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IMP Reference Guide  develop.50fdd7fa33,2025/08/31
The Integrative Modeling Platform
pmi/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.3.1
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 2007-2025 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_BOOST_SYSTEM = _IMP_pmi.IMP_KERNEL_HAS_BOOST_SYSTEM
188 
189 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi.IMP_KERNEL_HAS_GPERFTOOLS
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 
193 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 
195 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi.IMPKERNEL_SHOW_WARNINGS
196 
197 
198 import sys
199 class _DirectorObjects:
200  """@internal Simple class to keep references to director objects
201  to prevent premature deletion."""
202  def __init__(self):
203  self._objects = []
204  def register(self, obj):
205  """Take a reference to a director object; will only work for
206  refcounted C++ classes"""
207  if hasattr(obj, 'get_ref_count'):
208  self._objects.append(obj)
209  def cleanup(self):
210  """Only drop our reference and allow cleanup by Python if no other
211  Python references exist (we hold 3 references: one in self._objects,
212  one in x, and one in the argument list for getrefcount) *and* no
213  other C++ references exist (the Python object always holds one)"""
214  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
215  or x.get_ref_count() > 1]
216 # Do in two steps so the references are kept until the end of the
217 # function (deleting references may trigger a fresh call to this method)
218  self._objects = objs
219  def get_object_count(self):
220  """Get number of director objects (useful for testing only)"""
221  return len(self._objects)
222 _director_objects = _DirectorObjects()
223 
224 class _ostream(object):
225  r"""Proxy of C++ std::ostream class."""
226 
227  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
228 
229  def __init__(self, *args, **kwargs):
230  raise AttributeError("No constructor defined")
231  __repr__ = _swig_repr
232 
233  def write(self, osa_buf):
234  r"""write(_ostream self, char const * osa_buf)"""
235  return _IMP_pmi._ostream_write(self, osa_buf)
236 
237 # Register _ostream in _IMP_pmi:
238 _IMP_pmi._ostream_swigregister(_ostream)
239 IMP_C_OPEN_BINARY = _IMP_pmi.IMP_C_OPEN_BINARY
240 
241 import IMP
242 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 
246 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CGAL_HAS_BOOST_RANDOM
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_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_CGAL
262 
263 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi.IMP_ALGEBRA_HAS_NUMPY
264 
265 IMP_ALGEBRA_HAS_ANN = _IMP_pmi.IMP_ALGEBRA_HAS_ANN
266 
267 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi.IMPALGEBRA_SHOW_WARNINGS
268 
269 import IMP.algebra
270 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_IMP_CGAL
271 
272 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
273 
274 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
275 
276 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_RANDOM
277 
278 IMP_DISPLAY_HAS_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_CGAL
279 
280 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi.IMP_DISPLAY_HAS_NUMPY
281 
282 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi.IMPDISPLAY_SHOW_WARNINGS
283 
284 import IMP.display
285 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
286 
287 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
288 
289 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
292 
293 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_CGAL
294 
295 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_HDF5
296 
297 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_NUMPY
298 
299 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi.IMPSCOREFUNCTOR_SHOW_WARNINGS
300 
301 import IMP.score_functor
302 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_IMP_CGAL
303 
304 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
305 
306 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
307 
308 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_RANDOM
309 
310 IMP_STATISTICS_HAS_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_CGAL
311 
312 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi.IMP_STATISTICS_HAS_NUMPY
313 
314 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi.IMPSTATISTICS_SHOW_WARNINGS
315 
316 import IMP.statistics
317 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi.IMP_CORE_HAS_IMP_CGAL
318 
319 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi.IMP_CORE_HAS_IMP_KERNEL
320 
321 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_FILESYSTEM
322 
323 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
324 
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CORE_HAS_BOOST_RANDOM
326 
327 IMP_CORE_HAS_CGAL = _IMP_pmi.IMP_CORE_HAS_CGAL
328 
329 IMP_CORE_HAS_HDF5 = _IMP_pmi.IMP_CORE_HAS_HDF5
330 
331 IMP_CORE_HAS_NUMPY = _IMP_pmi.IMP_CORE_HAS_NUMPY
332 
333 IMPCORE_SHOW_WARNINGS = _IMP_pmi.IMPCORE_SHOW_WARNINGS
334 
335 import IMP.core
336 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_CONTAINER_HAS_IMP_ALGEBRA
337 
338 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_CGAL
339 
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi.IMP_CONTAINER_HAS_IMP_DISPLAY
341 
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_KERNEL
343 
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 
346 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
347 
348 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
349 
350 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_RANDOM
351 
352 IMP_CONTAINER_HAS_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_CGAL
353 
354 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi.IMP_CONTAINER_HAS_HDF5
355 
356 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi.IMP_CONTAINER_HAS_NUMPY
357 
358 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi.IMP_CONTAINER_HAS_PYTHON_IHM
359 
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 
362 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi.IMP_CONTAINER_HAS_ROBIN_MAP
363 
364 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi.IMPCONTAINER_SHOW_WARNINGS
365 
366 import IMP.container
367 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi.IMP_ATOM_HAS_IMP_CGAL
368 
369 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi.IMP_ATOM_HAS_IMP_KERNEL
370 
371 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
372 
373 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
374 
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ATOM_HAS_BOOST_RANDOM
376 
377 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi.IMP_ATOM_HAS_BOOST_REGEX
378 
379 IMP_ATOM_HAS_CGAL = _IMP_pmi.IMP_ATOM_HAS_CGAL
380 
381 IMP_ATOM_HAS_HDF5 = _IMP_pmi.IMP_ATOM_HAS_HDF5
382 
383 IMP_ATOM_HAS_NUMPY = _IMP_pmi.IMP_ATOM_HAS_NUMPY
384 
385 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi.IMP_ATOM_HAS_PYTHON_IHM
386 
387 IMPATOM_SHOW_WARNINGS = _IMP_pmi.IMPATOM_SHOW_WARNINGS
388 
389 IMP_ATOM_TYPE_INDEX = _IMP_pmi.IMP_ATOM_TYPE_INDEX
390 
391 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi.IMP_RESIDUE_TYPE_INDEX
392 
393 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi.IMP_HIERARCHY_TYPE_INDEX
394 
395 IMP_CHAIN_TYPE_INDEX = _IMP_pmi.IMP_CHAIN_TYPE_INDEX
396 
397 import IMP.atom
398 IMP_EM_HAS_IMP_CGAL = _IMP_pmi.IMP_EM_HAS_IMP_CGAL
399 
400 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi.IMP_EM_HAS_IMP_CONTAINER
401 
402 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi.IMP_EM_HAS_IMP_DISPLAY
403 
404 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_EM_HAS_IMP_SCORE_FUNCTOR
405 
406 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_FILESYSTEM
407 
408 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
409 
410 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_EM_HAS_BOOST_RANDOM
411 
412 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi.IMP_EM_HAS_BOOST_REGEX
413 
414 IMP_EM_HAS_CGAL = _IMP_pmi.IMP_EM_HAS_CGAL
415 
416 IMP_EM_HAS_HDF5 = _IMP_pmi.IMP_EM_HAS_HDF5
417 
418 IMP_EM_HAS_NUMPY = _IMP_pmi.IMP_EM_HAS_NUMPY
419 
420 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi.IMP_EM_HAS_PYTHON_IHM
421 
422 IMPEM_SHOW_WARNINGS = _IMP_pmi.IMPEM_SHOW_WARNINGS
423 
424 import IMP.em
425 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi.IMP_SAXS_HAS_IMP_CGAL
426 
427 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi.IMP_SAXS_HAS_IMP_CONTAINER
428 
429 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi.IMP_SAXS_HAS_IMP_DISPLAY
430 
431 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi.IMP_SAXS_HAS_IMP_KERNEL
432 
433 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
434 
435 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_FILESYSTEM
436 
437 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
438 
439 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SAXS_HAS_BOOST_RANDOM
440 
441 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi.IMP_SAXS_HAS_BOOST_REGEX
442 
443 IMP_SAXS_HAS_CGAL = _IMP_pmi.IMP_SAXS_HAS_CGAL
444 
445 IMP_SAXS_HAS_HDF5 = _IMP_pmi.IMP_SAXS_HAS_HDF5
446 
447 IMP_SAXS_HAS_NUMPY = _IMP_pmi.IMP_SAXS_HAS_NUMPY
448 
449 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi.IMP_SAXS_HAS_PYTHON_IHM
450 
451 IMPSAXS_SHOW_WARNINGS = _IMP_pmi.IMPSAXS_SHOW_WARNINGS
452 
453 import IMP.saxs
454 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi.IMP_ISD_HAS_IMP_CGAL
455 
456 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi.IMP_ISD_HAS_IMP_DISPLAY
457 
458 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
459 
460 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_FILESYSTEM
461 
462 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
463 
464 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ISD_HAS_BOOST_RANDOM
465 
466 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi.IMP_ISD_HAS_BOOST_REGEX
467 
468 IMP_ISD_HAS_CGAL = _IMP_pmi.IMP_ISD_HAS_CGAL
469 
470 IMP_ISD_HAS_HDF5 = _IMP_pmi.IMP_ISD_HAS_HDF5
471 
472 IMP_ISD_HAS_NUMPY = _IMP_pmi.IMP_ISD_HAS_NUMPY
473 
474 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi.IMP_ISD_HAS_PYTHON_IHM
475 
476 IMPISD_SHOW_WARNINGS = _IMP_pmi.IMPISD_SHOW_WARNINGS
477 
478 import IMP.isd
479 IMP_PMI_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_PMI_HAS_IMP_ALGEBRA
480 
481 IMP_PMI_HAS_IMP_ATOM = _IMP_pmi.IMP_PMI_HAS_IMP_ATOM
482 
483 IMP_PMI_HAS_IMP_CGAL = _IMP_pmi.IMP_PMI_HAS_IMP_CGAL
484 
485 IMP_PMI_HAS_IMP_DISPLAY = _IMP_pmi.IMP_PMI_HAS_IMP_DISPLAY
486 
487 IMP_PMI_HAS_IMP_EM = _IMP_pmi.IMP_PMI_HAS_IMP_EM
488 
489 IMP_PMI_HAS_IMP_KERNEL = _IMP_pmi.IMP_PMI_HAS_IMP_KERNEL
490 
491 IMP_PMI_HAS_IMP_SAXS = _IMP_pmi.IMP_PMI_HAS_IMP_SAXS
492 
493 IMP_PMI_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_PMI_HAS_IMP_SCORE_FUNCTOR
494 
495 IMP_PMI_HAS_IMP_STATISTICS = _IMP_pmi.IMP_PMI_HAS_IMP_STATISTICS
496 
497 IMP_PMI_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_FILESYSTEM
498 
499 IMP_PMI_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_PMI_HAS_BOOST_PROGRAMOPTIONS
500 
501 IMP_PMI_HAS_BOOST_RANDOM = _IMP_pmi.IMP_PMI_HAS_BOOST_RANDOM
502 
503 IMP_PMI_HAS_BOOST_REGEX = _IMP_pmi.IMP_PMI_HAS_BOOST_REGEX
504 
505 IMP_PMI_HAS_CGAL = _IMP_pmi.IMP_PMI_HAS_CGAL
506 
507 IMP_PMI_HAS_HDF5 = _IMP_pmi.IMP_PMI_HAS_HDF5
508 
509 IMP_PMI_HAS_NUMPY = _IMP_pmi.IMP_PMI_HAS_NUMPY
510 
511 IMP_PMI_HAS_PYTHON_IHM = _IMP_pmi.IMP_PMI_HAS_PYTHON_IHM
512 
513 IMPPMI_SHOW_WARNINGS = _IMP_pmi.IMPPMI_SHOW_WARNINGS
514 
515 
516 _object_types.append("CompositeRestraint")
517 
518 
519 def _object_cast_to_CompositeRestraint(o):
520  r"""_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
521  return _IMP_pmi._object_cast_to_CompositeRestraint(o)
522 
523 _object_types.append("CrossLinkRestraintSet")
524 
525 
526 def _object_cast_to_CrossLinkRestraintSet(o):
527  r"""_object_cast_to_CrossLinkRestraintSet(Object o) -> CrossLinkRestraintSet"""
528  return _IMP_pmi._object_cast_to_CrossLinkRestraintSet(o)
529 
530 def Uncertainties(l=[]):
531  return [Uncertainty(x) for x in l]
532 _plural_types.append("Uncertainties")
533 
534 
535 _value_types.append("Uncertainty")
536 
537 
538 def Resolutions(l=[]):
539  return [Resolution(x) for x in l]
540 _plural_types.append("Resolutions")
541 
542 
543 _value_types.append("Resolution")
544 
545 
546 def Symmetrics(l=[]):
547  return [Symmetric(x) for x in l]
548 _plural_types.append("Symmetrics")
549 
550 
551 _value_types.append("Symmetric")
552 
553 
554 _object_types.append("TransformMover")
555 
556 
557 def _object_cast_to_TransformMover(o):
558  r"""_object_cast_to_TransformMover(Object o) -> TransformMover"""
559  return _IMP_pmi._object_cast_to_TransformMover(o)
560 
561 _object_types.append("MembraneRestraint")
562 
563 
564 def _object_cast_to_MembraneRestraint(o):
565  r"""_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
566  return _IMP_pmi._object_cast_to_MembraneRestraint(o)
567 
568 class StructureWarning(UserWarning):
569  """Warning related to handling of structures"""
570  pass
571 
572 
573 class ParameterWarning(UserWarning):
574  """Warning for probably incorrect input parameters"""
575  pass
576 
577 
578 class MissingFileWarning(UserWarning):
579  """Warning for an expected, but missing, file"""
580  pass
581 
582 class MembraneRestraint(IMP.isd.ISDRestraint):
583  r"""Proxy of C++ IMP::pmi::MembraneRestraint class."""
584 
585  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
586 
587  def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
588  r"""__init__(MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
589  _IMP_pmi.MembraneRestraint_swiginit(self, _IMP_pmi.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear))
590 
591  def add_particles_below(self, particles):
592  r"""add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
593  return _IMP_pmi.MembraneRestraint_add_particles_below(self, particles)
594 
595  def add_particles_above(self, particles):
596  r"""add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
597  return _IMP_pmi.MembraneRestraint_add_particles_above(self, particles)
598 
599  def add_particles_inside(self, particles):
600  r"""add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
601  return _IMP_pmi.MembraneRestraint_add_particles_inside(self, particles)
602 
603  def get_score(self, prob):
604  r"""get_score(MembraneRestraint self, double prob) -> double"""
605  return _IMP_pmi.MembraneRestraint_get_score(self, prob)
606 
607  def get_probability_above(self, z, z_slope_center_upper):
608  r"""get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
609  return _IMP_pmi.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
610 
611  def get_score_above(self, z, z_slope_center_upper):
612  r"""get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
613  return _IMP_pmi.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
614 
615  def get_probability_below(self, z, z_slope_center_lower):
616  r"""get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
617  return _IMP_pmi.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
618 
619  def get_score_below(self, z, z_slope_center_lower):
620  r"""get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
621  return _IMP_pmi.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
622 
623  def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
624  r"""get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
625  return _IMP_pmi.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
626  __swig_destroy__ = _IMP_pmi.delete_MembraneRestraint
627 
628  def __str__(self):
629  r"""__str__(MembraneRestraint self) -> std::string"""
630  return _IMP_pmi.MembraneRestraint___str__(self)
631 
632  def __repr__(self):
633  r"""__repr__(MembraneRestraint self) -> std::string"""
634  return _IMP_pmi.MembraneRestraint___repr__(self)
635 
636  @staticmethod
637  def get_from(o):
638  return _object_cast_to_MembraneRestraint(o)
639 
640 
641 # Register MembraneRestraint in _IMP_pmi:
642 _IMP_pmi.MembraneRestraint_swigregister(MembraneRestraint)
643 class CompositeRestraint(IMP.Restraint):
644  r"""Proxy of C++ IMP::pmi::CompositeRestraint class."""
645 
646  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
647 
648  def __init__(self, *args):
649  r"""__init__(CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%") -> CompositeRestraint"""
650  _IMP_pmi.CompositeRestraint_swiginit(self, _IMP_pmi.new_CompositeRestraint(*args))
651 
652  def add_composite_particle(self, pi):
653  r"""add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
654  return _IMP_pmi.CompositeRestraint_add_composite_particle(self, pi)
655 
656  def get_number_of_elements(self):
657  r"""get_number_of_elements(CompositeRestraint self) -> unsigned int"""
658  return _IMP_pmi.CompositeRestraint_get_number_of_elements(self)
659 
660  def do_get_inputs(self):
661  r"""do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
662  return _IMP_pmi.CompositeRestraint_do_get_inputs(self)
663 
664  def get_version_info(self):
665  r"""get_version_info(CompositeRestraint self) -> VersionInfo"""
666  return _IMP_pmi.CompositeRestraint_get_version_info(self)
667  __swig_destroy__ = _IMP_pmi.delete_CompositeRestraint
668 
669  def get_probability(self):
670  r"""get_probability(CompositeRestraint self) -> double"""
671  return _IMP_pmi.CompositeRestraint_get_probability(self)
672 
673  def __str__(self):
674  r"""__str__(CompositeRestraint self) -> std::string"""
675  return _IMP_pmi.CompositeRestraint___str__(self)
676 
677  def __repr__(self):
678  r"""__repr__(CompositeRestraint self) -> std::string"""
679  return _IMP_pmi.CompositeRestraint___repr__(self)
680 
681  @staticmethod
682  def get_from(o):
683  return _object_cast_to_CompositeRestraint(o)
684 
685 
686 # Register CompositeRestraint in _IMP_pmi:
687 _IMP_pmi.CompositeRestraint_swigregister(CompositeRestraint)
688 class CrossLinkRestraintSet(IMP.RestraintSet):
689  r"""Proxy of C++ IMP::pmi::CrossLinkRestraintSet class."""
690 
691  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
692 
693  def __init__(self, *args):
694  r"""
695  __init__(CrossLinkRestraintSet self, Model m, std::string const & name="CrossLinkRestraintSet %1%") -> CrossLinkRestraintSet
696  __init__(CrossLinkRestraintSet self) -> CrossLinkRestraintSet
697  """
698  _IMP_pmi.CrossLinkRestraintSet_swiginit(self, _IMP_pmi.new_CrossLinkRestraintSet(*args))
699 
700  def set_metadata(self, filename, length, slope):
701  r"""set_metadata(CrossLinkRestraintSet self, std::string filename, double length, double slope)"""
702  return _IMP_pmi.CrossLinkRestraintSet_set_metadata(self, filename, length, slope)
703 
704  def set_linker_auth_name(self, name):
705  r"""set_linker_auth_name(CrossLinkRestraintSet self, std::string name)"""
706  return _IMP_pmi.CrossLinkRestraintSet_set_linker_auth_name(self, name)
707 
708  def set_linker_chemical_name(self, name):
709  r"""set_linker_chemical_name(CrossLinkRestraintSet self, std::string name)"""
710  return _IMP_pmi.CrossLinkRestraintSet_set_linker_chemical_name(self, name)
711 
712  def set_linker_smiles(self, name):
713  r"""set_linker_smiles(CrossLinkRestraintSet self, std::string name)"""
714  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles(self, name)
715 
716  def set_linker_smiles_canonical(self, name):
717  r"""set_linker_smiles_canonical(CrossLinkRestraintSet self, std::string name)"""
718  return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles_canonical(self, name)
719 
720  def set_linker_inchi(self, name):
721  r"""set_linker_inchi(CrossLinkRestraintSet self, std::string name)"""
722  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi(self, name)
723 
724  def set_linker_inchi_key(self, name):
725  r"""set_linker_inchi_key(CrossLinkRestraintSet self, std::string name)"""
726  return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi_key(self, name)
727  __swig_destroy__ = _IMP_pmi.delete_CrossLinkRestraintSet
728 
729  def __str__(self):
730  r"""__str__(CrossLinkRestraintSet self) -> std::string"""
731  return _IMP_pmi.CrossLinkRestraintSet___str__(self)
732 
733  def __repr__(self):
734  r"""__repr__(CrossLinkRestraintSet self) -> std::string"""
735  return _IMP_pmi.CrossLinkRestraintSet___repr__(self)
736 
737  @staticmethod
738  def get_from(o):
739  return _object_cast_to_CrossLinkRestraintSet(o)
740 
741 
742  def _get_as_binary(self):
743  r"""_get_as_binary(CrossLinkRestraintSet self) -> PyObject *"""
744  return _IMP_pmi.CrossLinkRestraintSet__get_as_binary(self)
745 
746  def _set_from_binary(self, p):
747  r"""_set_from_binary(CrossLinkRestraintSet self, PyObject * p)"""
748  return _IMP_pmi.CrossLinkRestraintSet__set_from_binary(self, p)
749 
750  def __getstate__(self):
751  p = self._get_as_binary()
752  if len(self.__dict__) > 1:
753  d = self.__dict__.copy()
754  del d['this']
755  p = (d, p)
756  return p
757 
758  def __setstate__(self, p):
759  if not hasattr(self, 'this'):
760  self.__init__()
761  if isinstance(p, tuple):
762  d, p = p
763  self.__dict__.update(d)
764  return self._set_from_binary(p)
765 
766 
767 # Register CrossLinkRestraintSet in _IMP_pmi:
768 _IMP_pmi.CrossLinkRestraintSet_swigregister(CrossLinkRestraintSet)
769 class Uncertainty(IMP.Decorator):
770  r"""Proxy of C++ IMP::pmi::Uncertainty class."""
771 
772  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
773 
774  def get_uncertainty(self):
775  r"""get_uncertainty(Uncertainty self) -> IMP::Float"""
776  return _IMP_pmi.Uncertainty_get_uncertainty(self)
777 
778  def set_uncertainty(self, d):
779  r"""set_uncertainty(Uncertainty self, IMP::Float d)"""
780  return _IMP_pmi.Uncertainty_set_uncertainty(self, d)
781 
782  def __init__(self, *args):
783  r"""
784  __init__(Uncertainty self) -> Uncertainty
785  __init__(Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
786  __init__(Uncertainty self, _ParticleAdaptor d) -> Uncertainty
787  """
788  _IMP_pmi.Uncertainty_swiginit(self, _IMP_pmi.new_Uncertainty(*args))
789 
790  @staticmethod
791  def get_is_setup(*args):
792  r"""
793  get_is_setup(Model m, ParticleIndex pi) -> bool
794  get_is_setup(_ParticleAdaptor p) -> bool
795  """
796  return _IMP_pmi.Uncertainty_get_is_setup(*args)
797 
798  def show(self, *args):
799  r"""show(Uncertainty self, _ostream out=std::cout)"""
800  return _IMP_pmi.Uncertainty_show(self, *args)
801 
802  @staticmethod
803  def setup_particle(*args):
804  r"""
805  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
806  setup_particle(_ParticleAdaptor pa, IMP::Float uncertainty) -> Uncertainty
807  """
808  return _IMP_pmi.Uncertainty_setup_particle(*args)
809 
810  @staticmethod
811  def get_uncertainty_key():
812  r"""get_uncertainty_key() -> FloatKey"""
813  return _IMP_pmi.Uncertainty_get_uncertainty_key()
814 
815  def add_attribute(self, *args):
816  r"""
817  add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
818  add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
819  add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
820  add_attribute(Uncertainty self, FloatsKey a0, IMP::Floats a1)
821  add_attribute(Uncertainty self, IntsKey a0, IMP::Ints a1)
822  add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
823  add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
824  add_attribute(Uncertainty self, ObjectKey a0, Object a1)
825  add_attribute(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
826  add_attribute(Uncertainty self, SparseIntKey a0, IMP::Int a1)
827  add_attribute(Uncertainty self, SparseStringKey a0, IMP::String a1)
828  add_attribute(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
829  """
830  return _IMP_pmi.Uncertainty_add_attribute(self, *args)
831 
832  def get_value(self, *args):
833  r"""
834  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
835  get_value(Uncertainty self, IntKey a0) -> IMP::Int
836  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
837  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
838  get_value(Uncertainty self, StringKey a0) -> IMP::String
839  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
840  get_value(Uncertainty self, ObjectKey a0) -> Object
841  get_value(Uncertainty self, SparseFloatKey a0) -> IMP::Float
842  get_value(Uncertainty self, SparseIntKey a0) -> IMP::Int
843  get_value(Uncertainty self, SparseStringKey a0) -> IMP::String
844  get_value(Uncertainty self, SparseParticleIndexKey a0) -> ParticleIndex
845  """
846  return _IMP_pmi.Uncertainty_get_value(self, *args)
847 
848  def set_value(self, *args):
849  r"""
850  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
851  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
852  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
853  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
854  set_value(Uncertainty self, StringKey a0, IMP::String a1)
855  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
856  set_value(Uncertainty self, ObjectKey a0, Object a1)
857  set_value(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
858  set_value(Uncertainty self, SparseIntKey a0, IMP::Int a1)
859  set_value(Uncertainty self, SparseStringKey a0, IMP::String a1)
860  set_value(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
861  """
862  return _IMP_pmi.Uncertainty_set_value(self, *args)
863 
864  def remove_attribute(self, *args):
865  r"""
866  remove_attribute(Uncertainty self, FloatKey a0)
867  remove_attribute(Uncertainty self, IntKey a0)
868  remove_attribute(Uncertainty self, FloatsKey a0)
869  remove_attribute(Uncertainty self, IntsKey a0)
870  remove_attribute(Uncertainty self, StringKey a0)
871  remove_attribute(Uncertainty self, ParticleIndexKey a0)
872  remove_attribute(Uncertainty self, ObjectKey a0)
873  remove_attribute(Uncertainty self, SparseFloatKey a0)
874  remove_attribute(Uncertainty self, SparseIntKey a0)
875  remove_attribute(Uncertainty self, SparseStringKey a0)
876  remove_attribute(Uncertainty self, SparseParticleIndexKey a0)
877  """
878  return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
879 
880  def has_attribute(self, *args):
881  r"""
882  has_attribute(Uncertainty self, FloatKey a0) -> bool
883  has_attribute(Uncertainty self, IntKey a0) -> bool
884  has_attribute(Uncertainty self, FloatsKey a0) -> bool
885  has_attribute(Uncertainty self, IntsKey a0) -> bool
886  has_attribute(Uncertainty self, StringKey a0) -> bool
887  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
888  has_attribute(Uncertainty self, ObjectKey a0) -> bool
889  has_attribute(Uncertainty self, SparseFloatKey a0) -> bool
890  has_attribute(Uncertainty self, SparseIntKey a0) -> bool
891  has_attribute(Uncertainty self, SparseStringKey a0) -> bool
892  has_attribute(Uncertainty self, SparseParticleIndexKey a0) -> bool
893  """
894  return _IMP_pmi.Uncertainty_has_attribute(self, *args)
895 
896  def get_derivative(self, a0):
897  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
898  return _IMP_pmi.Uncertainty_get_derivative(self, a0)
899 
900  def get_name(self):
901  r"""get_name(Uncertainty self) -> std::string"""
902  return _IMP_pmi.Uncertainty_get_name(self)
903 
904  def clear_caches(self):
905  r"""clear_caches(Uncertainty self)"""
906  return _IMP_pmi.Uncertainty_clear_caches(self)
907 
908  def set_name(self, a0):
909  r"""set_name(Uncertainty self, std::string a0)"""
910  return _IMP_pmi.Uncertainty_set_name(self, a0)
911 
912  def set_check_level(self, a0):
913  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
914  return _IMP_pmi.Uncertainty_set_check_level(self, a0)
915 
916  def add_to_derivative(self, a0, a1, a2):
917  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
918  return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
919 
920  def set_is_optimized(self, a0, a1):
921  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
922  return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
923 
924  def get_is_optimized(self, a0):
925  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
926  return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
927 
928  def get_check_level(self):
929  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
930  return _IMP_pmi.Uncertainty_get_check_level(self)
931 
932  def __eq__(self, *args):
933  r"""
934  __eq__(Uncertainty self, Uncertainty o) -> bool
935  __eq__(Uncertainty self, Particle d) -> bool
936  """
937  return _IMP_pmi.Uncertainty___eq__(self, *args)
938 
939  def __ne__(self, *args):
940  r"""
941  __ne__(Uncertainty self, Uncertainty o) -> bool
942  __ne__(Uncertainty self, Particle d) -> bool
943  """
944  return _IMP_pmi.Uncertainty___ne__(self, *args)
945 
946  def __le__(self, *args):
947  r"""
948  __le__(Uncertainty self, Uncertainty o) -> bool
949  __le__(Uncertainty self, Particle d) -> bool
950  """
951  return _IMP_pmi.Uncertainty___le__(self, *args)
952 
953  def __lt__(self, *args):
954  r"""
955  __lt__(Uncertainty self, Uncertainty o) -> bool
956  __lt__(Uncertainty self, Particle d) -> bool
957  """
958  return _IMP_pmi.Uncertainty___lt__(self, *args)
959 
960  def __ge__(self, *args):
961  r"""
962  __ge__(Uncertainty self, Uncertainty o) -> bool
963  __ge__(Uncertainty self, Particle d) -> bool
964  """
965  return _IMP_pmi.Uncertainty___ge__(self, *args)
966 
967  def __gt__(self, *args):
968  r"""
969  __gt__(Uncertainty self, Uncertainty o) -> bool
970  __gt__(Uncertainty self, Particle d) -> bool
971  """
972  return _IMP_pmi.Uncertainty___gt__(self, *args)
973 
974  def __hash__(self):
975  r"""__hash__(Uncertainty self) -> std::size_t"""
976  return _IMP_pmi.Uncertainty___hash__(self)
977 
978  def __str__(self):
979  r"""__str__(Uncertainty self) -> std::string"""
980  return _IMP_pmi.Uncertainty___str__(self)
981 
982  def __repr__(self):
983  r"""__repr__(Uncertainty self) -> std::string"""
984  return _IMP_pmi.Uncertainty___repr__(self)
985 
986  def _get_as_binary(self):
987  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
988  return _IMP_pmi.Uncertainty__get_as_binary(self)
989 
990  def _set_from_binary(self, p):
991  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
992  return _IMP_pmi.Uncertainty__set_from_binary(self, p)
993 
994  def __getstate__(self):
995  p = self._get_as_binary()
996  if len(self.__dict__) > 1:
997  d = self.__dict__.copy()
998  del d['this']
999  p = (d, p)
1000  return p
1001 
1002  def __setstate__(self, p):
1003  if not hasattr(self, 'this'):
1004  self.__init__()
1005  if isinstance(p, tuple):
1006  d, p = p
1007  self.__dict__.update(d)
1008  return self._set_from_binary(p)
1009 
1010  __swig_destroy__ = _IMP_pmi.delete_Uncertainty
1011 
1012 # Register Uncertainty in _IMP_pmi:
1013 _IMP_pmi.Uncertainty_swigregister(Uncertainty)
1014 class Resolution(IMP.Decorator):
1015  r"""Proxy of C++ IMP::pmi::Resolution class."""
1016 
1017  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1018 
1019  def get_resolution(self):
1020  r"""get_resolution(Resolution self) -> IMP::Float"""
1021  return _IMP_pmi.Resolution_get_resolution(self)
1022 
1023  def set_resolution(self, d):
1024  r"""set_resolution(Resolution self, IMP::Float d)"""
1025  return _IMP_pmi.Resolution_set_resolution(self, d)
1026 
1027  def __init__(self, *args):
1028  r"""
1029  __init__(Resolution self) -> Resolution
1030  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
1031  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
1032  """
1033  _IMP_pmi.Resolution_swiginit(self, _IMP_pmi.new_Resolution(*args))
1034 
1035  @staticmethod
1036  def get_is_setup(*args):
1037  r"""
1038  get_is_setup(Model m, ParticleIndex pi) -> bool
1039  get_is_setup(_ParticleAdaptor p) -> bool
1040  """
1041  return _IMP_pmi.Resolution_get_is_setup(*args)
1042 
1043  def show(self, *args):
1044  r"""show(Resolution self, _ostream out=std::cout)"""
1045  return _IMP_pmi.Resolution_show(self, *args)
1046 
1047  @staticmethod
1048  def setup_particle(*args):
1049  r"""
1050  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1051  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
1052  """
1053  return _IMP_pmi.Resolution_setup_particle(*args)
1054 
1055  @staticmethod
1056  def get_resolution_key():
1057  r"""get_resolution_key() -> FloatKey"""
1058  return _IMP_pmi.Resolution_get_resolution_key()
1059 
1060  def add_attribute(self, *args):
1061  r"""
1062  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1063  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1064  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1065  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1066  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1067  add_attribute(Resolution self, StringKey a0, IMP::String a1)
1068  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1069  add_attribute(Resolution self, ObjectKey a0, Object a1)
1070  add_attribute(Resolution self, SparseFloatKey a0, IMP::Float a1)
1071  add_attribute(Resolution self, SparseIntKey a0, IMP::Int a1)
1072  add_attribute(Resolution self, SparseStringKey a0, IMP::String a1)
1073  add_attribute(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1074  """
1075  return _IMP_pmi.Resolution_add_attribute(self, *args)
1076 
1077  def get_value(self, *args):
1078  r"""
1079  get_value(Resolution self, FloatKey a0) -> IMP::Float
1080  get_value(Resolution self, IntKey a0) -> IMP::Int
1081  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1082  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1083  get_value(Resolution self, StringKey a0) -> IMP::String
1084  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1085  get_value(Resolution self, ObjectKey a0) -> Object
1086  get_value(Resolution self, SparseFloatKey a0) -> IMP::Float
1087  get_value(Resolution self, SparseIntKey a0) -> IMP::Int
1088  get_value(Resolution self, SparseStringKey a0) -> IMP::String
1089  get_value(Resolution self, SparseParticleIndexKey a0) -> ParticleIndex
1090  """
1091  return _IMP_pmi.Resolution_get_value(self, *args)
1092 
1093  def set_value(self, *args):
1094  r"""
1095  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1096  set_value(Resolution self, IntKey a0, IMP::Int a1)
1097  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1098  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1099  set_value(Resolution self, StringKey a0, IMP::String a1)
1100  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1101  set_value(Resolution self, ObjectKey a0, Object a1)
1102  set_value(Resolution self, SparseFloatKey a0, IMP::Float a1)
1103  set_value(Resolution self, SparseIntKey a0, IMP::Int a1)
1104  set_value(Resolution self, SparseStringKey a0, IMP::String a1)
1105  set_value(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1106  """
1107  return _IMP_pmi.Resolution_set_value(self, *args)
1108 
1109  def remove_attribute(self, *args):
1110  r"""
1111  remove_attribute(Resolution self, FloatKey a0)
1112  remove_attribute(Resolution self, IntKey a0)
1113  remove_attribute(Resolution self, FloatsKey a0)
1114  remove_attribute(Resolution self, IntsKey a0)
1115  remove_attribute(Resolution self, StringKey a0)
1116  remove_attribute(Resolution self, ParticleIndexKey a0)
1117  remove_attribute(Resolution self, ObjectKey a0)
1118  remove_attribute(Resolution self, SparseFloatKey a0)
1119  remove_attribute(Resolution self, SparseIntKey a0)
1120  remove_attribute(Resolution self, SparseStringKey a0)
1121  remove_attribute(Resolution self, SparseParticleIndexKey a0)
1122  """
1123  return _IMP_pmi.Resolution_remove_attribute(self, *args)
1124 
1125  def has_attribute(self, *args):
1126  r"""
1127  has_attribute(Resolution self, FloatKey a0) -> bool
1128  has_attribute(Resolution self, IntKey a0) -> bool
1129  has_attribute(Resolution self, FloatsKey a0) -> bool
1130  has_attribute(Resolution self, IntsKey a0) -> bool
1131  has_attribute(Resolution self, StringKey a0) -> bool
1132  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1133  has_attribute(Resolution self, ObjectKey a0) -> bool
1134  has_attribute(Resolution self, SparseFloatKey a0) -> bool
1135  has_attribute(Resolution self, SparseIntKey a0) -> bool
1136  has_attribute(Resolution self, SparseStringKey a0) -> bool
1137  has_attribute(Resolution self, SparseParticleIndexKey a0) -> bool
1138  """
1139  return _IMP_pmi.Resolution_has_attribute(self, *args)
1140 
1141  def get_derivative(self, a0):
1142  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1143  return _IMP_pmi.Resolution_get_derivative(self, a0)
1144 
1145  def get_name(self):
1146  r"""get_name(Resolution self) -> std::string"""
1147  return _IMP_pmi.Resolution_get_name(self)
1148 
1149  def clear_caches(self):
1150  r"""clear_caches(Resolution self)"""
1151  return _IMP_pmi.Resolution_clear_caches(self)
1152 
1153  def set_name(self, a0):
1154  r"""set_name(Resolution self, std::string a0)"""
1155  return _IMP_pmi.Resolution_set_name(self, a0)
1156 
1157  def set_check_level(self, a0):
1158  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1159  return _IMP_pmi.Resolution_set_check_level(self, a0)
1160 
1161  def add_to_derivative(self, a0, a1, a2):
1162  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1163  return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1164 
1165  def set_is_optimized(self, a0, a1):
1166  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1167  return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1168 
1169  def get_is_optimized(self, a0):
1170  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1171  return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1172 
1173  def get_check_level(self):
1174  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1175  return _IMP_pmi.Resolution_get_check_level(self)
1176 
1177  def __eq__(self, *args):
1178  r"""
1179  __eq__(Resolution self, Resolution o) -> bool
1180  __eq__(Resolution self, Particle d) -> bool
1181  """
1182  return _IMP_pmi.Resolution___eq__(self, *args)
1183 
1184  def __ne__(self, *args):
1185  r"""
1186  __ne__(Resolution self, Resolution o) -> bool
1187  __ne__(Resolution self, Particle d) -> bool
1188  """
1189  return _IMP_pmi.Resolution___ne__(self, *args)
1190 
1191  def __le__(self, *args):
1192  r"""
1193  __le__(Resolution self, Resolution o) -> bool
1194  __le__(Resolution self, Particle d) -> bool
1195  """
1196  return _IMP_pmi.Resolution___le__(self, *args)
1197 
1198  def __lt__(self, *args):
1199  r"""
1200  __lt__(Resolution self, Resolution o) -> bool
1201  __lt__(Resolution self, Particle d) -> bool
1202  """
1203  return _IMP_pmi.Resolution___lt__(self, *args)
1204 
1205  def __ge__(self, *args):
1206  r"""
1207  __ge__(Resolution self, Resolution o) -> bool
1208  __ge__(Resolution self, Particle d) -> bool
1209  """
1210  return _IMP_pmi.Resolution___ge__(self, *args)
1211 
1212  def __gt__(self, *args):
1213  r"""
1214  __gt__(Resolution self, Resolution o) -> bool
1215  __gt__(Resolution self, Particle d) -> bool
1216  """
1217  return _IMP_pmi.Resolution___gt__(self, *args)
1218 
1219  def __hash__(self):
1220  r"""__hash__(Resolution self) -> std::size_t"""
1221  return _IMP_pmi.Resolution___hash__(self)
1222 
1223  def __str__(self):
1224  r"""__str__(Resolution self) -> std::string"""
1225  return _IMP_pmi.Resolution___str__(self)
1226 
1227  def __repr__(self):
1228  r"""__repr__(Resolution self) -> std::string"""
1229  return _IMP_pmi.Resolution___repr__(self)
1230 
1231  def _get_as_binary(self):
1232  r"""_get_as_binary(Resolution self) -> PyObject *"""
1233  return _IMP_pmi.Resolution__get_as_binary(self)
1234 
1235  def _set_from_binary(self, p):
1236  r"""_set_from_binary(Resolution self, PyObject * p)"""
1237  return _IMP_pmi.Resolution__set_from_binary(self, p)
1238 
1239  def __getstate__(self):
1240  p = self._get_as_binary()
1241  if len(self.__dict__) > 1:
1242  d = self.__dict__.copy()
1243  del d['this']
1244  p = (d, p)
1245  return p
1246 
1247  def __setstate__(self, p):
1248  if not hasattr(self, 'this'):
1249  self.__init__()
1250  if isinstance(p, tuple):
1251  d, p = p
1252  self.__dict__.update(d)
1253  return self._set_from_binary(p)
1254 
1255  __swig_destroy__ = _IMP_pmi.delete_Resolution
1256 
1257 # Register Resolution in _IMP_pmi:
1258 _IMP_pmi.Resolution_swigregister(Resolution)
1259 class Symmetric(IMP.Decorator):
1260  r"""Proxy of C++ IMP::pmi::Symmetric class."""
1261 
1262  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1263 
1264  def get_symmetric(self):
1265  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1266  return _IMP_pmi.Symmetric_get_symmetric(self)
1267 
1268  def set_symmetric(self, d):
1269  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1270  return _IMP_pmi.Symmetric_set_symmetric(self, d)
1271 
1272  def __init__(self, *args):
1273  r"""
1274  __init__(Symmetric self) -> Symmetric
1275  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1276  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1277  """
1278  _IMP_pmi.Symmetric_swiginit(self, _IMP_pmi.new_Symmetric(*args))
1279 
1280  @staticmethod
1281  def get_is_setup(*args):
1282  r"""
1283  get_is_setup(Model m, ParticleIndex pi) -> bool
1284  get_is_setup(_ParticleAdaptor p) -> bool
1285  """
1286  return _IMP_pmi.Symmetric_get_is_setup(*args)
1287 
1288  def show(self, *args):
1289  r"""show(Symmetric self, _ostream out=std::cout)"""
1290  return _IMP_pmi.Symmetric_show(self, *args)
1291 
1292  @staticmethod
1293  def setup_particle(*args):
1294  r"""
1295  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1296  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1297  """
1298  return _IMP_pmi.Symmetric_setup_particle(*args)
1299 
1300  @staticmethod
1301  def get_symmetric_key():
1302  r"""get_symmetric_key() -> FloatKey"""
1303  return _IMP_pmi.Symmetric_get_symmetric_key()
1304 
1305  def add_attribute(self, *args):
1306  r"""
1307  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1308  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1309  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1310  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1311  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1312  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1313  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1314  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1315  add_attribute(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1316  add_attribute(Symmetric self, SparseIntKey a0, IMP::Int a1)
1317  add_attribute(Symmetric self, SparseStringKey a0, IMP::String a1)
1318  add_attribute(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1319  """
1320  return _IMP_pmi.Symmetric_add_attribute(self, *args)
1321 
1322  def get_value(self, *args):
1323  r"""
1324  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1325  get_value(Symmetric self, IntKey a0) -> IMP::Int
1326  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1327  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1328  get_value(Symmetric self, StringKey a0) -> IMP::String
1329  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1330  get_value(Symmetric self, ObjectKey a0) -> Object
1331  get_value(Symmetric self, SparseFloatKey a0) -> IMP::Float
1332  get_value(Symmetric self, SparseIntKey a0) -> IMP::Int
1333  get_value(Symmetric self, SparseStringKey a0) -> IMP::String
1334  get_value(Symmetric self, SparseParticleIndexKey a0) -> ParticleIndex
1335  """
1336  return _IMP_pmi.Symmetric_get_value(self, *args)
1337 
1338  def set_value(self, *args):
1339  r"""
1340  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1341  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1342  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1343  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1344  set_value(Symmetric self, StringKey a0, IMP::String a1)
1345  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1346  set_value(Symmetric self, ObjectKey a0, Object a1)
1347  set_value(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1348  set_value(Symmetric self, SparseIntKey a0, IMP::Int a1)
1349  set_value(Symmetric self, SparseStringKey a0, IMP::String a1)
1350  set_value(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1351  """
1352  return _IMP_pmi.Symmetric_set_value(self, *args)
1353 
1354  def remove_attribute(self, *args):
1355  r"""
1356  remove_attribute(Symmetric self, FloatKey a0)
1357  remove_attribute(Symmetric self, IntKey a0)
1358  remove_attribute(Symmetric self, FloatsKey a0)
1359  remove_attribute(Symmetric self, IntsKey a0)
1360  remove_attribute(Symmetric self, StringKey a0)
1361  remove_attribute(Symmetric self, ParticleIndexKey a0)
1362  remove_attribute(Symmetric self, ObjectKey a0)
1363  remove_attribute(Symmetric self, SparseFloatKey a0)
1364  remove_attribute(Symmetric self, SparseIntKey a0)
1365  remove_attribute(Symmetric self, SparseStringKey a0)
1366  remove_attribute(Symmetric self, SparseParticleIndexKey a0)
1367  """
1368  return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1369 
1370  def has_attribute(self, *args):
1371  r"""
1372  has_attribute(Symmetric self, FloatKey a0) -> bool
1373  has_attribute(Symmetric self, IntKey a0) -> bool
1374  has_attribute(Symmetric self, FloatsKey a0) -> bool
1375  has_attribute(Symmetric self, IntsKey a0) -> bool
1376  has_attribute(Symmetric self, StringKey a0) -> bool
1377  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1378  has_attribute(Symmetric self, ObjectKey a0) -> bool
1379  has_attribute(Symmetric self, SparseFloatKey a0) -> bool
1380  has_attribute(Symmetric self, SparseIntKey a0) -> bool
1381  has_attribute(Symmetric self, SparseStringKey a0) -> bool
1382  has_attribute(Symmetric self, SparseParticleIndexKey a0) -> bool
1383  """
1384  return _IMP_pmi.Symmetric_has_attribute(self, *args)
1385 
1386  def get_derivative(self, a0):
1387  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1388  return _IMP_pmi.Symmetric_get_derivative(self, a0)
1389 
1390  def get_name(self):
1391  r"""get_name(Symmetric self) -> std::string"""
1392  return _IMP_pmi.Symmetric_get_name(self)
1393 
1394  def clear_caches(self):
1395  r"""clear_caches(Symmetric self)"""
1396  return _IMP_pmi.Symmetric_clear_caches(self)
1397 
1398  def set_name(self, a0):
1399  r"""set_name(Symmetric self, std::string a0)"""
1400  return _IMP_pmi.Symmetric_set_name(self, a0)
1401 
1402  def set_check_level(self, a0):
1403  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1404  return _IMP_pmi.Symmetric_set_check_level(self, a0)
1405 
1406  def add_to_derivative(self, a0, a1, a2):
1407  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1408  return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1409 
1410  def set_is_optimized(self, a0, a1):
1411  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1412  return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1413 
1414  def get_is_optimized(self, a0):
1415  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1416  return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1417 
1418  def get_check_level(self):
1419  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1420  return _IMP_pmi.Symmetric_get_check_level(self)
1421 
1422  def __eq__(self, *args):
1423  r"""
1424  __eq__(Symmetric self, Symmetric o) -> bool
1425  __eq__(Symmetric self, Particle d) -> bool
1426  """
1427  return _IMP_pmi.Symmetric___eq__(self, *args)
1428 
1429  def __ne__(self, *args):
1430  r"""
1431  __ne__(Symmetric self, Symmetric o) -> bool
1432  __ne__(Symmetric self, Particle d) -> bool
1433  """
1434  return _IMP_pmi.Symmetric___ne__(self, *args)
1435 
1436  def __le__(self, *args):
1437  r"""
1438  __le__(Symmetric self, Symmetric o) -> bool
1439  __le__(Symmetric self, Particle d) -> bool
1440  """
1441  return _IMP_pmi.Symmetric___le__(self, *args)
1442 
1443  def __lt__(self, *args):
1444  r"""
1445  __lt__(Symmetric self, Symmetric o) -> bool
1446  __lt__(Symmetric self, Particle d) -> bool
1447  """
1448  return _IMP_pmi.Symmetric___lt__(self, *args)
1449 
1450  def __ge__(self, *args):
1451  r"""
1452  __ge__(Symmetric self, Symmetric o) -> bool
1453  __ge__(Symmetric self, Particle d) -> bool
1454  """
1455  return _IMP_pmi.Symmetric___ge__(self, *args)
1456 
1457  def __gt__(self, *args):
1458  r"""
1459  __gt__(Symmetric self, Symmetric o) -> bool
1460  __gt__(Symmetric self, Particle d) -> bool
1461  """
1462  return _IMP_pmi.Symmetric___gt__(self, *args)
1463 
1464  def __hash__(self):
1465  r"""__hash__(Symmetric self) -> std::size_t"""
1466  return _IMP_pmi.Symmetric___hash__(self)
1467 
1468  def __str__(self):
1469  r"""__str__(Symmetric self) -> std::string"""
1470  return _IMP_pmi.Symmetric___str__(self)
1471 
1472  def __repr__(self):
1473  r"""__repr__(Symmetric self) -> std::string"""
1474  return _IMP_pmi.Symmetric___repr__(self)
1475 
1476  def _get_as_binary(self):
1477  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1478  return _IMP_pmi.Symmetric__get_as_binary(self)
1479 
1480  def _set_from_binary(self, p):
1481  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1482  return _IMP_pmi.Symmetric__set_from_binary(self, p)
1483 
1484  def __getstate__(self):
1485  p = self._get_as_binary()
1486  if len(self.__dict__) > 1:
1487  d = self.__dict__.copy()
1488  del d['this']
1489  p = (d, p)
1490  return p
1491 
1492  def __setstate__(self, p):
1493  if not hasattr(self, 'this'):
1494  self.__init__()
1495  if isinstance(p, tuple):
1496  d, p = p
1497  self.__dict__.update(d)
1498  return self._set_from_binary(p)
1499 
1500  __swig_destroy__ = _IMP_pmi.delete_Symmetric
1501 
1502 # Register Symmetric in _IMP_pmi:
1503 _IMP_pmi.Symmetric_swigregister(Symmetric)
1504 class TransformMover(IMP.core.MonteCarloMover):
1505  r"""Proxy of C++ IMP::pmi::TransformMover class."""
1506 
1507  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1508 
1509  def __init__(self, *args):
1510  r"""
1511  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1512  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1513  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1514  __init__(TransformMover self) -> TransformMover
1515  """
1516  _IMP_pmi.TransformMover_swiginit(self, _IMP_pmi.new_TransformMover(*args))
1517 
1518  def add_xyz_particle(self, pi):
1519  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1520  return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1521 
1522  def add_rigid_body_particle(self, pi):
1523  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1524  return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1525 
1526  def set_maximum_translation(self, mt):
1527  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1528  return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1529 
1530  def set_maximum_rotation(self, mr):
1531  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1532  return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1533 
1534  def get_maximum_translation(self):
1535  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1536  return _IMP_pmi.TransformMover_get_maximum_translation(self)
1537 
1538  def get_maximum_rotation(self):
1539  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1540  return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1541 
1542  def get_last_transformation(self):
1543  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1544  return _IMP_pmi.TransformMover_get_last_transformation(self)
1545 
1546  def get_version_info(self):
1547  r"""get_version_info(TransformMover self) -> VersionInfo"""
1548  return _IMP_pmi.TransformMover_get_version_info(self)
1549  __swig_destroy__ = _IMP_pmi.delete_TransformMover
1550 
1551  def __str__(self):
1552  r"""__str__(TransformMover self) -> std::string"""
1553  return _IMP_pmi.TransformMover___str__(self)
1554 
1555  def __repr__(self):
1556  r"""__repr__(TransformMover self) -> std::string"""
1557  return _IMP_pmi.TransformMover___repr__(self)
1558 
1559  @staticmethod
1560  def get_from(o):
1561  return _object_cast_to_TransformMover(o)
1562 
1563 
1564  def _get_as_binary(self):
1565  r"""_get_as_binary(TransformMover self) -> PyObject *"""
1566  return _IMP_pmi.TransformMover__get_as_binary(self)
1567 
1568  def _set_from_binary(self, p):
1569  r"""_set_from_binary(TransformMover self, PyObject * p)"""
1570  return _IMP_pmi.TransformMover__set_from_binary(self, p)
1571 
1572  def __getstate__(self):
1573  p = self._get_as_binary()
1574  if len(self.__dict__) > 1:
1575  d = self.__dict__.copy()
1576  del d['this']
1577  p = (d, p)
1578  return p
1579 
1580  def __setstate__(self, p):
1581  if not hasattr(self, 'this'):
1582  self.__init__()
1583  if isinstance(p, tuple):
1584  d, p = p
1585  self.__dict__.update(d)
1586  return self._set_from_binary(p)
1587 
1588 
1589 # Register TransformMover in _IMP_pmi:
1590 _IMP_pmi.TransformMover_swigregister(TransformMover)
1591 
1592 def create_elastic_network(ps, dist_cutoff, strength):
1593  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1594  return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1595 
1596 def get_dihedral_angle(p1, p2, p3, p4):
1597  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1598  return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1599 
1600 def get_bipartite_minimum_sphere_distance(m1, m2):
1601  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1602  return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1603 
1604 def get_list_of_bipartite_minimum_sphere_distance(pss):
1605  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1606  return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1607 
1609  r"""get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1610  return _IMP_pmi.get_molecule_name_and_copy(h)
1611 
1612 def get_module_name():
1613  r"""get_module_name() -> std::string const"""
1614  return _IMP_pmi.get_module_name()
1615 
1616 def get_module_version():
1617  r"""get_module_version() -> std::string const"""
1618  return _IMP_pmi.get_module_version()
1619 
1620 def get_example_path(fname):
1621  r"""get_example_path(std::string fname) -> std::string"""
1622  return _IMP_pmi.get_example_path(fname)
1623 
1624 def get_data_path(fname):
1625  r"""get_data_path(std::string fname) -> std::string"""
1626  return _IMP_pmi.get_data_path(fname)
1627 
1628 from . import _version_check
1629 _version_check.check_version(get_module_version())
1630 __version__ = get_module_version()
1631 
1632 
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