig_destroy__ = _IMP_atom.delete__SPSFT
7695  __del__ = lambda self: None
7696 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7697 _SPSFT_swigregister(_SPSFT)
7698 
7699 class ProteinLigandAtomPairScore(_SPSTF):
7700  """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class"""
7701  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7702 
7703  def __init__(self, *args):
7704  """
7705  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7706  __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7707  __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7708  """
7709  this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7710  try:
7711  self.this.append(this)
7712  except:
7713  self.this = this
7714 
7715  def get_maximum_distance(self):
7716  """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7717  return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7718 
7719 
7720  def __str__(self):
7721  """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7722  return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7723 
7724 
7725  def __repr__(self):
7726  """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7727  return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7728 
7729 
7730  @staticmethod
7731  def get_from(o):
7732  return _object_cast_to_ProteinLigandAtomPairScore(o)
7733 
7734  __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7735  __del__ = lambda self: None
7736 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7737 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7738 
7739 class ProteinLigandRestraint(IMP.container.PairsRestraint):
7740  """Proxy of C++ IMP::atom::ProteinLigandRestraint class"""
7741  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7742 
7743  def __init__(self, *args):
7744  """
7745  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7746  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7747  __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7748  """
7749  this = _IMP_atom.new_ProteinLigandRestraint(*args)
7750  try:
7751  self.this.append(this)
7752  except:
7753  self.this = this
7754 
7755  def __str__(self):
7756  """__str__(ProteinLigandRestraint self) -> std::string"""
7757  return _IMP_atom.ProteinLigandRestraint___str__(self)
7758 
7759 
7760  def __repr__(self):
7761  """__repr__(ProteinLigandRestraint self) -> std::string"""
7762  return _IMP_atom.ProteinLigandRestraint___repr__(self)
7763 
7764 
7765  @staticmethod
7766  def get_from(o):
7767  return _object_cast_to_ProteinLigandRestraint(o)
7768 
7769  __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7770  __del__ = lambda self: None
7771 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7772 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7773 
7774 
7776  """add_protein_ligand_score_data(Hierarchy h)"""
7777  return _IMP_atom.add_protein_ligand_score_data(h)
7778 class AtomType(IMP._Value):
7779  """Proxy of C++ IMP::Key<(8974343,false)> class"""
7780  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7781 
7782  def __init__(self, *args):
7783  """
7784  __init__(IMP::Key<(8974343,false)> self) -> AtomType
7785  __init__(IMP::Key<(8974343,false)> self, std::string c) -> AtomType
7786  __init__(IMP::Key<(8974343,false)> self, unsigned int i) -> AtomType
7787  """
7788  this = _IMP_atom.new_AtomType(*args)
7789  try:
7790  self.this.append(this)
7791  except:
7792  self.this = this
7793 
7794  def add_key(sc):
7795  """add_key(std::string sc) -> unsigned int"""
7796  return _IMP_atom.AtomType_add_key(sc)
7797 
7798  add_key = staticmethod(add_key)
7799 
7800  def get_key_exists(sc):
7801  """get_key_exists(std::string sc) -> bool"""
7802  return _IMP_atom.AtomType_get_key_exists(sc)
7803 
7804  get_key_exists = staticmethod(get_key_exists)
7805 
7806  def get_string(self):
7807  """get_string(AtomType self) -> std::string const"""
7808  return _IMP_atom.AtomType_get_string(self)
7809 
7810 
7811  def __cmp__(self, o):
7812  """__cmp__(AtomType self, AtomType o) -> int"""
7813  return _IMP_atom.AtomType___cmp__(self, o)
7814 
7815 
7816  def __eq__(self, o):
7817  """__eq__(AtomType self, AtomType o) -> bool"""
7818  return _IMP_atom.AtomType___eq__(self, o)
7819 
7820 
7821  def __ne__(self, o):
7822  """__ne__(AtomType self, AtomType o) -> bool"""
7823  return _IMP_atom.AtomType___ne__(self, o)
7824 
7825 
7826  def __lt__(self, o):
7827  """__lt__(AtomType self, AtomType o) -> bool"""
7828  return _IMP_atom.AtomType___lt__(self, o)
7829 
7830 
7831  def __gt__(self, o):
7832  """__gt__(AtomType self, AtomType o) -> bool"""
7833  return _IMP_atom.AtomType___gt__(self, o)
7834 
7835 
7836  def __ge__(self, o):
7837  """__ge__(AtomType self, AtomType o) -> bool"""
7838  return _IMP_atom.AtomType___ge__(self, o)
7839 
7840 
7841  def __le__(self, o):
7842  """__le__(AtomType self, AtomType o) -> bool"""
7843  return _IMP_atom.AtomType___le__(self, o)
7844 
7845 
7846  def __hash__(self):
7847  """__hash__(AtomType self) -> std::size_t"""
7848  return _IMP_atom.AtomType___hash__(self)
7849 
7850 
7851  def show(self, *args):
7852  """
7853  show(AtomType self, _ostream out)
7854  show(AtomType self)
7855  """
7856  return _IMP_atom.AtomType_show(self, *args)
7857 
7858 
7859  def add_alias(old_key, new_name):
7860  """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7861  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7862 
7863  add_alias = staticmethod(add_alias)
7864 
7865  def get_index(self):
7866  """get_index(AtomType self) -> unsigned int"""
7867  return _IMP_atom.AtomType_get_index(self)
7868 
7869 
7870  def show_all(out):
7871  """show_all(_ostream out)"""
7872  return _IMP_atom.AtomType_show_all(out)
7873 
7874  show_all = staticmethod(show_all)
7875 
7876  def get_all_strings():
7877  """get_all_strings() -> IMP::Vector< std::string >"""
7878  return _IMP_atom.AtomType_get_all_strings()
7879 
7880  get_all_strings = staticmethod(get_all_strings)
7881 
7882  def get_number_unique():
7883  """get_number_unique() -> unsigned int"""
7884  return _IMP_atom.AtomType_get_number_unique()
7885 
7886  get_number_unique = staticmethod(get_number_unique)
7887 
7888  def __str__(self):
7889  """__str__(AtomType self) -> std::string"""
7890  return _IMP_atom.AtomType___str__(self)
7891 
7892 
7893  def __repr__(self):
7894  """__repr__(AtomType self) -> std::string"""
7895  return _IMP_atom.AtomType___repr__(self)
7896 
7897  __swig_destroy__ = _IMP_atom.delete_AtomType
7898  __del__ = lambda self: None
7899 AtomType_swigregister = _IMP_atom.AtomType_swigregister
7900 AtomType_swigregister(AtomType)
7901 
7902 def AtomType_add_key(sc):
7903  """AtomType_add_key(std::string sc) -> unsigned int"""
7904  return _IMP_atom.AtomType_add_key(sc)
7905 
7906 def AtomType_get_key_exists(sc):
7907  """AtomType_get_key_exists(std::string sc) -> bool"""
7908  return _IMP_atom.AtomType_get_key_exists(sc)
7909 
7910 def AtomType_add_alias(old_key, new_name):
7911  """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7912  return _IMP_atom.AtomType_add_alias(old_key, new_name)
7913 
7914 def AtomType_show_all(out):
7915  """AtomType_show_all(_ostream out)"""
7916  return _IMP_atom.AtomType_show_all(out)
7917 
7918 def AtomType_get_all_strings():
7919  """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
7920  return _IMP_atom.AtomType_get_all_strings()
7921 
7922 def AtomType_get_number_unique():
7923  """AtomType_get_number_unique() -> unsigned int"""
7924  return _IMP_atom.AtomType_get_number_unique()
7925 
7926 class ResidueType(IMP._Value):
7927  """Proxy of C++ IMP::Key<(90784334,true)> class"""
7928  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
7929 
7930  def __init__(self, *args):
7931  """
7932  __init__(IMP::Key<(90784334,true)> self) -> ResidueType
7933  __init__(IMP::Key<(90784334,true)> self, std::string c) -> ResidueType
7934  __init__(IMP::Key<(90784334,true)> self, unsigned int i) -> ResidueType
7935  """
7936  this = _IMP_atom.new_ResidueType(*args)
7937  try:
7938  self.this.append(this)
7939  except:
7940  self.this = this
7941 
7942  def add_key(sc):
7943  """add_key(std::string sc) -> unsigned int"""
7944  return _IMP_atom.ResidueType_add_key(sc)
7945 
7946  add_key = staticmethod(add_key)
7947 
7948  def get_key_exists(sc):
7949  """get_key_exists(std::string sc) -> bool"""
7950  return _IMP_atom.ResidueType_get_key_exists(sc)
7951 
7952  get_key_exists = staticmethod(get_key_exists)
7953 
7954  def get_string(self):
7955  """get_string(ResidueType self) -> std::string const"""
7956  return _IMP_atom.ResidueType_get_string(self)
7957 
7958 
7959  def __cmp__(self, o):
7960  """__cmp__(ResidueType self, ResidueType o) -> int"""
7961  return _IMP_atom.ResidueType___cmp__(self, o)
7962 
7963 
7964  def __eq__(self, o):
7965  """__eq__(ResidueType self, ResidueType o) -> bool"""
7966  return _IMP_atom.ResidueType___eq__(self, o)
7967 
7968 
7969  def __ne__(self, o):
7970  """__ne__(ResidueType self, ResidueType o) -> bool"""
7971  return _IMP_atom.ResidueType___ne__(self, o)
7972 
7973 
7974  def __lt__(self, o):
7975  """__lt__(ResidueType self, ResidueType o) -> bool"""
7976  return _IMP_atom.ResidueType___lt__(self, o)
7977 
7978 
7979  def __gt__(self, o):
7980  """__gt__(ResidueType self, ResidueType o) -> bool"""
7981  return _IMP_atom.ResidueType___gt__(self, o)
7982 
7983 
7984  def __ge__(self, o):
7985  """__ge__(ResidueType self, ResidueType o) -> bool"""
7986  return _IMP_atom.ResidueType___ge__(self, o)
7987 
7988 
7989  def __le__(self, o):
7990  """__le__(ResidueType self, ResidueType o) -> bool"""
7991  return _IMP_atom.ResidueType___le__(self, o)
7992 
7993 
7994  def __hash__(self):
7995  """__hash__(ResidueType self) -> std::size_t"""
7996  return _IMP_atom.ResidueType___hash__(self)
7997 
7998 
7999  def show(self, *args):
8000  """
8001  show(ResidueType self, _ostream out)
8002  show(ResidueType self)
8003  """
8004  return _IMP_atom.ResidueType_show(self, *args)
8005 
8006 
8007  def add_alias(old_key, new_name):
8008  """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8009  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8010 
8011  add_alias = staticmethod(add_alias)
8012 
8013  def get_index(self):
8014  """get_index(ResidueType self) -> unsigned int"""
8015  return _IMP_atom.ResidueType_get_index(self)
8016 
8017 
8018  def show_all(out):
8019  """show_all(_ostream out)"""
8020  return _IMP_atom.ResidueType_show_all(out)
8021 
8022  show_all = staticmethod(show_all)
8023 
8024  def get_all_strings():
8025  """get_all_strings() -> IMP::Vector< std::string >"""
8026  return _IMP_atom.ResidueType_get_all_strings()
8027 
8028  get_all_strings = staticmethod(get_all_strings)
8029 
8030  def get_number_unique():
8031  """get_number_unique() -> unsigned int"""
8032  return _IMP_atom.ResidueType_get_number_unique()
8033 
8034  get_number_unique = staticmethod(get_number_unique)
8035 
8036  def __str__(self):
8037  """__str__(ResidueType self) -> std::string"""
8038  return _IMP_atom.ResidueType___str__(self)
8039 
8040 
8041  def __repr__(self):
8042  """__repr__(ResidueType self) -> std::string"""
8043  return _IMP_atom.ResidueType___repr__(self)
8044 
8045  __swig_destroy__ = _IMP_atom.delete_ResidueType
8046  __del__ = lambda self: None
8047 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
8048 ResidueType_swigregister(ResidueType)
8049 
8050 def ResidueType_add_key(sc):
8051  """ResidueType_add_key(std::string sc) -> unsigned int"""
8052  return _IMP_atom.ResidueType_add_key(sc)
8053 
8054 def ResidueType_get_key_exists(sc):
8055  """ResidueType_get_key_exists(std::string sc) -> bool"""
8056  return _IMP_atom.ResidueType_get_key_exists(sc)
8057 
8058 def ResidueType_add_alias(old_key, new_name):
8059  """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8060  return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8061 
8062 def ResidueType_show_all(out):
8063  """ResidueType_show_all(_ostream out)"""
8064  return _IMP_atom.ResidueType_show_all(out)
8065 
8066 def ResidueType_get_all_strings():
8067  """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
8068  return _IMP_atom.ResidueType_get_all_strings()
8069 
8070 def ResidueType_get_number_unique():
8071  """ResidueType_get_number_unique() -> unsigned int"""
8072  return _IMP_atom.ResidueType_get_number_unique()
8073 
8074 
8075 _IMP_atom.UNKNOWN_ELEMENT_swigconstant(_IMP_atom)
8076 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8077 
8078 _IMP_atom.OH_swigconstant(_IMP_atom)
8079 OH = _IMP_atom.OH
8080 
8081 _IMP_atom.H2O_swigconstant(_IMP_atom)
8082 H2O = _IMP_atom.H2O
8083 
8084 _IMP_atom.H_swigconstant(_IMP_atom)
8085 H = _IMP_atom.H
8086 
8087 _IMP_atom.He_swigconstant(_IMP_atom)
8088 He = _IMP_atom.He
8089 
8090 _IMP_atom.Li_swigconstant(_IMP_atom)
8091 Li = _IMP_atom.Li
8092 
8093 _IMP_atom.Be_swigconstant(_IMP_atom)
8094 Be = _IMP_atom.Be
8095 
8096 _IMP_atom.B_swigconstant(_IMP_atom)
8097 B = _IMP_atom.B
8098 
8099 _IMP_atom.C_swigconstant(_IMP_atom)
8100 C = _IMP_atom.C
8101 
8102 _IMP_atom.N_swigconstant(_IMP_atom)
8103 N = _IMP_atom.N
8104 
8105 _IMP_atom.O_swigconstant(_IMP_atom)
8106 O = _IMP_atom.O
8107 
8108 _IMP_atom.F_swigconstant(_IMP_atom)
8109 F = _IMP_atom.F
8110 
8111 _IMP_atom.Ne_swigconstant(_IMP_atom)
8112 Ne = _IMP_atom.Ne
8113 
8114 _IMP_atom.Na_swigconstant(_IMP_atom)
8115 Na = _IMP_atom.Na
8116 
8117 _IMP_atom.Mg_swigconstant(_IMP_atom)
8118 Mg = _IMP_atom.Mg
8119 
8120 _IMP_atom.Al_swigconstant(_IMP_atom)
8121 Al = _IMP_atom.Al
8122 
8123 _IMP_atom.Si_swigconstant(_IMP_atom)
8124 Si = _IMP_atom.Si
8125 
8126 _IMP_atom.P_swigconstant(_IMP_atom)
8127 P = _IMP_atom.P
8128 
8129 _IMP_atom.S_swigconstant(_IMP_atom)
8130 S = _IMP_atom.S
8131 
8132 _IMP_atom.Cl_swigconstant(_IMP_atom)
8133 Cl = _IMP_atom.Cl
8134 
8135 _IMP_atom.Ar_swigconstant(_IMP_atom)
8136 Ar = _IMP_atom.Ar
8137 
8138 _IMP_atom.K_swigconstant(_IMP_atom)
8139 K = _IMP_atom.K
8140 
8141 _IMP_atom.Ca_swigconstant(_IMP_atom)
8142 Ca = _IMP_atom.Ca
8143 
8144 _IMP_atom.Sc_swigconstant(_IMP_atom)
8145 Sc = _IMP_atom.Sc
8146 
8147 _IMP_atom.Ti_swigconstant(_IMP_atom)
8148 Ti = _IMP_atom.Ti
8149 
8150 _IMP_atom.V_swigconstant(_IMP_atom)
8151 V = _IMP_atom.V
8152 
8153 _IMP_atom.Cr_swigconstant(_IMP_atom)
8154 Cr = _IMP_atom.Cr
8155 
8156 _IMP_atom.Mn_swigconstant(_IMP_atom)
8157 Mn = _IMP_atom.Mn
8158 
8159 _IMP_atom.Fe_swigconstant(_IMP_atom)
8160 Fe = _IMP_atom.Fe
8161 
8162 _IMP_atom.Co_swigconstant(_IMP_atom)
8163 Co = _IMP_atom.Co
8164 
8165 _IMP_atom.Ni_swigconstant(_IMP_atom)
8166 Ni = _IMP_atom.Ni
8167 
8168 _IMP_atom.Cu_swigconstant(_IMP_atom)
8169 Cu = _IMP_atom.Cu
8170 
8171 _IMP_atom.Zn_swigconstant(_IMP_atom)
8172 Zn = _IMP_atom.Zn
8173 
8174 _IMP_atom.Ga_swigconstant(_IMP_atom)
8175 Ga = _IMP_atom.Ga
8176 
8177 _IMP_atom.Ge_swigconstant(_IMP_atom)
8178 Ge = _IMP_atom.Ge
8179 
8180 _IMP_atom.As_swigconstant(_IMP_atom)
8181 As = _IMP_atom.As
8182 
8183 _IMP_atom.Se_swigconstant(_IMP_atom)
8184 Se = _IMP_atom.Se
8185 
8186 _IMP_atom.Br_swigconstant(_IMP_atom)
8187 Br = _IMP_atom.Br
8188 
8189 _IMP_atom.Kr_swigconstant(_IMP_atom)
8190 Kr = _IMP_atom.Kr
8191 
8192 _IMP_atom.Rb_swigconstant(_IMP_atom)
8193 Rb = _IMP_atom.Rb
8194 
8195 _IMP_atom.Sr_swigconstant(_IMP_atom)
8196 Sr = _IMP_atom.Sr
8197 
8198 _IMP_atom.Y_swigconstant(_IMP_atom)
8199 Y = _IMP_atom.Y
8200 
8201 _IMP_atom.Zr_swigconstant(_IMP_atom)
8202 Zr = _IMP_atom.Zr
8203 
8204 _IMP_atom.Nb_swigconstant(_IMP_atom)
8205 Nb = _IMP_atom.Nb
8206 
8207 _IMP_atom.Mo_swigconstant(_IMP_atom)
8208 Mo = _IMP_atom.Mo
8209 
8210 _IMP_atom.Tc_swigconstant(_IMP_atom)
8211 Tc = _IMP_atom.Tc
8212 
8213 _IMP_atom.Ru_swigconstant(_IMP_atom)
8214 Ru = _IMP_atom.Ru
8215 
8216 _IMP_atom.Rh_swigconstant(_IMP_atom)
8217 Rh = _IMP_atom.Rh
8218 
8219 _IMP_atom.Pd_swigconstant(_IMP_atom)
8220 Pd = _IMP_atom.Pd
8221 
8222 _IMP_atom.Ag_swigconstant(_IMP_atom)
8223 Ag = _IMP_atom.Ag
8224 
8225 _IMP_atom.Cd_swigconstant(_IMP_atom)
8226 Cd = _IMP_atom.Cd
8227 
8228 _IMP_atom.In_swigconstant(_IMP_atom)
8229 In = _IMP_atom.In
8230 
8231 _IMP_atom.Sn_swigconstant(_IMP_atom)
8232 Sn = _IMP_atom.Sn
8233 
8234 _IMP_atom.Sb_swigconstant(_IMP_atom)
8235 Sb = _IMP_atom.Sb
8236 
8237 _IMP_atom.Te_swigconstant(_IMP_atom)
8238 Te = _IMP_atom.Te
8239 
8240 _IMP_atom.I_swigconstant(_IMP_atom)
8241 I = _IMP_atom.I
8242 
8243 _IMP_atom.Xe_swigconstant(_IMP_atom)
8244 Xe = _IMP_atom.Xe
8245 
8246 _IMP_atom.Cs_swigconstant(_IMP_atom)
8247 Cs = _IMP_atom.Cs
8248 
8249 _IMP_atom.Ba_swigconstant(_IMP_atom)
8250 Ba = _IMP_atom.Ba
8251 
8252 _IMP_atom.La_swigconstant(_IMP_atom)
8253 La = _IMP_atom.La
8254 
8255 _IMP_atom.Ce_swigconstant(_IMP_atom)
8256 Ce = _IMP_atom.Ce
8257 
8258 _IMP_atom.Pr_swigconstant(_IMP_atom)
8259 Pr = _IMP_atom.Pr
8260 
8261 _IMP_atom.Nd_swigconstant(_IMP_atom)
8262 Nd = _IMP_atom.Nd
8263 
8264 _IMP_atom.Pm_swigconstant(_IMP_atom)
8265 Pm = _IMP_atom.Pm
8266 
8267 _IMP_atom.Sm_swigconstant(_IMP_atom)
8268 Sm = _IMP_atom.Sm
8269 
8270 _IMP_atom.Eu_swigconstant(_IMP_atom)
8271 Eu = _IMP_atom.Eu
8272 
8273 _IMP_atom.Gd_swigconstant(_IMP_atom)
8274 Gd = _IMP_atom.Gd
8275 
8276 _IMP_atom.Tb_swigconstant(_IMP_atom)
8277 Tb = _IMP_atom.Tb
8278 
8279 _IMP_atom.Dy_swigconstant(_IMP_atom)
8280 Dy = _IMP_atom.Dy
8281 
8282 _IMP_atom.Ho_swigconstant(_IMP_atom)
8283 Ho = _IMP_atom.Ho
8284 
8285 _IMP_atom.Er_swigconstant(_IMP_atom)
8286 Er = _IMP_atom.Er
8287 
8288 _IMP_atom.Tm_swigconstant(_IMP_atom)
8289 Tm = _IMP_atom.Tm
8290 
8291 _IMP_atom.Yb_swigconstant(_IMP_atom)
8292 Yb = _IMP_atom.Yb
8293 
8294 _IMP_atom.Lu_swigconstant(_IMP_atom)
8295 Lu = _IMP_atom.Lu
8296 
8297 _IMP_atom.Hf_swigconstant(_IMP_atom)
8298 Hf = _IMP_atom.Hf
8299 
8300 _IMP_atom.Ta_swigconstant(_IMP_atom)
8301 Ta = _IMP_atom.Ta
8302 
8303 _IMP_atom.W_swigconstant(_IMP_atom)
8304 W = _IMP_atom.W
8305 
8306 _IMP_atom.Re_swigconstant(_IMP_atom)
8307 Re = _IMP_atom.Re
8308 
8309 _IMP_atom.Os_swigconstant(_IMP_atom)
8310 Os = _IMP_atom.Os
8311 
8312 _IMP_atom.Ir_swigconstant(_IMP_atom)
8313 Ir = _IMP_atom.Ir
8314 
8315 _IMP_atom.Pt_swigconstant(_IMP_atom)
8316 Pt = _IMP_atom.Pt
8317 
8318 _IMP_atom.Au_swigconstant(_IMP_atom)
8319 Au = _IMP_atom.Au
8320 
8321 _IMP_atom.Hg_swigconstant(_IMP_atom)
8322 Hg = _IMP_atom.Hg
8323 
8324 _IMP_atom.Tl_swigconstant(_IMP_atom)
8325 Tl = _IMP_atom.Tl
8326 
8327 _IMP_atom.Pb_swigconstant(_IMP_atom)
8328 Pb = _IMP_atom.Pb
8329 
8330 _IMP_atom.Bi_swigconstant(_IMP_atom)
8331 Bi = _IMP_atom.Bi
8332 
8333 _IMP_atom.Po_swigconstant(_IMP_atom)
8334 Po = _IMP_atom.Po
8335 
8336 _IMP_atom.At_swigconstant(_IMP_atom)
8337 At = _IMP_atom.At
8338 
8339 _IMP_atom.Rn_swigconstant(_IMP_atom)
8340 Rn = _IMP_atom.Rn
8341 
8342 _IMP_atom.Fr_swigconstant(_IMP_atom)
8343 Fr = _IMP_atom.Fr
8344 
8345 _IMP_atom.Ra_swigconstant(_IMP_atom)
8346 Ra = _IMP_atom.Ra
8347 
8348 _IMP_atom.Ac_swigconstant(_IMP_atom)
8349 Ac = _IMP_atom.Ac
8350 
8351 _IMP_atom.Th_swigconstant(_IMP_atom)
8352 Th = _IMP_atom.Th
8353 
8354 _IMP_atom.Pa_swigconstant(_IMP_atom)
8355 Pa = _IMP_atom.Pa
8356 
8357 _IMP_atom.U_swigconstant(_IMP_atom)
8358 U = _IMP_atom.U
8359 
8360 _IMP_atom.Np_swigconstant(_IMP_atom)
8361 Np = _IMP_atom.Np
8362 
8363 _IMP_atom.Pu_swigconstant(_IMP_atom)
8364 Pu = _IMP_atom.Pu
8365 
8366 _IMP_atom.Am_swigconstant(_IMP_atom)
8367 Am = _IMP_atom.Am
8368 
8369 _IMP_atom.Cm_swigconstant(_IMP_atom)
8370 Cm = _IMP_atom.Cm
8371 
8372 _IMP_atom.Bk_swigconstant(_IMP_atom)
8373 Bk = _IMP_atom.Bk
8374 
8375 _IMP_atom.Cf_swigconstant(_IMP_atom)
8376 Cf = _IMP_atom.Cf
8377 
8378 _IMP_atom.Es_swigconstant(_IMP_atom)
8379 Es = _IMP_atom.Es
8380 
8381 _IMP_atom.Fm_swigconstant(_IMP_atom)
8382 Fm = _IMP_atom.Fm
8383 
8384 _IMP_atom.Md_swigconstant(_IMP_atom)
8385 Md = _IMP_atom.Md
8386 
8387 _IMP_atom.No_swigconstant(_IMP_atom)
8388 No = _IMP_atom.No
8389 
8390 _IMP_atom.Lr_swigconstant(_IMP_atom)
8391 Lr = _IMP_atom.Lr
8392 
8393 _IMP_atom.Db_swigconstant(_IMP_atom)
8394 Db = _IMP_atom.Db
8395 
8396 _IMP_atom.Jl_swigconstant(_IMP_atom)
8397 Jl = _IMP_atom.Jl
8398 
8399 _IMP_atom.Rf_swigconstant(_IMP_atom)
8400 Rf = _IMP_atom.Rf
8401 
8402 _IMP_atom.NUMBER_OF_ELEMENTS_swigconstant(_IMP_atom)
8403 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8404 
8405 def hash_value(e):
8406  """hash_value(IMP::atom::Element e) -> size_t"""
8407  return _IMP_atom.hash_value(e)
8408 class ElementTable(object):
8409  """Proxy of C++ IMP::atom::ElementTable class"""
8410  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8411  __repr__ = _swig_repr
8412 
8413  def __init__(self):
8414  """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8415  this = _IMP_atom.new_ElementTable()
8416  try:
8417  self.this.append(this)
8418  except:
8419  self.this = this
8420 
8421  def get_element(self, s):
8422  """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8423  return _IMP_atom.ElementTable_get_element(self, s)
8424 
8425 
8426  def get_name(self, e):
8427  """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8428  return _IMP_atom.ElementTable_get_name(self, e)
8429 
8430 
8431  def get_mass(self, e):
8432  """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8433  return _IMP_atom.ElementTable_get_mass(self, e)
8434 
8435  __swig_destroy__ = _IMP_atom.delete_ElementTable
8436  __del__ = lambda self: None
8437 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8438 ElementTable_swigregister(ElementTable)
8439 
8440 
8441 def get_element_table():
8442  """get_element_table() -> ElementTable"""
8443  return _IMP_atom.get_element_table()
8444 class Atom(Hierarchy):
8445  """Proxy of C++ IMP::atom::Atom class"""
8446  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8447 
8448  def __init__(self, *args):
8449  """
8450  __init__(IMP::atom::Atom self) -> Atom
8451  __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8452  __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8453  """
8454  this = _IMP_atom.new_Atom(*args)
8455  try:
8456  self.this.append(this)
8457  except:
8458  self.this = this
8459 
8460  def show(self, *args):
8461  """
8462  show(Atom self, _ostream out)
8463  show(Atom self)
8464  """
8465  return _IMP_atom.Atom_show(self, *args)
8466 
8467 
8468  def setup_particle(*args):
8469  """
8470  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8471  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8472  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8473  setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8474  """
8475  return _IMP_atom.Atom_setup_particle(*args)
8476 
8477  setup_particle = staticmethod(setup_particle)
8478 
8479  def get_is_setup(*args):
8480  """
8481  get_is_setup(_ParticleAdaptor p) -> bool
8482  get_is_setup(Model m, ParticleIndex pi) -> bool
8483  """
8484  return _IMP_atom.Atom_get_is_setup(*args)
8485 
8486  get_is_setup = staticmethod(get_is_setup)
8487 
8488  def get_atom_type(self):
8489  """get_atom_type(Atom self) -> AtomType"""
8490  return _IMP_atom.Atom_get_atom_type(self)
8491 
8492 
8493  def set_atom_type(self, t):
8494  """set_atom_type(Atom self, AtomType t)"""
8495  return _IMP_atom.Atom_set_atom_type(self, t)
8496 
8497 
8498  def get_element(self):
8499  """get_element(Atom self) -> IMP::atom::Element"""
8500  return _IMP_atom.Atom_get_element(self)
8501 
8502 
8503  def set_element(self, e):
8504  """set_element(Atom self, IMP::atom::Element e)"""
8505  return _IMP_atom.Atom_set_element(self, e)
8506 
8507 
8508  def get_occupancy(self):
8509  """get_occupancy(Atom self) -> double"""
8510  return _IMP_atom.Atom_get_occupancy(self)
8511 
8512 
8513  def set_occupancy(self, occupancy):
8514  """set_occupancy(Atom self, double occupancy)"""
8515  return _IMP_atom.Atom_set_occupancy(self, occupancy)
8516 
8517 
8518  def get_temperature_factor(self):
8519  """get_temperature_factor(Atom self) -> double"""
8520  return _IMP_atom.Atom_get_temperature_factor(self)
8521 
8522 
8523  def set_temperature_factor(self, tempFactor):
8524  """set_temperature_factor(Atom self, double tempFactor)"""
8525  return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8526 
8527 
8528  def get_input_index(self):
8529  """get_input_index(Atom self) -> IMP::Int"""
8530  return _IMP_atom.Atom_get_input_index(self)
8531 
8532 
8533  def set_input_index(self, t):
8534  """set_input_index(Atom self, IMP::Int t)"""
8535  return _IMP_atom.Atom_set_input_index(self, t)
8536 
8537 
8538  def get_atom_type_key():
8539  """get_atom_type_key() -> IntKey"""
8540  return _IMP_atom.Atom_get_atom_type_key()
8541 
8542  get_atom_type_key = staticmethod(get_atom_type_key)
8543 
8544  def get_element_key():
8545  """get_element_key() -> IntKey"""
8546  return _IMP_atom.Atom_get_element_key()
8547 
8548  get_element_key = staticmethod(get_element_key)
8549 
8550  def get_input_index_key():
8551  """get_input_index_key() -> IntKey"""
8552  return _IMP_atom.Atom_get_input_index_key()
8553 
8554  get_input_index_key = staticmethod(get_input_index_key)
8555 
8556  def get_occupancy_key():
8557  """get_occupancy_key() -> FloatKey"""
8558  return _IMP_atom.Atom_get_occupancy_key()
8559 
8560  get_occupancy_key = staticmethod(get_occupancy_key)
8561 
8562  def get_temperature_factor_key():
8563  """get_temperature_factor_key() -> FloatKey"""
8564  return _IMP_atom.Atom_get_temperature_factor_key()
8565 
8566  get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8567 
8568  def add_attribute(self, *args):
8569  """
8570  add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8571  add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8572  add_attribute(Atom self, IntKey a0, IMP::Int a1)
8573  add_attribute(Atom self, StringKey a0, IMP::String a1)
8574  add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8575  add_attribute(Atom self, ObjectKey a0, Object a1)
8576  """
8577  return _IMP_atom.Atom_add_attribute(self, *args)
8578 
8579 
8580  def get_value(self, *args):
8581  """
8582  get_value(Atom self, FloatKey a0) -> IMP::Float
8583  get_value(Atom self, IntKey a0) -> IMP::Int
8584  get_value(Atom self, StringKey a0) -> IMP::String
8585  get_value(Atom self, ParticleIndexKey a0) -> Particle
8586  get_value(Atom self, ObjectKey a0) -> Object
8587  """
8588  return _IMP_atom.Atom_get_value(self, *args)
8589 
8590 
8591  def set_value(self, *args):
8592  """
8593  set_value(Atom self, FloatKey a0, IMP::Float a1)
8594  set_value(Atom self, IntKey a0, IMP::Int a1)
8595  set_value(Atom self, StringKey a0, IMP::String a1)
8596  set_value(Atom self, ParticleIndexKey a0, Particle a1)
8597  set_value(Atom self, ObjectKey a0, Object a1)
8598  """
8599  return _IMP_atom.Atom_set_value(self, *args)
8600 
8601 
8602  def remove_attribute(self, *args):
8603  """
8604  remove_attribute(Atom self, FloatKey a0)
8605  remove_attribute(Atom self, IntKey a0)
8606  remove_attribute(Atom self, StringKey a0)
8607  remove_attribute(Atom self, ParticleIndexKey a0)
8608  remove_attribute(Atom self, ObjectKey a0)
8609  """
8610  return _IMP_atom.Atom_remove_attribute(self, *args)
8611 
8612 
8613  def has_attribute(self, *args):
8614  """
8615  has_attribute(Atom self, FloatKey a0) -> bool
8616  has_attribute(Atom self, IntKey a0) -> bool
8617  has_attribute(Atom self, StringKey a0) -> bool
8618  has_attribute(Atom self, ParticleIndexKey a0) -> bool
8619  has_attribute(Atom self, ObjectKey a0) -> bool
8620  """
8621  return _IMP_atom.Atom_has_attribute(self, *args)
8622 
8623 
8624  def get_derivative(self, a0):
8625  """get_derivative(Atom self, FloatKey a0) -> double"""
8626  return _IMP_atom.Atom_get_derivative(self, a0)
8627 
8628 
8629  def get_name(self):
8630  """get_name(Atom self) -> std::string"""
8631  return _IMP_atom.Atom_get_name(self)
8632 
8633 
8634  def clear_caches(self):
8635  """clear_caches(Atom self)"""
8636  return _IMP_atom.Atom_clear_caches(self)
8637 
8638 
8639  def set_name(self, a0):
8640  """set_name(Atom self, std::string a0)"""
8641  return _IMP_atom.Atom_set_name(self, a0)
8642 
8643 
8644  def set_check_level(self, a0):
8645  """set_check_level(Atom self, IMP::CheckLevel a0)"""
8646  return _IMP_atom.Atom_set_check_level(self, a0)
8647 
8648 
8649  def add_to_derivative(self, a0, a1, a2):
8650  """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8651  return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8652 
8653 
8654  def set_is_optimized(self, a0, a1):
8655  """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8656  return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8657 
8658 
8659  def get_is_optimized(self, a0):
8660  """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8661  return _IMP_atom.Atom_get_is_optimized(self, a0)
8662 
8663 
8664  def get_check_level(self):
8665  """get_check_level(Atom self) -> IMP::CheckLevel"""
8666  return _IMP_atom.Atom_get_check_level(self)
8667 
8668 
8669  def __eq__(self, *args):
8670  """
8671  __eq__(Atom self, Atom o) -> bool
8672  __eq__(Atom self, Particle d) -> bool
8673  """
8674  return _IMP_atom.Atom___eq__(self, *args)
8675 
8676 
8677  def __ne__(self, *args):
8678  """
8679  __ne__(Atom self, Atom o) -> bool
8680  __ne__(Atom self, Particle d) -> bool
8681  """
8682  return _IMP_atom.Atom___ne__(self, *args)
8683 
8684 
8685  def __le__(self, *args):
8686  """
8687  __le__(Atom self, Atom o) -> bool
8688  __le__(Atom self, Particle d) -> bool
8689  """
8690  return _IMP_atom.Atom___le__(self, *args)
8691 
8692 
8693  def __lt__(self, *args):
8694  """
8695  __lt__(Atom self, Atom o) -> bool
8696  __lt__(Atom self, Particle d) -> bool
8697  """
8698  return _IMP_atom.Atom___lt__(self, *args)
8699 
8700 
8701  def __ge__(self, *args):
8702  """
8703  __ge__(Atom self, Atom o) -> bool
8704  __ge__(Atom self, Particle d) -> bool
8705  """
8706  return _IMP_atom.Atom___ge__(self, *args)
8707 
8708 
8709  def __gt__(self, *args):
8710  """
8711  __gt__(Atom self, Atom o) -> bool
8712  __gt__(Atom self, Particle d) -> bool
8713  """
8714  return _IMP_atom.Atom___gt__(self, *args)
8715 
8716 
8717  def __hash__(self):
8718  """__hash__(Atom self) -> std::size_t"""
8719  return _IMP_atom.Atom___hash__(self)
8720 
8721 
8722  def __str__(self):
8723  """__str__(Atom self) -> std::string"""
8724  return _IMP_atom.Atom___str__(self)
8725 
8726 
8727  def __repr__(self):
8728  """__repr__(Atom self) -> std::string"""
8729  return _IMP_atom.Atom___repr__(self)
8730 
8731  __swig_destroy__ = _IMP_atom.delete_Atom
8732  __del__ = lambda self: None
8733 Atom_swigregister = _IMP_atom.Atom_swigregister
8734 Atom_swigregister(Atom)
8735 cvar = _IMP_atom.cvar
8736 AT_UNKNOWN = cvar.AT_UNKNOWN
8737 AT_N = cvar.AT_N
8738 AT_CA = cvar.AT_CA
8739 AT_C = cvar.AT_C
8740 AT_O = cvar.AT_O
8741 AT_H = cvar.AT_H
8742 AT_H1 = cvar.AT_H1
8743 AT_H2 = cvar.AT_H2
8744 AT_H3 = cvar.AT_H3
8745 AT_HA = cvar.AT_HA
8746 AT_HA1 = cvar.AT_HA1
8747 AT_HA2 = cvar.AT_HA2
8748 AT_HA3 = cvar.AT_HA3
8749 AT_CB = cvar.AT_CB
8750 AT_HB = cvar.AT_HB
8751 AT_HB1 = cvar.AT_HB1
8752 AT_HB2 = cvar.AT_HB2
8753 AT_HB3 = cvar.AT_HB3
8754 AT_OXT = cvar.AT_OXT
8755 AT_CH3 = cvar.AT_CH3
8756 AT_CH = cvar.AT_CH
8757 AT_CG = cvar.AT_CG
8758 AT_CG1 = cvar.AT_CG1
8759 AT_CG2 = cvar.AT_CG2
8760 AT_HG = cvar.AT_HG
8761 AT_HG1 = cvar.AT_HG1
8762 AT_HG2 = cvar.AT_HG2
8763 AT_HG3 = cvar.AT_HG3
8764 AT_HG11 = cvar.AT_HG11
8765 AT_HG21 = cvar.AT_HG21
8766 AT_HG31 = cvar.AT_HG31
8767 AT_HG12 = cvar.AT_HG12
8768 AT_HG13 = cvar.AT_HG13
8769 AT_HG22 = cvar.AT_HG22
8770 AT_HG23 = cvar.AT_HG23
8771 AT_HG32 = cvar.AT_HG32
8772 AT_OG = cvar.AT_OG
8773 AT_OG1 = cvar.AT_OG1
8774 AT_SG = cvar.AT_SG
8775 AT_CD = cvar.AT_CD
8776 AT_CD1 = cvar.AT_CD1
8777 AT_CD2 = cvar.AT_CD2
8778 AT_HD = cvar.AT_HD
8779 AT_HD1 = cvar.AT_HD1
8780 AT_HD2 = cvar.AT_HD2
8781 AT_HD3 = cvar.AT_HD3
8782 AT_HD11 = cvar.AT_HD11
8783 AT_HD21 = cvar.AT_HD21
8784 AT_HD31 = cvar.AT_HD31
8785 AT_HD12 = cvar.AT_HD12
8786 AT_HD13 = cvar.AT_HD13
8787 AT_HD22 = cvar.AT_HD22
8788 AT_HD23 = cvar.AT_HD23
8789 AT_HD32 = cvar.AT_HD32
8790 AT_SD = cvar.AT_SD
8791 AT_OD1 = cvar.AT_OD1
8792 AT_OD2 = cvar.AT_OD2
8793 AT_ND1 = cvar.AT_ND1
8794 AT_ND2 = cvar.AT_ND2
8795 AT_CE = cvar.AT_CE
8796 AT_CE1 = cvar.AT_CE1
8797 AT_CE2 = cvar.AT_CE2
8798 AT_CE3 = cvar.AT_CE3
8799 AT_HE = cvar.AT_HE
8800 AT_HE1 = cvar.AT_HE1
8801 AT_HE2 = cvar.AT_HE2
8802 AT_HE3 = cvar.AT_HE3
8803 AT_HE21 = cvar.AT_HE21
8804 AT_HE22 = cvar.AT_HE22
8805 AT_OE1 = cvar.AT_OE1
8806 AT_OE2 = cvar.AT_OE2
8807 AT_NE = cvar.AT_NE
8808 AT_NE1 = cvar.AT_NE1
8809 AT_NE2 = cvar.AT_NE2
8810 AT_CZ = cvar.AT_CZ
8811 AT_CZ2 = cvar.AT_CZ2
8812 AT_CZ3 = cvar.AT_CZ3
8813 AT_NZ = cvar.AT_NZ
8814 AT_HZ = cvar.AT_HZ
8815 AT_HZ1 = cvar.AT_HZ1
8816 AT_HZ2 = cvar.AT_HZ2
8817 AT_HZ3 = cvar.AT_HZ3
8818 AT_CH2 = cvar.AT_CH2
8819 AT_NH1 = cvar.AT_NH1
8820 AT_NH2 = cvar.AT_NH2
8821 AT_OH = cvar.AT_OH
8822 AT_HH = cvar.AT_HH
8823 AT_HH11 = cvar.AT_HH11
8824 AT_HH21 = cvar.AT_HH21
8825 AT_HH2 = cvar.AT_HH2
8826 AT_HH12 = cvar.AT_HH12
8827 AT_HH22 = cvar.AT_HH22
8828 AT_HH13 = cvar.AT_HH13
8829 AT_HH23 = cvar.AT_HH23
8830 AT_HH33 = cvar.AT_HH33
8831 AT_P = cvar.AT_P
8832 AT_OP1 = cvar.AT_OP1
8833 AT_OP2 = cvar.AT_OP2
8834 AT_OP3 = cvar.AT_OP3
8835 AT_O5p = cvar.AT_O5p
8836 AT_C5p = cvar.AT_C5p
8837 AT_H5p = cvar.AT_H5p
8838 AT_H5pp = cvar.AT_H5pp
8839 AT_C4p = cvar.AT_C4p
8840 AT_H4p = cvar.AT_H4p
8841 AT_O4p = cvar.AT_O4p
8842 AT_C1p = cvar.AT_C1p
8843 AT_H1p = cvar.AT_H1p
8844 AT_C3p = cvar.AT_C3p
8845 AT_H3p = cvar.AT_H3p
8846 AT_O3p = cvar.AT_O3p
8847 AT_C2p = cvar.AT_C2p
8848 AT_H2p = cvar.AT_H2p
8849 AT_H2pp = cvar.AT_H2pp
8850 AT_O2p = cvar.AT_O2p
8851 AT_HO2p = cvar.AT_HO2p
8852 AT_N9 = cvar.AT_N9
8853 AT_C8 = cvar.AT_C8
8854 AT_H8 = cvar.AT_H8
8855 AT_N7 = cvar.AT_N7
8856 AT_C5 = cvar.AT_C5
8857 AT_C4 = cvar.AT_C4
8858 AT_N3 = cvar.AT_N3
8859 AT_C2 = cvar.AT_C2
8860 AT_N1 = cvar.AT_N1
8861 AT_C6 = cvar.AT_C6
8862 AT_N6 = cvar.AT_N6
8863 AT_H61 = cvar.AT_H61
8864 AT_H62 = cvar.AT_H62
8865 AT_O6 = cvar.AT_O6
8866 AT_N2 = cvar.AT_N2
8867 AT_NT = cvar.AT_NT
8868 AT_H21 = cvar.AT_H21
8869 AT_H22 = cvar.AT_H22
8870 AT_H6 = cvar.AT_H6
8871 AT_H5 = cvar.AT_H5
8872 AT_O2 = cvar.AT_O2
8873 AT_N4 = cvar.AT_N4
8874 AT_H41 = cvar.AT_H41
8875 AT_H42 = cvar.AT_H42
8876 AT_O4 = cvar.AT_O4
8877 AT_C7 = cvar.AT_C7
8878 AT_H71 = cvar.AT_H71
8879 AT_H72 = cvar.AT_H72
8880 AT_H73 = cvar.AT_H73
8881 AT_O1A = cvar.AT_O1A
8882 AT_O2A = cvar.AT_O2A
8883 AT_O3A = cvar.AT_O3A
8884 AT_O1B = cvar.AT_O1B
8885 AT_O2B = cvar.AT_O2B
8886 AT_O3B = cvar.AT_O3B
8887 
8888 def Atom_setup_particle(*args):
8889  """
8890  setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8891  setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8892  setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8893  Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8894  """
8895  return _IMP_atom.Atom_setup_particle(*args)
8896 
8897 def Atom_get_is_setup(*args):
8898  """
8899  get_is_setup(_ParticleAdaptor p) -> bool
8900  Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
8901  """
8902  return _IMP_atom.Atom_get_is_setup(*args)
8903 
8904 def Atom_get_atom_type_key():
8905  """Atom_get_atom_type_key() -> IntKey"""
8906  return _IMP_atom.Atom_get_atom_type_key()
8907 
8908 def Atom_get_element_key():
8909  """Atom_get_element_key() -> IntKey"""
8910  return _IMP_atom.Atom_get_element_key()
8911 
8912 def Atom_get_input_index_key():
8913  """Atom_get_input_index_key() -> IntKey"""
8914  return _IMP_atom.Atom_get_input_index_key()
8915 
8916 def Atom_get_occupancy_key():
8917  """Atom_get_occupancy_key() -> FloatKey"""
8918  return _IMP_atom.Atom_get_occupancy_key()
8919 
8920 def Atom_get_temperature_factor_key():
8921  """Atom_get_temperature_factor_key() -> FloatKey"""
8922  return _IMP_atom.Atom_get_temperature_factor_key()
8923 
8924 
8925 def get_residue(*args):
8926  """
8927  get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8928  get_residue(Atom d, bool nothrow=False) -> Residue
8929  get_residue(Atom d) -> Residue
8930  """
8931  return _IMP_atom.get_residue(*args)
8932 
8933 def get_atom(rd, at):
8934  """get_atom(Residue rd, AtomType at) -> Atom"""
8935  return _IMP_atom.get_atom(rd, at)
8936 
8937 def add_atom_type(name, e):
8938  """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8939  return _IMP_atom.add_atom_type(name, e)
8940 
8941 def get_element_for_atom_type(at):
8942  """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8943  return _IMP_atom.get_element_for_atom_type(at)
8944 
8945 def get_atom_type_exists(name):
8946  """get_atom_type_exists(std::string name) -> bool"""
8947  return _IMP_atom.get_atom_type_exists(name)
8948 class Residue(Hierarchy):
8949  """Proxy of C++ IMP::atom::Residue class"""
8950  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
8951 
8952  def __init__(self, *args):
8953  """
8954  __init__(IMP::atom::Residue self) -> Residue
8955  __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
8956  __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
8957  """
8958  this = _IMP_atom.new_Residue(*args)
8959  try:
8960  self.this.append(this)
8961  except:
8962  self.this = this
8963 
8964  def show(self, *args):
8965  """
8966  show(Residue self, _ostream out)
8967  show(Residue self)
8968  """
8969  return _IMP_atom.Residue_show(self, *args)
8970 
8971 
8972  def setup_particle(*args):
8973  """
8974  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8975  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8976  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8977  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8978  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8979  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8980  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8981  setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8982  """
8983  return _IMP_atom.Residue_setup_particle(*args)
8984 
8985  setup_particle = staticmethod(setup_particle)
8986 
8987  def get_is_setup(*args):
8988  """
8989  get_is_setup(_ParticleAdaptor p) -> bool
8990  get_is_setup(Model m, ParticleIndex pi) -> bool
8991  """
8992  return _IMP_atom.Residue_get_is_setup(*args)
8993 
8994  get_is_setup = staticmethod(get_is_setup)
8995 
8996  def get_residue_type(self):
8997  """get_residue_type(Residue self) -> ResidueType"""
8998  return _IMP_atom.Residue_get_residue_type(self)
8999 
9000 
9001  def set_residue_type(self, t):
9002  """set_residue_type(Residue self, ResidueType t)"""
9003  return _IMP_atom.Residue_set_residue_type(self, t)
9004 
9005 
9006  def get_is_protein(self):
9007  """get_is_protein(Residue self) -> bool"""
9008  return _IMP_atom.Residue_get_is_protein(self)
9009 
9010 
9011  def get_is_dna(self):
9012  """get_is_dna(Residue self) -> bool"""
9013  return _IMP_atom.Residue_get_is_dna(self)
9014 
9015 
9016  def get_is_rna(self):
9017  """get_is_rna(Residue self) -> bool"""
9018  return _IMP_atom.Residue_get_is_rna(self)
9019 
9020 
9021  def get_index(self):
9022  """get_index(Residue self) -> IMP::Int"""
9023  return _IMP_atom.Residue_get_index(self)
9024 
9025 
9026  def set_index(self, t):
9027  """set_index(Residue self, IMP::Int t)"""
9028  return _IMP_atom.Residue_set_index(self, t)
9029 
9030 
9031  def get_insertion_code(self):
9032  """get_insertion_code(Residue self) -> char"""
9033  return _IMP_atom.Residue_get_insertion_code(self)
9034 
9035 
9036  def set_insertion_code(self, insertion_code):
9037  """set_insertion_code(Residue self, char insertion_code)"""
9038  return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
9039 
9040 
9041  def get_index_key():
9042  """get_index_key() -> IntKey"""
9043  return _IMP_atom.Residue_get_index_key()
9044 
9045  get_index_key = staticmethod(get_index_key)
9046 
9047  def get_residue_type_key():
9048  """get_residue_type_key() -> IntKey"""
9049  return _IMP_atom.Residue_get_residue_type_key()
9050 
9051  get_residue_type_key = staticmethod(get_residue_type_key)
9052 
9053  def get_insertion_code_key():
9054  """get_insertion_code_key() -> IntKey"""
9055  return _IMP_atom.Residue_get_insertion_code_key()
9056 
9057  get_insertion_code_key = staticmethod(get_insertion_code_key)
9058 
9059  def add_attribute(self, *args):
9060  """
9061  add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
9062  add_attribute(Residue self, FloatKey a0, IMP::Float a1)
9063  add_attribute(Residue self, IntKey a0, IMP::Int a1)
9064  add_attribute(Residue self, StringKey a0, IMP::String a1)
9065  add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
9066  add_attribute(Residue self, ObjectKey a0, Object a1)
9067  """
9068  return _IMP_atom.Residue_add_attribute(self, *args)
9069 
9070 
9071  def get_value(self, *args):
9072  """
9073  get_value(Residue self, FloatKey a0) -> IMP::Float
9074  get_value(Residue self, IntKey a0) -> IMP::Int
9075  get_value(Residue self, StringKey a0) -> IMP::String
9076  get_value(Residue self, ParticleIndexKey a0) -> Particle
9077  get_value(Residue self, ObjectKey a0) -> Object
9078  """
9079  return _IMP_atom.Residue_get_value(self, *args)
9080 
9081 
9082  def set_value(self, *args):
9083  """
9084  set_value(Residue self, FloatKey a0, IMP::Float a1)
9085  set_value(Residue self, IntKey a0, IMP::Int a1)
9086  set_value(Residue self, StringKey a0, IMP::String a1)
9087  set_value(Residue self, ParticleIndexKey a0, Particle a1)
9088  set_value(Residue self, ObjectKey a0, Object a1)
9089  """
9090  return _IMP_atom.Residue_set_value(self, *args)
9091 
9092 
9093  def remove_attribute(self, *args):
9094  """
9095  remove_attribute(Residue self, FloatKey a0)
9096  remove_attribute(Residue self, IntKey a0)
9097  remove_attribute(Residue self, StringKey a0)
9098  remove_attribute(Residue self, ParticleIndexKey a0)
9099  remove_attribute(Residue self, ObjectKey a0)
9100  """
9101  return _IMP_atom.Residue_remove_attribute(self, *args)
9102 
9103 
9104  def has_attribute(self, *args):
9105  """
9106  has_attribute(Residue self, FloatKey a0) -> bool
9107  has_attribute(Residue self, IntKey a0) -> bool
9108  has_attribute(Residue self, StringKey a0) -> bool
9109  has_attribute(Residue self, ParticleIndexKey a0) -> bool
9110  has_attribute(Residue self, ObjectKey a0) -> bool
9111  """
9112  return _IMP_atom.Residue_has_attribute(self, *args)
9113 
9114 
9115  def get_derivative(self, a0):
9116  """get_derivative(Residue self, FloatKey a0) -> double"""
9117  return _IMP_atom.Residue_get_derivative(self, a0)
9118 
9119 
9120  def get_name(self):
9121  """get_name(Residue self) -> std::string"""
9122  return _IMP_atom.Residue_get_name(self)
9123 
9124 
9125  def clear_caches(self):
9126  """clear_caches(Residue self)"""
9127  return _IMP_atom.Residue_clear_caches(self)
9128 
9129 
9130  def set_name(self, a0):
9131  """set_name(Residue self, std::string a0)"""
9132  return _IMP_atom.Residue_set_name(self, a0)
9133 
9134 
9135  def set_check_level(self, a0):
9136  """set_check_level(Residue self, IMP::CheckLevel a0)"""
9137  return _IMP_atom.Residue_set_check_level(self, a0)
9138 
9139 
9140  def add_to_derivative(self, a0, a1, a2):
9141  """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9142  return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
9143 
9144 
9145  def set_is_optimized(self, a0, a1):
9146  """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
9147  return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
9148 
9149 
9150  def get_is_optimized(self, a0):
9151  """get_is_optimized(Residue self, FloatKey a0) -> bool"""
9152  return _IMP_atom.Residue_get_is_optimized(self, a0)
9153 
9154 
9155  def get_check_level(self):
9156  """get_check_level(Residue self) -> IMP::CheckLevel"""
9157  return _IMP_atom.Residue_get_check_level(self)
9158 
9159 
9160  def __eq__(self, *args):
9161  """
9162  __eq__(Residue self, Residue o) -> bool
9163  __eq__(Residue self, Particle d) -> bool
9164  """
9165  return _IMP_atom.Residue___eq__(self, *args)
9166 
9167 
9168  def __ne__(self, *args):
9169  """
9170  __ne__(Residue self, Residue o) -> bool
9171  __ne__(Residue self, Particle d) -> bool
9172  """
9173  return _IMP_atom.Residue___ne__(self, *args)
9174 
9175 
9176  def __le__(self, *args):
9177  """
9178  __le__(Residue self, Residue o) -> bool
9179  __le__(Residue self, Particle d) -> bool
9180  """
9181  return _IMP_atom.Residue___le__(self, *args)
9182 
9183 
9184  def __lt__(self, *args):
9185  """
9186  __lt__(Residue self, Residue o) -> bool
9187  __lt__(Residue self, Particle d) -> bool
9188  """
9189  return _IMP_atom.Residue___lt__(self, *args)
9190 
9191 
9192  def __ge__(self, *args):
9193  """
9194  __ge__(Residue self, Residue o) -> bool
9195  __ge__(Residue self, Particle d) -> bool
9196  """
9197  return _IMP_atom.Residue___ge__(self, *args)
9198 
9199 
9200  def __gt__(self, *args):
9201  """
9202  __gt__(Residue self, Residue o) -> bool
9203  __gt__(Residue self, Particle d) -> bool
9204  """
9205  return _IMP_atom.Residue___gt__(self, *args)
9206 
9207 
9208  def __hash__(self):
9209  """__hash__(Residue self) -> std::size_t"""
9210  return _IMP_atom.Residue___hash__(self)
9211 
9212 
9213  def __str__(self):
9214  """__str__(Residue self) -> std::string"""
9215  return _IMP_atom.Residue___str__(self)
9216 
9217 
9218  def __repr__(self):
9219  """__repr__(Residue self) -> std::string"""
9220  return _IMP_atom.Residue___repr__(self)
9221 
9222  __swig_destroy__ = _IMP_atom.delete_Residue
9223  __del__ = lambda self: None
9224 Residue_swigregister = _IMP_atom.Residue_swigregister
9225 Residue_swigregister(Residue)
9226 UNK = cvar.UNK
9227 GLY = cvar.GLY
9228 ALA = cvar.ALA
9229 VAL = cvar.VAL
9230 LEU = cvar.LEU
9231 ILE = cvar.ILE
9232 SER = cvar.SER
9233 THR = cvar.THR
9234 CYS = cvar.CYS
9235 MET = cvar.MET
9236 PRO = cvar.PRO
9237 ASP = cvar.ASP
9238 ASN = cvar.ASN
9239 GLU = cvar.GLU
9240 GLN = cvar.GLN
9241 LYS = cvar.LYS
9242 ARG = cvar.ARG
9243 HIS = cvar.HIS
9244 PHE = cvar.PHE
9245 TYR = cvar.TYR
9246 TRP = cvar.TRP
9247 ACE = cvar.ACE
9248 NH2 = cvar.NH2
9249 ADE = cvar.ADE
9250 URA = cvar.URA
9251 CYT = cvar.CYT
9252 GUA = cvar.GUA
9253 THY = cvar.THY
9254 DADE = cvar.DADE
9255 DURA = cvar.DURA
9256 DCYT = cvar.DCYT
9257 DGUA = cvar.DGUA
9258 DTHY = cvar.DTHY
9259 HOH = cvar.HOH
9260 HEME = cvar.HEME
9261 
9262 def Residue_setup_particle(*args):
9263  """
9264  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9265  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9266  setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9267  setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9268  setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9269  setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9270  setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9271  Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9272  """
9273  return _IMP_atom.Residue_setup_particle(*args)
9274 
9275 def Residue_get_is_setup(*args):
9276  """
9277  get_is_setup(_ParticleAdaptor p) -> bool
9278  Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
9279  """
9280  return _IMP_atom.Residue_get_is_setup(*args)
9281 
9282 def Residue_get_index_key():
9283  """Residue_get_index_key() -> IntKey"""
9284  return _IMP_atom.Residue_get_index_key()
9285 
9286 def Residue_get_residue_type_key():
9287  """Residue_get_residue_type_key() -> IntKey"""
9288  return _IMP_atom.Residue_get_residue_type_key()
9289 
9290 def Residue_get_insertion_code_key():
9291  """Residue_get_insertion_code_key() -> IntKey"""
9292  return _IMP_atom.Residue_get_insertion_code_key()
9293 
9294 
9295 def get_next_residue(rd):
9296  """get_next_residue(Residue rd) -> Hierarchy"""
9297  return _IMP_atom.get_next_residue(rd)
9298 
9299 def get_previous_residue(rd):
9300  """get_previous_residue(Residue rd) -> Hierarchy"""
9301  return _IMP_atom.get_previous_residue(rd)
9302 
9303 def get_one_letter_code(c):
9304  """get_one_letter_code(ResidueType c) -> char"""
9305  return _IMP_atom.get_one_letter_code(c)
9306 
9307 _IMP_atom.BALLS_swigconstant(_IMP_atom)
9308 BALLS = _IMP_atom.BALLS
9309 
9310 _IMP_atom.DENSITIES_swigconstant(_IMP_atom)
9311 DENSITIES = _IMP_atom.DENSITIES
9312 class Representation(Hierarchy):
9313  """Proxy of C++ IMP::atom::Representation class"""
9314  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9315 
9316  def setup_particle(*args):
9317  """
9318  setup_particle(Model m, ParticleIndex pi) -> Representation
9319  setup_particle(_ParticleAdaptor decorator) -> Representation
9320  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9321  setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9322  """
9323  return _IMP_atom.Representation_setup_particle(*args)
9324 
9325  setup_particle = staticmethod(setup_particle)
9326 
9327  def __init__(self, *args):
9328  """
9329  __init__(IMP::atom::Representation self) -> Representation
9330  __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
9331  __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
9332  """
9333  this = _IMP_atom.new_Representation(*args)
9334  try:
9335  self.this.append(this)
9336  except:
9337  self.this = this
9338 
9339  def show(self, *args):
9340  """
9341  show(Representation self, _ostream out)
9342  show(Representation self)
9343  """
9344  return _IMP_atom.Representation_show(self, *args)
9345 
9346 
9347  def get_is_setup(*args):
9348  """
9349  get_is_setup(_ParticleAdaptor p) -> bool
9350  get_is_setup(Model m, ParticleIndex pi) -> bool
9351  """
9352  return _IMP_atom.Representation_get_is_setup(*args)
9353 
9354  get_is_setup = staticmethod(get_is_setup)
9355 
9356  def get_representation(self, *args):
9357  """
9358  get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
9359  get_representation(Representation self, double resolution) -> Hierarchy
9360  """
9361  return _IMP_atom.Representation_get_representation(self, *args)
9362 
9363 
9364  def get_representations(self, *args):
9365  """
9366  get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
9367  get_representations(Representation self) -> IMP::atom::Hierarchies
9368  """
9369  return _IMP_atom.Representation_get_representations(self, *args)
9370 
9371 
9372  def add_representation(self, *args):
9373  """
9374  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
9375  add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
9376  add_representation(Representation self, _ParticleIndexAdaptor rep)
9377  """
9378  return _IMP_atom.Representation_add_representation(self, *args)
9379 
9380 
9381  def get_resolutions(self, *args):
9382  """
9383  get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9384  get_resolutions(Representation self) -> IMP::Floats
9385  """
9386  return _IMP_atom.Representation_get_resolutions(self, *args)
9387 
9388 
9389  def add_attribute(self, *args):
9390  """
9391  add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9392  add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9393  add_attribute(Representation self, IntKey a0, IMP::Int a1)
9394  add_attribute(Representation self, StringKey a0, IMP::String a1)
9395  add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9396  add_attribute(Representation self, ObjectKey a0, Object a1)
9397  """
9398  return _IMP_atom.Representation_add_attribute(self, *args)
9399 
9400 
9401  def get_value(self, *args):
9402  """
9403  get_value(Representation self, FloatKey a0) -> IMP::Float
9404  get_value(Representation self, IntKey a0) -> IMP::Int
9405  get_value(Representation self, StringKey a0) -> IMP::String
9406  get_value(Representation self, ParticleIndexKey a0) -> Particle
9407  get_value(Representation self, ObjectKey a0) -> Object
9408  """
9409  return _IMP_atom.Representation_get_value(self, *args)
9410 
9411 
9412  def set_value(self, *args):
9413  """
9414  set_value(Representation self, FloatKey a0, IMP::Float a1)
9415  set_value(Representation self, IntKey a0, IMP::Int a1)
9416  set_value(Representation self, StringKey a0, IMP::String a1)
9417  set_value(Representation self, ParticleIndexKey a0, Particle a1)
9418  set_value(Representation self, ObjectKey a0, Object a1)
9419  """
9420  return _IMP_atom.Representation_set_value(self, *args)
9421 
9422 
9423  def remove_attribute(self, *args):
9424  """
9425  remove_attribute(Representation self, FloatKey a0)
9426  remove_attribute(Representation self, IntKey a0)
9427  remove_attribute(Representation self, StringKey a0)
9428  remove_attribute(Representation self, ParticleIndexKey a0)
9429  remove_attribute(Representation self, ObjectKey a0)
9430  """
9431  return _IMP_atom.Representation_remove_attribute(self, *args)
9432 
9433 
9434  def has_attribute(self, *args):
9435  """
9436  has_attribute(Representation self, FloatKey a0) -> bool
9437  has_attribute(Representation self, IntKey a0) -> bool
9438  has_attribute(Representation self, StringKey a0) -> bool
9439  has_attribute(Representation self, ParticleIndexKey a0) -> bool
9440  has_attribute(Representation self, ObjectKey a0) -> bool
9441  """
9442  return _IMP_atom.Representation_has_attribute(self, *args)
9443 
9444 
9445  def get_derivative(self, a0):
9446  """get_derivative(Representation self, FloatKey a0) -> double"""
9447  return _IMP_atom.Representation_get_derivative(self, a0)
9448 
9449 
9450  def get_name(self):
9451  """get_name(Representation self) -> std::string"""
9452  return _IMP_atom.Representation_get_name(self)
9453 
9454 
9455  def clear_caches(self):
9456  """clear_caches(Representation self)"""
9457  return _IMP_atom.Representation_clear_caches(self)
9458 
9459 
9460  def set_name(self, a0):
9461  """set_name(Representation self, std::string a0)"""
9462  return _IMP_atom.Representation_set_name(self, a0)
9463 
9464 
9465  def set_check_level(self, a0):
9466  """set_check_level(Representation self, IMP::CheckLevel a0)"""
9467  return _IMP_atom.Representation_set_check_level(self, a0)
9468 
9469 
9470  def add_to_derivative(self, a0, a1, a2):
9471  """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9472  return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9473 
9474 
9475  def set_is_optimized(self, a0, a1):
9476  """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9477  return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9478 
9479 
9480  def get_is_optimized(self, a0):
9481  """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9482  return _IMP_atom.Representation_get_is_optimized(self, a0)
9483 
9484 
9485  def get_check_level(self):
9486  """get_check_level(Representation self) -> IMP::CheckLevel"""
9487  return _IMP_atom.Representation_get_check_level(self)
9488 
9489 
9490  def __eq__(self, *args):
9491  """
9492  __eq__(Representation self, Representation o) -> bool
9493  __eq__(Representation self, Particle d) -> bool
9494  """
9495  return _IMP_atom.Representation___eq__(self, *args)
9496 
9497 
9498  def __ne__(self, *args):
9499  """
9500  __ne__(Representation self, Representation o) -> bool
9501  __ne__(Representation self, Particle d) -> bool
9502  """
9503  return _IMP_atom.Representation___ne__(self, *args)
9504 
9505 
9506  def __le__(self, *args):
9507  """
9508  __le__(Representation self, Representation o) -> bool
9509  __le__(Representation self, Particle d) -> bool
9510  """
9511  return _IMP_atom.Representation___le__(self, *args)
9512 
9513 
9514  def __lt__(self, *args):
9515  """
9516  __lt__(Representation self, Representation o) -> bool
9517  __lt__(Representation self, Particle d) -> bool
9518  """
9519  return _IMP_atom.Representation___lt__(self, *args)
9520 
9521 
9522  def __ge__(self, *args):
9523  """
9524  __ge__(Representation self, Representation o) -> bool
9525  __ge__(Representation self, Particle d) -> bool
9526  """
9527  return _IMP_atom.Representation___ge__(self, *args)
9528 
9529 
9530  def __gt__(self, *args):
9531  """
9532  __gt__(Representation self, Representation o) -> bool
9533  __gt__(Representation self, Particle d) -> bool
9534  """
9535  return _IMP_atom.Representation___gt__(self, *args)
9536 
9537 
9538  def __hash__(self):
9539  """__hash__(Representation self) -> std::size_t"""
9540  return _IMP_atom.Representation___hash__(self)
9541 
9542 
9543  def __str__(self):
9544  """__str__(Representation self) -> std::string"""
9545  return _IMP_atom.Representation___str__(self)
9546 
9547 
9548  def __repr__(self):
9549  """__repr__(Representation self) -> std::string"""
9550  return _IMP_atom.Representation___repr__(self)
9551 
9552  __swig_destroy__ = _IMP_atom.delete_Representation
9553  __del__ = lambda self: None
9554 Representation_swigregister = _IMP_atom.Representation_swigregister
9555 Representation_swigregister(Representation)
9556 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9557 
9558 def Representation_setup_particle(*args):
9559  """
9560  setup_particle(Model m, ParticleIndex pi) -> Representation
9561  setup_particle(_ParticleAdaptor decorator) -> Representation
9562  setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9563  Representation_setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9564  """
9565  return _IMP_atom.Representation_setup_particle(*args)
9566 
9567 def Representation_get_is_setup(*args):
9568  """
9569  get_is_setup(_ParticleAdaptor p) -> bool
9570  Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9571  """
9572  return _IMP_atom.Representation_get_is_setup(*args)
9573 
9574 
9575 def get_resolution(*args):
9576  """
9577  get_resolution(Model m, ParticleIndex pi) -> double
9578  get_resolution(Hierarchy h) -> double
9579  """
9580  return _IMP_atom.get_resolution(*args)
9581 
9582 def get_representation(h, nothrow=False):
9583  """
9584  get_representation(Hierarchy h, bool nothrow=False) -> Representation
9585  get_representation(Hierarchy h) -> Representation
9586  """
9587  return _IMP_atom.get_representation(h, nothrow)
9588 
9589 def show_with_representations(*args):
9590  """
9591  show_with_representations(Hierarchy h, _ostream out)
9592  show_with_representations(Hierarchy h)
9593  """
9594  return _IMP_atom.show_with_representations(*args)
9595 class State(Hierarchy):
9596  """Proxy of C++ IMP::atom::State class"""
9597  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9598 
9599  def setup_particle(*args):
9600  """
9601  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9602  setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9603  """
9604  return _IMP_atom.State_setup_particle(*args)
9605 
9606  setup_particle = staticmethod(setup_particle)
9607 
9608  def __init__(self, *args):
9609  """
9610  __init__(IMP::atom::State self) -> State
9611  __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9612  __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9613  """
9614  this = _IMP_atom.new_State(*args)
9615  try:
9616  self.this.append(this)
9617  except:
9618  self.this = this
9619 
9620  def show(self, *args):
9621  """
9622  show(State self, _ostream out)
9623  show(State self)
9624  """
9625  return _IMP_atom.State_show(self, *args)
9626 
9627 
9628  def get_is_setup(*args):
9629  """
9630  get_is_setup(_ParticleAdaptor p) -> bool
9631  get_is_setup(Model m, ParticleIndex pi) -> bool
9632  """
9633  return _IMP_atom.State_get_is_setup(*args)
9634 
9635  get_is_setup = staticmethod(get_is_setup)
9636 
9637  def get_state_index(self):
9638  """get_state_index(State self) -> unsigned int"""
9639  return _IMP_atom.State_get_state_index(self)
9640 
9641 
9642  def add_attribute(self, *args):
9643  """
9644  add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9645  add_attribute(State self, FloatKey a0, IMP::Float a1)
9646  add_attribute(State self, IntKey a0, IMP::Int a1)
9647  add_attribute(State self, StringKey a0, IMP::String a1)
9648  add_attribute(State self, ParticleIndexKey a0, Particle a1)
9649  add_attribute(State self, ObjectKey a0, Object a1)
9650  """
9651  return _IMP_atom.State_add_attribute(self, *args)
9652 
9653 
9654  def get_value(self, *args):
9655  """
9656  get_value(State self, FloatKey a0) -> IMP::Float
9657  get_value(State self, IntKey a0) -> IMP::Int
9658  get_value(State self, StringKey a0) -> IMP::String
9659  get_value(State self, ParticleIndexKey a0) -> Particle
9660  get_value(State self, ObjectKey a0) -> Object
9661  """
9662  return _IMP_atom.State_get_value(self, *args)
9663 
9664 
9665  def set_value(self, *args):
9666  """
9667  set_value(State self, FloatKey a0, IMP::Float a1)
9668  set_value(State self, IntKey a0, IMP::Int a1)
9669  set_value(State self, StringKey a0, IMP::String a1)
9670  set_value(State self, ParticleIndexKey a0, Particle a1)
9671  set_value(State self, ObjectKey a0, Object a1)
9672  """
9673  return _IMP_atom.State_set_value(self, *args)
9674 
9675 
9676  def remove_attribute(self, *args):
9677  """
9678  remove_attribute(State self, FloatKey a0)
9679  remove_attribute(State self, IntKey a0)
9680  remove_attribute(State self, StringKey a0)
9681  remove_attribute(State self, ParticleIndexKey a0)
9682  remove_attribute(State self, ObjectKey a0)
9683  """
9684  return _IMP_atom.State_remove_attribute(self, *args)
9685 
9686 
9687  def has_attribute(self, *args):
9688  """
9689  has_attribute(State self, FloatKey a0) -> bool
9690  has_attribute(State self, IntKey a0) -> bool
9691  has_attribute(State self, StringKey a0) -> bool
9692  has_attribute(State self, ParticleIndexKey a0) -> bool
9693  has_attribute(State self, ObjectKey a0) -> bool
9694  """
9695  return _IMP_atom.State_has_attribute(self, *args)
9696 
9697 
9698  def get_derivative(self, a0):
9699  """get_derivative(State self, FloatKey a0) -> double"""
9700  return _IMP_atom.State_get_derivative(self, a0)
9701 
9702 
9703  def get_name(self):
9704  """get_name(State self) -> std::string"""
9705  return _IMP_atom.State_get_name(self)
9706 
9707 
9708  def clear_caches(self):
9709  """clear_caches(State self)"""
9710  return _IMP_atom.State_clear_caches(self)
9711 
9712 
9713  def set_name(self, a0):
9714  """set_name(State self, std::string a0)"""
9715  return _IMP_atom.State_set_name(self, a0)
9716 
9717 
9718  def set_check_level(self, a0):
9719  """set_check_level(State self, IMP::CheckLevel a0)"""
9720  return _IMP_atom.State_set_check_level(self, a0)
9721 
9722 
9723  def add_to_derivative(self, a0, a1, a2):
9724  """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9725  return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9726 
9727 
9728  def set_is_optimized(self, a0, a1):
9729  """set_is_optimized(State self, FloatKey a0, bool a1)"""
9730  return _IMP_atom.State_set_is_optimized(self, a0, a1)
9731 
9732 
9733  def get_is_optimized(self, a0):
9734  """get_is_optimized(State self, FloatKey a0) -> bool"""
9735  return _IMP_atom.State_get_is_optimized(self, a0)
9736 
9737 
9738  def get_check_level(self):
9739  """get_check_level(State self) -> IMP::CheckLevel"""
9740  return _IMP_atom.State_get_check_level(self)
9741 
9742 
9743  def __eq__(self, *args):
9744  """
9745  __eq__(State self, State o) -> bool
9746  __eq__(State self, Particle d) -> bool
9747  """
9748  return _IMP_atom.State___eq__(self, *args)
9749 
9750 
9751  def __ne__(self, *args):
9752  """
9753  __ne__(State self, State o) -> bool
9754  __ne__(State self, Particle d) -> bool
9755  """
9756  return _IMP_atom.State___ne__(self, *args)
9757 
9758 
9759  def __le__(self, *args):
9760  """
9761  __le__(State self, State o) -> bool
9762  __le__(State self, Particle d) -> bool
9763  """
9764  return _IMP_atom.State___le__(self, *args)
9765 
9766 
9767  def __lt__(self, *args):
9768  """
9769  __lt__(State self, State o) -> bool
9770  __lt__(State self, Particle d) -> bool
9771  """
9772  return _IMP_atom.State___lt__(self, *args)
9773 
9774 
9775  def __ge__(self, *args):
9776  """
9777  __ge__(State self, State o) -> bool
9778  __ge__(State self, Particle d) -> bool
9779  """
9780  return _IMP_atom.State___ge__(self, *args)
9781 
9782 
9783  def __gt__(self, *args):
9784  """
9785  __gt__(State self, State o) -> bool
9786  __gt__(State self, Particle d) -> bool
9787  """
9788  return _IMP_atom.State___gt__(self, *args)
9789 
9790 
9791  def __hash__(self):
9792  """__hash__(State self) -> std::size_t"""
9793  return _IMP_atom.State___hash__(self)
9794 
9795 
9796  def __str__(self):
9797  """__str__(State self) -> std::string"""
9798  return _IMP_atom.State___str__(self)
9799 
9800 
9801  def __repr__(self):
9802  """__repr__(State self) -> std::string"""
9803  return _IMP_atom.State___repr__(self)
9804 
9805  __swig_destroy__ = _IMP_atom.delete_State
9806  __del__ = lambda self: None
9807 State_swigregister = _IMP_atom.State_swigregister
9808 State_swigregister(State)
9809 
9810 def State_setup_particle(*args):
9811  """
9812  setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9813  State_setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9814  """
9815  return _IMP_atom.State_setup_particle(*args)
9816 
9817 def State_get_is_setup(*args):
9818  """
9819  get_is_setup(_ParticleAdaptor p) -> bool
9820  State_get_is_setup(Model m, ParticleIndex pi) -> bool
9821  """
9822  return _IMP_atom.State_get_is_setup(*args)
9823 
9824 
9825 def get_state_index(h):
9826  """get_state_index(Hierarchy h) -> int"""
9827  return _IMP_atom.get_state_index(h)
9828 
9829 def get_phi_dihedral_atoms(rd):
9830  """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9831  return _IMP_atom.get_phi_dihedral_atoms(rd)
9832 
9833 def get_psi_dihedral_atoms(rd):
9834  """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9835  return _IMP_atom.get_psi_dihedral_atoms(rd)
9836 class Molecule(Hierarchy):
9837  """Proxy of C++ IMP::atom::Molecule class"""
9838  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
9839 
9840  def __init__(self, *args):
9841  """
9842  __init__(IMP::atom::Molecule self) -> Molecule
9843  __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
9844  __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
9845  """
9846  this = _IMP_atom.new_Molecule(*args)
9847  try:
9848  self.this.append(this)
9849  except:
9850  self.this = this
9851 
9852  def show(self, *args):
9853  """
9854  show(Molecule self, _ostream out)
9855  show(Molecule self)
9856  """
9857  return _IMP_atom.Molecule_show(self, *args)
9858 
9859 
9860  def setup_particle(*args):
9861  """
9862  setup_particle(Model m, ParticleIndex pi) -> Molecule
9863  setup_particle(_ParticleAdaptor decorator) -> Molecule
9864  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9865  setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9866  """
9867  return _IMP_atom.Molecule_setup_particle(*args)
9868 
9869  setup_particle = staticmethod(setup_particle)
9870 
9871  def get_is_setup(*args):
9872  """
9873  get_is_setup(_ParticleAdaptor p) -> bool
9874  get_is_setup(Model m, ParticleIndex pi) -> bool
9875  """
9876  return _IMP_atom.Molecule_get_is_setup(*args)
9877 
9878  get_is_setup = staticmethod(get_is_setup)
9879 
9880  def add_attribute(self, *args):
9881  """
9882  add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9883  add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9884  add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9885  add_attribute(Molecule self, StringKey a0, IMP::String a1)
9886  add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9887  add_attribute(Molecule self, ObjectKey a0, Object a1)
9888  """
9889  return _IMP_atom.Molecule_add_attribute(self, *args)
9890 
9891 
9892  def get_value(self, *args):
9893  """
9894  get_value(Molecule self, FloatKey a0) -> IMP::Float
9895  get_value(Molecule self, IntKey a0) -> IMP::Int
9896  get_value(Molecule self, StringKey a0) -> IMP::String
9897  get_value(Molecule self, ParticleIndexKey a0) -> Particle
9898  get_value(Molecule self, ObjectKey a0) -> Object
9899  """
9900  return _IMP_atom.Molecule_get_value(self, *args)
9901 
9902 
9903  def set_value(self, *args):
9904  """
9905  set_value(Molecule self, FloatKey a0, IMP::Float a1)
9906  set_value(Molecule self, IntKey a0, IMP::Int a1)
9907  set_value(Molecule self, StringKey a0, IMP::String a1)
9908  set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9909  set_value(Molecule self, ObjectKey a0, Object a1)
9910  """
9911  return _IMP_atom.Molecule_set_value(self, *args)
9912 
9913 
9914  def remove_attribute(self, *args):
9915  """
9916  remove_attribute(Molecule self, FloatKey a0)
9917  remove_attribute(Molecule self, IntKey a0)
9918  remove_attribute(Molecule self, StringKey a0)
9919  remove_attribute(Molecule self, ParticleIndexKey a0)
9920  remove_attribute(Molecule self, ObjectKey a0)
9921  """
9922  return _IMP_atom.Molecule_remove_attribute(self, *args)
9923 
9924 
9925  def has_attribute(self, *args):
9926  """
9927  has_attribute(Molecule self, FloatKey a0) -> bool
9928  has_attribute(Molecule self, IntKey a0) -> bool
9929  has_attribute(Molecule self, StringKey a0) -> bool
9930  has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9931  has_attribute(Molecule self, ObjectKey a0) -> bool
9932  """
9933  return _IMP_atom.Molecule_has_attribute(self, *args)
9934 
9935 
9936  def get_derivative(self, a0):
9937  """get_derivative(Molecule self, FloatKey a0) -> double"""
9938  return _IMP_atom.Molecule_get_derivative(self, a0)
9939 
9940 
9941  def get_name(self):
9942  """get_name(Molecule self) -> std::string"""
9943  return _IMP_atom.Molecule_get_name(self)
9944 
9945 
9946  def clear_caches(self):
9947  """clear_caches(Molecule self)"""
9948  return _IMP_atom.Molecule_clear_caches(self)
9949 
9950 
9951  def set_name(self, a0):
9952  """set_name(Molecule self, std::string a0)"""
9953  return _IMP_atom.Molecule_set_name(self, a0)
9954 
9955 
9956  def set_check_level(self, a0):
9957  """set_check_level(Molecule self, IMP::CheckLevel a0)"""
9958  return _IMP_atom.Molecule_set_check_level(self, a0)
9959 
9960 
9961  def add_to_derivative(self, a0, a1, a2):
9962  """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9963  return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9964 
9965 
9966  def set_is_optimized(self, a0, a1):
9967  """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9968  return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9969 
9970 
9971  def get_is_optimized(self, a0):
9972  """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9973  return _IMP_atom.Molecule_get_is_optimized(self, a0)
9974 
9975 
9976  def get_check_level(self):
9977  """get_check_level(Molecule self) -> IMP::CheckLevel"""
9978  return _IMP_atom.Molecule_get_check_level(self)
9979 
9980 
9981  def __eq__(self, *args):
9982  """
9983  __eq__(Molecule self, Molecule o) -> bool
9984  __eq__(Molecule self, Particle d) -> bool
9985  """
9986  return _IMP_atom.Molecule___eq__(self, *args)
9987 
9988 
9989  def __ne__(self, *args):
9990  """
9991  __ne__(Molecule self, Molecule o) -> bool
9992  __ne__(Molecule self, Particle d) -> bool
9993  """
9994  return _IMP_atom.Molecule___ne__(self, *args)
9995 
9996 
9997  def __le__(self, *args):
9998  """
9999  __le__(Molecule self, Molecule o) -> bool
10000  __le__(Molecule self, Particle d) -> bool
10001  """
10002  return _IMP_atom.Molecule___le__(self, *args)
10003 
10004 
10005  def __lt__(self, *args):
10006  """
10007  __lt__(Molecule self, Molecule o) -> bool
10008  __lt__(Molecule self, Particle d) -> bool
10009  """
10010  return _IMP_atom.Molecule___lt__(self, *args)
10011 
10012 
10013  def __ge__(self, *args):
10014  """
10015  __ge__(Molecule self, Molecule o) -> bool
10016  __ge__(Molecule self, Particle d) -> bool
10017  """
10018  return _IMP_atom.Molecule___ge__(self, *args)
10019 
10020 
10021  def __gt__(self, *args):
10022  """
10023  __gt__(Molecule self, Molecule o) -> bool
10024  __gt__(Molecule self, Particle d) -> bool
10025  """
10026  return _IMP_atom.Molecule___gt__(self, *args)
10027 
10028 
10029  def __hash__(self):
10030  """__hash__(Molecule self) -> std::size_t"""
10031  return _IMP_atom.Molecule___hash__(self)
10032 
10033 
10034  def __str__(self):
10035  """__str__(Molecule self) -> std::string"""
10036  return _IMP_atom.Molecule___str__(self)
10037 
10038 
10039  def __repr__(self):
10040  """__repr__(Molecule self) -> std::string"""
10041  return _IMP_atom.Molecule___repr__(self)
10042 
10043  __swig_destroy__ = _IMP_atom.delete_Molecule
10044  __del__ = lambda self: None
10045 Molecule_swigregister = _IMP_atom.Molecule_swigregister
10046 Molecule_swigregister(Molecule)
10047 
10048 def Molecule_setup_particle(*args):
10049  """
10050  setup_particle(Model m, ParticleIndex pi) -> Molecule
10051  setup_particle(_ParticleAdaptor decorator) -> Molecule
10052  setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10053  Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10054  """
10055  return _IMP_atom.Molecule_setup_particle(*args)
10056 
10057 def Molecule_get_is_setup(*args):
10058  """
10059  get_is_setup(_ParticleAdaptor p) -> bool
10060  Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
10061  """
10062  return _IMP_atom.Molecule_get_is_setup(*args)
10063 
10064 
10065 def get_molecule_name(h):
10066  """get_molecule_name(Hierarchy h) -> std::string"""
10067  return _IMP_atom.get_molecule_name(h)
10068 class Copy(Molecule):
10069  """Proxy of C++ IMP::atom::Copy class"""
10070  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10071 
10072  def get_copy_index_key():
10073  """get_copy_index_key() -> IntKey"""
10074  return _IMP_atom.Copy_get_copy_index_key()
10075 
10076  get_copy_index_key = staticmethod(get_copy_index_key)
10077 
10078  def __init__(self, *args):
10079  """
10080  __init__(IMP::atom::Copy self) -> Copy
10081  __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
10082  __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
10083  """
10084  this = _IMP_atom.new_Copy(*args)
10085  try:
10086  self.this.append(this)
10087  except:
10088  self.this = this
10089 
10090  def show(self, *args):
10091  """
10092  show(Copy self, _ostream out)
10093  show(Copy self)
10094  """
10095  return _IMP_atom.Copy_show(self, *args)
10096 
10097 
10098  def setup_particle(*args):
10099  """
10100  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10101  setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10102  """
10103  return _IMP_atom.Copy_setup_particle(*args)
10104 
10105  setup_particle = staticmethod(setup_particle)
10106 
10107  def get_is_setup(*args):
10108  """
10109  get_is_setup(_ParticleAdaptor p) -> bool
10110  get_is_setup(Model m, ParticleIndex pi) -> bool
10111  """
10112  return _IMP_atom.Copy_get_is_setup(*args)
10113 
10114  get_is_setup = staticmethod(get_is_setup)
10115 
10116  def get_copy_index(self):
10117  """get_copy_index(Copy self) -> int"""
10118  return _IMP_atom.Copy_get_copy_index(self)
10119 
10120 
10121  def add_attribute(self, *args):
10122  """
10123  add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
10124  add_attribute(Copy self, FloatKey a0, IMP::Float a1)
10125  add_attribute(Copy self, IntKey a0, IMP::Int a1)
10126  add_attribute(Copy self, StringKey a0, IMP::String a1)
10127  add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
10128  add_attribute(Copy self, ObjectKey a0, Object a1)
10129  """
10130  return _IMP_atom.Copy_add_attribute(self, *args)
10131 
10132 
10133  def get_value(self, *args):
10134  """
10135  get_value(Copy self, FloatKey a0) -> IMP::Float
10136  get_value(Copy self, IntKey a0) -> IMP::Int
10137  get_value(Copy self, StringKey a0) -> IMP::String
10138  get_value(Copy self, ParticleIndexKey a0) -> Particle
10139  get_value(Copy self, ObjectKey a0) -> Object
10140  """
10141  return _IMP_atom.Copy_get_value(self, *args)
10142 
10143 
10144  def set_value(self, *args):
10145  """
10146  set_value(Copy self, FloatKey a0, IMP::Float a1)
10147  set_value(Copy self, IntKey a0, IMP::Int a1)
10148  set_value(Copy self, StringKey a0, IMP::String a1)
10149  set_value(Copy self, ParticleIndexKey a0, Particle a1)
10150  set_value(Copy self, ObjectKey a0, Object a1)
10151  """
10152  return _IMP_atom.Copy_set_value(self, *args)
10153 
10154 
10155  def remove_attribute(self, *args):
10156  """
10157  remove_attribute(Copy self, FloatKey a0)
10158  remove_attribute(Copy self, IntKey a0)
10159  remove_attribute(Copy self, StringKey a0)
10160  remove_attribute(Copy self, ParticleIndexKey a0)
10161  remove_attribute(Copy self, ObjectKey a0)
10162  """
10163  return _IMP_atom.Copy_remove_attribute(self, *args)
10164 
10165 
10166  def has_attribute(self, *args):
10167  """
10168  has_attribute(Copy self, FloatKey a0) -> bool
10169  has_attribute(Copy self, IntKey a0) -> bool
10170  has_attribute(Copy self, StringKey a0) -> bool
10171  has_attribute(Copy self, ParticleIndexKey a0) -> bool
10172  has_attribute(Copy self, ObjectKey a0) -> bool
10173  """
10174  return _IMP_atom.Copy_has_attribute(self, *args)
10175 
10176 
10177  def get_derivative(self, a0):
10178  """get_derivative(Copy self, FloatKey a0) -> double"""
10179  return _IMP_atom.Copy_get_derivative(self, a0)
10180 
10181 
10182  def get_name(self):
10183  """get_name(Copy self) -> std::string"""
10184  return _IMP_atom.Copy_get_name(self)
10185 
10186 
10187  def clear_caches(self):
10188  """clear_caches(Copy self)"""
10189  return _IMP_atom.Copy_clear_caches(self)
10190 
10191 
10192  def set_name(self, a0):
10193  """set_name(Copy self, std::string a0)"""
10194  return _IMP_atom.Copy_set_name(self, a0)
10195 
10196 
10197  def set_check_level(self, a0):
10198  """set_check_level(Copy self, IMP::CheckLevel a0)"""
10199  return _IMP_atom.Copy_set_check_level(self, a0)
10200 
10201 
10202  def add_to_derivative(self, a0, a1, a2):
10203  """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10204  return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
10205 
10206 
10207  def set_is_optimized(self, a0, a1):
10208  """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
10209  return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
10210 
10211 
10212  def get_is_optimized(self, a0):
10213  """get_is_optimized(Copy self, FloatKey a0) -> bool"""
10214  return _IMP_atom.Copy_get_is_optimized(self, a0)
10215 
10216 
10217  def get_check_level(self):
10218  """get_check_level(Copy self) -> IMP::CheckLevel"""
10219  return _IMP_atom.Copy_get_check_level(self)
10220 
10221 
10222  def __eq__(self, *args):
10223  """
10224  __eq__(Copy self, Copy o) -> bool
10225  __eq__(Copy self, Particle d) -> bool
10226  """
10227  return _IMP_atom.Copy___eq__(self, *args)
10228 
10229 
10230  def __ne__(self, *args):
10231  """
10232  __ne__(Copy self, Copy o) -> bool
10233  __ne__(Copy self, Particle d) -> bool
10234  """
10235  return _IMP_atom.Copy___ne__(self, *args)
10236 
10237 
10238  def __le__(self, *args):
10239  """
10240  __le__(Copy self, Copy o) -> bool
10241  __le__(Copy self, Particle d) -> bool
10242  """
10243  return _IMP_atom.Copy___le__(self, *args)
10244 
10245 
10246  def __lt__(self, *args):
10247  """
10248  __lt__(Copy self, Copy o) -> bool
10249  __lt__(Copy self, Particle d) -> bool
10250  """
10251  return _IMP_atom.Copy___lt__(self, *args)
10252 
10253 
10254  def __ge__(self, *args):
10255  """
10256  __ge__(Copy self, Copy o) -> bool
10257  __ge__(Copy self, Particle d) -> bool
10258  """
10259  return _IMP_atom.Copy___ge__(self, *args)
10260 
10261 
10262  def __gt__(self, *args):
10263  """
10264  __gt__(Copy self, Copy o) -> bool
10265  __gt__(Copy self, Particle d) -> bool
10266  """
10267  return _IMP_atom.Copy___gt__(self, *args)
10268 
10269 
10270  def __hash__(self):
10271  """__hash__(Copy self) -> std::size_t"""
10272  return _IMP_atom.Copy___hash__(self)
10273 
10274 
10275  def __str__(self):
10276  """__str__(Copy self) -> std::string"""
10277  return _IMP_atom.Copy___str__(self)
10278 
10279 
10280  def __repr__(self):
10281  """__repr__(Copy self) -> std::string"""
10282  return _IMP_atom.Copy___repr__(self)
10283 
10284  __swig_destroy__ = _IMP_atom.delete_Copy
10285  __del__ = lambda self: None
10286 Copy_swigregister = _IMP_atom.Copy_swigregister
10287 Copy_swigregister(Copy)
10288 
10289 def Copy_get_copy_index_key():
10290  """Copy_get_copy_index_key() -> IntKey"""
10291  return _IMP_atom.Copy_get_copy_index_key()
10292 
10293 def Copy_setup_particle(*args):
10294  """
10295  setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10296  Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10297  """
10298  return _IMP_atom.Copy_setup_particle(*args)
10299 
10300 def Copy_get_is_setup(*args):
10301  """
10302  get_is_setup(_ParticleAdaptor p) -> bool
10303  Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
10304  """
10305  return _IMP_atom.Copy_get_is_setup(*args)
10306 
10307 
10308 def get_copy_index(h):
10309  """get_copy_index(Hierarchy h) -> int"""
10310  return _IMP_atom.get_copy_index(h)
10311 class Selection(IMP._ParticleIndexesAdaptor):
10312  """Proxy of C++ IMP::atom::Selection class"""
10313  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10314  NONE = _IMP_atom.Selection_NONE
10315  C = _IMP_atom.Selection_C
10316  N = _IMP_atom.Selection_N
10317 
10318  def __init__(self, *args):
10319  """
10320  __init__(IMP::atom::Selection self) -> Selection
10321  __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
10322  __init__(IMP::atom::Selection self, Particle h) -> Selection
10323  __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10324  __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
10325  """
10326  this = _IMP_atom.new_Selection(*args)
10327  try:
10328  self.this.append(this)
10329  except:
10330  self.this = this
10331 
10332  def create_clone(self):
10333  """create_clone(Selection self) -> Selection"""
10334  return _IMP_atom.Selection_create_clone(self)
10335 
10336 
10337  def get_hierarchies(self):
10338  """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10339  return _IMP_atom.Selection_get_hierarchies(self)
10340 
10341 
10342  def set_molecules(self, mols):
10343  """set_molecules(Selection self, IMP::Strings mols)"""
10344  return _IMP_atom.Selection_set_molecules(self, mols)
10345 
10346 
10347  def set_resolution(self, r):
10348  """set_resolution(Selection self, double r)"""
10349  return _IMP_atom.Selection_set_resolution(self, r)
10350 
10351 
10352  def set_representation_type(self, t):
10353  """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10354  return _IMP_atom.Selection_set_representation_type(self, t)
10355 
10356 
10357  def set_state_index(self, state):
10358  """set_state_index(Selection self, int state)"""
10359  return _IMP_atom.Selection_set_state_index(self, state)
10360 
10361 
10362  def set_state_indexes(self, states):
10363  """set_state_indexes(Selection self, IMP::Ints states)"""
10364  return _IMP_atom.Selection_set_state_indexes(self, states)
10365 
10366 
10367  def set_terminus(self, t):
10368  """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10369  return _IMP_atom.Selection_set_terminus(self, t)
10370 
10371 
10372  def set_element(self, e):
10373  """set_element(Selection self, IMP::atom::Element e)"""
10374  return _IMP_atom.Selection_set_element(self, e)
10375 
10376 
10377  def set_chain_ids(self, chains):
10378  """set_chain_ids(Selection self, IMP::Strings chains)"""
10379  return _IMP_atom.Selection_set_chain_ids(self, chains)
10380 
10381 
10382  def set_chains(self, chains):
10383  """set_chains(Selection self, IMP::Strings chains)"""
10384  return _IMP_atom.Selection_set_chains(self, chains)
10385 
10386 
10387  def set_residue_indexes(self, indexes):
10388  """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10389  return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10390 
10391 
10392  def set_atom_types(self, types):
10393  """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10394  return _IMP_atom.Selection_set_atom_types(self, types)
10395 
10396 
10397  def set_residue_types(self, types):
10398  """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10399  return _IMP_atom.Selection_set_residue_types(self, types)
10400 
10401 
10402  def set_domains(self, names):
10403  """set_domains(Selection self, IMP::Strings names)"""
10404  return _IMP_atom.Selection_set_domains(self, names)
10405 
10406 
10407  def set_molecule(self, mol):
10408  """set_molecule(Selection self, std::string mol)"""
10409  return _IMP_atom.Selection_set_molecule(self, mol)
10410 
10411 
10412  def set_chain_id(self, c):
10413  """set_chain_id(Selection self, std::string c)"""
10414  return _IMP_atom.Selection_set_chain_id(self, c)
10415 
10416 
10417  def set_chain(self, c):
10418  """set_chain(Selection self, std::string c)"""
10419  return _IMP_atom.Selection_set_chain(self, c)
10420 
10421 
10422  def set_residue_index(self, i):
10423  """set_residue_index(Selection self, int i)"""
10424  return _IMP_atom.Selection_set_residue_index(self, i)
10425 
10426 
10427  def set_atom_type(self, types):
10428  """set_atom_type(Selection self, AtomType types)"""
10429  return _IMP_atom.Selection_set_atom_type(self, types)
10430 
10431 
10432  def set_residue_type(self, type):
10433  """set_residue_type(Selection self, ResidueType type)"""
10434  return _IMP_atom.Selection_set_residue_type(self, type)
10435 
10436 
10437  def set_domain(self, name):
10438  """set_domain(Selection self, std::string name)"""
10439  return _IMP_atom.Selection_set_domain(self, name)
10440 
10441 
10442  def set_copy_index(self, copy):
10443  """set_copy_index(Selection self, unsigned int copy)"""
10444  return _IMP_atom.Selection_set_copy_index(self, copy)
10445 
10446 
10447  def set_copy_indexes(self, copies):
10448  """set_copy_indexes(Selection self, IMP::Ints copies)"""
10449  return _IMP_atom.Selection_set_copy_indexes(self, copies)
10450 
10451 
10452  def set_particle_type(self, t):
10453  """set_particle_type(Selection self, ParticleType t)"""
10454  return _IMP_atom.Selection_set_particle_type(self, t)
10455 
10456 
10457  def set_particle_types(self, t):
10458  """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10459  return _IMP_atom.Selection_set_particle_types(self, t)
10460 
10461 
10462  def set_hierarchy_types(self, types):
10463  """set_hierarchy_types(Selection self, IMP::Ints types)"""
10464  return _IMP_atom.Selection_set_hierarchy_types(self, types)
10465 
10466 
10467  def set_intersection(self, s):
10468  """set_intersection(Selection self, Selection s)"""
10469  return _IMP_atom.Selection_set_intersection(self, s)
10470 
10471 
10472  def set_union(self, s):
10473  """set_union(Selection self, Selection s)"""
10474  return _IMP_atom.Selection_set_union(self, s)
10475 
10476 
10477  def set_symmetric_difference(self, s):
10478  """set_symmetric_difference(Selection self, Selection s)"""
10479  return _IMP_atom.Selection_set_symmetric_difference(self, s)
10480 
10481 
10482  def set_difference(self, s):
10483  """set_difference(Selection self, Selection s)"""
10484  return _IMP_atom.Selection_set_difference(self, s)
10485 
10486 
10487  def get_selected_particles(self, with_representation=True):
10488  """
10489  get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10490  get_selected_particles(Selection self) -> IMP::ParticlesTemp
10491  """
10492  return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10493 
10494 
10495  def get_selected_particle_indexes(self, with_representation=True):
10496  """
10497  get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10498  get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10499  """
10500  return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10501 
10502 
10503  def show(self, *args):
10504  """
10505  show(Selection self, _ostream out)
10506  show(Selection self)
10507  """
10508  return _IMP_atom.Selection_show(self, *args)
10509 
10510 
10511  def __str__(self):
10512  """__str__(Selection self) -> std::string"""
10513  return _IMP_atom.Selection___str__(self)
10514 
10515 
10516  def __repr__(self):
10517  """__repr__(Selection self) -> std::string"""
10518  return _IMP_atom.Selection___repr__(self)
10519 
10520 
10521  def __init__(self, hierarchy=None,
10522  hierarchies=None, **params):
10523  if hierarchy and hierarchies:
10524  raise RuntimeError("You can't pass both hierarchy and hierarchies to Selection")
10525  if hierarchy:
10526  this = _IMP_atom.new_Selection(hierarchy)
10527  try: self.this.append(this)
10528  except: self.this = this
10529  elif hierarchies:
10530  this = _IMP_atom.new_Selection(hierarchies)
10531  try: self.this.append(this)
10532  except: self.this = this
10533  else:
10534  raise ValueError("Either hierarchy or hierarchies must be provided.")
10535  for k in params.keys():
10536  eval("self.set_%s(params[k])"%k)
10537 
10538  def union(self, s):
10539  news = self.create_clone()
10540  news.union_update(s)
10541  return news
10542  def intersection(self, s):
10543  news = self.create_clone()
10544  news.intersection_update(s)
10545  return news
10546  def symmetric_difference(self, s):
10547  news = self.create_clone()
10548  news.symmetric_difference_update(s)
10549  return news
10550  def difference(self, s):
10551  news = self.create_clone()
10552  news.difference_update(s)
10553  return news
10554  def union_update(self, s):
10555  self.set_union(s)
10556  return self
10557  def intersection_update(self, s):
10558  self.set_intersection(s)
10559  return self
10560  def symmetric_difference_update(self, s):
10561  self.set_symmetric_difference(s)
10562  return self
10563  def difference_update(self, s):
10564  self.set_difference(s)
10565  return self
10566  __or__ = union
10567  __and__ = intersection
10568  __xor__ = symmetric_difference
10569  __sub__ = difference
10570  __ior__ = union_update
10571  __iand__ = intersection_update
10572  __ixor__ = symmetric_difference_update
10573  __isub__ = difference_update
10574 
10575  __swig_destroy__ = _IMP_atom.delete_Selection
10576  __del__ = lambda self: None
10577 Selection_swigregister = _IMP_atom.Selection_swigregister
10578 Selection_swigregister(Selection)
10579 
10580 
10581 def create_distance_restraint(*args):
10582  """
10583  create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10584  create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10585  """
10586  return _IMP_atom.create_distance_restraint(*args)
10587 
10589  """
10590  create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10591  create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10592  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10593  create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10594  """
10595  return _IMP_atom.create_connectivity_restraint(*args)
10596 
10598  """
10599  create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10600  create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10601  create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10602  create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10603  """
10604  return _IMP_atom.create_internal_connectivity_restraint(*args)
10605 
10606 def create_cover(*args):
10607  """
10608  create_cover(Selection s, std::string name) -> XYZR
10609  create_cover(Selection s) -> XYZR
10610  """
10611  return _IMP_atom.create_cover(*args)
10612 
10613 def get_mass(*args):
10614  """
10615  get_mass(ResidueType c) -> double
10616  get_mass(Selection s) -> double
10617  """
10618  return _IMP_atom.get_mass(*args)
10619 
10620 def get_volume(s):
10621  """get_volume(Selection s) -> double"""
10622  return _IMP_atom.get_volume(s)
10623 
10624 def get_surface_area(s):
10625  """get_surface_area(Selection s) -> double"""
10626  return _IMP_atom.get_surface_area(s)
10627 
10628 def get_leaves(*args):
10629  """
10630  get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10631  get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10632  get_leaves(Selection h) -> IMP::atom::Hierarchies
10633  """
10634  return _IMP_atom.get_leaves(*args)
10635 class SelectionGeometry(IMP.display.Geometry):
10636  """Proxy of C++ IMP::atom::SelectionGeometry class"""
10637  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10638 
10639  def __init__(self, *args):
10640  """
10641  __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10642  __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10643  """
10644  this = _IMP_atom.new_SelectionGeometry(*args)
10645  try:
10646  self.this.append(this)
10647  except:
10648  self.this = this
10649 
10650  def get_version_info(self):
10651  """get_version_info(SelectionGeometry self) -> VersionInfo"""
10652  return _IMP_atom.SelectionGeometry_get_version_info(self)
10653 
10654 
10655  def __str__(self):
10656  """__str__(SelectionGeometry self) -> std::string"""
10657  return _IMP_atom.SelectionGeometry___str__(self)
10658 
10659 
10660  def __repr__(self):
10661  """__repr__(SelectionGeometry self) -> std::string"""
10662  return _IMP_atom.SelectionGeometry___repr__(self)
10663 
10664 
10665  @staticmethod
10666  def get_from(o):
10667  return _object_cast_to_SelectionGeometry(o)
10668 
10669 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10670 SelectionGeometry_swigregister(SelectionGeometry)
10671 
10672 
10673 def get_rmsd(*args):
10674  """
10675  get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10676  get_rmsd(Selection s0, Selection s1) -> double
10677  """
10678  return _IMP_atom.get_rmsd(*args)
10679 
10680 def get_rmsd_transforming_first(*args):
10681  """
10682  get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10683  get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10684  """
10685  return _IMP_atom.get_rmsd_transforming_first(*args)
10686 
10687 def get_placement_score(source, target):
10688  """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10689  return _IMP_atom.get_placement_score(source, target)
10690 
10691 def get_component_placement_score(ref1, ref2, mdl1, mdl2):
10692  """get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> IMP::FloatPair"""
10693  return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10694 
10695 def get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2):
10696  """get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> double"""
10697  return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10698 
10699 def get_radius_of_gyration(*args):
10700  """
10701  get_radius_of_gyration(Selection s) -> double
10702  get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10703  """
10704  return _IMP_atom.get_radius_of_gyration(*args)
10705 class ForceFieldParameters(IMP.Object):
10706  """Proxy of C++ IMP::atom::ForceFieldParameters class"""
10707  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10708 
10709  def __init__(self):
10710  """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10711  this = _IMP_atom.new_ForceFieldParameters()
10712  try:
10713  self.this.append(this)
10714  except:
10715  self.this = this
10716 
10717  def get_radius(self, atom):
10718  """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10719  return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10720 
10721 
10722  def get_epsilon(self, atom):
10723  """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10724  return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10725 
10726 
10727  def add_radii(self, *args):
10728  """
10729  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10730  add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10731  add_radii(ForceFieldParameters self, Hierarchy mhd)
10732  """
10733  return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10734 
10735 
10736  def add_well_depths(self, mhd):
10737  """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10738  return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10739 
10740 
10741  def add_bonds(self, mhd):
10742  """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10743  return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10744 
10745  __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10746  __del__ = lambda self: None
10747 
10748  def __str__(self):
10749  """__str__(ForceFieldParameters self) -> std::string"""
10750  return _IMP_atom.ForceFieldParameters___str__(self)
10751 
10752 
10753  def __repr__(self):
10754  """__repr__(ForceFieldParameters self) -> std::string"""
10755  return _IMP_atom.ForceFieldParameters___repr__(self)
10756 
10757 
10758  @staticmethod
10759  def get_from(o):
10760  return _object_cast_to_ForceFieldParameters(o)
10761 
10762 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10763 ForceFieldParameters_swigregister(ForceFieldParameters)
10764 
10765 class CHARMMAtomTopology(object):
10766  """Proxy of C++ IMP::atom::CHARMMAtomTopology class"""
10767  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10768 
10769  def __init__(self, *args):
10770  """
10771  __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10772  __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10773  """
10774  this = _IMP_atom.new_CHARMMAtomTopology(*args)
10775  try:
10776  self.this.append(this)
10777  except:
10778  self.this = this
10779 
10780  def get_name(self):
10781  """get_name(CHARMMAtomTopology self) -> std::string"""
10782  return _IMP_atom.CHARMMAtomTopology_get_name(self)
10783 
10784 
10785  def get_charmm_type(self):
10786  """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10787  return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10788 
10789 
10790  def get_charge(self):
10791  """get_charge(CHARMMAtomTopology self) -> double"""
10792  return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10793 
10794 
10795  def set_charmm_type(self, charmm_type):
10796  """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10797  return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10798 
10799 
10800  def set_charge(self, charge):
10801  """set_charge(CHARMMAtomTopology self, double charge)"""
10802  return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10803 
10804 
10805  def show(self, *args):
10806  """
10807  show(CHARMMAtomTopology self, _ostream out)
10808  show(CHARMMAtomTopology self)
10809  """
10810  return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10811 
10812 
10813  def __str__(self):
10814  """__str__(CHARMMAtomTopology self) -> std::string"""
10815  return _IMP_atom.CHARMMAtomTopology___str__(self)
10816 
10817 
10818  def __repr__(self):
10819  """__repr__(CHARMMAtomTopology self) -> std::string"""
10820  return _IMP_atom.CHARMMAtomTopology___repr__(self)
10821 
10822  __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10823  __del__ = lambda self: None
10824 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
10825 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10826 
10827 class CHARMMBondEndpoint(object):
10828  """Proxy of C++ IMP::atom::CHARMMBondEndpoint class"""
10829  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10830 
10831  def __init__(self, atom_name, residue=None):
10832  """
10833  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
10834  __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
10835  """
10836  this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
10837  try:
10838  self.this.append(this)
10839  except:
10840  self.this = this
10841 
10842  def get_atom_name(self):
10843  """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10844  return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10845 
10846 
10847  def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10848  """get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue, std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom"""
10849  return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10850 
10851 
10852  def show(self, *args):
10853  """
10854  show(CHARMMBondEndpoint self, _ostream out)
10855  show(CHARMMBondEndpoint self)
10856  """
10857  return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10858 
10859 
10860  def __str__(self):
10861  """__str__(CHARMMBondEndpoint self) -> std::string"""
10862  return _IMP_atom.CHARMMBondEndpoint___str__(self)
10863 
10864 
10865  def __repr__(self):
10866  """__repr__(CHARMMBondEndpoint self) -> std::string"""
10867  return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10868 
10869  __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10870  __del__ = lambda self: None
10871 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
10872 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10873 
10874 class CHARMMDihedral(object):
10875  """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class"""
10876  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10877  __repr__ = _swig_repr
10878 
10879  def __init__(self, atoms):
10880  """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10881  this = _IMP_atom.new_CHARMMDihedral(atoms)
10882  try:
10883  self.this.append(this)
10884  except:
10885  self.this = this
10886 
10887  def get_endpoint(self, i):
10888  """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10889  return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10890 
10891 
10892  def get_contains_atom(self, name):
10893  """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10894  return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10895 
10896 
10897  def show(self, *args):
10898  """
10899  show(CHARMMDihedral self, _ostream out)
10900  show(CHARMMDihedral self)
10901  """
10902  return _IMP_atom.CHARMMDihedral_show(self, *args)
10903 
10904  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10905  __del__ = lambda self: None
10906 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
10907 CHARMMDihedral_swigregister(CHARMMDihedral)
10908 
10909 class CHARMMInternalCoordinate(CHARMMDihedral):
10910  """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class"""
10911  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10912 
10913  def __init__(self, *args):
10914  """
10915  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10916  __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10917  """
10918  this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
10919  try:
10920  self.this.append(this)
10921  except:
10922  self.this = this
10923 
10924  def get_first_distance(self):
10925  """get_first_distance(CHARMMInternalCoordinate self) -> float"""
10926  return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10927 
10928 
10929  def get_second_distance(self):
10930  """get_second_distance(CHARMMInternalCoordinate self) -> float"""
10931  return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10932 
10933 
10934  def get_first_angle(self):
10935  """get_first_angle(CHARMMInternalCoordinate self) -> float"""
10936  return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10937 
10938 
10939  def get_second_angle(self):
10940  """get_second_angle(CHARMMInternalCoordinate self) -> float"""
10941  return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10942 
10943 
10944  def get_dihedral(self):
10945  """get_dihedral(CHARMMInternalCoordinate self) -> float"""
10946  return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10947 
10948 
10949  def get_improper(self):
10950  """get_improper(CHARMMInternalCoordinate self) -> bool"""
10951  return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10952 
10953 
10954  def show(self, *args):
10955  """
10956  show(CHARMMInternalCoordinate self, _ostream out)
10957  show(CHARMMInternalCoordinate self)
10958  """
10959  return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10960 
10961 
10962  def __str__(self):
10963  """__str__(CHARMMInternalCoordinate self) -> std::string"""
10964  return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10965 
10966 
10967  def __repr__(self):
10968  """__repr__(CHARMMInternalCoordinate self) -> std::string"""
10969  return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10970 
10971  __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10972  __del__ = lambda self: None
10973 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
10974 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10975 
10976 class CHARMMResidueTopologyBase(IMP.Object):
10977  """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class"""
10978  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
10979 
10980  def __init__(self, *args, **kwargs):
10981  raise AttributeError("No constructor defined")
10982 
10983  def get_type(self):
10984  """get_type(CHARMMResidueTopologyBase self) -> std::string"""
10985  return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10986 
10987 
10988  def get_number_of_atoms(self):
10989  """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10990  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10991 
10992 
10993  def add_atom(self, atom):
10994  """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10995  return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10996 
10997 
10998  def get_atom(self, *args):
10999  """
11000  get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
11001  get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
11002  get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
11003  """
11004  return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
11005 
11006 
11007  def get_number_of_bonds(self):
11008  """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
11009  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
11010 
11011 
11012  def add_bond(self, bond):
11013  """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
11014  return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
11015 
11016 
11017  def get_number_of_angles(self):
11018  """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
11019  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
11020 
11021 
11022  def add_angle(self, bond):
11023  """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
11024  return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
11025 
11026 
11027  def get_number_of_dihedrals(self):
11028  """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
11029  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
11030 
11031 
11032  def add_dihedral(self, bond):
11033  """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11034  return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
11035 
11036 
11037  def get_number_of_impropers(self):
11038  """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
11039  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
11040 
11041 
11042  def add_improper(self, bond):
11043  """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11044  return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
11045 
11046 
11047  def get_number_of_internal_coordinates(self):
11048  """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11049  return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11050 
11051 
11052  def add_internal_coordinate(self, ic):
11053  """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11054  return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11055 
11056 
11057  def get_internal_coordinate(self, index):
11058  """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11059  return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11060 
11061 
11062  def get_bond(self, index):
11063  """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
11064  return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11065 
11066 
11067  def get_angle(self, index):
11068  """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
11069  return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11070 
11071 
11072  def get_dihedral(self, index):
11073  """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11074  return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11075 
11076 
11077  def get_improper(self, index):
11078  """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11079  return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11080 
11081 
11082  def get_version_info(self):
11083  """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11084  return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11085 
11086 
11087  def __str__(self):
11088  """__str__(CHARMMResidueTopologyBase self) -> std::string"""
11089  return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11090 
11091 
11092  def __repr__(self):
11093  """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11094  return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11095 
11096 
11097  @staticmethod
11098  def get_from(o):
11099  return _object_cast_to_CHARMMResidueTopologyBase(o)
11100 
11101 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
11102 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11103 
11104 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11105  """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class"""
11106  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11107 
11108  def __init__(self, *args):
11109  """
11110  __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11111  __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11112  """
11113  this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
11114  try:
11115  self.this.append(this)
11116  except:
11117  self.this = this
11118 
11119  def remove_atom(self, name):
11120  """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11121  return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11122 
11123 
11124  def set_default_first_patch(self, patch):
11125  """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11126  return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11127 
11128 
11129  def set_default_last_patch(self, patch):
11130  """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11131  return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11132 
11133 
11134  def get_default_first_patch(self):
11135  """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11136  return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11137 
11138 
11139  def get_default_last_patch(self):
11140  """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11141  return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11142 
11143 
11144  def __str__(self):
11145  """__str__(CHARMMIdealResidueTopology self) -> std::string"""
11146  return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11147 
11148 
11149  def __repr__(self):
11150  """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11151  return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11152 
11153 
11154  @staticmethod
11155  def get_from(o):
11156  return _object_cast_to_CHARMMIdealResidueTopology(o)
11157 
11158 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
11159 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11160 
11161 class CHARMMPatch(CHARMMResidueTopologyBase):
11162  """Proxy of C++ IMP::atom::CHARMMPatch class"""
11163  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11164 
11165  def __init__(self, type):
11166  """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
11167  this = _IMP_atom.new_CHARMMPatch(type)
11168  try:
11169  self.this.append(this)
11170  except:
11171  self.this = this
11172 
11173  def add_removed_atom(self, name):
11174  """add_removed_atom(CHARMMPatch self, std::string name)"""
11175  return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11176 
11177 
11178  def get_number_of_removed_atoms(self):
11179  """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11180  return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11181 
11182 
11183  def get_removed_atom(self, i):
11184  """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11185  return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11186 
11187 
11188  def apply(self, *args):
11189  """
11190  apply(CHARMMPatch self, CHARMMResidueTopology res)
11191  apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11192  """
11193  return _IMP_atom.CHARMMPatch_apply(self, *args)
11194 
11195 
11196  def __str__(self):
11197  """__str__(CHARMMPatch self) -> std::string"""
11198  return _IMP_atom.CHARMMPatch___str__(self)
11199 
11200 
11201  def __repr__(self):
11202  """__repr__(CHARMMPatch self) -> std::string"""
11203  return _IMP_atom.CHARMMPatch___repr__(self)
11204 
11205 
11206  @staticmethod
11207  def get_from(o):
11208  return _object_cast_to_CHARMMPatch(o)
11209 
11210 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
11211 CHARMMPatch_swigregister(CHARMMPatch)
11212 
11213 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11214  """Proxy of C++ IMP::atom::CHARMMResidueTopology class"""
11215  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11216 
11217  def __init__(self, *args):
11218  """
11219  __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11220  __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11221  """
11222  this = _IMP_atom.new_CHARMMResidueTopology(*args)
11223  try:
11224  self.this.append(this)
11225  except:
11226  self.this = this
11227 
11228  def get_patched(self):
11229  """get_patched(CHARMMResidueTopology self) -> bool"""
11230  return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11231 
11232 
11233  def set_patched(self, patched):
11234  """set_patched(CHARMMResidueTopology self, bool patched)"""
11235  return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11236 
11237 
11238  def __str__(self):
11239  """__str__(CHARMMResidueTopology self) -> std::string"""
11240  return _IMP_atom.CHARMMResidueTopology___str__(self)
11241 
11242 
11243  def __repr__(self):
11244  """__repr__(CHARMMResidueTopology self) -> std::string"""
11245  return _IMP_atom.CHARMMResidueTopology___repr__(self)
11246 
11247 
11248  @staticmethod
11249  def get_from(o):
11250  return _object_cast_to_CHARMMResidueTopology(o)
11251 
11252 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
11253 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11254 
11255 class CHARMMAtom(Atom):
11256  """Proxy of C++ IMP::atom::CHARMMAtom class"""
11257  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11258 
11259  def __init__(self, *args):
11260  """
11261  __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
11262  __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11263  __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11264  """
11265  this = _IMP_atom.new_CHARMMAtom(*args)
11266  try:
11267  self.this.append(this)
11268  except:
11269  self.this = this
11270 
11271  def show(self, *args):
11272  """
11273  show(CHARMMAtom self, _ostream out)
11274  show(CHARMMAtom self)
11275  """
11276  return _IMP_atom.CHARMMAtom_show(self, *args)
11277 
11278 
11279  def setup_particle(*args):
11280  """
11281  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11282  setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11283  """
11284  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11285 
11286  setup_particle = staticmethod(setup_particle)
11287 
11288  def get_charmm_type(self):
11289  """get_charmm_type(CHARMMAtom self) -> IMP::String"""
11290  return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11291 
11292 
11293  def set_charmm_type(self, t):
11294  """set_charmm_type(CHARMMAtom self, IMP::String t)"""
11295  return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11296 
11297 
11298  def get_is_setup(*args):
11299  """
11300  get_is_setup(_ParticleAdaptor p) -> bool
11301  get_is_setup(Model m, ParticleIndex pi) -> bool
11302  """
11303  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11304 
11305  get_is_setup = staticmethod(get_is_setup)
11306 
11307  def get_charmm_type_key():
11308  """get_charmm_type_key() -> StringKey"""
11309  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11310 
11311  get_charmm_type_key = staticmethod(get_charmm_type_key)
11312 
11313  def add_attribute(self, *args):
11314  """
11315  add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11316  add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11317  add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11318  add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11319  add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11320  add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11321  """
11322  return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11323 
11324 
11325  def get_value(self, *args):
11326  """
11327  get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11328  get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11329  get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11330  get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11331  get_value(CHARMMAtom self, ObjectKey a0) -> Object
11332  """
11333  return _IMP_atom.CHARMMAtom_get_value(self, *args)
11334 
11335 
11336  def set_value(self, *args):
11337  """
11338  set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11339  set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11340  set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11341  set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11342  set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11343  """
11344  return _IMP_atom.CHARMMAtom_set_value(self, *args)
11345 
11346 
11347  def remove_attribute(self, *args):
11348  """
11349  remove_attribute(CHARMMAtom self, FloatKey a0)
11350  remove_attribute(CHARMMAtom self, IntKey a0)
11351  remove_attribute(CHARMMAtom self, StringKey a0)
11352  remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11353  remove_attribute(CHARMMAtom self, ObjectKey a0)
11354  """
11355  return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11356 
11357 
11358  def has_attribute(self, *args):
11359  """
11360  has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11361  has_attribute(CHARMMAtom self, IntKey a0) -> bool
11362  has_attribute(CHARMMAtom self, StringKey a0) -> bool
11363  has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11364  has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11365  """
11366  return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11367 
11368 
11369  def get_derivative(self, a0):
11370  """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11371  return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11372 
11373 
11374  def get_name(self):
11375  """get_name(CHARMMAtom self) -> std::string"""
11376  return _IMP_atom.CHARMMAtom_get_name(self)
11377 
11378 
11379  def clear_caches(self):
11380  """clear_caches(CHARMMAtom self)"""
11381  return _IMP_atom.CHARMMAtom_clear_caches(self)
11382 
11383 
11384  def set_name(self, a0):
11385  """set_name(CHARMMAtom self, std::string a0)"""
11386  return _IMP_atom.CHARMMAtom_set_name(self, a0)
11387 
11388 
11389  def set_check_level(self, a0):
11390  """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11391  return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11392 
11393 
11394  def add_to_derivative(self, a0, a1, a2):
11395  """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11396  return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11397 
11398 
11399  def set_is_optimized(self, a0, a1):
11400  """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11401  return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11402 
11403 
11404  def get_is_optimized(self, a0):
11405  """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11406  return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11407 
11408 
11409  def get_check_level(self):
11410  """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11411  return _IMP_atom.CHARMMAtom_get_check_level(self)
11412 
11413 
11414  def __eq__(self, *args):
11415  """
11416  __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11417  __eq__(CHARMMAtom self, Particle d) -> bool
11418  """
11419  return _IMP_atom.CHARMMAtom___eq__(self, *args)
11420 
11421 
11422  def __ne__(self, *args):
11423  """
11424  __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11425  __ne__(CHARMMAtom self, Particle d) -> bool
11426  """
11427  return _IMP_atom.CHARMMAtom___ne__(self, *args)
11428 
11429 
11430  def __le__(self, *args):
11431  """
11432  __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11433  __le__(CHARMMAtom self, Particle d) -> bool
11434  """
11435  return _IMP_atom.CHARMMAtom___le__(self, *args)
11436 
11437 
11438  def __lt__(self, *args):
11439  """
11440  __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11441  __lt__(CHARMMAtom self, Particle d) -> bool
11442  """
11443  return _IMP_atom.CHARMMAtom___lt__(self, *args)
11444 
11445 
11446  def __ge__(self, *args):
11447  """
11448  __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11449  __ge__(CHARMMAtom self, Particle d) -> bool
11450  """
11451  return _IMP_atom.CHARMMAtom___ge__(self, *args)
11452 
11453 
11454  def __gt__(self, *args):
11455  """
11456  __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11457  __gt__(CHARMMAtom self, Particle d) -> bool
11458  """
11459  return _IMP_atom.CHARMMAtom___gt__(self, *args)
11460 
11461 
11462  def __hash__(self):
11463  """__hash__(CHARMMAtom self) -> std::size_t"""
11464  return _IMP_atom.CHARMMAtom___hash__(self)
11465 
11466 
11467  def __str__(self):
11468  """__str__(CHARMMAtom self) -> std::string"""
11469  return _IMP_atom.CHARMMAtom___str__(self)
11470 
11471 
11472  def __repr__(self):
11473  """__repr__(CHARMMAtom self) -> std::string"""
11474  return _IMP_atom.CHARMMAtom___repr__(self)
11475 
11476  __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11477  __del__ = lambda self: None
11478 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11479 CHARMMAtom_swigregister(CHARMMAtom)
11480 
11481 def CHARMMAtom_setup_particle(*args):
11482  """
11483  setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11484  CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11485  """
11486  return _IMP_atom.CHARMMAtom_setup_particle(*args)
11487 
11488 def CHARMMAtom_get_is_setup(*args):
11489  """
11490  get_is_setup(_ParticleAdaptor p) -> bool
11491  CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11492  """
11493  return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11494 
11495 def CHARMMAtom_get_charmm_type_key():
11496  """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11497  return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11498 
11499 
11500 def get_charmm_untyped_atoms(hierarchy):
11501  """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11502  return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11503 
11504 def remove_charmm_untyped_atoms(hierarchy):
11505  """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11506  return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11507 class CHARMMBondParameters(object):
11508  """Proxy of C++ IMP::atom::CHARMMBondParameters class"""
11509  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11510  force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11511  ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11512 
11513  def __init__(self):
11514  """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11515  this = _IMP_atom.new_CHARMMBondParameters()
11516  try:
11517  self.this.append(this)
11518  except:
11519  self.this = this
11520 
11521  def show(self, *args):
11522  """
11523  show(CHARMMBondParameters self, _ostream out)
11524  show(CHARMMBondParameters self)
11525  """
11526  return _IMP_atom.CHARMMBondParameters_show(self, *args)
11527 
11528 
11529  def __str__(self):
11530  """__str__(CHARMMBondParameters self) -> std::string"""
11531  return _IMP_atom.CHARMMBondParameters___str__(self)
11532 
11533 
11534  def __repr__(self):
11535  """__repr__(CHARMMBondParameters self) -> std::string"""
11536  return _IMP_atom.CHARMMBondParameters___repr__(self)
11537 
11538  __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11539  __del__ = lambda self: None
11540 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11541 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11542 
11543 class CHARMMDihedralParameters(object):
11544  """Proxy of C++ IMP::atom::CHARMMDihedralParameters class"""
11545  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11546  force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11547  multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11548  ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11549 
11550  def __init__(self):
11551  """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11552  this = _IMP_atom.new_CHARMMDihedralParameters()
11553  try:
11554  self.this.append(this)
11555  except:
11556  self.this = this
11557 
11558  def show(self, *args):
11559  """
11560  show(CHARMMDihedralParameters self, _ostream out)
11561  show(CHARMMDihedralParameters self)
11562  """
11563  return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11564 
11565 
11566  def __str__(self):
11567  """__str__(CHARMMDihedralParameters self) -> std::string"""
11568  return _IMP_atom.CHARMMDihedralParameters___str__(self)
11569 
11570 
11571  def __repr__(self):
11572  """__repr__(CHARMMDihedralParameters self) -> std::string"""
11573  return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11574 
11575  __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11576  __del__ = lambda self: None
11577 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11578 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11579 
11580 class CHARMMParameters(ForceFieldParameters):
11581  """Proxy of C++ IMP::atom::CHARMMParameters class"""
11582  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11583 
11584  def __init__(self, *args):
11585  """
11586  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11587  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11588  __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11589  """
11590  this = _IMP_atom.new_CHARMMParameters(*args)
11591  try:
11592  self.this.append(this)
11593  except:
11594  self.this = this
11595 
11596  def add_residue_topology(self, res):
11597  """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11598  return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11599 
11600 
11601  def get_residue_topology(self, type):
11602  """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11603  return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11604 
11605 
11606  def add_patch(self, patch):
11607  """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11608  return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11609 
11610 
11611  def get_patch(self, name):
11612  """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11613  return _IMP_atom.CHARMMParameters_get_patch(self, name)
11614 
11615 
11616  def create_topology(self, hierarchy):
11617  """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11618  return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11619 
11620 
11621  def get_bond_parameters(self, type1, type2):
11622  """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11623  return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11624 
11625 
11626  def get_angle_parameters(self, type1, type2, type3):
11627  """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11628  return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11629 
11630 
11631  def get_dihedral_parameters(self, type1, type2, type3, type4):
11632  """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11633  return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11634 
11635 
11636  def get_improper_parameters(self, type1, type2, type3, type4):
11637  """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11638  return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11639 
11640 
11641  def create_angles(self, bonds):
11642  """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11643  return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11644 
11645 
11646  def create_dihedrals(self, bonds):
11647  """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11648  return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11649 
11650 
11651  def get_version_info(self):
11652  """get_version_info(CHARMMParameters self) -> VersionInfo"""
11653  return _IMP_atom.CHARMMParameters_get_version_info(self)
11654 
11655 
11656  def __str__(self):
11657  """__str__(CHARMMParameters self) -> std::string"""
11658  return _IMP_atom.CHARMMParameters___str__(self)
11659 
11660 
11661  def __repr__(self):
11662  """__repr__(CHARMMParameters self) -> std::string"""
11663  return _IMP_atom.CHARMMParameters___repr__(self)
11664 
11665 
11666  @staticmethod
11667  def get_from(o):
11668  return _object_cast_to_CHARMMParameters(o)
11669 
11670 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11671 CHARMMParameters_swigregister(CHARMMParameters)
11672 
11673 
11675  """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11676  return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11677 
11679  """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11680  return _IMP_atom.get_all_atom_CHARMM_parameters()
11681 class CHARMMSegmentTopology(IMP.Object):
11682  """Proxy of C++ IMP::atom::CHARMMSegmentTopology class"""
11683  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11684 
11685  def remove_residue(self, d):
11686  """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11687  return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11688 
11689 
11690  def remove_residues(self, d):
11691  """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11692  return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11693 
11694 
11695  def set_residues(self, ps):
11696  """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11697  return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11698 
11699 
11700  def set_residues_order(self, objs):
11701  """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11702  return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11703 
11704 
11705  def add_residue(self, obj):
11706  """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11707  return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11708 
11709 
11710  def add_residues(self, objs):
11711  """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11712  return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11713 
11714 
11715  def clear_residues(self):
11716  """clear_residues(CHARMMSegmentTopology self)"""
11717  return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11718 
11719 
11720  def get_number_of_residues(self):
11721  """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11722  return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11723 
11724 
11725  def get_has_residues(self):
11726  """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11727  return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11728 
11729 
11730  def get_residue(self, i):
11731  """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11732  return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11733 
11734 
11735  def get_residues(self):
11736  """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11737  return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11738 
11739 
11740  def reserve_residues(self, sz):
11741  """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11742  return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11743 
11744 
11745  def get_version_info(self):
11746  """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11747  return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11748 
11749 
11750  def __init__(self, *args):
11751  """
11752  __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11753  __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11754  """
11755  this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11756  try:
11757  self.this.append(this)
11758  except:
11759  self.this = this
11760 
11761  def apply_default_patches(self, ff):
11762  """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11763  return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11764 
11765 
11766  def __str__(self):
11767  """__str__(CHARMMSegmentTopology self) -> std::string"""
11768  return _IMP_atom.CHARMMSegmentTopology___str__(self)
11769 
11770 
11771  def __repr__(self):
11772  """__repr__(CHARMMSegmentTopology self) -> std::string"""
11773  return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11774 
11775 
11776  @staticmethod
11777  def get_from(o):
11778  return _object_cast_to_CHARMMSegmentTopology(o)
11779 
11780 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
11781 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11782 
11783 class CHARMMTopology(IMP.Object):
11784  """Proxy of C++ IMP::atom::CHARMMTopology class"""
11785  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11786 
11787  def __init__(self, *args):
11788  """
11789  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
11790  __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
11791  """
11792  this = _IMP_atom.new_CHARMMTopology(*args)
11793  try:
11794  self.this.append(this)
11795  except:
11796  self.this = this
11797 
11798  def get_parameters(self):
11799  """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11800  return _IMP_atom.CHARMMTopology_get_parameters(self)
11801 
11802 
11803  def add_sequence(self, sequence):
11804  """add_sequence(CHARMMTopology self, std::string sequence)"""
11805  return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11806 
11807 
11808  def apply_default_patches(self):
11809  """apply_default_patches(CHARMMTopology self)"""
11810  return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11811 
11812 
11813  def create_hierarchy(self, model):
11814  """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11815  return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11816 
11817 
11818  def add_atom_types(self, hierarchy):
11819  """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11820  return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11821 
11822 
11823  def add_coordinates(self, hierarchy):
11824  """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11825  return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11826 
11827 
11828  def add_missing_atoms(self, hierarchy):
11829  """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11830  return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11831 
11832 
11833  def setup_hierarchy(self, hierarchy):
11834  """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11835  return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11836 
11837 
11838  def add_charges(self, hierarchy):
11839  """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11840  return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11841 
11842 
11843  def add_bonds(self, hierarchy):
11844  """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11845  return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11846 
11847 
11848  def add_dihedrals(self, hierarchy):
11849  """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11850  return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11851 
11852 
11853  def add_impropers(self, hierarchy):
11854  """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11855  return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11856 
11857 
11858  def remove_segment(self, d):
11859  """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11860  return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11861 
11862 
11863  def remove_segments(self, d):
11864  """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11865  return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11866 
11867 
11868  def set_segments(self, ps):
11869  """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11870  return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11871 
11872 
11873  def set_segments_order(self, objs):
11874  """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11875  return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11876 
11877 
11878  def add_segment(self, obj):
11879  """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11880  return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11881 
11882 
11883  def add_segments(self, objs):
11884  """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11885  return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11886 
11887 
11888  def clear_segments(self):
11889  """clear_segments(CHARMMTopology self)"""
11890  return _IMP_atom.CHARMMTopology_clear_segments(self)
11891 
11892 
11893  def get_number_of_segments(self):
11894  """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11895  return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11896 
11897 
11898  def get_has_segments(self):
11899  """get_has_segments(CHARMMTopology self) -> bool"""
11900  return _IMP_atom.CHARMMTopology_get_has_segments(self)
11901 
11902 
11903  def get_segment(self, i):
11904  """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11905  return _IMP_atom.CHARMMTopology_get_segment(self, i)
11906 
11907 
11908  def get_segments(self):
11909  """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11910  return _IMP_atom.CHARMMTopology_get_segments(self)
11911 
11912 
11913  def reserve_segments(self, sz):
11914  """reserve_segments(CHARMMTopology self, unsigned int sz)"""
11915  return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11916 
11917 
11918  def get_version_info(self):
11919  """get_version_info(CHARMMTopology self) -> VersionInfo"""
11920  return _IMP_atom.CHARMMTopology_get_version_info(self)
11921 
11922 
11923  def __str__(self):
11924  """__str__(CHARMMTopology self) -> std::string"""
11925  return _IMP_atom.CHARMMTopology___str__(self)
11926 
11927 
11928  def __repr__(self):
11929  """__repr__(CHARMMTopology self) -> std::string"""
11930  return _IMP_atom.CHARMMTopology___repr__(self)
11931 
11932 
11933  @staticmethod
11934  def get_from(o):
11935  return _object_cast_to_CHARMMTopology(o)
11936 
11937 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
11938 CHARMMTopology_swigregister(CHARMMTopology)
11939 
11940 class CHARMMStereochemistryRestraint(IMP.Restraint):
11941  """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class"""
11942  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
11943 
11944  def __init__(self, *args):
11945  """
11946  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11947  __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11948  """
11949  this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
11950  try:
11951  self.this.append(this)
11952  except:
11953  self.this = this
11954 
11955  def get_pair_filter(self):
11956  """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11957  return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11958 
11959 
11960  def get_full_pair_filter(self):
11961  """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11962  return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11963 
11964 
11965  def do_get_inputs(self):
11966  """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11967  return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11968 
11969 
11970  def get_version_info(self):
11971  """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11972  return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11973 
11974 
11975  def __str__(self):
11976  """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11977  return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11978 
11979 
11980  def __repr__(self):
11981  """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11982  return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11983 
11984 
11985  @staticmethod
11986  def get_from(o):
11987  return _object_cast_to_CHARMMStereochemistryRestraint(o)
11988 
11989 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
11990 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11991 
11992 
11993 def add_bonds(*args):
11994  """
11995  add_bonds(Hierarchy d, ForceFieldParameters ffp)
11996  add_bonds(Hierarchy d)
11997  """
11998  return _IMP_atom.add_bonds(*args)
11999 
12000 def add_radii(*args):
12001  """
12002  add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
12003  add_radii(Hierarchy d, ForceFieldParameters ffp)
12004  add_radii(Hierarchy d)
12005  """
12006  return _IMP_atom.add_radii(*args)
12007 
12008 _IMP_atom.ALBER_swigconstant(_IMP_atom)
12009 ALBER = _IMP_atom.ALBER
12010 
12011 _IMP_atom.HARPAZ_swigconstant(_IMP_atom)
12012 HARPAZ = _IMP_atom.HARPAZ
12013 
12014 _IMP_atom.ANDERSSON_swigconstant(_IMP_atom)
12015 ANDERSSON = _IMP_atom.ANDERSSON
12016 
12017 _IMP_atom.TSAI_swigconstant(_IMP_atom)
12018 TSAI = _IMP_atom.TSAI
12019 
12020 _IMP_atom.QUILLIN_swigconstant(_IMP_atom)
12021 QUILLIN = _IMP_atom.QUILLIN
12022 
12023 _IMP_atom.SQUIRE_swigconstant(_IMP_atom)
12024 SQUIRE = _IMP_atom.SQUIRE
12025 
12026 def get_protein_density_from_reference(densityReference):
12027  """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
12028  return _IMP_atom.get_protein_density_from_reference(densityReference)
12029 
12030 def get_volume_from_mass(*args):
12031  """
12032  get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
12033  get_volume_from_mass(double m) -> double
12034  """
12035  return _IMP_atom.get_volume_from_mass(*args)
12036 
12037 def get_mass_from_volume(*args):
12038  """
12039  get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
12040  get_mass_from_volume(double v) -> double
12041  """
12042  return _IMP_atom.get_mass_from_volume(*args)
12043 
12045  """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
12046  return _IMP_atom.get_mass_from_number_of_residues(num_aa)
12047 
12049  """get_volume_from_residue_type(ResidueType rt) -> double"""
12050  return _IMP_atom.get_volume_from_residue_type(rt)
12051 
12052 def get_molarity(n, volume):
12053  """get_molarity(double n, double volume) -> double"""
12054  return _IMP_atom.get_molarity(n, volume)
12055 
12056 def get_kd(na, nb, nab, volume):
12057  """get_kd(double na, double nb, double nab, double volume) -> double"""
12058  return _IMP_atom.get_kd(na, nb, nab, volume)
12059 
12061  """get_einstein_diffusion_coefficient(double r) -> double"""
12062  return _IMP_atom.get_einstein_diffusion_coefficient(r)
12063 
12065  """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
12066  return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r)
12067 
12068 def get_diffusion_length(*args):
12069  """
12070  get_diffusion_length(double D, double t) -> double
12071  get_diffusion_length(double D, double force, double t, double temp=273) -> double
12072  get_diffusion_length(double D, double force, double t) -> double
12073  """
12074  return _IMP_atom.get_diffusion_length(*args)
12075 
12076 def get_diffusion_angle(D, dtfs):
12077  """get_diffusion_angle(double D, double dtfs) -> double"""
12078  return _IMP_atom.get_diffusion_angle(D, dtfs)
12079 
12080 def get_diffusion_coefficient(displacements, dt):
12081  """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
12082  return _IMP_atom.get_diffusion_coefficient(displacements, dt)
12083 
12084 def get_rotational_diffusion_coefficient(displacements, dt):
12085  """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
12086  return _IMP_atom.get_rotational_diffusion_coefficient(displacements, dt)
12087 class EzRestraint(IMP.Restraint):
12088  """Proxy of C++ IMP::atom::EzRestraint class"""
12089  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12090 
12091  def __init__(self, m, ps):
12092  """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
12093  this = _IMP_atom.new_EzRestraint(m, ps)
12094  try:
12095  self.this.append(this)
12096  except:
12097  self.this = this
12098 
12099  def get_version_info(self):
12100  """get_version_info(EzRestraint self) -> VersionInfo"""
12101  return _IMP_atom.EzRestraint_get_version_info(self)
12102 
12103 
12104  def __str__(self):
12105  """__str__(EzRestraint self) -> std::string"""
12106  return _IMP_atom.EzRestraint___str__(self)
12107 
12108 
12109  def __repr__(self):
12110  """__repr__(EzRestraint self) -> std::string"""
12111  return _IMP_atom.EzRestraint___repr__(self)
12112 
12113 
12114  @staticmethod
12115  def get_from(o):
12116  return _object_cast_to_EzRestraint(o)
12117 
12118 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
12119 EzRestraint_swigregister(EzRestraint)
12120 
12121 
12122 def create_protein(*args):
12123  """
12124  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1, bool ismol=True) -> Hierarchy
12125  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
12126  create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
12127  create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
12128  create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12129  """
12130  return _IMP_atom.create_protein(*args)
12131 
12133  """
12134  create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12135  create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
12136  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12137  create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
12138  """
12139  return _IMP_atom.create_simplified_along_backbone(*args)
12140 
12141 def create_simplified_from_volume(h, resolution):
12142  """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12143  return _IMP_atom.create_simplified_from_volume(h, resolution)
12144 
12145 def create_simplified_assembly_from_volume(h, resolution):
12146  """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12147  return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12148 
12149 def get_residue_indexes(h):
12150  """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12151  return _IMP_atom.get_residue_indexes(h)
12152 
12153 def get_residue_type(*args):
12154  """
12155  get_residue_type(char c) -> ResidueType
12156  get_residue_type(Hierarchy h) -> ResidueType
12157  """
12158  return _IMP_atom.get_residue_type(*args)
12159 
12160 def get_atom_type(h):
12161  """get_atom_type(Hierarchy h) -> AtomType"""
12162  return _IMP_atom.get_atom_type(h)
12163 
12164 def get_domain_name(h):
12165  """get_domain_name(Hierarchy h) -> std::string"""
12166  return _IMP_atom.get_domain_name(h)
12167 
12169  """
12170  create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12171  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12172  create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
12173  """
12174  return _IMP_atom.create_excluded_volume_restraint(*args)
12175 
12176 def setup_as_approximation(*args):
12177  """
12178  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12179  setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
12180  setup_as_approximation(Hierarchy h, double resolution=-1)
12181  setup_as_approximation(Hierarchy h)
12182  """
12183  return _IMP_atom.setup_as_approximation(*args)
12184 class _HierarchyTreeVertexIndex(object):
12185  """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class"""
12186  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12187  __repr__ = _swig_repr
12188 
12189  def __init__(self):
12190  """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12191  this = _IMP_atom.new__HierarchyTreeVertexIndex()
12192  try:
12193  self.this.append(this)
12194  except:
12195  self.this = this
12196  __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12197  __del__ = lambda self: None
12198 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
12199 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12200 
12201 
12202 def show_as_graphviz(name, out):
12203  """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12204  return _IMP_atom.show_as_graphviz(name, out)
12205 
12206 def get_vertex_index(g):
12207  """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12208  return _IMP_atom.get_vertex_index(g)
12209 
12210 def get_hierarchy_tree(h):
12211  """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12212  return _IMP_atom.get_hierarchy_tree(h)
12213 class HierarchyGeometry(IMP.display.SingletonGeometry):
12214  """Proxy of C++ IMP::atom::HierarchyGeometry class"""
12215  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12216 
12217  def __init__(self, d, resolution=0):
12218  """
12219  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
12220  __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
12221  """
12222  this = _IMP_atom.new_HierarchyGeometry(d, resolution)
12223  try:
12224  self.this.append(this)
12225  except:
12226  self.this = this
12227 
12228  def get_version_info(self):
12229  """get_version_info(HierarchyGeometry self) -> VersionInfo"""
12230  return _IMP_atom.HierarchyGeometry_get_version_info(self)
12231 
12232 
12233  def __str__(self):
12234  """__str__(HierarchyGeometry self) -> std::string"""
12235  return _IMP_atom.HierarchyGeometry___str__(self)
12236 
12237 
12238  def __repr__(self):
12239  """__repr__(HierarchyGeometry self) -> std::string"""
12240  return _IMP_atom.HierarchyGeometry___repr__(self)
12241 
12242 
12243  @staticmethod
12244  def get_from(o):
12245  return _object_cast_to_HierarchyGeometry(o)
12246 
12247 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
12248 HierarchyGeometry_swigregister(HierarchyGeometry)
12249 
12250 class HierarchiesGeometry(IMP.display.SingletonsGeometry):
12251  """Proxy of C++ IMP::atom::HierarchiesGeometry class"""
12252  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12253 
12254  def __init__(self, sc, resolution=-1):
12255  """
12256  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
12257  __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
12258  """
12259  this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
12260  try:
12261  self.this.append(this)
12262  except:
12263  self.this = this
12264 
12265  def get_version_info(self):
12266  """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12267  return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12268 
12269 
12270  def __str__(self):
12271  """__str__(HierarchiesGeometry self) -> std::string"""
12272  return _IMP_atom.HierarchiesGeometry___str__(self)
12273 
12274 
12275  def __repr__(self):
12276  """__repr__(HierarchiesGeometry self) -> std::string"""
12277  return _IMP_atom.HierarchiesGeometry___repr__(self)
12278 
12279 
12280  @staticmethod
12281  def get_from(o):
12282  return _object_cast_to_HierarchiesGeometry(o)
12283 
12284 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
12285 HierarchiesGeometry_swigregister(HierarchiesGeometry)
12286 
12287 
12288 def transform(*args):
12289  """
12290  transform(Hierarchy h, Transformation3D tr)
12291  transform(Hierarchy h, Transformation3D tr)
12292  """
12293  return _IMP_atom.transform(*args)
12294 class DopePairScore(_ADopeBase):
12295  """Proxy of C++ IMP::atom::DopePairScore class"""
12296  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12297 
12298  def __init__(self, *args):
12299  """
12300  __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
12301  __init__(IMP::atom::DopePairScore self) -> DopePairScore
12302  __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12303  """
12304  this = _IMP_atom.new_DopePairScore(*args)
12305  try:
12306  self.this.append(this)
12307  except:
12308  self.this = this
12309 
12310  def __str__(self):
12311  """__str__(DopePairScore self) -> std::string"""
12312  return _IMP_atom.DopePairScore___str__(self)
12313 
12314 
12315  def __repr__(self):
12316  """__repr__(DopePairScore self) -> std::string"""
12317  return _IMP_atom.DopePairScore___repr__(self)
12318 
12319 
12320  @staticmethod
12321  def get_from(o):
12322  return _object_cast_to_DopePairScore(o)
12323 
12324  __swig_destroy__ = _IMP_atom.delete_DopePairScore
12325  __del__ = lambda self: None
12326 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
12327 DopePairScore_swigregister(DopePairScore)
12328 
12329 
12330 def add_dope_score_data(h):
12331  """add_dope_score_data(Hierarchy h)"""
12332  return _IMP_atom.add_dope_score_data(h)
12333 class OrientedSoapPairScore(_OrientedSoapBase):
12334  """Proxy of C++ IMP::atom::OrientedSoapPairScore class"""
12335  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12336 
12337  def __init__(self, library):
12338  """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12339  this = _IMP_atom.new_OrientedSoapPairScore(library)
12340  try:
12341  self.this.append(this)
12342  except:
12343  self.this = this
12344 
12345  def get_pair_filter(self):
12346  """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12347  return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12348 
12349 
12350  def __str__(self):
12351  """__str__(OrientedSoapPairScore self) -> std::string"""
12352  return _IMP_atom.OrientedSoapPairScore___str__(self)
12353 
12354 
12355  def __repr__(self):
12356  """__repr__(OrientedSoapPairScore self) -> std::string"""
12357  return _IMP_atom.OrientedSoapPairScore___repr__(self)
12358 
12359 
12360  @staticmethod
12361  def get_from(o):
12362  return _object_cast_to_OrientedSoapPairScore(o)
12363 
12364  __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12365  __del__ = lambda self: None
12366 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12367 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12368 
12369 class SameResiduePairFilter(IMP.PairPredicate):
12370  """Proxy of C++ IMP::atom::SameResiduePairFilter class"""
12371  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12372 
12373  def __init__(self):
12374  """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12375  this = _IMP_atom.new_SameResiduePairFilter()
12376  try:
12377  self.this.append(this)
12378  except:
12379  self.this = this
12380 
12381  def do_get_inputs(self, m, pis):
12382  """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12383  return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12384 
12385 
12386  def get_value(self, *args):
12387  """
12388  get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12389  get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12390  """
12391  return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12392 
12393 
12394  def get_value_index(self, *args):
12395  """
12396  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12397  get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12398  """
12399  return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12400 
12401 
12402  def get_version_info(self):
12403  """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12404  return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12405 
12406 
12407  def __str__(self):
12408  """__str__(SameResiduePairFilter self) -> std::string"""
12409  return _IMP_atom.SameResiduePairFilter___str__(self)
12410 
12411 
12412  def __repr__(self):
12413  """__repr__(SameResiduePairFilter self) -> std::string"""
12414  return _IMP_atom.SameResiduePairFilter___repr__(self)
12415 
12416 
12417  @staticmethod
12418  def get_from(o):
12419  return _object_cast_to_SameResiduePairFilter(o)
12420 
12421 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12422 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12423 
12424 class RemoveRigidMotionOptimizerState(IMP.OptimizerState):
12425  """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class"""
12426  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12427 
12428  def __init__(self, m, pis):
12429  """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12430  this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12431  try:
12432  self.this.append(this)
12433  except:
12434  self.this = this
12435 
12436  def set_particles(self, pis):
12437  """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12438  return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12439 
12440 
12441  def remove_rigid_motion(self):
12442  """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12443  return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12444 
12445 
12446  def get_version_info(self):
12447  """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12448  return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12449 
12450 
12451  def __str__(self):
12452  """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12453  return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12454 
12455 
12456  def __repr__(self):
12457  """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12458  return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12459 
12460 
12461  @staticmethod
12462  def get_from(o):
12463  return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12464 
12465 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12466 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12467 
12468 class BerendsenThermostatOptimizerState(IMP.OptimizerState):
12469  """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class"""
12470  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12471 
12472  def __init__(self, pis, temperature, tau):
12473  """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12474  this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12475  try:
12476  self.this.append(this)
12477  except:
12478  self.this = this
12479 
12480  def set_particles(self, pis):
12481  """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12482  return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12483 
12484 
12485  def get_temperature(self):
12486  """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12487  return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12488 
12489 
12490  def get_tau(self):
12491  """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12492  return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12493 
12494 
12495  def set_temperature(self, temperature):
12496  """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12497  return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12498 
12499 
12500  def set_tau(self, tau):
12501  """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12502  return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12503 
12504 
12505  def rescale_velocities(self):
12506  """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12507  return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12508 
12509 
12510  def get_version_info(self):
12511  """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12512  return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12513 
12514 
12515  def __str__(self):
12516  """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12517  return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12518 
12519 
12520  def __repr__(self):
12521  """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12522  return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12523 
12524 
12525  @staticmethod
12526  def get_from(o):
12527  return _object_cast_to_BerendsenThermostatOptimizerState(o)
12528 
12529 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12530 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12531 
12532 class LangevinThermostatOptimizerState(IMP.OptimizerState):
12533  """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class"""
12534  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12535 
12536  def __init__(self, m, pis, temperature, gamma):
12537  """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12538  this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12539  try:
12540  self.this.append(this)
12541  except:
12542  self.this = this
12543 
12544  def set_particles(self, pis):
12545  """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12546  return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12547 
12548 
12549  def get_temperature(self):
12550  """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12551  return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12552 
12553 
12554  def get_gamma(self):
12555  """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12556  return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12557 
12558 
12559  def set_temperature(self, temperature):
12560  """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12561  return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12562 
12563 
12564  def set_gamma(self, gamma):
12565  """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12566  return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12567 
12568 
12569  def rescale_velocities(self):
12570  """rescale_velocities(LangevinThermostatOptimizerState self)"""
12571  return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12572 
12573 
12574  def get_version_info(self):
12575  """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12576  return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12577 
12578 
12579  def __str__(self):
12580  """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12581  return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12582 
12583 
12584  def __repr__(self):
12585  """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12586  return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12587 
12588 
12589  @staticmethod
12590  def get_from(o):
12591  return _object_cast_to_LangevinThermostatOptimizerState(o)
12592 
12593 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12594 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12595 
12596 class PDBSelector(IMP.Object):
12597  """Proxy of C++ IMP::atom::PDBSelector class"""
12598  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12599 
12600  def __init__(self, name):
12601  """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12602  if self.__class__ == PDBSelector:
12603  _self = None
12604  else:
12605  _self = self
12606  this = _IMP_atom.new_PDBSelector(_self, name)
12607  try:
12608  self.this.append(this)
12609  except:
12610  self.this = this
12611 
12612  if self.__class__ != PDBSelector:
12613  _director_objects.register(self)
12614 
12615 
12616 
12617 
12618  def get_is_selected(self, pdb_line):
12619  """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12620  return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12621 
12622  __swig_destroy__ = _IMP_atom.delete_PDBSelector
12623  __del__ = lambda self: None
12624 
12625  def __str__(self):
12626  """__str__(PDBSelector self) -> std::string"""
12627  return _IMP_atom.PDBSelector___str__(self)
12628 
12629 
12630  def __repr__(self):
12631  """__repr__(PDBSelector self) -> std::string"""
12632  return _IMP_atom.PDBSelector___repr__(self)
12633 
12634 
12635  @staticmethod
12636  def get_from(o):
12637  return _object_cast_to_PDBSelector(o)
12638 
12639 
12640  def get_type_name(self):
12641  return self.__class__.__name__
12642  def do_show(self, out):
12643  pass
12644  def get_version_info(self):
12645  if"IMP::atom" == "IMP":
12646  return VersionInfo(self.__module__,
12647  __import__(self.__module__).get_module_version())
12648  else:
12649  return IMP.VersionInfo(self.__module__,
12650  __import__(self.__module__).get_module_version())
12651  @staticmethod
12652  def get_from(o):
12653  return _object_cast_to_PDBSelector(o)
12654 
12655 
12656  def __and__(self, s):
12657  return AndPDBSelector(self, s)
12658  def __or__(self, s):
12659  return OrPDBSelector(self, s)
12660  def __xor__(self, s):
12661  return XorPDBSelector(self, s)
12662  def __invert__(self):
12663  return NotPDBSelector(self)
12664  def __sub__(self, s):
12665  return AndPDBSelector(self, NotPDBSelector(s))
12666 
12667  def __disown__(self):
12668  self.this.disown()
12669  _IMP_atom.disown_PDBSelector(self)
12670  return weakref_proxy(self)
12671 
12672  def do_destroy(self):
12673  """do_destroy(PDBSelector self)"""
12674  return _IMP_atom.PDBSelector_do_destroy(self)
12675 
12676 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12677 PDBSelector_swigregister(PDBSelector)
12678 
12679 class NonAlternativePDBSelector(PDBSelector):
12680  """Proxy of C++ IMP::atom::NonAlternativePDBSelector class"""
12681  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12682 
12683  def __init__(self, *args):
12684  """
12685  __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12686  __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12687  """
12688  this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12689  try:
12690  self.this.append(this)
12691  except:
12692  self.this = this
12693 
12694  def get_version_info(self):
12695  """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12696  return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12697 
12698 
12699  def __str__(self):
12700  """__str__(NonAlternativePDBSelector self) -> std::string"""
12701  return _IMP_atom.NonAlternativePDBSelector___str__(self)
12702 
12703 
12704  def __repr__(self):
12705  """__repr__(NonAlternativePDBSelector self) -> std::string"""
12706  return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12707 
12708 
12709  @staticmethod
12710  def get_from(o):
12711  return _object_cast_to_NonAlternativePDBSelector(o)
12712 
12713 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
12714 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12715 
12716 class ATOMPDBSelector(NonAlternativePDBSelector):
12717  """Proxy of C++ IMP::atom::ATOMPDBSelector class"""
12718  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12719 
12720  def __init__(self, *args):
12721  """
12722  __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
12723  __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
12724  """
12725  this = _IMP_atom.new_ATOMPDBSelector(*args)
12726  try:
12727  self.this.append(this)
12728  except:
12729  self.this = this
12730 
12731  def __str__(self):
12732  """__str__(ATOMPDBSelector self) -> std::string"""
12733  return _IMP_atom.ATOMPDBSelector___str__(self)
12734 
12735 
12736  def __repr__(self):
12737  """__repr__(ATOMPDBSelector self) -> std::string"""
12738  return _IMP_atom.ATOMPDBSelector___repr__(self)
12739 
12740 
12741  @staticmethod
12742  def get_from(o):
12743  return _object_cast_to_ATOMPDBSelector(o)
12744 
12745 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
12746 ATOMPDBSelector_swigregister(ATOMPDBSelector)
12747 
12748 class CAlphaPDBSelector(NonAlternativePDBSelector):
12749  """Proxy of C++ IMP::atom::CAlphaPDBSelector class"""
12750  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12751 
12752  def __init__(self, *args):
12753  """
12754  __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
12755  __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
12756  """
12757  this = _IMP_atom.new_CAlphaPDBSelector(*args)
12758  try:
12759  self.this.append(this)
12760  except:
12761  self.this = this
12762 
12763  def __str__(self):
12764  """__str__(CAlphaPDBSelector self) -> std::string"""
12765  return _IMP_atom.CAlphaPDBSelector___str__(self)
12766 
12767 
12768  def __repr__(self):
12769  """__repr__(CAlphaPDBSelector self) -> std::string"""
12770  return _IMP_atom.CAlphaPDBSelector___repr__(self)
12771 
12772 
12773  @staticmethod
12774  def get_from(o):
12775  return _object_cast_to_CAlphaPDBSelector(o)
12776 
12777 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
12778 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12779 
12780 class CBetaPDBSelector(NonAlternativePDBSelector):
12781  """Proxy of C++ IMP::atom::CBetaPDBSelector class"""
12782  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12783 
12784  def __init__(self, *args):
12785  """
12786  __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
12787  __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
12788  """
12789  this = _IMP_atom.new_CBetaPDBSelector(*args)
12790  try:
12791  self.this.append(this)
12792  except:
12793  self.this = this
12794 
12795  def __str__(self):
12796  """__str__(CBetaPDBSelector self) -> std::string"""
12797  return _IMP_atom.CBetaPDBSelector___str__(self)
12798 
12799 
12800  def __repr__(self):
12801  """__repr__(CBetaPDBSelector self) -> std::string"""
12802  return _IMP_atom.CBetaPDBSelector___repr__(self)
12803 
12804 
12805  @staticmethod
12806  def get_from(o):
12807  return _object_cast_to_CBetaPDBSelector(o)
12808 
12809 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
12810 CBetaPDBSelector_swigregister(CBetaPDBSelector)
12811 
12812 class AtomTypePDBSelector(PDBSelector):
12813  """Proxy of C++ IMP::atom::AtomTypePDBSelector class"""
12814  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12815 
12816  def __init__(self, *args):
12817  """
12818  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
12819  __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
12820  """
12821  this = _IMP_atom.new_AtomTypePDBSelector(*args)
12822  try:
12823  self.this.append(this)
12824  except:
12825  self.this = this
12826 
12827  def get_version_info(self):
12828  """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12829  return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12830 
12831 
12832  def __str__(self):
12833  """__str__(AtomTypePDBSelector self) -> std::string"""
12834  return _IMP_atom.AtomTypePDBSelector___str__(self)
12835 
12836 
12837  def __repr__(self):
12838  """__repr__(AtomTypePDBSelector self) -> std::string"""
12839  return _IMP_atom.AtomTypePDBSelector___repr__(self)
12840 
12841 
12842  @staticmethod
12843  def get_from(o):
12844  return _object_cast_to_AtomTypePDBSelector(o)
12845 
12846 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
12847 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12848 
12849 class ResidueTypePDBSelector(PDBSelector):
12850  """Proxy of C++ IMP::atom::ResidueTypePDBSelector class"""
12851  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12852 
12853  def __init__(self, *args):
12854  """
12855  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
12856  __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
12857  """
12858  this = _IMP_atom.new_ResidueTypePDBSelector(*args)
12859  try:
12860  self.this.append(this)
12861  except:
12862  self.this = this
12863 
12864  def get_version_info(self):
12865  """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12866  return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12867 
12868 
12869  def __str__(self):
12870  """__str__(ResidueTypePDBSelector self) -> std::string"""
12871  return _IMP_atom.ResidueTypePDBSelector___str__(self)
12872 
12873 
12874  def __repr__(self):
12875  """__repr__(ResidueTypePDBSelector self) -> std::string"""
12876  return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12877 
12878 
12879  @staticmethod
12880  def get_from(o):
12881  return _object_cast_to_ResidueTypePDBSelector(o)
12882 
12883 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
12884 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12885 
12886 class CPDBSelector(NonAlternativePDBSelector):
12887  """Proxy of C++ IMP::atom::CPDBSelector class"""
12888  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12889 
12890  def __init__(self, *args):
12891  """
12892  __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
12893  __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
12894  """
12895  this = _IMP_atom.new_CPDBSelector(*args)
12896  try:
12897  self.this.append(this)
12898  except:
12899  self.this = this
12900 
12901  def __str__(self):
12902  """__str__(CPDBSelector self) -> std::string"""
12903  return _IMP_atom.CPDBSelector___str__(self)
12904 
12905 
12906  def __repr__(self):
12907  """__repr__(CPDBSelector self) -> std::string"""
12908  return _IMP_atom.CPDBSelector___repr__(self)
12909 
12910 
12911  @staticmethod
12912  def get_from(o):
12913  return _object_cast_to_CPDBSelector(o)
12914 
12915 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
12916 CPDBSelector_swigregister(CPDBSelector)
12917 
12918 class NPDBSelector(NonAlternativePDBSelector):
12919  """Proxy of C++ IMP::atom::NPDBSelector class"""
12920  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12921 
12922  def __init__(self, *args):
12923  """
12924  __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
12925  __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
12926  """
12927  this = _IMP_atom.new_NPDBSelector(*args)
12928  try:
12929  self.this.append(this)
12930  except:
12931  self.this = this
12932 
12933  def __str__(self):
12934  """__str__(NPDBSelector self) -> std::string"""
12935  return _IMP_atom.NPDBSelector___str__(self)
12936 
12937 
12938  def __repr__(self):
12939  """__repr__(NPDBSelector self) -> std::string"""
12940  return _IMP_atom.NPDBSelector___repr__(self)
12941 
12942 
12943  @staticmethod
12944  def get_from(o):
12945  return _object_cast_to_NPDBSelector(o)
12946 
12947 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
12948 NPDBSelector_swigregister(NPDBSelector)
12949 
12950 class AllPDBSelector(PDBSelector):
12951  """Proxy of C++ IMP::atom::AllPDBSelector class"""
12952  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12953 
12954  def __init__(self, *args):
12955  """
12956  __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
12957  __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
12958  """
12959  this = _IMP_atom.new_AllPDBSelector(*args)
12960  try:
12961  self.this.append(this)
12962  except:
12963  self.this = this
12964 
12965  def get_version_info(self):
12966  """get_version_info(AllPDBSelector self) -> VersionInfo"""
12967  return _IMP_atom.AllPDBSelector_get_version_info(self)
12968 
12969 
12970  def __str__(self):
12971  """__str__(AllPDBSelector self) -> std::string"""
12972  return _IMP_atom.AllPDBSelector___str__(self)
12973 
12974 
12975  def __repr__(self):
12976  """__repr__(AllPDBSelector self) -> std::string"""
12977  return _IMP_atom.AllPDBSelector___repr__(self)
12978 
12979 
12980  @staticmethod
12981  def get_from(o):
12982  return _object_cast_to_AllPDBSelector(o)
12983 
12984 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
12985 AllPDBSelector_swigregister(AllPDBSelector)
12986 
12987 class ChainPDBSelector(NonAlternativePDBSelector):
12988  """Proxy of C++ IMP::atom::ChainPDBSelector class"""
12989  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
12990 
12991  def __init__(self, *args):
12992  """
12993  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
12994  __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
12995  """
12996  this = _IMP_atom.new_ChainPDBSelector(*args)
12997  try:
12998  self.this.append(this)
12999  except:
13000  self.this = this
13001 
13002  def __str__(self):
13003  """__str__(ChainPDBSelector self) -> std::string"""
13004  return _IMP_atom.ChainPDBSelector___str__(self)
13005 
13006 
13007  def __repr__(self):
13008  """__repr__(ChainPDBSelector self) -> std::string"""
13009  return _IMP_atom.ChainPDBSelector___repr__(self)
13010 
13011 
13012  @staticmethod
13013  def get_from(o):
13014  return _object_cast_to_ChainPDBSelector(o)
13015 
13016 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
13017 ChainPDBSelector_swigregister(ChainPDBSelector)
13018 
13019 class WaterPDBSelector(NonAlternativePDBSelector):
13020  """Proxy of C++ IMP::atom::WaterPDBSelector class"""
13021  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13022 
13023  def __init__(self, *args):
13024  """
13025  __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
13026  __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
13027  """
13028  this = _IMP_atom.new_WaterPDBSelector(*args)
13029  try:
13030  self.this.append(this)
13031  except:
13032  self.this = this
13033 
13034  def __str__(self):
13035  """__str__(WaterPDBSelector self) -> std::string"""
13036  return _IMP_atom.WaterPDBSelector___str__(self)
13037 
13038 
13039  def __repr__(self):
13040  """__repr__(WaterPDBSelector self) -> std::string"""
13041  return _IMP_atom.WaterPDBSelector___repr__(self)
13042 
13043 
13044  @staticmethod
13045  def get_from(o):
13046  return _object_cast_to_WaterPDBSelector(o)
13047 
13048 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
13049 WaterPDBSelector_swigregister(WaterPDBSelector)
13050 
13051 class HydrogenPDBSelector(NonAlternativePDBSelector):
13052  """Proxy of C++ IMP::atom::HydrogenPDBSelector class"""
13053  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13054 
13055  def __init__(self, *args):
13056  """
13057  __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
13058  __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
13059  """
13060  this = _IMP_atom.new_HydrogenPDBSelector(*args)
13061  try:
13062  self.this.append(this)
13063  except:
13064  self.this = this
13065 
13066  def __str__(self):
13067  """__str__(HydrogenPDBSelector self) -> std::string"""
13068  return _IMP_atom.HydrogenPDBSelector___str__(self)
13069 
13070 
13071  def __repr__(self):
13072  """__repr__(HydrogenPDBSelector self) -> std::string"""
13073  return _IMP_atom.HydrogenPDBSelector___repr__(self)
13074 
13075 
13076  @staticmethod
13077  def get_from(o):
13078  return _object_cast_to_HydrogenPDBSelector(o)
13079 
13080 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
13081 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
13082 
13083 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
13084  """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class"""
13085  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13086 
13087  def __init__(self, *args):
13088  """
13089  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
13090  __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
13091  """
13092  this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
13093  try:
13094  self.this.append(this)
13095  except:
13096  self.this = this
13097 
13098  def __str__(self):
13099  """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13100  return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
13101 
13102 
13103  def __repr__(self):
13104  """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13105  return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
13106 
13107 
13108  @staticmethod
13109  def get_from(o):
13110  return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
13111 
13112 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
13113 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
13114 
13115 class NonWaterPDBSelector(NonAlternativePDBSelector):
13116  """Proxy of C++ IMP::atom::NonWaterPDBSelector class"""
13117  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13118 
13119  def __init__(self, *args):
13120  """
13121  __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
13122  __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
13123  """
13124  this = _IMP_atom.new_NonWaterPDBSelector(*args)
13125  try:
13126  self.this.append(this)
13127  except:
13128  self.this = this
13129 
13130  def __str__(self):
13131  """__str__(NonWaterPDBSelector self) -> std::string"""
13132  return _IMP_atom.NonWaterPDBSelector___str__(self)
13133 
13134 
13135  def __repr__(self):
13136  """__repr__(NonWaterPDBSelector self) -> std::string"""
13137  return _IMP_atom.NonWaterPDBSelector___repr__(self)
13138 
13139 
13140  @staticmethod
13141  def get_from(o):
13142  return _object_cast_to_NonWaterPDBSelector(o)
13143 
13144 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
13145 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
13146 
13147 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
13148  """Proxy of C++ IMP::atom::BackbonePDBSelector class"""
13149  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13150 
13151  def __init__(self, *args):
13152  """
13153  __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
13154  __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
13155  """
13156  this = _IMP_atom.new_BackbonePDBSelector(*args)
13157  try:
13158  self.this.append(this)
13159  except:
13160  self.this = this
13161 
13162  def __str__(self):
13163  """__str__(BackbonePDBSelector self) -> std::string"""
13164  return _IMP_atom.BackbonePDBSelector___str__(self)
13165 
13166 
13167  def __repr__(self):
13168  """__repr__(BackbonePDBSelector self) -> std::string"""
13169  return _IMP_atom.BackbonePDBSelector___repr__(self)
13170 
13171 
13172  @staticmethod
13173  def get_from(o):
13174  return _object_cast_to_BackbonePDBSelector(o)
13175 
13176 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
13177 BackbonePDBSelector_swigregister(BackbonePDBSelector)
13178 
13179 class PPDBSelector(NonAlternativePDBSelector):
13180  """Proxy of C++ IMP::atom::PPDBSelector class"""
13181  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13182 
13183  def __init__(self, *args):
13184  """
13185  __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
13186  __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
13187  """
13188  this = _IMP_atom.new_PPDBSelector(*args)
13189  try:
13190  self.this.append(this)
13191  except:
13192  self.this = this
13193 
13194  def __str__(self):
13195  """__str__(PPDBSelector self) -> std::string"""
13196  return _IMP_atom.PPDBSelector___str__(self)
13197 
13198 
13199  def __repr__(self):
13200  """__repr__(PPDBSelector self) -> std::string"""
13201  return _IMP_atom.PPDBSelector___repr__(self)
13202 
13203 
13204  @staticmethod
13205  def get_from(o):
13206  return _object_cast_to_PPDBSelector(o)
13207 
13208 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
13209 PPDBSelector_swigregister(PPDBSelector)
13210 
13211 class AndPDBSelector(PDBSelector):
13212  """Proxy of C++ IMP::atom::AndPDBSelector class"""
13213  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13214 
13215  def get_version_info(self):
13216  """get_version_info(AndPDBSelector self) -> VersionInfo"""
13217  return _IMP_atom.AndPDBSelector_get_version_info(self)
13218 
13219 
13220  def __init__(self, a, b):
13221  """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13222  this = _IMP_atom.new_AndPDBSelector(a, b)
13223  try:
13224  self.this.append(this)
13225  except:
13226  self.this = this
13227 
13228  def __str__(self):
13229  """__str__(AndPDBSelector self) -> std::string"""
13230  return _IMP_atom.AndPDBSelector___str__(self)
13231 
13232 
13233  def __repr__(self):
13234  """__repr__(AndPDBSelector self) -> std::string"""
13235  return _IMP_atom.AndPDBSelector___repr__(self)
13236 
13237 
13238  @staticmethod
13239  def get_from(o):
13240  return _object_cast_to_AndPDBSelector(o)
13241 
13242 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
13243 AndPDBSelector_swigregister(AndPDBSelector)
13244 
13245 class OrPDBSelector(PDBSelector):
13246  """Proxy of C++ IMP::atom::OrPDBSelector class"""
13247  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13248 
13249  def get_version_info(self):
13250  """get_version_info(OrPDBSelector self) -> VersionInfo"""
13251  return _IMP_atom.OrPDBSelector_get_version_info(self)
13252 
13253 
13254  def __init__(self, a, b):
13255  """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13256  this = _IMP_atom.new_OrPDBSelector(a, b)
13257  try:
13258  self.this.append(this)
13259  except:
13260  self.this = this
13261 
13262  def __str__(self):
13263  """__str__(OrPDBSelector self) -> std::string"""
13264  return _IMP_atom.OrPDBSelector___str__(self)
13265 
13266 
13267  def __repr__(self):
13268  """__repr__(OrPDBSelector self) -> std::string"""
13269  return _IMP_atom.OrPDBSelector___repr__(self)
13270 
13271 
13272  @staticmethod
13273  def get_from(o):
13274  return _object_cast_to_OrPDBSelector(o)
13275 
13276 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
13277 OrPDBSelector_swigregister(OrPDBSelector)
13278 
13279 class XorPDBSelector(PDBSelector):
13280  """Proxy of C++ IMP::atom::XorPDBSelector class"""
13281  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13282 
13283  def get_version_info(self):
13284  """get_version_info(XorPDBSelector self) -> VersionInfo"""
13285  return _IMP_atom.XorPDBSelector_get_version_info(self)
13286 
13287 
13288  def __init__(self, a, b):
13289  """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13290  this = _IMP_atom.new_XorPDBSelector(a, b)
13291  try:
13292  self.this.append(this)
13293  except:
13294  self.this = this
13295 
13296  def __str__(self):
13297  """__str__(XorPDBSelector self) -> std::string"""
13298  return _IMP_atom.XorPDBSelector___str__(self)
13299 
13300 
13301  def __repr__(self):
13302  """__repr__(XorPDBSelector self) -> std::string"""
13303  return _IMP_atom.XorPDBSelector___repr__(self)
13304 
13305 
13306  @staticmethod
13307  def get_from(o):
13308  return _object_cast_to_XorPDBSelector(o)
13309 
13310 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13311 XorPDBSelector_swigregister(XorPDBSelector)
13312 
13313 class NotPDBSelector(PDBSelector):
13314  """Proxy of C++ IMP::atom::NotPDBSelector class"""
13315  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13316 
13317  def get_version_info(self):
13318  """get_version_info(NotPDBSelector self) -> VersionInfo"""
13319  return _IMP_atom.NotPDBSelector_get_version_info(self)
13320 
13321 
13322  def __init__(self, a):
13323  """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13324  this = _IMP_atom.new_NotPDBSelector(a)
13325  try:
13326  self.this.append(this)
13327  except:
13328  self.this = this
13329 
13330  def __str__(self):
13331  """__str__(NotPDBSelector self) -> std::string"""
13332  return _IMP_atom.NotPDBSelector___str__(self)
13333 
13334 
13335  def __repr__(self):
13336  """__repr__(NotPDBSelector self) -> std::string"""
13337  return _IMP_atom.NotPDBSelector___repr__(self)
13338 
13339 
13340  @staticmethod
13341  def get_from(o):
13342  return _object_cast_to_NotPDBSelector(o)
13343 
13344 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13345 NotPDBSelector_swigregister(NotPDBSelector)
13346 
13347 
13348 def get_default_pdb_selector():
13349  """get_default_pdb_selector() -> PDBSelector"""
13350  return _IMP_atom.get_default_pdb_selector()
13351 
13352 def read_pdb(*args):
13353  """
13354  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13355  read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13356  read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13357  read_pdb(TextInput input, Model model) -> Hierarchy
13358  read_pdb(TextInput input, int model, Hierarchy h)
13359  """
13360  return _IMP_atom.read_pdb(*args)
13361 
13362 def read_multimodel_pdb(*args):
13363  """
13364  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13365  read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13366  read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13367  """
13368  return _IMP_atom.read_multimodel_pdb(*args)
13369 
13370 def write_pdb(mhd, out, model=1):
13371  """
13372  write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13373  write_pdb(Selection mhd, TextOutput out)
13374  """
13375  return _IMP_atom.write_pdb(mhd, out, model)
13376 
13377 def write_pdb_of_c_alphas(mhd, out, model=1):
13378  """
13379  write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13380  write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13381  """
13382  return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13383 
13384 def write_multimodel_pdb(mhd, out):
13385  """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13386  return _IMP_atom.write_multimodel_pdb(mhd, out)
13387 
13388 def get_pdb_string(*args):
13389  """
13390  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00, double tempFactor=0.00, IMP::atom::Element e) -> std::string
13391  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00, double tempFactor=0.00) -> std::string
13392  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00) -> std::string
13393  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13394  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13395  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13396  get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13397  get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13398  get_pdb_string(Vector3D v, int index=-1) -> std::string
13399  get_pdb_string(Vector3D v) -> std::string
13400  """
13401  return _IMP_atom.get_pdb_string(*args)
13402 
13403 def get_pdb_conect_record_string(arg1, arg2):
13404  """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13405  return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13406 class WritePDBOptimizerState(IMP.OptimizerState):
13407  """Proxy of C++ IMP::atom::WritePDBOptimizerState class"""
13408  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13409 
13410  def __init__(self, *args):
13411  """
13412  __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13413  __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13414  """
13415  this = _IMP_atom.new_WritePDBOptimizerState(*args)
13416  try:
13417  self.this.append(this)
13418  except:
13419  self.this = this
13420 
13421  def get_version_info(self):
13422  """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13423  return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13424 
13425 
13426  def __str__(self):
13427  """__str__(WritePDBOptimizerState self) -> std::string"""
13428  return _IMP_atom.WritePDBOptimizerState___str__(self)
13429 
13430 
13431  def __repr__(self):
13432  """__repr__(WritePDBOptimizerState self) -> std::string"""
13433  return _IMP_atom.WritePDBOptimizerState___repr__(self)
13434 
13435 
13436  @staticmethod
13437  def get_from(o):
13438  return _object_cast_to_WritePDBOptimizerState(o)
13439 
13440 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13441 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13442 
13443 
13444 def get_kt(T):
13445  """get_kt(double T) -> double"""
13446  return _IMP_atom.get_kt(T)
13447 class CAAngleRestraint(IMP.Restraint):
13448  """Proxy of C++ IMP::atom::CAAngleRestraint class"""
13449  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13450 
13451  def __init__(self, m, p1, p2, p3, phi0, score):
13452  """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13453  this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13454  try:
13455  self.this.append(this)
13456  except:
13457  self.this = this
13458 
13459  def do_get_inputs(self):
13460  """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13461  return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13462 
13463 
13464  def get_version_info(self):
13465  """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13466  return _IMP_atom.CAAngleRestraint_get_version_info(self)
13467 
13468 
13469  def __str__(self):
13470  """__str__(CAAngleRestraint self) -> std::string"""
13471  return _IMP_atom.CAAngleRestraint___str__(self)
13472 
13473 
13474  def __repr__(self):
13475  """__repr__(CAAngleRestraint self) -> std::string"""
13476  return _IMP_atom.CAAngleRestraint___repr__(self)
13477 
13478 
13479  @staticmethod
13480  def get_from(o):
13481  return _object_cast_to_CAAngleRestraint(o)
13482 
13483 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13484 CAAngleRestraint_swigregister(CAAngleRestraint)
13485 
13486 class CADihedralRestraint(IMP.Restraint):
13487  """Proxy of C++ IMP::atom::CADihedralRestraint class"""
13488  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13489 
13490  def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13491  """__init__(IMP::atom::CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
13492  this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13493  try:
13494  self.this.append(this)
13495  except:
13496  self.this = this
13497 
13498  def do_get_inputs(self):
13499  """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13500  return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13501 
13502 
13503  def get_version_info(self):
13504  """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13505  return _IMP_atom.CADihedralRestraint_get_version_info(self)
13506 
13507 
13508  def __str__(self):
13509  """__str__(CADihedralRestraint self) -> std::string"""
13510  return _IMP_atom.CADihedralRestraint___str__(self)
13511 
13512 
13513  def __repr__(self):
13514  """__repr__(CADihedralRestraint self) -> std::string"""
13515  return _IMP_atom.CADihedralRestraint___repr__(self)
13516 
13517 
13518  @staticmethod
13519  def get_from(o):
13520  return _object_cast_to_CADihedralRestraint(o)
13521 
13522 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13523 CADihedralRestraint_swigregister(CADihedralRestraint)
13524 
13525 class StructureSource(IMP.Decorator):
13526  """Proxy of C++ IMP::atom::StructureSource class"""
13527  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13528 
13529  def get_source_id(self):
13530  """get_source_id(StructureSource self) -> std::string"""
13531  return _IMP_atom.StructureSource_get_source_id(self)
13532 
13533 
13534  def get_source_chain_id(self):
13535  """get_source_chain_id(StructureSource self) -> std::string"""
13536  return _IMP_atom.StructureSource_get_source_chain_id(self)
13537 
13538 
13539  def set_source_id(self, source_id):
13540  """set_source_id(StructureSource self, std::string source_id)"""
13541  return _IMP_atom.StructureSource_set_source_id(self, source_id)
13542 
13543 
13544  def set_source_chain_id(self, source_chain_id):
13545  """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13546  return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13547 
13548 
13549  def __init__(self, *args):
13550  """
13551  __init__(IMP::atom::StructureSource self) -> StructureSource
13552  __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13553  __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13554  """
13555  this = _IMP_atom.new_StructureSource(*args)
13556  try:
13557  self.this.append(this)
13558  except:
13559  self.this = this
13560 
13561  def get_is_setup(*args):
13562  """
13563  get_is_setup(Model m, ParticleIndex pi) -> bool
13564  get_is_setup(_ParticleAdaptor p) -> bool
13565  """
13566  return _IMP_atom.StructureSource_get_is_setup(*args)
13567 
13568  get_is_setup = staticmethod(get_is_setup)
13569 
13570  def show(self, *args):
13571  """
13572  show(StructureSource self, _ostream out)
13573  show(StructureSource self)
13574  """
13575  return _IMP_atom.StructureSource_show(self, *args)
13576 
13577 
13578  def setup_particle(*args):
13579  """
13580  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13581  setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13582  """
13583  return _IMP_atom.StructureSource_setup_particle(*args)
13584 
13585  setup_particle = staticmethod(setup_particle)
13586 
13587  def add_attribute(self, *args):
13588  """
13589  add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13590  add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13591  add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13592  add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13593  add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13594  add_attribute(StructureSource self, ObjectKey a0, Object a1)
13595  """
13596  return _IMP_atom.StructureSource_add_attribute(self, *args)
13597 
13598 
13599  def get_value(self, *args):
13600  """
13601  get_value(StructureSource self, FloatKey a0) -> IMP::Float
13602  get_value(StructureSource self, IntKey a0) -> IMP::Int
13603  get_value(StructureSource self, StringKey a0) -> IMP::String
13604  get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13605  get_value(StructureSource self, ObjectKey a0) -> Object
13606  """
13607  return _IMP_atom.StructureSource_get_value(self, *args)
13608 
13609 
13610  def set_value(self, *args):
13611  """
13612  set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13613  set_value(StructureSource self, IntKey a0, IMP::Int a1)
13614  set_value(StructureSource self, StringKey a0, IMP::String a1)
13615  set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13616  set_value(StructureSource self, ObjectKey a0, Object a1)
13617  """
13618  return _IMP_atom.StructureSource_set_value(self, *args)
13619 
13620 
13621  def remove_attribute(self, *args):
13622  """
13623  remove_attribute(StructureSource self, FloatKey a0)
13624  remove_attribute(StructureSource self, IntKey a0)
13625  remove_attribute(StructureSource self, StringKey a0)
13626  remove_attribute(StructureSource self, ParticleIndexKey a0)
13627  remove_attribute(StructureSource self, ObjectKey a0)
13628  """
13629  return _IMP_atom.StructureSource_remove_attribute(self, *args)
13630 
13631 
13632  def has_attribute(self, *args):
13633  """
13634  has_attribute(StructureSource self, FloatKey a0) -> bool
13635  has_attribute(StructureSource self, IntKey a0) -> bool
13636  has_attribute(StructureSource self, StringKey a0) -> bool
13637  has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13638  has_attribute(StructureSource self, ObjectKey a0) -> bool
13639  """
13640  return _IMP_atom.StructureSource_has_attribute(self, *args)
13641 
13642 
13643  def get_derivative(self, a0):
13644  """get_derivative(StructureSource self, FloatKey a0) -> double"""
13645  return _IMP_atom.StructureSource_get_derivative(self, a0)
13646 
13647 
13648  def get_name(self):
13649  """get_name(StructureSource self) -> std::string"""
13650  return _IMP_atom.StructureSource_get_name(self)
13651 
13652 
13653  def clear_caches(self):
13654  """clear_caches(StructureSource self)"""
13655  return _IMP_atom.StructureSource_clear_caches(self)
13656 
13657 
13658  def set_name(self, a0):
13659  """set_name(StructureSource self, std::string a0)"""
13660  return _IMP_atom.StructureSource_set_name(self, a0)
13661 
13662 
13663  def set_check_level(self, a0):
13664  """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13665  return _IMP_atom.StructureSource_set_check_level(self, a0)
13666 
13667 
13668  def add_to_derivative(self, a0, a1, a2):
13669  """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13670  return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13671 
13672 
13673  def set_is_optimized(self, a0, a1):
13674  """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13675  return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13676 
13677 
13678  def get_is_optimized(self, a0):
13679  """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13680  return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13681 
13682 
13683  def get_check_level(self):
13684  """get_check_level(StructureSource self) -> IMP::CheckLevel"""
13685  return _IMP_atom.StructureSource_get_check_level(self)
13686 
13687 
13688  def __eq__(self, *args):
13689  """
13690  __eq__(StructureSource self, StructureSource o) -> bool
13691  __eq__(StructureSource self, Particle d) -> bool
13692  """
13693  return _IMP_atom.StructureSource___eq__(self, *args)
13694 
13695 
13696  def __ne__(self, *args):
13697  """
13698  __ne__(StructureSource self, StructureSource o) -> bool
13699  __ne__(StructureSource self, Particle d) -> bool
13700  """
13701  return _IMP_atom.StructureSource___ne__(self, *args)
13702 
13703 
13704  def __le__(self, *args):
13705  """
13706  __le__(StructureSource self, StructureSource o) -> bool
13707  __le__(StructureSource self, Particle d) -> bool
13708  """
13709  return _IMP_atom.StructureSource___le__(self, *args)
13710 
13711 
13712  def __lt__(self, *args):
13713  """
13714  __lt__(StructureSource self, StructureSource o) -> bool
13715  __lt__(StructureSource self, Particle d) -> bool
13716  """
13717  return _IMP_atom.StructureSource___lt__(self, *args)
13718 
13719 
13720  def __ge__(self, *args):
13721  """
13722  __ge__(StructureSource self, StructureSource o) -> bool
13723  __ge__(StructureSource self, Particle d) -> bool
13724  """
13725  return _IMP_atom.StructureSource___ge__(self, *args)
13726 
13727 
13728  def __gt__(self, *args):
13729  """
13730  __gt__(StructureSource self, StructureSource o) -> bool
13731  __gt__(StructureSource self, Particle d) -> bool
13732  """
13733  return _IMP_atom.StructureSource___gt__(self, *args)
13734 
13735 
13736  def __hash__(self):
13737  """__hash__(StructureSource self) -> std::size_t"""
13738  return _IMP_atom.StructureSource___hash__(self)
13739 
13740 
13741  def __str__(self):
13742  """__str__(StructureSource self) -> std::string"""
13743  return _IMP_atom.StructureSource___str__(self)
13744 
13745 
13746  def __repr__(self):
13747  """__repr__(StructureSource self) -> std::string"""
13748  return _IMP_atom.StructureSource___repr__(self)
13749 
13750  __swig_destroy__ = _IMP_atom.delete_StructureSource
13751  __del__ = lambda self: None
13752 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
13753 StructureSource_swigregister(StructureSource)
13754 
13755 def StructureSource_get_is_setup(*args):
13756  """
13757  get_is_setup(Model m, ParticleIndex pi) -> bool
13758  StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
13759  """
13760  return _IMP_atom.StructureSource_get_is_setup(*args)
13761 
13762 def StructureSource_setup_particle(*args):
13763  """
13764  setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13765  StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13766  """
13767  return _IMP_atom.StructureSource_setup_particle(*args)
13768 
13769 
13770 def __lshift__(*args):
13771  """
13772  __lshift__(_ostream out, Bonded n) -> _ostream
13773  __lshift__(_ostream out, Bond n) -> _ostream
13774  __lshift__(_ostream out, Hierarchy n) -> _ostream
13775  __lshift__(_ostream out, Angle n) -> _ostream
13776  __lshift__(_ostream out, Dihedral n) -> _ostream
13777  __lshift__(_ostream out, CenterOfMass n) -> _ostream
13778  __lshift__(_ostream out, Diffusion n) -> _ostream
13779  __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13780  __lshift__(_ostream out, TAMDParticle n) -> _ostream
13781  __lshift__(_ostream out, Chain n) -> _ostream
13782  __lshift__(_ostream out, Charged n) -> _ostream
13783  __lshift__(_ostream out, Domain n) -> _ostream
13784  __lshift__(_ostream out, LennardJones n) -> _ostream
13785  __lshift__(_ostream out, Fragment n) -> _ostream
13786  __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13787  __lshift__(_ostream out, Atom n) -> _ostream
13788  __lshift__(_ostream out, Residue n) -> _ostream
13789  __lshift__(_ostream out, Representation n) -> _ostream
13790  __lshift__(_ostream out, State n) -> _ostream
13791  __lshift__(_ostream out, Molecule n) -> _ostream
13792  __lshift__(_ostream out, Copy n) -> _ostream
13793  __lshift__(_ostream out, StructureSource n) -> _ostream
13794  """
13795  return _IMP_atom.__lshift__(*args)
13796 
13797 def show_molecular_hierarchy(*args):
13798  """
13799  show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
13800  show_molecular_hierarchy(Hierarchy h) -> _ostream
13801  """
13802  return _IMP_atom.show_molecular_hierarchy(*args)
13803 class CHARMMBond(object):
13804  """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class"""
13805  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13806  __repr__ = _swig_repr
13807 
13808  def __init__(self, atoms):
13809  """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
13810  this = _IMP_atom.new_CHARMMBond(atoms)
13811  try:
13812  self.this.append(this)
13813  except:
13814  self.this = this
13815 
13816  def get_endpoint(self, i):
13817  """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13818  return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13819 
13820 
13821  def get_contains_atom(self, name):
13822  """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13823  return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13824 
13825 
13826  def show(self, *args):
13827  """
13828  show(CHARMMBond self, _ostream out)
13829  show(CHARMMBond self)
13830  """
13831  return _IMP_atom.CHARMMBond_show(self, *args)
13832 
13833  __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13834  __del__ = lambda self: None
13835 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
13836 CHARMMBond_swigregister(CHARMMBond)
13837 
13838 class CHARMMAngle(object):
13839  """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class"""
13840  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
13841  __repr__ = _swig_repr
13842 
13843  def __init__(self, atoms):
13844  """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
13845  this = _IMP_atom.new_CHARMMAngle(atoms)
13846  try:
13847  self.this.append(this)
13848  except:
13849  self.this = this
13850 
13851  def get_endpoint(self, i):
13852  """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13853  return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13854 
13855 
13856  def get_contains_atom(self, name):
13857  """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13858  return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13859 
13860 
13861  def show(self, *args):
13862  """
13863  show(CHARMMAngle self, _ostream out)
13864  show(CHARMMAngle self)
13865  """
13866  return _IMP_atom.CHARMMAngle_show(self, *args)
13867 
13868  __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13869  __del__ = lambda self: None
13870 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
13871 CHARMMAngle_swigregister(CHARMMAngle)
13872 
13873 
13874 def _get_native_overlap_cpp(m1, m2, threshold):
13875  """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13876  return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13877 
13878 def _get_drmsd_cpp(m0, m1):
13879  """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13880  return _IMP_atom._get_drmsd_cpp(m0, m1)
13881 
13882 def _get_drmsd_Q_cpp(m0, m1, threshold):
13883  """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13884  return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13885 
13886 def _get_drms_cpp(m1, m2):
13887  """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13888  return _IMP_atom._get_drms_cpp(m1, m2)
13889 
13890 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13891  """_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, IMP::IntRanges const & ranges) -> double"""
13892  return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13893 
13894 def get_native_overlap(a, b, d):
13895  va= [IMP.algebra.get_vector(x) for x in a]
13896  vb= [IMP.algebra.get_vector(x) for x in b]
13897  return _get_native_overlap_cpp(va, vb, d)
13898 
13899 def get_drmsd(a, b):
13900  va= [IMP.algebra.get_vector(x) for x in a]
13901  vb= [IMP.algebra.get_vector(x) for x in b]
13902  return _get_drmsd_cpp(va, vb)
13903 
13904 def get_drms(a, b):
13905  va= [IMP.algebra.get_vector(x) for x in a]
13906  vb= [IMP.algebra.get_vector(x) for x in b]
13907  return _get_drms_cpp(va, vb)
13908 
13909 def get_drmsd_Q(a, b, t):
13910  va= [IMP.algebra.get_vector(x) for x in a]
13911  vb= [IMP.algebra.get_vector(x) for x in b]
13912  return _get_drmsd_Q_cpp(va, vb, t)
13913 
13914 def get_rigid_bodies_drms(a, b, ranges):
13915  va= [IMP.algebra.get_vector(x) for x in a]
13916  vb= [IMP.algebra.get_vector(x) for x in b]
13917 #rs = [IMP.IntRange(r[0],r[1]) for r in ranges]
13918  return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13919 
13920 
13921 
13922 def get_module_version():
13923  """get_module_version() -> std::string const"""
13924  return _IMP_atom.get_module_version()
13925 
13926 def get_example_path(fname):
13927  """get_example_path(std::string fname) -> std::string"""
13928  return _IMP_atom.get_example_path(fname)
13929 
13930 def get_data_path(fname):
13931  """get_data_path(std::string fname) -> std::string"""
13932  return _IMP_atom.get_data_path(fname)
13933 
13934 from . import _version_check
13935 _version_check.check_version(get_module_version())
13936 __version__ = get_module_version()
13937 
13938 
13939 
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature.
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:37
A shared container for Pairs.
Definition: PairContainer.h:37
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
setup
Definition: setup.py:1
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_einstein_rotational_diffusion_coefficient(double r)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Definition: atom/distance.h:49
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
Definition: BoundingBoxD.h:274
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Composable functors to implement scores via compile-time composition.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
double get_kd(double na, double nb, double nab, double volume)
Definition: estimates.h:94
double get_diffusion_angle(double D, double dtfs)
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
Definition: BoundingBoxD.h:163
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &displacements, double dt)
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
Base class for all optimizers.
Definition: Optimizer.h:46
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
Definition: estimates.h:87
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
Definition: VersionInfo.h:28
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Definition: Vector3D.h:65
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:31
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
Definition: Refiner.h:34
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
Definition: atom/distance.h:85
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
double get_diffusion_length(double D, double t)
double get_einstein_diffusion_coefficient(double r)
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27