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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
misc/__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_misc
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_MISC_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_MISC_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_misc.delete_IMP_MISC_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_MISC_SwigPyIterator self) -> PyObject *"""
79  return _IMP_misc.IMP_MISC_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator"""
83  return _IMP_misc.IMP_MISC_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator"""
87  return _IMP_misc.IMP_MISC_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_misc.IMP_MISC_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
95  return _IMP_misc.IMP_MISC_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator"""
99  return _IMP_misc.IMP_MISC_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_MISC_SwigPyIterator self) -> PyObject *"""
103  return _IMP_misc.IMP_MISC_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_MISC_SwigPyIterator self) -> PyObject *"""
107  return _IMP_misc.IMP_MISC_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_MISC_SwigPyIterator self) -> PyObject *"""
111  return _IMP_misc.IMP_MISC_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
115  return _IMP_misc.IMP_MISC_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
119  return _IMP_misc.IMP_MISC_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
123  return _IMP_misc.IMP_MISC_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
127  return _IMP_misc.IMP_MISC_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
131  return _IMP_misc.IMP_MISC_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
135  return _IMP_misc.IMP_MISC_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator
140  __sub__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_misc.IMP_MISC_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_MISC_SwigPyIterator in _IMP_misc:
147 _IMP_misc.IMP_MISC_SwigPyIterator_swigregister(IMP_MISC_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_misc.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_misc.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_misc.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_misc.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_misc.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_misc.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_misc.IMP_MEMORY
167 
168 IMP_NONE = _IMP_misc.IMP_NONE
169 
170 IMP_USAGE = _IMP_misc.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_misc.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_misc.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_misc.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_misc.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_misc.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_misc.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_misc.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_misc._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_misc:
237 _IMP_misc._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_misc.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_misc.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_misc.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_misc.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_misc.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_misc.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_misc.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_misc.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_misc.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_CORE_HAS_IMP_CGAL = _IMP_misc.IMP_CORE_HAS_IMP_CGAL
310 
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_misc.IMP_CORE_HAS_IMP_KERNEL
312 
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM
314 
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM
318 
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM
320 
321 IMP_CORE_HAS_CGAL = _IMP_misc.IMP_CORE_HAS_CGAL
322 
323 IMP_CORE_HAS_HDF5 = _IMP_misc.IMP_CORE_HAS_HDF5
324 
325 IMP_CORE_HAS_NUMPY = _IMP_misc.IMP_CORE_HAS_NUMPY
326 
327 IMPCORE_SHOW_WARNINGS = _IMP_misc.IMPCORE_SHOW_WARNINGS
328 
329 import IMP.core
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL
333 
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY
335 
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL
337 
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM
345 
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 
348 IMP_CONTAINER_HAS_CGAL = _IMP_misc.IMP_CONTAINER_HAS_CGAL
349 
350 IMP_CONTAINER_HAS_HDF5 = _IMP_misc.IMP_CONTAINER_HAS_HDF5
351 
352 IMP_CONTAINER_HAS_NUMPY = _IMP_misc.IMP_CONTAINER_HAS_NUMPY
353 
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_misc.IMP_CONTAINER_HAS_PYTHON_IHM
355 
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_misc.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_misc.IMP_CONTAINER_HAS_ROBIN_MAP
359 
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_misc.IMPCONTAINER_SHOW_WARNINGS
361 
362 import IMP.container
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_misc.IMP_ATOM_HAS_IMP_CGAL
364 
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL
366 
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
368 
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
370 
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM
372 
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX
374 
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM
376 
377 IMP_ATOM_HAS_CGAL = _IMP_misc.IMP_ATOM_HAS_CGAL
378 
379 IMP_ATOM_HAS_HDF5 = _IMP_misc.IMP_ATOM_HAS_HDF5
380 
381 IMP_ATOM_HAS_NUMPY = _IMP_misc.IMP_ATOM_HAS_NUMPY
382 
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_misc.IMP_ATOM_HAS_PYTHON_IHM
384 
385 IMPATOM_SHOW_WARNINGS = _IMP_misc.IMPATOM_SHOW_WARNINGS
386 
387 IMP_ATOM_TYPE_INDEX = _IMP_misc.IMP_ATOM_TYPE_INDEX
388 
389 IMP_RESIDUE_TYPE_INDEX = _IMP_misc.IMP_RESIDUE_TYPE_INDEX
390 
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_misc.IMP_HIERARCHY_TYPE_INDEX
392 
393 IMP_CHAIN_TYPE_INDEX = _IMP_misc.IMP_CHAIN_TYPE_INDEX
394 
395 import IMP.atom
396 IMP_MISC_HAS_IMP_ALGEBRA = _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA
397 
398 IMP_MISC_HAS_IMP_CGAL = _IMP_misc.IMP_MISC_HAS_IMP_CGAL
399 
400 IMP_MISC_HAS_IMP_CONTAINER = _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER
401 
402 IMP_MISC_HAS_IMP_DISPLAY = _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY
403 
404 IMP_MISC_HAS_IMP_KERNEL = _IMP_misc.IMP_MISC_HAS_IMP_KERNEL
405 
406 IMP_MISC_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR
407 
408 IMP_MISC_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM
409 
410 IMP_MISC_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS
411 
412 IMP_MISC_HAS_BOOST_RANDOM = _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM
413 
414 IMP_MISC_HAS_BOOST_REGEX = _IMP_misc.IMP_MISC_HAS_BOOST_REGEX
415 
416 IMP_MISC_HAS_BOOST_SYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM
417 
418 IMP_MISC_HAS_CGAL = _IMP_misc.IMP_MISC_HAS_CGAL
419 
420 IMP_MISC_HAS_HDF5 = _IMP_misc.IMP_MISC_HAS_HDF5
421 
422 IMP_MISC_HAS_NUMPY = _IMP_misc.IMP_MISC_HAS_NUMPY
423 
424 IMP_MISC_HAS_PYTHON_IHM = _IMP_misc.IMP_MISC_HAS_PYTHON_IHM
425 
426 IMPMISC_SHOW_WARNINGS = _IMP_misc.IMPMISC_SHOW_WARNINGS
427 
428 
429 _object_types.append("WormLikeChain")
430 
431 
432 def _object_cast_to_WormLikeChain(o):
433  r"""_object_cast_to_WormLikeChain(Object o) -> WormLikeChain"""
434  return _IMP_misc._object_cast_to_WormLikeChain(o)
435 
436 _object_types.append("FreelyJointedChain")
437 
438 
439 def _object_cast_to_FreelyJointedChain(o):
440  r"""_object_cast_to_FreelyJointedChain(Object o) -> FreelyJointedChain"""
441  return _IMP_misc._object_cast_to_FreelyJointedChain(o)
442 
443 _object_types.append("StateAdaptor")
444 
445 
446 def _object_cast_to_StateAdaptor(o):
447  r"""_object_cast_to_StateAdaptor(Object o) -> StateAdaptor"""
448  return _IMP_misc._object_cast_to_StateAdaptor(o)
449 
450 _object_types.append("CommonEndpointPairFilter")
451 
452 
453 def _object_cast_to_CommonEndpointPairFilter(o):
454  r"""_object_cast_to_CommonEndpointPairFilter(Object o) -> CommonEndpointPairFilter"""
455  return _IMP_misc._object_cast_to_CommonEndpointPairFilter(o)
456 
457 _object_types.append("LogPairScore")
458 
459 
460 def _object_cast_to_LogPairScore(o):
461  r"""_object_cast_to_LogPairScore(Object o) -> LogPairScore"""
462  return _IMP_misc._object_cast_to_LogPairScore(o)
463 
464 _object_types.append("LowestRefinedPairScore")
465 
466 
467 def _object_cast_to_LowestRefinedPairScore(o):
468  r"""_object_cast_to_LowestRefinedPairScore(Object o) -> LowestRefinedPairScore"""
469  return _IMP_misc._object_cast_to_LowestRefinedPairScore(o)
470 
471 _object_types.append("SoftCylinderPairScore")
472 
473 
474 def _object_cast_to_SoftCylinderPairScore(o):
475  r"""_object_cast_to_SoftCylinderPairScore(Object o) -> SoftCylinderPairScore"""
476  return _IMP_misc._object_cast_to_SoftCylinderPairScore(o)
477 
478 _object_types.append("DecayPairContainerOptimizerState")
479 
480 
481 def _object_cast_to_DecayPairContainerOptimizerState(o):
482  r"""_object_cast_to_DecayPairContainerOptimizerState(Object o) -> DecayPairContainerOptimizerState"""
483  return _IMP_misc._object_cast_to_DecayPairContainerOptimizerState(o)
484 
485 def CustomXYZRs(l=[]):
486  return [CustomXYZR(x) for x in l]
487 _plural_types.append("CustomXYZRs")
488 
489 
490 _value_types.append("CustomXYZR")
491 
492 class WormLikeChain(IMP.UnaryFunction):
493  r"""Proxy of C++ IMP::misc::WormLikeChain class."""
494 
495  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
496 
497  def __init__(self, l_max, lp):
498  r"""__init__(WormLikeChain self, IMP::Float l_max, IMP::Float lp) -> WormLikeChain"""
499  _IMP_misc.WormLikeChain_swiginit(self, _IMP_misc.new_WormLikeChain(l_max, lp))
500 
501  def get_version_info(self):
502  r"""get_version_info(WormLikeChain self) -> VersionInfo"""
503  return _IMP_misc.WormLikeChain_get_version_info(self)
504  __swig_destroy__ = _IMP_misc.delete_WormLikeChain
505 
506  def do_show(self, out):
507  r"""do_show(WormLikeChain self, _ostream out)"""
508  return _IMP_misc.WormLikeChain_do_show(self, out)
509 
510  def __str__(self):
511  r"""__str__(WormLikeChain self) -> std::string"""
512  return _IMP_misc.WormLikeChain___str__(self)
513 
514  def __repr__(self):
515  r"""__repr__(WormLikeChain self) -> std::string"""
516  return _IMP_misc.WormLikeChain___repr__(self)
517 
518  @staticmethod
519  def get_from(o):
520  return _object_cast_to_WormLikeChain(o)
521 
522 
523 # Register WormLikeChain in _IMP_misc:
524 _IMP_misc.WormLikeChain_swigregister(WormLikeChain)
525 class FreelyJointedChain(IMP.UnaryFunction):
526  r"""Proxy of C++ IMP::misc::FreelyJointedChain class."""
527 
528  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
529 
530  def __init__(self, link_num, link_length):
531  r"""__init__(FreelyJointedChain self, int link_num, double link_length) -> FreelyJointedChain"""
532  _IMP_misc.FreelyJointedChain_swiginit(self, _IMP_misc.new_FreelyJointedChain(link_num, link_length))
533 
534  def get_version_info(self):
535  r"""get_version_info(FreelyJointedChain self) -> VersionInfo"""
536  return _IMP_misc.FreelyJointedChain_get_version_info(self)
537  __swig_destroy__ = _IMP_misc.delete_FreelyJointedChain
538 
539  def get_link_number(self):
540  r"""get_link_number(FreelyJointedChain self) -> int"""
541  return _IMP_misc.FreelyJointedChain_get_link_number(self)
542 
543  def get_link_length(self):
544  r"""get_link_length(FreelyJointedChain self) -> double"""
545  return _IMP_misc.FreelyJointedChain_get_link_length(self)
546 
547  def set_link_number(self, N):
548  r"""set_link_number(FreelyJointedChain self, int N)"""
549  return _IMP_misc.FreelyJointedChain_set_link_number(self, N)
550 
551  def set_link_length(self, b):
552  r"""set_link_length(FreelyJointedChain self, double b)"""
553  return _IMP_misc.FreelyJointedChain_set_link_length(self, b)
554 
555  def get_distance_at_minimum(self):
556  r"""get_distance_at_minimum(FreelyJointedChain self) -> double"""
557  return _IMP_misc.FreelyJointedChain_get_distance_at_minimum(self)
558 
559  def get_average_distance(self):
560  r"""get_average_distance(FreelyJointedChain self) -> double"""
561  return _IMP_misc.FreelyJointedChain_get_average_distance(self)
562 
563  def __str__(self):
564  r"""__str__(FreelyJointedChain self) -> std::string"""
565  return _IMP_misc.FreelyJointedChain___str__(self)
566 
567  def __repr__(self):
568  r"""__repr__(FreelyJointedChain self) -> std::string"""
569  return _IMP_misc.FreelyJointedChain___repr__(self)
570 
571  @staticmethod
572  def get_from(o):
573  return _object_cast_to_FreelyJointedChain(o)
574 
575 
576 # Register FreelyJointedChain in _IMP_misc:
577 _IMP_misc.FreelyJointedChain_swigregister(FreelyJointedChain)
578 class LowestRefinedPairScore(IMP.PairScore):
579  r"""Proxy of C++ IMP::misc::LowestRefinedPairScore class."""
580 
581  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
582 
583  def __init__(self, r, f):
584  r"""__init__(LowestRefinedPairScore self, Refiner r, PairScore f) -> LowestRefinedPairScore"""
585  _IMP_misc.LowestRefinedPairScore_swiginit(self, _IMP_misc.new_LowestRefinedPairScore(r, f))
586 
587  def do_get_inputs(self, m, pis):
588  r"""do_get_inputs(LowestRefinedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
589  return _IMP_misc.LowestRefinedPairScore_do_get_inputs(self, m, pis)
590 
591  def get_version_info(self):
592  r"""get_version_info(LowestRefinedPairScore self) -> VersionInfo"""
593  return _IMP_misc.LowestRefinedPairScore_get_version_info(self)
594  __swig_destroy__ = _IMP_misc.delete_LowestRefinedPairScore
595 
596  def __str__(self):
597  r"""__str__(LowestRefinedPairScore self) -> std::string"""
598  return _IMP_misc.LowestRefinedPairScore___str__(self)
599 
600  def __repr__(self):
601  r"""__repr__(LowestRefinedPairScore self) -> std::string"""
602  return _IMP_misc.LowestRefinedPairScore___repr__(self)
603 
604  @staticmethod
605  def get_from(o):
606  return _object_cast_to_LowestRefinedPairScore(o)
607 
608 
609 # Register LowestRefinedPairScore in _IMP_misc:
610 _IMP_misc.LowestRefinedPairScore_swigregister(LowestRefinedPairScore)
611 class LogPairScore(IMP.PairScore):
612  r"""Proxy of C++ IMP::misc::LogPairScore class."""
613 
614  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
615 
616  def __init__(self):
617  r"""__init__(LogPairScore self) -> LogPairScore"""
618  _IMP_misc.LogPairScore_swiginit(self, _IMP_misc.new_LogPairScore())
619 
620  def do_get_inputs(self, arg2, arg3):
621  r"""do_get_inputs(LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
622  return _IMP_misc.LogPairScore_do_get_inputs(self, arg2, arg3)
623 
624  def get_version_info(self):
625  r"""get_version_info(LogPairScore self) -> VersionInfo"""
626  return _IMP_misc.LogPairScore_get_version_info(self)
627  __swig_destroy__ = _IMP_misc.delete_LogPairScore
628 
629  def get_particle_pairs(self):
630  r"""get_particle_pairs(LogPairScore self) -> IMP::ParticlePairsTemp"""
631  return _IMP_misc.LogPairScore_get_particle_pairs(self)
632 
633  def clear(self):
634  r"""clear(LogPairScore self)"""
635  return _IMP_misc.LogPairScore_clear(self)
636 
637  def get_contains(self, pp):
638  r"""get_contains(LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
639  return _IMP_misc.LogPairScore_get_contains(self, pp)
640 
641  def __str__(self):
642  r"""__str__(LogPairScore self) -> std::string"""
643  return _IMP_misc.LogPairScore___str__(self)
644 
645  def __repr__(self):
646  r"""__repr__(LogPairScore self) -> std::string"""
647  return _IMP_misc.LogPairScore___repr__(self)
648 
649  @staticmethod
650  def get_from(o):
651  return _object_cast_to_LogPairScore(o)
652 
653 
654 # Register LogPairScore in _IMP_misc:
655 _IMP_misc.LogPairScore_swigregister(LogPairScore)
656 class StateAdaptor(IMP.ScoreState):
657  r"""Proxy of C++ IMP::misc::StateAdaptor class."""
658 
659  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
660 
661  def __init__(self, m, before, after):
662  r"""__init__(StateAdaptor self, Model m, OptimizerState before, OptimizerState after) -> StateAdaptor"""
663  _IMP_misc.StateAdaptor_swiginit(self, _IMP_misc.new_StateAdaptor(m, before, after))
664 
665  def do_before_evaluate(self):
666  r"""do_before_evaluate(StateAdaptor self)"""
667  return _IMP_misc.StateAdaptor_do_before_evaluate(self)
668 
669  def do_after_evaluate(self, da):
670  r"""do_after_evaluate(StateAdaptor self, DerivativeAccumulator da)"""
671  return _IMP_misc.StateAdaptor_do_after_evaluate(self, da)
672 
673  def do_get_inputs(self):
674  r"""do_get_inputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
675  return _IMP_misc.StateAdaptor_do_get_inputs(self)
676 
677  def do_get_outputs(self):
678  r"""do_get_outputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
679  return _IMP_misc.StateAdaptor_do_get_outputs(self)
680 
681  def get_version_info(self):
682  r"""get_version_info(StateAdaptor self) -> VersionInfo"""
683  return _IMP_misc.StateAdaptor_get_version_info(self)
684  __swig_destroy__ = _IMP_misc.delete_StateAdaptor
685 
686  def __str__(self):
687  r"""__str__(StateAdaptor self) -> std::string"""
688  return _IMP_misc.StateAdaptor___str__(self)
689 
690  def __repr__(self):
691  r"""__repr__(StateAdaptor self) -> std::string"""
692  return _IMP_misc.StateAdaptor___repr__(self)
693 
694  @staticmethod
695  def get_from(o):
696  return _object_cast_to_StateAdaptor(o)
697 
698 
699 # Register StateAdaptor in _IMP_misc:
700 _IMP_misc.StateAdaptor_swigregister(StateAdaptor)
701 class CommonEndpointPairFilter(IMP.PairPredicate):
702  r"""Proxy of C++ IMP::misc::CommonEndpointPairFilter class."""
703 
704  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
705 
706  def __init__(self):
707  r"""__init__(CommonEndpointPairFilter self) -> CommonEndpointPairFilter"""
708  _IMP_misc.CommonEndpointPairFilter_swiginit(self, _IMP_misc.new_CommonEndpointPairFilter())
709 
710  def do_get_inputs(self, m, pis):
711  r"""do_get_inputs(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
712  return _IMP_misc.CommonEndpointPairFilter_do_get_inputs(self, m, pis)
713 
714  def get_value(self, *args):
715  r"""
716  get_value(CommonEndpointPairFilter self, IMP::ParticlePair const & a) -> int
717  get_value(CommonEndpointPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
718  """
719  return _IMP_misc.CommonEndpointPairFilter_get_value(self, *args)
720 
721  def get_value_index(self, *args):
722  r"""
723  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
724  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
725  """
726  return _IMP_misc.CommonEndpointPairFilter_get_value_index(self, *args)
727 
728  def get_version_info(self):
729  r"""get_version_info(CommonEndpointPairFilter self) -> VersionInfo"""
730  return _IMP_misc.CommonEndpointPairFilter_get_version_info(self)
731  __swig_destroy__ = _IMP_misc.delete_CommonEndpointPairFilter
732 
733  def __str__(self):
734  r"""__str__(CommonEndpointPairFilter self) -> std::string"""
735  return _IMP_misc.CommonEndpointPairFilter___str__(self)
736 
737  def __repr__(self):
738  r"""__repr__(CommonEndpointPairFilter self) -> std::string"""
739  return _IMP_misc.CommonEndpointPairFilter___repr__(self)
740 
741  @staticmethod
742  def get_from(o):
743  return _object_cast_to_CommonEndpointPairFilter(o)
744 
745 
746 # Register CommonEndpointPairFilter in _IMP_misc:
747 _IMP_misc.CommonEndpointPairFilter_swigregister(CommonEndpointPairFilter)
748 class CustomXYZR(IMP.core.XYZ):
749  r"""Proxy of C++ IMP::misc::CustomXYZR class."""
750 
751  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
752 
753  def get_decorator_traits(self):
754  r"""get_decorator_traits(CustomXYZR self) -> FloatKey"""
755  return _IMP_misc.CustomXYZR_get_decorator_traits(self)
756 
757  @staticmethod
758  def get_default_decorator_traits():
759  r"""get_default_decorator_traits() -> FloatKey"""
760  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
761 
762  def __init__(self, *args):
763  r"""
764  __init__(CustomXYZR self) -> CustomXYZR
765  __init__(CustomXYZR self, Model m, ParticleIndex id, FloatKey tr=IMP::core::XYZR::get_radius_key()) -> CustomXYZR
766  __init__(CustomXYZR self, _ParticleAdaptor d, FloatKey tr=IMP::core::XYZR::get_radius_key()) -> CustomXYZR
767  """
768  _IMP_misc.CustomXYZR_swiginit(self, _IMP_misc.new_CustomXYZR(*args))
769 
770  def show(self, *args):
771  r"""show(CustomXYZR self, _ostream out=std::cout)"""
772  return _IMP_misc.CustomXYZR_show(self, *args)
773 
774  @staticmethod
775  def setup_particle(*args):
776  r"""
777  setup_particle(Model m, ParticleIndex pi, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
778  setup_particle(_ParticleAdaptor d, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
779  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
780  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
781  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
782  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr=IMP::misc::CustomXYZR::get_default_decorator_traits()) -> CustomXYZR
783  """
784  return _IMP_misc.CustomXYZR_setup_particle(*args)
785 
786  @staticmethod
787  def get_is_setup(*args):
788  r"""
789  get_is_setup(_ParticleAdaptor p, FloatKey tr=IMP::core::XYZR::get_radius_key()) -> bool
790  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key=get_default_radius_key()) -> bool
791  """
792  return _IMP_misc.CustomXYZR_get_is_setup(*args)
793 
794  def get_radius(self):
795  r"""get_radius(CustomXYZR self) -> IMP::Float"""
796  return _IMP_misc.CustomXYZR_get_radius(self)
797 
798  def set_radius(self, t):
799  r"""set_radius(CustomXYZR self, IMP::Float t)"""
800  return _IMP_misc.CustomXYZR_set_radius(self, t)
801 
802  def get_sphere(self):
803  r"""get_sphere(CustomXYZR self) -> Sphere3D"""
804  return _IMP_misc.CustomXYZR_get_sphere(self)
805 
806  def set_sphere(self, s):
807  r"""set_sphere(CustomXYZR self, Sphere3D s)"""
808  return _IMP_misc.CustomXYZR_set_sphere(self, s)
809 
810  @staticmethod
811  def get_default_radius_key():
812  r"""get_default_radius_key() -> FloatKey"""
813  return _IMP_misc.CustomXYZR_get_default_radius_key()
814 
815  def add_to_radius_derivative(self, v, d):
816  r"""add_to_radius_derivative(CustomXYZR self, double v, DerivativeAccumulator d)"""
817  return _IMP_misc.CustomXYZR_add_to_radius_derivative(self, v, d)
818 
819  def get_traits(self):
820  r"""get_traits(CustomXYZR self) -> FloatKey"""
821  return _IMP_misc.CustomXYZR_get_traits(self)
822 
823  def add_attribute(self, *args):
824  r"""
825  add_attribute(CustomXYZR self, FloatKey k, IMP::Float v, bool opt)
826  add_attribute(CustomXYZR self, FloatKey a0, IMP::Float a1)
827  add_attribute(CustomXYZR self, IntKey a0, IMP::Int a1)
828  add_attribute(CustomXYZR self, FloatsKey a0, IMP::Floats a1)
829  add_attribute(CustomXYZR self, IntsKey a0, IMP::Ints a1)
830  add_attribute(CustomXYZR self, StringKey a0, IMP::String a1)
831  add_attribute(CustomXYZR self, ParticleIndexKey a0, Particle a1)
832  add_attribute(CustomXYZR self, ObjectKey a0, Object a1)
833  add_attribute(CustomXYZR self, SparseFloatKey a0, IMP::Float a1)
834  add_attribute(CustomXYZR self, SparseIntKey a0, IMP::Int a1)
835  add_attribute(CustomXYZR self, SparseStringKey a0, IMP::String a1)
836  add_attribute(CustomXYZR self, SparseParticleIndexKey a0, ParticleIndex a1)
837  """
838  return _IMP_misc.CustomXYZR_add_attribute(self, *args)
839 
840  def get_value(self, *args):
841  r"""
842  get_value(CustomXYZR self, FloatKey a0) -> IMP::Float
843  get_value(CustomXYZR self, IntKey a0) -> IMP::Int
844  get_value(CustomXYZR self, FloatsKey a0) -> IMP::Floats
845  get_value(CustomXYZR self, IntsKey a0) -> IMP::Ints
846  get_value(CustomXYZR self, StringKey a0) -> IMP::String
847  get_value(CustomXYZR self, ParticleIndexKey a0) -> Particle
848  get_value(CustomXYZR self, ObjectKey a0) -> Object
849  get_value(CustomXYZR self, SparseFloatKey a0) -> IMP::Float
850  get_value(CustomXYZR self, SparseIntKey a0) -> IMP::Int
851  get_value(CustomXYZR self, SparseStringKey a0) -> IMP::String
852  get_value(CustomXYZR self, SparseParticleIndexKey a0) -> ParticleIndex
853  """
854  return _IMP_misc.CustomXYZR_get_value(self, *args)
855 
856  def set_value(self, *args):
857  r"""
858  set_value(CustomXYZR self, FloatKey a0, IMP::Float a1)
859  set_value(CustomXYZR self, IntKey a0, IMP::Int a1)
860  set_value(CustomXYZR self, FloatsKey a0, IMP::Floats a1)
861  set_value(CustomXYZR self, IntsKey a0, IMP::Ints a1)
862  set_value(CustomXYZR self, StringKey a0, IMP::String a1)
863  set_value(CustomXYZR self, ParticleIndexKey a0, Particle a1)
864  set_value(CustomXYZR self, ObjectKey a0, Object a1)
865  set_value(CustomXYZR self, SparseFloatKey a0, IMP::Float a1)
866  set_value(CustomXYZR self, SparseIntKey a0, IMP::Int a1)
867  set_value(CustomXYZR self, SparseStringKey a0, IMP::String a1)
868  set_value(CustomXYZR self, SparseParticleIndexKey a0, ParticleIndex a1)
869  """
870  return _IMP_misc.CustomXYZR_set_value(self, *args)
871 
872  def remove_attribute(self, *args):
873  r"""
874  remove_attribute(CustomXYZR self, FloatKey a0)
875  remove_attribute(CustomXYZR self, IntKey a0)
876  remove_attribute(CustomXYZR self, FloatsKey a0)
877  remove_attribute(CustomXYZR self, IntsKey a0)
878  remove_attribute(CustomXYZR self, StringKey a0)
879  remove_attribute(CustomXYZR self, ParticleIndexKey a0)
880  remove_attribute(CustomXYZR self, ObjectKey a0)
881  remove_attribute(CustomXYZR self, SparseFloatKey a0)
882  remove_attribute(CustomXYZR self, SparseIntKey a0)
883  remove_attribute(CustomXYZR self, SparseStringKey a0)
884  remove_attribute(CustomXYZR self, SparseParticleIndexKey a0)
885  """
886  return _IMP_misc.CustomXYZR_remove_attribute(self, *args)
887 
888  def has_attribute(self, *args):
889  r"""
890  has_attribute(CustomXYZR self, FloatKey a0) -> bool
891  has_attribute(CustomXYZR self, IntKey a0) -> bool
892  has_attribute(CustomXYZR self, FloatsKey a0) -> bool
893  has_attribute(CustomXYZR self, IntsKey a0) -> bool
894  has_attribute(CustomXYZR self, StringKey a0) -> bool
895  has_attribute(CustomXYZR self, ParticleIndexKey a0) -> bool
896  has_attribute(CustomXYZR self, ObjectKey a0) -> bool
897  has_attribute(CustomXYZR self, SparseFloatKey a0) -> bool
898  has_attribute(CustomXYZR self, SparseIntKey a0) -> bool
899  has_attribute(CustomXYZR self, SparseStringKey a0) -> bool
900  has_attribute(CustomXYZR self, SparseParticleIndexKey a0) -> bool
901  """
902  return _IMP_misc.CustomXYZR_has_attribute(self, *args)
903 
904  def get_derivative(self, a0):
905  r"""get_derivative(CustomXYZR self, FloatKey a0) -> double"""
906  return _IMP_misc.CustomXYZR_get_derivative(self, a0)
907 
908  def get_name(self):
909  r"""get_name(CustomXYZR self) -> std::string"""
910  return _IMP_misc.CustomXYZR_get_name(self)
911 
912  def clear_caches(self):
913  r"""clear_caches(CustomXYZR self)"""
914  return _IMP_misc.CustomXYZR_clear_caches(self)
915 
916  def set_name(self, a0):
917  r"""set_name(CustomXYZR self, std::string a0)"""
918  return _IMP_misc.CustomXYZR_set_name(self, a0)
919 
920  def set_check_level(self, a0):
921  r"""set_check_level(CustomXYZR self, IMP::CheckLevel a0)"""
922  return _IMP_misc.CustomXYZR_set_check_level(self, a0)
923 
924  def add_to_derivative(self, a0, a1, a2):
925  r"""add_to_derivative(CustomXYZR self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
926  return _IMP_misc.CustomXYZR_add_to_derivative(self, a0, a1, a2)
927 
928  def set_is_optimized(self, a0, a1):
929  r"""set_is_optimized(CustomXYZR self, FloatKey a0, bool a1)"""
930  return _IMP_misc.CustomXYZR_set_is_optimized(self, a0, a1)
931 
932  def get_is_optimized(self, a0):
933  r"""get_is_optimized(CustomXYZR self, FloatKey a0) -> bool"""
934  return _IMP_misc.CustomXYZR_get_is_optimized(self, a0)
935 
936  def get_check_level(self):
937  r"""get_check_level(CustomXYZR self) -> IMP::CheckLevel"""
938  return _IMP_misc.CustomXYZR_get_check_level(self)
939 
940  def __eq__(self, *args):
941  r"""
942  __eq__(CustomXYZR self, CustomXYZR o) -> bool
943  __eq__(CustomXYZR self, Particle d) -> bool
944  """
945  return _IMP_misc.CustomXYZR___eq__(self, *args)
946 
947  def __ne__(self, *args):
948  r"""
949  __ne__(CustomXYZR self, CustomXYZR o) -> bool
950  __ne__(CustomXYZR self, Particle d) -> bool
951  """
952  return _IMP_misc.CustomXYZR___ne__(self, *args)
953 
954  def __le__(self, *args):
955  r"""
956  __le__(CustomXYZR self, CustomXYZR o) -> bool
957  __le__(CustomXYZR self, Particle d) -> bool
958  """
959  return _IMP_misc.CustomXYZR___le__(self, *args)
960 
961  def __lt__(self, *args):
962  r"""
963  __lt__(CustomXYZR self, CustomXYZR o) -> bool
964  __lt__(CustomXYZR self, Particle d) -> bool
965  """
966  return _IMP_misc.CustomXYZR___lt__(self, *args)
967 
968  def __ge__(self, *args):
969  r"""
970  __ge__(CustomXYZR self, CustomXYZR o) -> bool
971  __ge__(CustomXYZR self, Particle d) -> bool
972  """
973  return _IMP_misc.CustomXYZR___ge__(self, *args)
974 
975  def __gt__(self, *args):
976  r"""
977  __gt__(CustomXYZR self, CustomXYZR o) -> bool
978  __gt__(CustomXYZR self, Particle d) -> bool
979  """
980  return _IMP_misc.CustomXYZR___gt__(self, *args)
981 
982  def __hash__(self):
983  r"""__hash__(CustomXYZR self) -> std::size_t"""
984  return _IMP_misc.CustomXYZR___hash__(self)
985 
986  def __str__(self):
987  r"""__str__(CustomXYZR self) -> std::string"""
988  return _IMP_misc.CustomXYZR___str__(self)
989 
990  def __repr__(self):
991  r"""__repr__(CustomXYZR self) -> std::string"""
992  return _IMP_misc.CustomXYZR___repr__(self)
993  __swig_destroy__ = _IMP_misc.delete_CustomXYZR
994 
995 # Register CustomXYZR in _IMP_misc:
996 _IMP_misc.CustomXYZR_swigregister(CustomXYZR)
997 
998 def __lshift__(out, n):
999  r"""__lshift__(_ostream out, CustomXYZR n) -> _ostream"""
1000  return _IMP_misc.__lshift__(out, n)
1001 
1002 def get_distance(a, b):
1003  r"""get_distance(CustomXYZR a, CustomXYZR b) -> double"""
1004  return _IMP_misc.get_distance(a, b)
1005 
1006 def get_sphere_d_geometry(d):
1007  r"""get_sphere_d_geometry(CustomXYZR d) -> Sphere3D"""
1008  return _IMP_misc.get_sphere_d_geometry(d)
1009 
1010 def set_sphere_d_geometry(d, v):
1011  r"""set_sphere_d_geometry(CustomXYZR d, Sphere3D v)"""
1012  return _IMP_misc.set_sphere_d_geometry(d, v)
1013 class SoftCylinderPairScore(IMP.PairScore):
1014  r"""Proxy of C++ IMP::misc::SoftCylinderPairScore class."""
1015 
1016  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1017 
1018  def __init__(self, k):
1019  r"""__init__(SoftCylinderPairScore self, double k) -> SoftCylinderPairScore"""
1020  _IMP_misc.SoftCylinderPairScore_swiginit(self, _IMP_misc.new_SoftCylinderPairScore(k))
1021 
1022  def do_get_inputs(self, m, pis):
1023  r"""do_get_inputs(SoftCylinderPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1024  return _IMP_misc.SoftCylinderPairScore_do_get_inputs(self, m, pis)
1025 
1026  def get_version_info(self):
1027  r"""get_version_info(SoftCylinderPairScore self) -> VersionInfo"""
1028  return _IMP_misc.SoftCylinderPairScore_get_version_info(self)
1029  __swig_destroy__ = _IMP_misc.delete_SoftCylinderPairScore
1030 
1031  def __str__(self):
1032  r"""__str__(SoftCylinderPairScore self) -> std::string"""
1033  return _IMP_misc.SoftCylinderPairScore___str__(self)
1034 
1035  def __repr__(self):
1036  r"""__repr__(SoftCylinderPairScore self) -> std::string"""
1037  return _IMP_misc.SoftCylinderPairScore___repr__(self)
1038 
1039  @staticmethod
1040  def get_from(o):
1041  return _object_cast_to_SoftCylinderPairScore(o)
1042 
1043 
1044 # Register SoftCylinderPairScore in _IMP_misc:
1045 _IMP_misc.SoftCylinderPairScore_swigregister(SoftCylinderPairScore)
1046 class DecayPairContainerOptimizerState(IMP.OptimizerState):
1047  r"""Proxy of C++ IMP::misc::DecayPairContainerOptimizerState class."""
1048 
1049  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1050 
1051  def __init__(self, *args):
1052  r"""__init__(DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list, std::string name="DecayPairContainerOptimizerState%1%") -> DecayPairContainerOptimizerState"""
1053  _IMP_misc.DecayPairContainerOptimizerState_swiginit(self, _IMP_misc.new_DecayPairContainerOptimizerState(*args))
1054 
1055  def get_output_container(self):
1056  r"""get_output_container(DecayPairContainerOptimizerState self) -> PairContainer"""
1057  return _IMP_misc.DecayPairContainerOptimizerState_get_output_container(self)
1058 
1059  def do_update(self, call_num):
1060  r"""do_update(DecayPairContainerOptimizerState self, unsigned int call_num)"""
1061  return _IMP_misc.DecayPairContainerOptimizerState_do_update(self, call_num)
1062 
1063  def get_version_info(self):
1064  r"""get_version_info(DecayPairContainerOptimizerState self) -> VersionInfo"""
1065  return _IMP_misc.DecayPairContainerOptimizerState_get_version_info(self)
1066  __swig_destroy__ = _IMP_misc.delete_DecayPairContainerOptimizerState
1067 
1068  def __str__(self):
1069  r"""__str__(DecayPairContainerOptimizerState self) -> std::string"""
1070  return _IMP_misc.DecayPairContainerOptimizerState___str__(self)
1071 
1072  def __repr__(self):
1073  r"""__repr__(DecayPairContainerOptimizerState self) -> std::string"""
1074  return _IMP_misc.DecayPairContainerOptimizerState___repr__(self)
1075 
1076  @staticmethod
1077  def get_from(o):
1078  return _object_cast_to_DecayPairContainerOptimizerState(o)
1079 
1080 
1081 # Register DecayPairContainerOptimizerState in _IMP_misc:
1082 _IMP_misc.DecayPairContainerOptimizerState_swigregister(DecayPairContainerOptimizerState)
1083 
1084 def get_module_version():
1085  r"""get_module_version() -> std::string const"""
1086  return _IMP_misc.get_module_version()
1087 
1088 def get_example_path(fname):
1089  r"""get_example_path(std::string fname) -> std::string"""
1090  return _IMP_misc.get_example_path(fname)
1091 
1092 def get_data_path(fname):
1093  r"""get_data_path(std::string fname) -> std::string"""
1094  return _IMP_misc.get_data_path(fname)
1095 
1096 from . import _version_check
1097 _version_check.check_version(get_module_version())
1098 __version__ = get_module_version()
1099 
1100 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:44
Various classes to hold sets of particles.
const algebra::Sphere3D get_sphere_d_geometry(CustomXYZR d)
Definition: CustomXYZR.h:90
Make CGAL functionality available to IMP.
virtual void clear_caches()
Definition: Object.h:270
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
Composable functors to implement scores via compile-time composition.
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:56
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void set_sphere_d_geometry(CustomXYZR d, const algebra::Sphere3D &v)
Definition: CustomXYZR.h:95
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:31
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
std::string get_module_version()
Return the version of this module, as a string.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:206
Shared optimizer state that is invoked upon commitment of new coordinates.
void set_check_level(CheckLevel l)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:27
double get_distance(const Line3D &s, const Vector3D &p)
Get closest distance between a line and a point.