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IMP Reference Guide  develop.714915d50b,2024/12/07
The Integrative Modeling Platform
pmi/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.3.0
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 
12 
13 
14 from sys import version_info as _swig_python_version_info
15 import _IMP_pmi
16 
17 try:
18  import builtins as __builtin__
19 except ImportError:
20  import __builtin__
21 
22 def _swig_repr(self):
23  try:
24  strthis = "proxy of " + self.this.__repr__()
25  except __builtin__.Exception:
26  strthis = ""
27  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
28 
29 
30 def _swig_setattr_nondynamic_instance_variable(set):
31  def set_instance_attr(self, name, value):
32  if name == "this":
33  set(self, name, value)
34  elif name == "thisown":
35  self.this.own(value)
36  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
37  set(self, name, value)
38  else:
39  raise AttributeError("You cannot add instance attributes to %s" % self)
40  return set_instance_attr
41 
42 
43 def _swig_setattr_nondynamic_class_variable(set):
44  def set_class_attr(cls, name, value):
45  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
46  set(cls, name, value)
47  else:
48  raise AttributeError("You cannot add class attributes to %s" % cls)
49  return set_class_attr
50 
51 
52 def _swig_add_metaclass(metaclass):
53  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
54  def wrapper(cls):
55  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
56  return wrapper
57 
58 
59 class _SwigNonDynamicMeta(type):
60  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
62 
63 
64 import weakref
65 
66 class IMP_PMI_SwigPyIterator(object):
67  r"""Proxy of C++ swig::IMP_PMI_SwigPyIterator class."""
68 
69  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
70 
71  def __init__(self, *args, **kwargs):
72  raise AttributeError("No constructor defined - class is abstract")
73  __repr__ = _swig_repr
74  __swig_destroy__ = _IMP_pmi.delete_IMP_PMI_SwigPyIterator
75 
76  def value(self):
77  r"""value(IMP_PMI_SwigPyIterator self) -> PyObject *"""
78  return _IMP_pmi.IMP_PMI_SwigPyIterator_value(self)
79 
80  def incr(self, n=1):
81  r"""incr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
82  return _IMP_pmi.IMP_PMI_SwigPyIterator_incr(self, n)
83 
84  def decr(self, n=1):
85  r"""decr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
86  return _IMP_pmi.IMP_PMI_SwigPyIterator_decr(self, n)
87 
88  def distance(self, x):
89  r"""distance(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t"""
90  return _IMP_pmi.IMP_PMI_SwigPyIterator_distance(self, x)
91 
92  def equal(self, x):
93  r"""equal(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
94  return _IMP_pmi.IMP_PMI_SwigPyIterator_equal(self, x)
95 
96  def copy(self):
97  r"""copy(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator"""
98  return _IMP_pmi.IMP_PMI_SwigPyIterator_copy(self)
99 
100  def next(self):
101  r"""next(IMP_PMI_SwigPyIterator self) -> PyObject *"""
102  return _IMP_pmi.IMP_PMI_SwigPyIterator_next(self)
103 
104  def __next__(self):
105  r"""__next__(IMP_PMI_SwigPyIterator self) -> PyObject *"""
106  return _IMP_pmi.IMP_PMI_SwigPyIterator___next__(self)
107 
108  def previous(self):
109  r"""previous(IMP_PMI_SwigPyIterator self) -> PyObject *"""
110  return _IMP_pmi.IMP_PMI_SwigPyIterator_previous(self)
111 
112  def advance(self, n):
113  r"""advance(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
114  return _IMP_pmi.IMP_PMI_SwigPyIterator_advance(self, n)
115 
116  def __eq__(self, x):
117  r"""__eq__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
118  return _IMP_pmi.IMP_PMI_SwigPyIterator___eq__(self, x)
119 
120  def __ne__(self, x):
121  r"""__ne__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
122  return _IMP_pmi.IMP_PMI_SwigPyIterator___ne__(self, x)
123 
124  def __iadd__(self, n):
125  r"""__iadd__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
126  return _IMP_pmi.IMP_PMI_SwigPyIterator___iadd__(self, n)
127 
128  def __isub__(self, n):
129  r"""__isub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
130  return _IMP_pmi.IMP_PMI_SwigPyIterator___isub__(self, n)
131 
132  def __add__(self, n):
133  r"""__add__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
134  return _IMP_pmi.IMP_PMI_SwigPyIterator___add__(self, n)
135 
136  def __sub__(self, *args):
137  r"""
138  __sub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator
139  __sub__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t
140  """
141  return _IMP_pmi.IMP_PMI_SwigPyIterator___sub__(self, *args)
142  def __iter__(self):
143  return self
144 
145 # Register IMP_PMI_SwigPyIterator in _IMP_pmi:
146 _IMP_pmi.IMP_PMI_SwigPyIterator_swigregister(IMP_PMI_SwigPyIterator)
147 
148 _value_types=[]
149 _object_types=[]
150 _raii_types=[]
151 _plural_types=[]
152 
153 IMP_DEBUG = _IMP_pmi.IMP_DEBUG
154 
155 IMP_RELEASE = _IMP_pmi.IMP_RELEASE
156 
157 IMP_SILENT = _IMP_pmi.IMP_SILENT
158 
159 IMP_PROGRESS = _IMP_pmi.IMP_PROGRESS
160 
161 IMP_TERSE = _IMP_pmi.IMP_TERSE
162 
163 IMP_VERBOSE = _IMP_pmi.IMP_VERBOSE
164 
165 IMP_MEMORY = _IMP_pmi.IMP_MEMORY
166 
167 IMP_NONE = _IMP_pmi.IMP_NONE
168 
169 IMP_USAGE = _IMP_pmi.IMP_USAGE
170 
171 IMP_INTERNAL = _IMP_pmi.IMP_INTERNAL
172 
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_pmi.IMP_KERNEL_HAS_LOG4CXX
174 
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_pmi.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
176 
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_pmi.IMP_COMPILER_HAS_DEBUG_VECTOR
178 
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_pmi.IMP_COMPILER_HAS_RANDOM_SHUFFLE
180 
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_pmi.IMP_COMPILER_HAS_THREE_WAY
182 
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_KERNEL_HAS_BOOST_RANDOM
184 
185 IMP_KERNEL_HAS_NUMPY = _IMP_pmi.IMP_KERNEL_HAS_NUMPY
186 
187 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi.IMP_KERNEL_HAS_GPERFTOOLS
188 
189 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
192 
193 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi.IMPKERNEL_SHOW_WARNINGS
194 
195 
196 import sys
197 class _DirectorObjects:
198  """@internal Simple class to keep references to director objects
199  to prevent premature deletion."""
200  def __init__(self):
201  self._objects = []
202  def register(self, obj):
203  """Take a reference to a director object; will only work for
204  refcounted C++ classes"""
205  if hasattr(obj, 'get_ref_count'):
206  self._objects.append(obj)
207  def cleanup(self):
208  """Only drop our reference and allow cleanup by Python if no other
209  Python references exist (we hold 3 references: one in self._objects,
210  one in x, and one in the argument list for getrefcount) *and* no
211  other C++ references exist (the Python object always holds one)"""
212  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
213  or x.get_ref_count() > 1]
214 # Do in two steps so the references are kept until the end of the
215 # function (deleting references may trigger a fresh call to this method)
216  self._objects = objs
217  def get_object_count(self):
218  """Get number of director objects (useful for testing only)"""
219  return len(self._objects)
220 _director_objects = _DirectorObjects()
221 
222 class _ostream(object):
223  r"""Proxy of C++ std::ostream class."""
224 
225  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
226 
227  def __init__(self, *args, **kwargs):
228  raise AttributeError("No constructor defined")
229  __repr__ = _swig_repr
230 
231  def write(self, osa_buf):
232  r"""write(_ostream self, char const * osa_buf)"""
233  return _IMP_pmi._ostream_write(self, osa_buf)
234 
235 # Register _ostream in _IMP_pmi:
236 _IMP_pmi._ostream_swigregister(_ostream)
237 IMP_C_OPEN_BINARY = _IMP_pmi.IMP_C_OPEN_BINARY
238 
239 import IMP
240 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_FILESYSTEM
241 
242 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
243 
244 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CGAL_HAS_BOOST_RANDOM
245 
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_SYSTEM
247 
248 IMP_CGAL_HAS_NUMPY = _IMP_pmi.IMP_CGAL_HAS_NUMPY
249 
250 IMPCGAL_SHOW_WARNINGS = _IMP_pmi.IMPCGAL_SHOW_WARNINGS
251 
252 import IMP.cgal
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_IMP_CGAL
254 
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
256 
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
258 
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_RANDOM
260 
261 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_SYSTEM
262 
263 IMP_ALGEBRA_HAS_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_CGAL
264 
265 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi.IMP_ALGEBRA_HAS_NUMPY
266 
267 IMP_ALGEBRA_HAS_ANN = _IMP_pmi.IMP_ALGEBRA_HAS_ANN
268 
269 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi.IMPALGEBRA_SHOW_WARNINGS
270 
271 import IMP.algebra
272 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_IMP_CGAL
273 
274 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
275 
276 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
277 
278 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_RANDOM
279 
280 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_SYSTEM
281 
282 IMP_DISPLAY_HAS_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_CGAL
283 
284 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi.IMP_DISPLAY_HAS_NUMPY
285 
286 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi.IMPDISPLAY_SHOW_WARNINGS
287 
288 import IMP.display
289 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
292 
293 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
294 
295 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
296 
297 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
298 
299 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_CGAL
300 
301 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_HDF5
302 
303 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_NUMPY
304 
305 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi.IMPSCOREFUNCTOR_SHOW_WARNINGS
306 
307 import IMP.score_functor
308 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_IMP_CGAL
309 
310 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
311 
312 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
313 
314 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_RANDOM
315 
316 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_SYSTEM
317 
318 IMP_STATISTICS_HAS_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_CGAL
319 
320 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi.IMP_STATISTICS_HAS_NUMPY
321 
322 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi.IMPSTATISTICS_SHOW_WARNINGS
323 
324 import IMP.statistics
325 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi.IMP_CORE_HAS_IMP_CGAL
326 
327 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi.IMP_CORE_HAS_IMP_KERNEL
328 
329 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_FILESYSTEM
330 
331 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
332 
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CORE_HAS_BOOST_RANDOM
334 
335 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_SYSTEM
336 
337 IMP_CORE_HAS_CGAL = _IMP_pmi.IMP_CORE_HAS_CGAL
338 
339 IMP_CORE_HAS_HDF5 = _IMP_pmi.IMP_CORE_HAS_HDF5
340 
341 IMP_CORE_HAS_NUMPY = _IMP_pmi.IMP_CORE_HAS_NUMPY
342 
343 IMPCORE_SHOW_WARNINGS = _IMP_pmi.IMPCORE_SHOW_WARNINGS
344 
345 import IMP.core
346 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_CONTAINER_HAS_IMP_ALGEBRA
347 
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_CGAL
349 
350 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi.IMP_CONTAINER_HAS_IMP_DISPLAY
351 
352 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_KERNEL
353 
354 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
355 
356 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
357 
358 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
359 
360 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_RANDOM
361 
362 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_SYSTEM
363 
364 IMP_CONTAINER_HAS_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_CGAL
365 
366 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi.IMP_CONTAINER_HAS_HDF5
367 
368 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi.IMP_CONTAINER_HAS_NUMPY
369 
370 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi.IMP_CONTAINER_HAS_PYTHON_IHM
371 
372 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
373 
374 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi.IMP_CONTAINER_HAS_ROBIN_MAP
375 
376 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi.IMPCONTAINER_SHOW_WARNINGS
377 
378 import IMP.container
379 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi.IMP_ATOM_HAS_IMP_CGAL
380 
381 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi.IMP_ATOM_HAS_IMP_KERNEL
382 
383 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
384 
385 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
386 
387 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ATOM_HAS_BOOST_RANDOM
388 
389 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi.IMP_ATOM_HAS_BOOST_REGEX
390 
391 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ATOM_HAS_BOOST_SYSTEM
392 
393 IMP_ATOM_HAS_CGAL = _IMP_pmi.IMP_ATOM_HAS_CGAL
394 
395 IMP_ATOM_HAS_HDF5 = _IMP_pmi.IMP_ATOM_HAS_HDF5
396 
397 IMP_ATOM_HAS_NUMPY = _IMP_pmi.IMP_ATOM_HAS_NUMPY
398 
399 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi.IMP_ATOM_HAS_PYTHON_IHM
400 
401 IMPATOM_SHOW_WARNINGS = _IMP_pmi.IMPATOM_SHOW_WARNINGS
402 
403 IMP_ATOM_TYPE_INDEX = _IMP_pmi.IMP_ATOM_TYPE_INDEX
404 
405 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi.IMP_RESIDUE_TYPE_INDEX
406 
407 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi.IMP_HIERARCHY_TYPE_INDEX
408 
409 IMP_CHAIN_TYPE_INDEX = _IMP_pmi.IMP_CHAIN_TYPE_INDEX
410 
411 import IMP.atom
412 IMP_EM_HAS_IMP_CGAL = _IMP_pmi.IMP_EM_HAS_IMP_CGAL
413 
414 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi.IMP_EM_HAS_IMP_CONTAINER
415 
416 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi.IMP_EM_HAS_IMP_DISPLAY
417 
418 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_EM_HAS_IMP_SCORE_FUNCTOR
419 
420 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_FILESYSTEM
421 
422 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
423 
424 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_EM_HAS_BOOST_RANDOM
425 
426 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi.IMP_EM_HAS_BOOST_REGEX
427 
428 IMP_EM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_SYSTEM
429 
430 IMP_EM_HAS_CGAL = _IMP_pmi.IMP_EM_HAS_CGAL
431 
432 IMP_EM_HAS_HDF5 = _IMP_pmi.IMP_EM_HAS_HDF5
433 
434 IMP_EM_HAS_NUMPY = _IMP_pmi.IMP_EM_HAS_NUMPY
435 
436 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi.IMP_EM_HAS_PYTHON_IHM
437 
438 IMPEM_SHOW_WARNINGS = _IMP_pmi.IMPEM_SHOW_WARNINGS
439 
440 import IMP.em
441 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi.IMP_SAXS_HAS_IMP_CGAL
442 
443 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi.IMP_SAXS_HAS_IMP_CONTAINER
444 
445 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi.IMP_SAXS_HAS_IMP_DISPLAY
446 
447 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi.IMP_SAXS_HAS_IMP_KERNEL
448 
449 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
450 
451 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_FILESYSTEM
452 
453 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
454 
455 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SAXS_HAS_BOOST_RANDOM
456 
457 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi.IMP_SAXS_HAS_BOOST_REGEX
458 
459 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_SYSTEM
460 
461 IMP_SAXS_HAS_CGAL = _IMP_pmi.IMP_SAXS_HAS_CGAL
462 
463 IMP_SAXS_HAS_HDF5 = _IMP_pmi.IMP_SAXS_HAS_HDF5
464 
465 IMP_SAXS_HAS_NUMPY = _IMP_pmi.IMP_SAXS_HAS_NUMPY
466 
467 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi.IMP_SAXS_HAS_PYTHON_IHM
468 
469 IMPSAXS_SHOW_WARNINGS = _IMP_pmi.IMPSAXS_SHOW_WARNINGS
470 
471 import IMP.saxs
472 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi.IMP_ISD_HAS_IMP_CGAL
473 
474 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi.IMP_ISD_HAS_IMP_DISPLAY
475 
476 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
477 
478 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_FILESYSTEM
479 
480 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
481 
482 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ISD_HAS_BOOST_RANDOM
483 
484 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi.IMP_ISD_HAS_BOOST_REGEX
485 
486 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_SYSTEM
487 
488 IMP_ISD_HAS_CGAL = _IMP_pmi.IMP_ISD_HAS_CGAL
489 
490 IMP_ISD_HAS_HDF5 = _IMP_pmi.IMP_ISD_HAS_HDF5
491 
492 IMP_ISD_HAS_NUMPY = _IMP_pmi.IMP_ISD_HAS_NUMPY
493 
494 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi.IMP_ISD_HAS_PYTHON_IHM
495 
496 IMPISD_SHOW_WARNINGS = _IMP_pmi.IMPISD_SHOW_WARNINGS
497 
498 import IMP.isd
499 IMP_PMI_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_PMI_HAS_IMP_ALGEBRA
500 
501 IMP_PMI_HAS_IMP_ATOM = _IMP_pmi.IMP_PMI_HAS_IMP_ATOM
502 
503 IMP_PMI_HAS_IMP_CGAL = _IMP_pmi.IMP_PMI_HAS_IMP_CGAL
504 
505 IMP_PMI_HAS_IMP_DISPLAY = _IMP_pmi.IMP_PMI_HAS_IMP_DISPLAY
506 
507 IMP_PMI_HAS_IMP_EM = _IMP_pmi.IMP_PMI_HAS_IMP_EM
508 
509 IMP_PMI_HAS_IMP_KERNEL = _IMP_pmi.IMP_PMI_HAS_IMP_KERNEL
510 
511 IMP_PMI_HAS_IMP_SAXS = _IMP_pmi.IMP_PMI_HAS_IMP_SAXS
512 
513 IMP_PMI_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_PMI_HAS_IMP_SCORE_FUNCTOR
514 
515 IMP_PMI_HAS_IMP_STATISTICS = _IMP_pmi.IMP_PMI_HAS_IMP_STATISTICS
516 
517 IMP_PMI_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_FILESYSTEM
518 
519 IMP_PMI_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_PMI_HAS_BOOST_PROGRAMOPTIONS
520 
521 IMP_PMI_HAS_BOOST_RANDOM = _IMP_pmi.IMP_PMI_HAS_BOOST_RANDOM
522 
523 IMP_PMI_HAS_BOOST_REGEX = _IMP_pmi.IMP_PMI_HAS_BOOST_REGEX
524 
525 IMP_PMI_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_SYSTEM
526 
527 IMP_PMI_HAS_CGAL = _IMP_pmi.IMP_PMI_HAS_CGAL
528 
529 IMP_PMI_HAS_HDF5 = _IMP_pmi.IMP_PMI_HAS_HDF5
530 
531 IMP_PMI_HAS_NUMPY = _IMP_pmi.IMP_PMI_HAS_NUMPY
532 
533 IMP_PMI_HAS_PYTHON_IHM = _IMP_pmi.IMP_PMI_HAS_PYTHON_IHM
534 
535 IMPPMI_SHOW_WARNINGS = _IMP_pmi.IMPPMI_SHOW_WARNINGS
536 
537 
538 _object_types.append("CompositeRestraint")
539 
540 
541 def _object_cast_to_CompositeRestraint(o):
542  r"""_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
543  return _IMP_pmi._object_cast_to_CompositeRestraint(o)
544 
545 _object_types.append("CrossLinkRestraintSet")
546 
547 
548 def _object_cast_to_CrossLinkRestraintSet(o):
549  r"""_object_cast_to_CrossLinkRestraintSet(Object o) -> CrossLinkRestraintSet"""
550  return _IMP_pmi._object_cast_to_CrossLinkRestraintSet(o)
551 
552 def Uncertainties(l=[]):
553  return [Uncertainty(x) for x in l]
554 _plural_types.append("Uncertainties")
555 
556 
557 _value_types.append("Uncertainty")
558 
559 
560 def Resolutions(l=[]):
561  return [Resolution(x) for x in l]
562 _plural_types.append("Resolutions")
563 
564 
565 _value_types.append("Resolution")
566 
567 
568 def Symmetrics(l=[]):
569  return [Symmetric(x) for x in l]
570 _plural_types.append("Symmetrics")
571 
572 
573 _value_types.append("Symmetric")
574 
575 
576 _object_types.append("TransformMover")
577 
578 
579 def _object_cast_to_TransformMover(o):
580  r"""_object_cast_to_TransformMover(Object o) -> TransformMover"""
581  return _IMP_pmi._object_cast_to_TransformMover(o)
582 
583 _object_types.append("MembraneRestraint")
584 
585 
586 def _object_cast_to_MembraneRestraint(o):
587  r"""_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
588  return _IMP_pmi._object_cast_to_MembraneRestraint(o)
589 
590 class StructureWarning(UserWarning):
591  """Warning related to handling of structures"""
592  pass
593 
594 
595 class ParameterWarning(UserWarning):
596  """Warning for probably incorrect input parameters"""
597  pass
598 
599 
600 class MissingFileWarning(UserWarning):
601  """Warning for an expected, but missing, file"""
602  pass
603 
604 class MembraneRestraint(IMP.isd.ISDRestraint):
605  r"""Proxy of C++ IMP::pmi::MembraneRestraint class."""
606 
607  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
608 
609  def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
610  r"""__init__(MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
611  _IMP_pmi.MembraneRestraint_swiginit(self, _IMP_pmi.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear))
612 
613  def add_particles_below(self, particles):
614  r"""add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
615  return _IMP_pmi.MembraneRestraint_add_particles_below(self, particles)
616 
617  def add_particles_above(self, particles):
618  r"""add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
619  return _IMP_pmi.MembraneRestraint_add_particles_above(self, particles)
620 
621  def add_particles_inside(self, particles):
622  r"""add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
623  return _IMP_pmi.MembraneRestraint_add_particles_inside(self, particles)
624 
625  def get_score(self, prob):
626  r"""get_score(MembraneRestraint self, double prob) -> double"""
627  return _IMP_pmi.MembraneRestraint_get_score(self, prob)
628 
629  def get_probability_above(self, z, z_slope_center_upper):
630  r"""get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
631  return _IMP_pmi.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
632 
633  def get_score_above(self, z, z_slope_center_upper):
634  r"""get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
635  return _IMP_pmi.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
636 
637  def get_probability_below(self, z, z_slope_center_lower):
638  r"""get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
639  return _IMP_pmi.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
640 
641  def get_score_below(self, z, z_slope_center_lower):
642  r"""get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
643  return _IMP_pmi.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
644 
645  def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
646  r"""get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
647  return _IMP_pmi.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
648  __swig_destroy__ = _IMP_pmi.delete_MembraneRestraint
649 
650  def __str__(self):
651  r"""__str__(MembraneRestraint self) -> std::string"""
652  return _IMP_pmi.MembraneRestraint___str__(self)
653 
654  def __repr__(self):
655  r"""__repr__(MembraneRestraint self) -> std::string"""
656  return _IMP_pmi.MembraneRestraint___repr__(self)
657 
658  @staticmethod
659  def get_from(o):
660  return _object_cast_to_MembraneRestraint(o)
661 
662 
663 # Register MembraneRestraint in _IMP_pmi:
664 _IMP_pmi.MembraneRestraint_swigregister(MembraneRestraint)
665 class CompositeRestraint(IMP.Restraint):
666  r"""Proxy of C++ IMP::pmi::CompositeRestraint class."""
667 
668  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
669 
670  def __init__(self, *args):
671  r"""__init__(CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%") -> CompositeRestraint"""
672  _IMP_pmi.CompositeRestraint_swiginit(self, _IMP_pmi.new_CompositeRestraint(*args))
673 
674  def add_composite_particle(self, pi):
675  r"""add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
676  return _IMP_pmi.CompositeRestraint_add_composite_particle(self, pi)
677 
678  def get_number_of_elements(self):
679  r"""get_number_of_elements(CompositeRestraint self) -> unsigned int"""
680  return _IMP_pmi.CompositeRestraint_get_number_of_elements(self)
681 
682  def do_get_inputs(self):
683  r"""do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
684  return _IMP_pmi.CompositeRestraint_do_get_inputs(self)
685 
686  def get_version_info(self):
687  r"""get_version_info(CompositeRestraint self) -> VersionInfo"""
688  return _IMP_pmi.CompositeRestraint_get_version_info(self)
689  __swig_destroy__ = _IMP_pmi.delete_CompositeRestraint
690 
691  def get_probability(self):
692  r"""get_probability(CompositeRestraint self) -> double"""
693  return _IMP_pmi.CompositeRestraint_get_probability(self)
694 
695  def __str__(self):
696  r"""__str__(CompositeRestraint self) -> std::string"""
697  return _IMP_pmi.CompositeRestraint___str__(self)
698 
699  def __repr__(self):
700  r"""__repr__(CompositeRestraint self) -> std::string"""
701  return _IMP_pmi.CompositeRestraint___repr__(self)
702 
703  @staticmethod
704  def get_from(o):
705  return _object_cast_to_CompositeRestraint(o)
706 
707 
708 # Register CompositeRestraint in _IMP_pmi:
709 _IMP_pmi.CompositeRestraint_swigregister(CompositeRestraint)
710 class CrossLinkRestraintSet(IMP.RestraintSet):
711  r"""Proxy of C++ IMP::pmi::CrossLinkRestraintSet class."""
712 
713  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
714 
715  def __init__(self, *args):
716  r"""
717  __init__(CrossLinkRestraintSet self, Model m, std::string const & name="CrossLinkRestraintSet %1%") -> CrossLinkRestraintSet
718  __init__(CrossLinkRestraintSet self) -> CrossLinkRestraintSet
719  """
720  _IMP_pmi.CrossLinkRestraintSet_swiginit(self, _IMP_pmi.new_CrossLinkRestraintSet(*args))
721 
722  def set_metadata(self, filename, length, slope):
723  r"""set_metadata(CrossLinkRestraintSet self, std::string filename, double length, double slope)"""
724  return _IMP_pmi.CrossLinkRestraintSet_set_metadata(self, filename, length, slope)
725 
726  def set_linker_auth_name(self, name):
727  r"""set_linker_auth_name(CrossLinkRestraintSet self, std::string name)"""
728  return _IMP_pmi.CrossLinkRestraintSet_set_linker_auth_name(self, name)
729 
730  def set_linker_chemical_name(self, name):
731  r"""set_linker_chemical_name(CrossLinkRestraintSet self, std::string name)"""
732  return _IMP_pmi.CrossLinkRestraintSet_set_linker_chemical_name(self, name)
733 
734  def set_linker_smiles(self, name):
735  r"""set_linker_smiles(CrossLinkRestraintSet self, std::string name)"""
736  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles(self, name)
737 
738  def set_linker_smiles_canonical(self, name):
739  r"""set_linker_smiles_canonical(CrossLinkRestraintSet self, std::string name)"""
740  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles_canonical(self, name)
741 
742  def set_linker_inchi(self, name):
743  r"""set_linker_inchi(CrossLinkRestraintSet self, std::string name)"""
744  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi(self, name)
745 
746  def set_linker_inchi_key(self, name):
747  r"""set_linker_inchi_key(CrossLinkRestraintSet self, std::string name)"""
748  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi_key(self, name)
749  __swig_destroy__ = _IMP_pmi.delete_CrossLinkRestraintSet
750 
751  def __str__(self):
752  r"""__str__(CrossLinkRestraintSet self) -> std::string"""
753  return _IMP_pmi.CrossLinkRestraintSet___str__(self)
754 
755  def __repr__(self):
756  r"""__repr__(CrossLinkRestraintSet self) -> std::string"""
757  return _IMP_pmi.CrossLinkRestraintSet___repr__(self)
758 
759  @staticmethod
760  def get_from(o):
761  return _object_cast_to_CrossLinkRestraintSet(o)
762 
763 
764  def _get_as_binary(self):
765  r"""_get_as_binary(CrossLinkRestraintSet self) -> PyObject *"""
766  return _IMP_pmi.CrossLinkRestraintSet__get_as_binary(self)
767 
768  def _set_from_binary(self, p):
769  r"""_set_from_binary(CrossLinkRestraintSet self, PyObject * p)"""
770  return _IMP_pmi.CrossLinkRestraintSet__set_from_binary(self, p)
771 
772  def __getstate__(self):
773  p = self._get_as_binary()
774  if len(self.__dict__) > 1:
775  d = self.__dict__.copy()
776  del d['this']
777  p = (d, p)
778  return p
779 
780  def __setstate__(self, p):
781  if not hasattr(self, 'this'):
782  self.__init__()
783  if isinstance(p, tuple):
784  d, p = p
785  self.__dict__.update(d)
786  return self._set_from_binary(p)
787 
788 
789 # Register CrossLinkRestraintSet in _IMP_pmi:
790 _IMP_pmi.CrossLinkRestraintSet_swigregister(CrossLinkRestraintSet)
791 class Uncertainty(IMP.Decorator):
792  r"""Proxy of C++ IMP::pmi::Uncertainty class."""
793 
794  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
795 
796  def get_uncertainty(self):
797  r"""get_uncertainty(Uncertainty self) -> IMP::Float"""
798  return _IMP_pmi.Uncertainty_get_uncertainty(self)
799 
800  def set_uncertainty(self, d):
801  r"""set_uncertainty(Uncertainty self, IMP::Float d)"""
802  return _IMP_pmi.Uncertainty_set_uncertainty(self, d)
803 
804  def __init__(self, *args):
805  r"""
806  __init__(Uncertainty self) -> Uncertainty
807  __init__(Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
808  __init__(Uncertainty self, _ParticleAdaptor d) -> Uncertainty
809  """
810  _IMP_pmi.Uncertainty_swiginit(self, _IMP_pmi.new_Uncertainty(*args))
811 
812  @staticmethod
813  def get_is_setup(*args):
814  r"""
815  get_is_setup(Model m, ParticleIndex pi) -> bool
816  get_is_setup(_ParticleAdaptor p) -> bool
817  """
818  return _IMP_pmi.Uncertainty_get_is_setup(*args)
819 
820  def show(self, *args):
821  r"""show(Uncertainty self, _ostream out=std::cout)"""
822  return _IMP_pmi.Uncertainty_show(self, *args)
823 
824  @staticmethod
825  def setup_particle(*args):
826  r"""
827  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
828  setup_particle(_ParticleAdaptor pa, IMP::Float uncertainty) -> Uncertainty
829  """
830  return _IMP_pmi.Uncertainty_setup_particle(*args)
831 
832  @staticmethod
833  def get_uncertainty_key():
834  r"""get_uncertainty_key() -> FloatKey"""
835  return _IMP_pmi.Uncertainty_get_uncertainty_key()
836 
837  def add_attribute(self, *args):
838  r"""
839  add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
840  add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
841  add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
842  add_attribute(Uncertainty self, FloatsKey a0, IMP::Floats a1)
843  add_attribute(Uncertainty self, IntsKey a0, IMP::Ints a1)
844  add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
845  add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
846  add_attribute(Uncertainty self, ObjectKey a0, Object a1)
847  add_attribute(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
848  add_attribute(Uncertainty self, SparseIntKey a0, IMP::Int a1)
849  add_attribute(Uncertainty self, SparseStringKey a0, IMP::String a1)
850  add_attribute(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
851  """
852  return _IMP_pmi.Uncertainty_add_attribute(self, *args)
853 
854  def get_value(self, *args):
855  r"""
856  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
857  get_value(Uncertainty self, IntKey a0) -> IMP::Int
858  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
859  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
860  get_value(Uncertainty self, StringKey a0) -> IMP::String
861  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
862  get_value(Uncertainty self, ObjectKey a0) -> Object
863  get_value(Uncertainty self, SparseFloatKey a0) -> IMP::Float
864  get_value(Uncertainty self, SparseIntKey a0) -> IMP::Int
865  get_value(Uncertainty self, SparseStringKey a0) -> IMP::String
866  get_value(Uncertainty self, SparseParticleIndexKey a0) -> ParticleIndex
867  """
868  return _IMP_pmi.Uncertainty_get_value(self, *args)
869 
870  def set_value(self, *args):
871  r"""
872  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
873  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
874  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
875  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
876  set_value(Uncertainty self, StringKey a0, IMP::String a1)
877  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
878  set_value(Uncertainty self, ObjectKey a0, Object a1)
879  set_value(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
880  set_value(Uncertainty self, SparseIntKey a0, IMP::Int a1)
881  set_value(Uncertainty self, SparseStringKey a0, IMP::String a1)
882  set_value(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
883  """
884  return _IMP_pmi.Uncertainty_set_value(self, *args)
885 
886  def remove_attribute(self, *args):
887  r"""
888  remove_attribute(Uncertainty self, FloatKey a0)
889  remove_attribute(Uncertainty self, IntKey a0)
890  remove_attribute(Uncertainty self, FloatsKey a0)
891  remove_attribute(Uncertainty self, IntsKey a0)
892  remove_attribute(Uncertainty self, StringKey a0)
893  remove_attribute(Uncertainty self, ParticleIndexKey a0)
894  remove_attribute(Uncertainty self, ObjectKey a0)
895  remove_attribute(Uncertainty self, SparseFloatKey a0)
896  remove_attribute(Uncertainty self, SparseIntKey a0)
897  remove_attribute(Uncertainty self, SparseStringKey a0)
898  remove_attribute(Uncertainty self, SparseParticleIndexKey a0)
899  """
900  return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
901 
902  def has_attribute(self, *args):
903  r"""
904  has_attribute(Uncertainty self, FloatKey a0) -> bool
905  has_attribute(Uncertainty self, IntKey a0) -> bool
906  has_attribute(Uncertainty self, FloatsKey a0) -> bool
907  has_attribute(Uncertainty self, IntsKey a0) -> bool
908  has_attribute(Uncertainty self, StringKey a0) -> bool
909  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
910  has_attribute(Uncertainty self, ObjectKey a0) -> bool
911  has_attribute(Uncertainty self, SparseFloatKey a0) -> bool
912  has_attribute(Uncertainty self, SparseIntKey a0) -> bool
913  has_attribute(Uncertainty self, SparseStringKey a0) -> bool
914  has_attribute(Uncertainty self, SparseParticleIndexKey a0) -> bool
915  """
916  return _IMP_pmi.Uncertainty_has_attribute(self, *args)
917 
918  def get_derivative(self, a0):
919  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
920  return _IMP_pmi.Uncertainty_get_derivative(self, a0)
921 
922  def get_name(self):
923  r"""get_name(Uncertainty self) -> std::string"""
924  return _IMP_pmi.Uncertainty_get_name(self)
925 
926  def clear_caches(self):
927  r"""clear_caches(Uncertainty self)"""
928  return _IMP_pmi.Uncertainty_clear_caches(self)
929 
930  def set_name(self, a0):
931  r"""set_name(Uncertainty self, std::string a0)"""
932  return _IMP_pmi.Uncertainty_set_name(self, a0)
933 
934  def set_check_level(self, a0):
935  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
936  return _IMP_pmi.Uncertainty_set_check_level(self, a0)
937 
938  def add_to_derivative(self, a0, a1, a2):
939  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
940  return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
941 
942  def set_is_optimized(self, a0, a1):
943  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
944  return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
945 
946  def get_is_optimized(self, a0):
947  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
948  return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
949 
950  def get_check_level(self):
951  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
952  return _IMP_pmi.Uncertainty_get_check_level(self)
953 
954  def __eq__(self, *args):
955  r"""
956  __eq__(Uncertainty self, Uncertainty o) -> bool
957  __eq__(Uncertainty self, Particle d) -> bool
958  """
959  return _IMP_pmi.Uncertainty___eq__(self, *args)
960 
961  def __ne__(self, *args):
962  r"""
963  __ne__(Uncertainty self, Uncertainty o) -> bool
964  __ne__(Uncertainty self, Particle d) -> bool
965  """
966  return _IMP_pmi.Uncertainty___ne__(self, *args)
967 
968  def __le__(self, *args):
969  r"""
970  __le__(Uncertainty self, Uncertainty o) -> bool
971  __le__(Uncertainty self, Particle d) -> bool
972  """
973  return _IMP_pmi.Uncertainty___le__(self, *args)
974 
975  def __lt__(self, *args):
976  r"""
977  __lt__(Uncertainty self, Uncertainty o) -> bool
978  __lt__(Uncertainty self, Particle d) -> bool
979  """
980  return _IMP_pmi.Uncertainty___lt__(self, *args)
981 
982  def __ge__(self, *args):
983  r"""
984  __ge__(Uncertainty self, Uncertainty o) -> bool
985  __ge__(Uncertainty self, Particle d) -> bool
986  """
987  return _IMP_pmi.Uncertainty___ge__(self, *args)
988 
989  def __gt__(self, *args):
990  r"""
991  __gt__(Uncertainty self, Uncertainty o) -> bool
992  __gt__(Uncertainty self, Particle d) -> bool
993  """
994  return _IMP_pmi.Uncertainty___gt__(self, *args)
995 
996  def __hash__(self):
997  r"""__hash__(Uncertainty self) -> std::size_t"""
998  return _IMP_pmi.Uncertainty___hash__(self)
999 
1000  def __str__(self):
1001  r"""__str__(Uncertainty self) -> std::string"""
1002  return _IMP_pmi.Uncertainty___str__(self)
1003 
1004  def __repr__(self):
1005  r"""__repr__(Uncertainty self) -> std::string"""
1006  return _IMP_pmi.Uncertainty___repr__(self)
1007 
1008  def _get_as_binary(self):
1009  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
1010  return _IMP_pmi.Uncertainty__get_as_binary(self)
1011 
1012  def _set_from_binary(self, p):
1013  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
1014  return _IMP_pmi.Uncertainty__set_from_binary(self, p)
1015 
1016  def __getstate__(self):
1017  p = self._get_as_binary()
1018  if len(self.__dict__) > 1:
1019  d = self.__dict__.copy()
1020  del d['this']
1021  p = (d, p)
1022  return p
1023 
1024  def __setstate__(self, p):
1025  if not hasattr(self, 'this'):
1026  self.__init__()
1027  if isinstance(p, tuple):
1028  d, p = p
1029  self.__dict__.update(d)
1030  return self._set_from_binary(p)
1031 
1032  __swig_destroy__ = _IMP_pmi.delete_Uncertainty
1033 
1034 # Register Uncertainty in _IMP_pmi:
1035 _IMP_pmi.Uncertainty_swigregister(Uncertainty)
1036 class Resolution(IMP.Decorator):
1037  r"""Proxy of C++ IMP::pmi::Resolution class."""
1038 
1039  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1040 
1041  def get_resolution(self):
1042  r"""get_resolution(Resolution self) -> IMP::Float"""
1043  return _IMP_pmi.Resolution_get_resolution(self)
1044 
1045  def set_resolution(self, d):
1046  r"""set_resolution(Resolution self, IMP::Float d)"""
1047  return _IMP_pmi.Resolution_set_resolution(self, d)
1048 
1049  def __init__(self, *args):
1050  r"""
1051  __init__(Resolution self) -> Resolution
1052  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
1053  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
1054  """
1055  _IMP_pmi.Resolution_swiginit(self, _IMP_pmi.new_Resolution(*args))
1056 
1057  @staticmethod
1058  def get_is_setup(*args):
1059  r"""
1060  get_is_setup(Model m, ParticleIndex pi) -> bool
1061  get_is_setup(_ParticleAdaptor p) -> bool
1062  """
1063  return _IMP_pmi.Resolution_get_is_setup(*args)
1064 
1065  def show(self, *args):
1066  r"""show(Resolution self, _ostream out=std::cout)"""
1067  return _IMP_pmi.Resolution_show(self, *args)
1068 
1069  @staticmethod
1070  def setup_particle(*args):
1071  r"""
1072  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1073  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
1074  """
1075  return _IMP_pmi.Resolution_setup_particle(*args)
1076 
1077  @staticmethod
1078  def get_resolution_key():
1079  r"""get_resolution_key() -> FloatKey"""
1080  return _IMP_pmi.Resolution_get_resolution_key()
1081 
1082  def add_attribute(self, *args):
1083  r"""
1084  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1085  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1086  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1087  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1088  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1089  add_attribute(Resolution self, StringKey a0, IMP::String a1)
1090  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1091  add_attribute(Resolution self, ObjectKey a0, Object a1)
1092  add_attribute(Resolution self, SparseFloatKey a0, IMP::Float a1)
1093  add_attribute(Resolution self, SparseIntKey a0, IMP::Int a1)
1094  add_attribute(Resolution self, SparseStringKey a0, IMP::String a1)
1095  add_attribute(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1096  """
1097  return _IMP_pmi.Resolution_add_attribute(self, *args)
1098 
1099  def get_value(self, *args):
1100  r"""
1101  get_value(Resolution self, FloatKey a0) -> IMP::Float
1102  get_value(Resolution self, IntKey a0) -> IMP::Int
1103  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1104  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1105  get_value(Resolution self, StringKey a0) -> IMP::String
1106  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1107  get_value(Resolution self, ObjectKey a0) -> Object
1108  get_value(Resolution self, SparseFloatKey a0) -> IMP::Float
1109  get_value(Resolution self, SparseIntKey a0) -> IMP::Int
1110  get_value(Resolution self, SparseStringKey a0) -> IMP::String
1111  get_value(Resolution self, SparseParticleIndexKey a0) -> ParticleIndex
1112  """
1113  return _IMP_pmi.Resolution_get_value(self, *args)
1114 
1115  def set_value(self, *args):
1116  r"""
1117  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1118  set_value(Resolution self, IntKey a0, IMP::Int a1)
1119  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1120  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1121  set_value(Resolution self, StringKey a0, IMP::String a1)
1122  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1123  set_value(Resolution self, ObjectKey a0, Object a1)
1124  set_value(Resolution self, SparseFloatKey a0, IMP::Float a1)
1125  set_value(Resolution self, SparseIntKey a0, IMP::Int a1)
1126  set_value(Resolution self, SparseStringKey a0, IMP::String a1)
1127  set_value(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1128  """
1129  return _IMP_pmi.Resolution_set_value(self, *args)
1130 
1131  def remove_attribute(self, *args):
1132  r"""
1133  remove_attribute(Resolution self, FloatKey a0)
1134  remove_attribute(Resolution self, IntKey a0)
1135  remove_attribute(Resolution self, FloatsKey a0)
1136  remove_attribute(Resolution self, IntsKey a0)
1137  remove_attribute(Resolution self, StringKey a0)
1138  remove_attribute(Resolution self, ParticleIndexKey a0)
1139  remove_attribute(Resolution self, ObjectKey a0)
1140  remove_attribute(Resolution self, SparseFloatKey a0)
1141  remove_attribute(Resolution self, SparseIntKey a0)
1142  remove_attribute(Resolution self, SparseStringKey a0)
1143  remove_attribute(Resolution self, SparseParticleIndexKey a0)
1144  """
1145  return _IMP_pmi.Resolution_remove_attribute(self, *args)
1146 
1147  def has_attribute(self, *args):
1148  r"""
1149  has_attribute(Resolution self, FloatKey a0) -> bool
1150  has_attribute(Resolution self, IntKey a0) -> bool
1151  has_attribute(Resolution self, FloatsKey a0) -> bool
1152  has_attribute(Resolution self, IntsKey a0) -> bool
1153  has_attribute(Resolution self, StringKey a0) -> bool
1154  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1155  has_attribute(Resolution self, ObjectKey a0) -> bool
1156  has_attribute(Resolution self, SparseFloatKey a0) -> bool
1157  has_attribute(Resolution self, SparseIntKey a0) -> bool
1158  has_attribute(Resolution self, SparseStringKey a0) -> bool
1159  has_attribute(Resolution self, SparseParticleIndexKey a0) -> bool
1160  """
1161  return _IMP_pmi.Resolution_has_attribute(self, *args)
1162 
1163  def get_derivative(self, a0):
1164  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1165  return _IMP_pmi.Resolution_get_derivative(self, a0)
1166 
1167  def get_name(self):
1168  r"""get_name(Resolution self) -> std::string"""
1169  return _IMP_pmi.Resolution_get_name(self)
1170 
1171  def clear_caches(self):
1172  r"""clear_caches(Resolution self)"""
1173  return _IMP_pmi.Resolution_clear_caches(self)
1174 
1175  def set_name(self, a0):
1176  r"""set_name(Resolution self, std::string a0)"""
1177  return _IMP_pmi.Resolution_set_name(self, a0)
1178 
1179  def set_check_level(self, a0):
1180  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1181  return _IMP_pmi.Resolution_set_check_level(self, a0)
1182 
1183  def add_to_derivative(self, a0, a1, a2):
1184  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1185  return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1186 
1187  def set_is_optimized(self, a0, a1):
1188  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1189  return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1190 
1191  def get_is_optimized(self, a0):
1192  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1193  return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1194 
1195  def get_check_level(self):
1196  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1197  return _IMP_pmi.Resolution_get_check_level(self)
1198 
1199  def __eq__(self, *args):
1200  r"""
1201  __eq__(Resolution self, Resolution o) -> bool
1202  __eq__(Resolution self, Particle d) -> bool
1203  """
1204  return _IMP_pmi.Resolution___eq__(self, *args)
1205 
1206  def __ne__(self, *args):
1207  r"""
1208  __ne__(Resolution self, Resolution o) -> bool
1209  __ne__(Resolution self, Particle d) -> bool
1210  """
1211  return _IMP_pmi.Resolution___ne__(self, *args)
1212 
1213  def __le__(self, *args):
1214  r"""
1215  __le__(Resolution self, Resolution o) -> bool
1216  __le__(Resolution self, Particle d) -> bool
1217  """
1218  return _IMP_pmi.Resolution___le__(self, *args)
1219 
1220  def __lt__(self, *args):
1221  r"""
1222  __lt__(Resolution self, Resolution o) -> bool
1223  __lt__(Resolution self, Particle d) -> bool
1224  """
1225  return _IMP_pmi.Resolution___lt__(self, *args)
1226 
1227  def __ge__(self, *args):
1228  r"""
1229  __ge__(Resolution self, Resolution o) -> bool
1230  __ge__(Resolution self, Particle d) -> bool
1231  """
1232  return _IMP_pmi.Resolution___ge__(self, *args)
1233 
1234  def __gt__(self, *args):
1235  r"""
1236  __gt__(Resolution self, Resolution o) -> bool
1237  __gt__(Resolution self, Particle d) -> bool
1238  """
1239  return _IMP_pmi.Resolution___gt__(self, *args)
1240 
1241  def __hash__(self):
1242  r"""__hash__(Resolution self) -> std::size_t"""
1243  return _IMP_pmi.Resolution___hash__(self)
1244 
1245  def __str__(self):
1246  r"""__str__(Resolution self) -> std::string"""
1247  return _IMP_pmi.Resolution___str__(self)
1248 
1249  def __repr__(self):
1250  r"""__repr__(Resolution self) -> std::string"""
1251  return _IMP_pmi.Resolution___repr__(self)
1252 
1253  def _get_as_binary(self):
1254  r"""_get_as_binary(Resolution self) -> PyObject *"""
1255  return _IMP_pmi.Resolution__get_as_binary(self)
1256 
1257  def _set_from_binary(self, p):
1258  r"""_set_from_binary(Resolution self, PyObject * p)"""
1259  return _IMP_pmi.Resolution__set_from_binary(self, p)
1260 
1261  def __getstate__(self):
1262  p = self._get_as_binary()
1263  if len(self.__dict__) > 1:
1264  d = self.__dict__.copy()
1265  del d['this']
1266  p = (d, p)
1267  return p
1268 
1269  def __setstate__(self, p):
1270  if not hasattr(self, 'this'):
1271  self.__init__()
1272  if isinstance(p, tuple):
1273  d, p = p
1274  self.__dict__.update(d)
1275  return self._set_from_binary(p)
1276 
1277  __swig_destroy__ = _IMP_pmi.delete_Resolution
1278 
1279 # Register Resolution in _IMP_pmi:
1280 _IMP_pmi.Resolution_swigregister(Resolution)
1281 class Symmetric(IMP.Decorator):
1282  r"""Proxy of C++ IMP::pmi::Symmetric class."""
1283 
1284  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1285 
1286  def get_symmetric(self):
1287  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1288  return _IMP_pmi.Symmetric_get_symmetric(self)
1289 
1290  def set_symmetric(self, d):
1291  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1292  return _IMP_pmi.Symmetric_set_symmetric(self, d)
1293 
1294  def __init__(self, *args):
1295  r"""
1296  __init__(Symmetric self) -> Symmetric
1297  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1298  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1299  """
1300  _IMP_pmi.Symmetric_swiginit(self, _IMP_pmi.new_Symmetric(*args))
1301 
1302  @staticmethod
1303  def get_is_setup(*args):
1304  r"""
1305  get_is_setup(Model m, ParticleIndex pi) -> bool
1306  get_is_setup(_ParticleAdaptor p) -> bool
1307  """
1308  return _IMP_pmi.Symmetric_get_is_setup(*args)
1309 
1310  def show(self, *args):
1311  r"""show(Symmetric self, _ostream out=std::cout)"""
1312  return _IMP_pmi.Symmetric_show(self, *args)
1313 
1314  @staticmethod
1315  def setup_particle(*args):
1316  r"""
1317  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1318  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1319  """
1320  return _IMP_pmi.Symmetric_setup_particle(*args)
1321 
1322  @staticmethod
1323  def get_symmetric_key():
1324  r"""get_symmetric_key() -> FloatKey"""
1325  return _IMP_pmi.Symmetric_get_symmetric_key()
1326 
1327  def add_attribute(self, *args):
1328  r"""
1329  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1330  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1331  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1332  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1333  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1334  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1335  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1336  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1337  add_attribute(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1338  add_attribute(Symmetric self, SparseIntKey a0, IMP::Int a1)
1339  add_attribute(Symmetric self, SparseStringKey a0, IMP::String a1)
1340  add_attribute(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1341  """
1342  return _IMP_pmi.Symmetric_add_attribute(self, *args)
1343 
1344  def get_value(self, *args):
1345  r"""
1346  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1347  get_value(Symmetric self, IntKey a0) -> IMP::Int
1348  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1349  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1350  get_value(Symmetric self, StringKey a0) -> IMP::String
1351  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1352  get_value(Symmetric self, ObjectKey a0) -> Object
1353  get_value(Symmetric self, SparseFloatKey a0) -> IMP::Float
1354  get_value(Symmetric self, SparseIntKey a0) -> IMP::Int
1355  get_value(Symmetric self, SparseStringKey a0) -> IMP::String
1356  get_value(Symmetric self, SparseParticleIndexKey a0) -> ParticleIndex
1357  """
1358  return _IMP_pmi.Symmetric_get_value(self, *args)
1359 
1360  def set_value(self, *args):
1361  r"""
1362  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1363  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1364  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1365  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1366  set_value(Symmetric self, StringKey a0, IMP::String a1)
1367  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1368  set_value(Symmetric self, ObjectKey a0, Object a1)
1369  set_value(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1370  set_value(Symmetric self, SparseIntKey a0, IMP::Int a1)
1371  set_value(Symmetric self, SparseStringKey a0, IMP::String a1)
1372  set_value(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1373  """
1374  return _IMP_pmi.Symmetric_set_value(self, *args)
1375 
1376  def remove_attribute(self, *args):
1377  r"""
1378  remove_attribute(Symmetric self, FloatKey a0)
1379  remove_attribute(Symmetric self, IntKey a0)
1380  remove_attribute(Symmetric self, FloatsKey a0)
1381  remove_attribute(Symmetric self, IntsKey a0)
1382  remove_attribute(Symmetric self, StringKey a0)
1383  remove_attribute(Symmetric self, ParticleIndexKey a0)
1384  remove_attribute(Symmetric self, ObjectKey a0)
1385  remove_attribute(Symmetric self, SparseFloatKey a0)
1386  remove_attribute(Symmetric self, SparseIntKey a0)
1387  remove_attribute(Symmetric self, SparseStringKey a0)
1388  remove_attribute(Symmetric self, SparseParticleIndexKey a0)
1389  """
1390  return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1391 
1392  def has_attribute(self, *args):
1393  r"""
1394  has_attribute(Symmetric self, FloatKey a0) -> bool
1395  has_attribute(Symmetric self, IntKey a0) -> bool
1396  has_attribute(Symmetric self, FloatsKey a0) -> bool
1397  has_attribute(Symmetric self, IntsKey a0) -> bool
1398  has_attribute(Symmetric self, StringKey a0) -> bool
1399  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1400  has_attribute(Symmetric self, ObjectKey a0) -> bool
1401  has_attribute(Symmetric self, SparseFloatKey a0) -> bool
1402  has_attribute(Symmetric self, SparseIntKey a0) -> bool
1403  has_attribute(Symmetric self, SparseStringKey a0) -> bool
1404  has_attribute(Symmetric self, SparseParticleIndexKey a0) -> bool
1405  """
1406  return _IMP_pmi.Symmetric_has_attribute(self, *args)
1407 
1408  def get_derivative(self, a0):
1409  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1410  return _IMP_pmi.Symmetric_get_derivative(self, a0)
1411 
1412  def get_name(self):
1413  r"""get_name(Symmetric self) -> std::string"""
1414  return _IMP_pmi.Symmetric_get_name(self)
1415 
1416  def clear_caches(self):
1417  r"""clear_caches(Symmetric self)"""
1418  return _IMP_pmi.Symmetric_clear_caches(self)
1419 
1420  def set_name(self, a0):
1421  r"""set_name(Symmetric self, std::string a0)"""
1422  return _IMP_pmi.Symmetric_set_name(self, a0)
1423 
1424  def set_check_level(self, a0):
1425  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1426  return _IMP_pmi.Symmetric_set_check_level(self, a0)
1427 
1428  def add_to_derivative(self, a0, a1, a2):
1429  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1430  return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1431 
1432  def set_is_optimized(self, a0, a1):
1433  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1434  return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1435 
1436  def get_is_optimized(self, a0):
1437  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1438  return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1439 
1440  def get_check_level(self):
1441  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1442  return _IMP_pmi.Symmetric_get_check_level(self)
1443 
1444  def __eq__(self, *args):
1445  r"""
1446  __eq__(Symmetric self, Symmetric o) -> bool
1447  __eq__(Symmetric self, Particle d) -> bool
1448  """
1449  return _IMP_pmi.Symmetric___eq__(self, *args)
1450 
1451  def __ne__(self, *args):
1452  r"""
1453  __ne__(Symmetric self, Symmetric o) -> bool
1454  __ne__(Symmetric self, Particle d) -> bool
1455  """
1456  return _IMP_pmi.Symmetric___ne__(self, *args)
1457 
1458  def __le__(self, *args):
1459  r"""
1460  __le__(Symmetric self, Symmetric o) -> bool
1461  __le__(Symmetric self, Particle d) -> bool
1462  """
1463  return _IMP_pmi.Symmetric___le__(self, *args)
1464 
1465  def __lt__(self, *args):
1466  r"""
1467  __lt__(Symmetric self, Symmetric o) -> bool
1468  __lt__(Symmetric self, Particle d) -> bool
1469  """
1470  return _IMP_pmi.Symmetric___lt__(self, *args)
1471 
1472  def __ge__(self, *args):
1473  r"""
1474  __ge__(Symmetric self, Symmetric o) -> bool
1475  __ge__(Symmetric self, Particle d) -> bool
1476  """
1477  return _IMP_pmi.Symmetric___ge__(self, *args)
1478 
1479  def __gt__(self, *args):
1480  r"""
1481  __gt__(Symmetric self, Symmetric o) -> bool
1482  __gt__(Symmetric self, Particle d) -> bool
1483  """
1484  return _IMP_pmi.Symmetric___gt__(self, *args)
1485 
1486  def __hash__(self):
1487  r"""__hash__(Symmetric self) -> std::size_t"""
1488  return _IMP_pmi.Symmetric___hash__(self)
1489 
1490  def __str__(self):
1491  r"""__str__(Symmetric self) -> std::string"""
1492  return _IMP_pmi.Symmetric___str__(self)
1493 
1494  def __repr__(self):
1495  r"""__repr__(Symmetric self) -> std::string"""
1496  return _IMP_pmi.Symmetric___repr__(self)
1497 
1498  def _get_as_binary(self):
1499  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1500  return _IMP_pmi.Symmetric__get_as_binary(self)
1501 
1502  def _set_from_binary(self, p):
1503  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1504  return _IMP_pmi.Symmetric__set_from_binary(self, p)
1505 
1506  def __getstate__(self):
1507  p = self._get_as_binary()
1508  if len(self.__dict__) > 1:
1509  d = self.__dict__.copy()
1510  del d['this']
1511  p = (d, p)
1512  return p
1513 
1514  def __setstate__(self, p):
1515  if not hasattr(self, 'this'):
1516  self.__init__()
1517  if isinstance(p, tuple):
1518  d, p = p
1519  self.__dict__.update(d)
1520  return self._set_from_binary(p)
1521 
1522  __swig_destroy__ = _IMP_pmi.delete_Symmetric
1523 
1524 # Register Symmetric in _IMP_pmi:
1525 _IMP_pmi.Symmetric_swigregister(Symmetric)
1526 class TransformMover(IMP.core.MonteCarloMover):
1527  r"""Proxy of C++ IMP::pmi::TransformMover class."""
1528 
1529  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1530 
1531  def __init__(self, *args):
1532  r"""
1533  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1534  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1535  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1536  __init__(TransformMover self) -> TransformMover
1537  """
1538  _IMP_pmi.TransformMover_swiginit(self, _IMP_pmi.new_TransformMover(*args))
1539 
1540  def add_xyz_particle(self, pi):
1541  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1542  return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1543 
1544  def add_rigid_body_particle(self, pi):
1545  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1546  return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1547 
1548  def set_maximum_translation(self, mt):
1549  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1550  return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1551 
1552  def set_maximum_rotation(self, mr):
1553  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1554  return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1555 
1556  def get_maximum_translation(self):
1557  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1558  return _IMP_pmi.TransformMover_get_maximum_translation(self)
1559 
1560  def get_maximum_rotation(self):
1561  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1562  return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1563 
1564  def get_last_transformation(self):
1565  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1566  return _IMP_pmi.TransformMover_get_last_transformation(self)
1567 
1568  def get_version_info(self):
1569  r"""get_version_info(TransformMover self) -> VersionInfo"""
1570  return _IMP_pmi.TransformMover_get_version_info(self)
1571  __swig_destroy__ = _IMP_pmi.delete_TransformMover
1572 
1573  def __str__(self):
1574  r"""__str__(TransformMover self) -> std::string"""
1575  return _IMP_pmi.TransformMover___str__(self)
1576 
1577  def __repr__(self):
1578  r"""__repr__(TransformMover self) -> std::string"""
1579  return _IMP_pmi.TransformMover___repr__(self)
1580 
1581  @staticmethod
1582  def get_from(o):
1583  return _object_cast_to_TransformMover(o)
1584 
1585 
1586  def _get_as_binary(self):
1587  r"""_get_as_binary(TransformMover self) -> PyObject *"""
1588  return _IMP_pmi.TransformMover__get_as_binary(self)
1589 
1590  def _set_from_binary(self, p):
1591  r"""_set_from_binary(TransformMover self, PyObject * p)"""
1592  return _IMP_pmi.TransformMover__set_from_binary(self, p)
1593 
1594  def __getstate__(self):
1595  p = self._get_as_binary()
1596  if len(self.__dict__) > 1:
1597  d = self.__dict__.copy()
1598  del d['this']
1599  p = (d, p)
1600  return p
1601 
1602  def __setstate__(self, p):
1603  if not hasattr(self, 'this'):
1604  self.__init__()
1605  if isinstance(p, tuple):
1606  d, p = p
1607  self.__dict__.update(d)
1608  return self._set_from_binary(p)
1609 
1610 
1611 # Register TransformMover in _IMP_pmi:
1612 _IMP_pmi.TransformMover_swigregister(TransformMover)
1613 
1614 def create_elastic_network(ps, dist_cutoff, strength):
1615  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1616  return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1617 
1618 def get_dihedral_angle(p1, p2, p3, p4):
1619  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1620  return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1621 
1622 def get_bipartite_minimum_sphere_distance(m1, m2):
1623  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1624  return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1625 
1626 def get_list_of_bipartite_minimum_sphere_distance(pss):
1627  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1628  return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1629 
1631  r"""get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1632  return _IMP_pmi.get_molecule_name_and_copy(h)
1633 
1634 def get_module_version():
1635  r"""get_module_version() -> std::string const"""
1636  return _IMP_pmi.get_module_version()
1637 
1638 def get_example_path(fname):
1639  r"""get_example_path(std::string fname) -> std::string"""
1640  return _IMP_pmi.get_example_path(fname)
1641 
1642 def get_data_path(fname):
1643  r"""get_data_path(std::string fname) -> std::string"""
1644  return _IMP_pmi.get_data_path(fname)
1645 
1646 from . import _version_check
1647 _version_check.check_version(get_module_version())
1648 __version__ = get_module_version()
1649 
1650 
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