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IMP Reference Guide  2.20.1
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 2007-2024 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  add_attribute(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
849  add_attribute(Uncertainty self, SparseIntKey a0, IMP::Int a1)
850  add_attribute(Uncertainty self, SparseStringKey a0, IMP::String a1)
851  add_attribute(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
852  """
853  return _IMP_pmi.Uncertainty_add_attribute(self, *args)
854 
855  def get_value(self, *args):
856  r"""
857  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
858  get_value(Uncertainty self, IntKey a0) -> IMP::Int
859  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
860  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
861  get_value(Uncertainty self, StringKey a0) -> IMP::String
862  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
863  get_value(Uncertainty self, ObjectKey a0) -> Object
864  get_value(Uncertainty self, SparseFloatKey a0) -> IMP::Float
865  get_value(Uncertainty self, SparseIntKey a0) -> IMP::Int
866  get_value(Uncertainty self, SparseStringKey a0) -> IMP::String
867  get_value(Uncertainty self, SparseParticleIndexKey a0) -> ParticleIndex
868  """
869  return _IMP_pmi.Uncertainty_get_value(self, *args)
870 
871  def set_value(self, *args):
872  r"""
873  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
874  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
875  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
876  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
877  set_value(Uncertainty self, StringKey a0, IMP::String a1)
878  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
879  set_value(Uncertainty self, ObjectKey a0, Object a1)
880  set_value(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
881  set_value(Uncertainty self, SparseIntKey a0, IMP::Int a1)
882  set_value(Uncertainty self, SparseStringKey a0, IMP::String a1)
883  set_value(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
884  """
885  return _IMP_pmi.Uncertainty_set_value(self, *args)
886 
887  def remove_attribute(self, *args):
888  r"""
889  remove_attribute(Uncertainty self, FloatKey a0)
890  remove_attribute(Uncertainty self, IntKey a0)
891  remove_attribute(Uncertainty self, FloatsKey a0)
892  remove_attribute(Uncertainty self, IntsKey a0)
893  remove_attribute(Uncertainty self, StringKey a0)
894  remove_attribute(Uncertainty self, ParticleIndexKey a0)
895  remove_attribute(Uncertainty self, ObjectKey a0)
896  remove_attribute(Uncertainty self, SparseFloatKey a0)
897  remove_attribute(Uncertainty self, SparseIntKey a0)
898  remove_attribute(Uncertainty self, SparseStringKey a0)
899  remove_attribute(Uncertainty self, SparseParticleIndexKey a0)
900  """
901  return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
902 
903  def has_attribute(self, *args):
904  r"""
905  has_attribute(Uncertainty self, FloatKey a0) -> bool
906  has_attribute(Uncertainty self, IntKey a0) -> bool
907  has_attribute(Uncertainty self, FloatsKey a0) -> bool
908  has_attribute(Uncertainty self, IntsKey a0) -> bool
909  has_attribute(Uncertainty self, StringKey a0) -> bool
910  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
911  has_attribute(Uncertainty self, ObjectKey a0) -> bool
912  has_attribute(Uncertainty self, SparseFloatKey a0) -> bool
913  has_attribute(Uncertainty self, SparseIntKey a0) -> bool
914  has_attribute(Uncertainty self, SparseStringKey a0) -> bool
915  has_attribute(Uncertainty self, SparseParticleIndexKey a0) -> bool
916  """
917  return _IMP_pmi.Uncertainty_has_attribute(self, *args)
918 
919  def get_derivative(self, a0):
920  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
921  return _IMP_pmi.Uncertainty_get_derivative(self, a0)
922 
923  def get_name(self):
924  r"""get_name(Uncertainty self) -> std::string"""
925  return _IMP_pmi.Uncertainty_get_name(self)
926 
927  def clear_caches(self):
928  r"""clear_caches(Uncertainty self)"""
929  return _IMP_pmi.Uncertainty_clear_caches(self)
930 
931  def set_name(self, a0):
932  r"""set_name(Uncertainty self, std::string a0)"""
933  return _IMP_pmi.Uncertainty_set_name(self, a0)
934 
935  def set_check_level(self, a0):
936  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
937  return _IMP_pmi.Uncertainty_set_check_level(self, a0)
938 
939  def add_to_derivative(self, a0, a1, a2):
940  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
941  return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
942 
943  def set_is_optimized(self, a0, a1):
944  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
945  return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
946 
947  def get_is_optimized(self, a0):
948  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
949  return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
950 
951  def get_check_level(self):
952  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
953  return _IMP_pmi.Uncertainty_get_check_level(self)
954 
955  def __eq__(self, *args):
956  r"""
957  __eq__(Uncertainty self, Uncertainty o) -> bool
958  __eq__(Uncertainty self, Particle d) -> bool
959  """
960  return _IMP_pmi.Uncertainty___eq__(self, *args)
961 
962  def __ne__(self, *args):
963  r"""
964  __ne__(Uncertainty self, Uncertainty o) -> bool
965  __ne__(Uncertainty self, Particle d) -> bool
966  """
967  return _IMP_pmi.Uncertainty___ne__(self, *args)
968 
969  def __le__(self, *args):
970  r"""
971  __le__(Uncertainty self, Uncertainty o) -> bool
972  __le__(Uncertainty self, Particle d) -> bool
973  """
974  return _IMP_pmi.Uncertainty___le__(self, *args)
975 
976  def __lt__(self, *args):
977  r"""
978  __lt__(Uncertainty self, Uncertainty o) -> bool
979  __lt__(Uncertainty self, Particle d) -> bool
980  """
981  return _IMP_pmi.Uncertainty___lt__(self, *args)
982 
983  def __ge__(self, *args):
984  r"""
985  __ge__(Uncertainty self, Uncertainty o) -> bool
986  __ge__(Uncertainty self, Particle d) -> bool
987  """
988  return _IMP_pmi.Uncertainty___ge__(self, *args)
989 
990  def __gt__(self, *args):
991  r"""
992  __gt__(Uncertainty self, Uncertainty o) -> bool
993  __gt__(Uncertainty self, Particle d) -> bool
994  """
995  return _IMP_pmi.Uncertainty___gt__(self, *args)
996 
997  def __hash__(self):
998  r"""__hash__(Uncertainty self) -> std::size_t"""
999  return _IMP_pmi.Uncertainty___hash__(self)
1000 
1001  def __str__(self):
1002  r"""__str__(Uncertainty self) -> std::string"""
1003  return _IMP_pmi.Uncertainty___str__(self)
1004 
1005  def __repr__(self):
1006  r"""__repr__(Uncertainty self) -> std::string"""
1007  return _IMP_pmi.Uncertainty___repr__(self)
1008 
1009  def _get_as_binary(self):
1010  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
1011  return _IMP_pmi.Uncertainty__get_as_binary(self)
1012 
1013  def _set_from_binary(self, p):
1014  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
1015  return _IMP_pmi.Uncertainty__set_from_binary(self, p)
1016 
1017  def __getstate__(self):
1018  p = self._get_as_binary()
1019  if len(self.__dict__) > 1:
1020  d = self.__dict__.copy()
1021  del d['this']
1022  p = (d, p)
1023  return p
1024 
1025  def __setstate__(self, p):
1026  if not hasattr(self, 'this'):
1027  self.__init__()
1028  if isinstance(p, tuple):
1029  d, p = p
1030  self.__dict__.update(d)
1031  return self._set_from_binary(p)
1032 
1033  __swig_destroy__ = _IMP_pmi.delete_Uncertainty
1034 
1035 # Register Uncertainty in _IMP_pmi:
1036 _IMP_pmi.Uncertainty_swigregister(Uncertainty)
1037 class Resolution(IMP.Decorator):
1038  r"""Proxy of C++ IMP::pmi::Resolution class."""
1039 
1040  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1041 
1042  def get_resolution(self):
1043  r"""get_resolution(Resolution self) -> IMP::Float"""
1044  return _IMP_pmi.Resolution_get_resolution(self)
1045 
1046  def set_resolution(self, d):
1047  r"""set_resolution(Resolution self, IMP::Float d)"""
1048  return _IMP_pmi.Resolution_set_resolution(self, d)
1049 
1050  def __init__(self, *args):
1051  r"""
1052  __init__(Resolution self) -> Resolution
1053  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
1054  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
1055  """
1056  _IMP_pmi.Resolution_swiginit(self, _IMP_pmi.new_Resolution(*args))
1057 
1058  @staticmethod
1059  def get_is_setup(*args):
1060  r"""
1061  get_is_setup(Model m, ParticleIndex pi) -> bool
1062  get_is_setup(_ParticleAdaptor p) -> bool
1063  """
1064  return _IMP_pmi.Resolution_get_is_setup(*args)
1065 
1066  def show(self, *args):
1067  r"""show(Resolution self, _ostream out=std::cout)"""
1068  return _IMP_pmi.Resolution_show(self, *args)
1069 
1070  @staticmethod
1071  def setup_particle(*args):
1072  r"""
1073  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1074  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
1075  """
1076  return _IMP_pmi.Resolution_setup_particle(*args)
1077 
1078  @staticmethod
1079  def get_resolution_key():
1080  r"""get_resolution_key() -> FloatKey"""
1081  return _IMP_pmi.Resolution_get_resolution_key()
1082 
1083  def add_attribute(self, *args):
1084  r"""
1085  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1086  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1087  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1088  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1089  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1090  add_attribute(Resolution self, StringKey a0, IMP::String a1)
1091  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1092  add_attribute(Resolution self, ObjectKey a0, Object a1)
1093  add_attribute(Resolution self, SparseFloatKey a0, IMP::Float a1)
1094  add_attribute(Resolution self, SparseIntKey a0, IMP::Int a1)
1095  add_attribute(Resolution self, SparseStringKey a0, IMP::String a1)
1096  add_attribute(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1097  """
1098  return _IMP_pmi.Resolution_add_attribute(self, *args)
1099 
1100  def get_value(self, *args):
1101  r"""
1102  get_value(Resolution self, FloatKey a0) -> IMP::Float
1103  get_value(Resolution self, IntKey a0) -> IMP::Int
1104  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1105  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1106  get_value(Resolution self, StringKey a0) -> IMP::String
1107  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1108  get_value(Resolution self, ObjectKey a0) -> Object
1109  get_value(Resolution self, SparseFloatKey a0) -> IMP::Float
1110  get_value(Resolution self, SparseIntKey a0) -> IMP::Int
1111  get_value(Resolution self, SparseStringKey a0) -> IMP::String
1112  get_value(Resolution self, SparseParticleIndexKey a0) -> ParticleIndex
1113  """
1114  return _IMP_pmi.Resolution_get_value(self, *args)
1115 
1116  def set_value(self, *args):
1117  r"""
1118  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1119  set_value(Resolution self, IntKey a0, IMP::Int a1)
1120  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1121  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1122  set_value(Resolution self, StringKey a0, IMP::String a1)
1123  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1124  set_value(Resolution self, ObjectKey a0, Object a1)
1125  set_value(Resolution self, SparseFloatKey a0, IMP::Float a1)
1126  set_value(Resolution self, SparseIntKey a0, IMP::Int a1)
1127  set_value(Resolution self, SparseStringKey a0, IMP::String a1)
1128  set_value(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1129  """
1130  return _IMP_pmi.Resolution_set_value(self, *args)
1131 
1132  def remove_attribute(self, *args):
1133  r"""
1134  remove_attribute(Resolution self, FloatKey a0)
1135  remove_attribute(Resolution self, IntKey a0)
1136  remove_attribute(Resolution self, FloatsKey a0)
1137  remove_attribute(Resolution self, IntsKey a0)
1138  remove_attribute(Resolution self, StringKey a0)
1139  remove_attribute(Resolution self, ParticleIndexKey a0)
1140  remove_attribute(Resolution self, ObjectKey a0)
1141  remove_attribute(Resolution self, SparseFloatKey a0)
1142  remove_attribute(Resolution self, SparseIntKey a0)
1143  remove_attribute(Resolution self, SparseStringKey a0)
1144  remove_attribute(Resolution self, SparseParticleIndexKey a0)
1145  """
1146  return _IMP_pmi.Resolution_remove_attribute(self, *args)
1147 
1148  def has_attribute(self, *args):
1149  r"""
1150  has_attribute(Resolution self, FloatKey a0) -> bool
1151  has_attribute(Resolution self, IntKey a0) -> bool
1152  has_attribute(Resolution self, FloatsKey a0) -> bool
1153  has_attribute(Resolution self, IntsKey a0) -> bool
1154  has_attribute(Resolution self, StringKey a0) -> bool
1155  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1156  has_attribute(Resolution self, ObjectKey a0) -> bool
1157  has_attribute(Resolution self, SparseFloatKey a0) -> bool
1158  has_attribute(Resolution self, SparseIntKey a0) -> bool
1159  has_attribute(Resolution self, SparseStringKey a0) -> bool
1160  has_attribute(Resolution self, SparseParticleIndexKey a0) -> bool
1161  """
1162  return _IMP_pmi.Resolution_has_attribute(self, *args)
1163 
1164  def get_derivative(self, a0):
1165  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1166  return _IMP_pmi.Resolution_get_derivative(self, a0)
1167 
1168  def get_name(self):
1169  r"""get_name(Resolution self) -> std::string"""
1170  return _IMP_pmi.Resolution_get_name(self)
1171 
1172  def clear_caches(self):
1173  r"""clear_caches(Resolution self)"""
1174  return _IMP_pmi.Resolution_clear_caches(self)
1175 
1176  def set_name(self, a0):
1177  r"""set_name(Resolution self, std::string a0)"""
1178  return _IMP_pmi.Resolution_set_name(self, a0)
1179 
1180  def set_check_level(self, a0):
1181  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1182  return _IMP_pmi.Resolution_set_check_level(self, a0)
1183 
1184  def add_to_derivative(self, a0, a1, a2):
1185  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1186  return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1187 
1188  def set_is_optimized(self, a0, a1):
1189  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1190  return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1191 
1192  def get_is_optimized(self, a0):
1193  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1194  return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1195 
1196  def get_check_level(self):
1197  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1198  return _IMP_pmi.Resolution_get_check_level(self)
1199 
1200  def __eq__(self, *args):
1201  r"""
1202  __eq__(Resolution self, Resolution o) -> bool
1203  __eq__(Resolution self, Particle d) -> bool
1204  """
1205  return _IMP_pmi.Resolution___eq__(self, *args)
1206 
1207  def __ne__(self, *args):
1208  r"""
1209  __ne__(Resolution self, Resolution o) -> bool
1210  __ne__(Resolution self, Particle d) -> bool
1211  """
1212  return _IMP_pmi.Resolution___ne__(self, *args)
1213 
1214  def __le__(self, *args):
1215  r"""
1216  __le__(Resolution self, Resolution o) -> bool
1217  __le__(Resolution self, Particle d) -> bool
1218  """
1219  return _IMP_pmi.Resolution___le__(self, *args)
1220 
1221  def __lt__(self, *args):
1222  r"""
1223  __lt__(Resolution self, Resolution o) -> bool
1224  __lt__(Resolution self, Particle d) -> bool
1225  """
1226  return _IMP_pmi.Resolution___lt__(self, *args)
1227 
1228  def __ge__(self, *args):
1229  r"""
1230  __ge__(Resolution self, Resolution o) -> bool
1231  __ge__(Resolution self, Particle d) -> bool
1232  """
1233  return _IMP_pmi.Resolution___ge__(self, *args)
1234 
1235  def __gt__(self, *args):
1236  r"""
1237  __gt__(Resolution self, Resolution o) -> bool
1238  __gt__(Resolution self, Particle d) -> bool
1239  """
1240  return _IMP_pmi.Resolution___gt__(self, *args)
1241 
1242  def __hash__(self):
1243  r"""__hash__(Resolution self) -> std::size_t"""
1244  return _IMP_pmi.Resolution___hash__(self)
1245 
1246  def __str__(self):
1247  r"""__str__(Resolution self) -> std::string"""
1248  return _IMP_pmi.Resolution___str__(self)
1249 
1250  def __repr__(self):
1251  r"""__repr__(Resolution self) -> std::string"""
1252  return _IMP_pmi.Resolution___repr__(self)
1253 
1254  def _get_as_binary(self):
1255  r"""_get_as_binary(Resolution self) -> PyObject *"""
1256  return _IMP_pmi.Resolution__get_as_binary(self)
1257 
1258  def _set_from_binary(self, p):
1259  r"""_set_from_binary(Resolution self, PyObject * p)"""
1260  return _IMP_pmi.Resolution__set_from_binary(self, p)
1261 
1262  def __getstate__(self):
1263  p = self._get_as_binary()
1264  if len(self.__dict__) > 1:
1265  d = self.__dict__.copy()
1266  del d['this']
1267  p = (d, p)
1268  return p
1269 
1270  def __setstate__(self, p):
1271  if not hasattr(self, 'this'):
1272  self.__init__()
1273  if isinstance(p, tuple):
1274  d, p = p
1275  self.__dict__.update(d)
1276  return self._set_from_binary(p)
1277 
1278  __swig_destroy__ = _IMP_pmi.delete_Resolution
1279 
1280 # Register Resolution in _IMP_pmi:
1281 _IMP_pmi.Resolution_swigregister(Resolution)
1282 class Symmetric(IMP.Decorator):
1283  r"""Proxy of C++ IMP::pmi::Symmetric class."""
1284 
1285  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1286 
1287  def get_symmetric(self):
1288  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1289  return _IMP_pmi.Symmetric_get_symmetric(self)
1290 
1291  def set_symmetric(self, d):
1292  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1293  return _IMP_pmi.Symmetric_set_symmetric(self, d)
1294 
1295  def __init__(self, *args):
1296  r"""
1297  __init__(Symmetric self) -> Symmetric
1298  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1299  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1300  """
1301  _IMP_pmi.Symmetric_swiginit(self, _IMP_pmi.new_Symmetric(*args))
1302 
1303  @staticmethod
1304  def get_is_setup(*args):
1305  r"""
1306  get_is_setup(Model m, ParticleIndex pi) -> bool
1307  get_is_setup(_ParticleAdaptor p) -> bool
1308  """
1309  return _IMP_pmi.Symmetric_get_is_setup(*args)
1310 
1311  def show(self, *args):
1312  r"""show(Symmetric self, _ostream out=std::cout)"""
1313  return _IMP_pmi.Symmetric_show(self, *args)
1314 
1315  @staticmethod
1316  def setup_particle(*args):
1317  r"""
1318  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1319  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1320  """
1321  return _IMP_pmi.Symmetric_setup_particle(*args)
1322 
1323  @staticmethod
1324  def get_symmetric_key():
1325  r"""get_symmetric_key() -> FloatKey"""
1326  return _IMP_pmi.Symmetric_get_symmetric_key()
1327 
1328  def add_attribute(self, *args):
1329  r"""
1330  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1331  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1332  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1333  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1334  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1335  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1336  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1337  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1338  add_attribute(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1339  add_attribute(Symmetric self, SparseIntKey a0, IMP::Int a1)
1340  add_attribute(Symmetric self, SparseStringKey a0, IMP::String a1)
1341  add_attribute(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1342  """
1343  return _IMP_pmi.Symmetric_add_attribute(self, *args)
1344 
1345  def get_value(self, *args):
1346  r"""
1347  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1348  get_value(Symmetric self, IntKey a0) -> IMP::Int
1349  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1350  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1351  get_value(Symmetric self, StringKey a0) -> IMP::String
1352  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1353  get_value(Symmetric self, ObjectKey a0) -> Object
1354  get_value(Symmetric self, SparseFloatKey a0) -> IMP::Float
1355  get_value(Symmetric self, SparseIntKey a0) -> IMP::Int
1356  get_value(Symmetric self, SparseStringKey a0) -> IMP::String
1357  get_value(Symmetric self, SparseParticleIndexKey a0) -> ParticleIndex
1358  """
1359  return _IMP_pmi.Symmetric_get_value(self, *args)
1360 
1361  def set_value(self, *args):
1362  r"""
1363  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1364  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1365  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1366  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1367  set_value(Symmetric self, StringKey a0, IMP::String a1)
1368  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1369  set_value(Symmetric self, ObjectKey a0, Object a1)
1370  set_value(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1371  set_value(Symmetric self, SparseIntKey a0, IMP::Int a1)
1372  set_value(Symmetric self, SparseStringKey a0, IMP::String a1)
1373  set_value(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1374  """
1375  return _IMP_pmi.Symmetric_set_value(self, *args)
1376 
1377  def remove_attribute(self, *args):
1378  r"""
1379  remove_attribute(Symmetric self, FloatKey a0)
1380  remove_attribute(Symmetric self, IntKey a0)
1381  remove_attribute(Symmetric self, FloatsKey a0)
1382  remove_attribute(Symmetric self, IntsKey a0)
1383  remove_attribute(Symmetric self, StringKey a0)
1384  remove_attribute(Symmetric self, ParticleIndexKey a0)
1385  remove_attribute(Symmetric self, ObjectKey a0)
1386  remove_attribute(Symmetric self, SparseFloatKey a0)
1387  remove_attribute(Symmetric self, SparseIntKey a0)
1388  remove_attribute(Symmetric self, SparseStringKey a0)
1389  remove_attribute(Symmetric self, SparseParticleIndexKey a0)
1390  """
1391  return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1392 
1393  def has_attribute(self, *args):
1394  r"""
1395  has_attribute(Symmetric self, FloatKey a0) -> bool
1396  has_attribute(Symmetric self, IntKey a0) -> bool
1397  has_attribute(Symmetric self, FloatsKey a0) -> bool
1398  has_attribute(Symmetric self, IntsKey a0) -> bool
1399  has_attribute(Symmetric self, StringKey a0) -> bool
1400  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1401  has_attribute(Symmetric self, ObjectKey a0) -> bool
1402  has_attribute(Symmetric self, SparseFloatKey a0) -> bool
1403  has_attribute(Symmetric self, SparseIntKey a0) -> bool
1404  has_attribute(Symmetric self, SparseStringKey a0) -> bool
1405  has_attribute(Symmetric self, SparseParticleIndexKey a0) -> bool
1406  """
1407  return _IMP_pmi.Symmetric_has_attribute(self, *args)
1408 
1409  def get_derivative(self, a0):
1410  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1411  return _IMP_pmi.Symmetric_get_derivative(self, a0)
1412 
1413  def get_name(self):
1414  r"""get_name(Symmetric self) -> std::string"""
1415  return _IMP_pmi.Symmetric_get_name(self)
1416 
1417  def clear_caches(self):
1418  r"""clear_caches(Symmetric self)"""
1419  return _IMP_pmi.Symmetric_clear_caches(self)
1420 
1421  def set_name(self, a0):
1422  r"""set_name(Symmetric self, std::string a0)"""
1423  return _IMP_pmi.Symmetric_set_name(self, a0)
1424 
1425  def set_check_level(self, a0):
1426  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1427  return _IMP_pmi.Symmetric_set_check_level(self, a0)
1428 
1429  def add_to_derivative(self, a0, a1, a2):
1430  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1431  return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1432 
1433  def set_is_optimized(self, a0, a1):
1434  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1435  return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1436 
1437  def get_is_optimized(self, a0):
1438  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1439  return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1440 
1441  def get_check_level(self):
1442  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1443  return _IMP_pmi.Symmetric_get_check_level(self)
1444 
1445  def __eq__(self, *args):
1446  r"""
1447  __eq__(Symmetric self, Symmetric o) -> bool
1448  __eq__(Symmetric self, Particle d) -> bool
1449  """
1450  return _IMP_pmi.Symmetric___eq__(self, *args)
1451 
1452  def __ne__(self, *args):
1453  r"""
1454  __ne__(Symmetric self, Symmetric o) -> bool
1455  __ne__(Symmetric self, Particle d) -> bool
1456  """
1457  return _IMP_pmi.Symmetric___ne__(self, *args)
1458 
1459  def __le__(self, *args):
1460  r"""
1461  __le__(Symmetric self, Symmetric o) -> bool
1462  __le__(Symmetric self, Particle d) -> bool
1463  """
1464  return _IMP_pmi.Symmetric___le__(self, *args)
1465 
1466  def __lt__(self, *args):
1467  r"""
1468  __lt__(Symmetric self, Symmetric o) -> bool
1469  __lt__(Symmetric self, Particle d) -> bool
1470  """
1471  return _IMP_pmi.Symmetric___lt__(self, *args)
1472 
1473  def __ge__(self, *args):
1474  r"""
1475  __ge__(Symmetric self, Symmetric o) -> bool
1476  __ge__(Symmetric self, Particle d) -> bool
1477  """
1478  return _IMP_pmi.Symmetric___ge__(self, *args)
1479 
1480  def __gt__(self, *args):
1481  r"""
1482  __gt__(Symmetric self, Symmetric o) -> bool
1483  __gt__(Symmetric self, Particle d) -> bool
1484  """
1485  return _IMP_pmi.Symmetric___gt__(self, *args)
1486 
1487  def __hash__(self):
1488  r"""__hash__(Symmetric self) -> std::size_t"""
1489  return _IMP_pmi.Symmetric___hash__(self)
1490 
1491  def __str__(self):
1492  r"""__str__(Symmetric self) -> std::string"""
1493  return _IMP_pmi.Symmetric___str__(self)
1494 
1495  def __repr__(self):
1496  r"""__repr__(Symmetric self) -> std::string"""
1497  return _IMP_pmi.Symmetric___repr__(self)
1498 
1499  def _get_as_binary(self):
1500  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1501  return _IMP_pmi.Symmetric__get_as_binary(self)
1502 
1503  def _set_from_binary(self, p):
1504  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1505  return _IMP_pmi.Symmetric__set_from_binary(self, p)
1506 
1507  def __getstate__(self):
1508  p = self._get_as_binary()
1509  if len(self.__dict__) > 1:
1510  d = self.__dict__.copy()
1511  del d['this']
1512  p = (d, p)
1513  return p
1514 
1515  def __setstate__(self, p):
1516  if not hasattr(self, 'this'):
1517  self.__init__()
1518  if isinstance(p, tuple):
1519  d, p = p
1520  self.__dict__.update(d)
1521  return self._set_from_binary(p)
1522 
1523  __swig_destroy__ = _IMP_pmi.delete_Symmetric
1524 
1525 # Register Symmetric in _IMP_pmi:
1526 _IMP_pmi.Symmetric_swigregister(Symmetric)
1527 class TransformMover(IMP.core.MonteCarloMover):
1528  r"""Proxy of C++ IMP::pmi::TransformMover class."""
1529 
1530  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1531 
1532  def __init__(self, *args):
1533  r"""
1534  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1535  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1536  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1537  __init__(TransformMover self) -> TransformMover
1538  """
1539  _IMP_pmi.TransformMover_swiginit(self, _IMP_pmi.new_TransformMover(*args))
1540 
1541  def add_xyz_particle(self, pi):
1542  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1543  return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1544 
1545  def add_rigid_body_particle(self, pi):
1546  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1547  return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1548 
1549  def set_maximum_translation(self, mt):
1550  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1551  return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1552 
1553  def set_maximum_rotation(self, mr):
1554  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1555  return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1556 
1557  def get_maximum_translation(self):
1558  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1559  return _IMP_pmi.TransformMover_get_maximum_translation(self)
1560 
1561  def get_maximum_rotation(self):
1562  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1563  return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1564 
1565  def get_last_transformation(self):
1566  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1567  return _IMP_pmi.TransformMover_get_last_transformation(self)
1568 
1569  def get_version_info(self):
1570  r"""get_version_info(TransformMover self) -> VersionInfo"""
1571  return _IMP_pmi.TransformMover_get_version_info(self)
1572  __swig_destroy__ = _IMP_pmi.delete_TransformMover
1573 
1574  def __str__(self):
1575  r"""__str__(TransformMover self) -> std::string"""
1576  return _IMP_pmi.TransformMover___str__(self)
1577 
1578  def __repr__(self):
1579  r"""__repr__(TransformMover self) -> std::string"""
1580  return _IMP_pmi.TransformMover___repr__(self)
1581 
1582  @staticmethod
1583  def get_from(o):
1584  return _object_cast_to_TransformMover(o)
1585 
1586 
1587  def _get_as_binary(self):
1588  r"""_get_as_binary(TransformMover self) -> PyObject *"""
1589  return _IMP_pmi.TransformMover__get_as_binary(self)
1590 
1591  def _set_from_binary(self, p):
1592  r"""_set_from_binary(TransformMover self, PyObject * p)"""
1593  return _IMP_pmi.TransformMover__set_from_binary(self, p)
1594 
1595  def __getstate__(self):
1596  p = self._get_as_binary()
1597  if len(self.__dict__) > 1:
1598  d = self.__dict__.copy()
1599  del d['this']
1600  p = (d, p)
1601  return p
1602 
1603  def __setstate__(self, p):
1604  if not hasattr(self, 'this'):
1605  self.__init__()
1606  if isinstance(p, tuple):
1607  d, p = p
1608  self.__dict__.update(d)
1609  return self._set_from_binary(p)
1610 
1611 
1612 # Register TransformMover in _IMP_pmi:
1613 _IMP_pmi.TransformMover_swigregister(TransformMover)
1614 
1615 def create_elastic_network(ps, dist_cutoff, strength):
1616  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1617  return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1618 
1619 def get_dihedral_angle(p1, p2, p3, p4):
1620  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1621  return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1622 
1623 def get_bipartite_minimum_sphere_distance(m1, m2):
1624  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1625  return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1626 
1627 def get_list_of_bipartite_minimum_sphere_distance(pss):
1628  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1629  return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1630 
1632  r"""get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1633  return _IMP_pmi.get_molecule_name_and_copy(h)
1634 
1635 def get_is_canonical(h):
1636  r"""get_is_canonical(Hierarchy h) -> bool"""
1637  return _IMP_pmi.get_is_canonical(h)
1638 
1639 def get_module_version():
1640  r"""get_module_version() -> std::string const"""
1641  return _IMP_pmi.get_module_version()
1642 
1643 def get_example_path(fname):
1644  r"""get_example_path(std::string fname) -> std::string"""
1645  return _IMP_pmi.get_example_path(fname)
1646 
1647 def get_data_path(fname):
1648  r"""get_data_path(std::string fname) -> std::string"""
1649  return _IMP_pmi.get_data_path(fname)
1650 
1651 from . import _version_check
1652 _version_check.check_version(get_module_version())
1653 __version__ = get_module_version()
1654 
1655 
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.
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