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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
rmf/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 2007-2020 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 as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_rmf')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_rmf')
25  _IMP_rmf = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_rmf', [dirname(__file__)])
34  except ImportError:
35  import _IMP_rmf
36  return _IMP_rmf
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_rmf', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_rmf = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_rmf
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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 __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_RMF_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_RMF_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_rmf.delete_IMP_RMF_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_RMF_SwigPyIterator self) -> PyObject *"""
126  return _IMP_rmf.IMP_RMF_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_RMF_SwigPyIterator self, size_t n=1) -> IMP_RMF_SwigPyIterator
132  incr(IMP_RMF_SwigPyIterator self) -> IMP_RMF_SwigPyIterator
133  """
134  return _IMP_rmf.IMP_RMF_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_RMF_SwigPyIterator self, size_t n=1) -> IMP_RMF_SwigPyIterator
140  decr(IMP_RMF_SwigPyIterator self) -> IMP_RMF_SwigPyIterator
141  """
142  return _IMP_rmf.IMP_RMF_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_rmf.IMP_RMF_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
152  return _IMP_rmf.IMP_RMF_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_RMF_SwigPyIterator self) -> IMP_RMF_SwigPyIterator"""
157  return _IMP_rmf.IMP_RMF_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_RMF_SwigPyIterator self) -> PyObject *"""
162  return _IMP_rmf.IMP_RMF_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_RMF_SwigPyIterator self) -> PyObject *"""
167  return _IMP_rmf.IMP_RMF_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_RMF_SwigPyIterator self) -> PyObject *"""
172  return _IMP_rmf.IMP_RMF_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
177  return _IMP_rmf.IMP_RMF_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
182  return _IMP_rmf.IMP_RMF_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> bool"""
187  return _IMP_rmf.IMP_RMF_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
192  return _IMP_rmf.IMP_RMF_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
197  return _IMP_rmf.IMP_RMF_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator"""
202  return _IMP_rmf.IMP_RMF_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_RMF_SwigPyIterator self, ptrdiff_t n) -> IMP_RMF_SwigPyIterator
208  __sub__(IMP_RMF_SwigPyIterator self, IMP_RMF_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_rmf.IMP_RMF_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_RMF_SwigPyIterator_swigregister = _IMP_rmf.IMP_RMF_SwigPyIterator_swigregister
215 IMP_RMF_SwigPyIterator_swigregister(IMP_RMF_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_rmf.IMP_DEBUG
224 IMP_RELEASE = _IMP_rmf.IMP_RELEASE
225 IMP_SILENT = _IMP_rmf.IMP_SILENT
226 IMP_PROGRESS = _IMP_rmf.IMP_PROGRESS
227 IMP_TERSE = _IMP_rmf.IMP_TERSE
228 IMP_VERBOSE = _IMP_rmf.IMP_VERBOSE
229 IMP_MEMORY = _IMP_rmf.IMP_MEMORY
230 IMP_NONE = _IMP_rmf.IMP_NONE
231 IMP_USAGE = _IMP_rmf.IMP_USAGE
232 IMP_INTERNAL = _IMP_rmf.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_rmf.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_rmf.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_rmf.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_rmf.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_rmf.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_rmf.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_rmf.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_rmf.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_rmf.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_rmf.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_rmf._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_rmf._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_rmf.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_rmf.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_rmf.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_rmf.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_rmf.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_rmf.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_rmf.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_rmf.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_rmf.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_rmf.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_rmf.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_rmf.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_rmf.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_rmf.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_rmf.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_rmf.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_rmf.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_rmf.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_rmf.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_rmf.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_rmf.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_rmf.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_rmf.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_rmf.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_rmf.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_rmf.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_rmf.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_rmf.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_rmf.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_rmf.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_rmf.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_rmf.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_rmf.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_rmf.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_rmf.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_rmf.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_rmf.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_rmf.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_rmf.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_rmf.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_rmf.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_rmf.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_rmf.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_rmf.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_rmf.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_rmf.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_rmf.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_rmf.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_rmf.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_rmf.IMP_CHAIN_TYPE_INDEX
380 import IMP.atom
381 IMP_EM_HAS_IMP_CGAL = _IMP_rmf.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_rmf.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_rmf.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_rmf.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_rmf.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_rmf.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_rmf.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_rmf.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_rmf.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_rmf.IMPEM_SHOW_WARNINGS
395 import IMP.em
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_rmf.IMP_SAXS_HAS_IMP_CGAL
397 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_rmf.IMP_SAXS_HAS_IMP_CONTAINER
398 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_rmf.IMP_SAXS_HAS_IMP_DISPLAY
399 IMP_SAXS_HAS_IMP_KERNEL = _IMP_rmf.IMP_SAXS_HAS_IMP_KERNEL
400 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
401 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_SAXS_HAS_BOOST_FILESYSTEM
402 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
403 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_rmf.IMP_SAXS_HAS_BOOST_RANDOM
404 IMP_SAXS_HAS_BOOST_REGEX = _IMP_rmf.IMP_SAXS_HAS_BOOST_REGEX
405 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_SAXS_HAS_BOOST_SYSTEM
406 IMP_SAXS_HAS_CGAL = _IMP_rmf.IMP_SAXS_HAS_CGAL
407 IMP_SAXS_HAS_HDF5 = _IMP_rmf.IMP_SAXS_HAS_HDF5
408 IMP_SAXS_HAS_NUMPY = _IMP_rmf.IMP_SAXS_HAS_NUMPY
409 IMP_SAXS_HAS_PYTHON_IHM = _IMP_rmf.IMP_SAXS_HAS_PYTHON_IHM
410 IMPSAXS_SHOW_WARNINGS = _IMP_rmf.IMPSAXS_SHOW_WARNINGS
411 import IMP.saxs
412 IMP_ISD_HAS_IMP_CGAL = _IMP_rmf.IMP_ISD_HAS_IMP_CGAL
413 IMP_ISD_HAS_IMP_DISPLAY = _IMP_rmf.IMP_ISD_HAS_IMP_DISPLAY
414 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
415 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_ISD_HAS_BOOST_FILESYSTEM
416 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
417 IMP_ISD_HAS_BOOST_RANDOM = _IMP_rmf.IMP_ISD_HAS_BOOST_RANDOM
418 IMP_ISD_HAS_BOOST_REGEX = _IMP_rmf.IMP_ISD_HAS_BOOST_REGEX
419 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_ISD_HAS_BOOST_SYSTEM
420 IMP_ISD_HAS_CGAL = _IMP_rmf.IMP_ISD_HAS_CGAL
421 IMP_ISD_HAS_HDF5 = _IMP_rmf.IMP_ISD_HAS_HDF5
422 IMP_ISD_HAS_NUMPY = _IMP_rmf.IMP_ISD_HAS_NUMPY
423 IMP_ISD_HAS_PYTHON_IHM = _IMP_rmf.IMP_ISD_HAS_PYTHON_IHM
424 IMPISD_SHOW_WARNINGS = _IMP_rmf.IMPISD_SHOW_WARNINGS
425 import IMP.isd
426 IMP_RMF_HAS_IMP_CGAL = _IMP_rmf.IMP_RMF_HAS_IMP_CGAL
427 IMP_RMF_HAS_IMP_EM = _IMP_rmf.IMP_RMF_HAS_IMP_EM
428 IMP_RMF_HAS_IMP_SAXS = _IMP_rmf.IMP_RMF_HAS_IMP_SAXS
429 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_rmf.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
430 IMP_RMF_HAS_IMP_STATISTICS = _IMP_rmf.IMP_RMF_HAS_IMP_STATISTICS
431 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_rmf.IMP_RMF_HAS_BOOST_FILESYSTEM
432 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_rmf.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
433 IMP_RMF_HAS_BOOST_RANDOM = _IMP_rmf.IMP_RMF_HAS_BOOST_RANDOM
434 IMP_RMF_HAS_BOOST_REGEX = _IMP_rmf.IMP_RMF_HAS_BOOST_REGEX
435 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_rmf.IMP_RMF_HAS_BOOST_SYSTEM
436 IMP_RMF_HAS_CGAL = _IMP_rmf.IMP_RMF_HAS_CGAL
437 IMP_RMF_HAS_HDF5 = _IMP_rmf.IMP_RMF_HAS_HDF5
438 IMP_RMF_HAS_NUMPY = _IMP_rmf.IMP_RMF_HAS_NUMPY
439 IMP_RMF_HAS_PYTHON_IHM = _IMP_rmf.IMP_RMF_HAS_PYTHON_IHM
440 IMPRMF_SHOW_WARNINGS = _IMP_rmf.IMPRMF_SHOW_WARNINGS
441 import RMF
442 
443 _object_types.append("SaveOptimizerState")
444 
445 
446 def _object_cast_to_SaveOptimizerState(o):
447  """_object_cast_to_SaveOptimizerState(Object o) -> SaveOptimizerState"""
448  return _IMP_rmf._object_cast_to_SaveOptimizerState(o)
449 
450 _object_types.append("LoadLink")
451 
452 
453 def _object_cast_to_LoadLink(o):
454  """_object_cast_to_LoadLink(Object o) -> LoadLink"""
455  return _IMP_rmf._object_cast_to_LoadLink(o)
456 
457 _object_types.append("SaveLink")
458 
459 
460 def _object_cast_to_SaveLink(o):
461  """_object_cast_to_SaveLink(Object o) -> SaveLink"""
462  return _IMP_rmf._object_cast_to_SaveLink(o)
463 
464 _object_types.append("HierarchySaveLink")
465 
466 
467 def _object_cast_to_HierarchySaveLink(o):
468  """_object_cast_to_HierarchySaveLink(Object o) -> HierarchySaveLink"""
469  return _IMP_rmf._object_cast_to_HierarchySaveLink(o)
470 
471 _object_types.append("HierarchyLoadLink")
472 
473 
474 def _object_cast_to_HierarchyLoadLink(o):
475  """_object_cast_to_HierarchyLoadLink(Object o) -> HierarchyLoadLink"""
476  return _IMP_rmf._object_cast_to_HierarchyLoadLink(o)
477 class LoadLink(IMP.Object):
478  """Proxy of C++ IMP::rmf::LoadLink class."""
479 
480  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
481 
482  def do_load(self, fh):
483  """do_load(LoadLink self, FileConstHandle fh)"""
484  return _IMP_rmf.LoadLink_do_load(self, fh)
485 
486 
487  def __init__(self, name):
488  """__init__(IMP::rmf::LoadLink self, std::string name) -> LoadLink"""
489  if self.__class__ == LoadLink:
490  _self = None
491  else:
492  _self = self
493  this = _IMP_rmf.new_LoadLink(_self, name)
494  try:
495  self.this.append(this)
496  except __builtin__.Exception:
497  self.this = this
498 
499  if self.__class__ != LoadLink:
500  _director_objects.register(self)
501 
502 
503 
504 
505  def load(self, fh):
506  """load(LoadLink self, FileConstHandle fh)"""
507  return _IMP_rmf.LoadLink_load(self, fh)
508 
509  __swig_destroy__ = _IMP_rmf.delete_LoadLink
510  __del__ = lambda self: None
511 
512  def __str__(self):
513  """__str__(LoadLink self) -> std::string"""
514  return _IMP_rmf.LoadLink___str__(self)
515 
516 
517  def __repr__(self):
518  """__repr__(LoadLink self) -> std::string"""
519  return _IMP_rmf.LoadLink___repr__(self)
520 
521 
522  @staticmethod
523  def get_from(o):
524  return _object_cast_to_LoadLink(o)
525 
526 
527  def get_type_name(self):
528  return self.__class__.__name__
529  def do_show(self, out):
530  pass
531  def get_version_info(self):
532  if"IMP::rmf" == "IMP":
533  return VersionInfo(self.__module__,
534  __import__(self.__module__).get_module_version())
535  else:
536  return IMP.VersionInfo(self.__module__,
537  __import__(self.__module__).get_module_version())
538  @staticmethod
539  def get_from(o):
540  return _object_cast_to_LoadLink(o)
541 
542  def __disown__(self):
543  self.this.disown()
544  _IMP_rmf.disown_LoadLink(self)
545  return weakref_proxy(self)
546 
547  def do_destroy(self):
548  """do_destroy(LoadLink self)"""
549  return _IMP_rmf.LoadLink_do_destroy(self)
550 
551 LoadLink_swigregister = _IMP_rmf.LoadLink_swigregister
552 LoadLink_swigregister(LoadLink)
553 
554 class SaveLink(IMP.Object):
555  """Proxy of C++ IMP::rmf::SaveLink class."""
556 
557  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
558 
559  def do_save(self, hf):
560  """do_save(SaveLink self, FileHandle hf)"""
561  return _IMP_rmf.SaveLink_do_save(self, hf)
562 
563 
564  def __init__(self, name):
565  """__init__(IMP::rmf::SaveLink self, std::string name) -> SaveLink"""
566  if self.__class__ == SaveLink:
567  _self = None
568  else:
569  _self = self
570  this = _IMP_rmf.new_SaveLink(_self, name)
571  try:
572  self.this.append(this)
573  except __builtin__.Exception:
574  self.this = this
575 
576  if self.__class__ != SaveLink:
577  _director_objects.register(self)
578 
579 
580 
581 
582  def save(self, fh):
583  """save(SaveLink self, FileHandle fh)"""
584  return _IMP_rmf.SaveLink_save(self, fh)
585 
586  __swig_destroy__ = _IMP_rmf.delete_SaveLink
587  __del__ = lambda self: None
588 
589  def __str__(self):
590  """__str__(SaveLink self) -> std::string"""
591  return _IMP_rmf.SaveLink___str__(self)
592 
593 
594  def __repr__(self):
595  """__repr__(SaveLink self) -> std::string"""
596  return _IMP_rmf.SaveLink___repr__(self)
597 
598 
599  @staticmethod
600  def get_from(o):
601  return _object_cast_to_SaveLink(o)
602 
603 
604  def get_type_name(self):
605  return self.__class__.__name__
606  def do_show(self, out):
607  pass
608  def get_version_info(self):
609  if"IMP::rmf" == "IMP":
610  return VersionInfo(self.__module__,
611  __import__(self.__module__).get_module_version())
612  else:
613  return IMP.VersionInfo(self.__module__,
614  __import__(self.__module__).get_module_version())
615  @staticmethod
616  def get_from(o):
617  return _object_cast_to_SaveLink(o)
618 
619  def __disown__(self):
620  self.this.disown()
621  _IMP_rmf.disown_SaveLink(self)
622  return weakref_proxy(self)
623 
624  def do_destroy(self):
625  """do_destroy(SaveLink self)"""
626  return _IMP_rmf.SaveLink_do_destroy(self)
627 
628 SaveLink_swigregister = _IMP_rmf.SaveLink_swigregister
629 SaveLink_swigregister(SaveLink)
630 
631 
632 def add_hierarchies(*args):
633  """
634  add_hierarchies(FileHandle fh, IMP::atom::Hierarchies const & hs)
635  add_hierarchies(NodeHandle fh, IMP::atom::Hierarchies const & hs)
636  """
637  return _IMP_rmf.add_hierarchies(*args)
638 
639 def add_hierarchy(fh, hs):
640  """add_hierarchy(FileHandle fh, Hierarchy hs)"""
641  return _IMP_rmf.add_hierarchy(fh, hs)
642 
643 def create_hierarchies(fh, m):
644  """create_hierarchies(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
645  return _IMP_rmf.create_hierarchies(fh, m)
646 
647 def link_hierarchies(fh, hs):
648  """link_hierarchies(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
649  return _IMP_rmf.link_hierarchies(fh, hs)
650 
651 def add_restraints(*args):
652  """
653  add_restraints(FileHandle fh, IMP::Restraints const & hs)
654  add_restraints(NodeHandle fh, IMP::Restraints const & hs)
655  """
656  return _IMP_rmf.add_restraints(*args)
657 
658 def add_restraint(fh, hs):
659  """add_restraint(FileHandle fh, Restraint hs)"""
660  return _IMP_rmf.add_restraint(fh, hs)
661 
662 def create_restraints(fh, m):
663  """create_restraints(FileConstHandle fh, Model m) -> IMP::Restraints"""
664  return _IMP_rmf.create_restraints(fh, m)
665 
666 def link_restraints(fh, hs):
667  """link_restraints(FileConstHandle fh, IMP::Restraints const & hs)"""
668  return _IMP_rmf.link_restraints(fh, hs)
669 
670 def add_restraints_as_bonds(fh, rs):
671  """add_restraints_as_bonds(FileHandle fh, IMP::Restraints const & rs)"""
672  return _IMP_rmf.add_restraints_as_bonds(fh, rs)
673 
674 def set_maximum_number_of_terms(fh, num):
675  """set_maximum_number_of_terms(FileHandle fh, unsigned int num)"""
676  return _IMP_rmf.set_maximum_number_of_terms(fh, num)
677 
678 def add_particles(*args):
679  """
680  add_particles(FileHandle fh, IMP::ParticlesTemp const & hs)
681  add_particles(NodeHandle fh, IMP::ParticlesTemp const & hs)
682  """
683  return _IMP_rmf.add_particles(*args)
684 
685 def add_particle(fh, hs):
686  """add_particle(FileHandle fh, Particle hs)"""
687  return _IMP_rmf.add_particle(fh, hs)
688 
689 def create_particles(fh, m):
690  """create_particles(FileConstHandle fh, Model m) -> IMP::ParticlesTemp"""
691  return _IMP_rmf.create_particles(fh, m)
692 
693 def link_particles(fh, hs):
694  """link_particles(FileConstHandle fh, IMP::ParticlesTemp const & hs)"""
695  return _IMP_rmf.link_particles(fh, hs)
696 
697 def add_geometries(*args):
698  """
699  add_geometries(FileHandle file, IMP::display::GeometriesTemp const & r)
700  add_geometries(NodeHandle parent, IMP::display::GeometriesTemp const & r)
701  """
702  return _IMP_rmf.add_geometries(*args)
703 
704 def add_static_geometries(parent, r):
705  """add_static_geometries(FileHandle parent, IMP::display::GeometriesTemp const & r)"""
706  return _IMP_rmf.add_static_geometries(parent, r)
707 
708 def add_geometry(file, r):
709  """add_geometry(FileHandle file, Geometry r)"""
710  return _IMP_rmf.add_geometry(file, r)
711 
712 def create_geometries(parent):
713  """create_geometries(FileConstHandle parent) -> IMP::display::Geometries"""
714  return _IMP_rmf.create_geometries(parent)
715 
716 def link_geometries(parent, r):
717  """link_geometries(FileConstHandle parent, IMP::display::GeometriesTemp const & r)"""
718  return _IMP_rmf.link_geometries(parent, r)
719 
720 def set_association(nh, o, overwrite=False):
721  """
722  set_association(NodeConstHandle nh, Object o, bool overwrite=False)
723  set_association(NodeConstHandle nh, Object o)
724  """
725  return _IMP_rmf.set_association(nh, o, overwrite)
726 
727 def get_node_from_association(*args):
728  """
729  get_node_from_association(FileConstHandle nh, Object oi) -> NodeConstHandle
730  get_node_from_association(FileHandle nh, Object oi) -> NodeHandle
731  """
732  return _IMP_rmf.get_node_from_association(*args)
733 
734 def get_has_associated_node(nh, oi):
735  """get_has_associated_node(FileConstHandle nh, Object oi) -> bool"""
736  return _IMP_rmf.get_has_associated_node(nh, oi)
737 class SaveOptimizerState(IMP.OptimizerState):
738  """Proxy of C++ IMP::rmf::SaveOptimizerState class."""
739 
740  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
741 
742  def __init__(self, m, fh):
743  """__init__(IMP::rmf::SaveOptimizerState self, Model m, FileHandle fh) -> SaveOptimizerState"""
744  this = _IMP_rmf.new_SaveOptimizerState(m, fh)
745  try:
746  self.this.append(this)
747  except __builtin__.Exception:
748  self.this = this
749 
750  def remove_hierarchy(self, d):
751  """remove_hierarchy(SaveOptimizerState self, Particle d)"""
752  return _IMP_rmf.SaveOptimizerState_remove_hierarchy(self, d)
753 
754 
755  def remove_hierarchies(self, d):
756  """remove_hierarchies(SaveOptimizerState self, IMP::Particles const & d)"""
757  return _IMP_rmf.SaveOptimizerState_remove_hierarchies(self, d)
758 
759 
760  def set_hierarchies(self, ps):
761  """set_hierarchies(SaveOptimizerState self, IMP::Particles const & ps)"""
762  return _IMP_rmf.SaveOptimizerState_set_hierarchies(self, ps)
763 
764 
765  def set_hierarchies_order(self, objs):
766  """set_hierarchies_order(SaveOptimizerState self, IMP::Particles const & objs)"""
767  return _IMP_rmf.SaveOptimizerState_set_hierarchies_order(self, objs)
768 
769 
770  def add_hierarchy(self, obj):
771  """add_hierarchy(SaveOptimizerState self, Particle obj) -> unsigned int"""
772  return _IMP_rmf.SaveOptimizerState_add_hierarchy(self, obj)
773 
774 
775  def add_hierarchies(self, objs):
776  """add_hierarchies(SaveOptimizerState self, IMP::Particles const & objs)"""
777  return _IMP_rmf.SaveOptimizerState_add_hierarchies(self, objs)
778 
779 
780  def clear_hierarchies(self):
781  """clear_hierarchies(SaveOptimizerState self)"""
782  return _IMP_rmf.SaveOptimizerState_clear_hierarchies(self)
783 
784 
785  def get_number_of_hierarchies(self):
786  """get_number_of_hierarchies(SaveOptimizerState self) -> unsigned int"""
787  return _IMP_rmf.SaveOptimizerState_get_number_of_hierarchies(self)
788 
789 
790  def get_has_hierarchies(self):
791  """get_has_hierarchies(SaveOptimizerState self) -> bool"""
792  return _IMP_rmf.SaveOptimizerState_get_has_hierarchies(self)
793 
794 
795  def get_hierarchy(self, i):
796  """get_hierarchy(SaveOptimizerState self, unsigned int i) -> Particle"""
797  return _IMP_rmf.SaveOptimizerState_get_hierarchy(self, i)
798 
799 
800  def get_hierarchies(self):
801  """get_hierarchies(SaveOptimizerState self) -> IMP::Particles"""
802  return _IMP_rmf.SaveOptimizerState_get_hierarchies(self)
803 
804 
805  def reserve_hierarchies(self, sz):
806  """reserve_hierarchies(SaveOptimizerState self, unsigned int sz)"""
807  return _IMP_rmf.SaveOptimizerState_reserve_hierarchies(self, sz)
808 
809 
810  def remove_restraint(self, d):
811  """remove_restraint(SaveOptimizerState self, Restraint d)"""
812  return _IMP_rmf.SaveOptimizerState_remove_restraint(self, d)
813 
814 
815  def remove_restraints(self, d):
816  """remove_restraints(SaveOptimizerState self, IMP::Restraints const & d)"""
817  return _IMP_rmf.SaveOptimizerState_remove_restraints(self, d)
818 
819 
820  def set_restraints(self, ps):
821  """set_restraints(SaveOptimizerState self, IMP::Restraints const & ps)"""
822  return _IMP_rmf.SaveOptimizerState_set_restraints(self, ps)
823 
824 
825  def set_restraints_order(self, objs):
826  """set_restraints_order(SaveOptimizerState self, IMP::Restraints const & objs)"""
827  return _IMP_rmf.SaveOptimizerState_set_restraints_order(self, objs)
828 
829 
830  def add_restraint(self, obj):
831  """add_restraint(SaveOptimizerState self, Restraint obj) -> unsigned int"""
832  return _IMP_rmf.SaveOptimizerState_add_restraint(self, obj)
833 
834 
835  def add_restraints(self, objs):
836  """add_restraints(SaveOptimizerState self, IMP::Restraints const & objs)"""
837  return _IMP_rmf.SaveOptimizerState_add_restraints(self, objs)
838 
839 
840  def clear_restraints(self):
841  """clear_restraints(SaveOptimizerState self)"""
842  return _IMP_rmf.SaveOptimizerState_clear_restraints(self)
843 
844 
845  def get_number_of_restraints(self):
846  """get_number_of_restraints(SaveOptimizerState self) -> unsigned int"""
847  return _IMP_rmf.SaveOptimizerState_get_number_of_restraints(self)
848 
849 
850  def get_has_restraints(self):
851  """get_has_restraints(SaveOptimizerState self) -> bool"""
852  return _IMP_rmf.SaveOptimizerState_get_has_restraints(self)
853 
854 
855  def get_restraint(self, i):
856  """get_restraint(SaveOptimizerState self, unsigned int i) -> Restraint"""
857  return _IMP_rmf.SaveOptimizerState_get_restraint(self, i)
858 
859 
860  def get_restraints(self):
861  """get_restraints(SaveOptimizerState self) -> IMP::Restraints"""
862  return _IMP_rmf.SaveOptimizerState_get_restraints(self)
863 
864 
865  def reserve_restraints(self, sz):
866  """reserve_restraints(SaveOptimizerState self, unsigned int sz)"""
867  return _IMP_rmf.SaveOptimizerState_reserve_restraints(self, sz)
868 
869 
870  def remove_particle(self, d):
871  """remove_particle(SaveOptimizerState self, Particle d)"""
872  return _IMP_rmf.SaveOptimizerState_remove_particle(self, d)
873 
874 
875  def remove_particles(self, d):
876  """remove_particles(SaveOptimizerState self, IMP::Particles const & d)"""
877  return _IMP_rmf.SaveOptimizerState_remove_particles(self, d)
878 
879 
880  def set_particles(self, ps):
881  """set_particles(SaveOptimizerState self, IMP::Particles const & ps)"""
882  return _IMP_rmf.SaveOptimizerState_set_particles(self, ps)
883 
884 
885  def set_particles_order(self, objs):
886  """set_particles_order(SaveOptimizerState self, IMP::Particles const & objs)"""
887  return _IMP_rmf.SaveOptimizerState_set_particles_order(self, objs)
888 
889 
890  def add_particle(self, obj):
891  """add_particle(SaveOptimizerState self, Particle obj) -> unsigned int"""
892  return _IMP_rmf.SaveOptimizerState_add_particle(self, obj)
893 
894 
895  def add_particles(self, objs):
896  """add_particles(SaveOptimizerState self, IMP::Particles const & objs)"""
897  return _IMP_rmf.SaveOptimizerState_add_particles(self, objs)
898 
899 
900  def clear_particles(self):
901  """clear_particles(SaveOptimizerState self)"""
902  return _IMP_rmf.SaveOptimizerState_clear_particles(self)
903 
904 
905  def get_number_of_particles(self):
906  """get_number_of_particles(SaveOptimizerState self) -> unsigned int"""
907  return _IMP_rmf.SaveOptimizerState_get_number_of_particles(self)
908 
909 
910  def get_has_particles(self):
911  """get_has_particles(SaveOptimizerState self) -> bool"""
912  return _IMP_rmf.SaveOptimizerState_get_has_particles(self)
913 
914 
915  def get_particle(self, i):
916  """get_particle(SaveOptimizerState self, unsigned int i) -> Particle"""
917  return _IMP_rmf.SaveOptimizerState_get_particle(self, i)
918 
919 
920  def get_particles(self):
921  """get_particles(SaveOptimizerState self) -> IMP::Particles"""
922  return _IMP_rmf.SaveOptimizerState_get_particles(self)
923 
924 
925  def reserve_particles(self, sz):
926  """reserve_particles(SaveOptimizerState self, unsigned int sz)"""
927  return _IMP_rmf.SaveOptimizerState_reserve_particles(self, sz)
928 
929 
930  def remove_geometry(self, d):
931  """remove_geometry(SaveOptimizerState self, Geometry d)"""
932  return _IMP_rmf.SaveOptimizerState_remove_geometry(self, d)
933 
934 
935  def remove_geometries(self, d):
936  """remove_geometries(SaveOptimizerState self, IMP::display::Geometries const & d)"""
937  return _IMP_rmf.SaveOptimizerState_remove_geometries(self, d)
938 
939 
940  def set_geometries(self, ps):
941  """set_geometries(SaveOptimizerState self, IMP::display::Geometries const & ps)"""
942  return _IMP_rmf.SaveOptimizerState_set_geometries(self, ps)
943 
944 
945  def set_geometries_order(self, objs):
946  """set_geometries_order(SaveOptimizerState self, IMP::display::Geometries const & objs)"""
947  return _IMP_rmf.SaveOptimizerState_set_geometries_order(self, objs)
948 
949 
950  def add_geometry(self, obj):
951  """add_geometry(SaveOptimizerState self, Geometry obj) -> unsigned int"""
952  return _IMP_rmf.SaveOptimizerState_add_geometry(self, obj)
953 
954 
955  def add_geometries(self, objs):
956  """add_geometries(SaveOptimizerState self, IMP::display::Geometries const & objs)"""
957  return _IMP_rmf.SaveOptimizerState_add_geometries(self, objs)
958 
959 
960  def clear_geometries(self):
961  """clear_geometries(SaveOptimizerState self)"""
962  return _IMP_rmf.SaveOptimizerState_clear_geometries(self)
963 
964 
965  def get_number_of_geometries(self):
966  """get_number_of_geometries(SaveOptimizerState self) -> unsigned int"""
967  return _IMP_rmf.SaveOptimizerState_get_number_of_geometries(self)
968 
969 
970  def get_has_geometries(self):
971  """get_has_geometries(SaveOptimizerState self) -> bool"""
972  return _IMP_rmf.SaveOptimizerState_get_has_geometries(self)
973 
974 
975  def get_geometry(self, i):
976  """get_geometry(SaveOptimizerState self, unsigned int i) -> Geometry"""
977  return _IMP_rmf.SaveOptimizerState_get_geometry(self, i)
978 
979 
980  def get_geometries(self):
981  """get_geometries(SaveOptimizerState self) -> IMP::display::Geometries"""
982  return _IMP_rmf.SaveOptimizerState_get_geometries(self)
983 
984 
985  def reserve_geometries(self, sz):
986  """reserve_geometries(SaveOptimizerState self, unsigned int sz)"""
987  return _IMP_rmf.SaveOptimizerState_reserve_geometries(self, sz)
988 
989 
990  def set_simulator(self, sim):
991  """set_simulator(SaveOptimizerState self, Simulator sim)"""
992  return _IMP_rmf.SaveOptimizerState_set_simulator(self, sim)
993 
994 
995  def update_always(self, *args):
996  """
997  update_always(SaveOptimizerState self, std::string name)
998  update_always(SaveOptimizerState self)
999  """
1000  return _IMP_rmf.SaveOptimizerState_update_always(self, *args)
1001 
1002 
1003  def do_update(self, call_num):
1004  """do_update(SaveOptimizerState self, unsigned int call_num)"""
1005  return _IMP_rmf.SaveOptimizerState_do_update(self, call_num)
1006 
1007 
1008  def get_version_info(self):
1009  """get_version_info(SaveOptimizerState self) -> VersionInfo"""
1010  return _IMP_rmf.SaveOptimizerState_get_version_info(self)
1011 
1012 
1013  def __str__(self):
1014  """__str__(SaveOptimizerState self) -> std::string"""
1015  return _IMP_rmf.SaveOptimizerState___str__(self)
1016 
1017 
1018  def __repr__(self):
1019  """__repr__(SaveOptimizerState self) -> std::string"""
1020  return _IMP_rmf.SaveOptimizerState___repr__(self)
1021 
1022 
1023  @staticmethod
1024  def get_from(o):
1025  return _object_cast_to_SaveOptimizerState(o)
1026 
1027 SaveOptimizerState_swigregister = _IMP_rmf.SaveOptimizerState_swigregister
1028 SaveOptimizerState_swigregister(SaveOptimizerState)
1029 
1030 
1031 def load_frame(file, frame):
1032  """load_frame(FileConstHandle file, FrameID frame)"""
1033  return _IMP_rmf.load_frame(file, frame)
1034 
1035 def save_frame(*args):
1036  """
1037  save_frame(FileHandle file, std::string name) -> FrameID
1038  save_frame(FileHandle file) -> FrameID
1039  """
1040  return _IMP_rmf.save_frame(*args)
1041 class _ParticleSaveLink(SaveLink):
1042  """Proxy of C++ IMP::rmf::SimpleSaveLink<(IMP::Particle)> class."""
1043 
1044  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1045 
1046  def __init__(self, *args, **kwargs):
1047  raise AttributeError("No constructor defined - class is abstract")
1048  __repr__ = _swig_repr
1049 
1050  def add(self, parent, os):
1051  """add(_ParticleSaveLink self, NodeHandle parent, IMP::Vector< Pointer< IMP::Particle > > const & os)"""
1052  return _IMP_rmf._ParticleSaveLink_add(self, parent, os)
1053 
1054  __swig_destroy__ = _IMP_rmf.delete__ParticleSaveLink
1055  __del__ = lambda self: None
1056 _ParticleSaveLink_swigregister = _IMP_rmf._ParticleSaveLink_swigregister
1057 _ParticleSaveLink_swigregister(_ParticleSaveLink)
1058 
1059 class _ParticleLoadLink(LoadLink):
1060  """Proxy of C++ IMP::rmf::SimpleLoadLink<(IMP::Particle)> class."""
1061 
1062  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1063 
1064  def __init__(self, *args, **kwargs):
1065  raise AttributeError("No constructor defined - class is abstract")
1066  __repr__ = _swig_repr
1067 
1068  def create(self, *args):
1069  """
1070  create(_ParticleLoadLink self, NodeConstHandle rt) -> IMP::Vector< Pointer< IMP::Particle > >
1071  create(_ParticleLoadLink self, NodeConstHandle rt, Model m) -> IMP::Vector< Pointer< IMP::Particle > >
1072  """
1073  return _IMP_rmf._ParticleLoadLink_create(self, *args)
1074 
1075 
1076  def link(self, rt, ps):
1077  """link(_ParticleLoadLink self, NodeConstHandle rt, IMP::Vector< Pointer< IMP::Particle > > const & ps)"""
1078  return _IMP_rmf._ParticleLoadLink_link(self, rt, ps)
1079 
1080  __swig_destroy__ = _IMP_rmf.delete__ParticleLoadLink
1081  __del__ = lambda self: None
1082 _ParticleLoadLink_swigregister = _IMP_rmf._ParticleLoadLink_swigregister
1083 _ParticleLoadLink_swigregister(_ParticleLoadLink)
1084 
1085 class HierarchyLoadLink(_ParticleLoadLink):
1086  """Proxy of C++ IMP::rmf::HierarchyLoadLink class."""
1087 
1088  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1089 
1090  def __init__(self, fh):
1091  """__init__(IMP::rmf::HierarchyLoadLink self, FileConstHandle fh) -> HierarchyLoadLink"""
1092  this = _IMP_rmf.new_HierarchyLoadLink(fh)
1093  try:
1094  self.this.append(this)
1095  except __builtin__.Exception:
1096  self.this = this
1097 
1098  def get_name():
1099  """get_name() -> char const *"""
1100  return _IMP_rmf.HierarchyLoadLink_get_name()
1101 
1102  get_name = staticmethod(get_name)
1103 
1104  def get_version_info(self):
1105  """get_version_info(HierarchyLoadLink self) -> VersionInfo"""
1106  return _IMP_rmf.HierarchyLoadLink_get_version_info(self)
1107 
1108 
1109  def __str__(self):
1110  """__str__(HierarchyLoadLink self) -> std::string"""
1111  return _IMP_rmf.HierarchyLoadLink___str__(self)
1112 
1113 
1114  def __repr__(self):
1115  """__repr__(HierarchyLoadLink self) -> std::string"""
1116  return _IMP_rmf.HierarchyLoadLink___repr__(self)
1117 
1118 
1119  @staticmethod
1120  def get_from(o):
1121  return _object_cast_to_HierarchyLoadLink(o)
1122 
1123 HierarchyLoadLink_swigregister = _IMP_rmf.HierarchyLoadLink_swigregister
1124 HierarchyLoadLink_swigregister(HierarchyLoadLink)
1125 
1126 def HierarchyLoadLink_get_name():
1127  """HierarchyLoadLink_get_name() -> char const *"""
1128  return _IMP_rmf.HierarchyLoadLink_get_name()
1129 
1130 class HierarchySaveLink(_ParticleSaveLink):
1131  """Proxy of C++ IMP::rmf::HierarchySaveLink class."""
1132 
1133  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1134 
1135  def __init__(self, fh):
1136  """__init__(IMP::rmf::HierarchySaveLink self, FileHandle fh) -> HierarchySaveLink"""
1137  this = _IMP_rmf.new_HierarchySaveLink(fh)
1138  try:
1139  self.this.append(this)
1140  except __builtin__.Exception:
1141  self.this = this
1142 
1143  def get_name():
1144  """get_name() -> char const *"""
1145  return _IMP_rmf.HierarchySaveLink_get_name()
1146 
1147  get_name = staticmethod(get_name)
1148 
1149  def get_version_info(self):
1150  """get_version_info(HierarchySaveLink self) -> VersionInfo"""
1151  return _IMP_rmf.HierarchySaveLink_get_version_info(self)
1152 
1153 
1154  def __str__(self):
1155  """__str__(HierarchySaveLink self) -> std::string"""
1156  return _IMP_rmf.HierarchySaveLink___str__(self)
1157 
1158 
1159  def __repr__(self):
1160  """__repr__(HierarchySaveLink self) -> std::string"""
1161  return _IMP_rmf.HierarchySaveLink___repr__(self)
1162 
1163 
1164  @staticmethod
1165  def get_from(o):
1166  return _object_cast_to_HierarchySaveLink(o)
1167 
1168 HierarchySaveLink_swigregister = _IMP_rmf.HierarchySaveLink_swigregister
1169 HierarchySaveLink_swigregister(HierarchySaveLink)
1170 
1171 def HierarchySaveLink_get_name():
1172  """HierarchySaveLink_get_name() -> char const *"""
1173  return _IMP_rmf.HierarchySaveLink_get_name()
1174 
1175 
1176 suffixes = [".rmf", ".rmfz"]
1177 
1178 
1179 def get_module_version():
1180  """get_module_version() -> std::string const"""
1181  return _IMP_rmf.get_module_version()
1182 
1183 def get_example_path(fname):
1184  """get_example_path(std::string fname) -> std::string"""
1185  return _IMP_rmf.get_example_path(fname)
1186 
1187 def get_data_path(fname):
1188  """get_data_path(std::string fname) -> std::string"""
1189  return _IMP_rmf.get_data_path(fname)
1190 
1191 from . import _version_check
1192 _version_check.check_version(get_module_version())
1193 __version__ = get_module_version()
1194 
1195 
1196 
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)
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:106
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:28
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:171
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 ...