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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
kinematics/__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_kinematics')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_kinematics')
25  _IMP_kinematics = 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_kinematics', [dirname(__file__)])
34  except ImportError:
35  import _IMP_kinematics
36  return _IMP_kinematics
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_kinematics', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_kinematics = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_kinematics
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_KINEMATICS_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_KINEMATICS_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_kinematics.delete_IMP_KINEMATICS_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
126  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator
132  incr(IMP_KINEMATICS_SwigPyIterator self) -> IMP_KINEMATICS_SwigPyIterator
133  """
134  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator
140  decr(IMP_KINEMATICS_SwigPyIterator self) -> IMP_KINEMATICS_SwigPyIterator
141  """
142  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
152  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_KINEMATICS_SwigPyIterator self) -> IMP_KINEMATICS_SwigPyIterator"""
157  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
162  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
167  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
172  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
177  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
182  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
187  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
192  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
197  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
202  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator
208  __sub__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_KINEMATICS_SwigPyIterator_swigregister = _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_swigregister
215 IMP_KINEMATICS_SwigPyIterator_swigregister(IMP_KINEMATICS_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_kinematics.IMP_DEBUG
224 IMP_RELEASE = _IMP_kinematics.IMP_RELEASE
225 IMP_SILENT = _IMP_kinematics.IMP_SILENT
226 IMP_PROGRESS = _IMP_kinematics.IMP_PROGRESS
227 IMP_TERSE = _IMP_kinematics.IMP_TERSE
228 IMP_VERBOSE = _IMP_kinematics.IMP_VERBOSE
229 IMP_MEMORY = _IMP_kinematics.IMP_MEMORY
230 IMP_NONE = _IMP_kinematics.IMP_NONE
231 IMP_USAGE = _IMP_kinematics.IMP_USAGE
232 IMP_INTERNAL = _IMP_kinematics.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_kinematics.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_kinematics.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kinematics.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_kinematics.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kinematics.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_kinematics.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_kinematics._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_kinematics._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_kinematics.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_kinematics.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_kinematics.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_kinematics.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_kinematics.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_kinematics.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_kinematics.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_kinematics.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_CORE_HAS_IMP_CGAL = _IMP_kinematics.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_kinematics.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_kinematics.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_kinematics.IMPCORE_SHOW_WARNINGS
330 import IMP.core
331 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_CGAL
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_DISPLAY
334 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_KERNEL
335 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
336 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
337 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_RANDOM
339 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_SYSTEM
340 IMP_CONTAINER_HAS_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_CGAL
341 IMP_CONTAINER_HAS_HDF5 = _IMP_kinematics.IMP_CONTAINER_HAS_HDF5
342 IMPCONTAINER_SHOW_WARNINGS = _IMP_kinematics.IMPCONTAINER_SHOW_WARNINGS
343 import IMP.container
344 IMP_ATOM_HAS_IMP_CGAL = _IMP_kinematics.IMP_ATOM_HAS_IMP_CGAL
345 IMP_ATOM_HAS_IMP_KERNEL = _IMP_kinematics.IMP_ATOM_HAS_IMP_KERNEL
346 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
347 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
348 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_RANDOM
349 IMP_ATOM_HAS_BOOST_REGEX = _IMP_kinematics.IMP_ATOM_HAS_BOOST_REGEX
350 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_SYSTEM
351 IMP_ATOM_HAS_CGAL = _IMP_kinematics.IMP_ATOM_HAS_CGAL
352 IMP_ATOM_HAS_HDF5 = _IMP_kinematics.IMP_ATOM_HAS_HDF5
353 IMPATOM_SHOW_WARNINGS = _IMP_kinematics.IMPATOM_SHOW_WARNINGS
354 IMP_ATOM_TYPE_INDEX = _IMP_kinematics.IMP_ATOM_TYPE_INDEX
355 IMP_RESIDUE_TYPE_INDEX = _IMP_kinematics.IMP_RESIDUE_TYPE_INDEX
356 IMP_HIERARCHY_TYPE_INDEX = _IMP_kinematics.IMP_HIERARCHY_TYPE_INDEX
357 import IMP.atom
358 IMP_SAXS_HAS_IMP_CGAL = _IMP_kinematics.IMP_SAXS_HAS_IMP_CGAL
359 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_kinematics.IMP_SAXS_HAS_IMP_CONTAINER
360 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_SAXS_HAS_IMP_DISPLAY
361 IMP_SAXS_HAS_IMP_KERNEL = _IMP_kinematics.IMP_SAXS_HAS_IMP_KERNEL
362 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
363 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_FILESYSTEM
364 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
365 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_RANDOM
366 IMP_SAXS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_SAXS_HAS_BOOST_REGEX
367 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_SYSTEM
368 IMP_SAXS_HAS_CGAL = _IMP_kinematics.IMP_SAXS_HAS_CGAL
369 IMP_SAXS_HAS_HDF5 = _IMP_kinematics.IMP_SAXS_HAS_HDF5
370 IMPSAXS_SHOW_WARNINGS = _IMP_kinematics.IMPSAXS_SHOW_WARNINGS
371 import IMP.saxs
372 IMP_KINEMATICS_HAS_IMP_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_CGAL
373 IMP_KINEMATICS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_DISPLAY
374 IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR
375 IMP_KINEMATICS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_FILESYSTEM
376 IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS
377 IMP_KINEMATICS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_RANDOM
378 IMP_KINEMATICS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_REGEX
379 IMP_KINEMATICS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_SYSTEM
380 IMP_KINEMATICS_HAS_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_CGAL
381 IMP_KINEMATICS_HAS_HDF5 = _IMP_kinematics.IMP_KINEMATICS_HAS_HDF5
382 IMPKINEMATICS_SHOW_WARNINGS = _IMP_kinematics.IMPKINEMATICS_SHOW_WARNINGS
383 
384 _object_types.append("Joint")
385 
386 
387 def _object_cast_to_Joint(o):
388  """_object_cast_to_Joint(Object o) -> Joint"""
389  return _IMP_kinematics._object_cast_to_Joint(o)
390 
391 _object_types.append("TransformationJoint")
392 
393 
394 def _object_cast_to_TransformationJoint(o):
395  """_object_cast_to_TransformationJoint(Object o) -> TransformationJoint"""
396  return _IMP_kinematics._object_cast_to_TransformationJoint(o)
397 
398 _object_types.append("RevoluteJoint")
399 
400 
401 def _object_cast_to_RevoluteJoint(o):
402  """_object_cast_to_RevoluteJoint(Object o) -> RevoluteJoint"""
403  return _IMP_kinematics._object_cast_to_RevoluteJoint(o)
404 
405 _object_types.append("DihedralAngleRevoluteJoint")
406 
407 
408 def _object_cast_to_DihedralAngleRevoluteJoint(o):
409  """_object_cast_to_DihedralAngleRevoluteJoint(Object o) -> DihedralAngleRevoluteJoint"""
410  return _IMP_kinematics._object_cast_to_DihedralAngleRevoluteJoint(o)
411 
412 _object_types.append("BondAngleRevoluteJoint")
413 
414 
415 def _object_cast_to_BondAngleRevoluteJoint(o):
416  """_object_cast_to_BondAngleRevoluteJoint(Object o) -> BondAngleRevoluteJoint"""
417  return _IMP_kinematics._object_cast_to_BondAngleRevoluteJoint(o)
418 
419 _object_types.append("PrismaticJoint")
420 
421 
422 def _object_cast_to_PrismaticJoint(o):
423  """_object_cast_to_PrismaticJoint(Object o) -> PrismaticJoint"""
424  return _IMP_kinematics._object_cast_to_PrismaticJoint(o)
425 
426 _object_types.append("KinematicForest")
427 
428 
429 def _object_cast_to_KinematicForest(o):
430  """_object_cast_to_KinematicForest(Object o) -> KinematicForest"""
431  return _IMP_kinematics._object_cast_to_KinematicForest(o)
432 
433 _object_types.append("KinematicForestScoreState")
434 
435 
436 def _object_cast_to_KinematicForestScoreState(o):
437  """_object_cast_to_KinematicForestScoreState(Object o) -> KinematicForestScoreState"""
438  return _IMP_kinematics._object_cast_to_KinematicForestScoreState(o)
439 
440 _object_types.append("CompositeJoint")
441 
442 
443 def _object_cast_to_CompositeJoint(o):
444  """_object_cast_to_CompositeJoint(Object o) -> CompositeJoint"""
445  return _IMP_kinematics._object_cast_to_CompositeJoint(o)
446 
447 _object_types.append("RevoluteJointMover")
448 
449 
450 def _object_cast_to_RevoluteJointMover(o):
451  """_object_cast_to_RevoluteJointMover(Object o) -> RevoluteJointMover"""
452  return _IMP_kinematics._object_cast_to_RevoluteJointMover(o)
453 
454 _object_types.append("DOF")
455 
456 
457 def _object_cast_to_DOF(o):
458  """_object_cast_to_DOF(Object o) -> DOF"""
459  return _IMP_kinematics._object_cast_to_DOF(o)
460 
461 DOFValuesList=list
462 _plural_types.append("DOFValuesList")
463 _value_types.append("DOFValues")
464 
465 
466 _object_types.append("DirectionalDOF")
467 
468 
469 def _object_cast_to_DirectionalDOF(o):
470  """_object_cast_to_DirectionalDOF(Object o) -> DirectionalDOF"""
471  return _IMP_kinematics._object_cast_to_DirectionalDOF(o)
472 
473 _object_types.append("DOFsSampler")
474 
475 
476 def _object_cast_to_DOFsSampler(o):
477  """_object_cast_to_DOFsSampler(Object o) -> DOFsSampler"""
478  return _IMP_kinematics._object_cast_to_DOFsSampler(o)
479 
480 _object_types.append("UniformBackboneSampler")
481 
482 
483 def _object_cast_to_UniformBackboneSampler(o):
484  """_object_cast_to_UniformBackboneSampler(Object o) -> UniformBackboneSampler"""
485  return _IMP_kinematics._object_cast_to_UniformBackboneSampler(o)
486 
487 _object_types.append("ProteinKinematics")
488 
489 
490 def _object_cast_to_ProteinKinematics(o):
491  """_object_cast_to_ProteinKinematics(Object o) -> ProteinKinematics"""
492  return _IMP_kinematics._object_cast_to_ProteinKinematics(o)
493 
494 _object_types.append("LocalPlanner")
495 
496 
497 def _object_cast_to_LocalPlanner(o):
498  """_object_cast_to_LocalPlanner(Object o) -> LocalPlanner"""
499  return _IMP_kinematics._object_cast_to_LocalPlanner(o)
500 
501 _object_types.append("PathLocalPlanner")
502 
503 
504 def _object_cast_to_PathLocalPlanner(o):
505  """_object_cast_to_PathLocalPlanner(Object o) -> PathLocalPlanner"""
506  return _IMP_kinematics._object_cast_to_PathLocalPlanner(o)
507 
508 _object_types.append("RRT")
509 
510 
511 def _object_cast_to_RRT(o):
512  """_object_cast_to_RRT(Object o) -> RRT"""
513  return _IMP_kinematics._object_cast_to_RRT(o)
514 class Joint(IMP.Object):
515  """Proxy of C++ IMP::kinematics::Joint class."""
516 
517  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
518 
519  def get_version_info(self):
520  """get_version_info(Joint self) -> VersionInfo"""
521  return _IMP_kinematics.Joint_get_version_info(self)
522 
523 
524  def __init__(self, parent, child):
525  """__init__(IMP::kinematics::Joint self, RigidBody parent, RigidBody child) -> Joint"""
526  this = _IMP_kinematics.new_Joint(parent, child)
527  try:
528  self.this.append(this)
529  except __builtin__.Exception:
530  self.this = this
531 
532  def get_owner_kf(self):
533  """get_owner_kf(Joint self) -> KinematicForest"""
534  return _IMP_kinematics.Joint_get_owner_kf(self)
535 
536 
537  def get_transformation_child_to_parent(self):
538  """get_transformation_child_to_parent(Joint self) -> Transformation3D"""
539  return _IMP_kinematics.Joint_get_transformation_child_to_parent(self)
540 
541 
542  def get_parent_node(self):
543  """get_parent_node(Joint self) -> RigidBody"""
544  return _IMP_kinematics.Joint_get_parent_node(self)
545 
546 
547  def get_child_node(self):
548  """get_child_node(Joint self) -> RigidBody"""
549  return _IMP_kinematics.Joint_get_child_node(self)
550 
551 
552  def __str__(self):
553  """__str__(Joint self) -> std::string"""
554  return _IMP_kinematics.Joint___str__(self)
555 
556 
557  def __repr__(self):
558  """__repr__(Joint self) -> std::string"""
559  return _IMP_kinematics.Joint___repr__(self)
560 
561 
562  @staticmethod
563  def get_from(o):
564  return _object_cast_to_Joint(o)
565 
566 Joint_swigregister = _IMP_kinematics.Joint_swigregister
567 Joint_swigregister(Joint)
568 
569 class TransformationJoint(Joint):
570  """Proxy of C++ IMP::kinematics::TransformationJoint class."""
571 
572  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
573 
574  def __init__(self, parent, child):
575  """__init__(IMP::kinematics::TransformationJoint self, RigidBody parent, RigidBody child) -> TransformationJoint"""
576  this = _IMP_kinematics.new_TransformationJoint(parent, child)
577  try:
578  self.this.append(this)
579  except __builtin__.Exception:
580  self.this = this
581 
582  def set_transformation_child_to_parent(self, transformation):
583  """set_transformation_child_to_parent(TransformationJoint self, Transformation3D transformation)"""
584  return _IMP_kinematics.TransformationJoint_set_transformation_child_to_parent(self, transformation)
585 
586 
587  def __str__(self):
588  """__str__(TransformationJoint self) -> std::string"""
589  return _IMP_kinematics.TransformationJoint___str__(self)
590 
591 
592  def __repr__(self):
593  """__repr__(TransformationJoint self) -> std::string"""
594  return _IMP_kinematics.TransformationJoint___repr__(self)
595 
596 
597  @staticmethod
598  def get_from(o):
599  return _object_cast_to_TransformationJoint(o)
600 
601  __swig_destroy__ = _IMP_kinematics.delete_TransformationJoint
602  __del__ = lambda self: None
603 TransformationJoint_swigregister = _IMP_kinematics.TransformationJoint_swigregister
604 TransformationJoint_swigregister(TransformationJoint)
605 
606 class PrismaticJoint(Joint):
607  """Proxy of C++ IMP::kinematics::PrismaticJoint class."""
608 
609  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
610 
611  def __init__(self, *args):
612  """
613  __init__(IMP::kinematics::PrismaticJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b) -> PrismaticJoint
614  __init__(IMP::kinematics::PrismaticJoint self, RigidBody parent, RigidBody child) -> PrismaticJoint
615  """
616  this = _IMP_kinematics.new_PrismaticJoint(*args)
617  try:
618  self.this.append(this)
619  except __builtin__.Exception:
620  self.this = this
621 
622  def get_length(self):
623  """get_length(PrismaticJoint self) -> double"""
624  return _IMP_kinematics.PrismaticJoint_get_length(self)
625 
626 
627  def set_length(self, l):
628  """set_length(PrismaticJoint self, double l)"""
629  return _IMP_kinematics.PrismaticJoint_set_length(self, l)
630 
631 
632  def __str__(self):
633  """__str__(PrismaticJoint self) -> std::string"""
634  return _IMP_kinematics.PrismaticJoint___str__(self)
635 
636 
637  def __repr__(self):
638  """__repr__(PrismaticJoint self) -> std::string"""
639  return _IMP_kinematics.PrismaticJoint___repr__(self)
640 
641 
642  @staticmethod
643  def get_from(o):
644  return _object_cast_to_PrismaticJoint(o)
645 
646  __swig_destroy__ = _IMP_kinematics.delete_PrismaticJoint
647  __del__ = lambda self: None
648 PrismaticJoint_swigregister = _IMP_kinematics.PrismaticJoint_swigregister
649 PrismaticJoint_swigregister(PrismaticJoint)
650 
651 class CompositeJoint(Joint):
652  """Proxy of C++ IMP::kinematics::CompositeJoint class."""
653 
654  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
655 
656  def __init__(self, *args):
657  """
658  __init__(IMP::kinematics::CompositeJoint self, RigidBody parent, RigidBody child, IMP::kinematics::Joints joints) -> CompositeJoint
659  __init__(IMP::kinematics::CompositeJoint self, RigidBody parent, RigidBody child) -> CompositeJoint
660  """
661  this = _IMP_kinematics.new_CompositeJoint(*args)
662  try:
663  self.this.append(this)
664  except __builtin__.Exception:
665  self.this = this
666 
667  def add_downstream_joint(self, j):
668  """add_downstream_joint(CompositeJoint self, Joint j)"""
669  return _IMP_kinematics.CompositeJoint_add_downstream_joint(self, j)
670 
671 
672  def add_upstream_joint(self, j):
673  """add_upstream_joint(CompositeJoint self, Joint j)"""
674  return _IMP_kinematics.CompositeJoint_add_upstream_joint(self, j)
675 
676 
677  def set_joints(self, joints):
678  """set_joints(CompositeJoint self, IMP::kinematics::Joints joints)"""
679  return _IMP_kinematics.CompositeJoint_set_joints(self, joints)
680 
681 
682  def get_inner_joints(self):
683  """get_inner_joints(CompositeJoint self) -> IMP::kinematics::Joints const &"""
684  return _IMP_kinematics.CompositeJoint_get_inner_joints(self)
685 
686 
687  def __str__(self):
688  """__str__(CompositeJoint self) -> std::string"""
689  return _IMP_kinematics.CompositeJoint___str__(self)
690 
691 
692  def __repr__(self):
693  """__repr__(CompositeJoint self) -> std::string"""
694  return _IMP_kinematics.CompositeJoint___repr__(self)
695 
696 
697  @staticmethod
698  def get_from(o):
699  return _object_cast_to_CompositeJoint(o)
700 
701  __swig_destroy__ = _IMP_kinematics.delete_CompositeJoint
702  __del__ = lambda self: None
703 CompositeJoint_swigregister = _IMP_kinematics.CompositeJoint_swigregister
704 CompositeJoint_swigregister(CompositeJoint)
705 
706 class RevoluteJoint(Joint):
707  """Proxy of C++ IMP::kinematics::RevoluteJoint class."""
708 
709  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
710 
711  def __init__(self, parent, child):
712  """__init__(IMP::kinematics::RevoluteJoint self, RigidBody parent, RigidBody child) -> RevoluteJoint"""
713  if self.__class__ == RevoluteJoint:
714  _self = None
715  else:
716  _self = self
717  this = _IMP_kinematics.new_RevoluteJoint(_self, parent, child)
718  try:
719  self.this.append(this)
720  except __builtin__.Exception:
721  self.this = this
722 
723  if self.__class__ != RevoluteJoint:
724  _director_objects.register(self)
725 
726 
727 
728  __swig_destroy__ = _IMP_kinematics.delete_RevoluteJoint
729  __del__ = lambda self: None
730 
731  def set_angle(self, angle):
732  """set_angle(RevoluteJoint self, double angle)"""
733  return _IMP_kinematics.RevoluteJoint_set_angle(self, angle)
734 
735 
736  def get_angle(self):
737  """get_angle(RevoluteJoint self) -> double"""
738  return _IMP_kinematics.RevoluteJoint_get_angle(self)
739 
740 
741  def get_rot_axis_origin(self):
742  """get_rot_axis_origin(RevoluteJoint self) -> Vector3D"""
743  return _IMP_kinematics.RevoluteJoint_get_rot_axis_origin(self)
744 
745 
746  def get_rot_axis_unit_vector(self):
747  """get_rot_axis_unit_vector(RevoluteJoint self) -> Vector3D"""
748  return _IMP_kinematics.RevoluteJoint_get_rot_axis_unit_vector(self)
749 
750 
751  def update_child_node_reference_frame(self):
752  """update_child_node_reference_frame(RevoluteJoint self)"""
753  return _IMP_kinematics.RevoluteJoint_update_child_node_reference_frame(self)
754 
755 
756  def update_axis_of_rotation_from_cartesian_witnesses(self):
757  """update_axis_of_rotation_from_cartesian_witnesses(RevoluteJoint self)"""
758  return _IMP_kinematics.RevoluteJoint_update_axis_of_rotation_from_cartesian_witnesses(self)
759 
760 
761  def get_current_angle_from_cartesian_witnesses(self):
762  """get_current_angle_from_cartesian_witnesses(RevoluteJoint self) -> double"""
763  return _IMP_kinematics.RevoluteJoint_get_current_angle_from_cartesian_witnesses(self)
764 
765 
766  def update_joint_from_cartesian_witnesses(self):
767  """update_joint_from_cartesian_witnesses(RevoluteJoint self)"""
768  return _IMP_kinematics.RevoluteJoint_update_joint_from_cartesian_witnesses(self)
769 
770 
771  def get_rotation_about_joint_in_parent_coordinates(self):
772  """get_rotation_about_joint_in_parent_coordinates(RevoluteJoint self) -> Transformation3D"""
773  return _IMP_kinematics.RevoluteJoint_get_rotation_about_joint_in_parent_coordinates(self)
774 
775  angle_ = _swig_property(_IMP_kinematics.RevoluteJoint_angle__get, _IMP_kinematics.RevoluteJoint_angle__set)
776  last_updated_angle_ = _swig_property(_IMP_kinematics.RevoluteJoint_last_updated_angle__get, _IMP_kinematics.RevoluteJoint_last_updated_angle__set)
777  rot_axis_unit_vector_ = _swig_property(_IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__get, _IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__set)
778  rot_axis_origin_ = _swig_property(_IMP_kinematics.RevoluteJoint_rot_axis_origin__get, _IMP_kinematics.RevoluteJoint_rot_axis_origin__set)
779 
780  def __str__(self):
781  """__str__(RevoluteJoint self) -> std::string"""
782  return _IMP_kinematics.RevoluteJoint___str__(self)
783 
784 
785  def __repr__(self):
786  """__repr__(RevoluteJoint self) -> std::string"""
787  return _IMP_kinematics.RevoluteJoint___repr__(self)
788 
789 
790  @staticmethod
791  def get_from(o):
792  return _object_cast_to_RevoluteJoint(o)
793 
794 
795  def get_type_name(self):
796  return self.__class__.__name__
797  def do_show(self, out):
798  pass
799  def get_version_info(self):
800  if"IMP::kinematics" == "IMP":
801  return VersionInfo(self.__module__,
802  __import__(self.__module__).get_module_version())
803  else:
804  return IMP.VersionInfo(self.__module__,
805  __import__(self.__module__).get_module_version())
806  @staticmethod
807  def get_from(o):
808  return _object_cast_to_RevoluteJoint(o)
809 
810  def __disown__(self):
811  self.this.disown()
812  _IMP_kinematics.disown_RevoluteJoint(self)
813  return weakref_proxy(self)
814 
815  def do_destroy(self):
816  """do_destroy(RevoluteJoint self)"""
817  return _IMP_kinematics.RevoluteJoint_do_destroy(self)
818 
819 RevoluteJoint_swigregister = _IMP_kinematics.RevoluteJoint_swigregister
820 RevoluteJoint_swigregister(RevoluteJoint)
821 
822 class DihedralAngleRevoluteJoint(RevoluteJoint):
823  """Proxy of C++ IMP::kinematics::DihedralAngleRevoluteJoint class."""
824 
825  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
826 
827  def __init__(self, parent, child, a, b, c, d):
828  """__init__(IMP::kinematics::DihedralAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c, XYZ d) -> DihedralAngleRevoluteJoint"""
829  this = _IMP_kinematics.new_DihedralAngleRevoluteJoint(parent, child, a, b, c, d)
830  try:
831  self.this.append(this)
832  except __builtin__.Exception:
833  self.this = this
834 
835  def get_a(self):
836  """get_a(DihedralAngleRevoluteJoint self) -> XYZ"""
837  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_a(self)
838 
839 
840  def get_b(self):
841  """get_b(DihedralAngleRevoluteJoint self) -> XYZ"""
842  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_b(self)
843 
844 
845  def get_c(self):
846  """get_c(DihedralAngleRevoluteJoint self) -> XYZ"""
847  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_c(self)
848 
849 
850  def get_d(self):
851  """get_d(DihedralAngleRevoluteJoint self) -> XYZ"""
852  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_d(self)
853 
854 
855  def __str__(self):
856  """__str__(DihedralAngleRevoluteJoint self) -> std::string"""
857  return _IMP_kinematics.DihedralAngleRevoluteJoint___str__(self)
858 
859 
860  def __repr__(self):
861  """__repr__(DihedralAngleRevoluteJoint self) -> std::string"""
862  return _IMP_kinematics.DihedralAngleRevoluteJoint___repr__(self)
863 
864 
865  @staticmethod
866  def get_from(o):
867  return _object_cast_to_DihedralAngleRevoluteJoint(o)
868 
869  __swig_destroy__ = _IMP_kinematics.delete_DihedralAngleRevoluteJoint
870  __del__ = lambda self: None
871 DihedralAngleRevoluteJoint_swigregister = _IMP_kinematics.DihedralAngleRevoluteJoint_swigregister
872 DihedralAngleRevoluteJoint_swigregister(DihedralAngleRevoluteJoint)
873 
874 class BondAngleRevoluteJoint(RevoluteJoint):
875  """Proxy of C++ IMP::kinematics::BondAngleRevoluteJoint class."""
876 
877  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
878 
879  def __init__(self, parent, child, a, b, c):
880  """__init__(IMP::kinematics::BondAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c) -> BondAngleRevoluteJoint"""
881  this = _IMP_kinematics.new_BondAngleRevoluteJoint(parent, child, a, b, c)
882  try:
883  self.this.append(this)
884  except __builtin__.Exception:
885  self.this = this
886 
887  def __str__(self):
888  """__str__(BondAngleRevoluteJoint self) -> std::string"""
889  return _IMP_kinematics.BondAngleRevoluteJoint___str__(self)
890 
891 
892  def __repr__(self):
893  """__repr__(BondAngleRevoluteJoint self) -> std::string"""
894  return _IMP_kinematics.BondAngleRevoluteJoint___repr__(self)
895 
896 
897  @staticmethod
898  def get_from(o):
899  return _object_cast_to_BondAngleRevoluteJoint(o)
900 
901  __swig_destroy__ = _IMP_kinematics.delete_BondAngleRevoluteJoint
902  __del__ = lambda self: None
903 BondAngleRevoluteJoint_swigregister = _IMP_kinematics.BondAngleRevoluteJoint_swigregister
904 BondAngleRevoluteJoint_swigregister(BondAngleRevoluteJoint)
905 
906 class RevoluteJointMover(IMP.core.MonteCarloMover):
907  """Proxy of C++ IMP::kinematics::RevoluteJointMover class."""
908 
909  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
910 
911  def __init__(self, m, joints, stddev=0.01):
912  """
913  __init__(IMP::kinematics::RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const stddev=0.01) -> RevoluteJointMover
914  __init__(IMP::kinematics::RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints) -> RevoluteJointMover
915  """
916  this = _IMP_kinematics.new_RevoluteJointMover(m, joints, stddev)
917  try:
918  self.this.append(this)
919  except __builtin__.Exception:
920  self.this = this
921 
922  def set_sigma(self, sigma):
923  """set_sigma(RevoluteJointMover self, IMP::Float sigma)"""
924  return _IMP_kinematics.RevoluteJointMover_set_sigma(self, sigma)
925 
926 
927  def get_sigma(self):
928  """get_sigma(RevoluteJointMover self) -> IMP::Float"""
929  return _IMP_kinematics.RevoluteJointMover_get_sigma(self)
930 
931 
932  def get_version_info(self):
933  """get_version_info(RevoluteJointMover self) -> VersionInfo"""
934  return _IMP_kinematics.RevoluteJointMover_get_version_info(self)
935 
936 
937  def __str__(self):
938  """__str__(RevoluteJointMover self) -> std::string"""
939  return _IMP_kinematics.RevoluteJointMover___str__(self)
940 
941 
942  def __repr__(self):
943  """__repr__(RevoluteJointMover self) -> std::string"""
944  return _IMP_kinematics.RevoluteJointMover___repr__(self)
945 
946 
947  @staticmethod
948  def get_from(o):
949  return _object_cast_to_RevoluteJointMover(o)
950 
951 RevoluteJointMover_swigregister = _IMP_kinematics.RevoluteJointMover_swigregister
952 RevoluteJointMover_swigregister(RevoluteJointMover)
953 
954 class KinematicForest(IMP.Object):
955  """Proxy of C++ IMP::kinematics::KinematicForest class."""
956 
957  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
958 
959  def get_version_info(self):
960  """get_version_info(KinematicForest self) -> VersionInfo"""
961  return _IMP_kinematics.KinematicForest_get_version_info(self)
962 
963 
964  def __init__(self, *args):
965  """
966  __init__(IMP::kinematics::KinematicForest self, Model m) -> KinematicForest
967  __init__(IMP::kinematics::KinematicForest self, Model m, Hierarchy hierarchy) -> KinematicForest
968  """
969  this = _IMP_kinematics.new_KinematicForest(*args)
970  try:
971  self.this.append(this)
972  except __builtin__.Exception:
973  self.this = this
974 
975  def add_edge(self, *args):
976  """
977  add_edge(KinematicForest self, RigidBody parent, RigidBody child) -> Joint
978  add_edge(KinematicForest self, Joint joint)
979  """
980  return _IMP_kinematics.KinematicForest_add_edge(self, *args)
981 
982 
983  def add_rigid_bodies_in_chain(self, rbs):
984  """add_rigid_bodies_in_chain(KinematicForest self, IMP::core::RigidBodies rbs)"""
985  return _IMP_kinematics.KinematicForest_add_rigid_bodies_in_chain(self, rbs)
986 
987 
988  def reset_root(self, new_root):
989  """reset_root(KinematicForest self, Particle new_root)"""
990  return _IMP_kinematics.KinematicForest_reset_root(self, new_root)
991 
992 
993  def update_all_internal_coordinates(self):
994  """update_all_internal_coordinates(KinematicForest self)"""
995  return _IMP_kinematics.KinematicForest_update_all_internal_coordinates(self)
996 
997 
998  def update_all_external_coordinates(self):
999  """update_all_external_coordinates(KinematicForest self)"""
1000  return _IMP_kinematics.KinematicForest_update_all_external_coordinates(self)
1001 
1002 
1003  def get_ordered_joints(self):
1004  """get_ordered_joints(KinematicForest self) -> IMP::kinematics::Joints"""
1005  return _IMP_kinematics.KinematicForest_get_ordered_joints(self)
1006 
1007 
1008  def mark_internal_coordinates_changed(self):
1009  """mark_internal_coordinates_changed(KinematicForest self)"""
1010  return _IMP_kinematics.KinematicForest_mark_internal_coordinates_changed(self)
1011 
1012 
1013  def mark_external_coordinates_changed(self):
1014  """mark_external_coordinates_changed(KinematicForest self)"""
1015  return _IMP_kinematics.KinematicForest_mark_external_coordinates_changed(self)
1016 
1017 
1018  def set_coordinates_safe(self, rb, c):
1019  """set_coordinates_safe(KinematicForest self, RigidBody rb, Vector3D c)"""
1020  return _IMP_kinematics.KinematicForest_set_coordinates_safe(self, rb, c)
1021 
1022 
1023  def get_coordinates_safe(self, rb):
1024  """get_coordinates_safe(KinematicForest self, RigidBody rb) -> Vector3D"""
1025  return _IMP_kinematics.KinematicForest_get_coordinates_safe(self, rb)
1026 
1027 
1028  def get_is_member(self, rb):
1029  """get_is_member(KinematicForest self, RigidBody rb) -> bool"""
1030  return _IMP_kinematics.KinematicForest_get_is_member(self, rb)
1031 
1032 
1033  def get_reference_frame_safe(self, rb):
1034  """get_reference_frame_safe(KinematicForest self, RigidBody rb) -> ReferenceFrame3D"""
1035  return _IMP_kinematics.KinematicForest_get_reference_frame_safe(self, rb)
1036 
1037 
1038  def set_reference_frame_safe(self, rb, r):
1039  """set_reference_frame_safe(KinematicForest self, RigidBody rb, ReferenceFrame3D r)"""
1040  return _IMP_kinematics.KinematicForest_set_reference_frame_safe(self, rb, r)
1041 
1042 
1043  def __str__(self):
1044  """__str__(KinematicForest self) -> std::string"""
1045  return _IMP_kinematics.KinematicForest___str__(self)
1046 
1047 
1048  def __repr__(self):
1049  """__repr__(KinematicForest self) -> std::string"""
1050  return _IMP_kinematics.KinematicForest___repr__(self)
1051 
1052 
1053  @staticmethod
1054  def get_from(o):
1055  return _object_cast_to_KinematicForest(o)
1056 
1057 KinematicForest_swigregister = _IMP_kinematics.KinematicForest_swigregister
1058 KinematicForest_swigregister(KinematicForest)
1059 
1060 class KinematicForestScoreState(IMP.ScoreState):
1061  """Proxy of C++ IMP::kinematics::KinematicForestScoreState class."""
1062 
1063  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1064 
1065  def get_version_info(self):
1066  """get_version_info(KinematicForestScoreState self) -> VersionInfo"""
1067  return _IMP_kinematics.KinematicForestScoreState_get_version_info(self)
1068 
1069 
1070  def __init__(self, kf, rbs, atoms):
1071  """__init__(IMP::kinematics::KinematicForestScoreState self, KinematicForest kf, IMP::core::RigidBodies rbs, IMP::ParticlesTemp atoms) -> KinematicForestScoreState"""
1072  this = _IMP_kinematics.new_KinematicForestScoreState(kf, rbs, atoms)
1073  try:
1074  self.this.append(this)
1075  except __builtin__.Exception:
1076  self.this = this
1077 
1078  def do_before_evaluate(self):
1079  """do_before_evaluate(KinematicForestScoreState self)"""
1080  return _IMP_kinematics.KinematicForestScoreState_do_before_evaluate(self)
1081 
1082 
1083  def do_after_evaluate(self, da):
1084  """do_after_evaluate(KinematicForestScoreState self, DerivativeAccumulator da)"""
1085  return _IMP_kinematics.KinematicForestScoreState_do_after_evaluate(self, da)
1086 
1087 
1088  def do_get_inputs(self):
1089  """do_get_inputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1090  return _IMP_kinematics.KinematicForestScoreState_do_get_inputs(self)
1091 
1092 
1093  def do_get_outputs(self):
1094  """do_get_outputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1095  return _IMP_kinematics.KinematicForestScoreState_do_get_outputs(self)
1096 
1097 
1098  def __str__(self):
1099  """__str__(KinematicForestScoreState self) -> std::string"""
1100  return _IMP_kinematics.KinematicForestScoreState___str__(self)
1101 
1102 
1103  def __repr__(self):
1104  """__repr__(KinematicForestScoreState self) -> std::string"""
1105  return _IMP_kinematics.KinematicForestScoreState___repr__(self)
1106 
1107 
1108  @staticmethod
1109  def get_from(o):
1110  return _object_cast_to_KinematicForestScoreState(o)
1111 
1112 KinematicForestScoreState_swigregister = _IMP_kinematics.KinematicForestScoreState_swigregister
1113 KinematicForestScoreState_swigregister(KinematicForestScoreState)
1114 
1115 class DOF(IMP.Object):
1116  """Proxy of C++ IMP::kinematics::DOF class."""
1117 
1118  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1119 
1120  def get_version_info(self):
1121  """get_version_info(DOF self) -> VersionInfo"""
1122  return _IMP_kinematics.DOF_get_version_info(self)
1123 
1124 
1125  def __init__(self, *args):
1126  """
1127  __init__(IMP::kinematics::DOF self, double v) -> DOF
1128  __init__(IMP::kinematics::DOF self, double v, double min, double max, double step_size) -> DOF
1129  """
1130  this = _IMP_kinematics.new_DOF(*args)
1131  try:
1132  self.this.append(this)
1133  except __builtin__.Exception:
1134  self.this = this
1135 
1136  def get_value(self):
1137  """get_value(DOF self) -> double"""
1138  return _IMP_kinematics.DOF_get_value(self)
1139 
1140 
1141  def set_value(self, v):
1142  """set_value(DOF self, double v)"""
1143  return _IMP_kinematics.DOF_set_value(self, v)
1144 
1145 
1146  def get_range(self):
1147  """get_range(DOF self) -> std::pair< double,double >"""
1148  return _IMP_kinematics.DOF_get_range(self)
1149 
1150 
1151  def set_range(self, range):
1152  """set_range(DOF self, std::pair< double,double > range)"""
1153  return _IMP_kinematics.DOF_set_range(self, range)
1154 
1155 
1156  def get_step_size(self):
1157  """get_step_size(DOF self) -> double"""
1158  return _IMP_kinematics.DOF_get_step_size(self)
1159 
1160 
1161  def set_step_size(self, step_size):
1162  """set_step_size(DOF self, double step_size)"""
1163  return _IMP_kinematics.DOF_set_step_size(self, step_size)
1164 
1165 
1166  def get_number_of_steps(self, *args):
1167  """
1168  get_number_of_steps(DOF self, double value) -> int
1169  get_number_of_steps(DOF self, double value1, double value2) -> int
1170  """
1171  return _IMP_kinematics.DOF_get_number_of_steps(self, *args)
1172 
1173 
1174  def __str__(self):
1175  """__str__(DOF self) -> std::string"""
1176  return _IMP_kinematics.DOF___str__(self)
1177 
1178 
1179  def __repr__(self):
1180  """__repr__(DOF self) -> std::string"""
1181  return _IMP_kinematics.DOF___repr__(self)
1182 
1183 
1184  @staticmethod
1185  def get_from(o):
1186  return _object_cast_to_DOF(o)
1187 
1188 DOF_swigregister = _IMP_kinematics.DOF_swigregister
1189 DOF_swigregister(DOF)
1190 
1191 class DOFValues(IMP.saxs.DistBase):
1192  """Proxy of C++ IMP::kinematics::DOFValues class."""
1193 
1194  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1195 
1196  def __init__(self, *args):
1197  """
1198  __init__(IMP::kinematics::DOFValues self, IMP::kinematics::DOFs const & dofs) -> DOFValues
1199  __init__(IMP::kinematics::DOFValues self) -> DOFValues
1200  """
1201  this = _IMP_kinematics.new_DOFValues(*args)
1202  try:
1203  self.this.append(this)
1204  except __builtin__.Exception:
1205  self.this = this
1206 
1207  def get_distance2(self, *args):
1208  """
1209  get_distance2(DOFValues self, DOFValues other_dof_values) -> double
1210  get_distance2(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1211  """
1212  return _IMP_kinematics.DOFValues_get_distance2(self, *args)
1213 
1214 
1215  def get_distance(self, *args):
1216  """
1217  get_distance(DOFValues self, DOFValues other_dof_values) -> double
1218  get_distance(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1219  """
1220  return _IMP_kinematics.DOFValues_get_distance(self, *args)
1221 
1222 
1223  def show(self, *args):
1224  """
1225  show(DOFValues self, _ostream out)
1226  show(DOFValues self)
1227  """
1228  return _IMP_kinematics.DOFValues_show(self, *args)
1229 
1230 
1231  def __str__(self):
1232  """__str__(DOFValues self) -> std::string"""
1233  return _IMP_kinematics.DOFValues___str__(self)
1234 
1235 
1236  def __repr__(self):
1237  """__repr__(DOFValues self) -> std::string"""
1238  return _IMP_kinematics.DOFValues___repr__(self)
1239 
1240  __swig_destroy__ = _IMP_kinematics.delete_DOFValues
1241  __del__ = lambda self: None
1242 DOFValues_swigregister = _IMP_kinematics.DOFValues_swigregister
1243 DOFValues_swigregister(DOFValues)
1244 
1245 class DirectionalDOF(IMP.Object):
1246  """Proxy of C++ IMP::kinematics::DirectionalDOF class."""
1247 
1248  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1249 
1250  def __init__(self, dofs):
1251  """__init__(IMP::kinematics::DirectionalDOF self, IMP::kinematics::DOFs const & dofs) -> DirectionalDOF"""
1252  this = _IMP_kinematics.new_DirectionalDOF(dofs)
1253  try:
1254  self.this.append(this)
1255  except __builtin__.Exception:
1256  self.this = this
1257 
1258  def set_end_points(self, q1, q2):
1259  """set_end_points(DirectionalDOF self, DOFValues q1, DOFValues q2)"""
1260  return _IMP_kinematics.DirectionalDOF_set_end_points(self, q1, q2)
1261 
1262 
1263  def get_dofs_values(self):
1264  """get_dofs_values(DirectionalDOF self) -> DOFValues"""
1265  return _IMP_kinematics.DirectionalDOF_get_dofs_values(self)
1266 
1267 
1268  def get_value(self):
1269  """get_value(DirectionalDOF self) -> double"""
1270  return _IMP_kinematics.DirectionalDOF_get_value(self)
1271 
1272 
1273  def get_version_info(self):
1274  """get_version_info(DirectionalDOF self) -> VersionInfo"""
1275  return _IMP_kinematics.DirectionalDOF_get_version_info(self)
1276 
1277 
1278  def __str__(self):
1279  """__str__(DirectionalDOF self) -> std::string"""
1280  return _IMP_kinematics.DirectionalDOF___str__(self)
1281 
1282 
1283  def __repr__(self):
1284  """__repr__(DirectionalDOF self) -> std::string"""
1285  return _IMP_kinematics.DirectionalDOF___repr__(self)
1286 
1287 
1288  @staticmethod
1289  def get_from(o):
1290  return _object_cast_to_DirectionalDOF(o)
1291 
1292 DirectionalDOF_swigregister = _IMP_kinematics.DirectionalDOF_swigregister
1293 DirectionalDOF_swigregister(DirectionalDOF)
1294 
1295 class DOFsSampler(IMP.Object):
1296  """Proxy of C++ IMP::kinematics::DOFsSampler class."""
1297 
1298  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1299 
1300  def get_type_name(self):
1301  """get_type_name(DOFsSampler self) -> std::string"""
1302  return _IMP_kinematics.DOFsSampler_get_type_name(self)
1303 
1304 
1305  def get_version_info(self):
1306  """get_version_info(DOFsSampler self) -> VersionInfo"""
1307  return _IMP_kinematics.DOFsSampler_get_version_info(self)
1308 
1309 
1310  def __init__(self, dofs):
1311  """__init__(IMP::kinematics::DOFsSampler self, IMP::kinematics::DOFs dofs) -> DOFsSampler"""
1312  if self.__class__ == DOFsSampler:
1313  _self = None
1314  else:
1315  _self = self
1316  this = _IMP_kinematics.new_DOFsSampler(_self, dofs)
1317  try:
1318  self.this.append(this)
1319  except __builtin__.Exception:
1320  self.this = this
1321 
1322  if self.__class__ != DOFsSampler:
1323  _director_objects.register(self)
1324 
1325 
1326 
1327 
1328  def get_sample(self):
1329  """get_sample(DOFsSampler self) -> DOFValues"""
1330  return _IMP_kinematics.DOFsSampler_get_sample(self)
1331 
1332 
1333  def apply(self, values):
1334  """apply(DOFsSampler self, DOFValues values)"""
1335  return _IMP_kinematics.DOFsSampler_apply(self, values)
1336 
1337 
1338  def apply_last_sample(self):
1339  """apply_last_sample(DOFsSampler self)"""
1340  return _IMP_kinematics.DOFsSampler_apply_last_sample(self)
1341 
1342 
1343  def sample_and_apply(self):
1344  """sample_and_apply(DOFsSampler self)"""
1345  return _IMP_kinematics.DOFsSampler_sample_and_apply(self)
1346 
1347 
1348  def get_dofs(self):
1349  """get_dofs(DOFsSampler self) -> IMP::kinematics::DOFs const &"""
1350  return _IMP_kinematics.DOFsSampler_get_dofs(self)
1351 
1352 
1353  def get_dof(self, i):
1354  """get_dof(DOFsSampler self, unsigned int i) -> DOF"""
1355  return _IMP_kinematics.DOFsSampler_get_dof(self, i)
1356 
1357 
1358  def get_number_of_dofs(self):
1359  """get_number_of_dofs(DOFsSampler self) -> unsigned int"""
1360  return _IMP_kinematics.DOFsSampler_get_number_of_dofs(self)
1361 
1362 
1363  def do_get_sample(self):
1364  """do_get_sample(DOFsSampler self) -> DOFValues"""
1365  return _IMP_kinematics.DOFsSampler_do_get_sample(self)
1366 
1367 
1368  def __str__(self):
1369  """__str__(DOFsSampler self) -> std::string"""
1370  return _IMP_kinematics.DOFsSampler___str__(self)
1371 
1372 
1373  def __repr__(self):
1374  """__repr__(DOFsSampler self) -> std::string"""
1375  return _IMP_kinematics.DOFsSampler___repr__(self)
1376 
1377 
1378  @staticmethod
1379  def get_from(o):
1380  return _object_cast_to_DOFsSampler(o)
1381 
1382 
1383  def get_type_name(self):
1384  return self.__class__.__name__
1385  def do_show(self, out):
1386  pass
1387  def get_version_info(self):
1388  if"IMP::kinematics" == "IMP":
1389  return VersionInfo(self.__module__,
1390  __import__(self.__module__).get_module_version())
1391  else:
1392  return IMP.VersionInfo(self.__module__,
1393  __import__(self.__module__).get_module_version())
1394  @staticmethod
1395  def get_from(o):
1396  return _object_cast_to_DOFsSampler(o)
1397 
1398  def __disown__(self):
1399  self.this.disown()
1400  _IMP_kinematics.disown_DOFsSampler(self)
1401  return weakref_proxy(self)
1402 
1403  def do_destroy(self):
1404  """do_destroy(DOFsSampler self)"""
1405  return _IMP_kinematics.DOFsSampler_do_destroy(self)
1406 
1407 DOFsSampler_swigregister = _IMP_kinematics.DOFsSampler_swigregister
1408 DOFsSampler_swigregister(DOFsSampler)
1409 
1410 class UniformBackboneSampler(DOFsSampler):
1411  """Proxy of C++ IMP::kinematics::UniformBackboneSampler class."""
1412 
1413  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1414 
1415  def __init__(self, joints, dofs):
1416  """__init__(IMP::kinematics::UniformBackboneSampler self, IMP::kinematics::DihedralAngleRevoluteJoints joints, IMP::kinematics::DOFs dofs) -> UniformBackboneSampler"""
1417  this = _IMP_kinematics.new_UniformBackboneSampler(joints, dofs)
1418  try:
1419  self.this.append(this)
1420  except __builtin__.Exception:
1421  self.this = this
1422 
1423  def __str__(self):
1424  """__str__(UniformBackboneSampler self) -> std::string"""
1425  return _IMP_kinematics.UniformBackboneSampler___str__(self)
1426 
1427 
1428  def __repr__(self):
1429  """__repr__(UniformBackboneSampler self) -> std::string"""
1430  return _IMP_kinematics.UniformBackboneSampler___repr__(self)
1431 
1432 
1433  @staticmethod
1434  def get_from(o):
1435  return _object_cast_to_UniformBackboneSampler(o)
1436 
1437  __swig_destroy__ = _IMP_kinematics.delete_UniformBackboneSampler
1438  __del__ = lambda self: None
1439 UniformBackboneSampler_swigregister = _IMP_kinematics.UniformBackboneSampler_swigregister
1440 UniformBackboneSampler_swigregister(UniformBackboneSampler)
1441 
1442 class ProteinKinematics(IMP.Object):
1443  """Proxy of C++ IMP::kinematics::ProteinKinematics class."""
1444 
1445  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1446 
1447  def __init__(self, *args):
1448  """
1449  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1450  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True) -> ProteinKinematics
1451  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd) -> ProteinKinematics
1452  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles, IMP::atom::Atoms open_loop_bond_atoms, bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1453  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles, IMP::atom::Atoms open_loop_bond_atoms, bool flexible_backbone=True) -> ProteinKinematics
1454  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles, IMP::atom::Atoms open_loop_bond_atoms) -> ProteinKinematics
1455  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles) -> ProteinKinematics
1456  """
1457  this = _IMP_kinematics.new_ProteinKinematics(*args)
1458  try:
1459  self.this.append(this)
1460  except __builtin__.Exception:
1461  self.this = this
1462 
1463  def get_phi(self, r):
1464  """get_phi(ProteinKinematics self, Residue r) -> double"""
1465  return _IMP_kinematics.ProteinKinematics_get_phi(self, r)
1466 
1467 
1468  def get_psi(self, r):
1469  """get_psi(ProteinKinematics self, Residue r) -> double"""
1470  return _IMP_kinematics.ProteinKinematics_get_psi(self, r)
1471 
1472 
1473  def get_joints(self):
1474  """get_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1475  return _IMP_kinematics.ProteinKinematics_get_joints(self)
1476 
1477 
1478  def get_loop_joints(self):
1479  """get_loop_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1480  return _IMP_kinematics.ProteinKinematics_get_loop_joints(self)
1481 
1482 
1483  def get_ordered_joints(self):
1484  """get_ordered_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1485  return _IMP_kinematics.ProteinKinematics_get_ordered_joints(self)
1486 
1487 
1488  def get_kinematic_forest(self):
1489  """get_kinematic_forest(ProteinKinematics self) -> KinematicForest"""
1490  return _IMP_kinematics.ProteinKinematics_get_kinematic_forest(self)
1491 
1492 
1493  def get_rigid_bodies(self):
1494  """get_rigid_bodies(ProteinKinematics self) -> IMP::core::RigidBodies"""
1495  return _IMP_kinematics.ProteinKinematics_get_rigid_bodies(self)
1496 
1497 
1498  def set_phi(self, r, angle):
1499  """set_phi(ProteinKinematics self, Residue r, double angle)"""
1500  return _IMP_kinematics.ProteinKinematics_set_phi(self, r, angle)
1501 
1502 
1503  def set_psi(self, r, angle):
1504  """set_psi(ProteinKinematics self, Residue r, double angle)"""
1505  return _IMP_kinematics.ProteinKinematics_set_psi(self, r, angle)
1506 
1507 
1508  def get_version_info(self):
1509  """get_version_info(ProteinKinematics self) -> VersionInfo"""
1510  return _IMP_kinematics.ProteinKinematics_get_version_info(self)
1511 
1512 
1513  def __str__(self):
1514  """__str__(ProteinKinematics self) -> std::string"""
1515  return _IMP_kinematics.ProteinKinematics___str__(self)
1516 
1517 
1518  def __repr__(self):
1519  """__repr__(ProteinKinematics self) -> std::string"""
1520  return _IMP_kinematics.ProteinKinematics___repr__(self)
1521 
1522 
1523  @staticmethod
1524  def get_from(o):
1525  return _object_cast_to_ProteinKinematics(o)
1526 
1527 ProteinKinematics_swigregister = _IMP_kinematics.ProteinKinematics_swigregister
1528 ProteinKinematics_swigregister(ProteinKinematics)
1529 
1530 class LocalPlanner(IMP.Object):
1531  """Proxy of C++ IMP::kinematics::LocalPlanner class."""
1532 
1533  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1534 
1535  def __init__(self, *args, **kwargs):
1536  raise AttributeError("No constructor defined - class is abstract")
1537 
1538  def get_version_info(self):
1539  """get_version_info(LocalPlanner self) -> VersionInfo"""
1540  return _IMP_kinematics.LocalPlanner_get_version_info(self)
1541 
1542 
1543  def plan(self, q_near, q_rand, sf):
1544  """plan(LocalPlanner self, DOFValues q_near, DOFValues q_rand, ScoringFunction sf) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1545  return _IMP_kinematics.LocalPlanner_plan(self, q_near, q_rand, sf)
1546 
1547 
1548  def is_valid(self, values, sf):
1549  """is_valid(LocalPlanner self, DOFValues values, ScoringFunction sf) -> bool"""
1550  return _IMP_kinematics.LocalPlanner_is_valid(self, values, sf)
1551 
1552 
1553  def __str__(self):
1554  """__str__(LocalPlanner self) -> std::string"""
1555  return _IMP_kinematics.LocalPlanner___str__(self)
1556 
1557 
1558  def __repr__(self):
1559  """__repr__(LocalPlanner self) -> std::string"""
1560  return _IMP_kinematics.LocalPlanner___repr__(self)
1561 
1562 
1563  @staticmethod
1564  def get_from(o):
1565  return _object_cast_to_LocalPlanner(o)
1566 
1567 LocalPlanner_swigregister = _IMP_kinematics.LocalPlanner_swigregister
1568 LocalPlanner_swigregister(LocalPlanner)
1569 
1570 class PathLocalPlanner(LocalPlanner):
1571  """Proxy of C++ IMP::kinematics::PathLocalPlanner class."""
1572 
1573  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1574 
1575  def __init__(self, model, dofs_sampler, directional_dof, save_step_interval=1):
1576  """
1577  __init__(IMP::kinematics::PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof, int save_step_interval=1) -> PathLocalPlanner
1578  __init__(IMP::kinematics::PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof) -> PathLocalPlanner
1579  """
1580  this = _IMP_kinematics.new_PathLocalPlanner(model, dofs_sampler, directional_dof, save_step_interval)
1581  try:
1582  self.this.append(this)
1583  except __builtin__.Exception:
1584  self.this = this
1585 
1586  def __str__(self):
1587  """__str__(PathLocalPlanner self) -> std::string"""
1588  return _IMP_kinematics.PathLocalPlanner___str__(self)
1589 
1590 
1591  def __repr__(self):
1592  """__repr__(PathLocalPlanner self) -> std::string"""
1593  return _IMP_kinematics.PathLocalPlanner___repr__(self)
1594 
1595 
1596  @staticmethod
1597  def get_from(o):
1598  return _object_cast_to_PathLocalPlanner(o)
1599 
1600  __swig_destroy__ = _IMP_kinematics.delete_PathLocalPlanner
1601  __del__ = lambda self: None
1602 PathLocalPlanner_swigregister = _IMP_kinematics.PathLocalPlanner_swigregister
1603 PathLocalPlanner_swigregister(PathLocalPlanner)
1604 
1605 class RRT(IMP.Sampler):
1606  """Proxy of C++ IMP::kinematics::RRT class."""
1607 
1608  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1609 
1610  def get_version_info(self):
1611  """get_version_info(RRT self) -> VersionInfo"""
1612  return _IMP_kinematics.RRT_get_version_info(self)
1613 
1614 
1615  def __init__(self, m, sampler, planner, cspace_dofs, iteration_number=1000, tree_size=100, number_of_sampled_dofs=0):
1616  """
1617  __init__(IMP::kinematics::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
1618  __init__(IMP::kinematics::RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs, unsigned int iteration_number=1000, unsigned int tree_size=100) -> RRT
1619  __init__(IMP::kinematics::RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs, unsigned int iteration_number=1000) -> RRT
1620  __init__(IMP::kinematics::RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs) -> RRT
1621  """
1622  this = _IMP_kinematics.new_RRT(m, sampler, planner, cspace_dofs, iteration_number, tree_size, number_of_sampled_dofs)
1623  try:
1624  self.this.append(this)
1625  except __builtin__.Exception:
1626  self.this = this
1627 
1628  def do_sample(self):
1629  """do_sample(RRT self) -> ConfigurationSet"""
1630  return _IMP_kinematics.RRT_do_sample(self)
1631 
1632 
1633  def run(self, number_of_iterations=0):
1634  """
1635  run(RRT self, unsigned int number_of_iterations=0) -> bool
1636  run(RRT self) -> bool
1637  """
1638  return _IMP_kinematics.RRT_run(self, number_of_iterations)
1639 
1640 
1641  def get_DOFValues(self):
1642  """get_DOFValues(RRT self) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1643  return _IMP_kinematics.RRT_get_DOFValues(self)
1644 
1645 
1646  def set_number_of_iterations(self, num):
1647  """set_number_of_iterations(RRT self, unsigned int num)"""
1648  return _IMP_kinematics.RRT_set_number_of_iterations(self, num)
1649 
1650 
1651  def set_tree_size(self, num):
1652  """set_tree_size(RRT self, unsigned int num)"""
1653  return _IMP_kinematics.RRT_set_tree_size(self, num)
1654 
1655 
1656  def set_actual_tree_size(self, num):
1657  """set_actual_tree_size(RRT self, unsigned int num)"""
1658  return _IMP_kinematics.RRT_set_actual_tree_size(self, num)
1659 
1660 
1661  def set_number_of_collisions(self, num):
1662  """set_number_of_collisions(RRT self, unsigned int num)"""
1663  return _IMP_kinematics.RRT_set_number_of_collisions(self, num)
1664 
1665 
1666  def __str__(self):
1667  """__str__(RRT self) -> std::string"""
1668  return _IMP_kinematics.RRT___str__(self)
1669 
1670 
1671  def __repr__(self):
1672  """__repr__(RRT self) -> std::string"""
1673  return _IMP_kinematics.RRT___repr__(self)
1674 
1675 
1676  @staticmethod
1677  def get_from(o):
1678  return _object_cast_to_RRT(o)
1679 
1680 RRT_swigregister = _IMP_kinematics.RRT_swigregister
1681 RRT_swigregister(RRT)
1682 
1683 
1684 def get_module_version():
1685  """get_module_version() -> std::string const"""
1686  return _IMP_kinematics.get_module_version()
1687 
1688 def get_example_path(fname):
1689  """get_example_path(std::string fname) -> std::string"""
1690  return _IMP_kinematics.get_example_path(fname)
1691 
1692 def get_data_path(fname):
1693  """get_data_path(std::string fname) -> std::string"""
1694  return _IMP_kinematics.get_data_path(fname)
1695 
1696 from . import _version_check
1697 _version_check.check_version(get_module_version())
1698 __version__ = get_module_version()
1699 
1700 
1701 
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:231
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
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:28
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...
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
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.