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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
rmf/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_rmf
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_RMF_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_RMF_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_rmf.delete_IMP_RMF_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_RMF_SwigPyIterator self) -> PyObject *"""
79  return _IMP_rmf.IMP_RMF_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_RMF_SwigPyIterator self, size_t n=1) -> IMP_RMF_SwigPyIterator"""
83  return _IMP_rmf.IMP_RMF_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_RMF_SwigPyIterator self, size_t n=1) -> IMP_RMF_SwigPyIterator"""
87  return _IMP_rmf.IMP_RMF_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_rmf.IMP_RMF_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
95  return _IMP_rmf.IMP_RMF_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_RMF_SwigPyIterator self) -> IMP_RMF_SwigPyIterator"""
99  return _IMP_rmf.IMP_RMF_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_RMF_SwigPyIterator self) -> PyObject *"""
103  return _IMP_rmf.IMP_RMF_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_RMF_SwigPyIterator self) -> PyObject *"""
107  return _IMP_rmf.IMP_RMF_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_RMF_SwigPyIterator self) -> PyObject *"""
111  return _IMP_rmf.IMP_RMF_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
115  return _IMP_rmf.IMP_RMF_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
119  return _IMP_rmf.IMP_RMF_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
123  return _IMP_rmf.IMP_RMF_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
127  return _IMP_rmf.IMP_RMF_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
131  return _IMP_rmf.IMP_RMF_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
135  return _IMP_rmf.IMP_RMF_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator
140  __sub__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_rmf.IMP_RMF_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_RMF_SwigPyIterator in _IMP_rmf:
147 _IMP_rmf.IMP_RMF_SwigPyIterator_swigregister(IMP_RMF_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_rmf.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_rmf.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_rmf.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_rmf.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_rmf.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_rmf.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_rmf.IMP_MEMORY
167 
168 IMP_NONE = _IMP_rmf.IMP_NONE
169 
170 IMP_USAGE = _IMP_rmf.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_rmf.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_rmf.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_rmf.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_rmf.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_rmf.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_rmf.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_rmf.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_rmf.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_rmf.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_rmf.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_rmf.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_rmf.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_rmf._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_rmf:
237 _IMP_rmf._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_rmf.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_rmf.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_rmf.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_rmf.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_rmf.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_rmf.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_rmf.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_rmf.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_rmf.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_rmf.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_rmf.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_rmf.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_rmf.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_rmf.IMP_STATISTICS_HAS_IMP_CGAL
310 
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
312 
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
314 
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_RANDOM
316 
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_SYSTEM
318 
319 IMP_STATISTICS_HAS_CGAL = _IMP_rmf.IMP_STATISTICS_HAS_CGAL
320 
321 IMP_STATISTICS_HAS_NUMPY = _IMP_rmf.IMP_STATISTICS_HAS_NUMPY
322 
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_rmf.IMPSTATISTICS_SHOW_WARNINGS
324 
325 import IMP.statistics
326 IMP_CORE_HAS_IMP_CGAL = _IMP_rmf.IMP_CORE_HAS_IMP_CGAL
327 
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_rmf.IMP_CORE_HAS_IMP_KERNEL
329 
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CORE_HAS_BOOST_FILESYSTEM
331 
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CORE_HAS_BOOST_RANDOM
335 
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CORE_HAS_BOOST_SYSTEM
337 
338 IMP_CORE_HAS_CGAL = _IMP_rmf.IMP_CORE_HAS_CGAL
339 
340 IMP_CORE_HAS_HDF5 = _IMP_rmf.IMP_CORE_HAS_HDF5
341 
342 IMP_CORE_HAS_NUMPY = _IMP_rmf.IMP_CORE_HAS_NUMPY
343 
344 IMPCORE_SHOW_WARNINGS = _IMP_rmf.IMPCORE_SHOW_WARNINGS
345 
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_rmf.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_rmf.IMP_CONTAINER_HAS_IMP_CGAL
350 
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_rmf.IMP_CONTAINER_HAS_IMP_DISPLAY
352 
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_rmf.IMP_CONTAINER_HAS_IMP_KERNEL
354 
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
356 
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
358 
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
360 
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_RANDOM
362 
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_SYSTEM
364 
365 IMP_CONTAINER_HAS_CGAL = _IMP_rmf.IMP_CONTAINER_HAS_CGAL
366 
367 IMP_CONTAINER_HAS_HDF5 = _IMP_rmf.IMP_CONTAINER_HAS_HDF5
368 
369 IMP_CONTAINER_HAS_NUMPY = _IMP_rmf.IMP_CONTAINER_HAS_NUMPY
370 
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_rmf.IMP_CONTAINER_HAS_PYTHON_IHM
372 
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_rmf.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
374 
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_rmf.IMP_CONTAINER_HAS_ROBIN_MAP
376 
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_rmf.IMPCONTAINER_SHOW_WARNINGS
378 
379 import IMP.container
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_rmf.IMP_ATOM_HAS_IMP_CGAL
381 
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_rmf.IMP_ATOM_HAS_IMP_KERNEL
383 
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
385 
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
387 
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ATOM_HAS_BOOST_RANDOM
389 
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_rmf.IMP_ATOM_HAS_BOOST_REGEX
391 
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ATOM_HAS_BOOST_SYSTEM
393 
394 IMP_ATOM_HAS_CGAL = _IMP_rmf.IMP_ATOM_HAS_CGAL
395 
396 IMP_ATOM_HAS_HDF5 = _IMP_rmf.IMP_ATOM_HAS_HDF5
397 
398 IMP_ATOM_HAS_NUMPY = _IMP_rmf.IMP_ATOM_HAS_NUMPY
399 
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_rmf.IMP_ATOM_HAS_PYTHON_IHM
401 
402 IMPATOM_SHOW_WARNINGS = _IMP_rmf.IMPATOM_SHOW_WARNINGS
403 
404 IMP_ATOM_TYPE_INDEX = _IMP_rmf.IMP_ATOM_TYPE_INDEX
405 
406 IMP_RESIDUE_TYPE_INDEX = _IMP_rmf.IMP_RESIDUE_TYPE_INDEX
407 
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_rmf.IMP_HIERARCHY_TYPE_INDEX
409 
410 IMP_CHAIN_TYPE_INDEX = _IMP_rmf.IMP_CHAIN_TYPE_INDEX
411 
412 import IMP.atom
413 IMP_EM_HAS_IMP_CGAL = _IMP_rmf.IMP_EM_HAS_IMP_CGAL
414 
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_rmf.IMP_EM_HAS_IMP_CONTAINER
416 
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_rmf.IMP_EM_HAS_IMP_DISPLAY
418 
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_EM_HAS_IMP_SCORE_FUNCTOR
420 
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_EM_HAS_BOOST_FILESYSTEM
422 
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
424 
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_rmf.IMP_EM_HAS_BOOST_RANDOM
426 
427 IMP_EM_HAS_BOOST_REGEX = _IMP_rmf.IMP_EM_HAS_BOOST_REGEX
428 
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_EM_HAS_BOOST_SYSTEM
430 
431 IMP_EM_HAS_CGAL = _IMP_rmf.IMP_EM_HAS_CGAL
432 
433 IMP_EM_HAS_HDF5 = _IMP_rmf.IMP_EM_HAS_HDF5
434 
435 IMP_EM_HAS_NUMPY = _IMP_rmf.IMP_EM_HAS_NUMPY
436 
437 IMP_EM_HAS_PYTHON_IHM = _IMP_rmf.IMP_EM_HAS_PYTHON_IHM
438 
439 IMPEM_SHOW_WARNINGS = _IMP_rmf.IMPEM_SHOW_WARNINGS
440 
441 import IMP.em
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_rmf.IMP_SAXS_HAS_IMP_CGAL
443 
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_rmf.IMP_SAXS_HAS_IMP_CONTAINER
445 
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_rmf.IMP_SAXS_HAS_IMP_DISPLAY
447 
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_rmf.IMP_SAXS_HAS_IMP_KERNEL
449 
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
451 
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_SAXS_HAS_BOOST_FILESYSTEM
453 
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
455 
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_rmf.IMP_SAXS_HAS_BOOST_RANDOM
457 
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_rmf.IMP_SAXS_HAS_BOOST_REGEX
459 
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_SAXS_HAS_BOOST_SYSTEM
461 
462 IMP_SAXS_HAS_CGAL = _IMP_rmf.IMP_SAXS_HAS_CGAL
463 
464 IMP_SAXS_HAS_HDF5 = _IMP_rmf.IMP_SAXS_HAS_HDF5
465 
466 IMP_SAXS_HAS_NUMPY = _IMP_rmf.IMP_SAXS_HAS_NUMPY
467 
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_rmf.IMP_SAXS_HAS_PYTHON_IHM
469 
470 IMPSAXS_SHOW_WARNINGS = _IMP_rmf.IMPSAXS_SHOW_WARNINGS
471 
472 import IMP.saxs
473 IMP_ISD_HAS_IMP_CGAL = _IMP_rmf.IMP_ISD_HAS_IMP_CGAL
474 
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_rmf.IMP_ISD_HAS_IMP_DISPLAY
476 
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
478 
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_ISD_HAS_BOOST_FILESYSTEM
480 
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
482 
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ISD_HAS_BOOST_RANDOM
484 
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_rmf.IMP_ISD_HAS_BOOST_REGEX
486 
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ISD_HAS_BOOST_SYSTEM
488 
489 IMP_ISD_HAS_CGAL = _IMP_rmf.IMP_ISD_HAS_CGAL
490 
491 IMP_ISD_HAS_HDF5 = _IMP_rmf.IMP_ISD_HAS_HDF5
492 
493 IMP_ISD_HAS_NUMPY = _IMP_rmf.IMP_ISD_HAS_NUMPY
494 
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_rmf.IMP_ISD_HAS_PYTHON_IHM
496 
497 IMPISD_SHOW_WARNINGS = _IMP_rmf.IMPISD_SHOW_WARNINGS
498 
499 import IMP.isd
500 IMP_RMF_HAS_IMP_CGAL = _IMP_rmf.IMP_RMF_HAS_IMP_CGAL
501 
502 IMP_RMF_HAS_IMP_EM = _IMP_rmf.IMP_RMF_HAS_IMP_EM
503 
504 IMP_RMF_HAS_IMP_SAXS = _IMP_rmf.IMP_RMF_HAS_IMP_SAXS
505 
506 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
507 
508 IMP_RMF_HAS_IMP_STATISTICS = _IMP_rmf.IMP_RMF_HAS_IMP_STATISTICS
509 
510 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_RMF_HAS_BOOST_FILESYSTEM
511 
512 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
513 
514 IMP_RMF_HAS_BOOST_RANDOM = _IMP_rmf.IMP_RMF_HAS_BOOST_RANDOM
515 
516 IMP_RMF_HAS_BOOST_REGEX = _IMP_rmf.IMP_RMF_HAS_BOOST_REGEX
517 
518 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_RMF_HAS_BOOST_SYSTEM
519 
520 IMP_RMF_HAS_CGAL = _IMP_rmf.IMP_RMF_HAS_CGAL
521 
522 IMP_RMF_HAS_HDF5 = _IMP_rmf.IMP_RMF_HAS_HDF5
523 
524 IMP_RMF_HAS_NUMPY = _IMP_rmf.IMP_RMF_HAS_NUMPY
525 
526 IMP_RMF_HAS_PYTHON_IHM = _IMP_rmf.IMP_RMF_HAS_PYTHON_IHM
527 
528 IMPRMF_SHOW_WARNINGS = _IMP_rmf.IMPRMF_SHOW_WARNINGS
529 
530 import RMF
531 
532 _object_types.append("SaveOptimizerState")
533 
534 
535 def _object_cast_to_SaveOptimizerState(o):
536  r"""_object_cast_to_SaveOptimizerState(Object o) -> SaveOptimizerState"""
537  return _IMP_rmf._object_cast_to_SaveOptimizerState(o)
538 
539 _object_types.append("LoadLink")
540 
541 
542 def _object_cast_to_LoadLink(o):
543  r"""_object_cast_to_LoadLink(Object o) -> LoadLink"""
544  return _IMP_rmf._object_cast_to_LoadLink(o)
545 
546 _object_types.append("SaveLink")
547 
548 
549 def _object_cast_to_SaveLink(o):
550  r"""_object_cast_to_SaveLink(Object o) -> SaveLink"""
551  return _IMP_rmf._object_cast_to_SaveLink(o)
552 
553 _object_types.append("HierarchySaveLink")
554 
555 
556 def _object_cast_to_HierarchySaveLink(o):
557  r"""_object_cast_to_HierarchySaveLink(Object o) -> HierarchySaveLink"""
558  return _IMP_rmf._object_cast_to_HierarchySaveLink(o)
559 
560 _object_types.append("HierarchyLoadLink")
561 
562 
563 def _object_cast_to_HierarchyLoadLink(o):
564  r"""_object_cast_to_HierarchyLoadLink(Object o) -> HierarchyLoadLink"""
565  return _IMP_rmf._object_cast_to_HierarchyLoadLink(o)
566 class LoadLink(IMP.Object):
567  r"""Proxy of C++ IMP::rmf::LoadLink class."""
568 
569  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
570 
571  def do_load(self, fh):
572  r"""do_load(LoadLink self, FileConstHandle fh)"""
573  return _IMP_rmf.LoadLink_do_load(self, fh)
574 
575  def __init__(self, name):
576  r"""__init__(LoadLink self, std::string name) -> LoadLink"""
577  if self.__class__ == LoadLink:
578  _self = None
579  else:
580  _self = self
581  _IMP_rmf.LoadLink_swiginit(self, _IMP_rmf.new_LoadLink(_self, name))
582 
583  if self.__class__ != LoadLink:
584  _director_objects.register(self)
585 
586 
587 
588 
589  def load(self, fh):
590  r"""load(LoadLink self, FileConstHandle fh)"""
591  return _IMP_rmf.LoadLink_load(self, fh)
592  __swig_destroy__ = _IMP_rmf.delete_LoadLink
593 
594  def __str__(self):
595  r"""__str__(LoadLink self) -> std::string"""
596  return _IMP_rmf.LoadLink___str__(self)
597 
598  def __repr__(self):
599  r"""__repr__(LoadLink self) -> std::string"""
600  return _IMP_rmf.LoadLink___repr__(self)
601 
602  @staticmethod
603  def get_from(o):
604  return _object_cast_to_LoadLink(o)
605 
606 
607  def get_type_name(self):
608  return self.__class__.__name__
609  def do_show(self, out):
610  pass
611  def get_version_info(self):
612  if"IMP::rmf" == "IMP":
613  return VersionInfo(self.__module__,
614  __import__(self.__module__).get_module_version())
615  else:
616  return IMP.VersionInfo(self.__module__,
617  __import__(self.__module__).get_module_version())
618  @staticmethod
619  def get_from(o):
620  return _object_cast_to_LoadLink(o)
621 
622  def __disown__(self):
623  self.this.disown()
624  _IMP_rmf.disown_LoadLink(self)
625  return weakref.proxy(self)
626 
627  def do_destroy(self):
628  r"""do_destroy(LoadLink self)"""
629  return _IMP_rmf.LoadLink_do_destroy(self)
630 
631 # Register LoadLink in _IMP_rmf:
632 _IMP_rmf.LoadLink_swigregister(LoadLink)
633 class SaveLink(IMP.Object):
634  r"""Proxy of C++ IMP::rmf::SaveLink class."""
635 
636  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
637 
638  def do_save(self, hf):
639  r"""do_save(SaveLink self, FileHandle hf)"""
640  return _IMP_rmf.SaveLink_do_save(self, hf)
641 
642  def __init__(self, name):
643  r"""__init__(SaveLink self, std::string name) -> SaveLink"""
644  if self.__class__ == SaveLink:
645  _self = None
646  else:
647  _self = self
648  _IMP_rmf.SaveLink_swiginit(self, _IMP_rmf.new_SaveLink(_self, name))
649 
650  if self.__class__ != SaveLink:
651  _director_objects.register(self)
652 
653 
654 
655 
656  def save(self, fh):
657  r"""save(SaveLink self, FileHandle fh)"""
658  return _IMP_rmf.SaveLink_save(self, fh)
659  __swig_destroy__ = _IMP_rmf.delete_SaveLink
660 
661  def __str__(self):
662  r"""__str__(SaveLink self) -> std::string"""
663  return _IMP_rmf.SaveLink___str__(self)
664 
665  def __repr__(self):
666  r"""__repr__(SaveLink self) -> std::string"""
667  return _IMP_rmf.SaveLink___repr__(self)
668 
669  @staticmethod
670  def get_from(o):
671  return _object_cast_to_SaveLink(o)
672 
673 
674  def get_type_name(self):
675  return self.__class__.__name__
676  def do_show(self, out):
677  pass
678  def get_version_info(self):
679  if"IMP::rmf" == "IMP":
680  return VersionInfo(self.__module__,
681  __import__(self.__module__).get_module_version())
682  else:
683  return IMP.VersionInfo(self.__module__,
684  __import__(self.__module__).get_module_version())
685  @staticmethod
686  def get_from(o):
687  return _object_cast_to_SaveLink(o)
688 
689  def __disown__(self):
690  self.this.disown()
691  _IMP_rmf.disown_SaveLink(self)
692  return weakref.proxy(self)
693 
694  def do_destroy(self):
695  r"""do_destroy(SaveLink self)"""
696  return _IMP_rmf.SaveLink_do_destroy(self)
697 
698 # Register SaveLink in _IMP_rmf:
699 _IMP_rmf.SaveLink_swigregister(SaveLink)
700 
701 def add_hierarchies(*args):
702  r"""
703  add_hierarchies(FileHandle fh, IMP::atom::Hierarchies const & hs)
704  add_hierarchies(NodeHandle fh, IMP::atom::Hierarchies const & hs)
705  """
706  return _IMP_rmf.add_hierarchies(*args)
707 
708 def add_hierarchy(fh, hs):
709  r"""add_hierarchy(FileHandle fh, Hierarchy hs)"""
710  return _IMP_rmf.add_hierarchy(fh, hs)
711 
712 def create_hierarchies(fh, m):
713  r"""create_hierarchies(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
714  return _IMP_rmf.create_hierarchies(fh, m)
715 
716 def link_hierarchies(fh, hs):
717  r"""link_hierarchies(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
718  return _IMP_rmf.link_hierarchies(fh, hs)
719 
720 def add_restraints(*args):
721  r"""
722  add_restraints(FileHandle fh, IMP::Restraints const & hs)
723  add_restraints(NodeHandle fh, IMP::Restraints const & hs)
724  """
725  return _IMP_rmf.add_restraints(*args)
726 
727 def add_restraint(fh, hs):
728  r"""add_restraint(FileHandle fh, Restraint hs)"""
729  return _IMP_rmf.add_restraint(fh, hs)
730 
731 def create_restraints(fh, m):
732  r"""create_restraints(FileConstHandle fh, Model m) -> IMP::Restraints"""
733  return _IMP_rmf.create_restraints(fh, m)
734 
735 def link_restraints(fh, hs):
736  r"""link_restraints(FileConstHandle fh, IMP::Restraints const & hs)"""
737  return _IMP_rmf.link_restraints(fh, hs)
738 
739 def add_restraints_as_bonds(fh, rs):
740  r"""add_restraints_as_bonds(FileHandle fh, IMP::Restraints const & rs)"""
741  return _IMP_rmf.add_restraints_as_bonds(fh, rs)
742 
743 def set_maximum_number_of_terms(fh, num):
744  r"""set_maximum_number_of_terms(FileHandle fh, unsigned int num)"""
745  return _IMP_rmf.set_maximum_number_of_terms(fh, num)
746 
747 def add_particles(*args):
748  r"""
749  add_particles(FileHandle fh, IMP::ParticlesTemp const & hs)
750  add_particles(NodeHandle fh, IMP::ParticlesTemp const & hs)
751  """
752  return _IMP_rmf.add_particles(*args)
753 
754 def add_particle(fh, hs):
755  r"""add_particle(FileHandle fh, Particle hs)"""
756  return _IMP_rmf.add_particle(fh, hs)
757 
758 def create_particles(fh, m):
759  r"""create_particles(FileConstHandle fh, Model m) -> IMP::ParticlesTemp"""
760  return _IMP_rmf.create_particles(fh, m)
761 
762 def link_particles(fh, hs):
763  r"""link_particles(FileConstHandle fh, IMP::ParticlesTemp const & hs)"""
764  return _IMP_rmf.link_particles(fh, hs)
765 
766 def add_geometries(*args):
767  r"""
768  add_geometries(FileHandle file, IMP::display::GeometriesTemp const & r)
769  add_geometries(NodeHandle parent, IMP::display::GeometriesTemp const & r)
770  """
771  return _IMP_rmf.add_geometries(*args)
772 
773 def add_static_geometries(parent, r):
774  r"""add_static_geometries(FileHandle parent, IMP::display::GeometriesTemp const & r)"""
775  return _IMP_rmf.add_static_geometries(parent, r)
776 
777 def add_geometry(file, r):
778  r"""add_geometry(FileHandle file, Geometry r)"""
779  return _IMP_rmf.add_geometry(file, r)
780 
781 def create_geometries(parent):
782  r"""create_geometries(FileConstHandle parent) -> IMP::display::Geometries"""
783  return _IMP_rmf.create_geometries(parent)
784 
785 def link_geometries(parent, r):
786  r"""link_geometries(FileConstHandle parent, IMP::display::GeometriesTemp const & r)"""
787  return _IMP_rmf.link_geometries(parent, r)
788 
789 def set_association(nh, o, overwrite=False):
790  r"""set_association(NodeConstHandle nh, Object o, bool overwrite=False)"""
791  return _IMP_rmf.set_association(nh, o, overwrite)
792 
793 def get_node_from_association(*args):
794  r"""
795  get_node_from_association(FileConstHandle nh, Object oi) -> NodeConstHandle
796  get_node_from_association(FileHandle nh, Object oi) -> NodeHandle
797  """
798  return _IMP_rmf.get_node_from_association(*args)
799 
800 def get_has_associated_node(nh, oi):
801  r"""get_has_associated_node(FileConstHandle nh, Object oi) -> bool"""
802  return _IMP_rmf.get_has_associated_node(nh, oi)
803 class SaveOptimizerState(IMP.OptimizerState):
804  r"""Proxy of C++ IMP::rmf::SaveOptimizerState class."""
805 
806  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
807 
808  def __init__(self, m, fh):
809  r"""__init__(SaveOptimizerState self, Model m, FileHandle fh) -> SaveOptimizerState"""
810  _IMP_rmf.SaveOptimizerState_swiginit(self, _IMP_rmf.new_SaveOptimizerState(m, fh))
811  def __get_hierarchies(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_hierarchies, getfunc=self.get_hierarchy, erasefunc=self.erase_hierarchy, appendfunc=self.add_hierarchy, extendfunc=self.add_hierarchies, clearfunc=self.clear_hierarchies, indexfunc=self._python_index_hierarchy)
812  def __set_hierarchies(self, obj): IMP._list_util.set_varlist(self.hierarchies, obj)
813  def __del_hierarchies(self): IMP._list_util.del_varlist(self.hierarchies)
814  hierarchies = property(__get_hierarchies, __set_hierarchies, __del_hierarchies, doc="List of ##ucnames")
815 
816  def remove_hierarchy(self, d):
817  r"""remove_hierarchy(SaveOptimizerState self, Particle d)"""
818  return _IMP_rmf.SaveOptimizerState_remove_hierarchy(self, d)
819 
820  def _python_index_hierarchy(self, d, start, stop):
821  r"""_python_index_hierarchy(SaveOptimizerState self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
822  return _IMP_rmf.SaveOptimizerState__python_index_hierarchy(self, d, start, stop)
823 
824  def remove_hierarchies(self, d):
825  r"""remove_hierarchies(SaveOptimizerState self, IMP::Particles const & d)"""
826  return _IMP_rmf.SaveOptimizerState_remove_hierarchies(self, d)
827 
828  def set_hierarchies(self, ps):
829  r"""set_hierarchies(SaveOptimizerState self, IMP::Particles const & ps)"""
830  return _IMP_rmf.SaveOptimizerState_set_hierarchies(self, ps)
831 
832  def set_hierarchies_order(self, objs):
833  r"""set_hierarchies_order(SaveOptimizerState self, IMP::Particles const & objs)"""
834  return _IMP_rmf.SaveOptimizerState_set_hierarchies_order(self, objs)
835 
836  def add_hierarchy(self, obj):
837  r"""add_hierarchy(SaveOptimizerState self, Particle obj) -> unsigned int"""
838  return _IMP_rmf.SaveOptimizerState_add_hierarchy(self, obj)
839 
840  def add_hierarchies(self, objs):
841  r"""add_hierarchies(SaveOptimizerState self, IMP::Particles const & objs)"""
842  return _IMP_rmf.SaveOptimizerState_add_hierarchies(self, objs)
843 
844  def clear_hierarchies(self):
845  r"""clear_hierarchies(SaveOptimizerState self)"""
846  return _IMP_rmf.SaveOptimizerState_clear_hierarchies(self)
847 
848  def get_number_of_hierarchies(self):
849  r"""get_number_of_hierarchies(SaveOptimizerState self) -> unsigned int"""
850  return _IMP_rmf.SaveOptimizerState_get_number_of_hierarchies(self)
851 
852  def get_has_hierarchies(self):
853  r"""get_has_hierarchies(SaveOptimizerState self) -> bool"""
854  return _IMP_rmf.SaveOptimizerState_get_has_hierarchies(self)
855 
856  def get_hierarchy(self, i):
857  r"""get_hierarchy(SaveOptimizerState self, unsigned int i) -> Particle"""
858  return _IMP_rmf.SaveOptimizerState_get_hierarchy(self, i)
859 
860  def get_hierarchies(self):
861  r"""get_hierarchies(SaveOptimizerState self) -> IMP::Particles"""
862  return _IMP_rmf.SaveOptimizerState_get_hierarchies(self)
863 
864  def erase_hierarchy(self, i):
865  r"""erase_hierarchy(SaveOptimizerState self, unsigned int i)"""
866  return _IMP_rmf.SaveOptimizerState_erase_hierarchy(self, i)
867 
868  def reserve_hierarchies(self, sz):
869  r"""reserve_hierarchies(SaveOptimizerState self, unsigned int sz)"""
870  return _IMP_rmf.SaveOptimizerState_reserve_hierarchies(self, sz)
871  def __get_restraints(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_restraints, getfunc=self.get_restraint, erasefunc=self.erase_restraint, appendfunc=self.add_restraint, extendfunc=self.add_restraints, clearfunc=self.clear_restraints, indexfunc=self._python_index_restraint)
872  def __set_restraints(self, obj): IMP._list_util.set_varlist(self.restraints, obj)
873  def __del_restraints(self): IMP._list_util.del_varlist(self.restraints)
874  restraints = property(__get_restraints, __set_restraints, __del_restraints, doc="List of ##ucnames")
875 
876  def remove_restraint(self, d):
877  r"""remove_restraint(SaveOptimizerState self, Restraint d)"""
878  return _IMP_rmf.SaveOptimizerState_remove_restraint(self, d)
879 
880  def _python_index_restraint(self, d, start, stop):
881  r"""_python_index_restraint(SaveOptimizerState self, Restraint d, unsigned int start, unsigned int stop) -> unsigned int"""
882  return _IMP_rmf.SaveOptimizerState__python_index_restraint(self, d, start, stop)
883 
884  def remove_restraints(self, d):
885  r"""remove_restraints(SaveOptimizerState self, IMP::Restraints const & d)"""
886  return _IMP_rmf.SaveOptimizerState_remove_restraints(self, d)
887 
888  def set_restraints(self, ps):
889  r"""set_restraints(SaveOptimizerState self, IMP::Restraints const & ps)"""
890  return _IMP_rmf.SaveOptimizerState_set_restraints(self, ps)
891 
892  def set_restraints_order(self, objs):
893  r"""set_restraints_order(SaveOptimizerState self, IMP::Restraints const & objs)"""
894  return _IMP_rmf.SaveOptimizerState_set_restraints_order(self, objs)
895 
896  def add_restraint(self, obj):
897  r"""add_restraint(SaveOptimizerState self, Restraint obj) -> unsigned int"""
898  return _IMP_rmf.SaveOptimizerState_add_restraint(self, obj)
899 
900  def add_restraints(self, objs):
901  r"""add_restraints(SaveOptimizerState self, IMP::Restraints const & objs)"""
902  return _IMP_rmf.SaveOptimizerState_add_restraints(self, objs)
903 
904  def clear_restraints(self):
905  r"""clear_restraints(SaveOptimizerState self)"""
906  return _IMP_rmf.SaveOptimizerState_clear_restraints(self)
907 
908  def get_number_of_restraints(self):
909  r"""get_number_of_restraints(SaveOptimizerState self) -> unsigned int"""
910  return _IMP_rmf.SaveOptimizerState_get_number_of_restraints(self)
911 
912  def get_has_restraints(self):
913  r"""get_has_restraints(SaveOptimizerState self) -> bool"""
914  return _IMP_rmf.SaveOptimizerState_get_has_restraints(self)
915 
916  def get_restraint(self, i):
917  r"""get_restraint(SaveOptimizerState self, unsigned int i) -> Restraint"""
918  return _IMP_rmf.SaveOptimizerState_get_restraint(self, i)
919 
920  def get_restraints(self):
921  r"""get_restraints(SaveOptimizerState self) -> IMP::Restraints"""
922  return _IMP_rmf.SaveOptimizerState_get_restraints(self)
923 
924  def erase_restraint(self, i):
925  r"""erase_restraint(SaveOptimizerState self, unsigned int i)"""
926  return _IMP_rmf.SaveOptimizerState_erase_restraint(self, i)
927 
928  def reserve_restraints(self, sz):
929  r"""reserve_restraints(SaveOptimizerState self, unsigned int sz)"""
930  return _IMP_rmf.SaveOptimizerState_reserve_restraints(self, sz)
931  def __get_particles(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_particles, getfunc=self.get_particle, erasefunc=self.erase_particle, appendfunc=self.add_particle, extendfunc=self.add_particles, clearfunc=self.clear_particles, indexfunc=self._python_index_particle)
932  def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
933  def __del_particles(self): IMP._list_util.del_varlist(self.particles)
934  particles = property(__get_particles, __set_particles, __del_particles, doc="List of ##ucnames")
935 
936  def remove_particle(self, d):
937  r"""remove_particle(SaveOptimizerState self, Particle d)"""
938  return _IMP_rmf.SaveOptimizerState_remove_particle(self, d)
939 
940  def _python_index_particle(self, d, start, stop):
941  r"""_python_index_particle(SaveOptimizerState self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
942  return _IMP_rmf.SaveOptimizerState__python_index_particle(self, d, start, stop)
943 
944  def remove_particles(self, d):
945  r"""remove_particles(SaveOptimizerState self, IMP::Particles const & d)"""
946  return _IMP_rmf.SaveOptimizerState_remove_particles(self, d)
947 
948  def set_particles(self, ps):
949  r"""set_particles(SaveOptimizerState self, IMP::Particles const & ps)"""
950  return _IMP_rmf.SaveOptimizerState_set_particles(self, ps)
951 
952  def set_particles_order(self, objs):
953  r"""set_particles_order(SaveOptimizerState self, IMP::Particles const & objs)"""
954  return _IMP_rmf.SaveOptimizerState_set_particles_order(self, objs)
955 
956  def add_particle(self, obj):
957  r"""add_particle(SaveOptimizerState self, Particle obj) -> unsigned int"""
958  return _IMP_rmf.SaveOptimizerState_add_particle(self, obj)
959 
960  def add_particles(self, objs):
961  r"""add_particles(SaveOptimizerState self, IMP::Particles const & objs)"""
962  return _IMP_rmf.SaveOptimizerState_add_particles(self, objs)
963 
964  def clear_particles(self):
965  r"""clear_particles(SaveOptimizerState self)"""
966  return _IMP_rmf.SaveOptimizerState_clear_particles(self)
967 
968  def get_number_of_particles(self):
969  r"""get_number_of_particles(SaveOptimizerState self) -> unsigned int"""
970  return _IMP_rmf.SaveOptimizerState_get_number_of_particles(self)
971 
972  def get_has_particles(self):
973  r"""get_has_particles(SaveOptimizerState self) -> bool"""
974  return _IMP_rmf.SaveOptimizerState_get_has_particles(self)
975 
976  def get_particle(self, i):
977  r"""get_particle(SaveOptimizerState self, unsigned int i) -> Particle"""
978  return _IMP_rmf.SaveOptimizerState_get_particle(self, i)
979 
980  def get_particles(self):
981  r"""get_particles(SaveOptimizerState self) -> IMP::Particles"""
982  return _IMP_rmf.SaveOptimizerState_get_particles(self)
983 
984  def erase_particle(self, i):
985  r"""erase_particle(SaveOptimizerState self, unsigned int i)"""
986  return _IMP_rmf.SaveOptimizerState_erase_particle(self, i)
987 
988  def reserve_particles(self, sz):
989  r"""reserve_particles(SaveOptimizerState self, unsigned int sz)"""
990  return _IMP_rmf.SaveOptimizerState_reserve_particles(self, sz)
991  def __get_geometries(self): return IMP._list_util.VarList(getdimfunc=self.get_number_of_geometries, getfunc=self.get_geometry, erasefunc=self.erase_geometry, appendfunc=self.add_geometry, extendfunc=self.add_geometries, clearfunc=self.clear_geometries, indexfunc=self._python_index_geometry)
992  def __set_geometries(self, obj): IMP._list_util.set_varlist(self.geometries, obj)
993  def __del_geometries(self): IMP._list_util.del_varlist(self.geometries)
994  geometries = property(__get_geometries, __set_geometries, __del_geometries, doc="List of ##ucnames")
995 
996  def remove_geometry(self, d):
997  r"""remove_geometry(SaveOptimizerState self, Geometry d)"""
998  return _IMP_rmf.SaveOptimizerState_remove_geometry(self, d)
999 
1000  def _python_index_geometry(self, d, start, stop):
1001  r"""_python_index_geometry(SaveOptimizerState self, Geometry d, unsigned int start, unsigned int stop) -> unsigned int"""
1002  return _IMP_rmf.SaveOptimizerState__python_index_geometry(self, d, start, stop)
1003 
1004  def remove_geometries(self, d):
1005  r"""remove_geometries(SaveOptimizerState self, IMP::display::Geometries const & d)"""
1006  return _IMP_rmf.SaveOptimizerState_remove_geometries(self, d)
1007 
1008  def set_geometries(self, ps):
1009  r"""set_geometries(SaveOptimizerState self, IMP::display::Geometries const & ps)"""
1010  return _IMP_rmf.SaveOptimizerState_set_geometries(self, ps)
1011 
1012  def set_geometries_order(self, objs):
1013  r"""set_geometries_order(SaveOptimizerState self, IMP::display::Geometries const & objs)"""
1014  return _IMP_rmf.SaveOptimizerState_set_geometries_order(self, objs)
1015 
1016  def add_geometry(self, obj):
1017  r"""add_geometry(SaveOptimizerState self, Geometry obj) -> unsigned int"""
1018  return _IMP_rmf.SaveOptimizerState_add_geometry(self, obj)
1019 
1020  def add_geometries(self, objs):
1021  r"""add_geometries(SaveOptimizerState self, IMP::display::Geometries const & objs)"""
1022  return _IMP_rmf.SaveOptimizerState_add_geometries(self, objs)
1023 
1024  def clear_geometries(self):
1025  r"""clear_geometries(SaveOptimizerState self)"""
1026  return _IMP_rmf.SaveOptimizerState_clear_geometries(self)
1027 
1028  def get_number_of_geometries(self):
1029  r"""get_number_of_geometries(SaveOptimizerState self) -> unsigned int"""
1030  return _IMP_rmf.SaveOptimizerState_get_number_of_geometries(self)
1031 
1032  def get_has_geometries(self):
1033  r"""get_has_geometries(SaveOptimizerState self) -> bool"""
1034  return _IMP_rmf.SaveOptimizerState_get_has_geometries(self)
1035 
1036  def get_geometry(self, i):
1037  r"""get_geometry(SaveOptimizerState self, unsigned int i) -> Geometry"""
1038  return _IMP_rmf.SaveOptimizerState_get_geometry(self, i)
1039 
1040  def get_geometries(self):
1041  r"""get_geometries(SaveOptimizerState self) -> IMP::display::Geometries"""
1042  return _IMP_rmf.SaveOptimizerState_get_geometries(self)
1043 
1044  def erase_geometry(self, i):
1045  r"""erase_geometry(SaveOptimizerState self, unsigned int i)"""
1046  return _IMP_rmf.SaveOptimizerState_erase_geometry(self, i)
1047 
1048  def reserve_geometries(self, sz):
1049  r"""reserve_geometries(SaveOptimizerState self, unsigned int sz)"""
1050  return _IMP_rmf.SaveOptimizerState_reserve_geometries(self, sz)
1051 
1052  def set_simulator(self, sim):
1053  r"""set_simulator(SaveOptimizerState self, Simulator sim)"""
1054  return _IMP_rmf.SaveOptimizerState_set_simulator(self, sim)
1055 
1056  def update_always(self, *args):
1057  r"""
1058  update_always(SaveOptimizerState self, std::string name)
1059  update_always(SaveOptimizerState self)
1060  """
1061  return _IMP_rmf.SaveOptimizerState_update_always(self, *args)
1062 
1063  def do_update(self, call_num):
1064  r"""do_update(SaveOptimizerState self, unsigned int call_num)"""
1065  return _IMP_rmf.SaveOptimizerState_do_update(self, call_num)
1066 
1067  def get_version_info(self):
1068  r"""get_version_info(SaveOptimizerState self) -> VersionInfo"""
1069  return _IMP_rmf.SaveOptimizerState_get_version_info(self)
1070  __swig_destroy__ = _IMP_rmf.delete_SaveOptimizerState
1071 
1072  def __str__(self):
1073  r"""__str__(SaveOptimizerState self) -> std::string"""
1074  return _IMP_rmf.SaveOptimizerState___str__(self)
1075 
1076  def __repr__(self):
1077  r"""__repr__(SaveOptimizerState self) -> std::string"""
1078  return _IMP_rmf.SaveOptimizerState___repr__(self)
1079 
1080  @staticmethod
1081  def get_from(o):
1082  return _object_cast_to_SaveOptimizerState(o)
1083 
1084 
1085 # Register SaveOptimizerState in _IMP_rmf:
1086 _IMP_rmf.SaveOptimizerState_swigregister(SaveOptimizerState)
1087 
1088 def load_frame(file, frame):
1089  r"""load_frame(FileConstHandle file, FrameID frame)"""
1090  return _IMP_rmf.load_frame(file, frame)
1091 
1092 def save_frame(*args):
1093  r"""save_frame(FileHandle file, std::string name="") -> FrameID"""
1094  return _IMP_rmf.save_frame(*args)
1095 class _ParticleSaveLink(SaveLink):
1096  r"""Proxy of C++ IMP::rmf::SimpleSaveLink< IMP::Particle > class."""
1097 
1098  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1099 
1100  def __init__(self, *args, **kwargs):
1101  raise AttributeError("No constructor defined - class is abstract")
1102  __repr__ = _swig_repr
1103 
1104  def add(self, parent, os):
1105  r"""add(_ParticleSaveLink self, NodeHandle parent, IMP::Vector< Pointer< IMP::Particle > > const & os)"""
1106  return _IMP_rmf._ParticleSaveLink_add(self, parent, os)
1107  __swig_destroy__ = _IMP_rmf.delete__ParticleSaveLink
1108 
1109 # Register _ParticleSaveLink in _IMP_rmf:
1110 _IMP_rmf._ParticleSaveLink_swigregister(_ParticleSaveLink)
1111 class _ParticleLoadLink(LoadLink):
1112  r"""Proxy of C++ IMP::rmf::SimpleLoadLink< IMP::Particle > class."""
1113 
1114  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1115 
1116  def __init__(self, *args, **kwargs):
1117  raise AttributeError("No constructor defined - class is abstract")
1118  __repr__ = _swig_repr
1119 
1120  def create(self, *args):
1121  r"""
1122  create(_ParticleLoadLink self, NodeConstHandle rt) -> IMP::Vector< Pointer< IMP::Particle > >
1123  create(_ParticleLoadLink self, NodeConstHandle rt, Model m) -> IMP::Vector< Pointer< IMP::Particle > >
1124  """
1125  return _IMP_rmf._ParticleLoadLink_create(self, *args)
1126 
1127  def link(self, rt, ps):
1128  r"""link(_ParticleLoadLink self, NodeConstHandle rt, IMP::Vector< Pointer< IMP::Particle > > const & ps)"""
1129  return _IMP_rmf._ParticleLoadLink_link(self, rt, ps)
1130  __swig_destroy__ = _IMP_rmf.delete__ParticleLoadLink
1131 
1132 # Register _ParticleLoadLink in _IMP_rmf:
1133 _IMP_rmf._ParticleLoadLink_swigregister(_ParticleLoadLink)
1134 class HierarchyLoadLink(_ParticleLoadLink):
1135  r"""Proxy of C++ IMP::rmf::HierarchyLoadLink class."""
1136 
1137  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1138 
1139  def __init__(self, fh):
1140  r"""__init__(HierarchyLoadLink self, FileConstHandle fh) -> HierarchyLoadLink"""
1141  _IMP_rmf.HierarchyLoadLink_swiginit(self, _IMP_rmf.new_HierarchyLoadLink(fh))
1142 
1143  @staticmethod
1144  def get_name():
1145  r"""get_name() -> char const *"""
1146  return _IMP_rmf.HierarchyLoadLink_get_name()
1147 
1148  def get_version_info(self):
1149  r"""get_version_info(HierarchyLoadLink self) -> VersionInfo"""
1150  return _IMP_rmf.HierarchyLoadLink_get_version_info(self)
1151  __swig_destroy__ = _IMP_rmf.delete_HierarchyLoadLink
1152 
1153  def __str__(self):
1154  r"""__str__(HierarchyLoadLink self) -> std::string"""
1155  return _IMP_rmf.HierarchyLoadLink___str__(self)
1156 
1157  def __repr__(self):
1158  r"""__repr__(HierarchyLoadLink self) -> std::string"""
1159  return _IMP_rmf.HierarchyLoadLink___repr__(self)
1160 
1161  @staticmethod
1162  def get_from(o):
1163  return _object_cast_to_HierarchyLoadLink(o)
1164 
1165 
1166 # Register HierarchyLoadLink in _IMP_rmf:
1167 _IMP_rmf.HierarchyLoadLink_swigregister(HierarchyLoadLink)
1168 class HierarchySaveLink(_ParticleSaveLink):
1169  r"""Proxy of C++ IMP::rmf::HierarchySaveLink class."""
1170 
1171  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1172 
1173  def __init__(self, fh):
1174  r"""__init__(HierarchySaveLink self, FileHandle fh) -> HierarchySaveLink"""
1175  _IMP_rmf.HierarchySaveLink_swiginit(self, _IMP_rmf.new_HierarchySaveLink(fh))
1176 
1177  @staticmethod
1178  def get_name():
1179  r"""get_name() -> char const *"""
1180  return _IMP_rmf.HierarchySaveLink_get_name()
1181 
1182  def get_version_info(self):
1183  r"""get_version_info(HierarchySaveLink self) -> VersionInfo"""
1184  return _IMP_rmf.HierarchySaveLink_get_version_info(self)
1185  __swig_destroy__ = _IMP_rmf.delete_HierarchySaveLink
1186 
1187  def __str__(self):
1188  r"""__str__(HierarchySaveLink self) -> std::string"""
1189  return _IMP_rmf.HierarchySaveLink___str__(self)
1190 
1191  def __repr__(self):
1192  r"""__repr__(HierarchySaveLink self) -> std::string"""
1193  return _IMP_rmf.HierarchySaveLink___repr__(self)
1194 
1195  @staticmethod
1196  def get_from(o):
1197  return _object_cast_to_HierarchySaveLink(o)
1198 
1199 
1200 # Register HierarchySaveLink in _IMP_rmf:
1201 _IMP_rmf.HierarchySaveLink_swigregister(HierarchySaveLink)
1202 
1203 suffixes = [".rmf", ".rmfz"]
1204 
1205 
1206 def get_module_version():
1207  r"""get_module_version() -> std::string const"""
1208  return _IMP_rmf.get_module_version()
1209 
1210 def get_example_path(fname):
1211  r"""get_example_path(std::string fname) -> std::string"""
1212  return _IMP_rmf.get_example_path(fname)
1213 
1214 def get_data_path(fname):
1215  r"""get_data_path(std::string fname) -> std::string"""
1216  return _IMP_rmf.get_data_path(fname)
1217 
1218 from . import _version_check
1219 _version_check.check_version(get_module_version())
1220 __version__ = get_module_version()
1221 
1222 
void link_particles(RMF::FileConstHandle fh, const ParticlesTemp &hs)
display::Geometries create_geometries(RMF::FileConstHandle parent)
Create geometry objects for the geometry nodes found in the file.
ParticlesTemp create_particles(RMF::FileConstHandle fh, Model *m)
atom::Hierarchies create_hierarchies(RMF::FileConstHandle fh, Model *m)
RMF::FrameID save_frame(RMF::FileHandle file, std::string name="")
Save the current state of the linked objects as a new RMF frame.
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
Various classes to hold sets of particles.
void add_restraints_as_bonds(RMF::FileHandle fh, const Restraints &rs)
Add a list of restraints to the file as (static) bonds.
Make CGAL functionality available to IMP.
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
void link_restraints(RMF::FileConstHandle fh, const Restraints &hs)
void add_particle(RMF::FileHandle fh, Particle *hs)
void add_hierarchies(RMF::FileHandle fh, const atom::Hierarchies &hs)
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
void add_restraint(RMF::FileHandle fh, Restraint *hs)
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
std::string get_module_version()
Return the version of this module, as a string.
Common base class for heavy weight IMP objects.
Definition: Object.h:111
void add_restraints(RMF::FileHandle fh, const Restraints &hs)
void link_geometries(RMF::FileConstHandle parent, const display::GeometriesTemp &r)
Link the passed geometry objects to corresponding ones in the file.
Version and module information for Objects.
Definition: VersionInfo.h:29
Basic utilities for handling cryo-electron microscopy 3D density maps.
void load_frame(RMF::FileConstHandle file, RMF::FrameID frame)
Load the given RMF frame into the state of the linked objects.
Particle * get_particle() const
Returns the particle decorated by this decorator.
Definition: Decorator.h:194
void set_maximum_number_of_terms(RMF::FileHandle fh, unsigned int num)
Limit the number of restraint terms.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Restraints create_restraints(RMF::FileConstHandle fh, Model *m)
Shared optimizer state that is invoked upon commitment of new coordinates.
void link_hierarchies(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
void add_geometry(RMF::FileHandle file, display::Geometry *r)
Add a single geometry to the file.
void add_static_geometries(RMF::FileHandle parent, const display::GeometriesTemp &r)
Add geometries, assuming they do not move between frames.
void add_geometries(RMF::FileHandle file, const display::GeometriesTemp &r)
Add geometries to the file.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...