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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
kinematics/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_kinematics
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_KINEMATICS_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_KINEMATICS_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_kinematics.delete_IMP_KINEMATICS_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
79  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator"""
83  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator"""
87  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
95  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_KINEMATICS_SwigPyIterator self) -> IMP_KINEMATICS_SwigPyIterator"""
99  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
103  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
107  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
111  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
115  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
119  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
123  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
127  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
131  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
135  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator
140  __sub__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_KINEMATICS_SwigPyIterator in _IMP_kinematics:
147 _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_swigregister(IMP_KINEMATICS_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_kinematics.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_kinematics.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_kinematics.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_kinematics.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_kinematics.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_kinematics.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_kinematics.IMP_MEMORY
167 
168 IMP_NONE = _IMP_kinematics.IMP_NONE
169 
170 IMP_USAGE = _IMP_kinematics.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_kinematics.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_kinematics.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_kinematics.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kinematics.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_kinematics.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_kinematics.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_kinematics.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kinematics.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_kinematics.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_kinematics._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_kinematics:
237 _IMP_kinematics._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_kinematics.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_kinematics.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_kinematics.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_kinematics.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_kinematics.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_kinematics.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_kinematics.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_kinematics.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_kinematics.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_CORE_HAS_IMP_CGAL = _IMP_kinematics.IMP_CORE_HAS_IMP_CGAL
310 
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CORE_HAS_IMP_KERNEL
312 
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_FILESYSTEM
314 
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CORE_HAS_BOOST_RANDOM
318 
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_SYSTEM
320 
321 IMP_CORE_HAS_CGAL = _IMP_kinematics.IMP_CORE_HAS_CGAL
322 
323 IMP_CORE_HAS_HDF5 = _IMP_kinematics.IMP_CORE_HAS_HDF5
324 
325 IMP_CORE_HAS_NUMPY = _IMP_kinematics.IMP_CORE_HAS_NUMPY
326 
327 IMPCORE_SHOW_WARNINGS = _IMP_kinematics.IMPCORE_SHOW_WARNINGS
328 
329 import IMP.core
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_CGAL
333 
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_DISPLAY
335 
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_KERNEL
337 
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_RANDOM
345 
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 
348 IMP_CONTAINER_HAS_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_CGAL
349 
350 IMP_CONTAINER_HAS_HDF5 = _IMP_kinematics.IMP_CONTAINER_HAS_HDF5
351 
352 IMP_CONTAINER_HAS_NUMPY = _IMP_kinematics.IMP_CONTAINER_HAS_NUMPY
353 
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_kinematics.IMP_CONTAINER_HAS_PYTHON_IHM
355 
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_ROBIN_MAP
359 
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_kinematics.IMPCONTAINER_SHOW_WARNINGS
361 
362 import IMP.container
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_kinematics.IMP_ATOM_HAS_IMP_CGAL
364 
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_kinematics.IMP_ATOM_HAS_IMP_KERNEL
366 
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
368 
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
370 
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_RANDOM
372 
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_kinematics.IMP_ATOM_HAS_BOOST_REGEX
374 
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_SYSTEM
376 
377 IMP_ATOM_HAS_CGAL = _IMP_kinematics.IMP_ATOM_HAS_CGAL
378 
379 IMP_ATOM_HAS_HDF5 = _IMP_kinematics.IMP_ATOM_HAS_HDF5
380 
381 IMP_ATOM_HAS_NUMPY = _IMP_kinematics.IMP_ATOM_HAS_NUMPY
382 
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_kinematics.IMP_ATOM_HAS_PYTHON_IHM
384 
385 IMPATOM_SHOW_WARNINGS = _IMP_kinematics.IMPATOM_SHOW_WARNINGS
386 
387 IMP_ATOM_TYPE_INDEX = _IMP_kinematics.IMP_ATOM_TYPE_INDEX
388 
389 IMP_RESIDUE_TYPE_INDEX = _IMP_kinematics.IMP_RESIDUE_TYPE_INDEX
390 
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_kinematics.IMP_HIERARCHY_TYPE_INDEX
392 
393 IMP_CHAIN_TYPE_INDEX = _IMP_kinematics.IMP_CHAIN_TYPE_INDEX
394 
395 import IMP.atom
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_kinematics.IMP_SAXS_HAS_IMP_CGAL
397 
398 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_kinematics.IMP_SAXS_HAS_IMP_CONTAINER
399 
400 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_SAXS_HAS_IMP_DISPLAY
401 
402 IMP_SAXS_HAS_IMP_KERNEL = _IMP_kinematics.IMP_SAXS_HAS_IMP_KERNEL
403 
404 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
405 
406 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_FILESYSTEM
407 
408 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
409 
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_RANDOM
411 
412 IMP_SAXS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_SAXS_HAS_BOOST_REGEX
413 
414 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_SYSTEM
415 
416 IMP_SAXS_HAS_CGAL = _IMP_kinematics.IMP_SAXS_HAS_CGAL
417 
418 IMP_SAXS_HAS_HDF5 = _IMP_kinematics.IMP_SAXS_HAS_HDF5
419 
420 IMP_SAXS_HAS_NUMPY = _IMP_kinematics.IMP_SAXS_HAS_NUMPY
421 
422 IMP_SAXS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_SAXS_HAS_PYTHON_IHM
423 
424 IMPSAXS_SHOW_WARNINGS = _IMP_kinematics.IMPSAXS_SHOW_WARNINGS
425 
426 import IMP.saxs
427 IMP_KINEMATICS_HAS_IMP_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_CGAL
428 
429 IMP_KINEMATICS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_DISPLAY
430 
431 IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR
432 
433 IMP_KINEMATICS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_FILESYSTEM
434 
435 IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS
436 
437 IMP_KINEMATICS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_RANDOM
438 
439 IMP_KINEMATICS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_REGEX
440 
441 IMP_KINEMATICS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_SYSTEM
442 
443 IMP_KINEMATICS_HAS_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_CGAL
444 
445 IMP_KINEMATICS_HAS_HDF5 = _IMP_kinematics.IMP_KINEMATICS_HAS_HDF5
446 
447 IMP_KINEMATICS_HAS_NUMPY = _IMP_kinematics.IMP_KINEMATICS_HAS_NUMPY
448 
449 IMP_KINEMATICS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_KINEMATICS_HAS_PYTHON_IHM
450 
451 IMPKINEMATICS_SHOW_WARNINGS = _IMP_kinematics.IMPKINEMATICS_SHOW_WARNINGS
452 
453 
454 _object_types.append("Joint")
455 
456 
457 def _object_cast_to_Joint(o):
458  r"""_object_cast_to_Joint(Object o) -> Joint"""
459  return _IMP_kinematics._object_cast_to_Joint(o)
460 
461 _object_types.append("TransformationJoint")
462 
463 
464 def _object_cast_to_TransformationJoint(o):
465  r"""_object_cast_to_TransformationJoint(Object o) -> TransformationJoint"""
466  return _IMP_kinematics._object_cast_to_TransformationJoint(o)
467 
468 _object_types.append("RevoluteJoint")
469 
470 
471 def _object_cast_to_RevoluteJoint(o):
472  r"""_object_cast_to_RevoluteJoint(Object o) -> RevoluteJoint"""
473  return _IMP_kinematics._object_cast_to_RevoluteJoint(o)
474 
475 _object_types.append("DihedralAngleRevoluteJoint")
476 
477 
478 def _object_cast_to_DihedralAngleRevoluteJoint(o):
479  r"""_object_cast_to_DihedralAngleRevoluteJoint(Object o) -> DihedralAngleRevoluteJoint"""
480  return _IMP_kinematics._object_cast_to_DihedralAngleRevoluteJoint(o)
481 
482 _object_types.append("BondAngleRevoluteJoint")
483 
484 
485 def _object_cast_to_BondAngleRevoluteJoint(o):
486  r"""_object_cast_to_BondAngleRevoluteJoint(Object o) -> BondAngleRevoluteJoint"""
487  return _IMP_kinematics._object_cast_to_BondAngleRevoluteJoint(o)
488 
489 _object_types.append("PrismaticJoint")
490 
491 
492 def _object_cast_to_PrismaticJoint(o):
493  r"""_object_cast_to_PrismaticJoint(Object o) -> PrismaticJoint"""
494  return _IMP_kinematics._object_cast_to_PrismaticJoint(o)
495 
496 _object_types.append("KinematicForest")
497 
498 
499 def _object_cast_to_KinematicForest(o):
500  r"""_object_cast_to_KinematicForest(Object o) -> KinematicForest"""
501  return _IMP_kinematics._object_cast_to_KinematicForest(o)
502 
503 _object_types.append("KinematicForestScoreState")
504 
505 
506 def _object_cast_to_KinematicForestScoreState(o):
507  r"""_object_cast_to_KinematicForestScoreState(Object o) -> KinematicForestScoreState"""
508  return _IMP_kinematics._object_cast_to_KinematicForestScoreState(o)
509 
510 _object_types.append("CompositeJoint")
511 
512 
513 def _object_cast_to_CompositeJoint(o):
514  r"""_object_cast_to_CompositeJoint(Object o) -> CompositeJoint"""
515  return _IMP_kinematics._object_cast_to_CompositeJoint(o)
516 
517 _object_types.append("RevoluteJointMover")
518 
519 
520 def _object_cast_to_RevoluteJointMover(o):
521  r"""_object_cast_to_RevoluteJointMover(Object o) -> RevoluteJointMover"""
522  return _IMP_kinematics._object_cast_to_RevoluteJointMover(o)
523 
524 _object_types.append("DihedralMover")
525 
526 
527 def _object_cast_to_DihedralMover(o):
528  r"""_object_cast_to_DihedralMover(Object o) -> DihedralMover"""
529  return _IMP_kinematics._object_cast_to_DihedralMover(o)
530 
531 _object_types.append("DOF")
532 
533 
534 def _object_cast_to_DOF(o):
535  r"""_object_cast_to_DOF(Object o) -> DOF"""
536  return _IMP_kinematics._object_cast_to_DOF(o)
537 
538 DOFValuesList=list
539 _plural_types.append("DOFValuesList")
540 _value_types.append("DOFValues")
541 
542 
543 _object_types.append("DirectionalDOF")
544 
545 
546 def _object_cast_to_DirectionalDOF(o):
547  r"""_object_cast_to_DirectionalDOF(Object o) -> DirectionalDOF"""
548  return _IMP_kinematics._object_cast_to_DirectionalDOF(o)
549 
550 _object_types.append("DOFsSampler")
551 
552 
553 def _object_cast_to_DOFsSampler(o):
554  r"""_object_cast_to_DOFsSampler(Object o) -> DOFsSampler"""
555  return _IMP_kinematics._object_cast_to_DOFsSampler(o)
556 
557 _object_types.append("UniformBackboneSampler")
558 
559 
560 def _object_cast_to_UniformBackboneSampler(o):
561  r"""_object_cast_to_UniformBackboneSampler(Object o) -> UniformBackboneSampler"""
562  return _IMP_kinematics._object_cast_to_UniformBackboneSampler(o)
563 
564 _object_types.append("FibrilSampler")
565 
566 
567 def _object_cast_to_FibrilSampler(o):
568  r"""_object_cast_to_FibrilSampler(Object o) -> FibrilSampler"""
569  return _IMP_kinematics._object_cast_to_FibrilSampler(o)
570 
571 _object_types.append("ProteinKinematics")
572 
573 
574 def _object_cast_to_ProteinKinematics(o):
575  r"""_object_cast_to_ProteinKinematics(Object o) -> ProteinKinematics"""
576  return _IMP_kinematics._object_cast_to_ProteinKinematics(o)
577 
578 _object_types.append("LocalPlanner")
579 
580 
581 def _object_cast_to_LocalPlanner(o):
582  r"""_object_cast_to_LocalPlanner(Object o) -> LocalPlanner"""
583  return _IMP_kinematics._object_cast_to_LocalPlanner(o)
584 
585 _object_types.append("PathLocalPlanner")
586 
587 
588 def _object_cast_to_PathLocalPlanner(o):
589  r"""_object_cast_to_PathLocalPlanner(Object o) -> PathLocalPlanner"""
590  return _IMP_kinematics._object_cast_to_PathLocalPlanner(o)
591 
592 _object_types.append("RRT")
593 
594 
595 def _object_cast_to_RRT(o):
596  r"""_object_cast_to_RRT(Object o) -> RRT"""
597  return _IMP_kinematics._object_cast_to_RRT(o)
598 class Joint(IMP.Object):
599  r"""Proxy of C++ IMP::kinematics::Joint class."""
600 
601  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
602 
603  def get_version_info(self):
604  r"""get_version_info(Joint self) -> VersionInfo"""
605  return _IMP_kinematics.Joint_get_version_info(self)
606  __swig_destroy__ = _IMP_kinematics.delete_Joint
607 
608  def __init__(self, parent, child):
609  r"""__init__(Joint self, RigidBody parent, RigidBody child) -> Joint"""
610  _IMP_kinematics.Joint_swiginit(self, _IMP_kinematics.new_Joint(parent, child))
611 
612  def get_owner_kf(self):
613  r"""get_owner_kf(Joint self) -> KinematicForest"""
614  return _IMP_kinematics.Joint_get_owner_kf(self)
615 
616  def get_transformation_child_to_parent(self):
617  r"""get_transformation_child_to_parent(Joint self) -> Transformation3D"""
618  return _IMP_kinematics.Joint_get_transformation_child_to_parent(self)
619 
620  def get_parent_node(self):
621  r"""get_parent_node(Joint self) -> RigidBody"""
622  return _IMP_kinematics.Joint_get_parent_node(self)
623 
624  def get_child_node(self):
625  r"""get_child_node(Joint self) -> RigidBody"""
626  return _IMP_kinematics.Joint_get_child_node(self)
627 
628  def __str__(self):
629  r"""__str__(Joint self) -> std::string"""
630  return _IMP_kinematics.Joint___str__(self)
631 
632  def __repr__(self):
633  r"""__repr__(Joint self) -> std::string"""
634  return _IMP_kinematics.Joint___repr__(self)
635 
636  @staticmethod
637  def get_from(o):
638  return _object_cast_to_Joint(o)
639 
640 
641 # Register Joint in _IMP_kinematics:
642 _IMP_kinematics.Joint_swigregister(Joint)
643 class TransformationJoint(Joint):
644  r"""Proxy of C++ IMP::kinematics::TransformationJoint class."""
645 
646  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
647 
648  def __init__(self, parent, child):
649  r"""__init__(TransformationJoint self, RigidBody parent, RigidBody child) -> TransformationJoint"""
650  _IMP_kinematics.TransformationJoint_swiginit(self, _IMP_kinematics.new_TransformationJoint(parent, child))
651 
652  def set_transformation_child_to_parent(self, transformation):
653  r"""set_transformation_child_to_parent(TransformationJoint self, Transformation3D transformation)"""
654  return _IMP_kinematics.TransformationJoint_set_transformation_child_to_parent(self, transformation)
655 
656  def __str__(self):
657  r"""__str__(TransformationJoint self) -> std::string"""
658  return _IMP_kinematics.TransformationJoint___str__(self)
659 
660  def __repr__(self):
661  r"""__repr__(TransformationJoint self) -> std::string"""
662  return _IMP_kinematics.TransformationJoint___repr__(self)
663 
664  @staticmethod
665  def get_from(o):
666  return _object_cast_to_TransformationJoint(o)
667 
668  __swig_destroy__ = _IMP_kinematics.delete_TransformationJoint
669 
670 # Register TransformationJoint in _IMP_kinematics:
671 _IMP_kinematics.TransformationJoint_swigregister(TransformationJoint)
672 class PrismaticJoint(Joint):
673  r"""Proxy of C++ IMP::kinematics::PrismaticJoint class."""
674 
675  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
676 
677  def __init__(self, *args):
678  r"""
679  __init__(PrismaticJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b) -> PrismaticJoint
680  __init__(PrismaticJoint self, RigidBody parent, RigidBody child) -> PrismaticJoint
681  """
682  _IMP_kinematics.PrismaticJoint_swiginit(self, _IMP_kinematics.new_PrismaticJoint(*args))
683 
684  def get_length(self):
685  r"""get_length(PrismaticJoint self) -> double"""
686  return _IMP_kinematics.PrismaticJoint_get_length(self)
687 
688  def set_length(self, l):
689  r"""set_length(PrismaticJoint self, double l)"""
690  return _IMP_kinematics.PrismaticJoint_set_length(self, l)
691 
692  def __str__(self):
693  r"""__str__(PrismaticJoint self) -> std::string"""
694  return _IMP_kinematics.PrismaticJoint___str__(self)
695 
696  def __repr__(self):
697  r"""__repr__(PrismaticJoint self) -> std::string"""
698  return _IMP_kinematics.PrismaticJoint___repr__(self)
699 
700  @staticmethod
701  def get_from(o):
702  return _object_cast_to_PrismaticJoint(o)
703 
704  __swig_destroy__ = _IMP_kinematics.delete_PrismaticJoint
705 
706 # Register PrismaticJoint in _IMP_kinematics:
707 _IMP_kinematics.PrismaticJoint_swigregister(PrismaticJoint)
708 class CompositeJoint(Joint):
709  r"""Proxy of C++ IMP::kinematics::CompositeJoint class."""
710 
711  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
712 
713  def __init__(self, *args):
714  r"""__init__(CompositeJoint self, RigidBody parent, RigidBody child, IMP::kinematics::Joints joints=IMP::kinematics::Joints()) -> CompositeJoint"""
715  _IMP_kinematics.CompositeJoint_swiginit(self, _IMP_kinematics.new_CompositeJoint(*args))
716 
717  def add_downstream_joint(self, j):
718  r"""add_downstream_joint(CompositeJoint self, Joint j)"""
719  return _IMP_kinematics.CompositeJoint_add_downstream_joint(self, j)
720 
721  def add_upstream_joint(self, j):
722  r"""add_upstream_joint(CompositeJoint self, Joint j)"""
723  return _IMP_kinematics.CompositeJoint_add_upstream_joint(self, j)
724 
725  def set_joints(self, joints):
726  r"""set_joints(CompositeJoint self, IMP::kinematics::Joints joints)"""
727  return _IMP_kinematics.CompositeJoint_set_joints(self, joints)
728 
729  def get_inner_joints(self):
730  r"""get_inner_joints(CompositeJoint self) -> IMP::kinematics::Joints const &"""
731  return _IMP_kinematics.CompositeJoint_get_inner_joints(self)
732 
733  def __str__(self):
734  r"""__str__(CompositeJoint self) -> std::string"""
735  return _IMP_kinematics.CompositeJoint___str__(self)
736 
737  def __repr__(self):
738  r"""__repr__(CompositeJoint self) -> std::string"""
739  return _IMP_kinematics.CompositeJoint___repr__(self)
740 
741  @staticmethod
742  def get_from(o):
743  return _object_cast_to_CompositeJoint(o)
744 
745  __swig_destroy__ = _IMP_kinematics.delete_CompositeJoint
746 
747 # Register CompositeJoint in _IMP_kinematics:
748 _IMP_kinematics.CompositeJoint_swigregister(CompositeJoint)
749 class RevoluteJoint(Joint):
750  r"""Proxy of C++ IMP::kinematics::RevoluteJoint class."""
751 
752  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
753 
754  def __init__(self, parent, child):
755  r"""__init__(RevoluteJoint self, RigidBody parent, RigidBody child) -> RevoluteJoint"""
756  if self.__class__ == RevoluteJoint:
757  _self = None
758  else:
759  _self = self
760  _IMP_kinematics.RevoluteJoint_swiginit(self, _IMP_kinematics.new_RevoluteJoint(_self, parent, child))
761 
762  if self.__class__ != RevoluteJoint:
763  _director_objects.register(self)
764 
765 
766 
767  __swig_destroy__ = _IMP_kinematics.delete_RevoluteJoint
768 
769  def set_angle(self, angle):
770  r"""set_angle(RevoluteJoint self, double angle)"""
771  return _IMP_kinematics.RevoluteJoint_set_angle(self, angle)
772 
773  def get_angle(self):
774  r"""get_angle(RevoluteJoint self) -> double"""
775  return _IMP_kinematics.RevoluteJoint_get_angle(self)
776 
777  def get_rot_axis_origin(self):
778  r"""get_rot_axis_origin(RevoluteJoint self) -> Vector3D"""
779  return _IMP_kinematics.RevoluteJoint_get_rot_axis_origin(self)
780 
781  def get_rot_axis_unit_vector(self):
782  r"""get_rot_axis_unit_vector(RevoluteJoint self) -> Vector3D"""
783  return _IMP_kinematics.RevoluteJoint_get_rot_axis_unit_vector(self)
784 
785  def update_child_node_reference_frame(self):
786  r"""update_child_node_reference_frame(RevoluteJoint self)"""
787  return _IMP_kinematics.RevoluteJoint_update_child_node_reference_frame(self)
788 
789  def update_axis_of_rotation_from_cartesian_witnesses(self):
790  r"""update_axis_of_rotation_from_cartesian_witnesses(RevoluteJoint self)"""
791  return _IMP_kinematics.RevoluteJoint_update_axis_of_rotation_from_cartesian_witnesses(self)
792 
793  def get_current_angle_from_cartesian_witnesses(self):
794  r"""get_current_angle_from_cartesian_witnesses(RevoluteJoint self) -> double"""
795  return _IMP_kinematics.RevoluteJoint_get_current_angle_from_cartesian_witnesses(self)
796 
797  def update_joint_from_cartesian_witnesses(self):
798  r"""update_joint_from_cartesian_witnesses(RevoluteJoint self)"""
799  return _IMP_kinematics.RevoluteJoint_update_joint_from_cartesian_witnesses(self)
800 
801  def get_rotation_about_joint_in_parent_coordinates(self):
802  r"""get_rotation_about_joint_in_parent_coordinates(RevoluteJoint self) -> Transformation3D"""
803  return _IMP_kinematics.RevoluteJoint_get_rotation_about_joint_in_parent_coordinates(self)
804  angle_ = property(_IMP_kinematics.RevoluteJoint_angle__get, _IMP_kinematics.RevoluteJoint_angle__set, doc=r"""angle_ : double""")
805  last_updated_angle_ = property(_IMP_kinematics.RevoluteJoint_last_updated_angle__get, _IMP_kinematics.RevoluteJoint_last_updated_angle__set, doc=r"""last_updated_angle_ : double""")
806  rot_axis_unit_vector_ = property(_IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__get, _IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__set, doc=r"""rot_axis_unit_vector_ : IMP::algebra::Vector3D""")
807  rot_axis_origin_ = property(_IMP_kinematics.RevoluteJoint_rot_axis_origin__get, _IMP_kinematics.RevoluteJoint_rot_axis_origin__set, doc=r"""rot_axis_origin_ : IMP::algebra::Vector3D""")
808 
809  def __str__(self):
810  r"""__str__(RevoluteJoint self) -> std::string"""
811  return _IMP_kinematics.RevoluteJoint___str__(self)
812 
813  def __repr__(self):
814  r"""__repr__(RevoluteJoint self) -> std::string"""
815  return _IMP_kinematics.RevoluteJoint___repr__(self)
816 
817  @staticmethod
818  def get_from(o):
819  return _object_cast_to_RevoluteJoint(o)
820 
821 
822  def get_type_name(self):
823  return self.__class__.__name__
824  def do_show(self, out):
825  pass
826  def get_version_info(self):
827  if"IMP::kinematics" == "IMP":
828  return VersionInfo(self.__module__,
829  __import__(self.__module__).get_module_version())
830  else:
831  return IMP.VersionInfo(self.__module__,
832  __import__(self.__module__).get_module_version())
833  @staticmethod
834  def get_from(o):
835  return _object_cast_to_RevoluteJoint(o)
836 
837  def __disown__(self):
838  self.this.disown()
839  _IMP_kinematics.disown_RevoluteJoint(self)
840  return weakref.proxy(self)
841 
842  def do_destroy(self):
843  r"""do_destroy(RevoluteJoint self)"""
844  return _IMP_kinematics.RevoluteJoint_do_destroy(self)
845 
846 # Register RevoluteJoint in _IMP_kinematics:
847 _IMP_kinematics.RevoluteJoint_swigregister(RevoluteJoint)
848 class DihedralAngleRevoluteJoint(RevoluteJoint):
849  r"""Proxy of C++ IMP::kinematics::DihedralAngleRevoluteJoint class."""
850 
851  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
852 
853  def __init__(self, parent, child, a, b, c, d):
854  r"""__init__(DihedralAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c, XYZ d) -> DihedralAngleRevoluteJoint"""
855  _IMP_kinematics.DihedralAngleRevoluteJoint_swiginit(self, _IMP_kinematics.new_DihedralAngleRevoluteJoint(parent, child, a, b, c, d))
856 
857  def get_a(self):
858  r"""get_a(DihedralAngleRevoluteJoint self) -> XYZ"""
859  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_a(self)
860 
861  def get_b(self):
862  r"""get_b(DihedralAngleRevoluteJoint self) -> XYZ"""
863  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_b(self)
864 
865  def get_c(self):
866  r"""get_c(DihedralAngleRevoluteJoint self) -> XYZ"""
867  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_c(self)
868 
869  def get_d(self):
870  r"""get_d(DihedralAngleRevoluteJoint self) -> XYZ"""
871  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_d(self)
872 
873  def __str__(self):
874  r"""__str__(DihedralAngleRevoluteJoint self) -> std::string"""
875  return _IMP_kinematics.DihedralAngleRevoluteJoint___str__(self)
876 
877  def __repr__(self):
878  r"""__repr__(DihedralAngleRevoluteJoint self) -> std::string"""
879  return _IMP_kinematics.DihedralAngleRevoluteJoint___repr__(self)
880 
881  @staticmethod
882  def get_from(o):
883  return _object_cast_to_DihedralAngleRevoluteJoint(o)
884 
885  __swig_destroy__ = _IMP_kinematics.delete_DihedralAngleRevoluteJoint
886 
887 # Register DihedralAngleRevoluteJoint in _IMP_kinematics:
888 _IMP_kinematics.DihedralAngleRevoluteJoint_swigregister(DihedralAngleRevoluteJoint)
889 class BondAngleRevoluteJoint(RevoluteJoint):
890  r"""Proxy of C++ IMP::kinematics::BondAngleRevoluteJoint class."""
891 
892  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
893 
894  def __init__(self, parent, child, a, b, c):
895  r"""__init__(BondAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c) -> BondAngleRevoluteJoint"""
896  _IMP_kinematics.BondAngleRevoluteJoint_swiginit(self, _IMP_kinematics.new_BondAngleRevoluteJoint(parent, child, a, b, c))
897 
898  def __str__(self):
899  r"""__str__(BondAngleRevoluteJoint self) -> std::string"""
900  return _IMP_kinematics.BondAngleRevoluteJoint___str__(self)
901 
902  def __repr__(self):
903  r"""__repr__(BondAngleRevoluteJoint self) -> std::string"""
904  return _IMP_kinematics.BondAngleRevoluteJoint___repr__(self)
905 
906  @staticmethod
907  def get_from(o):
908  return _object_cast_to_BondAngleRevoluteJoint(o)
909 
910  __swig_destroy__ = _IMP_kinematics.delete_BondAngleRevoluteJoint
911 
912 # Register BondAngleRevoluteJoint in _IMP_kinematics:
913 _IMP_kinematics.BondAngleRevoluteJoint_swigregister(BondAngleRevoluteJoint)
914 class RevoluteJointMover(IMP.core.MonteCarloMover):
915  r"""Proxy of C++ IMP::kinematics::RevoluteJointMover class."""
916 
917  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
918 
919  def __init__(self, m, joints, stddev=0.01):
920  r"""__init__(RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const stddev=0.01) -> RevoluteJointMover"""
921  _IMP_kinematics.RevoluteJointMover_swiginit(self, _IMP_kinematics.new_RevoluteJointMover(m, joints, stddev))
922 
923  def set_sigma(self, sigma):
924  r"""set_sigma(RevoluteJointMover self, IMP::Float sigma)"""
925  return _IMP_kinematics.RevoluteJointMover_set_sigma(self, sigma)
926 
927  def get_sigma(self):
928  r"""get_sigma(RevoluteJointMover self) -> IMP::Float"""
929  return _IMP_kinematics.RevoluteJointMover_get_sigma(self)
930 
931  def get_version_info(self):
932  r"""get_version_info(RevoluteJointMover self) -> VersionInfo"""
933  return _IMP_kinematics.RevoluteJointMover_get_version_info(self)
934  __swig_destroy__ = _IMP_kinematics.delete_RevoluteJointMover
935 
936  def __str__(self):
937  r"""__str__(RevoluteJointMover self) -> std::string"""
938  return _IMP_kinematics.RevoluteJointMover___str__(self)
939 
940  def __repr__(self):
941  r"""__repr__(RevoluteJointMover self) -> std::string"""
942  return _IMP_kinematics.RevoluteJointMover___repr__(self)
943 
944  @staticmethod
945  def get_from(o):
946  return _object_cast_to_RevoluteJointMover(o)
947 
948 
949 # Register RevoluteJointMover in _IMP_kinematics:
950 _IMP_kinematics.RevoluteJointMover_swigregister(RevoluteJointMover)
951 class DihedralMover(IMP.core.MonteCarloMover):
952  r"""Proxy of C++ IMP::kinematics::DihedralMover class."""
953 
954  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
955 
956  def __init__(self, m, joints, max_rot=0.1):
957  r"""__init__(DihedralMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const max_rot=0.1) -> DihedralMover"""
958  _IMP_kinematics.DihedralMover_swiginit(self, _IMP_kinematics.new_DihedralMover(m, joints, max_rot))
959 
960  def get_version_info(self):
961  r"""get_version_info(DihedralMover self) -> VersionInfo"""
962  return _IMP_kinematics.DihedralMover_get_version_info(self)
963  __swig_destroy__ = _IMP_kinematics.delete_DihedralMover
964 
965  def __str__(self):
966  r"""__str__(DihedralMover self) -> std::string"""
967  return _IMP_kinematics.DihedralMover___str__(self)
968 
969  def __repr__(self):
970  r"""__repr__(DihedralMover self) -> std::string"""
971  return _IMP_kinematics.DihedralMover___repr__(self)
972 
973  @staticmethod
974  def get_from(o):
975  return _object_cast_to_DihedralMover(o)
976 
977 
978 # Register DihedralMover in _IMP_kinematics:
979 _IMP_kinematics.DihedralMover_swigregister(DihedralMover)
980 class KinematicForest(IMP.Object):
981  r"""Proxy of C++ IMP::kinematics::KinematicForest class."""
982 
983  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
984 
985  def get_version_info(self):
986  r"""get_version_info(KinematicForest self) -> VersionInfo"""
987  return _IMP_kinematics.KinematicForest_get_version_info(self)
988  __swig_destroy__ = _IMP_kinematics.delete_KinematicForest
989 
990  def __init__(self, *args):
991  r"""
992  __init__(KinematicForest self, Model m) -> KinematicForest
993  __init__(KinematicForest self, Model m, Hierarchy hierarchy) -> KinematicForest
994  """
995  _IMP_kinematics.KinematicForest_swiginit(self, _IMP_kinematics.new_KinematicForest(*args))
996 
997  def add_edge(self, *args):
998  r"""
999  add_edge(KinematicForest self, RigidBody parent, RigidBody child) -> Joint
1000  add_edge(KinematicForest self, Joint joint)
1001  """
1002  return _IMP_kinematics.KinematicForest_add_edge(self, *args)
1003 
1004  def add_rigid_bodies_in_chain(self, rbs):
1005  r"""add_rigid_bodies_in_chain(KinematicForest self, IMP::core::RigidBodies rbs)"""
1006  return _IMP_kinematics.KinematicForest_add_rigid_bodies_in_chain(self, rbs)
1007 
1008  def reset_root(self, new_root):
1009  r"""reset_root(KinematicForest self, Particle new_root)"""
1010  return _IMP_kinematics.KinematicForest_reset_root(self, new_root)
1011 
1012  def update_all_internal_coordinates(self):
1013  r"""update_all_internal_coordinates(KinematicForest self)"""
1014  return _IMP_kinematics.KinematicForest_update_all_internal_coordinates(self)
1015 
1016  def update_all_external_coordinates(self):
1017  r"""update_all_external_coordinates(KinematicForest self)"""
1018  return _IMP_kinematics.KinematicForest_update_all_external_coordinates(self)
1019 
1020  def get_ordered_joints(self):
1021  r"""get_ordered_joints(KinematicForest self) -> IMP::kinematics::Joints"""
1022  return _IMP_kinematics.KinematicForest_get_ordered_joints(self)
1023 
1024  def transform_safe(self, tr):
1025  r"""transform_safe(KinematicForest self, Transformation3D tr)"""
1026  return _IMP_kinematics.KinematicForest_transform_safe(self, tr)
1027 
1028  def mark_internal_coordinates_changed(self):
1029  r"""mark_internal_coordinates_changed(KinematicForest self)"""
1030  return _IMP_kinematics.KinematicForest_mark_internal_coordinates_changed(self)
1031 
1032  def mark_external_coordinates_changed(self):
1033  r"""mark_external_coordinates_changed(KinematicForest self)"""
1034  return _IMP_kinematics.KinematicForest_mark_external_coordinates_changed(self)
1035 
1036  def set_coordinates_safe(self, rb, c):
1037  r"""set_coordinates_safe(KinematicForest self, RigidBody rb, Vector3D c)"""
1038  return _IMP_kinematics.KinematicForest_set_coordinates_safe(self, rb, c)
1039 
1040  def get_coordinates_safe(self, rb):
1041  r"""get_coordinates_safe(KinematicForest self, RigidBody rb) -> Vector3D"""
1042  return _IMP_kinematics.KinematicForest_get_coordinates_safe(self, rb)
1043 
1044  def get_is_member(self, rb):
1045  r"""get_is_member(KinematicForest self, RigidBody rb) -> bool"""
1046  return _IMP_kinematics.KinematicForest_get_is_member(self, rb)
1047 
1048  def get_reference_frame_safe(self, rb):
1049  r"""get_reference_frame_safe(KinematicForest self, RigidBody rb) -> ReferenceFrame3D"""
1050  return _IMP_kinematics.KinematicForest_get_reference_frame_safe(self, rb)
1051 
1052  def set_reference_frame_safe(self, rb, r):
1053  r"""set_reference_frame_safe(KinematicForest self, RigidBody rb, ReferenceFrame3D r)"""
1054  return _IMP_kinematics.KinematicForest_set_reference_frame_safe(self, rb, r)
1055 
1056  def apply_transform_safely(self, tr):
1057  r"""apply_transform_safely(KinematicForest self, Transformation3D tr)"""
1058  return _IMP_kinematics.KinematicForest_apply_transform_safely(self, tr)
1059 
1060  def __str__(self):
1061  r"""__str__(KinematicForest self) -> std::string"""
1062  return _IMP_kinematics.KinematicForest___str__(self)
1063 
1064  def __repr__(self):
1065  r"""__repr__(KinematicForest self) -> std::string"""
1066  return _IMP_kinematics.KinematicForest___repr__(self)
1067 
1068  @staticmethod
1069  def get_from(o):
1070  return _object_cast_to_KinematicForest(o)
1071 
1072 
1073 # Register KinematicForest in _IMP_kinematics:
1074 _IMP_kinematics.KinematicForest_swigregister(KinematicForest)
1075 class KinematicForestScoreState(IMP.ScoreState):
1076  r"""Proxy of C++ IMP::kinematics::KinematicForestScoreState class."""
1077 
1078  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1079 
1080  def get_version_info(self):
1081  r"""get_version_info(KinematicForestScoreState self) -> VersionInfo"""
1082  return _IMP_kinematics.KinematicForestScoreState_get_version_info(self)
1083  __swig_destroy__ = _IMP_kinematics.delete_KinematicForestScoreState
1084 
1085  def __init__(self, kf, rbs, atoms):
1086  r"""__init__(KinematicForestScoreState self, KinematicForest kf, IMP::core::RigidBodies rbs, IMP::ParticlesTemp atoms) -> KinematicForestScoreState"""
1087  _IMP_kinematics.KinematicForestScoreState_swiginit(self, _IMP_kinematics.new_KinematicForestScoreState(kf, rbs, atoms))
1088 
1089  def do_before_evaluate(self):
1090  r"""do_before_evaluate(KinematicForestScoreState self)"""
1091  return _IMP_kinematics.KinematicForestScoreState_do_before_evaluate(self)
1092 
1093  def do_after_evaluate(self, da):
1094  r"""do_after_evaluate(KinematicForestScoreState self, DerivativeAccumulator da)"""
1095  return _IMP_kinematics.KinematicForestScoreState_do_after_evaluate(self, da)
1096 
1097  def do_get_inputs(self):
1098  r"""do_get_inputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1099  return _IMP_kinematics.KinematicForestScoreState_do_get_inputs(self)
1100 
1101  def do_get_outputs(self):
1102  r"""do_get_outputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1103  return _IMP_kinematics.KinematicForestScoreState_do_get_outputs(self)
1104 
1105  def __str__(self):
1106  r"""__str__(KinematicForestScoreState self) -> std::string"""
1107  return _IMP_kinematics.KinematicForestScoreState___str__(self)
1108 
1109  def __repr__(self):
1110  r"""__repr__(KinematicForestScoreState self) -> std::string"""
1111  return _IMP_kinematics.KinematicForestScoreState___repr__(self)
1112 
1113  @staticmethod
1114  def get_from(o):
1115  return _object_cast_to_KinematicForestScoreState(o)
1116 
1117 
1118 # Register KinematicForestScoreState in _IMP_kinematics:
1119 _IMP_kinematics.KinematicForestScoreState_swigregister(KinematicForestScoreState)
1120 class DOF(IMP.Object):
1121  r"""Proxy of C++ IMP::kinematics::DOF class."""
1122 
1123  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1124 
1125  def get_version_info(self):
1126  r"""get_version_info(DOF self) -> VersionInfo"""
1127  return _IMP_kinematics.DOF_get_version_info(self)
1128  __swig_destroy__ = _IMP_kinematics.delete_DOF
1129 
1130  def __init__(self, *args):
1131  r"""
1132  __init__(DOF self, double v) -> DOF
1133  __init__(DOF self, double v, double min, double max, double step_size) -> DOF
1134  """
1135  _IMP_kinematics.DOF_swiginit(self, _IMP_kinematics.new_DOF(*args))
1136 
1137  def get_value(self):
1138  r"""get_value(DOF self) -> double"""
1139  return _IMP_kinematics.DOF_get_value(self)
1140 
1141  def set_value(self, v):
1142  r"""set_value(DOF self, double v)"""
1143  return _IMP_kinematics.DOF_set_value(self, v)
1144 
1145  def get_range(self):
1146  r"""get_range(DOF self) -> std::pair< double,double >"""
1147  return _IMP_kinematics.DOF_get_range(self)
1148 
1149  def set_range(self, range):
1150  r"""set_range(DOF self, std::pair< double,double > range)"""
1151  return _IMP_kinematics.DOF_set_range(self, range)
1152 
1153  def get_step_size(self):
1154  r"""get_step_size(DOF self) -> double"""
1155  return _IMP_kinematics.DOF_get_step_size(self)
1156 
1157  def set_step_size(self, step_size):
1158  r"""set_step_size(DOF self, double step_size)"""
1159  return _IMP_kinematics.DOF_set_step_size(self, step_size)
1160 
1161  def get_number_of_steps(self, *args):
1162  r"""
1163  get_number_of_steps(DOF self, double value) -> int
1164  get_number_of_steps(DOF self, double value1, double value2) -> int
1165  """
1166  return _IMP_kinematics.DOF_get_number_of_steps(self, *args)
1167 
1168  def __str__(self):
1169  r"""__str__(DOF self) -> std::string"""
1170  return _IMP_kinematics.DOF___str__(self)
1171 
1172  def __repr__(self):
1173  r"""__repr__(DOF self) -> std::string"""
1174  return _IMP_kinematics.DOF___repr__(self)
1175 
1176  @staticmethod
1177  def get_from(o):
1178  return _object_cast_to_DOF(o)
1179 
1180 
1181 # Register DOF in _IMP_kinematics:
1182 _IMP_kinematics.DOF_swigregister(DOF)
1183 class DOFValues(IMP.saxs.DistBase):
1184  r"""Proxy of C++ IMP::kinematics::DOFValues class."""
1185 
1186  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1187 
1188  def __init__(self, *args):
1189  r"""
1190  __init__(DOFValues self, IMP::kinematics::DOFs const & dofs) -> DOFValues
1191  __init__(DOFValues self) -> DOFValues
1192  """
1193  _IMP_kinematics.DOFValues_swiginit(self, _IMP_kinematics.new_DOFValues(*args))
1194 
1195  def get_distance2(self, *args):
1196  r"""
1197  get_distance2(DOFValues self, DOFValues other_dof_values) -> double
1198  get_distance2(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1199  """
1200  return _IMP_kinematics.DOFValues_get_distance2(self, *args)
1201 
1202  def get_distance(self, *args):
1203  r"""
1204  get_distance(DOFValues self, DOFValues other_dof_values) -> double
1205  get_distance(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1206  """
1207  return _IMP_kinematics.DOFValues_get_distance(self, *args)
1208 
1209  def show(self, *args):
1210  r"""show(DOFValues self, _ostream out=std::cout)"""
1211  return _IMP_kinematics.DOFValues_show(self, *args)
1212 
1213  def __str__(self):
1214  r"""__str__(DOFValues self) -> std::string"""
1215  return _IMP_kinematics.DOFValues___str__(self)
1216 
1217  def __repr__(self):
1218  r"""__repr__(DOFValues self) -> std::string"""
1219  return _IMP_kinematics.DOFValues___repr__(self)
1220 
1221  def _get_as_binary(self):
1222  r"""_get_as_binary(DOFValues self) -> PyObject *"""
1223  return _IMP_kinematics.DOFValues__get_as_binary(self)
1224 
1225  def _set_from_binary(self, p):
1226  r"""_set_from_binary(DOFValues self, PyObject * p)"""
1227  return _IMP_kinematics.DOFValues__set_from_binary(self, p)
1228 
1229  def __getstate__(self):
1230  p = self._get_as_binary()
1231  if len(self.__dict__) > 1:
1232  d = self.__dict__.copy()
1233  del d['this']
1234  p = (d, p)
1235  return p
1236 
1237  def __setstate__(self, p):
1238  if not hasattr(self, 'this'):
1239  self.__init__()
1240  if isinstance(p, tuple):
1241  d, p = p
1242  self.__dict__.update(d)
1243  return self._set_from_binary(p)
1244 
1245  __swig_destroy__ = _IMP_kinematics.delete_DOFValues
1246 
1247 # Register DOFValues in _IMP_kinematics:
1248 _IMP_kinematics.DOFValues_swigregister(DOFValues)
1249 class DirectionalDOF(IMP.Object):
1250  r"""Proxy of C++ IMP::kinematics::DirectionalDOF class."""
1251 
1252  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1253 
1254  def __init__(self, dofs):
1255  r"""__init__(DirectionalDOF self, IMP::kinematics::DOFs const & dofs) -> DirectionalDOF"""
1256  _IMP_kinematics.DirectionalDOF_swiginit(self, _IMP_kinematics.new_DirectionalDOF(dofs))
1257 
1258  def set_end_points(self, q1, q2):
1259  r"""set_end_points(DirectionalDOF self, DOFValues q1, DOFValues q2)"""
1260  return _IMP_kinematics.DirectionalDOF_set_end_points(self, q1, q2)
1261 
1262  def get_dofs_values(self):
1263  r"""get_dofs_values(DirectionalDOF self) -> DOFValues"""
1264  return _IMP_kinematics.DirectionalDOF_get_dofs_values(self)
1265 
1266  def get_value(self):
1267  r"""get_value(DirectionalDOF self) -> double"""
1268  return _IMP_kinematics.DirectionalDOF_get_value(self)
1269 
1270  def get_version_info(self):
1271  r"""get_version_info(DirectionalDOF self) -> VersionInfo"""
1272  return _IMP_kinematics.DirectionalDOF_get_version_info(self)
1273  __swig_destroy__ = _IMP_kinematics.delete_DirectionalDOF
1274 
1275  def __str__(self):
1276  r"""__str__(DirectionalDOF self) -> std::string"""
1277  return _IMP_kinematics.DirectionalDOF___str__(self)
1278 
1279  def __repr__(self):
1280  r"""__repr__(DirectionalDOF self) -> std::string"""
1281  return _IMP_kinematics.DirectionalDOF___repr__(self)
1282 
1283  @staticmethod
1284  def get_from(o):
1285  return _object_cast_to_DirectionalDOF(o)
1286 
1287 
1288 # Register DirectionalDOF in _IMP_kinematics:
1289 _IMP_kinematics.DirectionalDOF_swigregister(DirectionalDOF)
1290 class DOFsSampler(IMP.Object):
1291  r"""Proxy of C++ IMP::kinematics::DOFsSampler class."""
1292 
1293  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1294 
1295  def get_type_name(self):
1296  r"""get_type_name(DOFsSampler self) -> std::string"""
1297  return _IMP_kinematics.DOFsSampler_get_type_name(self)
1298 
1299  def get_version_info(self):
1300  r"""get_version_info(DOFsSampler self) -> VersionInfo"""
1301  return _IMP_kinematics.DOFsSampler_get_version_info(self)
1302  __swig_destroy__ = _IMP_kinematics.delete_DOFsSampler
1303 
1304  def __init__(self, dofs):
1305  r"""__init__(DOFsSampler self, IMP::kinematics::DOFs dofs) -> DOFsSampler"""
1306  if self.__class__ == DOFsSampler:
1307  _self = None
1308  else:
1309  _self = self
1310  _IMP_kinematics.DOFsSampler_swiginit(self, _IMP_kinematics.new_DOFsSampler(_self, dofs))
1311 
1312  if self.__class__ != DOFsSampler:
1313  _director_objects.register(self)
1314 
1315 
1316 
1317 
1318  def get_sample(self):
1319  r"""get_sample(DOFsSampler self) -> DOFValues"""
1320  return _IMP_kinematics.DOFsSampler_get_sample(self)
1321 
1322  def apply(self, values):
1323  r"""apply(DOFsSampler self, DOFValues values)"""
1324  return _IMP_kinematics.DOFsSampler_apply(self, values)
1325 
1326  def apply_last_sample(self):
1327  r"""apply_last_sample(DOFsSampler self)"""
1328  return _IMP_kinematics.DOFsSampler_apply_last_sample(self)
1329 
1330  def sample_and_apply(self):
1331  r"""sample_and_apply(DOFsSampler self)"""
1332  return _IMP_kinematics.DOFsSampler_sample_and_apply(self)
1333 
1334  def get_dofs(self):
1335  r"""get_dofs(DOFsSampler self) -> IMP::kinematics::DOFs const &"""
1336  return _IMP_kinematics.DOFsSampler_get_dofs(self)
1337 
1338  def get_dof(self, i):
1339  r"""get_dof(DOFsSampler self, unsigned int i) -> DOF"""
1340  return _IMP_kinematics.DOFsSampler_get_dof(self, i)
1341 
1342  def get_number_of_dofs(self):
1343  r"""get_number_of_dofs(DOFsSampler self) -> unsigned int"""
1344  return _IMP_kinematics.DOFsSampler_get_number_of_dofs(self)
1345 
1346  def do_get_sample(self):
1347  r"""do_get_sample(DOFsSampler self) -> DOFValues"""
1348  return _IMP_kinematics.DOFsSampler_do_get_sample(self)
1349 
1350  def __str__(self):
1351  r"""__str__(DOFsSampler self) -> std::string"""
1352  return _IMP_kinematics.DOFsSampler___str__(self)
1353 
1354  def __repr__(self):
1355  r"""__repr__(DOFsSampler self) -> std::string"""
1356  return _IMP_kinematics.DOFsSampler___repr__(self)
1357 
1358  @staticmethod
1359  def get_from(o):
1360  return _object_cast_to_DOFsSampler(o)
1361 
1362 
1363  def get_type_name(self):
1364  return self.__class__.__name__
1365  def do_show(self, out):
1366  pass
1367  def get_version_info(self):
1368  if"IMP::kinematics" == "IMP":
1369  return VersionInfo(self.__module__,
1370  __import__(self.__module__).get_module_version())
1371  else:
1372  return IMP.VersionInfo(self.__module__,
1373  __import__(self.__module__).get_module_version())
1374  @staticmethod
1375  def get_from(o):
1376  return _object_cast_to_DOFsSampler(o)
1377 
1378  def __disown__(self):
1379  self.this.disown()
1380  _IMP_kinematics.disown_DOFsSampler(self)
1381  return weakref.proxy(self)
1382 
1383  def do_destroy(self):
1384  r"""do_destroy(DOFsSampler self)"""
1385  return _IMP_kinematics.DOFsSampler_do_destroy(self)
1386 
1387 # Register DOFsSampler in _IMP_kinematics:
1388 _IMP_kinematics.DOFsSampler_swigregister(DOFsSampler)
1389 class FibrilSampler(DOFsSampler):
1390  r"""Proxy of C++ IMP::kinematics::FibrilSampler class."""
1391 
1392  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1393 
1394  def __init__(self, trans_joint, dihedral_joints, dofs):
1395  r"""__init__(FibrilSampler self, IMP::kinematics::TransformationJoints trans_joint, IMP::kinematics::DihedralAngleRevoluteJoints dihedral_joints, IMP::kinematics::DOFs dofs) -> FibrilSampler"""
1396  _IMP_kinematics.FibrilSampler_swiginit(self, _IMP_kinematics.new_FibrilSampler(trans_joint, dihedral_joints, dofs))
1397 
1398  def apply_floats(self, values):
1399  r"""apply_floats(FibrilSampler self, IMP::Floats const & values)"""
1400  return _IMP_kinematics.FibrilSampler_apply_floats(self, values)
1401 
1402  def get_dihedral_joints(self):
1403  r"""get_dihedral_joints(FibrilSampler self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1404  return _IMP_kinematics.FibrilSampler_get_dihedral_joints(self)
1405 
1406  def get_transformation_joint(self):
1407  r"""get_transformation_joint(FibrilSampler self) -> IMP::kinematics::TransformationJoints"""
1408  return _IMP_kinematics.FibrilSampler_get_transformation_joint(self)
1409 
1410  def __str__(self):
1411  r"""__str__(FibrilSampler self) -> std::string"""
1412  return _IMP_kinematics.FibrilSampler___str__(self)
1413 
1414  def __repr__(self):
1415  r"""__repr__(FibrilSampler self) -> std::string"""
1416  return _IMP_kinematics.FibrilSampler___repr__(self)
1417 
1418  @staticmethod
1419  def get_from(o):
1420  return _object_cast_to_FibrilSampler(o)
1421 
1422  __swig_destroy__ = _IMP_kinematics.delete_FibrilSampler
1423 
1424 # Register FibrilSampler in _IMP_kinematics:
1425 _IMP_kinematics.FibrilSampler_swigregister(FibrilSampler)
1426 class UniformBackboneSampler(DOFsSampler):
1427  r"""Proxy of C++ IMP::kinematics::UniformBackboneSampler class."""
1428 
1429  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1430 
1431  def __init__(self, joints, dofs):
1432  r"""__init__(UniformBackboneSampler self, IMP::kinematics::DihedralAngleRevoluteJoints joints, IMP::kinematics::DOFs dofs) -> UniformBackboneSampler"""
1433  _IMP_kinematics.UniformBackboneSampler_swiginit(self, _IMP_kinematics.new_UniformBackboneSampler(joints, dofs))
1434 
1435  def apply_floats(self, values):
1436  r"""apply_floats(UniformBackboneSampler self, IMP::Floats const & values)"""
1437  return _IMP_kinematics.UniformBackboneSampler_apply_floats(self, values)
1438 
1439  def get_joints(self):
1440  r"""get_joints(UniformBackboneSampler self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1441  return _IMP_kinematics.UniformBackboneSampler_get_joints(self)
1442 
1443  def __str__(self):
1444  r"""__str__(UniformBackboneSampler self) -> std::string"""
1445  return _IMP_kinematics.UniformBackboneSampler___str__(self)
1446 
1447  def __repr__(self):
1448  r"""__repr__(UniformBackboneSampler self) -> std::string"""
1449  return _IMP_kinematics.UniformBackboneSampler___repr__(self)
1450 
1451  @staticmethod
1452  def get_from(o):
1453  return _object_cast_to_UniformBackboneSampler(o)
1454 
1455  __swig_destroy__ = _IMP_kinematics.delete_UniformBackboneSampler
1456 
1457 # Register UniformBackboneSampler in _IMP_kinematics:
1458 _IMP_kinematics.UniformBackboneSampler_swigregister(UniformBackboneSampler)
1459 PHI = _IMP_kinematics.PHI
1460 
1461 PSI = _IMP_kinematics.PSI
1462 
1463 CHI = _IMP_kinematics.CHI
1464 
1465 CHI1 = _IMP_kinematics.CHI1
1466 
1467 CHI2 = _IMP_kinematics.CHI2
1468 
1469 CHI3 = _IMP_kinematics.CHI3
1470 
1471 CHI4 = _IMP_kinematics.CHI4
1472 
1473 CHI5 = _IMP_kinematics.CHI5
1474 
1475 OTHER = _IMP_kinematics.OTHER
1476 
1477 OTHER2 = _IMP_kinematics.OTHER2
1478 
1479 OTHER3 = _IMP_kinematics.OTHER3
1480 
1481 OTHER4 = _IMP_kinematics.OTHER4
1482 
1483 OTHER5 = _IMP_kinematics.OTHER5
1484 
1485 TOTAL = _IMP_kinematics.TOTAL
1486 
1487 class ProteinKinematics(IMP.Object):
1488  r"""Proxy of C++ IMP::kinematics::ProteinKinematics class."""
1489 
1490  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1491 
1492  def __init__(self, *args):
1493  r"""
1494  __init__(ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1495  __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, IMP::ParticleIndexQuads const custom_dihedral_angles, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1496  __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & custom_dihedral_atoms, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1497  __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, IMP::ParticleIndexQuads const custom_dihedral_angles, std::vector< IMP::kinematics::ProteinAngleType,std::allocator< IMP::kinematics::ProteinAngleType > > const & custom_dihedral_angle_types, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1498  """
1499  _IMP_kinematics.ProteinKinematics_swiginit(self, _IMP_kinematics.new_ProteinKinematics(*args))
1500 
1501  def get_phi(self, r):
1502  r"""get_phi(ProteinKinematics self, Residue r) -> double"""
1503  return _IMP_kinematics.ProteinKinematics_get_phi(self, r)
1504 
1505  def get_psi(self, r):
1506  r"""get_psi(ProteinKinematics self, Residue r) -> double"""
1507  return _IMP_kinematics.ProteinKinematics_get_psi(self, r)
1508 
1509  def get_joints(self):
1510  r"""get_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1511  return _IMP_kinematics.ProteinKinematics_get_joints(self)
1512 
1513  def get_loop_joints(self):
1514  r"""get_loop_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1515  return _IMP_kinematics.ProteinKinematics_get_loop_joints(self)
1516 
1517  def get_ordered_joints(self):
1518  r"""get_ordered_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1519  return _IMP_kinematics.ProteinKinematics_get_ordered_joints(self)
1520 
1521  def get_kinematic_forest(self):
1522  r"""get_kinematic_forest(ProteinKinematics self) -> KinematicForest"""
1523  return _IMP_kinematics.ProteinKinematics_get_kinematic_forest(self)
1524 
1525  def get_rigid_bodies(self):
1526  r"""get_rigid_bodies(ProteinKinematics self) -> IMP::core::RigidBodies"""
1527  return _IMP_kinematics.ProteinKinematics_get_rigid_bodies(self)
1528 
1529  def set_phi(self, r, angle):
1530  r"""set_phi(ProteinKinematics self, Residue r, double angle)"""
1531  return _IMP_kinematics.ProteinKinematics_set_phi(self, r, angle)
1532 
1533  def set_psi(self, r, angle):
1534  r"""set_psi(ProteinKinematics self, Residue r, double angle)"""
1535  return _IMP_kinematics.ProteinKinematics_set_psi(self, r, angle)
1536 
1537  def get_version_info(self):
1538  r"""get_version_info(ProteinKinematics self) -> VersionInfo"""
1539  return _IMP_kinematics.ProteinKinematics_get_version_info(self)
1540  __swig_destroy__ = _IMP_kinematics.delete_ProteinKinematics
1541 
1542  def build_topology_graph(self):
1543  r"""build_topology_graph(ProteinKinematics self)"""
1544  return _IMP_kinematics.ProteinKinematics_build_topology_graph(self)
1545 
1546  def order_rigid_bodies(self, dihedral_angles, phi_angles, psi_angles, chi1_angles, chi2_angles, chi3_angles, chi4_angles, chi5_angles, open_loop_bond_atoms):
1547  r"""order_rigid_bodies(ProteinKinematics self, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & phi_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & psi_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi1_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi2_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi3_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi4_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi5_angles, IMP::atom::Atoms open_loop_bond_atoms)"""
1548  return _IMP_kinematics.ProteinKinematics_order_rigid_bodies(self, dihedral_angles, phi_angles, psi_angles, chi1_angles, chi2_angles, chi3_angles, chi4_angles, chi5_angles, open_loop_bond_atoms)
1549 
1550  def mark_rotatable_angles(self, dihedral_angles):
1551  r"""mark_rotatable_angles(ProteinKinematics self, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles)"""
1552  return _IMP_kinematics.ProteinKinematics_mark_rotatable_angles(self, dihedral_angles)
1553 
1554  def mark_rotatable_angle(self, dihedral_angle):
1555  r"""mark_rotatable_angle(ProteinKinematics self, std::vector< IMP::atom::Atom,std::allocator< IMP::atom::Atom > > const & dihedral_angle)"""
1556  return _IMP_kinematics.ProteinKinematics_mark_rotatable_angle(self, dihedral_angle)
1557 
1558  def build_rigid_bodies(self):
1559  r"""build_rigid_bodies(ProteinKinematics self)"""
1560  return _IMP_kinematics.ProteinKinematics_build_rigid_bodies(self)
1561 
1562  def add_dihedral_joints(self, residues, angle_type, dihedral_angles):
1563  r"""add_dihedral_joints(ProteinKinematics self, std::vector< IMP::atom::Residue,std::allocator< IMP::atom::Residue > > const & residues, IMP::kinematics::ProteinAngleType angle_type, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles)"""
1564  return _IMP_kinematics.ProteinKinematics_add_dihedral_joints(self, residues, angle_type, dihedral_angles)
1565 
1566  def add_dihedral_joint(self, r, angle_type, atoms):
1567  r"""add_dihedral_joint(ProteinKinematics self, Residue r, IMP::kinematics::ProteinAngleType angle_type, IMP::atom::Atoms const & atoms)"""
1568  return _IMP_kinematics.ProteinKinematics_add_dihedral_joint(self, r, angle_type, atoms)
1569 
1570  def open_loop(self, open_loop_bond_atoms):
1571  r"""open_loop(ProteinKinematics self, IMP::atom::Atoms open_loop_bond_atoms)"""
1572  return _IMP_kinematics.ProteinKinematics_open_loop(self, open_loop_bond_atoms)
1573 
1574  def get_phi_joint(self, r):
1575  r"""get_phi_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1576  return _IMP_kinematics.ProteinKinematics_get_phi_joint(self, r)
1577 
1578  def get_psi_joint(self, r):
1579  r"""get_psi_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1580  return _IMP_kinematics.ProteinKinematics_get_psi_joint(self, r)
1581 
1582  def get_other_joint(self, r):
1583  r"""get_other_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1584  return _IMP_kinematics.ProteinKinematics_get_other_joint(self, r)
1585 
1586  def get_chi1_joint(self, r):
1587  r"""get_chi1_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1588  return _IMP_kinematics.ProteinKinematics_get_chi1_joint(self, r)
1589 
1590  def get_chi2_joint(self, r):
1591  r"""get_chi2_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1592  return _IMP_kinematics.ProteinKinematics_get_chi2_joint(self, r)
1593 
1594  def get_chi3_joint(self, r):
1595  r"""get_chi3_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1596  return _IMP_kinematics.ProteinKinematics_get_chi3_joint(self, r)
1597 
1598  def get_chi4_joint(self, r):
1599  r"""get_chi4_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1600  return _IMP_kinematics.ProteinKinematics_get_chi4_joint(self, r)
1601 
1602  def get_chi5_joint(self, r):
1603  r"""get_chi5_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1604  return _IMP_kinematics.ProteinKinematics_get_chi5_joint(self, r)
1605 
1606  def get_joint(self, r, angle):
1607  r"""get_joint(ProteinKinematics self, Residue r, IMP::kinematics::ProteinAngleType angle) -> DihedralAngleRevoluteJoint"""
1608  return _IMP_kinematics.ProteinKinematics_get_joint(self, r, angle)
1609 
1610  def __str__(self):
1611  r"""__str__(ProteinKinematics self) -> std::string"""
1612  return _IMP_kinematics.ProteinKinematics___str__(self)
1613 
1614  def __repr__(self):
1615  r"""__repr__(ProteinKinematics self) -> std::string"""
1616  return _IMP_kinematics.ProteinKinematics___repr__(self)
1617 
1618  @staticmethod
1619  def get_from(o):
1620  return _object_cast_to_ProteinKinematics(o)
1621 
1622 
1623 # Register ProteinKinematics in _IMP_kinematics:
1624 _IMP_kinematics.ProteinKinematics_swigregister(ProteinKinematics)
1625 class LocalPlanner(IMP.Object):
1626  r"""Proxy of C++ IMP::kinematics::LocalPlanner class."""
1627 
1628  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1629 
1630  def __init__(self, *args, **kwargs):
1631  raise AttributeError("No constructor defined - class is abstract")
1632 
1633  def get_version_info(self):
1634  r"""get_version_info(LocalPlanner self) -> VersionInfo"""
1635  return _IMP_kinematics.LocalPlanner_get_version_info(self)
1636  __swig_destroy__ = _IMP_kinematics.delete_LocalPlanner
1637 
1638  def plan(self, q_near, q_rand, sf):
1639  r"""plan(LocalPlanner self, DOFValues q_near, DOFValues q_rand, ScoringFunction sf) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1640  return _IMP_kinematics.LocalPlanner_plan(self, q_near, q_rand, sf)
1641 
1642  def is_valid(self, values, sf):
1643  r"""is_valid(LocalPlanner self, DOFValues values, ScoringFunction sf) -> bool"""
1644  return _IMP_kinematics.LocalPlanner_is_valid(self, values, sf)
1645 
1646  def __str__(self):
1647  r"""__str__(LocalPlanner self) -> std::string"""
1648  return _IMP_kinematics.LocalPlanner___str__(self)
1649 
1650  def __repr__(self):
1651  r"""__repr__(LocalPlanner self) -> std::string"""
1652  return _IMP_kinematics.LocalPlanner___repr__(self)
1653 
1654  @staticmethod
1655  def get_from(o):
1656  return _object_cast_to_LocalPlanner(o)
1657 
1658 
1659 # Register LocalPlanner in _IMP_kinematics:
1660 _IMP_kinematics.LocalPlanner_swigregister(LocalPlanner)
1661 class PathLocalPlanner(LocalPlanner):
1662  r"""Proxy of C++ IMP::kinematics::PathLocalPlanner class."""
1663 
1664  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1665 
1666  def __init__(self, model, dofs_sampler, directional_dof, save_step_interval=1):
1667  r"""__init__(PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof, int save_step_interval=1) -> PathLocalPlanner"""
1668  _IMP_kinematics.PathLocalPlanner_swiginit(self, _IMP_kinematics.new_PathLocalPlanner(model, dofs_sampler, directional_dof, save_step_interval))
1669 
1670  def __str__(self):
1671  r"""__str__(PathLocalPlanner self) -> std::string"""
1672  return _IMP_kinematics.PathLocalPlanner___str__(self)
1673 
1674  def __repr__(self):
1675  r"""__repr__(PathLocalPlanner self) -> std::string"""
1676  return _IMP_kinematics.PathLocalPlanner___repr__(self)
1677 
1678  @staticmethod
1679  def get_from(o):
1680  return _object_cast_to_PathLocalPlanner(o)
1681 
1682  __swig_destroy__ = _IMP_kinematics.delete_PathLocalPlanner
1683 
1684 # Register PathLocalPlanner in _IMP_kinematics:
1685 _IMP_kinematics.PathLocalPlanner_swigregister(PathLocalPlanner)
1686 class RRT(IMP.Sampler):
1687  r"""Proxy of C++ IMP::kinematics::RRT class."""
1688 
1689  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1690 
1691  def get_version_info(self):
1692  r"""get_version_info(RRT self) -> VersionInfo"""
1693  return _IMP_kinematics.RRT_get_version_info(self)
1694  __swig_destroy__ = _IMP_kinematics.delete_RRT
1695 
1696  def __init__(self, m, sampler, planner, cspace_dofs, iteration_number=1000, tree_size=100, number_of_sampled_dofs=0):
1697  r"""__init__(RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs, unsigned int iteration_number=1000, unsigned int tree_size=100, unsigned int number_of_sampled_dofs=0) -> RRT"""
1698  _IMP_kinematics.RRT_swiginit(self, _IMP_kinematics.new_RRT(m, sampler, planner, cspace_dofs, iteration_number, tree_size, number_of_sampled_dofs))
1699 
1700  def do_sample(self):
1701  r"""do_sample(RRT self) -> ConfigurationSet"""
1702  return _IMP_kinematics.RRT_do_sample(self)
1703 
1704  def run(self, number_of_iterations=0):
1705  r"""run(RRT self, unsigned int number_of_iterations=0) -> bool"""
1706  return _IMP_kinematics.RRT_run(self, number_of_iterations)
1707 
1708  def get_DOFValuesList(self):
1709  r"""get_DOFValuesList(RRT self) -> IMP::kinematics::DOFValuesList"""
1710  return _IMP_kinematics.RRT_get_DOFValuesList(self)
1711 
1712  def set_number_of_iterations(self, num):
1713  r"""set_number_of_iterations(RRT self, unsigned int num)"""
1714  return _IMP_kinematics.RRT_set_number_of_iterations(self, num)
1715 
1716  def set_tree_size(self, num):
1717  r"""set_tree_size(RRT self, unsigned int num)"""
1718  return _IMP_kinematics.RRT_set_tree_size(self, num)
1719 
1720  def set_actual_tree_size(self, num):
1721  r"""set_actual_tree_size(RRT self, unsigned int num)"""
1722  return _IMP_kinematics.RRT_set_actual_tree_size(self, num)
1723 
1724  def set_number_of_collisions(self, num):
1725  r"""set_number_of_collisions(RRT self, unsigned int num)"""
1726  return _IMP_kinematics.RRT_set_number_of_collisions(self, num)
1727 
1728  def check_initial_configuration(self, sf):
1729  r"""check_initial_configuration(RRT self, ScoringFunction sf)"""
1730  return _IMP_kinematics.RRT_check_initial_configuration(self, sf)
1731 
1732  def __str__(self):
1733  r"""__str__(RRT self) -> std::string"""
1734  return _IMP_kinematics.RRT___str__(self)
1735 
1736  def __repr__(self):
1737  r"""__repr__(RRT self) -> std::string"""
1738  return _IMP_kinematics.RRT___repr__(self)
1739 
1740  @staticmethod
1741  def get_from(o):
1742  return _object_cast_to_RRT(o)
1743 
1744 
1745 # Register RRT in _IMP_kinematics:
1746 _IMP_kinematics.RRT_swigregister(RRT)
1747 
1748 def get_module_version():
1749  r"""get_module_version() -> std::string const"""
1750  return _IMP_kinematics.get_module_version()
1751 
1752 def get_example_path(fname):
1753  r"""get_example_path(std::string fname) -> std::string"""
1754  return _IMP_kinematics.get_example_path(fname)
1755 
1756 def get_data_path(fname):
1757  r"""get_data_path(std::string fname) -> std::string"""
1758  return _IMP_kinematics.get_data_path(fname)
1759 
1760 from . import _version_check
1761 _version_check.check_version(get_module_version())
1762 __version__ = get_module_version()
1763 
1764 
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
Base class for all samplers.
Definition: Sampler.h:31
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.
double get_angle(const Line3D &a, const Line3D &b)
Get angle in radians between two lines around their closest points.
virtual void do_destroy()
Definition: Object.h:274
Common base class for heavy weight IMP objects.
Definition: Object.h:111
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:56
A base class for classes which perturb particles.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
Version and module information for Objects.
Definition: VersionInfo.h:29
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
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
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.
double get_distance(const Line3D &s, const Vector3D &p)
Get closest distance between a line and a point.
Support for small angle X-ray scattering (SAXS) data.