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IMP Reference Guide  develop.27926d84dc,2024/04/20
The Integrative Modeling Platform
pmi1/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.2.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2024 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_pmi1
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_PMI1_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_PMI1_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_pmi1.delete_IMP_PMI1_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_PMI1_SwigPyIterator self) -> PyObject *"""
79  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_PMI1_SwigPyIterator self, size_t n=1) -> IMP_PMI1_SwigPyIterator"""
83  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_PMI1_SwigPyIterator self, size_t n=1) -> IMP_PMI1_SwigPyIterator"""
87  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_PMI1_SwigPyIterator self, IMP_PMI1_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_PMI1_SwigPyIterator self, IMP_PMI1_SwigPyIterator x) -> bool"""
95  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_PMI1_SwigPyIterator self) -> IMP_PMI1_SwigPyIterator"""
99  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_PMI1_SwigPyIterator self) -> PyObject *"""
103  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_PMI1_SwigPyIterator self) -> PyObject *"""
107  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_PMI1_SwigPyIterator self) -> PyObject *"""
111  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_PMI1_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI1_SwigPyIterator"""
115  return _IMP_pmi1.IMP_PMI1_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_PMI1_SwigPyIterator self, IMP_PMI1_SwigPyIterator x) -> bool"""
119  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_PMI1_SwigPyIterator self, IMP_PMI1_SwigPyIterator x) -> bool"""
123  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_PMI1_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI1_SwigPyIterator"""
127  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_PMI1_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI1_SwigPyIterator"""
131  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_PMI1_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI1_SwigPyIterator"""
135  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_PMI1_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI1_SwigPyIterator
140  __sub__(IMP_PMI1_SwigPyIterator self, IMP_PMI1_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_pmi1.IMP_PMI1_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_PMI1_SwigPyIterator in _IMP_pmi1:
147 _IMP_pmi1.IMP_PMI1_SwigPyIterator_swigregister(IMP_PMI1_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_pmi1.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_pmi1.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_pmi1.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_pmi1.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_pmi1.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_pmi1.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_pmi1.IMP_MEMORY
167 
168 IMP_NONE = _IMP_pmi1.IMP_NONE
169 
170 IMP_USAGE = _IMP_pmi1.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_pmi1.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_pmi1.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_pmi1.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_pmi1.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_pmi1.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_pmi1.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_pmi1.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi1.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi1.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi1.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi1.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_pmi1._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_pmi1:
237 _IMP_pmi1._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_pmi1.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_pmi1.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_pmi1.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_pmi1.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_pmi1.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi1.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_pmi1.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi1.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi1.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_pmi1.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi1.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi1.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi1.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi1.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi1.IMP_STATISTICS_HAS_IMP_CGAL
310 
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
312 
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
314 
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_STATISTICS_HAS_BOOST_RANDOM
316 
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_STATISTICS_HAS_BOOST_SYSTEM
318 
319 IMP_STATISTICS_HAS_CGAL = _IMP_pmi1.IMP_STATISTICS_HAS_CGAL
320 
321 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi1.IMP_STATISTICS_HAS_NUMPY
322 
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi1.IMPSTATISTICS_SHOW_WARNINGS
324 
325 import IMP.statistics
326 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi1.IMP_CORE_HAS_IMP_CGAL
327 
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi1.IMP_CORE_HAS_IMP_KERNEL
329 
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_CORE_HAS_BOOST_FILESYSTEM
331 
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_CORE_HAS_BOOST_RANDOM
335 
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_CORE_HAS_BOOST_SYSTEM
337 
338 IMP_CORE_HAS_CGAL = _IMP_pmi1.IMP_CORE_HAS_CGAL
339 
340 IMP_CORE_HAS_HDF5 = _IMP_pmi1.IMP_CORE_HAS_HDF5
341 
342 IMP_CORE_HAS_NUMPY = _IMP_pmi1.IMP_CORE_HAS_NUMPY
343 
344 IMPCORE_SHOW_WARNINGS = _IMP_pmi1.IMPCORE_SHOW_WARNINGS
345 
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi1.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi1.IMP_CONTAINER_HAS_IMP_CGAL
350 
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi1.IMP_CONTAINER_HAS_IMP_DISPLAY
352 
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi1.IMP_CONTAINER_HAS_IMP_KERNEL
354 
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
356 
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
358 
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
360 
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_CONTAINER_HAS_BOOST_RANDOM
362 
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_CONTAINER_HAS_BOOST_SYSTEM
364 
365 IMP_CONTAINER_HAS_CGAL = _IMP_pmi1.IMP_CONTAINER_HAS_CGAL
366 
367 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi1.IMP_CONTAINER_HAS_HDF5
368 
369 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi1.IMP_CONTAINER_HAS_NUMPY
370 
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi1.IMP_CONTAINER_HAS_PYTHON_IHM
372 
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi1.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
374 
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi1.IMP_CONTAINER_HAS_ROBIN_MAP
376 
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi1.IMPCONTAINER_SHOW_WARNINGS
378 
379 import IMP.container
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi1.IMP_ATOM_HAS_IMP_CGAL
381 
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi1.IMP_ATOM_HAS_IMP_KERNEL
383 
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
385 
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
387 
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_ATOM_HAS_BOOST_RANDOM
389 
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi1.IMP_ATOM_HAS_BOOST_REGEX
391 
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_ATOM_HAS_BOOST_SYSTEM
393 
394 IMP_ATOM_HAS_CGAL = _IMP_pmi1.IMP_ATOM_HAS_CGAL
395 
396 IMP_ATOM_HAS_HDF5 = _IMP_pmi1.IMP_ATOM_HAS_HDF5
397 
398 IMP_ATOM_HAS_NUMPY = _IMP_pmi1.IMP_ATOM_HAS_NUMPY
399 
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi1.IMP_ATOM_HAS_PYTHON_IHM
401 
402 IMPATOM_SHOW_WARNINGS = _IMP_pmi1.IMPATOM_SHOW_WARNINGS
403 
404 IMP_ATOM_TYPE_INDEX = _IMP_pmi1.IMP_ATOM_TYPE_INDEX
405 
406 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi1.IMP_RESIDUE_TYPE_INDEX
407 
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi1.IMP_HIERARCHY_TYPE_INDEX
409 
410 IMP_CHAIN_TYPE_INDEX = _IMP_pmi1.IMP_CHAIN_TYPE_INDEX
411 
412 import IMP.atom
413 IMP_EM_HAS_IMP_CGAL = _IMP_pmi1.IMP_EM_HAS_IMP_CGAL
414 
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi1.IMP_EM_HAS_IMP_CONTAINER
416 
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi1.IMP_EM_HAS_IMP_DISPLAY
418 
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_EM_HAS_IMP_SCORE_FUNCTOR
420 
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_EM_HAS_BOOST_FILESYSTEM
422 
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
424 
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_EM_HAS_BOOST_RANDOM
426 
427 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi1.IMP_EM_HAS_BOOST_REGEX
428 
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_EM_HAS_BOOST_SYSTEM
430 
431 IMP_EM_HAS_CGAL = _IMP_pmi1.IMP_EM_HAS_CGAL
432 
433 IMP_EM_HAS_HDF5 = _IMP_pmi1.IMP_EM_HAS_HDF5
434 
435 IMP_EM_HAS_NUMPY = _IMP_pmi1.IMP_EM_HAS_NUMPY
436 
437 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi1.IMP_EM_HAS_PYTHON_IHM
438 
439 IMPEM_SHOW_WARNINGS = _IMP_pmi1.IMPEM_SHOW_WARNINGS
440 
441 import IMP.em
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi1.IMP_SAXS_HAS_IMP_CGAL
443 
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi1.IMP_SAXS_HAS_IMP_CONTAINER
445 
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi1.IMP_SAXS_HAS_IMP_DISPLAY
447 
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi1.IMP_SAXS_HAS_IMP_KERNEL
449 
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
451 
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_SAXS_HAS_BOOST_FILESYSTEM
453 
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
455 
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_SAXS_HAS_BOOST_RANDOM
457 
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi1.IMP_SAXS_HAS_BOOST_REGEX
459 
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_SAXS_HAS_BOOST_SYSTEM
461 
462 IMP_SAXS_HAS_CGAL = _IMP_pmi1.IMP_SAXS_HAS_CGAL
463 
464 IMP_SAXS_HAS_HDF5 = _IMP_pmi1.IMP_SAXS_HAS_HDF5
465 
466 IMP_SAXS_HAS_NUMPY = _IMP_pmi1.IMP_SAXS_HAS_NUMPY
467 
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi1.IMP_SAXS_HAS_PYTHON_IHM
469 
470 IMPSAXS_SHOW_WARNINGS = _IMP_pmi1.IMPSAXS_SHOW_WARNINGS
471 
472 import IMP.saxs
473 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi1.IMP_ISD_HAS_IMP_CGAL
474 
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi1.IMP_ISD_HAS_IMP_DISPLAY
476 
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
478 
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_ISD_HAS_BOOST_FILESYSTEM
480 
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
482 
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_ISD_HAS_BOOST_RANDOM
484 
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi1.IMP_ISD_HAS_BOOST_REGEX
486 
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_ISD_HAS_BOOST_SYSTEM
488 
489 IMP_ISD_HAS_CGAL = _IMP_pmi1.IMP_ISD_HAS_CGAL
490 
491 IMP_ISD_HAS_HDF5 = _IMP_pmi1.IMP_ISD_HAS_HDF5
492 
493 IMP_ISD_HAS_NUMPY = _IMP_pmi1.IMP_ISD_HAS_NUMPY
494 
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi1.IMP_ISD_HAS_PYTHON_IHM
496 
497 IMPISD_SHOW_WARNINGS = _IMP_pmi1.IMPISD_SHOW_WARNINGS
498 
499 import IMP.isd
500 IMP_PMI1_HAS_IMP_ALGEBRA = _IMP_pmi1.IMP_PMI1_HAS_IMP_ALGEBRA
501 
502 IMP_PMI1_HAS_IMP_ATOM = _IMP_pmi1.IMP_PMI1_HAS_IMP_ATOM
503 
504 IMP_PMI1_HAS_IMP_CGAL = _IMP_pmi1.IMP_PMI1_HAS_IMP_CGAL
505 
506 IMP_PMI1_HAS_IMP_DISPLAY = _IMP_pmi1.IMP_PMI1_HAS_IMP_DISPLAY
507 
508 IMP_PMI1_HAS_IMP_EM = _IMP_pmi1.IMP_PMI1_HAS_IMP_EM
509 
510 IMP_PMI1_HAS_IMP_KERNEL = _IMP_pmi1.IMP_PMI1_HAS_IMP_KERNEL
511 
512 IMP_PMI1_HAS_IMP_SAXS = _IMP_pmi1.IMP_PMI1_HAS_IMP_SAXS
513 
514 IMP_PMI1_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi1.IMP_PMI1_HAS_IMP_SCORE_FUNCTOR
515 
516 IMP_PMI1_HAS_IMP_STATISTICS = _IMP_pmi1.IMP_PMI1_HAS_IMP_STATISTICS
517 
518 IMP_PMI1_HAS_BOOST_FILESYSTEM = _IMP_pmi1.IMP_PMI1_HAS_BOOST_FILESYSTEM
519 
520 IMP_PMI1_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi1.IMP_PMI1_HAS_BOOST_PROGRAMOPTIONS
521 
522 IMP_PMI1_HAS_BOOST_RANDOM = _IMP_pmi1.IMP_PMI1_HAS_BOOST_RANDOM
523 
524 IMP_PMI1_HAS_BOOST_REGEX = _IMP_pmi1.IMP_PMI1_HAS_BOOST_REGEX
525 
526 IMP_PMI1_HAS_BOOST_SYSTEM = _IMP_pmi1.IMP_PMI1_HAS_BOOST_SYSTEM
527 
528 IMP_PMI1_HAS_CGAL = _IMP_pmi1.IMP_PMI1_HAS_CGAL
529 
530 IMP_PMI1_HAS_HDF5 = _IMP_pmi1.IMP_PMI1_HAS_HDF5
531 
532 IMP_PMI1_HAS_NUMPY = _IMP_pmi1.IMP_PMI1_HAS_NUMPY
533 
534 IMP_PMI1_HAS_PYTHON_IHM = _IMP_pmi1.IMP_PMI1_HAS_PYTHON_IHM
535 
536 IMPPMI1_SHOW_WARNINGS = _IMP_pmi1.IMPPMI1_SHOW_WARNINGS
537 
538 
539 
540 IMP.deprecated_module('2.10', __name__,
541  "This module is provided to support legacy published applications "
542  "of IMP - it is no longer developed and should not be used for "
543  "new systems. Use the IMP.pmi module instead.")
544 
545 
546 
547 _object_types.append("CompositeRestraint")
548 
549 
550 def _object_cast_to_CompositeRestraint(o):
551  r"""_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
552  return _IMP_pmi1._object_cast_to_CompositeRestraint(o)
553 
554 def Uncertainties(l=[]):
555  return [Uncertainty(x) for x in l]
556 _plural_types.append("Uncertainties")
557 
558 
559 _value_types.append("Uncertainty")
560 
561 
562 def Resolutions(l=[]):
563  return [Resolution(x) for x in l]
564 _plural_types.append("Resolutions")
565 
566 
567 _value_types.append("Resolution")
568 
569 
570 def Symmetrics(l=[]):
571  return [Symmetric(x) for x in l]
572 _plural_types.append("Symmetrics")
573 
574 
575 _value_types.append("Symmetric")
576 
577 
578 _object_types.append("SigmoidRestraintSphere")
579 
580 
581 def _object_cast_to_SigmoidRestraintSphere(o):
582  r"""_object_cast_to_SigmoidRestraintSphere(Object o) -> SigmoidRestraintSphere"""
583  return _IMP_pmi1._object_cast_to_SigmoidRestraintSphere(o)
584 
585 _object_types.append("TransformMover")
586 
587 
588 def _object_cast_to_TransformMover(o):
589  r"""_object_cast_to_TransformMover(Object o) -> TransformMover"""
590  return _IMP_pmi1._object_cast_to_TransformMover(o)
591 
592 _object_types.append("MembraneRestraint")
593 
594 
595 def _object_cast_to_MembraneRestraint(o):
596  r"""_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
597  return _IMP_pmi1._object_cast_to_MembraneRestraint(o)
598 
599 _object_types.append("InternalCoordinatesConstraint")
600 
601 
602 def _object_cast_to_InternalCoordinatesConstraint(o):
603  r"""_object_cast_to_InternalCoordinatesConstraint(Object o) -> InternalCoordinatesConstraint"""
604  return _IMP_pmi1._object_cast_to_InternalCoordinatesConstraint(o)
605 class MembraneRestraint(IMP.isd.ISDRestraint):
606  r"""Proxy of C++ IMP::pmi1::MembraneRestraint class."""
607 
608  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
609 
610  def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
611  r"""__init__(MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
612  _IMP_pmi1.MembraneRestraint_swiginit(self, _IMP_pmi1.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear))
613 
614  def add_particles_below(self, particles):
615  r"""add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
616  return _IMP_pmi1.MembraneRestraint_add_particles_below(self, particles)
617 
618  def add_particles_above(self, particles):
619  r"""add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
620  return _IMP_pmi1.MembraneRestraint_add_particles_above(self, particles)
621 
622  def add_particles_inside(self, particles):
623  r"""add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
624  return _IMP_pmi1.MembraneRestraint_add_particles_inside(self, particles)
625 
626  def get_score(self, prob):
627  r"""get_score(MembraneRestraint self, double prob) -> double"""
628  return _IMP_pmi1.MembraneRestraint_get_score(self, prob)
629 
630  def get_probability_above(self, z, z_slope_center_upper):
631  r"""get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
632  return _IMP_pmi1.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
633 
634  def get_score_above(self, z, z_slope_center_upper):
635  r"""get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
636  return _IMP_pmi1.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
637 
638  def get_probability_below(self, z, z_slope_center_lower):
639  r"""get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
640  return _IMP_pmi1.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
641 
642  def get_score_below(self, z, z_slope_center_lower):
643  r"""get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
644  return _IMP_pmi1.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
645 
646  def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
647  r"""get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
648  return _IMP_pmi1.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
649  __swig_destroy__ = _IMP_pmi1.delete_MembraneRestraint
650 
651  def __str__(self):
652  r"""__str__(MembraneRestraint self) -> std::string"""
653  return _IMP_pmi1.MembraneRestraint___str__(self)
654 
655  def __repr__(self):
656  r"""__repr__(MembraneRestraint self) -> std::string"""
657  return _IMP_pmi1.MembraneRestraint___repr__(self)
658 
659  @staticmethod
660  def get_from(o):
661  return _object_cast_to_MembraneRestraint(o)
662 
663 
664 # Register MembraneRestraint in _IMP_pmi1:
665 _IMP_pmi1.MembraneRestraint_swigregister(MembraneRestraint)
666 class CompositeRestraint(IMP.Restraint):
667  r"""Proxy of C++ IMP::pmi1::CompositeRestraint class."""
668 
669  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
670 
671  def __init__(self, *args):
672  r"""__init__(CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%") -> CompositeRestraint"""
673  _IMP_pmi1.CompositeRestraint_swiginit(self, _IMP_pmi1.new_CompositeRestraint(*args))
674 
675  def add_composite_particle(self, pi):
676  r"""add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
677  return _IMP_pmi1.CompositeRestraint_add_composite_particle(self, pi)
678 
679  def get_number_of_elements(self):
680  r"""get_number_of_elements(CompositeRestraint self) -> unsigned int"""
681  return _IMP_pmi1.CompositeRestraint_get_number_of_elements(self)
682 
683  def do_get_inputs(self):
684  r"""do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
685  return _IMP_pmi1.CompositeRestraint_do_get_inputs(self)
686 
687  def get_version_info(self):
688  r"""get_version_info(CompositeRestraint self) -> VersionInfo"""
689  return _IMP_pmi1.CompositeRestraint_get_version_info(self)
690  __swig_destroy__ = _IMP_pmi1.delete_CompositeRestraint
691 
692  def get_probability(self):
693  r"""get_probability(CompositeRestraint self) -> double"""
694  return _IMP_pmi1.CompositeRestraint_get_probability(self)
695 
696  def __str__(self):
697  r"""__str__(CompositeRestraint self) -> std::string"""
698  return _IMP_pmi1.CompositeRestraint___str__(self)
699 
700  def __repr__(self):
701  r"""__repr__(CompositeRestraint self) -> std::string"""
702  return _IMP_pmi1.CompositeRestraint___repr__(self)
703 
704  @staticmethod
705  def get_from(o):
706  return _object_cast_to_CompositeRestraint(o)
707 
708 
709 # Register CompositeRestraint in _IMP_pmi1:
710 _IMP_pmi1.CompositeRestraint_swigregister(CompositeRestraint)
711 class Uncertainty(IMP.Decorator):
712  r"""Proxy of C++ IMP::pmi1::Uncertainty class."""
713 
714  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
715 
716  def get_uncertainty(self):
717  r"""get_uncertainty(Uncertainty self) -> IMP::Float"""
718  return _IMP_pmi1.Uncertainty_get_uncertainty(self)
719 
720  def set_uncertainty(self, d):
721  r"""set_uncertainty(Uncertainty self, IMP::Float d)"""
722  return _IMP_pmi1.Uncertainty_set_uncertainty(self, d)
723 
724  def __init__(self, *args):
725  r"""
726  __init__(Uncertainty self) -> Uncertainty
727  __init__(Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
728  __init__(Uncertainty self, _ParticleAdaptor d) -> Uncertainty
729  """
730  _IMP_pmi1.Uncertainty_swiginit(self, _IMP_pmi1.new_Uncertainty(*args))
731 
732  @staticmethod
733  def get_is_setup(*args):
734  r"""
735  get_is_setup(Model m, ParticleIndex pi) -> bool
736  get_is_setup(_ParticleAdaptor p) -> bool
737  """
738  return _IMP_pmi1.Uncertainty_get_is_setup(*args)
739 
740  def show(self, *args):
741  r"""show(Uncertainty self, _ostream out=std::cout)"""
742  return _IMP_pmi1.Uncertainty_show(self, *args)
743 
744  @staticmethod
745  def setup_particle(*args):
746  r"""
747  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
748  setup_particle(_ParticleAdaptor pa, IMP::Float uncertainty) -> Uncertainty
749  """
750  return _IMP_pmi1.Uncertainty_setup_particle(*args)
751 
752  @staticmethod
753  def get_uncertainty_key():
754  r"""get_uncertainty_key() -> FloatKey"""
755  return _IMP_pmi1.Uncertainty_get_uncertainty_key()
756 
757  def add_attribute(self, *args):
758  r"""
759  add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
760  add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
761  add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
762  add_attribute(Uncertainty self, FloatsKey a0, IMP::Floats a1)
763  add_attribute(Uncertainty self, IntsKey a0, IMP::Ints a1)
764  add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
765  add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
766  add_attribute(Uncertainty self, ObjectKey a0, Object a1)
767  add_attribute(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
768  add_attribute(Uncertainty self, SparseIntKey a0, IMP::Int a1)
769  add_attribute(Uncertainty self, SparseStringKey a0, IMP::String a1)
770  add_attribute(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
771  """
772  return _IMP_pmi1.Uncertainty_add_attribute(self, *args)
773 
774  def get_value(self, *args):
775  r"""
776  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
777  get_value(Uncertainty self, IntKey a0) -> IMP::Int
778  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
779  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
780  get_value(Uncertainty self, StringKey a0) -> IMP::String
781  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
782  get_value(Uncertainty self, ObjectKey a0) -> Object
783  get_value(Uncertainty self, SparseFloatKey a0) -> IMP::Float
784  get_value(Uncertainty self, SparseIntKey a0) -> IMP::Int
785  get_value(Uncertainty self, SparseStringKey a0) -> IMP::String
786  get_value(Uncertainty self, SparseParticleIndexKey a0) -> ParticleIndex
787  """
788  return _IMP_pmi1.Uncertainty_get_value(self, *args)
789 
790  def set_value(self, *args):
791  r"""
792  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
793  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
794  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
795  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
796  set_value(Uncertainty self, StringKey a0, IMP::String a1)
797  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
798  set_value(Uncertainty self, ObjectKey a0, Object a1)
799  set_value(Uncertainty self, SparseFloatKey a0, IMP::Float a1)
800  set_value(Uncertainty self, SparseIntKey a0, IMP::Int a1)
801  set_value(Uncertainty self, SparseStringKey a0, IMP::String a1)
802  set_value(Uncertainty self, SparseParticleIndexKey a0, ParticleIndex a1)
803  """
804  return _IMP_pmi1.Uncertainty_set_value(self, *args)
805 
806  def remove_attribute(self, *args):
807  r"""
808  remove_attribute(Uncertainty self, FloatKey a0)
809  remove_attribute(Uncertainty self, IntKey a0)
810  remove_attribute(Uncertainty self, FloatsKey a0)
811  remove_attribute(Uncertainty self, IntsKey a0)
812  remove_attribute(Uncertainty self, StringKey a0)
813  remove_attribute(Uncertainty self, ParticleIndexKey a0)
814  remove_attribute(Uncertainty self, ObjectKey a0)
815  remove_attribute(Uncertainty self, SparseFloatKey a0)
816  remove_attribute(Uncertainty self, SparseIntKey a0)
817  remove_attribute(Uncertainty self, SparseStringKey a0)
818  remove_attribute(Uncertainty self, SparseParticleIndexKey a0)
819  """
820  return _IMP_pmi1.Uncertainty_remove_attribute(self, *args)
821 
822  def has_attribute(self, *args):
823  r"""
824  has_attribute(Uncertainty self, FloatKey a0) -> bool
825  has_attribute(Uncertainty self, IntKey a0) -> bool
826  has_attribute(Uncertainty self, FloatsKey a0) -> bool
827  has_attribute(Uncertainty self, IntsKey a0) -> bool
828  has_attribute(Uncertainty self, StringKey a0) -> bool
829  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
830  has_attribute(Uncertainty self, ObjectKey a0) -> bool
831  has_attribute(Uncertainty self, SparseFloatKey a0) -> bool
832  has_attribute(Uncertainty self, SparseIntKey a0) -> bool
833  has_attribute(Uncertainty self, SparseStringKey a0) -> bool
834  has_attribute(Uncertainty self, SparseParticleIndexKey a0) -> bool
835  """
836  return _IMP_pmi1.Uncertainty_has_attribute(self, *args)
837 
838  def get_derivative(self, a0):
839  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
840  return _IMP_pmi1.Uncertainty_get_derivative(self, a0)
841 
842  def get_name(self):
843  r"""get_name(Uncertainty self) -> std::string"""
844  return _IMP_pmi1.Uncertainty_get_name(self)
845 
846  def clear_caches(self):
847  r"""clear_caches(Uncertainty self)"""
848  return _IMP_pmi1.Uncertainty_clear_caches(self)
849 
850  def set_name(self, a0):
851  r"""set_name(Uncertainty self, std::string a0)"""
852  return _IMP_pmi1.Uncertainty_set_name(self, a0)
853 
854  def set_check_level(self, a0):
855  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
856  return _IMP_pmi1.Uncertainty_set_check_level(self, a0)
857 
858  def add_to_derivative(self, a0, a1, a2):
859  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
860  return _IMP_pmi1.Uncertainty_add_to_derivative(self, a0, a1, a2)
861 
862  def set_is_optimized(self, a0, a1):
863  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
864  return _IMP_pmi1.Uncertainty_set_is_optimized(self, a0, a1)
865 
866  def get_is_optimized(self, a0):
867  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
868  return _IMP_pmi1.Uncertainty_get_is_optimized(self, a0)
869 
870  def get_check_level(self):
871  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
872  return _IMP_pmi1.Uncertainty_get_check_level(self)
873 
874  def __eq__(self, *args):
875  r"""
876  __eq__(Uncertainty self, Uncertainty o) -> bool
877  __eq__(Uncertainty self, Particle d) -> bool
878  """
879  return _IMP_pmi1.Uncertainty___eq__(self, *args)
880 
881  def __ne__(self, *args):
882  r"""
883  __ne__(Uncertainty self, Uncertainty o) -> bool
884  __ne__(Uncertainty self, Particle d) -> bool
885  """
886  return _IMP_pmi1.Uncertainty___ne__(self, *args)
887 
888  def __le__(self, *args):
889  r"""
890  __le__(Uncertainty self, Uncertainty o) -> bool
891  __le__(Uncertainty self, Particle d) -> bool
892  """
893  return _IMP_pmi1.Uncertainty___le__(self, *args)
894 
895  def __lt__(self, *args):
896  r"""
897  __lt__(Uncertainty self, Uncertainty o) -> bool
898  __lt__(Uncertainty self, Particle d) -> bool
899  """
900  return _IMP_pmi1.Uncertainty___lt__(self, *args)
901 
902  def __ge__(self, *args):
903  r"""
904  __ge__(Uncertainty self, Uncertainty o) -> bool
905  __ge__(Uncertainty self, Particle d) -> bool
906  """
907  return _IMP_pmi1.Uncertainty___ge__(self, *args)
908 
909  def __gt__(self, *args):
910  r"""
911  __gt__(Uncertainty self, Uncertainty o) -> bool
912  __gt__(Uncertainty self, Particle d) -> bool
913  """
914  return _IMP_pmi1.Uncertainty___gt__(self, *args)
915 
916  def __hash__(self):
917  r"""__hash__(Uncertainty self) -> std::size_t"""
918  return _IMP_pmi1.Uncertainty___hash__(self)
919 
920  def __str__(self):
921  r"""__str__(Uncertainty self) -> std::string"""
922  return _IMP_pmi1.Uncertainty___str__(self)
923 
924  def __repr__(self):
925  r"""__repr__(Uncertainty self) -> std::string"""
926  return _IMP_pmi1.Uncertainty___repr__(self)
927 
928  def _get_as_binary(self):
929  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
930  return _IMP_pmi1.Uncertainty__get_as_binary(self)
931 
932  def _set_from_binary(self, p):
933  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
934  return _IMP_pmi1.Uncertainty__set_from_binary(self, p)
935 
936  def __getstate__(self):
937  p = self._get_as_binary()
938  if len(self.__dict__) > 1:
939  d = self.__dict__.copy()
940  del d['this']
941  p = (d, p)
942  return p
943 
944  def __setstate__(self, p):
945  if not hasattr(self, 'this'):
946  self.__init__()
947  if isinstance(p, tuple):
948  d, p = p
949  self.__dict__.update(d)
950  return self._set_from_binary(p)
951 
952  __swig_destroy__ = _IMP_pmi1.delete_Uncertainty
953 
954 # Register Uncertainty in _IMP_pmi1:
955 _IMP_pmi1.Uncertainty_swigregister(Uncertainty)
956 class Resolution(IMP.Decorator):
957  r"""Proxy of C++ IMP::pmi1::Resolution class."""
958 
959  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
960 
961  def get_resolution(self):
962  r"""get_resolution(Resolution self) -> IMP::Float"""
963  return _IMP_pmi1.Resolution_get_resolution(self)
964 
965  def set_resolution(self, d):
966  r"""set_resolution(Resolution self, IMP::Float d)"""
967  return _IMP_pmi1.Resolution_set_resolution(self, d)
968 
969  def __init__(self, *args):
970  r"""
971  __init__(Resolution self) -> Resolution
972  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
973  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
974  """
975  _IMP_pmi1.Resolution_swiginit(self, _IMP_pmi1.new_Resolution(*args))
976 
977  @staticmethod
978  def get_is_setup(*args):
979  r"""
980  get_is_setup(Model m, ParticleIndex pi) -> bool
981  get_is_setup(_ParticleAdaptor p) -> bool
982  """
983  return _IMP_pmi1.Resolution_get_is_setup(*args)
984 
985  def show(self, *args):
986  r"""show(Resolution self, _ostream out=std::cout)"""
987  return _IMP_pmi1.Resolution_show(self, *args)
988 
989  @staticmethod
990  def setup_particle(*args):
991  r"""
992  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
993  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
994  """
995  return _IMP_pmi1.Resolution_setup_particle(*args)
996 
997  @staticmethod
998  def get_resolution_key():
999  r"""get_resolution_key() -> FloatKey"""
1000  return _IMP_pmi1.Resolution_get_resolution_key()
1001 
1002  def add_attribute(self, *args):
1003  r"""
1004  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1005  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1006  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1007  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1008  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1009  add_attribute(Resolution self, StringKey a0, IMP::String a1)
1010  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1011  add_attribute(Resolution self, ObjectKey a0, Object a1)
1012  add_attribute(Resolution self, SparseFloatKey a0, IMP::Float a1)
1013  add_attribute(Resolution self, SparseIntKey a0, IMP::Int a1)
1014  add_attribute(Resolution self, SparseStringKey a0, IMP::String a1)
1015  add_attribute(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1016  """
1017  return _IMP_pmi1.Resolution_add_attribute(self, *args)
1018 
1019  def get_value(self, *args):
1020  r"""
1021  get_value(Resolution self, FloatKey a0) -> IMP::Float
1022  get_value(Resolution self, IntKey a0) -> IMP::Int
1023  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1024  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1025  get_value(Resolution self, StringKey a0) -> IMP::String
1026  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1027  get_value(Resolution self, ObjectKey a0) -> Object
1028  get_value(Resolution self, SparseFloatKey a0) -> IMP::Float
1029  get_value(Resolution self, SparseIntKey a0) -> IMP::Int
1030  get_value(Resolution self, SparseStringKey a0) -> IMP::String
1031  get_value(Resolution self, SparseParticleIndexKey a0) -> ParticleIndex
1032  """
1033  return _IMP_pmi1.Resolution_get_value(self, *args)
1034 
1035  def set_value(self, *args):
1036  r"""
1037  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1038  set_value(Resolution self, IntKey a0, IMP::Int a1)
1039  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1040  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1041  set_value(Resolution self, StringKey a0, IMP::String a1)
1042  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1043  set_value(Resolution self, ObjectKey a0, Object a1)
1044  set_value(Resolution self, SparseFloatKey a0, IMP::Float a1)
1045  set_value(Resolution self, SparseIntKey a0, IMP::Int a1)
1046  set_value(Resolution self, SparseStringKey a0, IMP::String a1)
1047  set_value(Resolution self, SparseParticleIndexKey a0, ParticleIndex a1)
1048  """
1049  return _IMP_pmi1.Resolution_set_value(self, *args)
1050 
1051  def remove_attribute(self, *args):
1052  r"""
1053  remove_attribute(Resolution self, FloatKey a0)
1054  remove_attribute(Resolution self, IntKey a0)
1055  remove_attribute(Resolution self, FloatsKey a0)
1056  remove_attribute(Resolution self, IntsKey a0)
1057  remove_attribute(Resolution self, StringKey a0)
1058  remove_attribute(Resolution self, ParticleIndexKey a0)
1059  remove_attribute(Resolution self, ObjectKey a0)
1060  remove_attribute(Resolution self, SparseFloatKey a0)
1061  remove_attribute(Resolution self, SparseIntKey a0)
1062  remove_attribute(Resolution self, SparseStringKey a0)
1063  remove_attribute(Resolution self, SparseParticleIndexKey a0)
1064  """
1065  return _IMP_pmi1.Resolution_remove_attribute(self, *args)
1066 
1067  def has_attribute(self, *args):
1068  r"""
1069  has_attribute(Resolution self, FloatKey a0) -> bool
1070  has_attribute(Resolution self, IntKey a0) -> bool
1071  has_attribute(Resolution self, FloatsKey a0) -> bool
1072  has_attribute(Resolution self, IntsKey a0) -> bool
1073  has_attribute(Resolution self, StringKey a0) -> bool
1074  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1075  has_attribute(Resolution self, ObjectKey a0) -> bool
1076  has_attribute(Resolution self, SparseFloatKey a0) -> bool
1077  has_attribute(Resolution self, SparseIntKey a0) -> bool
1078  has_attribute(Resolution self, SparseStringKey a0) -> bool
1079  has_attribute(Resolution self, SparseParticleIndexKey a0) -> bool
1080  """
1081  return _IMP_pmi1.Resolution_has_attribute(self, *args)
1082 
1083  def get_derivative(self, a0):
1084  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1085  return _IMP_pmi1.Resolution_get_derivative(self, a0)
1086 
1087  def get_name(self):
1088  r"""get_name(Resolution self) -> std::string"""
1089  return _IMP_pmi1.Resolution_get_name(self)
1090 
1091  def clear_caches(self):
1092  r"""clear_caches(Resolution self)"""
1093  return _IMP_pmi1.Resolution_clear_caches(self)
1094 
1095  def set_name(self, a0):
1096  r"""set_name(Resolution self, std::string a0)"""
1097  return _IMP_pmi1.Resolution_set_name(self, a0)
1098 
1099  def set_check_level(self, a0):
1100  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1101  return _IMP_pmi1.Resolution_set_check_level(self, a0)
1102 
1103  def add_to_derivative(self, a0, a1, a2):
1104  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1105  return _IMP_pmi1.Resolution_add_to_derivative(self, a0, a1, a2)
1106 
1107  def set_is_optimized(self, a0, a1):
1108  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1109  return _IMP_pmi1.Resolution_set_is_optimized(self, a0, a1)
1110 
1111  def get_is_optimized(self, a0):
1112  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1113  return _IMP_pmi1.Resolution_get_is_optimized(self, a0)
1114 
1115  def get_check_level(self):
1116  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1117  return _IMP_pmi1.Resolution_get_check_level(self)
1118 
1119  def __eq__(self, *args):
1120  r"""
1121  __eq__(Resolution self, Resolution o) -> bool
1122  __eq__(Resolution self, Particle d) -> bool
1123  """
1124  return _IMP_pmi1.Resolution___eq__(self, *args)
1125 
1126  def __ne__(self, *args):
1127  r"""
1128  __ne__(Resolution self, Resolution o) -> bool
1129  __ne__(Resolution self, Particle d) -> bool
1130  """
1131  return _IMP_pmi1.Resolution___ne__(self, *args)
1132 
1133  def __le__(self, *args):
1134  r"""
1135  __le__(Resolution self, Resolution o) -> bool
1136  __le__(Resolution self, Particle d) -> bool
1137  """
1138  return _IMP_pmi1.Resolution___le__(self, *args)
1139 
1140  def __lt__(self, *args):
1141  r"""
1142  __lt__(Resolution self, Resolution o) -> bool
1143  __lt__(Resolution self, Particle d) -> bool
1144  """
1145  return _IMP_pmi1.Resolution___lt__(self, *args)
1146 
1147  def __ge__(self, *args):
1148  r"""
1149  __ge__(Resolution self, Resolution o) -> bool
1150  __ge__(Resolution self, Particle d) -> bool
1151  """
1152  return _IMP_pmi1.Resolution___ge__(self, *args)
1153 
1154  def __gt__(self, *args):
1155  r"""
1156  __gt__(Resolution self, Resolution o) -> bool
1157  __gt__(Resolution self, Particle d) -> bool
1158  """
1159  return _IMP_pmi1.Resolution___gt__(self, *args)
1160 
1161  def __hash__(self):
1162  r"""__hash__(Resolution self) -> std::size_t"""
1163  return _IMP_pmi1.Resolution___hash__(self)
1164 
1165  def __str__(self):
1166  r"""__str__(Resolution self) -> std::string"""
1167  return _IMP_pmi1.Resolution___str__(self)
1168 
1169  def __repr__(self):
1170  r"""__repr__(Resolution self) -> std::string"""
1171  return _IMP_pmi1.Resolution___repr__(self)
1172 
1173  def _get_as_binary(self):
1174  r"""_get_as_binary(Resolution self) -> PyObject *"""
1175  return _IMP_pmi1.Resolution__get_as_binary(self)
1176 
1177  def _set_from_binary(self, p):
1178  r"""_set_from_binary(Resolution self, PyObject * p)"""
1179  return _IMP_pmi1.Resolution__set_from_binary(self, p)
1180 
1181  def __getstate__(self):
1182  p = self._get_as_binary()
1183  if len(self.__dict__) > 1:
1184  d = self.__dict__.copy()
1185  del d['this']
1186  p = (d, p)
1187  return p
1188 
1189  def __setstate__(self, p):
1190  if not hasattr(self, 'this'):
1191  self.__init__()
1192  if isinstance(p, tuple):
1193  d, p = p
1194  self.__dict__.update(d)
1195  return self._set_from_binary(p)
1196 
1197  __swig_destroy__ = _IMP_pmi1.delete_Resolution
1198 
1199 # Register Resolution in _IMP_pmi1:
1200 _IMP_pmi1.Resolution_swigregister(Resolution)
1201 class Symmetric(IMP.Decorator):
1202  r"""Proxy of C++ IMP::pmi1::Symmetric class."""
1203 
1204  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1205 
1206  def get_symmetric(self):
1207  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1208  return _IMP_pmi1.Symmetric_get_symmetric(self)
1209 
1210  def set_symmetric(self, d):
1211  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1212  return _IMP_pmi1.Symmetric_set_symmetric(self, d)
1213 
1214  def __init__(self, *args):
1215  r"""
1216  __init__(Symmetric self) -> Symmetric
1217  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1218  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1219  """
1220  _IMP_pmi1.Symmetric_swiginit(self, _IMP_pmi1.new_Symmetric(*args))
1221 
1222  @staticmethod
1223  def get_is_setup(*args):
1224  r"""
1225  get_is_setup(Model m, ParticleIndex pi) -> bool
1226  get_is_setup(_ParticleAdaptor p) -> bool
1227  """
1228  return _IMP_pmi1.Symmetric_get_is_setup(*args)
1229 
1230  def show(self, *args):
1231  r"""show(Symmetric self, _ostream out=std::cout)"""
1232  return _IMP_pmi1.Symmetric_show(self, *args)
1233 
1234  @staticmethod
1235  def setup_particle(*args):
1236  r"""
1237  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1238  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1239  """
1240  return _IMP_pmi1.Symmetric_setup_particle(*args)
1241 
1242  @staticmethod
1243  def get_symmetric_key():
1244  r"""get_symmetric_key() -> FloatKey"""
1245  return _IMP_pmi1.Symmetric_get_symmetric_key()
1246 
1247  def add_attribute(self, *args):
1248  r"""
1249  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1250  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1251  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1252  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1253  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1254  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1255  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1256  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1257  add_attribute(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1258  add_attribute(Symmetric self, SparseIntKey a0, IMP::Int a1)
1259  add_attribute(Symmetric self, SparseStringKey a0, IMP::String a1)
1260  add_attribute(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1261  """
1262  return _IMP_pmi1.Symmetric_add_attribute(self, *args)
1263 
1264  def get_value(self, *args):
1265  r"""
1266  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1267  get_value(Symmetric self, IntKey a0) -> IMP::Int
1268  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1269  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1270  get_value(Symmetric self, StringKey a0) -> IMP::String
1271  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1272  get_value(Symmetric self, ObjectKey a0) -> Object
1273  get_value(Symmetric self, SparseFloatKey a0) -> IMP::Float
1274  get_value(Symmetric self, SparseIntKey a0) -> IMP::Int
1275  get_value(Symmetric self, SparseStringKey a0) -> IMP::String
1276  get_value(Symmetric self, SparseParticleIndexKey a0) -> ParticleIndex
1277  """
1278  return _IMP_pmi1.Symmetric_get_value(self, *args)
1279 
1280  def set_value(self, *args):
1281  r"""
1282  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1283  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1284  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1285  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1286  set_value(Symmetric self, StringKey a0, IMP::String a1)
1287  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1288  set_value(Symmetric self, ObjectKey a0, Object a1)
1289  set_value(Symmetric self, SparseFloatKey a0, IMP::Float a1)
1290  set_value(Symmetric self, SparseIntKey a0, IMP::Int a1)
1291  set_value(Symmetric self, SparseStringKey a0, IMP::String a1)
1292  set_value(Symmetric self, SparseParticleIndexKey a0, ParticleIndex a1)
1293  """
1294  return _IMP_pmi1.Symmetric_set_value(self, *args)
1295 
1296  def remove_attribute(self, *args):
1297  r"""
1298  remove_attribute(Symmetric self, FloatKey a0)
1299  remove_attribute(Symmetric self, IntKey a0)
1300  remove_attribute(Symmetric self, FloatsKey a0)
1301  remove_attribute(Symmetric self, IntsKey a0)
1302  remove_attribute(Symmetric self, StringKey a0)
1303  remove_attribute(Symmetric self, ParticleIndexKey a0)
1304  remove_attribute(Symmetric self, ObjectKey a0)
1305  remove_attribute(Symmetric self, SparseFloatKey a0)
1306  remove_attribute(Symmetric self, SparseIntKey a0)
1307  remove_attribute(Symmetric self, SparseStringKey a0)
1308  remove_attribute(Symmetric self, SparseParticleIndexKey a0)
1309  """
1310  return _IMP_pmi1.Symmetric_remove_attribute(self, *args)
1311 
1312  def has_attribute(self, *args):
1313  r"""
1314  has_attribute(Symmetric self, FloatKey a0) -> bool
1315  has_attribute(Symmetric self, IntKey a0) -> bool
1316  has_attribute(Symmetric self, FloatsKey a0) -> bool
1317  has_attribute(Symmetric self, IntsKey a0) -> bool
1318  has_attribute(Symmetric self, StringKey a0) -> bool
1319  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1320  has_attribute(Symmetric self, ObjectKey a0) -> bool
1321  has_attribute(Symmetric self, SparseFloatKey a0) -> bool
1322  has_attribute(Symmetric self, SparseIntKey a0) -> bool
1323  has_attribute(Symmetric self, SparseStringKey a0) -> bool
1324  has_attribute(Symmetric self, SparseParticleIndexKey a0) -> bool
1325  """
1326  return _IMP_pmi1.Symmetric_has_attribute(self, *args)
1327 
1328  def get_derivative(self, a0):
1329  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1330  return _IMP_pmi1.Symmetric_get_derivative(self, a0)
1331 
1332  def get_name(self):
1333  r"""get_name(Symmetric self) -> std::string"""
1334  return _IMP_pmi1.Symmetric_get_name(self)
1335 
1336  def clear_caches(self):
1337  r"""clear_caches(Symmetric self)"""
1338  return _IMP_pmi1.Symmetric_clear_caches(self)
1339 
1340  def set_name(self, a0):
1341  r"""set_name(Symmetric self, std::string a0)"""
1342  return _IMP_pmi1.Symmetric_set_name(self, a0)
1343 
1344  def set_check_level(self, a0):
1345  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1346  return _IMP_pmi1.Symmetric_set_check_level(self, a0)
1347 
1348  def add_to_derivative(self, a0, a1, a2):
1349  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1350  return _IMP_pmi1.Symmetric_add_to_derivative(self, a0, a1, a2)
1351 
1352  def set_is_optimized(self, a0, a1):
1353  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1354  return _IMP_pmi1.Symmetric_set_is_optimized(self, a0, a1)
1355 
1356  def get_is_optimized(self, a0):
1357  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1358  return _IMP_pmi1.Symmetric_get_is_optimized(self, a0)
1359 
1360  def get_check_level(self):
1361  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1362  return _IMP_pmi1.Symmetric_get_check_level(self)
1363 
1364  def __eq__(self, *args):
1365  r"""
1366  __eq__(Symmetric self, Symmetric o) -> bool
1367  __eq__(Symmetric self, Particle d) -> bool
1368  """
1369  return _IMP_pmi1.Symmetric___eq__(self, *args)
1370 
1371  def __ne__(self, *args):
1372  r"""
1373  __ne__(Symmetric self, Symmetric o) -> bool
1374  __ne__(Symmetric self, Particle d) -> bool
1375  """
1376  return _IMP_pmi1.Symmetric___ne__(self, *args)
1377 
1378  def __le__(self, *args):
1379  r"""
1380  __le__(Symmetric self, Symmetric o) -> bool
1381  __le__(Symmetric self, Particle d) -> bool
1382  """
1383  return _IMP_pmi1.Symmetric___le__(self, *args)
1384 
1385  def __lt__(self, *args):
1386  r"""
1387  __lt__(Symmetric self, Symmetric o) -> bool
1388  __lt__(Symmetric self, Particle d) -> bool
1389  """
1390  return _IMP_pmi1.Symmetric___lt__(self, *args)
1391 
1392  def __ge__(self, *args):
1393  r"""
1394  __ge__(Symmetric self, Symmetric o) -> bool
1395  __ge__(Symmetric self, Particle d) -> bool
1396  """
1397  return _IMP_pmi1.Symmetric___ge__(self, *args)
1398 
1399  def __gt__(self, *args):
1400  r"""
1401  __gt__(Symmetric self, Symmetric o) -> bool
1402  __gt__(Symmetric self, Particle d) -> bool
1403  """
1404  return _IMP_pmi1.Symmetric___gt__(self, *args)
1405 
1406  def __hash__(self):
1407  r"""__hash__(Symmetric self) -> std::size_t"""
1408  return _IMP_pmi1.Symmetric___hash__(self)
1409 
1410  def __str__(self):
1411  r"""__str__(Symmetric self) -> std::string"""
1412  return _IMP_pmi1.Symmetric___str__(self)
1413 
1414  def __repr__(self):
1415  r"""__repr__(Symmetric self) -> std::string"""
1416  return _IMP_pmi1.Symmetric___repr__(self)
1417 
1418  def _get_as_binary(self):
1419  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1420  return _IMP_pmi1.Symmetric__get_as_binary(self)
1421 
1422  def _set_from_binary(self, p):
1423  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1424  return _IMP_pmi1.Symmetric__set_from_binary(self, p)
1425 
1426  def __getstate__(self):
1427  p = self._get_as_binary()
1428  if len(self.__dict__) > 1:
1429  d = self.__dict__.copy()
1430  del d['this']
1431  p = (d, p)
1432  return p
1433 
1434  def __setstate__(self, p):
1435  if not hasattr(self, 'this'):
1436  self.__init__()
1437  if isinstance(p, tuple):
1438  d, p = p
1439  self.__dict__.update(d)
1440  return self._set_from_binary(p)
1441 
1442  __swig_destroy__ = _IMP_pmi1.delete_Symmetric
1443 
1444 # Register Symmetric in _IMP_pmi1:
1445 _IMP_pmi1.Symmetric_swigregister(Symmetric)
1446 class SigmoidRestraintSphere(IMP.Restraint):
1447  r"""Proxy of C++ IMP::pmi1::SigmoidRestraintSphere class."""
1448 
1449  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1450 
1451  def __init__(self, *args):
1452  r"""__init__(SigmoidRestraintSphere self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, double inflection, double slope, double amplitude, double line_slope_=0, std::string name="SigmoidRestraintSphere%1%") -> SigmoidRestraintSphere"""
1453  _IMP_pmi1.SigmoidRestraintSphere_swiginit(self, _IMP_pmi1.new_SigmoidRestraintSphere(*args))
1454 
1455  def set_amplitude(self, amplitude):
1456  r"""set_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1457  return _IMP_pmi1.SigmoidRestraintSphere_set_amplitude(self, amplitude)
1458 
1459  def increment_amplitude(self, amplitude):
1460  r"""increment_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1461  return _IMP_pmi1.SigmoidRestraintSphere_increment_amplitude(self, amplitude)
1462 
1463  def get_amplitude(self):
1464  r"""get_amplitude(SigmoidRestraintSphere self) -> double"""
1465  return _IMP_pmi1.SigmoidRestraintSphere_get_amplitude(self)
1466 
1467  def do_get_inputs(self):
1468  r"""do_get_inputs(SigmoidRestraintSphere self) -> IMP::ModelObjectsTemp"""
1469  return _IMP_pmi1.SigmoidRestraintSphere_do_get_inputs(self)
1470 
1471  def get_version_info(self):
1472  r"""get_version_info(SigmoidRestraintSphere self) -> VersionInfo"""
1473  return _IMP_pmi1.SigmoidRestraintSphere_get_version_info(self)
1474  __swig_destroy__ = _IMP_pmi1.delete_SigmoidRestraintSphere
1475 
1476  def __str__(self):
1477  r"""__str__(SigmoidRestraintSphere self) -> std::string"""
1478  return _IMP_pmi1.SigmoidRestraintSphere___str__(self)
1479 
1480  def __repr__(self):
1481  r"""__repr__(SigmoidRestraintSphere self) -> std::string"""
1482  return _IMP_pmi1.SigmoidRestraintSphere___repr__(self)
1483 
1484  @staticmethod
1485  def get_from(o):
1486  return _object_cast_to_SigmoidRestraintSphere(o)
1487 
1488 
1489 # Register SigmoidRestraintSphere in _IMP_pmi1:
1490 _IMP_pmi1.SigmoidRestraintSphere_swigregister(SigmoidRestraintSphere)
1491 class TransformMover(IMP.core.MonteCarloMover):
1492  r"""Proxy of C++ IMP::pmi1::TransformMover class."""
1493 
1494  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1495 
1496  def __init__(self, *args):
1497  r"""
1498  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1499  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1500  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1501  """
1502  _IMP_pmi1.TransformMover_swiginit(self, _IMP_pmi1.new_TransformMover(*args))
1503 
1504  def add_xyz_particle(self, pi):
1505  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1506  return _IMP_pmi1.TransformMover_add_xyz_particle(self, pi)
1507 
1508  def add_rigid_body_particle(self, pi):
1509  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1510  return _IMP_pmi1.TransformMover_add_rigid_body_particle(self, pi)
1511 
1512  def set_maximum_translation(self, mt):
1513  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1514  return _IMP_pmi1.TransformMover_set_maximum_translation(self, mt)
1515 
1516  def set_maximum_rotation(self, mr):
1517  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1518  return _IMP_pmi1.TransformMover_set_maximum_rotation(self, mr)
1519 
1520  def get_maximum_translation(self):
1521  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1522  return _IMP_pmi1.TransformMover_get_maximum_translation(self)
1523 
1524  def get_maximum_rotation(self):
1525  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1526  return _IMP_pmi1.TransformMover_get_maximum_rotation(self)
1527 
1528  def get_last_transformation(self):
1529  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1530  return _IMP_pmi1.TransformMover_get_last_transformation(self)
1531 
1532  def get_version_info(self):
1533  r"""get_version_info(TransformMover self) -> VersionInfo"""
1534  return _IMP_pmi1.TransformMover_get_version_info(self)
1535  __swig_destroy__ = _IMP_pmi1.delete_TransformMover
1536 
1537  def __str__(self):
1538  r"""__str__(TransformMover self) -> std::string"""
1539  return _IMP_pmi1.TransformMover___str__(self)
1540 
1541  def __repr__(self):
1542  r"""__repr__(TransformMover self) -> std::string"""
1543  return _IMP_pmi1.TransformMover___repr__(self)
1544 
1545  @staticmethod
1546  def get_from(o):
1547  return _object_cast_to_TransformMover(o)
1548 
1549 
1550 # Register TransformMover in _IMP_pmi1:
1551 _IMP_pmi1.TransformMover_swigregister(TransformMover)
1552 
1553 def create_elastic_network(ps, dist_cutoff, strength):
1554  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1555  return _IMP_pmi1.create_elastic_network(ps, dist_cutoff, strength)
1556 
1557 def get_dihedral_angle(p1, p2, p3, p4):
1558  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1559  return _IMP_pmi1.get_dihedral_angle(p1, p2, p3, p4)
1560 
1561 def get_bipartite_minimum_sphere_distance(m1, m2):
1562  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1563  return _IMP_pmi1.get_bipartite_minimum_sphere_distance(m1, m2)
1564 
1565 def get_list_of_bipartite_minimum_sphere_distance(pss):
1566  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1567  return _IMP_pmi1.get_list_of_bipartite_minimum_sphere_distance(pss)
1568 class InternalCoordinatesConstraint(IMP.SingletonModifier):
1569  r"""Proxy of C++ IMP::pmi1::InternalCoordinatesConstraint class."""
1570 
1571  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1572 
1573  def __init__(self):
1574  r"""__init__(InternalCoordinatesConstraint self) -> InternalCoordinatesConstraint"""
1575  _IMP_pmi1.InternalCoordinatesConstraint_swiginit(self, _IMP_pmi1.new_InternalCoordinatesConstraint())
1576 
1577  def do_get_inputs(self, m, pis):
1578  r"""do_get_inputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1579  return _IMP_pmi1.InternalCoordinatesConstraint_do_get_inputs(self, m, pis)
1580 
1581  def do_get_outputs(self, m, pis):
1582  r"""do_get_outputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1583  return _IMP_pmi1.InternalCoordinatesConstraint_do_get_outputs(self, m, pis)
1584 
1585  def get_version_info(self):
1586  r"""get_version_info(InternalCoordinatesConstraint self) -> VersionInfo"""
1587  return _IMP_pmi1.InternalCoordinatesConstraint_get_version_info(self)
1588  __swig_destroy__ = _IMP_pmi1.delete_InternalCoordinatesConstraint
1589 
1590  def __str__(self):
1591  r"""__str__(InternalCoordinatesConstraint self) -> std::string"""
1592  return _IMP_pmi1.InternalCoordinatesConstraint___str__(self)
1593 
1594  def __repr__(self):
1595  r"""__repr__(InternalCoordinatesConstraint self) -> std::string"""
1596  return _IMP_pmi1.InternalCoordinatesConstraint___repr__(self)
1597 
1598  @staticmethod
1599  def get_from(o):
1600  return _object_cast_to_InternalCoordinatesConstraint(o)
1601 
1602 
1603 # Register InternalCoordinatesConstraint in _IMP_pmi1:
1604 _IMP_pmi1.InternalCoordinatesConstraint_swigregister(InternalCoordinatesConstraint)
1605 
1606 def get_module_version():
1607  r"""get_module_version() -> std::string const"""
1608  return _IMP_pmi1.get_module_version()
1609 
1610 def get_example_path(fname):
1611  r"""get_example_path(std::string fname) -> std::string"""
1612  return _IMP_pmi1.get_example_path(fname)
1613 
1614 def get_data_path(fname):
1615  r"""get_data_path(std::string fname) -> std::string"""
1616  return _IMP_pmi1.get_data_path(fname)
1617 
1618 from . import _version_check
1619 _version_check.check_version(get_module_version())
1620 __version__ = get_module_version()
1621 
1622 
A base class for modifiers of ParticlesTemp.
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.
def deprecated_module
Mark a Python module as deprecated.
Definition: __init__.py:9515
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.
static Molecule setup_particle(Model *m, ParticleIndex pi)
Definition: Molecule.h:37
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.
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:119
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