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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
misc/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 # This wrapper is part of IMP,
8 # Copyright 2007-2017 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_misc')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_misc')
25  _IMP_misc = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_misc', [dirname(__file__)])
34  except ImportError:
35  import _IMP_misc
36  return _IMP_misc
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_misc', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_misc = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_misc
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_MISC_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_MISC_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_misc.delete_IMP_MISC_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_MISC_SwigPyIterator self) -> PyObject *"""
126  return _IMP_misc.IMP_MISC_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
132  incr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
133  """
134  return _IMP_misc.IMP_MISC_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
140  decr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
141  """
142  return _IMP_misc.IMP_MISC_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_misc.IMP_MISC_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
152  return _IMP_misc.IMP_MISC_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator"""
157  return _IMP_misc.IMP_MISC_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_MISC_SwigPyIterator self) -> PyObject *"""
162  return _IMP_misc.IMP_MISC_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_MISC_SwigPyIterator self) -> PyObject *"""
167  return _IMP_misc.IMP_MISC_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_MISC_SwigPyIterator self) -> PyObject *"""
172  return _IMP_misc.IMP_MISC_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
177  return _IMP_misc.IMP_MISC_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
182  return _IMP_misc.IMP_MISC_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
187  return _IMP_misc.IMP_MISC_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
192  return _IMP_misc.IMP_MISC_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
197  return _IMP_misc.IMP_MISC_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
202  return _IMP_misc.IMP_MISC_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator
208  __sub__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_misc.IMP_MISC_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_MISC_SwigPyIterator_swigregister = _IMP_misc.IMP_MISC_SwigPyIterator_swigregister
215 IMP_MISC_SwigPyIterator_swigregister(IMP_MISC_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_misc.IMP_DEBUG
224 IMP_RELEASE = _IMP_misc.IMP_RELEASE
225 IMP_SILENT = _IMP_misc.IMP_SILENT
226 IMP_PROGRESS = _IMP_misc.IMP_PROGRESS
227 IMP_TERSE = _IMP_misc.IMP_TERSE
228 IMP_VERBOSE = _IMP_misc.IMP_VERBOSE
229 IMP_MEMORY = _IMP_misc.IMP_MEMORY
230 IMP_NONE = _IMP_misc.IMP_NONE
231 IMP_USAGE = _IMP_misc.IMP_USAGE
232 IMP_INTERNAL = _IMP_misc.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_misc.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_misc.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_misc.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_misc.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_misc._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_misc._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_misc.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_misc.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_misc.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_misc.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_misc.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_misc.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_misc.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_misc.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_CORE_HAS_IMP_CGAL = _IMP_misc.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_misc.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_misc.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_misc.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_misc.IMPCORE_SHOW_WARNINGS
330 import IMP.core
331 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY
334 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL
335 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
336 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
337 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM
339 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM
340 IMP_CONTAINER_HAS_CGAL = _IMP_misc.IMP_CONTAINER_HAS_CGAL
341 IMP_CONTAINER_HAS_HDF5 = _IMP_misc.IMP_CONTAINER_HAS_HDF5
342 IMPCONTAINER_SHOW_WARNINGS = _IMP_misc.IMPCONTAINER_SHOW_WARNINGS
343 import IMP.container
344 IMP_ATOM_HAS_IMP_CGAL = _IMP_misc.IMP_ATOM_HAS_IMP_CGAL
345 IMP_ATOM_HAS_IMP_KERNEL = _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL
346 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
347 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
348 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM
349 IMP_ATOM_HAS_BOOST_REGEX = _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX
350 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM
351 IMP_ATOM_HAS_CGAL = _IMP_misc.IMP_ATOM_HAS_CGAL
352 IMP_ATOM_HAS_HDF5 = _IMP_misc.IMP_ATOM_HAS_HDF5
353 IMPATOM_SHOW_WARNINGS = _IMP_misc.IMPATOM_SHOW_WARNINGS
354 IMP_ATOM_TYPE_INDEX = _IMP_misc.IMP_ATOM_TYPE_INDEX
355 IMP_RESIDUE_TYPE_INDEX = _IMP_misc.IMP_RESIDUE_TYPE_INDEX
356 IMP_HIERARCHY_TYPE_INDEX = _IMP_misc.IMP_HIERARCHY_TYPE_INDEX
357 import IMP.atom
358 IMP_MISC_HAS_IMP_ALGEBRA = _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA
359 IMP_MISC_HAS_IMP_CGAL = _IMP_misc.IMP_MISC_HAS_IMP_CGAL
360 IMP_MISC_HAS_IMP_CONTAINER = _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER
361 IMP_MISC_HAS_IMP_DISPLAY = _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY
362 IMP_MISC_HAS_IMP_KERNEL = _IMP_misc.IMP_MISC_HAS_IMP_KERNEL
363 IMP_MISC_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR
364 IMP_MISC_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM
365 IMP_MISC_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS
366 IMP_MISC_HAS_BOOST_RANDOM = _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM
367 IMP_MISC_HAS_BOOST_REGEX = _IMP_misc.IMP_MISC_HAS_BOOST_REGEX
368 IMP_MISC_HAS_BOOST_SYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM
369 IMP_MISC_HAS_CGAL = _IMP_misc.IMP_MISC_HAS_CGAL
370 IMP_MISC_HAS_HDF5 = _IMP_misc.IMP_MISC_HAS_HDF5
371 IMPMISC_SHOW_WARNINGS = _IMP_misc.IMPMISC_SHOW_WARNINGS
372 
373 _object_types.append("WormLikeChain")
374 
375 
376 def _object_cast_to_WormLikeChain(o):
377  """_object_cast_to_WormLikeChain(Object o) -> WormLikeChain"""
378  return _IMP_misc._object_cast_to_WormLikeChain(o)
379 
380 _object_types.append("FreelyJointedChain")
381 
382 
383 def _object_cast_to_FreelyJointedChain(o):
384  """_object_cast_to_FreelyJointedChain(Object o) -> FreelyJointedChain"""
385  return _IMP_misc._object_cast_to_FreelyJointedChain(o)
386 
387 _object_types.append("StateAdaptor")
388 
389 
390 def _object_cast_to_StateAdaptor(o):
391  """_object_cast_to_StateAdaptor(Object o) -> StateAdaptor"""
392  return _IMP_misc._object_cast_to_StateAdaptor(o)
393 
394 _object_types.append("CommonEndpointPairFilter")
395 
396 
397 def _object_cast_to_CommonEndpointPairFilter(o):
398  """_object_cast_to_CommonEndpointPairFilter(Object o) -> CommonEndpointPairFilter"""
399  return _IMP_misc._object_cast_to_CommonEndpointPairFilter(o)
400 
401 _object_types.append("LogPairScore")
402 
403 
404 def _object_cast_to_LogPairScore(o):
405  """_object_cast_to_LogPairScore(Object o) -> LogPairScore"""
406  return _IMP_misc._object_cast_to_LogPairScore(o)
407 
408 _object_types.append("LowestRefinedPairScore")
409 
410 
411 def _object_cast_to_LowestRefinedPairScore(o):
412  """_object_cast_to_LowestRefinedPairScore(Object o) -> LowestRefinedPairScore"""
413  return _IMP_misc._object_cast_to_LowestRefinedPairScore(o)
414 
415 _object_types.append("SoftCylinderPairScore")
416 
417 
418 def _object_cast_to_SoftCylinderPairScore(o):
419  """_object_cast_to_SoftCylinderPairScore(Object o) -> SoftCylinderPairScore"""
420  return _IMP_misc._object_cast_to_SoftCylinderPairScore(o)
421 
422 _object_types.append("DecayPairContainerOptimizerState")
423 
424 
425 def _object_cast_to_DecayPairContainerOptimizerState(o):
426  """_object_cast_to_DecayPairContainerOptimizerState(Object o) -> DecayPairContainerOptimizerState"""
427  return _IMP_misc._object_cast_to_DecayPairContainerOptimizerState(o)
428 
429 def CustomXYZRs(l=[]):
430  return [CustomXYZR(x) for x in l]
431 _plural_types.append("CustomXYZRs")
432 
433 
434 _value_types.append("CustomXYZR")
435 
436 class WormLikeChain(IMP.UnaryFunction):
437  """Proxy of C++ IMP::misc::WormLikeChain class."""
438 
439  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
440 
441  def __init__(self, l_max, lp):
442  """__init__(IMP::misc::WormLikeChain self, IMP::Float l_max, IMP::Float lp) -> WormLikeChain"""
443  this = _IMP_misc.new_WormLikeChain(l_max, lp)
444  try:
445  self.this.append(this)
446  except __builtin__.Exception:
447  self.this = this
448 
449  def get_version_info(self):
450  """get_version_info(WormLikeChain self) -> VersionInfo"""
451  return _IMP_misc.WormLikeChain_get_version_info(self)
452 
453 
454  def do_show(self, out):
455  """do_show(WormLikeChain self, _ostream out)"""
456  return _IMP_misc.WormLikeChain_do_show(self, out)
457 
458 
459  def __str__(self):
460  """__str__(WormLikeChain self) -> std::string"""
461  return _IMP_misc.WormLikeChain___str__(self)
462 
463 
464  def __repr__(self):
465  """__repr__(WormLikeChain self) -> std::string"""
466  return _IMP_misc.WormLikeChain___repr__(self)
467 
468 
469  @staticmethod
470  def get_from(o):
471  return _object_cast_to_WormLikeChain(o)
472 
473 WormLikeChain_swigregister = _IMP_misc.WormLikeChain_swigregister
474 WormLikeChain_swigregister(WormLikeChain)
475 
476 class FreelyJointedChain(IMP.UnaryFunction):
477  """Proxy of C++ IMP::misc::FreelyJointedChain class."""
478 
479  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
480 
481  def __init__(self, link_num, link_length):
482  """__init__(IMP::misc::FreelyJointedChain self, int link_num, double link_length) -> FreelyJointedChain"""
483  this = _IMP_misc.new_FreelyJointedChain(link_num, link_length)
484  try:
485  self.this.append(this)
486  except __builtin__.Exception:
487  self.this = this
488 
489  def get_version_info(self):
490  """get_version_info(FreelyJointedChain self) -> VersionInfo"""
491  return _IMP_misc.FreelyJointedChain_get_version_info(self)
492 
493 
494  def get_link_number(self):
495  """get_link_number(FreelyJointedChain self) -> int"""
496  return _IMP_misc.FreelyJointedChain_get_link_number(self)
497 
498 
499  def get_link_length(self):
500  """get_link_length(FreelyJointedChain self) -> double"""
501  return _IMP_misc.FreelyJointedChain_get_link_length(self)
502 
503 
504  def set_link_number(self, N):
505  """set_link_number(FreelyJointedChain self, int N)"""
506  return _IMP_misc.FreelyJointedChain_set_link_number(self, N)
507 
508 
509  def set_link_length(self, b):
510  """set_link_length(FreelyJointedChain self, double b)"""
511  return _IMP_misc.FreelyJointedChain_set_link_length(self, b)
512 
513 
514  def get_distance_at_minimum(self):
515  """get_distance_at_minimum(FreelyJointedChain self) -> double"""
516  return _IMP_misc.FreelyJointedChain_get_distance_at_minimum(self)
517 
518 
519  def get_average_distance(self):
520  """get_average_distance(FreelyJointedChain self) -> double"""
521  return _IMP_misc.FreelyJointedChain_get_average_distance(self)
522 
523 
524  def __str__(self):
525  """__str__(FreelyJointedChain self) -> std::string"""
526  return _IMP_misc.FreelyJointedChain___str__(self)
527 
528 
529  def __repr__(self):
530  """__repr__(FreelyJointedChain self) -> std::string"""
531  return _IMP_misc.FreelyJointedChain___repr__(self)
532 
533 
534  @staticmethod
535  def get_from(o):
536  return _object_cast_to_FreelyJointedChain(o)
537 
538 FreelyJointedChain_swigregister = _IMP_misc.FreelyJointedChain_swigregister
539 FreelyJointedChain_swigregister(FreelyJointedChain)
540 
541 class LowestRefinedPairScore(IMP.PairScore):
542  """Proxy of C++ IMP::misc::LowestRefinedPairScore class."""
543 
544  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
545 
546  def __init__(self, r, f):
547  """__init__(IMP::misc::LowestRefinedPairScore self, Refiner r, PairScore f) -> LowestRefinedPairScore"""
548  this = _IMP_misc.new_LowestRefinedPairScore(r, f)
549  try:
550  self.this.append(this)
551  except __builtin__.Exception:
552  self.this = this
553 
554  def do_get_inputs(self, m, pis):
555  """do_get_inputs(LowestRefinedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
556  return _IMP_misc.LowestRefinedPairScore_do_get_inputs(self, m, pis)
557 
558 
559  def get_version_info(self):
560  """get_version_info(LowestRefinedPairScore self) -> VersionInfo"""
561  return _IMP_misc.LowestRefinedPairScore_get_version_info(self)
562 
563 
564  def __str__(self):
565  """__str__(LowestRefinedPairScore self) -> std::string"""
566  return _IMP_misc.LowestRefinedPairScore___str__(self)
567 
568 
569  def __repr__(self):
570  """__repr__(LowestRefinedPairScore self) -> std::string"""
571  return _IMP_misc.LowestRefinedPairScore___repr__(self)
572 
573 
574  @staticmethod
575  def get_from(o):
576  return _object_cast_to_LowestRefinedPairScore(o)
577 
578 LowestRefinedPairScore_swigregister = _IMP_misc.LowestRefinedPairScore_swigregister
579 LowestRefinedPairScore_swigregister(LowestRefinedPairScore)
580 
581 class LogPairScore(IMP.PairScore):
582  """Proxy of C++ IMP::misc::LogPairScore class."""
583 
584  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
585 
586  def __init__(self):
587  """__init__(IMP::misc::LogPairScore self) -> LogPairScore"""
588  this = _IMP_misc.new_LogPairScore()
589  try:
590  self.this.append(this)
591  except __builtin__.Exception:
592  self.this = this
593 
594  def do_get_inputs(self, arg2, arg3):
595  """do_get_inputs(LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
596  return _IMP_misc.LogPairScore_do_get_inputs(self, arg2, arg3)
597 
598 
599  def get_version_info(self):
600  """get_version_info(LogPairScore self) -> VersionInfo"""
601  return _IMP_misc.LogPairScore_get_version_info(self)
602 
603 
604  def get_particle_pairs(self):
605  """get_particle_pairs(LogPairScore self) -> IMP::ParticlePairsTemp"""
606  return _IMP_misc.LogPairScore_get_particle_pairs(self)
607 
608 
609  def clear(self):
610  """clear(LogPairScore self)"""
611  return _IMP_misc.LogPairScore_clear(self)
612 
613 
614  def get_contains(self, pp):
615  """get_contains(LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
616  return _IMP_misc.LogPairScore_get_contains(self, pp)
617 
618 
619  def __str__(self):
620  """__str__(LogPairScore self) -> std::string"""
621  return _IMP_misc.LogPairScore___str__(self)
622 
623 
624  def __repr__(self):
625  """__repr__(LogPairScore self) -> std::string"""
626  return _IMP_misc.LogPairScore___repr__(self)
627 
628 
629  @staticmethod
630  def get_from(o):
631  return _object_cast_to_LogPairScore(o)
632 
633 LogPairScore_swigregister = _IMP_misc.LogPairScore_swigregister
634 LogPairScore_swigregister(LogPairScore)
635 
636 class StateAdaptor(IMP.ScoreState):
637  """Proxy of C++ IMP::misc::StateAdaptor class."""
638 
639  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
640 
641  def __init__(self, m, before, after):
642  """__init__(IMP::misc::StateAdaptor self, Model m, OptimizerState before, OptimizerState after) -> StateAdaptor"""
643  this = _IMP_misc.new_StateAdaptor(m, before, after)
644  try:
645  self.this.append(this)
646  except __builtin__.Exception:
647  self.this = this
648 
649  def do_before_evaluate(self):
650  """do_before_evaluate(StateAdaptor self)"""
651  return _IMP_misc.StateAdaptor_do_before_evaluate(self)
652 
653 
654  def do_after_evaluate(self, da):
655  """do_after_evaluate(StateAdaptor self, DerivativeAccumulator da)"""
656  return _IMP_misc.StateAdaptor_do_after_evaluate(self, da)
657 
658 
659  def do_get_inputs(self):
660  """do_get_inputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
661  return _IMP_misc.StateAdaptor_do_get_inputs(self)
662 
663 
664  def do_get_outputs(self):
665  """do_get_outputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
666  return _IMP_misc.StateAdaptor_do_get_outputs(self)
667 
668 
669  def get_version_info(self):
670  """get_version_info(StateAdaptor self) -> VersionInfo"""
671  return _IMP_misc.StateAdaptor_get_version_info(self)
672 
673 
674  def __str__(self):
675  """__str__(StateAdaptor self) -> std::string"""
676  return _IMP_misc.StateAdaptor___str__(self)
677 
678 
679  def __repr__(self):
680  """__repr__(StateAdaptor self) -> std::string"""
681  return _IMP_misc.StateAdaptor___repr__(self)
682 
683 
684  @staticmethod
685  def get_from(o):
686  return _object_cast_to_StateAdaptor(o)
687 
688 StateAdaptor_swigregister = _IMP_misc.StateAdaptor_swigregister
689 StateAdaptor_swigregister(StateAdaptor)
690 
691 class CommonEndpointPairFilter(IMP.PairPredicate):
692  """Proxy of C++ IMP::misc::CommonEndpointPairFilter class."""
693 
694  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
695 
696  def __init__(self):
697  """__init__(IMP::misc::CommonEndpointPairFilter self) -> CommonEndpointPairFilter"""
698  this = _IMP_misc.new_CommonEndpointPairFilter()
699  try:
700  self.this.append(this)
701  except __builtin__.Exception:
702  self.this = this
703 
704  def do_get_inputs(self, m, pis):
705  """do_get_inputs(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
706  return _IMP_misc.CommonEndpointPairFilter_do_get_inputs(self, m, pis)
707 
708 
709  def get_value(self, *args):
710  """
711  get_value(CommonEndpointPairFilter self, IMP::ParticlePair const & a) -> int
712  get_value(CommonEndpointPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
713  """
714  return _IMP_misc.CommonEndpointPairFilter_get_value(self, *args)
715 
716 
717  def get_value_index(self, *args):
718  """
719  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
720  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
721  """
722  return _IMP_misc.CommonEndpointPairFilter_get_value_index(self, *args)
723 
724 
725  def get_version_info(self):
726  """get_version_info(CommonEndpointPairFilter self) -> VersionInfo"""
727  return _IMP_misc.CommonEndpointPairFilter_get_version_info(self)
728 
729 
730  def __str__(self):
731  """__str__(CommonEndpointPairFilter self) -> std::string"""
732  return _IMP_misc.CommonEndpointPairFilter___str__(self)
733 
734 
735  def __repr__(self):
736  """__repr__(CommonEndpointPairFilter self) -> std::string"""
737  return _IMP_misc.CommonEndpointPairFilter___repr__(self)
738 
739 
740  @staticmethod
741  def get_from(o):
742  return _object_cast_to_CommonEndpointPairFilter(o)
743 
744 CommonEndpointPairFilter_swigregister = _IMP_misc.CommonEndpointPairFilter_swigregister
745 CommonEndpointPairFilter_swigregister(CommonEndpointPairFilter)
746 
747 class CustomXYZR(IMP.core.XYZ):
748  """Proxy of C++ IMP::misc::CustomXYZR class."""
749 
750  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
751 
752  def get_decorator_traits(self):
753  """get_decorator_traits(CustomXYZR self) -> FloatKey"""
754  return _IMP_misc.CustomXYZR_get_decorator_traits(self)
755 
756 
757  def get_default_decorator_traits():
758  """get_default_decorator_traits() -> FloatKey"""
759  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
760 
761  get_default_decorator_traits = staticmethod(get_default_decorator_traits)
762 
763  def __init__(self, *args):
764  """
765  __init__(IMP::misc::CustomXYZR self) -> CustomXYZR
766  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id, FloatKey tr) -> CustomXYZR
767  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id) -> CustomXYZR
768  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d, FloatKey tr) -> CustomXYZR
769  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d) -> CustomXYZR
770  """
771  this = _IMP_misc.new_CustomXYZR(*args)
772  try:
773  self.this.append(this)
774  except __builtin__.Exception:
775  self.this = this
776 
777  def show(self, *args):
778  """
779  show(CustomXYZR self, _ostream out)
780  show(CustomXYZR self)
781  """
782  return _IMP_misc.CustomXYZR_show(self, *args)
783 
784 
785  def setup_particle(*args):
786  """
787  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
788  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
789  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
790  setup_particle(_ParticleAdaptor d) -> CustomXYZR
791  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
792  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
793  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
794  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
795  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
796  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
797  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
798  setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
799  """
800  return _IMP_misc.CustomXYZR_setup_particle(*args)
801 
802  setup_particle = staticmethod(setup_particle)
803 
804  def get_is_setup(*args):
805  """
806  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
807  get_is_setup(_ParticleAdaptor p) -> bool
808  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
809  get_is_setup(Model m, ParticleIndex pi) -> bool
810  """
811  return _IMP_misc.CustomXYZR_get_is_setup(*args)
812 
813  get_is_setup = staticmethod(get_is_setup)
814 
815  def get_radius(self):
816  """get_radius(CustomXYZR self) -> IMP::Float"""
817  return _IMP_misc.CustomXYZR_get_radius(self)
818 
819 
820  def set_radius(self, t):
821  """set_radius(CustomXYZR self, IMP::Float t)"""
822  return _IMP_misc.CustomXYZR_set_radius(self, t)
823 
824 
825  def get_sphere(self):
826  """get_sphere(CustomXYZR self) -> Sphere3D"""
827  return _IMP_misc.CustomXYZR_get_sphere(self)
828 
829 
830  def set_sphere(self, s):
831  """set_sphere(CustomXYZR self, Sphere3D s)"""
832  return _IMP_misc.CustomXYZR_set_sphere(self, s)
833 
834 
835  def get_default_radius_key():
836  """get_default_radius_key() -> FloatKey"""
837  return _IMP_misc.CustomXYZR_get_default_radius_key()
838 
839  get_default_radius_key = staticmethod(get_default_radius_key)
840 
841  def add_to_radius_derivative(self, v, d):
842  """add_to_radius_derivative(CustomXYZR self, double v, DerivativeAccumulator d)"""
843  return _IMP_misc.CustomXYZR_add_to_radius_derivative(self, v, d)
844 
845 
846  def get_traits(self):
847  """get_traits(CustomXYZR self) -> FloatKey"""
848  return _IMP_misc.CustomXYZR_get_traits(self)
849 
850 
851  def add_attribute(self, *args):
852  """
853  add_attribute(CustomXYZR self, FloatKey k, IMP::Float v, bool opt)
854  add_attribute(CustomXYZR self, FloatKey a0, IMP::Float a1)
855  add_attribute(CustomXYZR self, IntKey a0, IMP::Int a1)
856  add_attribute(CustomXYZR self, StringKey a0, IMP::String a1)
857  add_attribute(CustomXYZR self, ParticleIndexKey a0, Particle a1)
858  add_attribute(CustomXYZR self, ObjectKey a0, Object a1)
859  """
860  return _IMP_misc.CustomXYZR_add_attribute(self, *args)
861 
862 
863  def get_value(self, *args):
864  """
865  get_value(CustomXYZR self, FloatKey a0) -> IMP::Float
866  get_value(CustomXYZR self, IntKey a0) -> IMP::Int
867  get_value(CustomXYZR self, StringKey a0) -> IMP::String
868  get_value(CustomXYZR self, ParticleIndexKey a0) -> Particle
869  get_value(CustomXYZR self, ObjectKey a0) -> Object
870  """
871  return _IMP_misc.CustomXYZR_get_value(self, *args)
872 
873 
874  def set_value(self, *args):
875  """
876  set_value(CustomXYZR self, FloatKey a0, IMP::Float a1)
877  set_value(CustomXYZR self, IntKey a0, IMP::Int a1)
878  set_value(CustomXYZR self, StringKey a0, IMP::String a1)
879  set_value(CustomXYZR self, ParticleIndexKey a0, Particle a1)
880  set_value(CustomXYZR self, ObjectKey a0, Object a1)
881  """
882  return _IMP_misc.CustomXYZR_set_value(self, *args)
883 
884 
885  def remove_attribute(self, *args):
886  """
887  remove_attribute(CustomXYZR self, FloatKey a0)
888  remove_attribute(CustomXYZR self, IntKey a0)
889  remove_attribute(CustomXYZR self, StringKey a0)
890  remove_attribute(CustomXYZR self, ParticleIndexKey a0)
891  remove_attribute(CustomXYZR self, ObjectKey a0)
892  """
893  return _IMP_misc.CustomXYZR_remove_attribute(self, *args)
894 
895 
896  def has_attribute(self, *args):
897  """
898  has_attribute(CustomXYZR self, FloatKey a0) -> bool
899  has_attribute(CustomXYZR self, IntKey a0) -> bool
900  has_attribute(CustomXYZR self, StringKey a0) -> bool
901  has_attribute(CustomXYZR self, ParticleIndexKey a0) -> bool
902  has_attribute(CustomXYZR self, ObjectKey a0) -> bool
903  """
904  return _IMP_misc.CustomXYZR_has_attribute(self, *args)
905 
906 
907  def get_derivative(self, a0):
908  """get_derivative(CustomXYZR self, FloatKey a0) -> double"""
909  return _IMP_misc.CustomXYZR_get_derivative(self, a0)
910 
911 
912  def get_name(self):
913  """get_name(CustomXYZR self) -> std::string"""
914  return _IMP_misc.CustomXYZR_get_name(self)
915 
916 
917  def clear_caches(self):
918  """clear_caches(CustomXYZR self)"""
919  return _IMP_misc.CustomXYZR_clear_caches(self)
920 
921 
922  def set_name(self, a0):
923  """set_name(CustomXYZR self, std::string a0)"""
924  return _IMP_misc.CustomXYZR_set_name(self, a0)
925 
926 
927  def set_check_level(self, a0):
928  """set_check_level(CustomXYZR self, IMP::CheckLevel a0)"""
929  return _IMP_misc.CustomXYZR_set_check_level(self, a0)
930 
931 
932  def add_to_derivative(self, a0, a1, a2):
933  """add_to_derivative(CustomXYZR self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
934  return _IMP_misc.CustomXYZR_add_to_derivative(self, a0, a1, a2)
935 
936 
937  def set_is_optimized(self, a0, a1):
938  """set_is_optimized(CustomXYZR self, FloatKey a0, bool a1)"""
939  return _IMP_misc.CustomXYZR_set_is_optimized(self, a0, a1)
940 
941 
942  def get_is_optimized(self, a0):
943  """get_is_optimized(CustomXYZR self, FloatKey a0) -> bool"""
944  return _IMP_misc.CustomXYZR_get_is_optimized(self, a0)
945 
946 
947  def get_check_level(self):
948  """get_check_level(CustomXYZR self) -> IMP::CheckLevel"""
949  return _IMP_misc.CustomXYZR_get_check_level(self)
950 
951 
952  def __eq__(self, *args):
953  """
954  __eq__(CustomXYZR self, CustomXYZR o) -> bool
955  __eq__(CustomXYZR self, Particle d) -> bool
956  """
957  return _IMP_misc.CustomXYZR___eq__(self, *args)
958 
959 
960  def __ne__(self, *args):
961  """
962  __ne__(CustomXYZR self, CustomXYZR o) -> bool
963  __ne__(CustomXYZR self, Particle d) -> bool
964  """
965  return _IMP_misc.CustomXYZR___ne__(self, *args)
966 
967 
968  def __le__(self, *args):
969  """
970  __le__(CustomXYZR self, CustomXYZR o) -> bool
971  __le__(CustomXYZR self, Particle d) -> bool
972  """
973  return _IMP_misc.CustomXYZR___le__(self, *args)
974 
975 
976  def __lt__(self, *args):
977  """
978  __lt__(CustomXYZR self, CustomXYZR o) -> bool
979  __lt__(CustomXYZR self, Particle d) -> bool
980  """
981  return _IMP_misc.CustomXYZR___lt__(self, *args)
982 
983 
984  def __ge__(self, *args):
985  """
986  __ge__(CustomXYZR self, CustomXYZR o) -> bool
987  __ge__(CustomXYZR self, Particle d) -> bool
988  """
989  return _IMP_misc.CustomXYZR___ge__(self, *args)
990 
991 
992  def __gt__(self, *args):
993  """
994  __gt__(CustomXYZR self, CustomXYZR o) -> bool
995  __gt__(CustomXYZR self, Particle d) -> bool
996  """
997  return _IMP_misc.CustomXYZR___gt__(self, *args)
998 
999 
1000  def __hash__(self):
1001  """__hash__(CustomXYZR self) -> std::size_t"""
1002  return _IMP_misc.CustomXYZR___hash__(self)
1003 
1004 
1005  def __str__(self):
1006  """__str__(CustomXYZR self) -> std::string"""
1007  return _IMP_misc.CustomXYZR___str__(self)
1008 
1009 
1010  def __repr__(self):
1011  """__repr__(CustomXYZR self) -> std::string"""
1012  return _IMP_misc.CustomXYZR___repr__(self)
1013 
1014  __swig_destroy__ = _IMP_misc.delete_CustomXYZR
1015  __del__ = lambda self: None
1016 CustomXYZR_swigregister = _IMP_misc.CustomXYZR_swigregister
1017 CustomXYZR_swigregister(CustomXYZR)
1018 
1019 def CustomXYZR_get_default_decorator_traits():
1020  """CustomXYZR_get_default_decorator_traits() -> FloatKey"""
1021  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
1022 
1023 def CustomXYZR_setup_particle(*args):
1024  """
1025  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
1026  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
1027  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
1028  setup_particle(_ParticleAdaptor d) -> CustomXYZR
1029  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
1030  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
1031  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
1032  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
1033  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
1034  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
1035  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
1036  CustomXYZR_setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
1037  """
1038  return _IMP_misc.CustomXYZR_setup_particle(*args)
1039 
1040 def CustomXYZR_get_is_setup(*args):
1041  """
1042  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
1043  get_is_setup(_ParticleAdaptor p) -> bool
1044  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
1045  CustomXYZR_get_is_setup(Model m, ParticleIndex pi) -> bool
1046  """
1047  return _IMP_misc.CustomXYZR_get_is_setup(*args)
1048 
1049 def CustomXYZR_get_default_radius_key():
1050  """CustomXYZR_get_default_radius_key() -> FloatKey"""
1051  return _IMP_misc.CustomXYZR_get_default_radius_key()
1052 
1053 
1054 def __lshift__(out, n):
1055  """__lshift__(_ostream out, CustomXYZR n) -> _ostream"""
1056  return _IMP_misc.__lshift__(out, n)
1057 
1058 def get_distance(a, b):
1059  """get_distance(CustomXYZR a, CustomXYZR b) -> double"""
1060  return _IMP_misc.get_distance(a, b)
1061 
1062 def get_sphere_d_geometry(d):
1063  """get_sphere_d_geometry(CustomXYZR d) -> Sphere3D"""
1064  return _IMP_misc.get_sphere_d_geometry(d)
1065 
1066 def set_sphere_d_geometry(d, v):
1067  """set_sphere_d_geometry(CustomXYZR d, Sphere3D v)"""
1068  return _IMP_misc.set_sphere_d_geometry(d, v)
1069 class SoftCylinderPairScore(IMP.PairScore):
1070  """Proxy of C++ IMP::misc::SoftCylinderPairScore class."""
1071 
1072  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1073 
1074  def __init__(self, k):
1075  """__init__(IMP::misc::SoftCylinderPairScore self, double k) -> SoftCylinderPairScore"""
1076  this = _IMP_misc.new_SoftCylinderPairScore(k)
1077  try:
1078  self.this.append(this)
1079  except __builtin__.Exception:
1080  self.this = this
1081 
1082  def do_get_inputs(self, m, pis):
1083  """do_get_inputs(SoftCylinderPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1084  return _IMP_misc.SoftCylinderPairScore_do_get_inputs(self, m, pis)
1085 
1086 
1087  def get_version_info(self):
1088  """get_version_info(SoftCylinderPairScore self) -> VersionInfo"""
1089  return _IMP_misc.SoftCylinderPairScore_get_version_info(self)
1090 
1091 
1092  def __str__(self):
1093  """__str__(SoftCylinderPairScore self) -> std::string"""
1094  return _IMP_misc.SoftCylinderPairScore___str__(self)
1095 
1096 
1097  def __repr__(self):
1098  """__repr__(SoftCylinderPairScore self) -> std::string"""
1099  return _IMP_misc.SoftCylinderPairScore___repr__(self)
1100 
1101 
1102  @staticmethod
1103  def get_from(o):
1104  return _object_cast_to_SoftCylinderPairScore(o)
1105 
1106 SoftCylinderPairScore_swigregister = _IMP_misc.SoftCylinderPairScore_swigregister
1107 SoftCylinderPairScore_swigregister(SoftCylinderPairScore)
1108 
1109 class DecayPairContainerOptimizerState(IMP.OptimizerState):
1110  """Proxy of C++ IMP::misc::DecayPairContainerOptimizerState class."""
1111 
1112  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1113 
1114  def __init__(self, *args):
1115  """
1116  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list, std::string name) -> DecayPairContainerOptimizerState
1117  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list) -> DecayPairContainerOptimizerState
1118  """
1119  this = _IMP_misc.new_DecayPairContainerOptimizerState(*args)
1120  try:
1121  self.this.append(this)
1122  except __builtin__.Exception:
1123  self.this = this
1124 
1125  def get_output_container(self):
1126  """get_output_container(DecayPairContainerOptimizerState self) -> PairContainer"""
1127  return _IMP_misc.DecayPairContainerOptimizerState_get_output_container(self)
1128 
1129 
1130  def do_update(self, call_num):
1131  """do_update(DecayPairContainerOptimizerState self, unsigned int call_num)"""
1132  return _IMP_misc.DecayPairContainerOptimizerState_do_update(self, call_num)
1133 
1134 
1135  def get_version_info(self):
1136  """get_version_info(DecayPairContainerOptimizerState self) -> VersionInfo"""
1137  return _IMP_misc.DecayPairContainerOptimizerState_get_version_info(self)
1138 
1139 
1140  def __str__(self):
1141  """__str__(DecayPairContainerOptimizerState self) -> std::string"""
1142  return _IMP_misc.DecayPairContainerOptimizerState___str__(self)
1143 
1144 
1145  def __repr__(self):
1146  """__repr__(DecayPairContainerOptimizerState self) -> std::string"""
1147  return _IMP_misc.DecayPairContainerOptimizerState___repr__(self)
1148 
1149 
1150  @staticmethod
1151  def get_from(o):
1152  return _object_cast_to_DecayPairContainerOptimizerState(o)
1153 
1154 DecayPairContainerOptimizerState_swigregister = _IMP_misc.DecayPairContainerOptimizerState_swigregister
1155 DecayPairContainerOptimizerState_swigregister(DecayPairContainerOptimizerState)
1156 
1157 
1158 def get_module_version():
1159  """get_module_version() -> std::string const"""
1160  return _IMP_misc.get_module_version()
1161 
1162 def get_example_path(fname):
1163  """get_example_path(std::string fname) -> std::string"""
1164  return _IMP_misc.get_example_path(fname)
1165 
1166 def get_data_path(fname):
1167  """get_data_path(std::string fname) -> std::string"""
1168  return _IMP_misc.get_data_path(fname)
1169 
1170 from . import _version_check
1171 _version_check.check_version(get_module_version())
1172 __version__ = get_module_version()
1173 
1174 
1175 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:37
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:227
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:53
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...
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
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:25
double get_distance(const Line3D &s, const Vector3D &p)
Get closest distance between a line and a point.