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IMP Reference Guide  2.13.0
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 2007-2020 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_NUMPY = _IMP_kinematics.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kinematics.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_kinematics.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_kinematics._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_kinematics._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_kinematics.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_kinematics.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_kinematics.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_kinematics.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_kinematics.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_kinematics.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_kinematics.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_kinematics.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_kinematics.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_kinematics.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_kinematics.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_kinematics.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_CORE_HAS_IMP_CGAL = _IMP_kinematics.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CORE_HAS_IMP_KERNEL
329 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_FILESYSTEM
330 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
331 IMP_CORE_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CORE_HAS_BOOST_RANDOM
332 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_SYSTEM
333 IMP_CORE_HAS_CGAL = _IMP_kinematics.IMP_CORE_HAS_CGAL
334 IMP_CORE_HAS_HDF5 = _IMP_kinematics.IMP_CORE_HAS_HDF5
335 IMP_CORE_HAS_NUMPY = _IMP_kinematics.IMP_CORE_HAS_NUMPY
336 IMPCORE_SHOW_WARNINGS = _IMP_kinematics.IMPCORE_SHOW_WARNINGS
337 import IMP.core
338 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_ALGEBRA
339 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_CGAL
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_DISPLAY
341 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_KERNEL
342 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
343 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
344 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
345 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 IMP_CONTAINER_HAS_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_CGAL
348 IMP_CONTAINER_HAS_HDF5 = _IMP_kinematics.IMP_CONTAINER_HAS_HDF5
349 IMP_CONTAINER_HAS_NUMPY = _IMP_kinematics.IMP_CONTAINER_HAS_NUMPY
350 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_kinematics.IMP_CONTAINER_HAS_PYTHON_IHM
351 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
352 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_ROBIN_MAP
353 IMPCONTAINER_SHOW_WARNINGS = _IMP_kinematics.IMPCONTAINER_SHOW_WARNINGS
354 import IMP.container
355 IMP_ATOM_HAS_IMP_CGAL = _IMP_kinematics.IMP_ATOM_HAS_IMP_CGAL
356 IMP_ATOM_HAS_IMP_KERNEL = _IMP_kinematics.IMP_ATOM_HAS_IMP_KERNEL
357 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
358 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
359 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_RANDOM
360 IMP_ATOM_HAS_BOOST_REGEX = _IMP_kinematics.IMP_ATOM_HAS_BOOST_REGEX
361 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_SYSTEM
362 IMP_ATOM_HAS_CGAL = _IMP_kinematics.IMP_ATOM_HAS_CGAL
363 IMP_ATOM_HAS_HDF5 = _IMP_kinematics.IMP_ATOM_HAS_HDF5
364 IMP_ATOM_HAS_NUMPY = _IMP_kinematics.IMP_ATOM_HAS_NUMPY
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_kinematics.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_kinematics.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_kinematics.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_kinematics.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_kinematics.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_kinematics.IMP_CHAIN_TYPE_INDEX
371 import IMP.atom
372 IMP_SAXS_HAS_IMP_CGAL = _IMP_kinematics.IMP_SAXS_HAS_IMP_CGAL
373 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_kinematics.IMP_SAXS_HAS_IMP_CONTAINER
374 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_SAXS_HAS_IMP_DISPLAY
375 IMP_SAXS_HAS_IMP_KERNEL = _IMP_kinematics.IMP_SAXS_HAS_IMP_KERNEL
376 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
377 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_FILESYSTEM
378 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
379 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_RANDOM
380 IMP_SAXS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_SAXS_HAS_BOOST_REGEX
381 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_SYSTEM
382 IMP_SAXS_HAS_CGAL = _IMP_kinematics.IMP_SAXS_HAS_CGAL
383 IMP_SAXS_HAS_HDF5 = _IMP_kinematics.IMP_SAXS_HAS_HDF5
384 IMP_SAXS_HAS_NUMPY = _IMP_kinematics.IMP_SAXS_HAS_NUMPY
385 IMP_SAXS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_SAXS_HAS_PYTHON_IHM
386 IMPSAXS_SHOW_WARNINGS = _IMP_kinematics.IMPSAXS_SHOW_WARNINGS
387 import IMP.saxs
388 IMP_KINEMATICS_HAS_IMP_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_CGAL
389 IMP_KINEMATICS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_DISPLAY
390 IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR
391 IMP_KINEMATICS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_FILESYSTEM
392 IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS
393 IMP_KINEMATICS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_RANDOM
394 IMP_KINEMATICS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_REGEX
395 IMP_KINEMATICS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_SYSTEM
396 IMP_KINEMATICS_HAS_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_CGAL
397 IMP_KINEMATICS_HAS_HDF5 = _IMP_kinematics.IMP_KINEMATICS_HAS_HDF5
398 IMP_KINEMATICS_HAS_NUMPY = _IMP_kinematics.IMP_KINEMATICS_HAS_NUMPY
399 IMP_KINEMATICS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_KINEMATICS_HAS_PYTHON_IHM
400 IMPKINEMATICS_SHOW_WARNINGS = _IMP_kinematics.IMPKINEMATICS_SHOW_WARNINGS
401 
402 _object_types.append("Joint")
403 
404 
405 def _object_cast_to_Joint(o):
406  """_object_cast_to_Joint(Object o) -> Joint"""
407  return _IMP_kinematics._object_cast_to_Joint(o)
408 
409 _object_types.append("TransformationJoint")
410 
411 
412 def _object_cast_to_TransformationJoint(o):
413  """_object_cast_to_TransformationJoint(Object o) -> TransformationJoint"""
414  return _IMP_kinematics._object_cast_to_TransformationJoint(o)
415 
416 _object_types.append("RevoluteJoint")
417 
418 
419 def _object_cast_to_RevoluteJoint(o):
420  """_object_cast_to_RevoluteJoint(Object o) -> RevoluteJoint"""
421  return _IMP_kinematics._object_cast_to_RevoluteJoint(o)
422 
423 _object_types.append("DihedralAngleRevoluteJoint")
424 
425 
426 def _object_cast_to_DihedralAngleRevoluteJoint(o):
427  """_object_cast_to_DihedralAngleRevoluteJoint(Object o) -> DihedralAngleRevoluteJoint"""
428  return _IMP_kinematics._object_cast_to_DihedralAngleRevoluteJoint(o)
429 
430 _object_types.append("BondAngleRevoluteJoint")
431 
432 
433 def _object_cast_to_BondAngleRevoluteJoint(o):
434  """_object_cast_to_BondAngleRevoluteJoint(Object o) -> BondAngleRevoluteJoint"""
435  return _IMP_kinematics._object_cast_to_BondAngleRevoluteJoint(o)
436 
437 _object_types.append("PrismaticJoint")
438 
439 
440 def _object_cast_to_PrismaticJoint(o):
441  """_object_cast_to_PrismaticJoint(Object o) -> PrismaticJoint"""
442  return _IMP_kinematics._object_cast_to_PrismaticJoint(o)
443 
444 _object_types.append("KinematicForest")
445 
446 
447 def _object_cast_to_KinematicForest(o):
448  """_object_cast_to_KinematicForest(Object o) -> KinematicForest"""
449  return _IMP_kinematics._object_cast_to_KinematicForest(o)
450 
451 _object_types.append("KinematicForestScoreState")
452 
453 
454 def _object_cast_to_KinematicForestScoreState(o):
455  """_object_cast_to_KinematicForestScoreState(Object o) -> KinematicForestScoreState"""
456  return _IMP_kinematics._object_cast_to_KinematicForestScoreState(o)
457 
458 _object_types.append("CompositeJoint")
459 
460 
461 def _object_cast_to_CompositeJoint(o):
462  """_object_cast_to_CompositeJoint(Object o) -> CompositeJoint"""
463  return _IMP_kinematics._object_cast_to_CompositeJoint(o)
464 
465 _object_types.append("RevoluteJointMover")
466 
467 
468 def _object_cast_to_RevoluteJointMover(o):
469  """_object_cast_to_RevoluteJointMover(Object o) -> RevoluteJointMover"""
470  return _IMP_kinematics._object_cast_to_RevoluteJointMover(o)
471 
472 _object_types.append("DOF")
473 
474 
475 def _object_cast_to_DOF(o):
476  """_object_cast_to_DOF(Object o) -> DOF"""
477  return _IMP_kinematics._object_cast_to_DOF(o)
478 
479 DOFValuesList=list
480 _plural_types.append("DOFValuesList")
481 _value_types.append("DOFValues")
482 
483 
484 _object_types.append("DirectionalDOF")
485 
486 
487 def _object_cast_to_DirectionalDOF(o):
488  """_object_cast_to_DirectionalDOF(Object o) -> DirectionalDOF"""
489  return _IMP_kinematics._object_cast_to_DirectionalDOF(o)
490 
491 _object_types.append("DOFsSampler")
492 
493 
494 def _object_cast_to_DOFsSampler(o):
495  """_object_cast_to_DOFsSampler(Object o) -> DOFsSampler"""
496  return _IMP_kinematics._object_cast_to_DOFsSampler(o)
497 
498 _object_types.append("UniformBackboneSampler")
499 
500 
501 def _object_cast_to_UniformBackboneSampler(o):
502  """_object_cast_to_UniformBackboneSampler(Object o) -> UniformBackboneSampler"""
503  return _IMP_kinematics._object_cast_to_UniformBackboneSampler(o)
504 
505 _object_types.append("ProteinKinematics")
506 
507 
508 def _object_cast_to_ProteinKinematics(o):
509  """_object_cast_to_ProteinKinematics(Object o) -> ProteinKinematics"""
510  return _IMP_kinematics._object_cast_to_ProteinKinematics(o)
511 
512 _object_types.append("LocalPlanner")
513 
514 
515 def _object_cast_to_LocalPlanner(o):
516  """_object_cast_to_LocalPlanner(Object o) -> LocalPlanner"""
517  return _IMP_kinematics._object_cast_to_LocalPlanner(o)
518 
519 _object_types.append("PathLocalPlanner")
520 
521 
522 def _object_cast_to_PathLocalPlanner(o):
523  """_object_cast_to_PathLocalPlanner(Object o) -> PathLocalPlanner"""
524  return _IMP_kinematics._object_cast_to_PathLocalPlanner(o)
525 
526 _object_types.append("RRT")
527 
528 
529 def _object_cast_to_RRT(o):
530  """_object_cast_to_RRT(Object o) -> RRT"""
531  return _IMP_kinematics._object_cast_to_RRT(o)
532 class Joint(IMP.Object):
533  """Proxy of C++ IMP::kinematics::Joint class."""
534 
535  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
536 
537  def get_version_info(self):
538  """get_version_info(Joint self) -> VersionInfo"""
539  return _IMP_kinematics.Joint_get_version_info(self)
540 
541 
542  def __init__(self, parent, child):
543  """__init__(IMP::kinematics::Joint self, RigidBody parent, RigidBody child) -> Joint"""
544  this = _IMP_kinematics.new_Joint(parent, child)
545  try:
546  self.this.append(this)
547  except __builtin__.Exception:
548  self.this = this
549 
550  def get_owner_kf(self):
551  """get_owner_kf(Joint self) -> KinematicForest"""
552  return _IMP_kinematics.Joint_get_owner_kf(self)
553 
554 
555  def get_transformation_child_to_parent(self):
556  """get_transformation_child_to_parent(Joint self) -> Transformation3D"""
557  return _IMP_kinematics.Joint_get_transformation_child_to_parent(self)
558 
559 
560  def get_parent_node(self):
561  """get_parent_node(Joint self) -> RigidBody"""
562  return _IMP_kinematics.Joint_get_parent_node(self)
563 
564 
565  def get_child_node(self):
566  """get_child_node(Joint self) -> RigidBody"""
567  return _IMP_kinematics.Joint_get_child_node(self)
568 
569 
570  def __str__(self):
571  """__str__(Joint self) -> std::string"""
572  return _IMP_kinematics.Joint___str__(self)
573 
574 
575  def __repr__(self):
576  """__repr__(Joint self) -> std::string"""
577  return _IMP_kinematics.Joint___repr__(self)
578 
579 
580  @staticmethod
581  def get_from(o):
582  return _object_cast_to_Joint(o)
583 
584 Joint_swigregister = _IMP_kinematics.Joint_swigregister
585 Joint_swigregister(Joint)
586 
587 class TransformationJoint(Joint):
588  """Proxy of C++ IMP::kinematics::TransformationJoint class."""
589 
590  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
591 
592  def __init__(self, parent, child):
593  """__init__(IMP::kinematics::TransformationJoint self, RigidBody parent, RigidBody child) -> TransformationJoint"""
594  this = _IMP_kinematics.new_TransformationJoint(parent, child)
595  try:
596  self.this.append(this)
597  except __builtin__.Exception:
598  self.this = this
599 
600  def set_transformation_child_to_parent(self, transformation):
601  """set_transformation_child_to_parent(TransformationJoint self, Transformation3D transformation)"""
602  return _IMP_kinematics.TransformationJoint_set_transformation_child_to_parent(self, transformation)
603 
604 
605  def __str__(self):
606  """__str__(TransformationJoint self) -> std::string"""
607  return _IMP_kinematics.TransformationJoint___str__(self)
608 
609 
610  def __repr__(self):
611  """__repr__(TransformationJoint self) -> std::string"""
612  return _IMP_kinematics.TransformationJoint___repr__(self)
613 
614 
615  @staticmethod
616  def get_from(o):
617  return _object_cast_to_TransformationJoint(o)
618 
619  __swig_destroy__ = _IMP_kinematics.delete_TransformationJoint
620  __del__ = lambda self: None
621 TransformationJoint_swigregister = _IMP_kinematics.TransformationJoint_swigregister
622 TransformationJoint_swigregister(TransformationJoint)
623 
624 class PrismaticJoint(Joint):
625  """Proxy of C++ IMP::kinematics::PrismaticJoint class."""
626 
627  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
628 
629  def __init__(self, *args):
630  """
631  __init__(IMP::kinematics::PrismaticJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b) -> PrismaticJoint
632  __init__(IMP::kinematics::PrismaticJoint self, RigidBody parent, RigidBody child) -> PrismaticJoint
633  """
634  this = _IMP_kinematics.new_PrismaticJoint(*args)
635  try:
636  self.this.append(this)
637  except __builtin__.Exception:
638  self.this = this
639 
640  def get_length(self):
641  """get_length(PrismaticJoint self) -> double"""
642  return _IMP_kinematics.PrismaticJoint_get_length(self)
643 
644 
645  def set_length(self, l):
646  """set_length(PrismaticJoint self, double l)"""
647  return _IMP_kinematics.PrismaticJoint_set_length(self, l)
648 
649 
650  def __str__(self):
651  """__str__(PrismaticJoint self) -> std::string"""
652  return _IMP_kinematics.PrismaticJoint___str__(self)
653 
654 
655  def __repr__(self):
656  """__repr__(PrismaticJoint self) -> std::string"""
657  return _IMP_kinematics.PrismaticJoint___repr__(self)
658 
659 
660  @staticmethod
661  def get_from(o):
662  return _object_cast_to_PrismaticJoint(o)
663 
664  __swig_destroy__ = _IMP_kinematics.delete_PrismaticJoint
665  __del__ = lambda self: None
666 PrismaticJoint_swigregister = _IMP_kinematics.PrismaticJoint_swigregister
667 PrismaticJoint_swigregister(PrismaticJoint)
668 
669 class CompositeJoint(Joint):
670  """Proxy of C++ IMP::kinematics::CompositeJoint class."""
671 
672  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
673 
674  def __init__(self, *args):
675  """
676  __init__(IMP::kinematics::CompositeJoint self, RigidBody parent, RigidBody child, IMP::kinematics::Joints joints) -> CompositeJoint
677  __init__(IMP::kinematics::CompositeJoint self, RigidBody parent, RigidBody child) -> CompositeJoint
678  """
679  this = _IMP_kinematics.new_CompositeJoint(*args)
680  try:
681  self.this.append(this)
682  except __builtin__.Exception:
683  self.this = this
684 
685  def add_downstream_joint(self, j):
686  """add_downstream_joint(CompositeJoint self, Joint j)"""
687  return _IMP_kinematics.CompositeJoint_add_downstream_joint(self, j)
688 
689 
690  def add_upstream_joint(self, j):
691  """add_upstream_joint(CompositeJoint self, Joint j)"""
692  return _IMP_kinematics.CompositeJoint_add_upstream_joint(self, j)
693 
694 
695  def set_joints(self, joints):
696  """set_joints(CompositeJoint self, IMP::kinematics::Joints joints)"""
697  return _IMP_kinematics.CompositeJoint_set_joints(self, joints)
698 
699 
700  def get_inner_joints(self):
701  """get_inner_joints(CompositeJoint self) -> IMP::kinematics::Joints const &"""
702  return _IMP_kinematics.CompositeJoint_get_inner_joints(self)
703 
704 
705  def __str__(self):
706  """__str__(CompositeJoint self) -> std::string"""
707  return _IMP_kinematics.CompositeJoint___str__(self)
708 
709 
710  def __repr__(self):
711  """__repr__(CompositeJoint self) -> std::string"""
712  return _IMP_kinematics.CompositeJoint___repr__(self)
713 
714 
715  @staticmethod
716  def get_from(o):
717  return _object_cast_to_CompositeJoint(o)
718 
719  __swig_destroy__ = _IMP_kinematics.delete_CompositeJoint
720  __del__ = lambda self: None
721 CompositeJoint_swigregister = _IMP_kinematics.CompositeJoint_swigregister
722 CompositeJoint_swigregister(CompositeJoint)
723 
724 class RevoluteJoint(Joint):
725  """Proxy of C++ IMP::kinematics::RevoluteJoint class."""
726 
727  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
728 
729  def __init__(self, parent, child):
730  """__init__(IMP::kinematics::RevoluteJoint self, RigidBody parent, RigidBody child) -> RevoluteJoint"""
731  if self.__class__ == RevoluteJoint:
732  _self = None
733  else:
734  _self = self
735  this = _IMP_kinematics.new_RevoluteJoint(_self, parent, child)
736  try:
737  self.this.append(this)
738  except __builtin__.Exception:
739  self.this = this
740 
741  if self.__class__ != RevoluteJoint:
742  _director_objects.register(self)
743 
744 
745 
746  __swig_destroy__ = _IMP_kinematics.delete_RevoluteJoint
747  __del__ = lambda self: None
748 
749  def set_angle(self, angle):
750  """set_angle(RevoluteJoint self, double angle)"""
751  return _IMP_kinematics.RevoluteJoint_set_angle(self, angle)
752 
753 
754  def get_angle(self):
755  """get_angle(RevoluteJoint self) -> double"""
756  return _IMP_kinematics.RevoluteJoint_get_angle(self)
757 
758 
759  def get_rot_axis_origin(self):
760  """get_rot_axis_origin(RevoluteJoint self) -> Vector3D"""
761  return _IMP_kinematics.RevoluteJoint_get_rot_axis_origin(self)
762 
763 
764  def get_rot_axis_unit_vector(self):
765  """get_rot_axis_unit_vector(RevoluteJoint self) -> Vector3D"""
766  return _IMP_kinematics.RevoluteJoint_get_rot_axis_unit_vector(self)
767 
768 
769  def update_child_node_reference_frame(self):
770  """update_child_node_reference_frame(RevoluteJoint self)"""
771  return _IMP_kinematics.RevoluteJoint_update_child_node_reference_frame(self)
772 
773 
774  def update_axis_of_rotation_from_cartesian_witnesses(self):
775  """update_axis_of_rotation_from_cartesian_witnesses(RevoluteJoint self)"""
776  return _IMP_kinematics.RevoluteJoint_update_axis_of_rotation_from_cartesian_witnesses(self)
777 
778 
779  def get_current_angle_from_cartesian_witnesses(self):
780  """get_current_angle_from_cartesian_witnesses(RevoluteJoint self) -> double"""
781  return _IMP_kinematics.RevoluteJoint_get_current_angle_from_cartesian_witnesses(self)
782 
783 
784  def update_joint_from_cartesian_witnesses(self):
785  """update_joint_from_cartesian_witnesses(RevoluteJoint self)"""
786  return _IMP_kinematics.RevoluteJoint_update_joint_from_cartesian_witnesses(self)
787 
788 
789  def get_rotation_about_joint_in_parent_coordinates(self):
790  """get_rotation_about_joint_in_parent_coordinates(RevoluteJoint self) -> Transformation3D"""
791  return _IMP_kinematics.RevoluteJoint_get_rotation_about_joint_in_parent_coordinates(self)
792 
793  angle_ = _swig_property(_IMP_kinematics.RevoluteJoint_angle__get, _IMP_kinematics.RevoluteJoint_angle__set)
794  last_updated_angle_ = _swig_property(_IMP_kinematics.RevoluteJoint_last_updated_angle__get, _IMP_kinematics.RevoluteJoint_last_updated_angle__set)
795  rot_axis_unit_vector_ = _swig_property(_IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__get, _IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__set)
796  rot_axis_origin_ = _swig_property(_IMP_kinematics.RevoluteJoint_rot_axis_origin__get, _IMP_kinematics.RevoluteJoint_rot_axis_origin__set)
797 
798  def __str__(self):
799  """__str__(RevoluteJoint self) -> std::string"""
800  return _IMP_kinematics.RevoluteJoint___str__(self)
801 
802 
803  def __repr__(self):
804  """__repr__(RevoluteJoint self) -> std::string"""
805  return _IMP_kinematics.RevoluteJoint___repr__(self)
806 
807 
808  @staticmethod
809  def get_from(o):
810  return _object_cast_to_RevoluteJoint(o)
811 
812 
813  def get_type_name(self):
814  return self.__class__.__name__
815  def do_show(self, out):
816  pass
817  def get_version_info(self):
818  if"IMP::kinematics" == "IMP":
819  return VersionInfo(self.__module__,
820  __import__(self.__module__).get_module_version())
821  else:
822  return IMP.VersionInfo(self.__module__,
823  __import__(self.__module__).get_module_version())
824  @staticmethod
825  def get_from(o):
826  return _object_cast_to_RevoluteJoint(o)
827 
828  def __disown__(self):
829  self.this.disown()
830  _IMP_kinematics.disown_RevoluteJoint(self)
831  return weakref_proxy(self)
832 
833  def do_destroy(self):
834  """do_destroy(RevoluteJoint self)"""
835  return _IMP_kinematics.RevoluteJoint_do_destroy(self)
836 
837 RevoluteJoint_swigregister = _IMP_kinematics.RevoluteJoint_swigregister
838 RevoluteJoint_swigregister(RevoluteJoint)
839 
840 class DihedralAngleRevoluteJoint(RevoluteJoint):
841  """Proxy of C++ IMP::kinematics::DihedralAngleRevoluteJoint class."""
842 
843  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
844 
845  def __init__(self, parent, child, a, b, c, d):
846  """__init__(IMP::kinematics::DihedralAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c, XYZ d) -> DihedralAngleRevoluteJoint"""
847  this = _IMP_kinematics.new_DihedralAngleRevoluteJoint(parent, child, a, b, c, d)
848  try:
849  self.this.append(this)
850  except __builtin__.Exception:
851  self.this = this
852 
853  def get_a(self):
854  """get_a(DihedralAngleRevoluteJoint self) -> XYZ"""
855  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_a(self)
856 
857 
858  def get_b(self):
859  """get_b(DihedralAngleRevoluteJoint self) -> XYZ"""
860  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_b(self)
861 
862 
863  def get_c(self):
864  """get_c(DihedralAngleRevoluteJoint self) -> XYZ"""
865  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_c(self)
866 
867 
868  def get_d(self):
869  """get_d(DihedralAngleRevoluteJoint self) -> XYZ"""
870  return _IMP_kinematics.DihedralAngleRevoluteJoint_get_d(self)
871 
872 
873  def __str__(self):
874  """__str__(DihedralAngleRevoluteJoint self) -> std::string"""
875  return _IMP_kinematics.DihedralAngleRevoluteJoint___str__(self)
876 
877 
878  def __repr__(self):
879  """__repr__(DihedralAngleRevoluteJoint self) -> std::string"""
880  return _IMP_kinematics.DihedralAngleRevoluteJoint___repr__(self)
881 
882 
883  @staticmethod
884  def get_from(o):
885  return _object_cast_to_DihedralAngleRevoluteJoint(o)
886 
887  __swig_destroy__ = _IMP_kinematics.delete_DihedralAngleRevoluteJoint
888  __del__ = lambda self: None
889 DihedralAngleRevoluteJoint_swigregister = _IMP_kinematics.DihedralAngleRevoluteJoint_swigregister
890 DihedralAngleRevoluteJoint_swigregister(DihedralAngleRevoluteJoint)
891 
892 class BondAngleRevoluteJoint(RevoluteJoint):
893  """Proxy of C++ IMP::kinematics::BondAngleRevoluteJoint class."""
894 
895  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
896 
897  def __init__(self, parent, child, a, b, c):
898  """__init__(IMP::kinematics::BondAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c) -> BondAngleRevoluteJoint"""
899  this = _IMP_kinematics.new_BondAngleRevoluteJoint(parent, child, a, b, c)
900  try:
901  self.this.append(this)
902  except __builtin__.Exception:
903  self.this = this
904 
905  def __str__(self):
906  """__str__(BondAngleRevoluteJoint self) -> std::string"""
907  return _IMP_kinematics.BondAngleRevoluteJoint___str__(self)
908 
909 
910  def __repr__(self):
911  """__repr__(BondAngleRevoluteJoint self) -> std::string"""
912  return _IMP_kinematics.BondAngleRevoluteJoint___repr__(self)
913 
914 
915  @staticmethod
916  def get_from(o):
917  return _object_cast_to_BondAngleRevoluteJoint(o)
918 
919  __swig_destroy__ = _IMP_kinematics.delete_BondAngleRevoluteJoint
920  __del__ = lambda self: None
921 BondAngleRevoluteJoint_swigregister = _IMP_kinematics.BondAngleRevoluteJoint_swigregister
922 BondAngleRevoluteJoint_swigregister(BondAngleRevoluteJoint)
923 
924 class RevoluteJointMover(IMP.core.MonteCarloMover):
925  """Proxy of C++ IMP::kinematics::RevoluteJointMover class."""
926 
927  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
928 
929  def __init__(self, m, joints, stddev=0.01):
930  """
931  __init__(IMP::kinematics::RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const stddev=0.01) -> RevoluteJointMover
932  __init__(IMP::kinematics::RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints) -> RevoluteJointMover
933  """
934  this = _IMP_kinematics.new_RevoluteJointMover(m, joints, stddev)
935  try:
936  self.this.append(this)
937  except __builtin__.Exception:
938  self.this = this
939 
940  def set_sigma(self, sigma):
941  """set_sigma(RevoluteJointMover self, IMP::Float sigma)"""
942  return _IMP_kinematics.RevoluteJointMover_set_sigma(self, sigma)
943 
944 
945  def get_sigma(self):
946  """get_sigma(RevoluteJointMover self) -> IMP::Float"""
947  return _IMP_kinematics.RevoluteJointMover_get_sigma(self)
948 
949 
950  def get_version_info(self):
951  """get_version_info(RevoluteJointMover self) -> VersionInfo"""
952  return _IMP_kinematics.RevoluteJointMover_get_version_info(self)
953 
954 
955  def __str__(self):
956  """__str__(RevoluteJointMover self) -> std::string"""
957  return _IMP_kinematics.RevoluteJointMover___str__(self)
958 
959 
960  def __repr__(self):
961  """__repr__(RevoluteJointMover self) -> std::string"""
962  return _IMP_kinematics.RevoluteJointMover___repr__(self)
963 
964 
965  @staticmethod
966  def get_from(o):
967  return _object_cast_to_RevoluteJointMover(o)
968 
969 RevoluteJointMover_swigregister = _IMP_kinematics.RevoluteJointMover_swigregister
970 RevoluteJointMover_swigregister(RevoluteJointMover)
971 
972 class KinematicForest(IMP.Object):
973  """Proxy of C++ IMP::kinematics::KinematicForest class."""
974 
975  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
976 
977  def get_version_info(self):
978  """get_version_info(KinematicForest self) -> VersionInfo"""
979  return _IMP_kinematics.KinematicForest_get_version_info(self)
980 
981 
982  def __init__(self, *args):
983  """
984  __init__(IMP::kinematics::KinematicForest self, Model m) -> KinematicForest
985  __init__(IMP::kinematics::KinematicForest self, Model m, Hierarchy hierarchy) -> KinematicForest
986  """
987  this = _IMP_kinematics.new_KinematicForest(*args)
988  try:
989  self.this.append(this)
990  except __builtin__.Exception:
991  self.this = this
992 
993  def add_edge(self, *args):
994  """
995  add_edge(KinematicForest self, RigidBody parent, RigidBody child) -> Joint
996  add_edge(KinematicForest self, Joint joint)
997  """
998  return _IMP_kinematics.KinematicForest_add_edge(self, *args)
999 
1000 
1001  def add_rigid_bodies_in_chain(self, rbs):
1002  """add_rigid_bodies_in_chain(KinematicForest self, IMP::core::RigidBodies rbs)"""
1003  return _IMP_kinematics.KinematicForest_add_rigid_bodies_in_chain(self, rbs)
1004 
1005 
1006  def reset_root(self, new_root):
1007  """reset_root(KinematicForest self, Particle new_root)"""
1008  return _IMP_kinematics.KinematicForest_reset_root(self, new_root)
1009 
1010 
1011  def update_all_internal_coordinates(self):
1012  """update_all_internal_coordinates(KinematicForest self)"""
1013  return _IMP_kinematics.KinematicForest_update_all_internal_coordinates(self)
1014 
1015 
1016  def update_all_external_coordinates(self):
1017  """update_all_external_coordinates(KinematicForest self)"""
1018  return _IMP_kinematics.KinematicForest_update_all_external_coordinates(self)
1019 
1020 
1021  def get_ordered_joints(self):
1022  """get_ordered_joints(KinematicForest self) -> IMP::kinematics::Joints"""
1023  return _IMP_kinematics.KinematicForest_get_ordered_joints(self)
1024 
1025 
1026  def mark_internal_coordinates_changed(self):
1027  """mark_internal_coordinates_changed(KinematicForest self)"""
1028  return _IMP_kinematics.KinematicForest_mark_internal_coordinates_changed(self)
1029 
1030 
1031  def mark_external_coordinates_changed(self):
1032  """mark_external_coordinates_changed(KinematicForest self)"""
1033  return _IMP_kinematics.KinematicForest_mark_external_coordinates_changed(self)
1034 
1035 
1036  def set_coordinates_safe(self, rb, c):
1037  """set_coordinates_safe(KinematicForest self, RigidBody rb, Vector3D c)"""
1038  return _IMP_kinematics.KinematicForest_set_coordinates_safe(self, rb, c)
1039 
1040 
1041  def get_coordinates_safe(self, rb):
1042  """get_coordinates_safe(KinematicForest self, RigidBody rb) -> Vector3D"""
1043  return _IMP_kinematics.KinematicForest_get_coordinates_safe(self, rb)
1044 
1045 
1046  def get_is_member(self, rb):
1047  """get_is_member(KinematicForest self, RigidBody rb) -> bool"""
1048  return _IMP_kinematics.KinematicForest_get_is_member(self, rb)
1049 
1050 
1051  def get_reference_frame_safe(self, rb):
1052  """get_reference_frame_safe(KinematicForest self, RigidBody rb) -> ReferenceFrame3D"""
1053  return _IMP_kinematics.KinematicForest_get_reference_frame_safe(self, rb)
1054 
1055 
1056  def set_reference_frame_safe(self, rb, r):
1057  """set_reference_frame_safe(KinematicForest self, RigidBody rb, ReferenceFrame3D r)"""
1058  return _IMP_kinematics.KinematicForest_set_reference_frame_safe(self, rb, r)
1059 
1060 
1061  def apply_transform_safely(self, tr):
1062  """apply_transform_safely(KinematicForest self, Transformation3D tr)"""
1063  return _IMP_kinematics.KinematicForest_apply_transform_safely(self, tr)
1064 
1065 
1066  def __str__(self):
1067  """__str__(KinematicForest self) -> std::string"""
1068  return _IMP_kinematics.KinematicForest___str__(self)
1069 
1070 
1071  def __repr__(self):
1072  """__repr__(KinematicForest self) -> std::string"""
1073  return _IMP_kinematics.KinematicForest___repr__(self)
1074 
1075 
1076  @staticmethod
1077  def get_from(o):
1078  return _object_cast_to_KinematicForest(o)
1079 
1080 KinematicForest_swigregister = _IMP_kinematics.KinematicForest_swigregister
1081 KinematicForest_swigregister(KinematicForest)
1082 
1083 class KinematicForestScoreState(IMP.ScoreState):
1084  """Proxy of C++ IMP::kinematics::KinematicForestScoreState class."""
1085 
1086  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1087 
1088  def get_version_info(self):
1089  """get_version_info(KinematicForestScoreState self) -> VersionInfo"""
1090  return _IMP_kinematics.KinematicForestScoreState_get_version_info(self)
1091 
1092 
1093  def __init__(self, kf, rbs, atoms):
1094  """__init__(IMP::kinematics::KinematicForestScoreState self, KinematicForest kf, IMP::core::RigidBodies rbs, IMP::ParticlesTemp atoms) -> KinematicForestScoreState"""
1095  this = _IMP_kinematics.new_KinematicForestScoreState(kf, rbs, atoms)
1096  try:
1097  self.this.append(this)
1098  except __builtin__.Exception:
1099  self.this = this
1100 
1101  def do_before_evaluate(self):
1102  """do_before_evaluate(KinematicForestScoreState self)"""
1103  return _IMP_kinematics.KinematicForestScoreState_do_before_evaluate(self)
1104 
1105 
1106  def do_after_evaluate(self, da):
1107  """do_after_evaluate(KinematicForestScoreState self, DerivativeAccumulator da)"""
1108  return _IMP_kinematics.KinematicForestScoreState_do_after_evaluate(self, da)
1109 
1110 
1111  def do_get_inputs(self):
1112  """do_get_inputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1113  return _IMP_kinematics.KinematicForestScoreState_do_get_inputs(self)
1114 
1115 
1116  def do_get_outputs(self):
1117  """do_get_outputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1118  return _IMP_kinematics.KinematicForestScoreState_do_get_outputs(self)
1119 
1120 
1121  def __str__(self):
1122  """__str__(KinematicForestScoreState self) -> std::string"""
1123  return _IMP_kinematics.KinematicForestScoreState___str__(self)
1124 
1125 
1126  def __repr__(self):
1127  """__repr__(KinematicForestScoreState self) -> std::string"""
1128  return _IMP_kinematics.KinematicForestScoreState___repr__(self)
1129 
1130 
1131  @staticmethod
1132  def get_from(o):
1133  return _object_cast_to_KinematicForestScoreState(o)
1134 
1135 KinematicForestScoreState_swigregister = _IMP_kinematics.KinematicForestScoreState_swigregister
1136 KinematicForestScoreState_swigregister(KinematicForestScoreState)
1137 
1138 class DOF(IMP.Object):
1139  """Proxy of C++ IMP::kinematics::DOF class."""
1140 
1141  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1142 
1143  def get_version_info(self):
1144  """get_version_info(DOF self) -> VersionInfo"""
1145  return _IMP_kinematics.DOF_get_version_info(self)
1146 
1147 
1148  def __init__(self, *args):
1149  """
1150  __init__(IMP::kinematics::DOF self, double v) -> DOF
1151  __init__(IMP::kinematics::DOF self, double v, double min, double max, double step_size) -> DOF
1152  """
1153  this = _IMP_kinematics.new_DOF(*args)
1154  try:
1155  self.this.append(this)
1156  except __builtin__.Exception:
1157  self.this = this
1158 
1159  def get_value(self):
1160  """get_value(DOF self) -> double"""
1161  return _IMP_kinematics.DOF_get_value(self)
1162 
1163 
1164  def set_value(self, v):
1165  """set_value(DOF self, double v)"""
1166  return _IMP_kinematics.DOF_set_value(self, v)
1167 
1168 
1169  def get_range(self):
1170  """get_range(DOF self) -> std::pair< double,double >"""
1171  return _IMP_kinematics.DOF_get_range(self)
1172 
1173 
1174  def set_range(self, range):
1175  """set_range(DOF self, std::pair< double,double > range)"""
1176  return _IMP_kinematics.DOF_set_range(self, range)
1177 
1178 
1179  def get_step_size(self):
1180  """get_step_size(DOF self) -> double"""
1181  return _IMP_kinematics.DOF_get_step_size(self)
1182 
1183 
1184  def set_step_size(self, step_size):
1185  """set_step_size(DOF self, double step_size)"""
1186  return _IMP_kinematics.DOF_set_step_size(self, step_size)
1187 
1188 
1189  def get_number_of_steps(self, *args):
1190  """
1191  get_number_of_steps(DOF self, double value) -> int
1192  get_number_of_steps(DOF self, double value1, double value2) -> int
1193  """
1194  return _IMP_kinematics.DOF_get_number_of_steps(self, *args)
1195 
1196 
1197  def __str__(self):
1198  """__str__(DOF self) -> std::string"""
1199  return _IMP_kinematics.DOF___str__(self)
1200 
1201 
1202  def __repr__(self):
1203  """__repr__(DOF self) -> std::string"""
1204  return _IMP_kinematics.DOF___repr__(self)
1205 
1206 
1207  @staticmethod
1208  def get_from(o):
1209  return _object_cast_to_DOF(o)
1210 
1211 DOF_swigregister = _IMP_kinematics.DOF_swigregister
1212 DOF_swigregister(DOF)
1213 
1214 class DOFValues(IMP.saxs.DistBase):
1215  """Proxy of C++ IMP::kinematics::DOFValues class."""
1216 
1217  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1218 
1219  def __init__(self, *args):
1220  """
1221  __init__(IMP::kinematics::DOFValues self, IMP::kinematics::DOFs const & dofs) -> DOFValues
1222  __init__(IMP::kinematics::DOFValues self) -> DOFValues
1223  """
1224  this = _IMP_kinematics.new_DOFValues(*args)
1225  try:
1226  self.this.append(this)
1227  except __builtin__.Exception:
1228  self.this = this
1229 
1230  def get_distance2(self, *args):
1231  """
1232  get_distance2(DOFValues self, DOFValues other_dof_values) -> double
1233  get_distance2(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1234  """
1235  return _IMP_kinematics.DOFValues_get_distance2(self, *args)
1236 
1237 
1238  def get_distance(self, *args):
1239  """
1240  get_distance(DOFValues self, DOFValues other_dof_values) -> double
1241  get_distance(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1242  """
1243  return _IMP_kinematics.DOFValues_get_distance(self, *args)
1244 
1245 
1246  def show(self, *args):
1247  """
1248  show(DOFValues self, _ostream out)
1249  show(DOFValues self)
1250  """
1251  return _IMP_kinematics.DOFValues_show(self, *args)
1252 
1253 
1254  def __str__(self):
1255  """__str__(DOFValues self) -> std::string"""
1256  return _IMP_kinematics.DOFValues___str__(self)
1257 
1258 
1259  def __repr__(self):
1260  """__repr__(DOFValues self) -> std::string"""
1261  return _IMP_kinematics.DOFValues___repr__(self)
1262 
1263  __swig_destroy__ = _IMP_kinematics.delete_DOFValues
1264  __del__ = lambda self: None
1265 DOFValues_swigregister = _IMP_kinematics.DOFValues_swigregister
1266 DOFValues_swigregister(DOFValues)
1267 
1268 class DirectionalDOF(IMP.Object):
1269  """Proxy of C++ IMP::kinematics::DirectionalDOF class."""
1270 
1271  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1272 
1273  def __init__(self, dofs):
1274  """__init__(IMP::kinematics::DirectionalDOF self, IMP::kinematics::DOFs const & dofs) -> DirectionalDOF"""
1275  this = _IMP_kinematics.new_DirectionalDOF(dofs)
1276  try:
1277  self.this.append(this)
1278  except __builtin__.Exception:
1279  self.this = this
1280 
1281  def set_end_points(self, q1, q2):
1282  """set_end_points(DirectionalDOF self, DOFValues q1, DOFValues q2)"""
1283  return _IMP_kinematics.DirectionalDOF_set_end_points(self, q1, q2)
1284 
1285 
1286  def get_dofs_values(self):
1287  """get_dofs_values(DirectionalDOF self) -> DOFValues"""
1288  return _IMP_kinematics.DirectionalDOF_get_dofs_values(self)
1289 
1290 
1291  def get_value(self):
1292  """get_value(DirectionalDOF self) -> double"""
1293  return _IMP_kinematics.DirectionalDOF_get_value(self)
1294 
1295 
1296  def get_version_info(self):
1297  """get_version_info(DirectionalDOF self) -> VersionInfo"""
1298  return _IMP_kinematics.DirectionalDOF_get_version_info(self)
1299 
1300 
1301  def __str__(self):
1302  """__str__(DirectionalDOF self) -> std::string"""
1303  return _IMP_kinematics.DirectionalDOF___str__(self)
1304 
1305 
1306  def __repr__(self):
1307  """__repr__(DirectionalDOF self) -> std::string"""
1308  return _IMP_kinematics.DirectionalDOF___repr__(self)
1309 
1310 
1311  @staticmethod
1312  def get_from(o):
1313  return _object_cast_to_DirectionalDOF(o)
1314 
1315 DirectionalDOF_swigregister = _IMP_kinematics.DirectionalDOF_swigregister
1316 DirectionalDOF_swigregister(DirectionalDOF)
1317 
1318 class DOFsSampler(IMP.Object):
1319  """Proxy of C++ IMP::kinematics::DOFsSampler class."""
1320 
1321  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1322 
1323  def get_type_name(self):
1324  """get_type_name(DOFsSampler self) -> std::string"""
1325  return _IMP_kinematics.DOFsSampler_get_type_name(self)
1326 
1327 
1328  def get_version_info(self):
1329  """get_version_info(DOFsSampler self) -> VersionInfo"""
1330  return _IMP_kinematics.DOFsSampler_get_version_info(self)
1331 
1332 
1333  def __init__(self, dofs):
1334  """__init__(IMP::kinematics::DOFsSampler self, IMP::kinematics::DOFs dofs) -> DOFsSampler"""
1335  if self.__class__ == DOFsSampler:
1336  _self = None
1337  else:
1338  _self = self
1339  this = _IMP_kinematics.new_DOFsSampler(_self, dofs)
1340  try:
1341  self.this.append(this)
1342  except __builtin__.Exception:
1343  self.this = this
1344 
1345  if self.__class__ != DOFsSampler:
1346  _director_objects.register(self)
1347 
1348 
1349 
1350 
1351  def get_sample(self):
1352  """get_sample(DOFsSampler self) -> DOFValues"""
1353  return _IMP_kinematics.DOFsSampler_get_sample(self)
1354 
1355 
1356  def apply(self, values):
1357  """apply(DOFsSampler self, DOFValues values)"""
1358  return _IMP_kinematics.DOFsSampler_apply(self, values)
1359 
1360 
1361  def apply_last_sample(self):
1362  """apply_last_sample(DOFsSampler self)"""
1363  return _IMP_kinematics.DOFsSampler_apply_last_sample(self)
1364 
1365 
1366  def sample_and_apply(self):
1367  """sample_and_apply(DOFsSampler self)"""
1368  return _IMP_kinematics.DOFsSampler_sample_and_apply(self)
1369 
1370 
1371  def get_dofs(self):
1372  """get_dofs(DOFsSampler self) -> IMP::kinematics::DOFs const &"""
1373  return _IMP_kinematics.DOFsSampler_get_dofs(self)
1374 
1375 
1376  def get_dof(self, i):
1377  """get_dof(DOFsSampler self, unsigned int i) -> DOF"""
1378  return _IMP_kinematics.DOFsSampler_get_dof(self, i)
1379 
1380 
1381  def get_number_of_dofs(self):
1382  """get_number_of_dofs(DOFsSampler self) -> unsigned int"""
1383  return _IMP_kinematics.DOFsSampler_get_number_of_dofs(self)
1384 
1385 
1386  def do_get_sample(self):
1387  """do_get_sample(DOFsSampler self) -> DOFValues"""
1388  return _IMP_kinematics.DOFsSampler_do_get_sample(self)
1389 
1390 
1391  def __str__(self):
1392  """__str__(DOFsSampler self) -> std::string"""
1393  return _IMP_kinematics.DOFsSampler___str__(self)
1394 
1395 
1396  def __repr__(self):
1397  """__repr__(DOFsSampler self) -> std::string"""
1398  return _IMP_kinematics.DOFsSampler___repr__(self)
1399 
1400 
1401  @staticmethod
1402  def get_from(o):
1403  return _object_cast_to_DOFsSampler(o)
1404 
1405 
1406  def get_type_name(self):
1407  return self.__class__.__name__
1408  def do_show(self, out):
1409  pass
1410  def get_version_info(self):
1411  if"IMP::kinematics" == "IMP":
1412  return VersionInfo(self.__module__,
1413  __import__(self.__module__).get_module_version())
1414  else:
1415  return IMP.VersionInfo(self.__module__,
1416  __import__(self.__module__).get_module_version())
1417  @staticmethod
1418  def get_from(o):
1419  return _object_cast_to_DOFsSampler(o)
1420 
1421  def __disown__(self):
1422  self.this.disown()
1423  _IMP_kinematics.disown_DOFsSampler(self)
1424  return weakref_proxy(self)
1425 
1426  def do_destroy(self):
1427  """do_destroy(DOFsSampler self)"""
1428  return _IMP_kinematics.DOFsSampler_do_destroy(self)
1429 
1430 DOFsSampler_swigregister = _IMP_kinematics.DOFsSampler_swigregister
1431 DOFsSampler_swigregister(DOFsSampler)
1432 
1433 class UniformBackboneSampler(DOFsSampler):
1434  """Proxy of C++ IMP::kinematics::UniformBackboneSampler class."""
1435 
1436  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1437 
1438  def __init__(self, joints, dofs):
1439  """__init__(IMP::kinematics::UniformBackboneSampler self, IMP::kinematics::DihedralAngleRevoluteJoints joints, IMP::kinematics::DOFs dofs) -> UniformBackboneSampler"""
1440  this = _IMP_kinematics.new_UniformBackboneSampler(joints, dofs)
1441  try:
1442  self.this.append(this)
1443  except __builtin__.Exception:
1444  self.this = this
1445 
1446  def __str__(self):
1447  """__str__(UniformBackboneSampler self) -> std::string"""
1448  return _IMP_kinematics.UniformBackboneSampler___str__(self)
1449 
1450 
1451  def __repr__(self):
1452  """__repr__(UniformBackboneSampler self) -> std::string"""
1453  return _IMP_kinematics.UniformBackboneSampler___repr__(self)
1454 
1455 
1456  @staticmethod
1457  def get_from(o):
1458  return _object_cast_to_UniformBackboneSampler(o)
1459 
1460  __swig_destroy__ = _IMP_kinematics.delete_UniformBackboneSampler
1461  __del__ = lambda self: None
1462 UniformBackboneSampler_swigregister = _IMP_kinematics.UniformBackboneSampler_swigregister
1463 UniformBackboneSampler_swigregister(UniformBackboneSampler)
1464 
1465 class ProteinKinematics(IMP.Object):
1466  """Proxy of C++ IMP::kinematics::ProteinKinematics class."""
1467 
1468  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1469 
1470  def __init__(self, *args):
1471  """
1472  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1473  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True) -> ProteinKinematics
1474  __init__(IMP::kinematics::ProteinKinematics self, Hierarchy mhd) -> ProteinKinematics
1475  __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
1476  __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
1477  __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
1478  __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
1479  """
1480  this = _IMP_kinematics.new_ProteinKinematics(*args)
1481  try:
1482  self.this.append(this)
1483  except __builtin__.Exception:
1484  self.this = this
1485 
1486  def get_phi(self, r):
1487  """get_phi(ProteinKinematics self, Residue r) -> double"""
1488  return _IMP_kinematics.ProteinKinematics_get_phi(self, r)
1489 
1490 
1491  def get_psi(self, r):
1492  """get_psi(ProteinKinematics self, Residue r) -> double"""
1493  return _IMP_kinematics.ProteinKinematics_get_psi(self, r)
1494 
1495 
1496  def get_joints(self):
1497  """get_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1498  return _IMP_kinematics.ProteinKinematics_get_joints(self)
1499 
1500 
1501  def get_loop_joints(self):
1502  """get_loop_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1503  return _IMP_kinematics.ProteinKinematics_get_loop_joints(self)
1504 
1505 
1506  def get_ordered_joints(self):
1507  """get_ordered_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1508  return _IMP_kinematics.ProteinKinematics_get_ordered_joints(self)
1509 
1510 
1511  def get_kinematic_forest(self):
1512  """get_kinematic_forest(ProteinKinematics self) -> KinematicForest"""
1513  return _IMP_kinematics.ProteinKinematics_get_kinematic_forest(self)
1514 
1515 
1516  def get_rigid_bodies(self):
1517  """get_rigid_bodies(ProteinKinematics self) -> IMP::core::RigidBodies"""
1518  return _IMP_kinematics.ProteinKinematics_get_rigid_bodies(self)
1519 
1520 
1521  def set_phi(self, r, angle):
1522  """set_phi(ProteinKinematics self, Residue r, double angle)"""
1523  return _IMP_kinematics.ProteinKinematics_set_phi(self, r, angle)
1524 
1525 
1526  def set_psi(self, r, angle):
1527  """set_psi(ProteinKinematics self, Residue r, double angle)"""
1528  return _IMP_kinematics.ProteinKinematics_set_psi(self, r, angle)
1529 
1530 
1531  def get_version_info(self):
1532  """get_version_info(ProteinKinematics self) -> VersionInfo"""
1533  return _IMP_kinematics.ProteinKinematics_get_version_info(self)
1534 
1535 
1536  def __str__(self):
1537  """__str__(ProteinKinematics self) -> std::string"""
1538  return _IMP_kinematics.ProteinKinematics___str__(self)
1539 
1540 
1541  def __repr__(self):
1542  """__repr__(ProteinKinematics self) -> std::string"""
1543  return _IMP_kinematics.ProteinKinematics___repr__(self)
1544 
1545 
1546  @staticmethod
1547  def get_from(o):
1548  return _object_cast_to_ProteinKinematics(o)
1549 
1550 ProteinKinematics_swigregister = _IMP_kinematics.ProteinKinematics_swigregister
1551 ProteinKinematics_swigregister(ProteinKinematics)
1552 
1553 class LocalPlanner(IMP.Object):
1554  """Proxy of C++ IMP::kinematics::LocalPlanner class."""
1555 
1556  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1557 
1558  def __init__(self, *args, **kwargs):
1559  raise AttributeError("No constructor defined - class is abstract")
1560 
1561  def get_version_info(self):
1562  """get_version_info(LocalPlanner self) -> VersionInfo"""
1563  return _IMP_kinematics.LocalPlanner_get_version_info(self)
1564 
1565 
1566  def plan(self, q_near, q_rand, sf):
1567  """plan(LocalPlanner self, DOFValues q_near, DOFValues q_rand, ScoringFunction sf) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1568  return _IMP_kinematics.LocalPlanner_plan(self, q_near, q_rand, sf)
1569 
1570 
1571  def is_valid(self, values, sf):
1572  """is_valid(LocalPlanner self, DOFValues values, ScoringFunction sf) -> bool"""
1573  return _IMP_kinematics.LocalPlanner_is_valid(self, values, sf)
1574 
1575 
1576  def __str__(self):
1577  """__str__(LocalPlanner self) -> std::string"""
1578  return _IMP_kinematics.LocalPlanner___str__(self)
1579 
1580 
1581  def __repr__(self):
1582  """__repr__(LocalPlanner self) -> std::string"""
1583  return _IMP_kinematics.LocalPlanner___repr__(self)
1584 
1585 
1586  @staticmethod
1587  def get_from(o):
1588  return _object_cast_to_LocalPlanner(o)
1589 
1590 LocalPlanner_swigregister = _IMP_kinematics.LocalPlanner_swigregister
1591 LocalPlanner_swigregister(LocalPlanner)
1592 
1593 class PathLocalPlanner(LocalPlanner):
1594  """Proxy of C++ IMP::kinematics::PathLocalPlanner class."""
1595 
1596  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1597 
1598  def __init__(self, model, dofs_sampler, directional_dof, save_step_interval=1):
1599  """
1600  __init__(IMP::kinematics::PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof, int save_step_interval=1) -> PathLocalPlanner
1601  __init__(IMP::kinematics::PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof) -> PathLocalPlanner
1602  """
1603  this = _IMP_kinematics.new_PathLocalPlanner(model, dofs_sampler, directional_dof, save_step_interval)
1604  try:
1605  self.this.append(this)
1606  except __builtin__.Exception:
1607  self.this = this
1608 
1609  def __str__(self):
1610  """__str__(PathLocalPlanner self) -> std::string"""
1611  return _IMP_kinematics.PathLocalPlanner___str__(self)
1612 
1613 
1614  def __repr__(self):
1615  """__repr__(PathLocalPlanner self) -> std::string"""
1616  return _IMP_kinematics.PathLocalPlanner___repr__(self)
1617 
1618 
1619  @staticmethod
1620  def get_from(o):
1621  return _object_cast_to_PathLocalPlanner(o)
1622 
1623  __swig_destroy__ = _IMP_kinematics.delete_PathLocalPlanner
1624  __del__ = lambda self: None
1625 PathLocalPlanner_swigregister = _IMP_kinematics.PathLocalPlanner_swigregister
1626 PathLocalPlanner_swigregister(PathLocalPlanner)
1627 
1628 class RRT(IMP.Sampler):
1629  """Proxy of C++ IMP::kinematics::RRT class."""
1630 
1631  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1632 
1633  def get_version_info(self):
1634  """get_version_info(RRT self) -> VersionInfo"""
1635  return _IMP_kinematics.RRT_get_version_info(self)
1636 
1637 
1638  def __init__(self, m, sampler, planner, cspace_dofs, iteration_number=1000, tree_size=100, number_of_sampled_dofs=0):
1639  """
1640  __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
1641  __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
1642  __init__(IMP::kinematics::RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs, unsigned int iteration_number=1000) -> RRT
1643  __init__(IMP::kinematics::RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs) -> RRT
1644  """
1645  this = _IMP_kinematics.new_RRT(m, sampler, planner, cspace_dofs, iteration_number, tree_size, number_of_sampled_dofs)
1646  try:
1647  self.this.append(this)
1648  except __builtin__.Exception:
1649  self.this = this
1650 
1651  def do_sample(self):
1652  """do_sample(RRT self) -> ConfigurationSet"""
1653  return _IMP_kinematics.RRT_do_sample(self)
1654 
1655 
1656  def run(self, number_of_iterations=0):
1657  """
1658  run(RRT self, unsigned int number_of_iterations=0) -> bool
1659  run(RRT self) -> bool
1660  """
1661  return _IMP_kinematics.RRT_run(self, number_of_iterations)
1662 
1663 
1664  def get_DOFValues(self):
1665  """get_DOFValues(RRT self) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1666  return _IMP_kinematics.RRT_get_DOFValues(self)
1667 
1668 
1669  def set_number_of_iterations(self, num):
1670  """set_number_of_iterations(RRT self, unsigned int num)"""
1671  return _IMP_kinematics.RRT_set_number_of_iterations(self, num)
1672 
1673 
1674  def set_tree_size(self, num):
1675  """set_tree_size(RRT self, unsigned int num)"""
1676  return _IMP_kinematics.RRT_set_tree_size(self, num)
1677 
1678 
1679  def set_actual_tree_size(self, num):
1680  """set_actual_tree_size(RRT self, unsigned int num)"""
1681  return _IMP_kinematics.RRT_set_actual_tree_size(self, num)
1682 
1683 
1684  def set_number_of_collisions(self, num):
1685  """set_number_of_collisions(RRT self, unsigned int num)"""
1686  return _IMP_kinematics.RRT_set_number_of_collisions(self, num)
1687 
1688 
1689  def __str__(self):
1690  """__str__(RRT self) -> std::string"""
1691  return _IMP_kinematics.RRT___str__(self)
1692 
1693 
1694  def __repr__(self):
1695  """__repr__(RRT self) -> std::string"""
1696  return _IMP_kinematics.RRT___repr__(self)
1697 
1698 
1699  @staticmethod
1700  def get_from(o):
1701  return _object_cast_to_RRT(o)
1702 
1703 RRT_swigregister = _IMP_kinematics.RRT_swigregister
1704 RRT_swigregister(RRT)
1705 
1706 
1707 def get_module_version():
1708  """get_module_version() -> std::string const"""
1709  return _IMP_kinematics.get_module_version()
1710 
1711 def get_example_path(fname):
1712  """get_example_path(std::string fname) -> std::string"""
1713  return _IMP_kinematics.get_example_path(fname)
1714 
1715 def get_data_path(fname):
1716  """get_data_path(std::string fname) -> std::string"""
1717  return _IMP_kinematics.get_data_path(fname)
1718 
1719 from . import _version_check
1720 _version_check.check_version(get_module_version())
1721 __version__ = get_module_version()
1722 
1723 
1724 
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...
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: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.