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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
pmi/__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_pmi
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_PMI_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_PMI_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_pmi.delete_IMP_PMI_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_PMI_SwigPyIterator self) -> PyObject *"""
79  return _IMP_pmi.IMP_PMI_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
83  return _IMP_pmi.IMP_PMI_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
87  return _IMP_pmi.IMP_PMI_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_pmi.IMP_PMI_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
95  return _IMP_pmi.IMP_PMI_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator"""
99  return _IMP_pmi.IMP_PMI_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_PMI_SwigPyIterator self) -> PyObject *"""
103  return _IMP_pmi.IMP_PMI_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_PMI_SwigPyIterator self) -> PyObject *"""
107  return _IMP_pmi.IMP_PMI_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_PMI_SwigPyIterator self) -> PyObject *"""
111  return _IMP_pmi.IMP_PMI_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
115  return _IMP_pmi.IMP_PMI_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
119  return _IMP_pmi.IMP_PMI_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
123  return _IMP_pmi.IMP_PMI_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
127  return _IMP_pmi.IMP_PMI_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
131  return _IMP_pmi.IMP_PMI_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
135  return _IMP_pmi.IMP_PMI_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator
140  __sub__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_pmi.IMP_PMI_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_PMI_SwigPyIterator in _IMP_pmi:
147 _IMP_pmi.IMP_PMI_SwigPyIterator_swigregister(IMP_PMI_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_pmi.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_pmi.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_pmi.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_pmi.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_pmi.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_pmi.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_pmi.IMP_MEMORY
167 
168 IMP_NONE = _IMP_pmi.IMP_NONE
169 
170 IMP_USAGE = _IMP_pmi.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_pmi.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_pmi.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_pmi.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_pmi.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_pmi.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_pmi.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_pmi.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi.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_pmi._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_pmi:
237 _IMP_pmi._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_pmi.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_pmi.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_pmi.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_pmi.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_IMP_CGAL
310 
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
312 
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
314 
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_RANDOM
316 
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_SYSTEM
318 
319 IMP_STATISTICS_HAS_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_CGAL
320 
321 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi.IMP_STATISTICS_HAS_NUMPY
322 
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi.IMPSTATISTICS_SHOW_WARNINGS
324 
325 import IMP.statistics
326 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi.IMP_CORE_HAS_IMP_CGAL
327 
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi.IMP_CORE_HAS_IMP_KERNEL
329 
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_FILESYSTEM
331 
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CORE_HAS_BOOST_RANDOM
335 
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_SYSTEM
337 
338 IMP_CORE_HAS_CGAL = _IMP_pmi.IMP_CORE_HAS_CGAL
339 
340 IMP_CORE_HAS_HDF5 = _IMP_pmi.IMP_CORE_HAS_HDF5
341 
342 IMP_CORE_HAS_NUMPY = _IMP_pmi.IMP_CORE_HAS_NUMPY
343 
344 IMPCORE_SHOW_WARNINGS = _IMP_pmi.IMPCORE_SHOW_WARNINGS
345 
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_CGAL
350 
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi.IMP_CONTAINER_HAS_IMP_DISPLAY
352 
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_KERNEL
354 
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
356 
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
358 
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
360 
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_RANDOM
362 
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_SYSTEM
364 
365 IMP_CONTAINER_HAS_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_CGAL
366 
367 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi.IMP_CONTAINER_HAS_HDF5
368 
369 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi.IMP_CONTAINER_HAS_NUMPY
370 
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi.IMP_CONTAINER_HAS_PYTHON_IHM
372 
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
374 
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi.IMP_CONTAINER_HAS_ROBIN_MAP
376 
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi.IMPCONTAINER_SHOW_WARNINGS
378 
379 import IMP.container
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi.IMP_ATOM_HAS_IMP_CGAL
381 
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi.IMP_ATOM_HAS_IMP_KERNEL
383 
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
385 
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
387 
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ATOM_HAS_BOOST_RANDOM
389 
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi.IMP_ATOM_HAS_BOOST_REGEX
391 
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ATOM_HAS_BOOST_SYSTEM
393 
394 IMP_ATOM_HAS_CGAL = _IMP_pmi.IMP_ATOM_HAS_CGAL
395 
396 IMP_ATOM_HAS_HDF5 = _IMP_pmi.IMP_ATOM_HAS_HDF5
397 
398 IMP_ATOM_HAS_NUMPY = _IMP_pmi.IMP_ATOM_HAS_NUMPY
399 
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi.IMP_ATOM_HAS_PYTHON_IHM
401 
402 IMPATOM_SHOW_WARNINGS = _IMP_pmi.IMPATOM_SHOW_WARNINGS
403 
404 IMP_ATOM_TYPE_INDEX = _IMP_pmi.IMP_ATOM_TYPE_INDEX
405 
406 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi.IMP_RESIDUE_TYPE_INDEX
407 
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi.IMP_HIERARCHY_TYPE_INDEX
409 
410 IMP_CHAIN_TYPE_INDEX = _IMP_pmi.IMP_CHAIN_TYPE_INDEX
411 
412 import IMP.atom
413 IMP_EM_HAS_IMP_CGAL = _IMP_pmi.IMP_EM_HAS_IMP_CGAL
414 
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi.IMP_EM_HAS_IMP_CONTAINER
416 
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi.IMP_EM_HAS_IMP_DISPLAY
418 
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_EM_HAS_IMP_SCORE_FUNCTOR
420 
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_FILESYSTEM
422 
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
424 
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_EM_HAS_BOOST_RANDOM
426 
427 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi.IMP_EM_HAS_BOOST_REGEX
428 
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_SYSTEM
430 
431 IMP_EM_HAS_CGAL = _IMP_pmi.IMP_EM_HAS_CGAL
432 
433 IMP_EM_HAS_HDF5 = _IMP_pmi.IMP_EM_HAS_HDF5
434 
435 IMP_EM_HAS_NUMPY = _IMP_pmi.IMP_EM_HAS_NUMPY
436 
437 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi.IMP_EM_HAS_PYTHON_IHM
438 
439 IMPEM_SHOW_WARNINGS = _IMP_pmi.IMPEM_SHOW_WARNINGS
440 
441 import IMP.em
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi.IMP_SAXS_HAS_IMP_CGAL
443 
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi.IMP_SAXS_HAS_IMP_CONTAINER
445 
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi.IMP_SAXS_HAS_IMP_DISPLAY
447 
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi.IMP_SAXS_HAS_IMP_KERNEL
449 
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
451 
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_FILESYSTEM
453 
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
455 
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SAXS_HAS_BOOST_RANDOM
457 
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi.IMP_SAXS_HAS_BOOST_REGEX
459 
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_SYSTEM
461 
462 IMP_SAXS_HAS_CGAL = _IMP_pmi.IMP_SAXS_HAS_CGAL
463 
464 IMP_SAXS_HAS_HDF5 = _IMP_pmi.IMP_SAXS_HAS_HDF5
465 
466 IMP_SAXS_HAS_NUMPY = _IMP_pmi.IMP_SAXS_HAS_NUMPY
467 
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi.IMP_SAXS_HAS_PYTHON_IHM
469 
470 IMPSAXS_SHOW_WARNINGS = _IMP_pmi.IMPSAXS_SHOW_WARNINGS
471 
472 import IMP.saxs
473 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi.IMP_ISD_HAS_IMP_CGAL
474 
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi.IMP_ISD_HAS_IMP_DISPLAY
476 
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
478 
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_FILESYSTEM
480 
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
482 
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ISD_HAS_BOOST_RANDOM
484 
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi.IMP_ISD_HAS_BOOST_REGEX
486 
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_SYSTEM
488 
489 IMP_ISD_HAS_CGAL = _IMP_pmi.IMP_ISD_HAS_CGAL
490 
491 IMP_ISD_HAS_HDF5 = _IMP_pmi.IMP_ISD_HAS_HDF5
492 
493 IMP_ISD_HAS_NUMPY = _IMP_pmi.IMP_ISD_HAS_NUMPY
494 
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi.IMP_ISD_HAS_PYTHON_IHM
496 
497 IMPISD_SHOW_WARNINGS = _IMP_pmi.IMPISD_SHOW_WARNINGS
498 
499 import IMP.isd
500 IMP_PMI_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_PMI_HAS_IMP_ALGEBRA
501 
502 IMP_PMI_HAS_IMP_ATOM = _IMP_pmi.IMP_PMI_HAS_IMP_ATOM
503 
504 IMP_PMI_HAS_IMP_CGAL = _IMP_pmi.IMP_PMI_HAS_IMP_CGAL
505 
506 IMP_PMI_HAS_IMP_DISPLAY = _IMP_pmi.IMP_PMI_HAS_IMP_DISPLAY
507 
508 IMP_PMI_HAS_IMP_EM = _IMP_pmi.IMP_PMI_HAS_IMP_EM
509 
510 IMP_PMI_HAS_IMP_KERNEL = _IMP_pmi.IMP_PMI_HAS_IMP_KERNEL
511 
512 IMP_PMI_HAS_IMP_SAXS = _IMP_pmi.IMP_PMI_HAS_IMP_SAXS
513 
514 IMP_PMI_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_PMI_HAS_IMP_SCORE_FUNCTOR
515 
516 IMP_PMI_HAS_IMP_STATISTICS = _IMP_pmi.IMP_PMI_HAS_IMP_STATISTICS
517 
518 IMP_PMI_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_FILESYSTEM
519 
520 IMP_PMI_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_PMI_HAS_BOOST_PROGRAMOPTIONS
521 
522 IMP_PMI_HAS_BOOST_RANDOM = _IMP_pmi.IMP_PMI_HAS_BOOST_RANDOM
523 
524 IMP_PMI_HAS_BOOST_REGEX = _IMP_pmi.IMP_PMI_HAS_BOOST_REGEX
525 
526 IMP_PMI_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_SYSTEM
527 
528 IMP_PMI_HAS_CGAL = _IMP_pmi.IMP_PMI_HAS_CGAL
529 
530 IMP_PMI_HAS_HDF5 = _IMP_pmi.IMP_PMI_HAS_HDF5
531 
532 IMP_PMI_HAS_NUMPY = _IMP_pmi.IMP_PMI_HAS_NUMPY
533 
534 IMP_PMI_HAS_PYTHON_IHM = _IMP_pmi.IMP_PMI_HAS_PYTHON_IHM
535 
536 IMPPMI_SHOW_WARNINGS = _IMP_pmi.IMPPMI_SHOW_WARNINGS
537 
538 
539 _object_types.append("CompositeRestraint")
540 
541 
542 def _object_cast_to_CompositeRestraint(o):
543  r"""_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
544  return _IMP_pmi._object_cast_to_CompositeRestraint(o)
545 
546 _object_types.append("CrossLinkRestraintSet")
547 
548 
549 def _object_cast_to_CrossLinkRestraintSet(o):
550  r"""_object_cast_to_CrossLinkRestraintSet(Object o) -> CrossLinkRestraintSet"""
551  return _IMP_pmi._object_cast_to_CrossLinkRestraintSet(o)
552 
553 def Uncertainties(l=[]):
554  return [Uncertainty(x) for x in l]
555 _plural_types.append("Uncertainties")
556 
557 
558 _value_types.append("Uncertainty")
559 
560 
561 def Resolutions(l=[]):
562  return [Resolution(x) for x in l]
563 _plural_types.append("Resolutions")
564 
565 
566 _value_types.append("Resolution")
567 
568 
569 def Symmetrics(l=[]):
570  return [Symmetric(x) for x in l]
571 _plural_types.append("Symmetrics")
572 
573 
574 _value_types.append("Symmetric")
575 
576 
577 _object_types.append("TransformMover")
578 
579 
580 def _object_cast_to_TransformMover(o):
581  r"""_object_cast_to_TransformMover(Object o) -> TransformMover"""
582  return _IMP_pmi._object_cast_to_TransformMover(o)
583 
584 _object_types.append("MembraneRestraint")
585 
586 
587 def _object_cast_to_MembraneRestraint(o):
588  r"""_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
589  return _IMP_pmi._object_cast_to_MembraneRestraint(o)
590 
591 class StructureWarning(UserWarning):
592  """Warning related to handling of structures"""
593  pass
594 
595 
596 class ParameterWarning(UserWarning):
597  """Warning for probably incorrect input parameters"""
598  pass
599 
600 
601 class MissingFileWarning(UserWarning):
602  """Warning for an expected, but missing, file"""
603  pass
604 
605 class MembraneRestraint(IMP.isd.ISDRestraint):
606  r"""Proxy of C++ IMP::pmi::MembraneRestraint class."""
607 
608  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
609 
610  def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
611  r"""__init__(MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
612  _IMP_pmi.MembraneRestraint_swiginit(self, _IMP_pmi.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear))
613 
614  def add_particles_below(self, particles):
615  r"""add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
616  return _IMP_pmi.MembraneRestraint_add_particles_below(self, particles)
617 
618  def add_particles_above(self, particles):
619  r"""add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
620  return _IMP_pmi.MembraneRestraint_add_particles_above(self, particles)
621 
622  def add_particles_inside(self, particles):
623  r"""add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
624  return _IMP_pmi.MembraneRestraint_add_particles_inside(self, particles)
625 
626  def get_score(self, prob):
627  r"""get_score(MembraneRestraint self, double prob) -> double"""
628  return _IMP_pmi.MembraneRestraint_get_score(self, prob)
629 
630  def get_probability_above(self, z, z_slope_center_upper):
631  r"""get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
632  return _IMP_pmi.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
633 
634  def get_score_above(self, z, z_slope_center_upper):
635  r"""get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
636  return _IMP_pmi.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
637 
638  def get_probability_below(self, z, z_slope_center_lower):
639  r"""get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
640  return _IMP_pmi.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
641 
642  def get_score_below(self, z, z_slope_center_lower):
643  r"""get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
644  return _IMP_pmi.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
645 
646  def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
647  r"""get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
648  return _IMP_pmi.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
649  __swig_destroy__ = _IMP_pmi.delete_MembraneRestraint
650 
651  def __str__(self):
652  r"""__str__(MembraneRestraint self) -> std::string"""
653  return _IMP_pmi.MembraneRestraint___str__(self)
654 
655  def __repr__(self):
656  r"""__repr__(MembraneRestraint self) -> std::string"""
657  return _IMP_pmi.MembraneRestraint___repr__(self)
658 
659  @staticmethod
660  def get_from(o):
661  return _object_cast_to_MembraneRestraint(o)
662 
663 
664 # Register MembraneRestraint in _IMP_pmi:
665 _IMP_pmi.MembraneRestraint_swigregister(MembraneRestraint)
666 class CompositeRestraint(IMP.Restraint):
667  r"""Proxy of C++ IMP::pmi::CompositeRestraint class."""
668 
669  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
670 
671  def __init__(self, *args):
672  r"""__init__(CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%") -> CompositeRestraint"""
673  _IMP_pmi.CompositeRestraint_swiginit(self, _IMP_pmi.new_CompositeRestraint(*args))
674 
675  def add_composite_particle(self, pi):
676  r"""add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
677  return _IMP_pmi.CompositeRestraint_add_composite_particle(self, pi)
678 
679  def get_number_of_elements(self):
680  r"""get_number_of_elements(CompositeRestraint self) -> unsigned int"""
681  return _IMP_pmi.CompositeRestraint_get_number_of_elements(self)
682 
683  def do_get_inputs(self):
684  r"""do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
685  return _IMP_pmi.CompositeRestraint_do_get_inputs(self)
686 
687  def get_version_info(self):
688  r"""get_version_info(CompositeRestraint self) -> VersionInfo"""
689  return _IMP_pmi.CompositeRestraint_get_version_info(self)
690  __swig_destroy__ = _IMP_pmi.delete_CompositeRestraint
691 
692  def get_probability(self):
693  r"""get_probability(CompositeRestraint self) -> double"""
694  return _IMP_pmi.CompositeRestraint_get_probability(self)
695 
696  def __str__(self):
697  r"""__str__(CompositeRestraint self) -> std::string"""
698  return _IMP_pmi.CompositeRestraint___str__(self)
699 
700  def __repr__(self):
701  r"""__repr__(CompositeRestraint self) -> std::string"""
702  return _IMP_pmi.CompositeRestraint___repr__(self)
703 
704  @staticmethod
705  def get_from(o):
706  return _object_cast_to_CompositeRestraint(o)
707 
708 
709 # Register CompositeRestraint in _IMP_pmi:
710 _IMP_pmi.CompositeRestraint_swigregister(CompositeRestraint)
711 class CrossLinkRestraintSet(IMP.RestraintSet):
712  r"""Proxy of C++ IMP::pmi::CrossLinkRestraintSet class."""
713 
714  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
715 
716  def __init__(self, *args):
717  r"""
718  __init__(CrossLinkRestraintSet self, Model m, std::string const & name="CrossLinkRestraintSet %1%") -> CrossLinkRestraintSet
719  __init__(CrossLinkRestraintSet self) -> CrossLinkRestraintSet
720  """
721  _IMP_pmi.CrossLinkRestraintSet_swiginit(self, _IMP_pmi.new_CrossLinkRestraintSet(*args))
722 
723  def set_metadata(self, filename, length, slope):
724  r"""set_metadata(CrossLinkRestraintSet self, std::string filename, double length, double slope)"""
725  return _IMP_pmi.CrossLinkRestraintSet_set_metadata(self, filename, length, slope)
726 
727  def set_linker_auth_name(self, name):
728  r"""set_linker_auth_name(CrossLinkRestraintSet self, std::string name)"""
729  return _IMP_pmi.CrossLinkRestraintSet_set_linker_auth_name(self, name)
730 
731  def set_linker_chemical_name(self, name):
732  r"""set_linker_chemical_name(CrossLinkRestraintSet self, std::string name)"""
733  return _IMP_pmi.CrossLinkRestraintSet_set_linker_chemical_name(self, name)
734 
735  def set_linker_smiles(self, name):
736  r"""set_linker_smiles(CrossLinkRestraintSet self, std::string name)"""
737  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles(self, name)
738 
739  def set_linker_smiles_canonical(self, name):
740  r"""set_linker_smiles_canonical(CrossLinkRestraintSet self, std::string name)"""
741  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles_canonical(self, name)
742 
743  def set_linker_inchi(self, name):
744  r"""set_linker_inchi(CrossLinkRestraintSet self, std::string name)"""
745  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi(self, name)
746 
747  def set_linker_inchi_key(self, name):
748  r"""set_linker_inchi_key(CrossLinkRestraintSet self, std::string name)"""
749  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi_key(self, name)
750  __swig_destroy__ = _IMP_pmi.delete_CrossLinkRestraintSet
751 
752  def __str__(self):
753  r"""__str__(CrossLinkRestraintSet self) -> std::string"""
754  return _IMP_pmi.CrossLinkRestraintSet___str__(self)
755 
756  def __repr__(self):
757  r"""__repr__(CrossLinkRestraintSet self) -> std::string"""
758  return _IMP_pmi.CrossLinkRestraintSet___repr__(self)
759 
760  @staticmethod
761  def get_from(o):
762  return _object_cast_to_CrossLinkRestraintSet(o)
763 
764 
765  def _get_as_binary(self):
766  r"""_get_as_binary(CrossLinkRestraintSet self) -> PyObject *"""
767  return _IMP_pmi.CrossLinkRestraintSet__get_as_binary(self)
768 
769  def _set_from_binary(self, p):
770  r"""_set_from_binary(CrossLinkRestraintSet self, PyObject * p)"""
771  return _IMP_pmi.CrossLinkRestraintSet__set_from_binary(self, p)
772 
773  def __getstate__(self):
774  p = self._get_as_binary()
775  if len(self.__dict__) > 1:
776  d = self.__dict__.copy()
777  del d['this']
778  p = (d, p)
779  return p
780 
781  def __setstate__(self, p):
782  if not hasattr(self, 'this'):
783  self.__init__()
784  if isinstance(p, tuple):
785  d, p = p
786  self.__dict__.update(d)
787  return self._set_from_binary(p)
788 
789 
790 # Register CrossLinkRestraintSet in _IMP_pmi:
791 _IMP_pmi.CrossLinkRestraintSet_swigregister(CrossLinkRestraintSet)
792 class Uncertainty(IMP.Decorator):
793  r"""Proxy of C++ IMP::pmi::Uncertainty class."""
794 
795  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
796 
797  def get_uncertainty(self):
798  r"""get_uncertainty(Uncertainty self) -> IMP::Float"""
799  return _IMP_pmi.Uncertainty_get_uncertainty(self)
800 
801  def set_uncertainty(self, d):
802  r"""set_uncertainty(Uncertainty self, IMP::Float d)"""
803  return _IMP_pmi.Uncertainty_set_uncertainty(self, d)
804 
805  def __init__(self, *args):
806  r"""
807  __init__(Uncertainty self) -> Uncertainty
808  __init__(Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
809  __init__(Uncertainty self, _ParticleAdaptor d) -> Uncertainty
810  """
811  _IMP_pmi.Uncertainty_swiginit(self, _IMP_pmi.new_Uncertainty(*args))
812 
813  @staticmethod
814  def get_is_setup(*args):
815  r"""
816  get_is_setup(Model m, ParticleIndex pi) -> bool
817  get_is_setup(_ParticleAdaptor p) -> bool
818  """
819  return _IMP_pmi.Uncertainty_get_is_setup(*args)
820 
821  def show(self, *args):
822  r"""show(Uncertainty self, _ostream out=std::cout)"""
823  return _IMP_pmi.Uncertainty_show(self, *args)
824 
825  @staticmethod
826  def setup_particle(*args):
827  r"""
828  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
829  setup_particle(_ParticleAdaptor pa, IMP::Float uncertainty) -> Uncertainty
830  """
831  return _IMP_pmi.Uncertainty_setup_particle(*args)
832 
833  @staticmethod
834  def get_uncertainty_key():
835  r"""get_uncertainty_key() -> FloatKey"""
836  return _IMP_pmi.Uncertainty_get_uncertainty_key()
837 
838  def add_attribute(self, *args):
839  r"""
840  add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
841  add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
842  add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
843  add_attribute(Uncertainty self, FloatsKey a0, IMP::Floats a1)
844  add_attribute(Uncertainty self, IntsKey a0, IMP::Ints a1)
845  add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
846  add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
847  add_attribute(Uncertainty self, ObjectKey a0, Object a1)
848  """
849  return _IMP_pmi.Uncertainty_add_attribute(self, *args)
850 
851  def get_value(self, *args):
852  r"""
853  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
854  get_value(Uncertainty self, IntKey a0) -> IMP::Int
855  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
856  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
857  get_value(Uncertainty self, StringKey a0) -> IMP::String
858  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
859  get_value(Uncertainty self, ObjectKey a0) -> Object
860  """
861  return _IMP_pmi.Uncertainty_get_value(self, *args)
862 
863  def set_value(self, *args):
864  r"""
865  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
866  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
867  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
868  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
869  set_value(Uncertainty self, StringKey a0, IMP::String a1)
870  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
871  set_value(Uncertainty self, ObjectKey a0, Object a1)
872  """
873  return _IMP_pmi.Uncertainty_set_value(self, *args)
874 
875  def remove_attribute(self, *args):
876  r"""
877  remove_attribute(Uncertainty self, FloatKey a0)
878  remove_attribute(Uncertainty self, IntKey a0)
879  remove_attribute(Uncertainty self, FloatsKey a0)
880  remove_attribute(Uncertainty self, IntsKey a0)
881  remove_attribute(Uncertainty self, StringKey a0)
882  remove_attribute(Uncertainty self, ParticleIndexKey a0)
883  remove_attribute(Uncertainty self, ObjectKey a0)
884  """
885  return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
886 
887  def has_attribute(self, *args):
888  r"""
889  has_attribute(Uncertainty self, FloatKey a0) -> bool
890  has_attribute(Uncertainty self, IntKey a0) -> bool
891  has_attribute(Uncertainty self, FloatsKey a0) -> bool
892  has_attribute(Uncertainty self, IntsKey a0) -> bool
893  has_attribute(Uncertainty self, StringKey a0) -> bool
894  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
895  has_attribute(Uncertainty self, ObjectKey a0) -> bool
896  """
897  return _IMP_pmi.Uncertainty_has_attribute(self, *args)
898 
899  def get_derivative(self, a0):
900  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
901  return _IMP_pmi.Uncertainty_get_derivative(self, a0)
902 
903  def get_name(self):
904  r"""get_name(Uncertainty self) -> std::string"""
905  return _IMP_pmi.Uncertainty_get_name(self)
906 
907  def clear_caches(self):
908  r"""clear_caches(Uncertainty self)"""
909  return _IMP_pmi.Uncertainty_clear_caches(self)
910 
911  def set_name(self, a0):
912  r"""set_name(Uncertainty self, std::string a0)"""
913  return _IMP_pmi.Uncertainty_set_name(self, a0)
914 
915  def set_check_level(self, a0):
916  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
917  return _IMP_pmi.Uncertainty_set_check_level(self, a0)
918 
919  def add_to_derivative(self, a0, a1, a2):
920  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
921  return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
922 
923  def set_is_optimized(self, a0, a1):
924  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
925  return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
926 
927  def get_is_optimized(self, a0):
928  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
929  return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
930 
931  def get_check_level(self):
932  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
933  return _IMP_pmi.Uncertainty_get_check_level(self)
934 
935  def __eq__(self, *args):
936  r"""
937  __eq__(Uncertainty self, Uncertainty o) -> bool
938  __eq__(Uncertainty self, Particle d) -> bool
939  """
940  return _IMP_pmi.Uncertainty___eq__(self, *args)
941 
942  def __ne__(self, *args):
943  r"""
944  __ne__(Uncertainty self, Uncertainty o) -> bool
945  __ne__(Uncertainty self, Particle d) -> bool
946  """
947  return _IMP_pmi.Uncertainty___ne__(self, *args)
948 
949  def __le__(self, *args):
950  r"""
951  __le__(Uncertainty self, Uncertainty o) -> bool
952  __le__(Uncertainty self, Particle d) -> bool
953  """
954  return _IMP_pmi.Uncertainty___le__(self, *args)
955 
956  def __lt__(self, *args):
957  r"""
958  __lt__(Uncertainty self, Uncertainty o) -> bool
959  __lt__(Uncertainty self, Particle d) -> bool
960  """
961  return _IMP_pmi.Uncertainty___lt__(self, *args)
962 
963  def __ge__(self, *args):
964  r"""
965  __ge__(Uncertainty self, Uncertainty o) -> bool
966  __ge__(Uncertainty self, Particle d) -> bool
967  """
968  return _IMP_pmi.Uncertainty___ge__(self, *args)
969 
970  def __gt__(self, *args):
971  r"""
972  __gt__(Uncertainty self, Uncertainty o) -> bool
973  __gt__(Uncertainty self, Particle d) -> bool
974  """
975  return _IMP_pmi.Uncertainty___gt__(self, *args)
976 
977  def __hash__(self):
978  r"""__hash__(Uncertainty self) -> std::size_t"""
979  return _IMP_pmi.Uncertainty___hash__(self)
980 
981  def __str__(self):
982  r"""__str__(Uncertainty self) -> std::string"""
983  return _IMP_pmi.Uncertainty___str__(self)
984 
985  def __repr__(self):
986  r"""__repr__(Uncertainty self) -> std::string"""
987  return _IMP_pmi.Uncertainty___repr__(self)
988 
989  def _get_as_binary(self):
990  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
991  return _IMP_pmi.Uncertainty__get_as_binary(self)
992 
993  def _set_from_binary(self, p):
994  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
995  return _IMP_pmi.Uncertainty__set_from_binary(self, p)
996 
997  def __getstate__(self):
998  p = self._get_as_binary()
999  if len(self.__dict__) > 1:
1000  d = self.__dict__.copy()
1001  del d['this']
1002  p = (d, p)
1003  return p
1004 
1005  def __setstate__(self, p):
1006  if not hasattr(self, 'this'):
1007  self.__init__()
1008  if isinstance(p, tuple):
1009  d, p = p
1010  self.__dict__.update(d)
1011  return self._set_from_binary(p)
1012 
1013  __swig_destroy__ = _IMP_pmi.delete_Uncertainty
1014 
1015 # Register Uncertainty in _IMP_pmi:
1016 _IMP_pmi.Uncertainty_swigregister(Uncertainty)
1017 class Resolution(IMP.Decorator):
1018  r"""Proxy of C++ IMP::pmi::Resolution class."""
1019 
1020  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1021 
1022  def get_resolution(self):
1023  r"""get_resolution(Resolution self) -> IMP::Float"""
1024  return _IMP_pmi.Resolution_get_resolution(self)
1025 
1026  def set_resolution(self, d):
1027  r"""set_resolution(Resolution self, IMP::Float d)"""
1028  return _IMP_pmi.Resolution_set_resolution(self, d)
1029 
1030  def __init__(self, *args):
1031  r"""
1032  __init__(Resolution self) -> Resolution
1033  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
1034  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
1035  """
1036  _IMP_pmi.Resolution_swiginit(self, _IMP_pmi.new_Resolution(*args))
1037 
1038  @staticmethod
1039  def get_is_setup(*args):
1040  r"""
1041  get_is_setup(Model m, ParticleIndex pi) -> bool
1042  get_is_setup(_ParticleAdaptor p) -> bool
1043  """
1044  return _IMP_pmi.Resolution_get_is_setup(*args)
1045 
1046  def show(self, *args):
1047  r"""show(Resolution self, _ostream out=std::cout)"""
1048  return _IMP_pmi.Resolution_show(self, *args)
1049 
1050  @staticmethod
1051  def setup_particle(*args):
1052  r"""
1053  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1054  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
1055  """
1056  return _IMP_pmi.Resolution_setup_particle(*args)
1057 
1058  @staticmethod
1059  def get_resolution_key():
1060  r"""get_resolution_key() -> FloatKey"""
1061  return _IMP_pmi.Resolution_get_resolution_key()
1062 
1063  def add_attribute(self, *args):
1064  r"""
1065  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1066  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1067  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1068  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1069  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1070  add_attribute(Resolution self, StringKey a0, IMP::String a1)
1071  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1072  add_attribute(Resolution self, ObjectKey a0, Object a1)
1073  """
1074  return _IMP_pmi.Resolution_add_attribute(self, *args)
1075 
1076  def get_value(self, *args):
1077  r"""
1078  get_value(Resolution self, FloatKey a0) -> IMP::Float
1079  get_value(Resolution self, IntKey a0) -> IMP::Int
1080  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1081  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1082  get_value(Resolution self, StringKey a0) -> IMP::String
1083  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1084  get_value(Resolution self, ObjectKey a0) -> Object
1085  """
1086  return _IMP_pmi.Resolution_get_value(self, *args)
1087 
1088  def set_value(self, *args):
1089  r"""
1090  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1091  set_value(Resolution self, IntKey a0, IMP::Int a1)
1092  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1093  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1094  set_value(Resolution self, StringKey a0, IMP::String a1)
1095  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1096  set_value(Resolution self, ObjectKey a0, Object a1)
1097  """
1098  return _IMP_pmi.Resolution_set_value(self, *args)
1099 
1100  def remove_attribute(self, *args):
1101  r"""
1102  remove_attribute(Resolution self, FloatKey a0)
1103  remove_attribute(Resolution self, IntKey a0)
1104  remove_attribute(Resolution self, FloatsKey a0)
1105  remove_attribute(Resolution self, IntsKey a0)
1106  remove_attribute(Resolution self, StringKey a0)
1107  remove_attribute(Resolution self, ParticleIndexKey a0)
1108  remove_attribute(Resolution self, ObjectKey a0)
1109  """
1110  return _IMP_pmi.Resolution_remove_attribute(self, *args)
1111 
1112  def has_attribute(self, *args):
1113  r"""
1114  has_attribute(Resolution self, FloatKey a0) -> bool
1115  has_attribute(Resolution self, IntKey a0) -> bool
1116  has_attribute(Resolution self, FloatsKey a0) -> bool
1117  has_attribute(Resolution self, IntsKey a0) -> bool
1118  has_attribute(Resolution self, StringKey a0) -> bool
1119  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1120  has_attribute(Resolution self, ObjectKey a0) -> bool
1121  """
1122  return _IMP_pmi.Resolution_has_attribute(self, *args)
1123 
1124  def get_derivative(self, a0):
1125  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1126  return _IMP_pmi.Resolution_get_derivative(self, a0)
1127 
1128  def get_name(self):
1129  r"""get_name(Resolution self) -> std::string"""
1130  return _IMP_pmi.Resolution_get_name(self)
1131 
1132  def clear_caches(self):
1133  r"""clear_caches(Resolution self)"""
1134  return _IMP_pmi.Resolution_clear_caches(self)
1135 
1136  def set_name(self, a0):
1137  r"""set_name(Resolution self, std::string a0)"""
1138  return _IMP_pmi.Resolution_set_name(self, a0)
1139 
1140  def set_check_level(self, a0):
1141  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1142  return _IMP_pmi.Resolution_set_check_level(self, a0)
1143 
1144  def add_to_derivative(self, a0, a1, a2):
1145  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1146  return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1147 
1148  def set_is_optimized(self, a0, a1):
1149  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1150  return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1151 
1152  def get_is_optimized(self, a0):
1153  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1154  return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1155 
1156  def get_check_level(self):
1157  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1158  return _IMP_pmi.Resolution_get_check_level(self)
1159 
1160  def __eq__(self, *args):
1161  r"""
1162  __eq__(Resolution self, Resolution o) -> bool
1163  __eq__(Resolution self, Particle d) -> bool
1164  """
1165  return _IMP_pmi.Resolution___eq__(self, *args)
1166 
1167  def __ne__(self, *args):
1168  r"""
1169  __ne__(Resolution self, Resolution o) -> bool
1170  __ne__(Resolution self, Particle d) -> bool
1171  """
1172  return _IMP_pmi.Resolution___ne__(self, *args)
1173 
1174  def __le__(self, *args):
1175  r"""
1176  __le__(Resolution self, Resolution o) -> bool
1177  __le__(Resolution self, Particle d) -> bool
1178  """
1179  return _IMP_pmi.Resolution___le__(self, *args)
1180 
1181  def __lt__(self, *args):
1182  r"""
1183  __lt__(Resolution self, Resolution o) -> bool
1184  __lt__(Resolution self, Particle d) -> bool
1185  """
1186  return _IMP_pmi.Resolution___lt__(self, *args)
1187 
1188  def __ge__(self, *args):
1189  r"""
1190  __ge__(Resolution self, Resolution o) -> bool
1191  __ge__(Resolution self, Particle d) -> bool
1192  """
1193  return _IMP_pmi.Resolution___ge__(self, *args)
1194 
1195  def __gt__(self, *args):
1196  r"""
1197  __gt__(Resolution self, Resolution o) -> bool
1198  __gt__(Resolution self, Particle d) -> bool
1199  """
1200  return _IMP_pmi.Resolution___gt__(self, *args)
1201 
1202  def __hash__(self):
1203  r"""__hash__(Resolution self) -> std::size_t"""
1204  return _IMP_pmi.Resolution___hash__(self)
1205 
1206  def __str__(self):
1207  r"""__str__(Resolution self) -> std::string"""
1208  return _IMP_pmi.Resolution___str__(self)
1209 
1210  def __repr__(self):
1211  r"""__repr__(Resolution self) -> std::string"""
1212  return _IMP_pmi.Resolution___repr__(self)
1213 
1214  def _get_as_binary(self):
1215  r"""_get_as_binary(Resolution self) -> PyObject *"""
1216  return _IMP_pmi.Resolution__get_as_binary(self)
1217 
1218  def _set_from_binary(self, p):
1219  r"""_set_from_binary(Resolution self, PyObject * p)"""
1220  return _IMP_pmi.Resolution__set_from_binary(self, p)
1221 
1222  def __getstate__(self):
1223  p = self._get_as_binary()
1224  if len(self.__dict__) > 1:
1225  d = self.__dict__.copy()
1226  del d['this']
1227  p = (d, p)
1228  return p
1229 
1230  def __setstate__(self, p):
1231  if not hasattr(self, 'this'):
1232  self.__init__()
1233  if isinstance(p, tuple):
1234  d, p = p
1235  self.__dict__.update(d)
1236  return self._set_from_binary(p)
1237 
1238  __swig_destroy__ = _IMP_pmi.delete_Resolution
1239 
1240 # Register Resolution in _IMP_pmi:
1241 _IMP_pmi.Resolution_swigregister(Resolution)
1242 class Symmetric(IMP.Decorator):
1243  r"""Proxy of C++ IMP::pmi::Symmetric class."""
1244 
1245  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1246 
1247  def get_symmetric(self):
1248  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1249  return _IMP_pmi.Symmetric_get_symmetric(self)
1250 
1251  def set_symmetric(self, d):
1252  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1253  return _IMP_pmi.Symmetric_set_symmetric(self, d)
1254 
1255  def __init__(self, *args):
1256  r"""
1257  __init__(Symmetric self) -> Symmetric
1258  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1259  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1260  """
1261  _IMP_pmi.Symmetric_swiginit(self, _IMP_pmi.new_Symmetric(*args))
1262 
1263  @staticmethod
1264  def get_is_setup(*args):
1265  r"""
1266  get_is_setup(Model m, ParticleIndex pi) -> bool
1267  get_is_setup(_ParticleAdaptor p) -> bool
1268  """
1269  return _IMP_pmi.Symmetric_get_is_setup(*args)
1270 
1271  def show(self, *args):
1272  r"""show(Symmetric self, _ostream out=std::cout)"""
1273  return _IMP_pmi.Symmetric_show(self, *args)
1274 
1275  @staticmethod
1276  def setup_particle(*args):
1277  r"""
1278  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1279  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1280  """
1281  return _IMP_pmi.Symmetric_setup_particle(*args)
1282 
1283  @staticmethod
1284  def get_symmetric_key():
1285  r"""get_symmetric_key() -> FloatKey"""
1286  return _IMP_pmi.Symmetric_get_symmetric_key()
1287 
1288  def add_attribute(self, *args):
1289  r"""
1290  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1291  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1292  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1293  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1294  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1295  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1296  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1297  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1298  """
1299  return _IMP_pmi.Symmetric_add_attribute(self, *args)
1300 
1301  def get_value(self, *args):
1302  r"""
1303  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1304  get_value(Symmetric self, IntKey a0) -> IMP::Int
1305  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1306  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1307  get_value(Symmetric self, StringKey a0) -> IMP::String
1308  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1309  get_value(Symmetric self, ObjectKey a0) -> Object
1310  """
1311  return _IMP_pmi.Symmetric_get_value(self, *args)
1312 
1313  def set_value(self, *args):
1314  r"""
1315  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1316  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1317  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1318  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1319  set_value(Symmetric self, StringKey a0, IMP::String a1)
1320  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1321  set_value(Symmetric self, ObjectKey a0, Object a1)
1322  """
1323  return _IMP_pmi.Symmetric_set_value(self, *args)
1324 
1325  def remove_attribute(self, *args):
1326  r"""
1327  remove_attribute(Symmetric self, FloatKey a0)
1328  remove_attribute(Symmetric self, IntKey a0)
1329  remove_attribute(Symmetric self, FloatsKey a0)
1330  remove_attribute(Symmetric self, IntsKey a0)
1331  remove_attribute(Symmetric self, StringKey a0)
1332  remove_attribute(Symmetric self, ParticleIndexKey a0)
1333  remove_attribute(Symmetric self, ObjectKey a0)
1334  """
1335  return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1336 
1337  def has_attribute(self, *args):
1338  r"""
1339  has_attribute(Symmetric self, FloatKey a0) -> bool
1340  has_attribute(Symmetric self, IntKey a0) -> bool
1341  has_attribute(Symmetric self, FloatsKey a0) -> bool
1342  has_attribute(Symmetric self, IntsKey a0) -> bool
1343  has_attribute(Symmetric self, StringKey a0) -> bool
1344  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1345  has_attribute(Symmetric self, ObjectKey a0) -> bool
1346  """
1347  return _IMP_pmi.Symmetric_has_attribute(self, *args)
1348 
1349  def get_derivative(self, a0):
1350  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1351  return _IMP_pmi.Symmetric_get_derivative(self, a0)
1352 
1353  def get_name(self):
1354  r"""get_name(Symmetric self) -> std::string"""
1355  return _IMP_pmi.Symmetric_get_name(self)
1356 
1357  def clear_caches(self):
1358  r"""clear_caches(Symmetric self)"""
1359  return _IMP_pmi.Symmetric_clear_caches(self)
1360 
1361  def set_name(self, a0):
1362  r"""set_name(Symmetric self, std::string a0)"""
1363  return _IMP_pmi.Symmetric_set_name(self, a0)
1364 
1365  def set_check_level(self, a0):
1366  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1367  return _IMP_pmi.Symmetric_set_check_level(self, a0)
1368 
1369  def add_to_derivative(self, a0, a1, a2):
1370  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1371  return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1372 
1373  def set_is_optimized(self, a0, a1):
1374  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1375  return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1376 
1377  def get_is_optimized(self, a0):
1378  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1379  return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1380 
1381  def get_check_level(self):
1382  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1383  return _IMP_pmi.Symmetric_get_check_level(self)
1384 
1385  def __eq__(self, *args):
1386  r"""
1387  __eq__(Symmetric self, Symmetric o) -> bool
1388  __eq__(Symmetric self, Particle d) -> bool
1389  """
1390  return _IMP_pmi.Symmetric___eq__(self, *args)
1391 
1392  def __ne__(self, *args):
1393  r"""
1394  __ne__(Symmetric self, Symmetric o) -> bool
1395  __ne__(Symmetric self, Particle d) -> bool
1396  """
1397  return _IMP_pmi.Symmetric___ne__(self, *args)
1398 
1399  def __le__(self, *args):
1400  r"""
1401  __le__(Symmetric self, Symmetric o) -> bool
1402  __le__(Symmetric self, Particle d) -> bool
1403  """
1404  return _IMP_pmi.Symmetric___le__(self, *args)
1405 
1406  def __lt__(self, *args):
1407  r"""
1408  __lt__(Symmetric self, Symmetric o) -> bool
1409  __lt__(Symmetric self, Particle d) -> bool
1410  """
1411  return _IMP_pmi.Symmetric___lt__(self, *args)
1412 
1413  def __ge__(self, *args):
1414  r"""
1415  __ge__(Symmetric self, Symmetric o) -> bool
1416  __ge__(Symmetric self, Particle d) -> bool
1417  """
1418  return _IMP_pmi.Symmetric___ge__(self, *args)
1419 
1420  def __gt__(self, *args):
1421  r"""
1422  __gt__(Symmetric self, Symmetric o) -> bool
1423  __gt__(Symmetric self, Particle d) -> bool
1424  """
1425  return _IMP_pmi.Symmetric___gt__(self, *args)
1426 
1427  def __hash__(self):
1428  r"""__hash__(Symmetric self) -> std::size_t"""
1429  return _IMP_pmi.Symmetric___hash__(self)
1430 
1431  def __str__(self):
1432  r"""__str__(Symmetric self) -> std::string"""
1433  return _IMP_pmi.Symmetric___str__(self)
1434 
1435  def __repr__(self):
1436  r"""__repr__(Symmetric self) -> std::string"""
1437  return _IMP_pmi.Symmetric___repr__(self)
1438 
1439  def _get_as_binary(self):
1440  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1441  return _IMP_pmi.Symmetric__get_as_binary(self)
1442 
1443  def _set_from_binary(self, p):
1444  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1445  return _IMP_pmi.Symmetric__set_from_binary(self, p)
1446 
1447  def __getstate__(self):
1448  p = self._get_as_binary()
1449  if len(self.__dict__) > 1:
1450  d = self.__dict__.copy()
1451  del d['this']
1452  p = (d, p)
1453  return p
1454 
1455  def __setstate__(self, p):
1456  if not hasattr(self, 'this'):
1457  self.__init__()
1458  if isinstance(p, tuple):
1459  d, p = p
1460  self.__dict__.update(d)
1461  return self._set_from_binary(p)
1462 
1463  __swig_destroy__ = _IMP_pmi.delete_Symmetric
1464 
1465 # Register Symmetric in _IMP_pmi:
1466 _IMP_pmi.Symmetric_swigregister(Symmetric)
1467 class TransformMover(IMP.core.MonteCarloMover):
1468  r"""Proxy of C++ IMP::pmi::TransformMover class."""
1469 
1470  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1471 
1472  def __init__(self, *args):
1473  r"""
1474  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1475  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1476  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1477  __init__(TransformMover self) -> TransformMover
1478  """
1479  _IMP_pmi.TransformMover_swiginit(self, _IMP_pmi.new_TransformMover(*args))
1480 
1481  def add_xyz_particle(self, pi):
1482  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1483  return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1484 
1485  def add_rigid_body_particle(self, pi):
1486  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1487  return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1488 
1489  def set_maximum_translation(self, mt):
1490  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1491  return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1492 
1493  def set_maximum_rotation(self, mr):
1494  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1495  return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1496 
1497  def get_maximum_translation(self):
1498  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1499  return _IMP_pmi.TransformMover_get_maximum_translation(self)
1500 
1501  def get_maximum_rotation(self):
1502  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1503  return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1504 
1505  def get_last_transformation(self):
1506  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1507  return _IMP_pmi.TransformMover_get_last_transformation(self)
1508 
1509  def get_version_info(self):
1510  r"""get_version_info(TransformMover self) -> VersionInfo"""
1511  return _IMP_pmi.TransformMover_get_version_info(self)
1512  __swig_destroy__ = _IMP_pmi.delete_TransformMover
1513 
1514  def __str__(self):
1515  r"""__str__(TransformMover self) -> std::string"""
1516  return _IMP_pmi.TransformMover___str__(self)
1517 
1518  def __repr__(self):
1519  r"""__repr__(TransformMover self) -> std::string"""
1520  return _IMP_pmi.TransformMover___repr__(self)
1521 
1522  @staticmethod
1523  def get_from(o):
1524  return _object_cast_to_TransformMover(o)
1525 
1526 
1527  def _get_as_binary(self):
1528  r"""_get_as_binary(TransformMover self) -> PyObject *"""
1529  return _IMP_pmi.TransformMover__get_as_binary(self)
1530 
1531  def _set_from_binary(self, p):
1532  r"""_set_from_binary(TransformMover self, PyObject * p)"""
1533  return _IMP_pmi.TransformMover__set_from_binary(self, p)
1534 
1535  def __getstate__(self):
1536  p = self._get_as_binary()
1537  if len(self.__dict__) > 1:
1538  d = self.__dict__.copy()
1539  del d['this']
1540  p = (d, p)
1541  return p
1542 
1543  def __setstate__(self, p):
1544  if not hasattr(self, 'this'):
1545  self.__init__()
1546  if isinstance(p, tuple):
1547  d, p = p
1548  self.__dict__.update(d)
1549  return self._set_from_binary(p)
1550 
1551 
1552 # Register TransformMover in _IMP_pmi:
1553 _IMP_pmi.TransformMover_swigregister(TransformMover)
1554 
1555 def create_elastic_network(ps, dist_cutoff, strength):
1556  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1557  return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1558 
1559 def get_dihedral_angle(p1, p2, p3, p4):
1560  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1561  return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1562 
1563 def get_bipartite_minimum_sphere_distance(m1, m2):
1564  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1565  return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1566 
1567 def get_list_of_bipartite_minimum_sphere_distance(pss):
1568  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1569  return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1570 
1572  r"""get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1573  return _IMP_pmi.get_molecule_name_and_copy(h)
1574 
1575 def get_is_canonical(h):
1576  r"""get_is_canonical(Hierarchy h) -> bool"""
1577  return _IMP_pmi.get_is_canonical(h)
1578 
1579 def get_module_version():
1580  r"""get_module_version() -> std::string const"""
1581  return _IMP_pmi.get_module_version()
1582 
1583 def get_example_path(fname):
1584  r"""get_example_path(std::string fname) -> std::string"""
1585  return _IMP_pmi.get_example_path(fname)
1586 
1587 def get_data_path(fname):
1588  r"""get_data_path(std::string fname) -> std::string"""
1589  return _IMP_pmi.get_data_path(fname)
1590 
1591 from . import _version_check
1592 _version_check.check_version(get_module_version())
1593 __version__ = get_module_version()
1594 
1595 
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
A base class for ISD Restraints.
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.
std::string get_module_version()
Return the version of this module, as a string.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
Object used to hold a set of restraints.
Definition: RestraintSet.h:41
Warning related to handling of structures.
std::string get_molecule_name_and_copy(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and get the "molname.copynum".
Definition: pmi/utilities.h:85
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
Definition: pmi/utilities.h:26
A base class for classes which perturb particles.
Basic utilities for handling cryo-electron microscopy 3D density maps.
Warning for an expected, but missing, file.
bool get_is_canonical(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and check if the root is named System.
Definition: pmi/utilities.h:91
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:119
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
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...
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
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.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
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