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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
bayesianem/__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_bayesianem
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_BAYESIANEM_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_BAYESIANEM_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_bayesianem.delete_IMP_BAYESIANEM_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
79  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_BAYESIANEM_SwigPyIterator self, size_t n=1) -> IMP_BAYESIANEM_SwigPyIterator"""
83  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_BAYESIANEM_SwigPyIterator self, size_t n=1) -> IMP_BAYESIANEM_SwigPyIterator"""
87  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
95  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_BAYESIANEM_SwigPyIterator self) -> IMP_BAYESIANEM_SwigPyIterator"""
99  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
103  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
107  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
111  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
115  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
119  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
123  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
127  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
131  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
135  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator
140  __sub__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_BAYESIANEM_SwigPyIterator in _IMP_bayesianem:
147 _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_swigregister(IMP_BAYESIANEM_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_bayesianem.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_bayesianem.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_bayesianem.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_bayesianem.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_bayesianem.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_bayesianem.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_bayesianem.IMP_MEMORY
167 
168 IMP_NONE = _IMP_bayesianem.IMP_NONE
169 
170 IMP_USAGE = _IMP_bayesianem.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_bayesianem.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_bayesianem.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_bayesianem.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_bayesianem.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_bayesianem.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_bayesianem.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_bayesianem.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_bayesianem.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_bayesianem.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_bayesianem.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_bayesianem.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_bayesianem._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_bayesianem:
237 _IMP_bayesianem._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_bayesianem.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_bayesianem.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_bayesianem.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_bayesianem.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_bayesianem.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_bayesianem.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_bayesianem.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_bayesianem.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_bayesianem.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_bayesianem.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_bayesianem.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_bayesianem.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_bayesianem.IMP_STATISTICS_HAS_IMP_CGAL
310 
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
312 
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
314 
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_RANDOM
316 
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_SYSTEM
318 
319 IMP_STATISTICS_HAS_CGAL = _IMP_bayesianem.IMP_STATISTICS_HAS_CGAL
320 
321 IMP_STATISTICS_HAS_NUMPY = _IMP_bayesianem.IMP_STATISTICS_HAS_NUMPY
322 
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_bayesianem.IMPSTATISTICS_SHOW_WARNINGS
324 
325 import IMP.statistics
326 IMP_CORE_HAS_IMP_CGAL = _IMP_bayesianem.IMP_CORE_HAS_IMP_CGAL
327 
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_CORE_HAS_IMP_KERNEL
329 
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_FILESYSTEM
331 
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_RANDOM
335 
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_SYSTEM
337 
338 IMP_CORE_HAS_CGAL = _IMP_bayesianem.IMP_CORE_HAS_CGAL
339 
340 IMP_CORE_HAS_HDF5 = _IMP_bayesianem.IMP_CORE_HAS_HDF5
341 
342 IMP_CORE_HAS_NUMPY = _IMP_bayesianem.IMP_CORE_HAS_NUMPY
343 
344 IMPCORE_SHOW_WARNINGS = _IMP_bayesianem.IMPCORE_SHOW_WARNINGS
345 
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_CGAL
350 
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_DISPLAY
352 
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_KERNEL
354 
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
356 
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
358 
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
360 
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_RANDOM
362 
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_SYSTEM
364 
365 IMP_CONTAINER_HAS_CGAL = _IMP_bayesianem.IMP_CONTAINER_HAS_CGAL
366 
367 IMP_CONTAINER_HAS_HDF5 = _IMP_bayesianem.IMP_CONTAINER_HAS_HDF5
368 
369 IMP_CONTAINER_HAS_NUMPY = _IMP_bayesianem.IMP_CONTAINER_HAS_NUMPY
370 
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_CONTAINER_HAS_PYTHON_IHM
372 
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_bayesianem.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
374 
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_bayesianem.IMP_CONTAINER_HAS_ROBIN_MAP
376 
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_bayesianem.IMPCONTAINER_SHOW_WARNINGS
378 
379 import IMP.container
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ATOM_HAS_IMP_CGAL
381 
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_ATOM_HAS_IMP_KERNEL
383 
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
385 
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
387 
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_RANDOM
389 
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_REGEX
391 
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_SYSTEM
393 
394 IMP_ATOM_HAS_CGAL = _IMP_bayesianem.IMP_ATOM_HAS_CGAL
395 
396 IMP_ATOM_HAS_HDF5 = _IMP_bayesianem.IMP_ATOM_HAS_HDF5
397 
398 IMP_ATOM_HAS_NUMPY = _IMP_bayesianem.IMP_ATOM_HAS_NUMPY
399 
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_ATOM_HAS_PYTHON_IHM
401 
402 IMPATOM_SHOW_WARNINGS = _IMP_bayesianem.IMPATOM_SHOW_WARNINGS
403 
404 IMP_ATOM_TYPE_INDEX = _IMP_bayesianem.IMP_ATOM_TYPE_INDEX
405 
406 IMP_RESIDUE_TYPE_INDEX = _IMP_bayesianem.IMP_RESIDUE_TYPE_INDEX
407 
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_bayesianem.IMP_HIERARCHY_TYPE_INDEX
409 
410 IMP_CHAIN_TYPE_INDEX = _IMP_bayesianem.IMP_CHAIN_TYPE_INDEX
411 
412 import IMP.atom
413 IMP_EM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_EM_HAS_IMP_CGAL
414 
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_bayesianem.IMP_EM_HAS_IMP_CONTAINER
416 
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_EM_HAS_IMP_DISPLAY
418 
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_EM_HAS_IMP_SCORE_FUNCTOR
420 
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_EM_HAS_BOOST_FILESYSTEM
422 
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
424 
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_EM_HAS_BOOST_RANDOM
426 
427 IMP_EM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_EM_HAS_BOOST_REGEX
428 
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_EM_HAS_BOOST_SYSTEM
430 
431 IMP_EM_HAS_CGAL = _IMP_bayesianem.IMP_EM_HAS_CGAL
432 
433 IMP_EM_HAS_HDF5 = _IMP_bayesianem.IMP_EM_HAS_HDF5
434 
435 IMP_EM_HAS_NUMPY = _IMP_bayesianem.IMP_EM_HAS_NUMPY
436 
437 IMP_EM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_EM_HAS_PYTHON_IHM
438 
439 IMPEM_SHOW_WARNINGS = _IMP_bayesianem.IMPEM_SHOW_WARNINGS
440 
441 import IMP.em
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_bayesianem.IMP_SAXS_HAS_IMP_CGAL
443 
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_bayesianem.IMP_SAXS_HAS_IMP_CONTAINER
445 
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_SAXS_HAS_IMP_DISPLAY
447 
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_SAXS_HAS_IMP_KERNEL
449 
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
451 
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_FILESYSTEM
453 
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
455 
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_RANDOM
457 
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_REGEX
459 
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_SYSTEM
461 
462 IMP_SAXS_HAS_CGAL = _IMP_bayesianem.IMP_SAXS_HAS_CGAL
463 
464 IMP_SAXS_HAS_HDF5 = _IMP_bayesianem.IMP_SAXS_HAS_HDF5
465 
466 IMP_SAXS_HAS_NUMPY = _IMP_bayesianem.IMP_SAXS_HAS_NUMPY
467 
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_SAXS_HAS_PYTHON_IHM
469 
470 IMPSAXS_SHOW_WARNINGS = _IMP_bayesianem.IMPSAXS_SHOW_WARNINGS
471 
472 import IMP.saxs
473 IMP_ISD_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ISD_HAS_IMP_CGAL
474 
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_ISD_HAS_IMP_DISPLAY
476 
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
478 
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_FILESYSTEM
480 
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
482 
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_RANDOM
484 
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_ISD_HAS_BOOST_REGEX
486 
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_SYSTEM
488 
489 IMP_ISD_HAS_CGAL = _IMP_bayesianem.IMP_ISD_HAS_CGAL
490 
491 IMP_ISD_HAS_HDF5 = _IMP_bayesianem.IMP_ISD_HAS_HDF5
492 
493 IMP_ISD_HAS_NUMPY = _IMP_bayesianem.IMP_ISD_HAS_NUMPY
494 
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_ISD_HAS_PYTHON_IHM
496 
497 IMPISD_SHOW_WARNINGS = _IMP_bayesianem.IMPISD_SHOW_WARNINGS
498 
499 import IMP.isd
500 IMP_BAYESIANEM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_CGAL
501 
502 IMP_BAYESIANEM_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_DISPLAY
503 
504 IMP_BAYESIANEM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_SCORE_FUNCTOR
505 
506 IMP_BAYESIANEM_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_FILESYSTEM
507 
508 IMP_BAYESIANEM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_PROGRAMOPTIONS
509 
510 IMP_BAYESIANEM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_RANDOM
511 
512 IMP_BAYESIANEM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_REGEX
513 
514 IMP_BAYESIANEM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_SYSTEM
515 
516 IMP_BAYESIANEM_HAS_CGAL = _IMP_bayesianem.IMP_BAYESIANEM_HAS_CGAL
517 
518 IMP_BAYESIANEM_HAS_HDF5 = _IMP_bayesianem.IMP_BAYESIANEM_HAS_HDF5
519 
520 IMP_BAYESIANEM_HAS_NUMPY = _IMP_bayesianem.IMP_BAYESIANEM_HAS_NUMPY
521 
522 IMP_BAYESIANEM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_PYTHON_IHM
523 
524 IMPBAYESIANEM_SHOW_WARNINGS = _IMP_bayesianem.IMPBAYESIANEM_SHOW_WARNINGS
525 
526 
527 _object_types.append("GaussianEMRestraint")
528 
529 class GaussianEMRestraint(IMP.Restraint):
530  r"""Proxy of C++ IMP::bayesianem::GaussianEMRestraint class."""
531 
532  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
533 
534  def __init__(self, *args):
535  r"""__init__(GaussianEMRestraint self, Model mdl, IMP::ParticleIndexes model_ps, IMP::ParticleIndexes density_ps, ParticleIndex global_sigma, IMP::Float model_cutoff_dist, IMP::Float density_cutoff_dist, IMP::Float slope, bool update_model=True, bool backbone_slope=False, std::string name="GaussianEMRestraint%1%") -> GaussianEMRestraint"""
536  _IMP_bayesianem.GaussianEMRestraint_swiginit(self, _IMP_bayesianem.new_GaussianEMRestraint(*args))
537 
538  def get_probability(self):
539  r"""get_probability(GaussianEMRestraint self) -> double"""
540  return _IMP_bayesianem.GaussianEMRestraint_get_probability(self)
541 
542  def set_density_filename(self, density_fn):
543  r"""set_density_filename(GaussianEMRestraint self, std::string density_fn)"""
544  return _IMP_bayesianem.GaussianEMRestraint_set_density_filename(self, density_fn)
545 
546  def compute_initial_scores(self):
547  r"""compute_initial_scores(GaussianEMRestraint self)"""
548  return _IMP_bayesianem.GaussianEMRestraint_compute_initial_scores(self)
549 
550  def get_indexes(self):
551  r"""get_indexes(GaussianEMRestraint self) -> IMP::ParticleIndexes const"""
552  return _IMP_bayesianem.GaussianEMRestraint_get_indexes(self)
553 
554  def get_log2(self):
555  r"""get_log2(GaussianEMRestraint self) -> IMP::Floats const"""
556  return _IMP_bayesianem.GaussianEMRestraint_get_log2(self)
557 
558  def debug(self):
559  r"""debug(GaussianEMRestraint self)"""
560  return _IMP_bayesianem.GaussianEMRestraint_debug(self)
561 
562  def set_slope(self, s):
563  r"""set_slope(GaussianEMRestraint self, IMP::Float s)"""
564  return _IMP_bayesianem.GaussianEMRestraint_set_slope(self, s)
565 
566  def get_slope(self):
567  r"""get_slope(GaussianEMRestraint self) -> IMP::Float"""
568  return _IMP_bayesianem.GaussianEMRestraint_get_slope(self)
569 
570  def do_get_inputs(self):
571  r"""do_get_inputs(GaussianEMRestraint self) -> IMP::ModelObjectsTemp"""
572  return _IMP_bayesianem.GaussianEMRestraint_do_get_inputs(self)
573 
574  def show(self, out):
575  r"""show(GaussianEMRestraint self, _ostream out)"""
576  return _IMP_bayesianem.GaussianEMRestraint_show(self, out)
577 
578  def get_version_info(self):
579  r"""get_version_info(GaussianEMRestraint self) -> VersionInfo"""
580  return _IMP_bayesianem.GaussianEMRestraint_get_version_info(self)
581  __swig_destroy__ = _IMP_bayesianem.delete_GaussianEMRestraint
582 
583  def __str__(self):
584  r"""__str__(GaussianEMRestraint self) -> std::string"""
585  return _IMP_bayesianem.GaussianEMRestraint___str__(self)
586 
587  def __repr__(self):
588  r"""__repr__(GaussianEMRestraint self) -> std::string"""
589  return _IMP_bayesianem.GaussianEMRestraint___repr__(self)
590 
591  @staticmethod
592  def get_from(o):
593  return _object_cast_to_GaussianEMRestraint(o)
594 
595 
596 # Register GaussianEMRestraint in _IMP_bayesianem:
597 _IMP_bayesianem.GaussianEMRestraint_swigregister(GaussianEMRestraint)
598 
599 def get_rmsd_excluding_higher_than(m1, m2, t):
600  r"""get_rmsd_excluding_higher_than(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const t) -> double"""
601  return _IMP_bayesianem.get_rmsd_excluding_higher_than(m1, m2, t)
602 
603 def get_percentage_closer_than(m1, m2, t):
604  r"""get_percentage_closer_than(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const t) -> double"""
605  return _IMP_bayesianem.get_percentage_closer_than(m1, m2, t)
606 
608  r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
609  return _IMP_bayesianem.get_transformation_aligning_first_to_second(s1, s2)
610 
611 def get_rmsd_of_best_population(*args):
612  r"""
613  get_rmsd_of_best_population(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const percentage) -> double
614  get_rmsd_of_best_population(Selection s1, Selection s2, double const percentage) -> double
615  get_rmsd_of_best_population(IMP::algebra::Vector3Ds const & m1, IMP::algebra::Vector3Ds const & m2, double const percentage) -> double
616  """
617  return _IMP_bayesianem.get_rmsd_of_best_population(*args)
618 
619 def gem_score_cc(model_ps, density_ps):
620  r"""gem_score_cc(IMP::Particles model_ps, IMP::Particles density_ps) -> double"""
621  return _IMP_bayesianem.gem_score_cc(model_ps, density_ps)
622 
623 def get_grid(_in):
624  r"""get_grid(DensityMap _in) -> DenseDoubleGrid3D"""
625  return _IMP_bayesianem.get_grid(_in)
626 
627 def get_masked_map(gmm, weights, densitymap, threshold):
628  r"""get_masked_map(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap densitymap, double threshold) -> DensityMap"""
629  return _IMP_bayesianem.get_masked_map(gmm, weights, densitymap, threshold)
630 
631 def get_sub_map(dm, sub_gmm, gmm):
632  r"""get_sub_map(DensityMap dm, DensityMap sub_gmm, DensityMap gmm) -> DensityMap"""
633  return _IMP_bayesianem.get_sub_map(dm, sub_gmm, gmm)
634 
635 def get_overlap_fast(gmm, weights, dm, factor=2.5):
636  r"""get_overlap_fast(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap dm, double factor=2.5) -> double"""
637  return _IMP_bayesianem.get_overlap_fast(gmm, weights, dm, factor)
638 
639 def get_overlap_binned(gmm, weights, dm, factor=2.5, Nbin=100):
640  r"""get_overlap_binned(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap dm, double factor=2.5, int Nbin=100) -> IMP::algebra::Vector3Ds"""
641  return _IMP_bayesianem.get_overlap_binned(gmm, weights, dm, factor, Nbin)
642 
643 def get_rotation_matrix(x, y):
644  r"""get_rotation_matrix(Vector3D x, Vector3D y) -> Rotation3D"""
645  return _IMP_bayesianem.get_rotation_matrix(x, y)
646 
647 def sgn(v):
648  r"""sgn(double v) -> float"""
649  return _IMP_bayesianem.sgn(v)
650 
651 def NormalizePCA(pca, ps):
652  r"""NormalizePCA(PrincipalComponentAnalysis3D pca, IMP::Particles const & ps) -> PrincipalComponentAnalysis3D"""
653  return _IMP_bayesianem.NormalizePCA(pca, ps)
654 
655 def PCAalign(pca1, pca2):
656  r"""PCAalign(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2) -> IMP::algebra::Transformation3Ds"""
657  return _IMP_bayesianem.PCAalign(pca1, pca2)
658 
659 def get_module_version():
660  r"""get_module_version() -> std::string const"""
661  return _IMP_bayesianem.get_module_version()
662 
663 def get_example_path(fname):
664  r"""get_example_path(std::string fname) -> std::string"""
665  return _IMP_bayesianem.get_example_path(fname)
666 
667 def get_data_path(fname):
668  r"""get_data_path(std::string fname) -> std::string"""
669  return _IMP_bayesianem.get_data_path(fname)
670 
671 from . import _version_check
672 _version_check.check_version(get_module_version())
673 __version__ = get_module_version()
674 
675 
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
Basic utilities for handling cryo-electron microscopy 3D density maps.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
DensityGrid get_grid(IMP::em::DensityMap *in)
Return a dense grid containing the voxels of the passed density map.
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...
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
Support for small angle X-ray scattering (SAXS) data.
std::string get_module_version()
Return the version of this module, as a string.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56