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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
pmi1/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_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  """
768  return _IMP_pmi1.Uncertainty_add_attribute(self, *args)
769 
770  def get_value(self, *args):
771  r"""
772  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
773  get_value(Uncertainty self, IntKey a0) -> IMP::Int
774  get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
775  get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
776  get_value(Uncertainty self, StringKey a0) -> IMP::String
777  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
778  get_value(Uncertainty self, ObjectKey a0) -> Object
779  """
780  return _IMP_pmi1.Uncertainty_get_value(self, *args)
781 
782  def set_value(self, *args):
783  r"""
784  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
785  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
786  set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
787  set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
788  set_value(Uncertainty self, StringKey a0, IMP::String a1)
789  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
790  set_value(Uncertainty self, ObjectKey a0, Object a1)
791  """
792  return _IMP_pmi1.Uncertainty_set_value(self, *args)
793 
794  def remove_attribute(self, *args):
795  r"""
796  remove_attribute(Uncertainty self, FloatKey a0)
797  remove_attribute(Uncertainty self, IntKey a0)
798  remove_attribute(Uncertainty self, FloatsKey a0)
799  remove_attribute(Uncertainty self, IntsKey a0)
800  remove_attribute(Uncertainty self, StringKey a0)
801  remove_attribute(Uncertainty self, ParticleIndexKey a0)
802  remove_attribute(Uncertainty self, ObjectKey a0)
803  """
804  return _IMP_pmi1.Uncertainty_remove_attribute(self, *args)
805 
806  def has_attribute(self, *args):
807  r"""
808  has_attribute(Uncertainty self, FloatKey a0) -> bool
809  has_attribute(Uncertainty self, IntKey a0) -> bool
810  has_attribute(Uncertainty self, FloatsKey a0) -> bool
811  has_attribute(Uncertainty self, IntsKey a0) -> bool
812  has_attribute(Uncertainty self, StringKey a0) -> bool
813  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
814  has_attribute(Uncertainty self, ObjectKey a0) -> bool
815  """
816  return _IMP_pmi1.Uncertainty_has_attribute(self, *args)
817 
818  def get_derivative(self, a0):
819  r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
820  return _IMP_pmi1.Uncertainty_get_derivative(self, a0)
821 
822  def get_name(self):
823  r"""get_name(Uncertainty self) -> std::string"""
824  return _IMP_pmi1.Uncertainty_get_name(self)
825 
826  def clear_caches(self):
827  r"""clear_caches(Uncertainty self)"""
828  return _IMP_pmi1.Uncertainty_clear_caches(self)
829 
830  def set_name(self, a0):
831  r"""set_name(Uncertainty self, std::string a0)"""
832  return _IMP_pmi1.Uncertainty_set_name(self, a0)
833 
834  def set_check_level(self, a0):
835  r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
836  return _IMP_pmi1.Uncertainty_set_check_level(self, a0)
837 
838  def add_to_derivative(self, a0, a1, a2):
839  r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
840  return _IMP_pmi1.Uncertainty_add_to_derivative(self, a0, a1, a2)
841 
842  def set_is_optimized(self, a0, a1):
843  r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
844  return _IMP_pmi1.Uncertainty_set_is_optimized(self, a0, a1)
845 
846  def get_is_optimized(self, a0):
847  r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
848  return _IMP_pmi1.Uncertainty_get_is_optimized(self, a0)
849 
850  def get_check_level(self):
851  r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
852  return _IMP_pmi1.Uncertainty_get_check_level(self)
853 
854  def __eq__(self, *args):
855  r"""
856  __eq__(Uncertainty self, Uncertainty o) -> bool
857  __eq__(Uncertainty self, Particle d) -> bool
858  """
859  return _IMP_pmi1.Uncertainty___eq__(self, *args)
860 
861  def __ne__(self, *args):
862  r"""
863  __ne__(Uncertainty self, Uncertainty o) -> bool
864  __ne__(Uncertainty self, Particle d) -> bool
865  """
866  return _IMP_pmi1.Uncertainty___ne__(self, *args)
867 
868  def __le__(self, *args):
869  r"""
870  __le__(Uncertainty self, Uncertainty o) -> bool
871  __le__(Uncertainty self, Particle d) -> bool
872  """
873  return _IMP_pmi1.Uncertainty___le__(self, *args)
874 
875  def __lt__(self, *args):
876  r"""
877  __lt__(Uncertainty self, Uncertainty o) -> bool
878  __lt__(Uncertainty self, Particle d) -> bool
879  """
880  return _IMP_pmi1.Uncertainty___lt__(self, *args)
881 
882  def __ge__(self, *args):
883  r"""
884  __ge__(Uncertainty self, Uncertainty o) -> bool
885  __ge__(Uncertainty self, Particle d) -> bool
886  """
887  return _IMP_pmi1.Uncertainty___ge__(self, *args)
888 
889  def __gt__(self, *args):
890  r"""
891  __gt__(Uncertainty self, Uncertainty o) -> bool
892  __gt__(Uncertainty self, Particle d) -> bool
893  """
894  return _IMP_pmi1.Uncertainty___gt__(self, *args)
895 
896  def __hash__(self):
897  r"""__hash__(Uncertainty self) -> std::size_t"""
898  return _IMP_pmi1.Uncertainty___hash__(self)
899 
900  def __str__(self):
901  r"""__str__(Uncertainty self) -> std::string"""
902  return _IMP_pmi1.Uncertainty___str__(self)
903 
904  def __repr__(self):
905  r"""__repr__(Uncertainty self) -> std::string"""
906  return _IMP_pmi1.Uncertainty___repr__(self)
907 
908  def _get_as_binary(self):
909  r"""_get_as_binary(Uncertainty self) -> PyObject *"""
910  return _IMP_pmi1.Uncertainty__get_as_binary(self)
911 
912  def _set_from_binary(self, p):
913  r"""_set_from_binary(Uncertainty self, PyObject * p)"""
914  return _IMP_pmi1.Uncertainty__set_from_binary(self, p)
915 
916  def __getstate__(self):
917  p = self._get_as_binary()
918  if len(self.__dict__) > 1:
919  d = self.__dict__.copy()
920  del d['this']
921  p = (d, p)
922  return p
923 
924  def __setstate__(self, p):
925  if not hasattr(self, 'this'):
926  self.__init__()
927  if isinstance(p, tuple):
928  d, p = p
929  self.__dict__.update(d)
930  return self._set_from_binary(p)
931 
932  __swig_destroy__ = _IMP_pmi1.delete_Uncertainty
933 
934 # Register Uncertainty in _IMP_pmi1:
935 _IMP_pmi1.Uncertainty_swigregister(Uncertainty)
936 class Resolution(IMP.Decorator):
937  r"""Proxy of C++ IMP::pmi1::Resolution class."""
938 
939  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
940 
941  def get_resolution(self):
942  r"""get_resolution(Resolution self) -> IMP::Float"""
943  return _IMP_pmi1.Resolution_get_resolution(self)
944 
945  def set_resolution(self, d):
946  r"""set_resolution(Resolution self, IMP::Float d)"""
947  return _IMP_pmi1.Resolution_set_resolution(self, d)
948 
949  def __init__(self, *args):
950  r"""
951  __init__(Resolution self) -> Resolution
952  __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
953  __init__(Resolution self, _ParticleAdaptor d) -> Resolution
954  """
955  _IMP_pmi1.Resolution_swiginit(self, _IMP_pmi1.new_Resolution(*args))
956 
957  @staticmethod
958  def get_is_setup(*args):
959  r"""
960  get_is_setup(Model m, ParticleIndex pi) -> bool
961  get_is_setup(_ParticleAdaptor p) -> bool
962  """
963  return _IMP_pmi1.Resolution_get_is_setup(*args)
964 
965  def show(self, *args):
966  r"""show(Resolution self, _ostream out=std::cout)"""
967  return _IMP_pmi1.Resolution_show(self, *args)
968 
969  @staticmethod
970  def setup_particle(*args):
971  r"""
972  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
973  setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
974  """
975  return _IMP_pmi1.Resolution_setup_particle(*args)
976 
977  @staticmethod
978  def get_resolution_key():
979  r"""get_resolution_key() -> FloatKey"""
980  return _IMP_pmi1.Resolution_get_resolution_key()
981 
982  def add_attribute(self, *args):
983  r"""
984  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
985  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
986  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
987  add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
988  add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
989  add_attribute(Resolution self, StringKey a0, IMP::String a1)
990  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
991  add_attribute(Resolution self, ObjectKey a0, Object a1)
992  """
993  return _IMP_pmi1.Resolution_add_attribute(self, *args)
994 
995  def get_value(self, *args):
996  r"""
997  get_value(Resolution self, FloatKey a0) -> IMP::Float
998  get_value(Resolution self, IntKey a0) -> IMP::Int
999  get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1000  get_value(Resolution self, IntsKey a0) -> IMP::Ints
1001  get_value(Resolution self, StringKey a0) -> IMP::String
1002  get_value(Resolution self, ParticleIndexKey a0) -> Particle
1003  get_value(Resolution self, ObjectKey a0) -> Object
1004  """
1005  return _IMP_pmi1.Resolution_get_value(self, *args)
1006 
1007  def set_value(self, *args):
1008  r"""
1009  set_value(Resolution self, FloatKey a0, IMP::Float a1)
1010  set_value(Resolution self, IntKey a0, IMP::Int a1)
1011  set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1012  set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1013  set_value(Resolution self, StringKey a0, IMP::String a1)
1014  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1015  set_value(Resolution self, ObjectKey a0, Object a1)
1016  """
1017  return _IMP_pmi1.Resolution_set_value(self, *args)
1018 
1019  def remove_attribute(self, *args):
1020  r"""
1021  remove_attribute(Resolution self, FloatKey a0)
1022  remove_attribute(Resolution self, IntKey a0)
1023  remove_attribute(Resolution self, FloatsKey a0)
1024  remove_attribute(Resolution self, IntsKey a0)
1025  remove_attribute(Resolution self, StringKey a0)
1026  remove_attribute(Resolution self, ParticleIndexKey a0)
1027  remove_attribute(Resolution self, ObjectKey a0)
1028  """
1029  return _IMP_pmi1.Resolution_remove_attribute(self, *args)
1030 
1031  def has_attribute(self, *args):
1032  r"""
1033  has_attribute(Resolution self, FloatKey a0) -> bool
1034  has_attribute(Resolution self, IntKey a0) -> bool
1035  has_attribute(Resolution self, FloatsKey a0) -> bool
1036  has_attribute(Resolution self, IntsKey a0) -> bool
1037  has_attribute(Resolution self, StringKey a0) -> bool
1038  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1039  has_attribute(Resolution self, ObjectKey a0) -> bool
1040  """
1041  return _IMP_pmi1.Resolution_has_attribute(self, *args)
1042 
1043  def get_derivative(self, a0):
1044  r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1045  return _IMP_pmi1.Resolution_get_derivative(self, a0)
1046 
1047  def get_name(self):
1048  r"""get_name(Resolution self) -> std::string"""
1049  return _IMP_pmi1.Resolution_get_name(self)
1050 
1051  def clear_caches(self):
1052  r"""clear_caches(Resolution self)"""
1053  return _IMP_pmi1.Resolution_clear_caches(self)
1054 
1055  def set_name(self, a0):
1056  r"""set_name(Resolution self, std::string a0)"""
1057  return _IMP_pmi1.Resolution_set_name(self, a0)
1058 
1059  def set_check_level(self, a0):
1060  r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1061  return _IMP_pmi1.Resolution_set_check_level(self, a0)
1062 
1063  def add_to_derivative(self, a0, a1, a2):
1064  r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1065  return _IMP_pmi1.Resolution_add_to_derivative(self, a0, a1, a2)
1066 
1067  def set_is_optimized(self, a0, a1):
1068  r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1069  return _IMP_pmi1.Resolution_set_is_optimized(self, a0, a1)
1070 
1071  def get_is_optimized(self, a0):
1072  r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1073  return _IMP_pmi1.Resolution_get_is_optimized(self, a0)
1074 
1075  def get_check_level(self):
1076  r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1077  return _IMP_pmi1.Resolution_get_check_level(self)
1078 
1079  def __eq__(self, *args):
1080  r"""
1081  __eq__(Resolution self, Resolution o) -> bool
1082  __eq__(Resolution self, Particle d) -> bool
1083  """
1084  return _IMP_pmi1.Resolution___eq__(self, *args)
1085 
1086  def __ne__(self, *args):
1087  r"""
1088  __ne__(Resolution self, Resolution o) -> bool
1089  __ne__(Resolution self, Particle d) -> bool
1090  """
1091  return _IMP_pmi1.Resolution___ne__(self, *args)
1092 
1093  def __le__(self, *args):
1094  r"""
1095  __le__(Resolution self, Resolution o) -> bool
1096  __le__(Resolution self, Particle d) -> bool
1097  """
1098  return _IMP_pmi1.Resolution___le__(self, *args)
1099 
1100  def __lt__(self, *args):
1101  r"""
1102  __lt__(Resolution self, Resolution o) -> bool
1103  __lt__(Resolution self, Particle d) -> bool
1104  """
1105  return _IMP_pmi1.Resolution___lt__(self, *args)
1106 
1107  def __ge__(self, *args):
1108  r"""
1109  __ge__(Resolution self, Resolution o) -> bool
1110  __ge__(Resolution self, Particle d) -> bool
1111  """
1112  return _IMP_pmi1.Resolution___ge__(self, *args)
1113 
1114  def __gt__(self, *args):
1115  r"""
1116  __gt__(Resolution self, Resolution o) -> bool
1117  __gt__(Resolution self, Particle d) -> bool
1118  """
1119  return _IMP_pmi1.Resolution___gt__(self, *args)
1120 
1121  def __hash__(self):
1122  r"""__hash__(Resolution self) -> std::size_t"""
1123  return _IMP_pmi1.Resolution___hash__(self)
1124 
1125  def __str__(self):
1126  r"""__str__(Resolution self) -> std::string"""
1127  return _IMP_pmi1.Resolution___str__(self)
1128 
1129  def __repr__(self):
1130  r"""__repr__(Resolution self) -> std::string"""
1131  return _IMP_pmi1.Resolution___repr__(self)
1132 
1133  def _get_as_binary(self):
1134  r"""_get_as_binary(Resolution self) -> PyObject *"""
1135  return _IMP_pmi1.Resolution__get_as_binary(self)
1136 
1137  def _set_from_binary(self, p):
1138  r"""_set_from_binary(Resolution self, PyObject * p)"""
1139  return _IMP_pmi1.Resolution__set_from_binary(self, p)
1140 
1141  def __getstate__(self):
1142  p = self._get_as_binary()
1143  if len(self.__dict__) > 1:
1144  d = self.__dict__.copy()
1145  del d['this']
1146  p = (d, p)
1147  return p
1148 
1149  def __setstate__(self, p):
1150  if not hasattr(self, 'this'):
1151  self.__init__()
1152  if isinstance(p, tuple):
1153  d, p = p
1154  self.__dict__.update(d)
1155  return self._set_from_binary(p)
1156 
1157  __swig_destroy__ = _IMP_pmi1.delete_Resolution
1158 
1159 # Register Resolution in _IMP_pmi1:
1160 _IMP_pmi1.Resolution_swigregister(Resolution)
1161 class Symmetric(IMP.Decorator):
1162  r"""Proxy of C++ IMP::pmi1::Symmetric class."""
1163 
1164  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1165 
1166  def get_symmetric(self):
1167  r"""get_symmetric(Symmetric self) -> IMP::Float"""
1168  return _IMP_pmi1.Symmetric_get_symmetric(self)
1169 
1170  def set_symmetric(self, d):
1171  r"""set_symmetric(Symmetric self, IMP::Float d)"""
1172  return _IMP_pmi1.Symmetric_set_symmetric(self, d)
1173 
1174  def __init__(self, *args):
1175  r"""
1176  __init__(Symmetric self) -> Symmetric
1177  __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1178  __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1179  """
1180  _IMP_pmi1.Symmetric_swiginit(self, _IMP_pmi1.new_Symmetric(*args))
1181 
1182  @staticmethod
1183  def get_is_setup(*args):
1184  r"""
1185  get_is_setup(Model m, ParticleIndex pi) -> bool
1186  get_is_setup(_ParticleAdaptor p) -> bool
1187  """
1188  return _IMP_pmi1.Symmetric_get_is_setup(*args)
1189 
1190  def show(self, *args):
1191  r"""show(Symmetric self, _ostream out=std::cout)"""
1192  return _IMP_pmi1.Symmetric_show(self, *args)
1193 
1194  @staticmethod
1195  def setup_particle(*args):
1196  r"""
1197  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1198  setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1199  """
1200  return _IMP_pmi1.Symmetric_setup_particle(*args)
1201 
1202  @staticmethod
1203  def get_symmetric_key():
1204  r"""get_symmetric_key() -> FloatKey"""
1205  return _IMP_pmi1.Symmetric_get_symmetric_key()
1206 
1207  def add_attribute(self, *args):
1208  r"""
1209  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1210  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1211  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1212  add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1213  add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1214  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1215  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1216  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1217  """
1218  return _IMP_pmi1.Symmetric_add_attribute(self, *args)
1219 
1220  def get_value(self, *args):
1221  r"""
1222  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1223  get_value(Symmetric self, IntKey a0) -> IMP::Int
1224  get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1225  get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1226  get_value(Symmetric self, StringKey a0) -> IMP::String
1227  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1228  get_value(Symmetric self, ObjectKey a0) -> Object
1229  """
1230  return _IMP_pmi1.Symmetric_get_value(self, *args)
1231 
1232  def set_value(self, *args):
1233  r"""
1234  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1235  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1236  set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1237  set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1238  set_value(Symmetric self, StringKey a0, IMP::String a1)
1239  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1240  set_value(Symmetric self, ObjectKey a0, Object a1)
1241  """
1242  return _IMP_pmi1.Symmetric_set_value(self, *args)
1243 
1244  def remove_attribute(self, *args):
1245  r"""
1246  remove_attribute(Symmetric self, FloatKey a0)
1247  remove_attribute(Symmetric self, IntKey a0)
1248  remove_attribute(Symmetric self, FloatsKey a0)
1249  remove_attribute(Symmetric self, IntsKey a0)
1250  remove_attribute(Symmetric self, StringKey a0)
1251  remove_attribute(Symmetric self, ParticleIndexKey a0)
1252  remove_attribute(Symmetric self, ObjectKey a0)
1253  """
1254  return _IMP_pmi1.Symmetric_remove_attribute(self, *args)
1255 
1256  def has_attribute(self, *args):
1257  r"""
1258  has_attribute(Symmetric self, FloatKey a0) -> bool
1259  has_attribute(Symmetric self, IntKey a0) -> bool
1260  has_attribute(Symmetric self, FloatsKey a0) -> bool
1261  has_attribute(Symmetric self, IntsKey a0) -> bool
1262  has_attribute(Symmetric self, StringKey a0) -> bool
1263  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1264  has_attribute(Symmetric self, ObjectKey a0) -> bool
1265  """
1266  return _IMP_pmi1.Symmetric_has_attribute(self, *args)
1267 
1268  def get_derivative(self, a0):
1269  r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1270  return _IMP_pmi1.Symmetric_get_derivative(self, a0)
1271 
1272  def get_name(self):
1273  r"""get_name(Symmetric self) -> std::string"""
1274  return _IMP_pmi1.Symmetric_get_name(self)
1275 
1276  def clear_caches(self):
1277  r"""clear_caches(Symmetric self)"""
1278  return _IMP_pmi1.Symmetric_clear_caches(self)
1279 
1280  def set_name(self, a0):
1281  r"""set_name(Symmetric self, std::string a0)"""
1282  return _IMP_pmi1.Symmetric_set_name(self, a0)
1283 
1284  def set_check_level(self, a0):
1285  r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1286  return _IMP_pmi1.Symmetric_set_check_level(self, a0)
1287 
1288  def add_to_derivative(self, a0, a1, a2):
1289  r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1290  return _IMP_pmi1.Symmetric_add_to_derivative(self, a0, a1, a2)
1291 
1292  def set_is_optimized(self, a0, a1):
1293  r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1294  return _IMP_pmi1.Symmetric_set_is_optimized(self, a0, a1)
1295 
1296  def get_is_optimized(self, a0):
1297  r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1298  return _IMP_pmi1.Symmetric_get_is_optimized(self, a0)
1299 
1300  def get_check_level(self):
1301  r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1302  return _IMP_pmi1.Symmetric_get_check_level(self)
1303 
1304  def __eq__(self, *args):
1305  r"""
1306  __eq__(Symmetric self, Symmetric o) -> bool
1307  __eq__(Symmetric self, Particle d) -> bool
1308  """
1309  return _IMP_pmi1.Symmetric___eq__(self, *args)
1310 
1311  def __ne__(self, *args):
1312  r"""
1313  __ne__(Symmetric self, Symmetric o) -> bool
1314  __ne__(Symmetric self, Particle d) -> bool
1315  """
1316  return _IMP_pmi1.Symmetric___ne__(self, *args)
1317 
1318  def __le__(self, *args):
1319  r"""
1320  __le__(Symmetric self, Symmetric o) -> bool
1321  __le__(Symmetric self, Particle d) -> bool
1322  """
1323  return _IMP_pmi1.Symmetric___le__(self, *args)
1324 
1325  def __lt__(self, *args):
1326  r"""
1327  __lt__(Symmetric self, Symmetric o) -> bool
1328  __lt__(Symmetric self, Particle d) -> bool
1329  """
1330  return _IMP_pmi1.Symmetric___lt__(self, *args)
1331 
1332  def __ge__(self, *args):
1333  r"""
1334  __ge__(Symmetric self, Symmetric o) -> bool
1335  __ge__(Symmetric self, Particle d) -> bool
1336  """
1337  return _IMP_pmi1.Symmetric___ge__(self, *args)
1338 
1339  def __gt__(self, *args):
1340  r"""
1341  __gt__(Symmetric self, Symmetric o) -> bool
1342  __gt__(Symmetric self, Particle d) -> bool
1343  """
1344  return _IMP_pmi1.Symmetric___gt__(self, *args)
1345 
1346  def __hash__(self):
1347  r"""__hash__(Symmetric self) -> std::size_t"""
1348  return _IMP_pmi1.Symmetric___hash__(self)
1349 
1350  def __str__(self):
1351  r"""__str__(Symmetric self) -> std::string"""
1352  return _IMP_pmi1.Symmetric___str__(self)
1353 
1354  def __repr__(self):
1355  r"""__repr__(Symmetric self) -> std::string"""
1356  return _IMP_pmi1.Symmetric___repr__(self)
1357 
1358  def _get_as_binary(self):
1359  r"""_get_as_binary(Symmetric self) -> PyObject *"""
1360  return _IMP_pmi1.Symmetric__get_as_binary(self)
1361 
1362  def _set_from_binary(self, p):
1363  r"""_set_from_binary(Symmetric self, PyObject * p)"""
1364  return _IMP_pmi1.Symmetric__set_from_binary(self, p)
1365 
1366  def __getstate__(self):
1367  p = self._get_as_binary()
1368  if len(self.__dict__) > 1:
1369  d = self.__dict__.copy()
1370  del d['this']
1371  p = (d, p)
1372  return p
1373 
1374  def __setstate__(self, p):
1375  if not hasattr(self, 'this'):
1376  self.__init__()
1377  if isinstance(p, tuple):
1378  d, p = p
1379  self.__dict__.update(d)
1380  return self._set_from_binary(p)
1381 
1382  __swig_destroy__ = _IMP_pmi1.delete_Symmetric
1383 
1384 # Register Symmetric in _IMP_pmi1:
1385 _IMP_pmi1.Symmetric_swigregister(Symmetric)
1386 class SigmoidRestraintSphere(IMP.Restraint):
1387  r"""Proxy of C++ IMP::pmi1::SigmoidRestraintSphere class."""
1388 
1389  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1390 
1391  def __init__(self, *args):
1392  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"""
1393  _IMP_pmi1.SigmoidRestraintSphere_swiginit(self, _IMP_pmi1.new_SigmoidRestraintSphere(*args))
1394 
1395  def set_amplitude(self, amplitude):
1396  r"""set_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1397  return _IMP_pmi1.SigmoidRestraintSphere_set_amplitude(self, amplitude)
1398 
1399  def increment_amplitude(self, amplitude):
1400  r"""increment_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1401  return _IMP_pmi1.SigmoidRestraintSphere_increment_amplitude(self, amplitude)
1402 
1403  def get_amplitude(self):
1404  r"""get_amplitude(SigmoidRestraintSphere self) -> double"""
1405  return _IMP_pmi1.SigmoidRestraintSphere_get_amplitude(self)
1406 
1407  def do_get_inputs(self):
1408  r"""do_get_inputs(SigmoidRestraintSphere self) -> IMP::ModelObjectsTemp"""
1409  return _IMP_pmi1.SigmoidRestraintSphere_do_get_inputs(self)
1410 
1411  def get_version_info(self):
1412  r"""get_version_info(SigmoidRestraintSphere self) -> VersionInfo"""
1413  return _IMP_pmi1.SigmoidRestraintSphere_get_version_info(self)
1414  __swig_destroy__ = _IMP_pmi1.delete_SigmoidRestraintSphere
1415 
1416  def __str__(self):
1417  r"""__str__(SigmoidRestraintSphere self) -> std::string"""
1418  return _IMP_pmi1.SigmoidRestraintSphere___str__(self)
1419 
1420  def __repr__(self):
1421  r"""__repr__(SigmoidRestraintSphere self) -> std::string"""
1422  return _IMP_pmi1.SigmoidRestraintSphere___repr__(self)
1423 
1424  @staticmethod
1425  def get_from(o):
1426  return _object_cast_to_SigmoidRestraintSphere(o)
1427 
1428 
1429 # Register SigmoidRestraintSphere in _IMP_pmi1:
1430 _IMP_pmi1.SigmoidRestraintSphere_swigregister(SigmoidRestraintSphere)
1431 class TransformMover(IMP.core.MonteCarloMover):
1432  r"""Proxy of C++ IMP::pmi1::TransformMover class."""
1433 
1434  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1435 
1436  def __init__(self, *args):
1437  r"""
1438  __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1439  __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1440  __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1441  """
1442  _IMP_pmi1.TransformMover_swiginit(self, _IMP_pmi1.new_TransformMover(*args))
1443 
1444  def add_xyz_particle(self, pi):
1445  r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1446  return _IMP_pmi1.TransformMover_add_xyz_particle(self, pi)
1447 
1448  def add_rigid_body_particle(self, pi):
1449  r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1450  return _IMP_pmi1.TransformMover_add_rigid_body_particle(self, pi)
1451 
1452  def set_maximum_translation(self, mt):
1453  r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1454  return _IMP_pmi1.TransformMover_set_maximum_translation(self, mt)
1455 
1456  def set_maximum_rotation(self, mr):
1457  r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1458  return _IMP_pmi1.TransformMover_set_maximum_rotation(self, mr)
1459 
1460  def get_maximum_translation(self):
1461  r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1462  return _IMP_pmi1.TransformMover_get_maximum_translation(self)
1463 
1464  def get_maximum_rotation(self):
1465  r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1466  return _IMP_pmi1.TransformMover_get_maximum_rotation(self)
1467 
1468  def get_last_transformation(self):
1469  r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1470  return _IMP_pmi1.TransformMover_get_last_transformation(self)
1471 
1472  def get_version_info(self):
1473  r"""get_version_info(TransformMover self) -> VersionInfo"""
1474  return _IMP_pmi1.TransformMover_get_version_info(self)
1475  __swig_destroy__ = _IMP_pmi1.delete_TransformMover
1476 
1477  def __str__(self):
1478  r"""__str__(TransformMover self) -> std::string"""
1479  return _IMP_pmi1.TransformMover___str__(self)
1480 
1481  def __repr__(self):
1482  r"""__repr__(TransformMover self) -> std::string"""
1483  return _IMP_pmi1.TransformMover___repr__(self)
1484 
1485  @staticmethod
1486  def get_from(o):
1487  return _object_cast_to_TransformMover(o)
1488 
1489 
1490 # Register TransformMover in _IMP_pmi1:
1491 _IMP_pmi1.TransformMover_swigregister(TransformMover)
1492 
1493 def create_elastic_network(ps, dist_cutoff, strength):
1494  r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1495  return _IMP_pmi1.create_elastic_network(ps, dist_cutoff, strength)
1496 
1497 def get_dihedral_angle(p1, p2, p3, p4):
1498  r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1499  return _IMP_pmi1.get_dihedral_angle(p1, p2, p3, p4)
1500 
1501 def get_bipartite_minimum_sphere_distance(m1, m2):
1502  r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1503  return _IMP_pmi1.get_bipartite_minimum_sphere_distance(m1, m2)
1504 
1505 def get_list_of_bipartite_minimum_sphere_distance(pss):
1506  r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1507  return _IMP_pmi1.get_list_of_bipartite_minimum_sphere_distance(pss)
1508 class InternalCoordinatesConstraint(IMP.SingletonModifier):
1509  r"""Proxy of C++ IMP::pmi1::InternalCoordinatesConstraint class."""
1510 
1511  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1512 
1513  def __init__(self):
1514  r"""__init__(InternalCoordinatesConstraint self) -> InternalCoordinatesConstraint"""
1515  _IMP_pmi1.InternalCoordinatesConstraint_swiginit(self, _IMP_pmi1.new_InternalCoordinatesConstraint())
1516 
1517  def do_get_inputs(self, m, pis):
1518  r"""do_get_inputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1519  return _IMP_pmi1.InternalCoordinatesConstraint_do_get_inputs(self, m, pis)
1520 
1521  def do_get_outputs(self, m, pis):
1522  r"""do_get_outputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1523  return _IMP_pmi1.InternalCoordinatesConstraint_do_get_outputs(self, m, pis)
1524 
1525  def get_version_info(self):
1526  r"""get_version_info(InternalCoordinatesConstraint self) -> VersionInfo"""
1527  return _IMP_pmi1.InternalCoordinatesConstraint_get_version_info(self)
1528  __swig_destroy__ = _IMP_pmi1.delete_InternalCoordinatesConstraint
1529 
1530  def __str__(self):
1531  r"""__str__(InternalCoordinatesConstraint self) -> std::string"""
1532  return _IMP_pmi1.InternalCoordinatesConstraint___str__(self)
1533 
1534  def __repr__(self):
1535  r"""__repr__(InternalCoordinatesConstraint self) -> std::string"""
1536  return _IMP_pmi1.InternalCoordinatesConstraint___repr__(self)
1537 
1538  @staticmethod
1539  def get_from(o):
1540  return _object_cast_to_InternalCoordinatesConstraint(o)
1541 
1542 
1543 # Register InternalCoordinatesConstraint in _IMP_pmi1:
1544 _IMP_pmi1.InternalCoordinatesConstraint_swigregister(InternalCoordinatesConstraint)
1545 
1546 def get_module_version():
1547  r"""get_module_version() -> std::string const"""
1548  return _IMP_pmi1.get_module_version()
1549 
1550 def get_example_path(fname):
1551  r"""get_example_path(std::string fname) -> std::string"""
1552  return _IMP_pmi1.get_example_path(fname)
1553 
1554 def get_data_path(fname):
1555  r"""get_data_path(std::string fname) -> std::string"""
1556  return _IMP_pmi1.get_data_path(fname)
1557 
1558 from . import _version_check
1559 _version_check.check_version(get_module_version())
1560 __version__ = get_module_version()
1561 
1562 
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:8979
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