11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 import _IMP_kinematics
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_KINEMATICS_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_KINEMATICS_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
72 def __init__(self, *args, **kwargs):
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_kinematics.delete_IMP_KINEMATICS_SwigPyIterator
78 r"""value(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
79 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_value(self)
82 r"""incr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator"""
83 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_KINEMATICS_SwigPyIterator self, size_t n=1) -> IMP_KINEMATICS_SwigPyIterator"""
87 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
95 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_KINEMATICS_SwigPyIterator self) -> IMP_KINEMATICS_SwigPyIterator"""
99 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_copy(self)
102 r"""next(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
103 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_next(self)
106 r"""__next__(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
107 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___next__(self)
110 r"""previous(IMP_KINEMATICS_SwigPyIterator self) -> PyObject *"""
111 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
115 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
119 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> bool"""
123 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
127 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
131 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator"""
135 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_KINEMATICS_SwigPyIterator self, ptrdiff_t n) -> IMP_KINEMATICS_SwigPyIterator
140 __sub__(IMP_KINEMATICS_SwigPyIterator self, IMP_KINEMATICS_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator___sub__(self, *args)
147 _IMP_kinematics.IMP_KINEMATICS_SwigPyIterator_swigregister(IMP_KINEMATICS_SwigPyIterator)
154 IMP_DEBUG = _IMP_kinematics.IMP_DEBUG
156 IMP_RELEASE = _IMP_kinematics.IMP_RELEASE
158 IMP_SILENT = _IMP_kinematics.IMP_SILENT
160 IMP_PROGRESS = _IMP_kinematics.IMP_PROGRESS
162 IMP_TERSE = _IMP_kinematics.IMP_TERSE
164 IMP_VERBOSE = _IMP_kinematics.IMP_VERBOSE
166 IMP_MEMORY = _IMP_kinematics.IMP_MEMORY
168 IMP_NONE = _IMP_kinematics.IMP_NONE
170 IMP_USAGE = _IMP_kinematics.IMP_USAGE
172 IMP_INTERNAL = _IMP_kinematics.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_kinematics.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_kinematics.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kinematics.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_kinematics.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_kinematics.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_kinematics.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kinematics.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kinematics.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_kinematics.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_kinematics._ostream_write(self, osa_buf)
237 _IMP_kinematics._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_kinematics.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_kinematics.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_kinematics.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_kinematics.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_kinematics.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_kinematics.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_kinematics.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_kinematics.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_kinematics.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_kinematics.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_kinematics.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_kinematics.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_CORE_HAS_IMP_CGAL = _IMP_kinematics.IMP_CORE_HAS_IMP_CGAL
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CORE_HAS_IMP_KERNEL
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_FILESYSTEM
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_CORE_HAS_BOOST_RANDOM
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_CORE_HAS_BOOST_SYSTEM
321 IMP_CORE_HAS_CGAL = _IMP_kinematics.IMP_CORE_HAS_CGAL
323 IMP_CORE_HAS_HDF5 = _IMP_kinematics.IMP_CORE_HAS_HDF5
325 IMP_CORE_HAS_NUMPY = _IMP_kinematics.IMP_CORE_HAS_NUMPY
327 IMPCORE_SHOW_WARNINGS = _IMP_kinematics.IMPCORE_SHOW_WARNINGS
330 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
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_DISPLAY
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_KERNEL
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
344 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
348 IMP_CONTAINER_HAS_CGAL = _IMP_kinematics.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_kinematics.IMP_CONTAINER_HAS_HDF5
352 IMP_CONTAINER_HAS_NUMPY = _IMP_kinematics.IMP_CONTAINER_HAS_NUMPY
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_kinematics.IMP_CONTAINER_HAS_PYTHON_IHM
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_kinematics.IMP_CONTAINER_HAS_ROBIN_MAP
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_kinematics.IMPCONTAINER_SHOW_WARNINGS
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_kinematics.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_kinematics.IMP_ATOM_HAS_IMP_KERNEL
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_RANDOM
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_kinematics.IMP_ATOM_HAS_BOOST_REGEX
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_ATOM_HAS_BOOST_SYSTEM
377 IMP_ATOM_HAS_CGAL = _IMP_kinematics.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_kinematics.IMP_ATOM_HAS_HDF5
381 IMP_ATOM_HAS_NUMPY = _IMP_kinematics.IMP_ATOM_HAS_NUMPY
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_kinematics.IMP_ATOM_HAS_PYTHON_IHM
385 IMPATOM_SHOW_WARNINGS = _IMP_kinematics.IMPATOM_SHOW_WARNINGS
387 IMP_ATOM_TYPE_INDEX = _IMP_kinematics.IMP_ATOM_TYPE_INDEX
389 IMP_RESIDUE_TYPE_INDEX = _IMP_kinematics.IMP_RESIDUE_TYPE_INDEX
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_kinematics.IMP_HIERARCHY_TYPE_INDEX
393 IMP_CHAIN_TYPE_INDEX = _IMP_kinematics.IMP_CHAIN_TYPE_INDEX
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_kinematics.IMP_SAXS_HAS_IMP_CGAL
398 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_kinematics.IMP_SAXS_HAS_IMP_CONTAINER
400 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_SAXS_HAS_IMP_DISPLAY
402 IMP_SAXS_HAS_IMP_KERNEL = _IMP_kinematics.IMP_SAXS_HAS_IMP_KERNEL
404 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
406 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_FILESYSTEM
408 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_RANDOM
412 IMP_SAXS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_SAXS_HAS_BOOST_REGEX
414 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_SAXS_HAS_BOOST_SYSTEM
416 IMP_SAXS_HAS_CGAL = _IMP_kinematics.IMP_SAXS_HAS_CGAL
418 IMP_SAXS_HAS_HDF5 = _IMP_kinematics.IMP_SAXS_HAS_HDF5
420 IMP_SAXS_HAS_NUMPY = _IMP_kinematics.IMP_SAXS_HAS_NUMPY
422 IMP_SAXS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_SAXS_HAS_PYTHON_IHM
424 IMPSAXS_SHOW_WARNINGS = _IMP_kinematics.IMPSAXS_SHOW_WARNINGS
427 IMP_KINEMATICS_HAS_IMP_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_CGAL
429 IMP_KINEMATICS_HAS_IMP_DISPLAY = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_DISPLAY
431 IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR = _IMP_kinematics.IMP_KINEMATICS_HAS_IMP_SCORE_FUNCTOR
433 IMP_KINEMATICS_HAS_BOOST_FILESYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_FILESYSTEM
435 IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_PROGRAMOPTIONS
437 IMP_KINEMATICS_HAS_BOOST_RANDOM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_RANDOM
439 IMP_KINEMATICS_HAS_BOOST_REGEX = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_REGEX
441 IMP_KINEMATICS_HAS_BOOST_SYSTEM = _IMP_kinematics.IMP_KINEMATICS_HAS_BOOST_SYSTEM
443 IMP_KINEMATICS_HAS_CGAL = _IMP_kinematics.IMP_KINEMATICS_HAS_CGAL
445 IMP_KINEMATICS_HAS_HDF5 = _IMP_kinematics.IMP_KINEMATICS_HAS_HDF5
447 IMP_KINEMATICS_HAS_NUMPY = _IMP_kinematics.IMP_KINEMATICS_HAS_NUMPY
449 IMP_KINEMATICS_HAS_PYTHON_IHM = _IMP_kinematics.IMP_KINEMATICS_HAS_PYTHON_IHM
451 IMPKINEMATICS_SHOW_WARNINGS = _IMP_kinematics.IMPKINEMATICS_SHOW_WARNINGS
454 _object_types.append(
"Joint")
457 def _object_cast_to_Joint(o):
458 r"""_object_cast_to_Joint(Object o) -> Joint"""
459 return _IMP_kinematics._object_cast_to_Joint(o)
461 _object_types.append(
"TransformationJoint")
464 def _object_cast_to_TransformationJoint(o):
465 r"""_object_cast_to_TransformationJoint(Object o) -> TransformationJoint"""
466 return _IMP_kinematics._object_cast_to_TransformationJoint(o)
468 _object_types.append(
"RevoluteJoint")
471 def _object_cast_to_RevoluteJoint(o):
472 r"""_object_cast_to_RevoluteJoint(Object o) -> RevoluteJoint"""
473 return _IMP_kinematics._object_cast_to_RevoluteJoint(o)
475 _object_types.append(
"DihedralAngleRevoluteJoint")
478 def _object_cast_to_DihedralAngleRevoluteJoint(o):
479 r"""_object_cast_to_DihedralAngleRevoluteJoint(Object o) -> DihedralAngleRevoluteJoint"""
480 return _IMP_kinematics._object_cast_to_DihedralAngleRevoluteJoint(o)
482 _object_types.append(
"BondAngleRevoluteJoint")
485 def _object_cast_to_BondAngleRevoluteJoint(o):
486 r"""_object_cast_to_BondAngleRevoluteJoint(Object o) -> BondAngleRevoluteJoint"""
487 return _IMP_kinematics._object_cast_to_BondAngleRevoluteJoint(o)
489 _object_types.append(
"PrismaticJoint")
492 def _object_cast_to_PrismaticJoint(o):
493 r"""_object_cast_to_PrismaticJoint(Object o) -> PrismaticJoint"""
494 return _IMP_kinematics._object_cast_to_PrismaticJoint(o)
496 _object_types.append(
"KinematicForest")
499 def _object_cast_to_KinematicForest(o):
500 r"""_object_cast_to_KinematicForest(Object o) -> KinematicForest"""
501 return _IMP_kinematics._object_cast_to_KinematicForest(o)
503 _object_types.append(
"KinematicForestScoreState")
506 def _object_cast_to_KinematicForestScoreState(o):
507 r"""_object_cast_to_KinematicForestScoreState(Object o) -> KinematicForestScoreState"""
508 return _IMP_kinematics._object_cast_to_KinematicForestScoreState(o)
510 _object_types.append(
"CompositeJoint")
513 def _object_cast_to_CompositeJoint(o):
514 r"""_object_cast_to_CompositeJoint(Object o) -> CompositeJoint"""
515 return _IMP_kinematics._object_cast_to_CompositeJoint(o)
517 _object_types.append(
"RevoluteJointMover")
520 def _object_cast_to_RevoluteJointMover(o):
521 r"""_object_cast_to_RevoluteJointMover(Object o) -> RevoluteJointMover"""
522 return _IMP_kinematics._object_cast_to_RevoluteJointMover(o)
524 _object_types.append(
"DihedralMover")
527 def _object_cast_to_DihedralMover(o):
528 r"""_object_cast_to_DihedralMover(Object o) -> DihedralMover"""
529 return _IMP_kinematics._object_cast_to_DihedralMover(o)
531 _object_types.append(
"DOF")
534 def _object_cast_to_DOF(o):
535 r"""_object_cast_to_DOF(Object o) -> DOF"""
536 return _IMP_kinematics._object_cast_to_DOF(o)
539 _plural_types.append(
"DOFValuesList")
540 _value_types.append(
"DOFValues")
543 _object_types.append(
"DirectionalDOF")
546 def _object_cast_to_DirectionalDOF(o):
547 r"""_object_cast_to_DirectionalDOF(Object o) -> DirectionalDOF"""
548 return _IMP_kinematics._object_cast_to_DirectionalDOF(o)
550 _object_types.append(
"DOFsSampler")
553 def _object_cast_to_DOFsSampler(o):
554 r"""_object_cast_to_DOFsSampler(Object o) -> DOFsSampler"""
555 return _IMP_kinematics._object_cast_to_DOFsSampler(o)
557 _object_types.append(
"UniformBackboneSampler")
560 def _object_cast_to_UniformBackboneSampler(o):
561 r"""_object_cast_to_UniformBackboneSampler(Object o) -> UniformBackboneSampler"""
562 return _IMP_kinematics._object_cast_to_UniformBackboneSampler(o)
564 _object_types.append(
"FibrilSampler")
567 def _object_cast_to_FibrilSampler(o):
568 r"""_object_cast_to_FibrilSampler(Object o) -> FibrilSampler"""
569 return _IMP_kinematics._object_cast_to_FibrilSampler(o)
571 _object_types.append(
"ProteinKinematics")
574 def _object_cast_to_ProteinKinematics(o):
575 r"""_object_cast_to_ProteinKinematics(Object o) -> ProteinKinematics"""
576 return _IMP_kinematics._object_cast_to_ProteinKinematics(o)
578 _object_types.append(
"LocalPlanner")
581 def _object_cast_to_LocalPlanner(o):
582 r"""_object_cast_to_LocalPlanner(Object o) -> LocalPlanner"""
583 return _IMP_kinematics._object_cast_to_LocalPlanner(o)
585 _object_types.append(
"PathLocalPlanner")
588 def _object_cast_to_PathLocalPlanner(o):
589 r"""_object_cast_to_PathLocalPlanner(Object o) -> PathLocalPlanner"""
590 return _IMP_kinematics._object_cast_to_PathLocalPlanner(o)
592 _object_types.append(
"RRT")
595 def _object_cast_to_RRT(o):
596 r"""_object_cast_to_RRT(Object o) -> RRT"""
597 return _IMP_kinematics._object_cast_to_RRT(o)
599 r"""Proxy of C++ IMP::kinematics::Joint class."""
601 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
604 r"""get_version_info(Joint self) -> VersionInfo"""
605 return _IMP_kinematics.Joint_get_version_info(self)
606 __swig_destroy__ = _IMP_kinematics.delete_Joint
608 def __init__(self, parent, child):
609 r"""__init__(Joint self, RigidBody parent, RigidBody child) -> Joint"""
610 _IMP_kinematics.Joint_swiginit(self, _IMP_kinematics.new_Joint(parent, child))
612 def get_owner_kf(self):
613 r"""get_owner_kf(Joint self) -> KinematicForest"""
614 return _IMP_kinematics.Joint_get_owner_kf(self)
616 def get_transformation_child_to_parent(self):
617 r"""get_transformation_child_to_parent(Joint self) -> Transformation3D"""
618 return _IMP_kinematics.Joint_get_transformation_child_to_parent(self)
620 def get_parent_node(self):
621 r"""get_parent_node(Joint self) -> RigidBody"""
622 return _IMP_kinematics.Joint_get_parent_node(self)
624 def get_child_node(self):
625 r"""get_child_node(Joint self) -> RigidBody"""
626 return _IMP_kinematics.Joint_get_child_node(self)
629 r"""__str__(Joint self) -> std::string"""
630 return _IMP_kinematics.Joint___str__(self)
633 r"""__repr__(Joint self) -> std::string"""
634 return _IMP_kinematics.Joint___repr__(self)
638 return _object_cast_to_Joint(o)
642 _IMP_kinematics.Joint_swigregister(Joint)
643 class TransformationJoint(Joint):
644 r"""Proxy of C++ IMP::kinematics::TransformationJoint class."""
646 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
648 def __init__(self, parent, child):
649 r"""__init__(TransformationJoint self, RigidBody parent, RigidBody child) -> TransformationJoint"""
650 _IMP_kinematics.TransformationJoint_swiginit(self, _IMP_kinematics.new_TransformationJoint(parent, child))
652 def set_transformation_child_to_parent(self, transformation):
653 r"""set_transformation_child_to_parent(TransformationJoint self, Transformation3D transformation)"""
654 return _IMP_kinematics.TransformationJoint_set_transformation_child_to_parent(self, transformation)
657 r"""__str__(TransformationJoint self) -> std::string"""
658 return _IMP_kinematics.TransformationJoint___str__(self)
661 r"""__repr__(TransformationJoint self) -> std::string"""
662 return _IMP_kinematics.TransformationJoint___repr__(self)
666 return _object_cast_to_TransformationJoint(o)
668 __swig_destroy__ = _IMP_kinematics.delete_TransformationJoint
671 _IMP_kinematics.TransformationJoint_swigregister(TransformationJoint)
672 class PrismaticJoint(Joint):
673 r"""Proxy of C++ IMP::kinematics::PrismaticJoint class."""
675 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
677 def __init__(self, *args):
679 __init__(PrismaticJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b) -> PrismaticJoint
680 __init__(PrismaticJoint self, RigidBody parent, RigidBody child) -> PrismaticJoint
682 _IMP_kinematics.PrismaticJoint_swiginit(self, _IMP_kinematics.new_PrismaticJoint(*args))
684 def get_length(self):
685 r"""get_length(PrismaticJoint self) -> double"""
686 return _IMP_kinematics.PrismaticJoint_get_length(self)
688 def set_length(self, l):
689 r"""set_length(PrismaticJoint self, double l)"""
690 return _IMP_kinematics.PrismaticJoint_set_length(self, l)
693 r"""__str__(PrismaticJoint self) -> std::string"""
694 return _IMP_kinematics.PrismaticJoint___str__(self)
697 r"""__repr__(PrismaticJoint self) -> std::string"""
698 return _IMP_kinematics.PrismaticJoint___repr__(self)
702 return _object_cast_to_PrismaticJoint(o)
704 __swig_destroy__ = _IMP_kinematics.delete_PrismaticJoint
707 _IMP_kinematics.PrismaticJoint_swigregister(PrismaticJoint)
708 class CompositeJoint(Joint):
709 r"""Proxy of C++ IMP::kinematics::CompositeJoint class."""
711 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
713 def __init__(self, *args):
714 r"""__init__(CompositeJoint self, RigidBody parent, RigidBody child, IMP::kinematics::Joints joints=IMP::kinematics::Joints()) -> CompositeJoint"""
715 _IMP_kinematics.CompositeJoint_swiginit(self, _IMP_kinematics.new_CompositeJoint(*args))
717 def add_downstream_joint(self, j):
718 r"""add_downstream_joint(CompositeJoint self, Joint j)"""
719 return _IMP_kinematics.CompositeJoint_add_downstream_joint(self, j)
721 def add_upstream_joint(self, j):
722 r"""add_upstream_joint(CompositeJoint self, Joint j)"""
723 return _IMP_kinematics.CompositeJoint_add_upstream_joint(self, j)
725 def set_joints(self, joints):
726 r"""set_joints(CompositeJoint self, IMP::kinematics::Joints joints)"""
727 return _IMP_kinematics.CompositeJoint_set_joints(self, joints)
729 def get_inner_joints(self):
730 r"""get_inner_joints(CompositeJoint self) -> IMP::kinematics::Joints const &"""
731 return _IMP_kinematics.CompositeJoint_get_inner_joints(self)
734 r"""__str__(CompositeJoint self) -> std::string"""
735 return _IMP_kinematics.CompositeJoint___str__(self)
738 r"""__repr__(CompositeJoint self) -> std::string"""
739 return _IMP_kinematics.CompositeJoint___repr__(self)
743 return _object_cast_to_CompositeJoint(o)
745 __swig_destroy__ = _IMP_kinematics.delete_CompositeJoint
748 _IMP_kinematics.CompositeJoint_swigregister(CompositeJoint)
749 class RevoluteJoint(Joint):
750 r"""Proxy of C++ IMP::kinematics::RevoluteJoint class."""
752 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
754 def __init__(self, parent, child):
755 r"""__init__(RevoluteJoint self, RigidBody parent, RigidBody child) -> RevoluteJoint"""
756 if self.__class__ == RevoluteJoint:
760 _IMP_kinematics.RevoluteJoint_swiginit(self, _IMP_kinematics.new_RevoluteJoint(_self, parent, child))
762 if self.__class__ != RevoluteJoint:
763 _director_objects.register(self)
767 __swig_destroy__ = _IMP_kinematics.delete_RevoluteJoint
769 def set_angle(self, angle):
770 r"""set_angle(RevoluteJoint self, double angle)"""
771 return _IMP_kinematics.RevoluteJoint_set_angle(self, angle)
774 r"""get_angle(RevoluteJoint self) -> double"""
775 return _IMP_kinematics.RevoluteJoint_get_angle(self)
777 def get_rot_axis_origin(self):
778 r"""get_rot_axis_origin(RevoluteJoint self) -> Vector3D"""
779 return _IMP_kinematics.RevoluteJoint_get_rot_axis_origin(self)
781 def get_rot_axis_unit_vector(self):
782 r"""get_rot_axis_unit_vector(RevoluteJoint self) -> Vector3D"""
783 return _IMP_kinematics.RevoluteJoint_get_rot_axis_unit_vector(self)
785 def update_child_node_reference_frame(self):
786 r"""update_child_node_reference_frame(RevoluteJoint self)"""
787 return _IMP_kinematics.RevoluteJoint_update_child_node_reference_frame(self)
789 def update_axis_of_rotation_from_cartesian_witnesses(self):
790 r"""update_axis_of_rotation_from_cartesian_witnesses(RevoluteJoint self)"""
791 return _IMP_kinematics.RevoluteJoint_update_axis_of_rotation_from_cartesian_witnesses(self)
793 def get_current_angle_from_cartesian_witnesses(self):
794 r"""get_current_angle_from_cartesian_witnesses(RevoluteJoint self) -> double"""
795 return _IMP_kinematics.RevoluteJoint_get_current_angle_from_cartesian_witnesses(self)
797 def update_joint_from_cartesian_witnesses(self):
798 r"""update_joint_from_cartesian_witnesses(RevoluteJoint self)"""
799 return _IMP_kinematics.RevoluteJoint_update_joint_from_cartesian_witnesses(self)
801 def get_rotation_about_joint_in_parent_coordinates(self):
802 r"""get_rotation_about_joint_in_parent_coordinates(RevoluteJoint self) -> Transformation3D"""
803 return _IMP_kinematics.RevoluteJoint_get_rotation_about_joint_in_parent_coordinates(self)
804 angle_ = property(_IMP_kinematics.RevoluteJoint_angle__get, _IMP_kinematics.RevoluteJoint_angle__set, doc=
r"""angle_ : double""")
805 last_updated_angle_ = property(_IMP_kinematics.RevoluteJoint_last_updated_angle__get, _IMP_kinematics.RevoluteJoint_last_updated_angle__set, doc=
r"""last_updated_angle_ : double""")
806 rot_axis_unit_vector_ = property(_IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__get, _IMP_kinematics.RevoluteJoint_rot_axis_unit_vector__set, doc=
r"""rot_axis_unit_vector_ : IMP::algebra::Vector3D""")
807 rot_axis_origin_ = property(_IMP_kinematics.RevoluteJoint_rot_axis_origin__get, _IMP_kinematics.RevoluteJoint_rot_axis_origin__set, doc=
r"""rot_axis_origin_ : IMP::algebra::Vector3D""")
810 r"""__str__(RevoluteJoint self) -> std::string"""
811 return _IMP_kinematics.RevoluteJoint___str__(self)
814 r"""__repr__(RevoluteJoint self) -> std::string"""
815 return _IMP_kinematics.RevoluteJoint___repr__(self)
819 return _object_cast_to_RevoluteJoint(o)
822 def get_type_name(self):
823 return self.__class__.__name__
824 def do_show(self, out):
827 if"IMP::kinematics" ==
"IMP":
828 return VersionInfo(self.__module__,
835 return _object_cast_to_RevoluteJoint(o)
837 def __disown__(self):
839 _IMP_kinematics.disown_RevoluteJoint(self)
840 return weakref.proxy(self)
843 r"""do_destroy(RevoluteJoint self)"""
844 return _IMP_kinematics.RevoluteJoint_do_destroy(self)
847 _IMP_kinematics.RevoluteJoint_swigregister(RevoluteJoint)
848 class DihedralAngleRevoluteJoint(RevoluteJoint):
849 r"""Proxy of C++ IMP::kinematics::DihedralAngleRevoluteJoint class."""
851 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
853 def __init__(self, parent, child, a, b, c, d):
854 r"""__init__(DihedralAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c, XYZ d) -> DihedralAngleRevoluteJoint"""
855 _IMP_kinematics.DihedralAngleRevoluteJoint_swiginit(self, _IMP_kinematics.new_DihedralAngleRevoluteJoint(parent, child, a, b, c, d))
858 r"""get_a(DihedralAngleRevoluteJoint self) -> XYZ"""
859 return _IMP_kinematics.DihedralAngleRevoluteJoint_get_a(self)
862 r"""get_b(DihedralAngleRevoluteJoint self) -> XYZ"""
863 return _IMP_kinematics.DihedralAngleRevoluteJoint_get_b(self)
866 r"""get_c(DihedralAngleRevoluteJoint self) -> XYZ"""
867 return _IMP_kinematics.DihedralAngleRevoluteJoint_get_c(self)
870 r"""get_d(DihedralAngleRevoluteJoint self) -> XYZ"""
871 return _IMP_kinematics.DihedralAngleRevoluteJoint_get_d(self)
874 r"""__str__(DihedralAngleRevoluteJoint self) -> std::string"""
875 return _IMP_kinematics.DihedralAngleRevoluteJoint___str__(self)
878 r"""__repr__(DihedralAngleRevoluteJoint self) -> std::string"""
879 return _IMP_kinematics.DihedralAngleRevoluteJoint___repr__(self)
883 return _object_cast_to_DihedralAngleRevoluteJoint(o)
885 __swig_destroy__ = _IMP_kinematics.delete_DihedralAngleRevoluteJoint
888 _IMP_kinematics.DihedralAngleRevoluteJoint_swigregister(DihedralAngleRevoluteJoint)
889 class BondAngleRevoluteJoint(RevoluteJoint):
890 r"""Proxy of C++ IMP::kinematics::BondAngleRevoluteJoint class."""
892 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
894 def __init__(self, parent, child, a, b, c):
895 r"""__init__(BondAngleRevoluteJoint self, RigidBody parent, RigidBody child, XYZ a, XYZ b, XYZ c) -> BondAngleRevoluteJoint"""
896 _IMP_kinematics.BondAngleRevoluteJoint_swiginit(self, _IMP_kinematics.new_BondAngleRevoluteJoint(parent, child, a, b, c))
899 r"""__str__(BondAngleRevoluteJoint self) -> std::string"""
900 return _IMP_kinematics.BondAngleRevoluteJoint___str__(self)
903 r"""__repr__(BondAngleRevoluteJoint self) -> std::string"""
904 return _IMP_kinematics.BondAngleRevoluteJoint___repr__(self)
908 return _object_cast_to_BondAngleRevoluteJoint(o)
910 __swig_destroy__ = _IMP_kinematics.delete_BondAngleRevoluteJoint
913 _IMP_kinematics.BondAngleRevoluteJoint_swigregister(BondAngleRevoluteJoint)
915 r"""Proxy of C++ IMP::kinematics::RevoluteJointMover class."""
917 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
919 def __init__(self, m, joints, stddev=0.01):
920 r"""__init__(RevoluteJointMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const stddev=0.01) -> RevoluteJointMover"""
921 _IMP_kinematics.RevoluteJointMover_swiginit(self, _IMP_kinematics.new_RevoluteJointMover(m, joints, stddev))
923 def set_sigma(self, sigma):
924 r"""set_sigma(RevoluteJointMover self, IMP::Float sigma)"""
925 return _IMP_kinematics.RevoluteJointMover_set_sigma(self, sigma)
928 r"""get_sigma(RevoluteJointMover self) -> IMP::Float"""
929 return _IMP_kinematics.RevoluteJointMover_get_sigma(self)
932 r"""get_version_info(RevoluteJointMover self) -> VersionInfo"""
933 return _IMP_kinematics.RevoluteJointMover_get_version_info(self)
934 __swig_destroy__ = _IMP_kinematics.delete_RevoluteJointMover
937 r"""__str__(RevoluteJointMover self) -> std::string"""
938 return _IMP_kinematics.RevoluteJointMover___str__(self)
941 r"""__repr__(RevoluteJointMover self) -> std::string"""
942 return _IMP_kinematics.RevoluteJointMover___repr__(self)
946 return _object_cast_to_RevoluteJointMover(o)
950 _IMP_kinematics.RevoluteJointMover_swigregister(RevoluteJointMover)
952 r"""Proxy of C++ IMP::kinematics::DihedralMover class."""
954 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
956 def __init__(self, m, joints, max_rot=0.1):
957 r"""__init__(DihedralMover self, Model m, IMP::kinematics::RevoluteJoints const & joints, double const max_rot=0.1) -> DihedralMover"""
958 _IMP_kinematics.DihedralMover_swiginit(self, _IMP_kinematics.new_DihedralMover(m, joints, max_rot))
961 r"""get_version_info(DihedralMover self) -> VersionInfo"""
962 return _IMP_kinematics.DihedralMover_get_version_info(self)
963 __swig_destroy__ = _IMP_kinematics.delete_DihedralMover
966 r"""__str__(DihedralMover self) -> std::string"""
967 return _IMP_kinematics.DihedralMover___str__(self)
970 r"""__repr__(DihedralMover self) -> std::string"""
971 return _IMP_kinematics.DihedralMover___repr__(self)
975 return _object_cast_to_DihedralMover(o)
979 _IMP_kinematics.DihedralMover_swigregister(DihedralMover)
981 r"""Proxy of C++ IMP::kinematics::KinematicForest class."""
983 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
986 r"""get_version_info(KinematicForest self) -> VersionInfo"""
987 return _IMP_kinematics.KinematicForest_get_version_info(self)
988 __swig_destroy__ = _IMP_kinematics.delete_KinematicForest
990 def __init__(self, *args):
992 __init__(KinematicForest self, Model m) -> KinematicForest
993 __init__(KinematicForest self, Model m, Hierarchy hierarchy) -> KinematicForest
995 _IMP_kinematics.KinematicForest_swiginit(self, _IMP_kinematics.new_KinematicForest(*args))
997 def add_edge(self, *args):
999 add_edge(KinematicForest self, RigidBody parent, RigidBody child) -> Joint
1000 add_edge(KinematicForest self, Joint joint)
1002 return _IMP_kinematics.KinematicForest_add_edge(self, *args)
1004 def add_rigid_bodies_in_chain(self, rbs):
1005 r"""add_rigid_bodies_in_chain(KinematicForest self, IMP::core::RigidBodies rbs)"""
1006 return _IMP_kinematics.KinematicForest_add_rigid_bodies_in_chain(self, rbs)
1008 def reset_root(self, new_root):
1009 r"""reset_root(KinematicForest self, Particle new_root)"""
1010 return _IMP_kinematics.KinematicForest_reset_root(self, new_root)
1012 def update_all_internal_coordinates(self):
1013 r"""update_all_internal_coordinates(KinematicForest self)"""
1014 return _IMP_kinematics.KinematicForest_update_all_internal_coordinates(self)
1016 def update_all_external_coordinates(self):
1017 r"""update_all_external_coordinates(KinematicForest self)"""
1018 return _IMP_kinematics.KinematicForest_update_all_external_coordinates(self)
1020 def get_ordered_joints(self):
1021 r"""get_ordered_joints(KinematicForest self) -> IMP::kinematics::Joints"""
1022 return _IMP_kinematics.KinematicForest_get_ordered_joints(self)
1024 def transform_safe(self, tr):
1025 r"""transform_safe(KinematicForest self, Transformation3D tr)"""
1026 return _IMP_kinematics.KinematicForest_transform_safe(self, tr)
1028 def mark_internal_coordinates_changed(self):
1029 r"""mark_internal_coordinates_changed(KinematicForest self)"""
1030 return _IMP_kinematics.KinematicForest_mark_internal_coordinates_changed(self)
1032 def mark_external_coordinates_changed(self):
1033 r"""mark_external_coordinates_changed(KinematicForest self)"""
1034 return _IMP_kinematics.KinematicForest_mark_external_coordinates_changed(self)
1036 def set_coordinates_safe(self, rb, c):
1037 r"""set_coordinates_safe(KinematicForest self, RigidBody rb, Vector3D c)"""
1038 return _IMP_kinematics.KinematicForest_set_coordinates_safe(self, rb, c)
1040 def get_coordinates_safe(self, rb):
1041 r"""get_coordinates_safe(KinematicForest self, RigidBody rb) -> Vector3D"""
1042 return _IMP_kinematics.KinematicForest_get_coordinates_safe(self, rb)
1044 def get_is_member(self, rb):
1045 r"""get_is_member(KinematicForest self, RigidBody rb) -> bool"""
1046 return _IMP_kinematics.KinematicForest_get_is_member(self, rb)
1048 def get_reference_frame_safe(self, rb):
1049 r"""get_reference_frame_safe(KinematicForest self, RigidBody rb) -> ReferenceFrame3D"""
1050 return _IMP_kinematics.KinematicForest_get_reference_frame_safe(self, rb)
1052 def set_reference_frame_safe(self, rb, r):
1053 r"""set_reference_frame_safe(KinematicForest self, RigidBody rb, ReferenceFrame3D r)"""
1054 return _IMP_kinematics.KinematicForest_set_reference_frame_safe(self, rb, r)
1056 def apply_transform_safely(self, tr):
1057 r"""apply_transform_safely(KinematicForest self, Transformation3D tr)"""
1058 return _IMP_kinematics.KinematicForest_apply_transform_safely(self, tr)
1061 r"""__str__(KinematicForest self) -> std::string"""
1062 return _IMP_kinematics.KinematicForest___str__(self)
1065 r"""__repr__(KinematicForest self) -> std::string"""
1066 return _IMP_kinematics.KinematicForest___repr__(self)
1070 return _object_cast_to_KinematicForest(o)
1074 _IMP_kinematics.KinematicForest_swigregister(KinematicForest)
1076 r"""Proxy of C++ IMP::kinematics::KinematicForestScoreState class."""
1078 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1081 r"""get_version_info(KinematicForestScoreState self) -> VersionInfo"""
1082 return _IMP_kinematics.KinematicForestScoreState_get_version_info(self)
1083 __swig_destroy__ = _IMP_kinematics.delete_KinematicForestScoreState
1085 def __init__(self, kf, rbs, atoms):
1086 r"""__init__(KinematicForestScoreState self, KinematicForest kf, IMP::core::RigidBodies rbs, IMP::ParticlesTemp atoms) -> KinematicForestScoreState"""
1087 _IMP_kinematics.KinematicForestScoreState_swiginit(self, _IMP_kinematics.new_KinematicForestScoreState(kf, rbs, atoms))
1089 def do_before_evaluate(self):
1090 r"""do_before_evaluate(KinematicForestScoreState self)"""
1091 return _IMP_kinematics.KinematicForestScoreState_do_before_evaluate(self)
1093 def do_after_evaluate(self, da):
1094 r"""do_after_evaluate(KinematicForestScoreState self, DerivativeAccumulator da)"""
1095 return _IMP_kinematics.KinematicForestScoreState_do_after_evaluate(self, da)
1098 r"""do_get_inputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1099 return _IMP_kinematics.KinematicForestScoreState_do_get_inputs(self)
1102 r"""do_get_outputs(KinematicForestScoreState self) -> IMP::ModelObjectsTemp"""
1103 return _IMP_kinematics.KinematicForestScoreState_do_get_outputs(self)
1106 r"""__str__(KinematicForestScoreState self) -> std::string"""
1107 return _IMP_kinematics.KinematicForestScoreState___str__(self)
1110 r"""__repr__(KinematicForestScoreState self) -> std::string"""
1111 return _IMP_kinematics.KinematicForestScoreState___repr__(self)
1115 return _object_cast_to_KinematicForestScoreState(o)
1119 _IMP_kinematics.KinematicForestScoreState_swigregister(KinematicForestScoreState)
1121 r"""Proxy of C++ IMP::kinematics::DOF class."""
1123 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1126 r"""get_version_info(DOF self) -> VersionInfo"""
1127 return _IMP_kinematics.DOF_get_version_info(self)
1128 __swig_destroy__ = _IMP_kinematics.delete_DOF
1130 def __init__(self, *args):
1132 __init__(DOF self, double v) -> DOF
1133 __init__(DOF self, double v, double min, double max, double step_size) -> DOF
1135 _IMP_kinematics.DOF_swiginit(self, _IMP_kinematics.new_DOF(*args))
1137 def get_value(self):
1138 r"""get_value(DOF self) -> double"""
1139 return _IMP_kinematics.DOF_get_value(self)
1141 def set_value(self, v):
1142 r"""set_value(DOF self, double v)"""
1143 return _IMP_kinematics.DOF_set_value(self, v)
1145 def get_range(self):
1146 r"""get_range(DOF self) -> std::pair< double,double >"""
1147 return _IMP_kinematics.DOF_get_range(self)
1149 def set_range(self, range):
1150 r"""set_range(DOF self, std::pair< double,double > range)"""
1151 return _IMP_kinematics.DOF_set_range(self, range)
1153 def get_step_size(self):
1154 r"""get_step_size(DOF self) -> double"""
1155 return _IMP_kinematics.DOF_get_step_size(self)
1157 def set_step_size(self, step_size):
1158 r"""set_step_size(DOF self, double step_size)"""
1159 return _IMP_kinematics.DOF_set_step_size(self, step_size)
1161 def get_number_of_steps(self, *args):
1163 get_number_of_steps(DOF self, double value) -> int
1164 get_number_of_steps(DOF self, double value1, double value2) -> int
1166 return _IMP_kinematics.DOF_get_number_of_steps(self, *args)
1169 r"""__str__(DOF self) -> std::string"""
1170 return _IMP_kinematics.DOF___str__(self)
1173 r"""__repr__(DOF self) -> std::string"""
1174 return _IMP_kinematics.DOF___repr__(self)
1178 return _object_cast_to_DOF(o)
1182 _IMP_kinematics.DOF_swigregister(DOF)
1183 class DOFValues(IMP.saxs.DistBase):
1184 r"""Proxy of C++ IMP::kinematics::DOFValues class."""
1186 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1188 def __init__(self, *args):
1190 __init__(DOFValues self, IMP::kinematics::DOFs const & dofs) -> DOFValues
1191 __init__(DOFValues self) -> DOFValues
1193 _IMP_kinematics.DOFValues_swiginit(self, _IMP_kinematics.new_DOFValues(*args))
1195 def get_distance2(self, *args):
1197 get_distance2(DOFValues self, DOFValues other_dof_values) -> double
1198 get_distance2(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1200 return _IMP_kinematics.DOFValues_get_distance2(self, *args)
1204 get_distance(DOFValues self, DOFValues other_dof_values) -> double
1205 get_distance(DOFValues self, DOFValues other_dof_values, std::vector< bool,std::allocator< bool > > const & active_dofs) -> double
1207 return _IMP_kinematics.DOFValues_get_distance(self, *args)
1209 def show(self, *args):
1210 r"""show(DOFValues self, _ostream out=std::cout)"""
1211 return _IMP_kinematics.DOFValues_show(self, *args)
1214 r"""__str__(DOFValues self) -> std::string"""
1215 return _IMP_kinematics.DOFValues___str__(self)
1218 r"""__repr__(DOFValues self) -> std::string"""
1219 return _IMP_kinematics.DOFValues___repr__(self)
1221 def _get_as_binary(self):
1222 r"""_get_as_binary(DOFValues self) -> PyObject *"""
1223 return _IMP_kinematics.DOFValues__get_as_binary(self)
1225 def _set_from_binary(self, p):
1226 r"""_set_from_binary(DOFValues self, PyObject * p)"""
1227 return _IMP_kinematics.DOFValues__set_from_binary(self, p)
1229 def __getstate__(self):
1230 p = self._get_as_binary()
1231 if len(self.__dict__) > 1:
1232 d = self.__dict__.copy()
1237 def __setstate__(self, p):
1238 if not hasattr(self,
'this'):
1240 if isinstance(p, tuple):
1242 self.__dict__.update(d)
1243 return self._set_from_binary(p)
1245 __swig_destroy__ = _IMP_kinematics.delete_DOFValues
1248 _IMP_kinematics.DOFValues_swigregister(DOFValues)
1250 r"""Proxy of C++ IMP::kinematics::DirectionalDOF class."""
1252 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1254 def __init__(self, dofs):
1255 r"""__init__(DirectionalDOF self, IMP::kinematics::DOFs const & dofs) -> DirectionalDOF"""
1256 _IMP_kinematics.DirectionalDOF_swiginit(self, _IMP_kinematics.new_DirectionalDOF(dofs))
1258 def set_end_points(self, q1, q2):
1259 r"""set_end_points(DirectionalDOF self, DOFValues q1, DOFValues q2)"""
1260 return _IMP_kinematics.DirectionalDOF_set_end_points(self, q1, q2)
1262 def get_dofs_values(self):
1263 r"""get_dofs_values(DirectionalDOF self) -> DOFValues"""
1264 return _IMP_kinematics.DirectionalDOF_get_dofs_values(self)
1266 def get_value(self):
1267 r"""get_value(DirectionalDOF self) -> double"""
1268 return _IMP_kinematics.DirectionalDOF_get_value(self)
1271 r"""get_version_info(DirectionalDOF self) -> VersionInfo"""
1272 return _IMP_kinematics.DirectionalDOF_get_version_info(self)
1273 __swig_destroy__ = _IMP_kinematics.delete_DirectionalDOF
1276 r"""__str__(DirectionalDOF self) -> std::string"""
1277 return _IMP_kinematics.DirectionalDOF___str__(self)
1280 r"""__repr__(DirectionalDOF self) -> std::string"""
1281 return _IMP_kinematics.DirectionalDOF___repr__(self)
1285 return _object_cast_to_DirectionalDOF(o)
1289 _IMP_kinematics.DirectionalDOF_swigregister(DirectionalDOF)
1291 r"""Proxy of C++ IMP::kinematics::DOFsSampler class."""
1293 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1295 def get_type_name(self):
1296 r"""get_type_name(DOFsSampler self) -> std::string"""
1297 return _IMP_kinematics.DOFsSampler_get_type_name(self)
1300 r"""get_version_info(DOFsSampler self) -> VersionInfo"""
1301 return _IMP_kinematics.DOFsSampler_get_version_info(self)
1302 __swig_destroy__ = _IMP_kinematics.delete_DOFsSampler
1304 def __init__(self, dofs):
1305 r"""__init__(DOFsSampler self, IMP::kinematics::DOFs dofs) -> DOFsSampler"""
1306 if self.__class__ == DOFsSampler:
1310 _IMP_kinematics.DOFsSampler_swiginit(self, _IMP_kinematics.new_DOFsSampler(_self, dofs))
1312 if self.__class__ != DOFsSampler:
1313 _director_objects.register(self)
1318 def get_sample(self):
1319 r"""get_sample(DOFsSampler self) -> DOFValues"""
1320 return _IMP_kinematics.DOFsSampler_get_sample(self)
1322 def apply(self, values):
1323 r"""apply(DOFsSampler self, DOFValues values)"""
1324 return _IMP_kinematics.DOFsSampler_apply(self, values)
1326 def apply_last_sample(self):
1327 r"""apply_last_sample(DOFsSampler self)"""
1328 return _IMP_kinematics.DOFsSampler_apply_last_sample(self)
1330 def sample_and_apply(self):
1331 r"""sample_and_apply(DOFsSampler self)"""
1332 return _IMP_kinematics.DOFsSampler_sample_and_apply(self)
1335 r"""get_dofs(DOFsSampler self) -> IMP::kinematics::DOFs const &"""
1336 return _IMP_kinematics.DOFsSampler_get_dofs(self)
1338 def get_dof(self, i):
1339 r"""get_dof(DOFsSampler self, unsigned int i) -> DOF"""
1340 return _IMP_kinematics.DOFsSampler_get_dof(self, i)
1342 def get_number_of_dofs(self):
1343 r"""get_number_of_dofs(DOFsSampler self) -> unsigned int"""
1344 return _IMP_kinematics.DOFsSampler_get_number_of_dofs(self)
1346 def do_get_sample(self):
1347 r"""do_get_sample(DOFsSampler self) -> DOFValues"""
1348 return _IMP_kinematics.DOFsSampler_do_get_sample(self)
1351 r"""__str__(DOFsSampler self) -> std::string"""
1352 return _IMP_kinematics.DOFsSampler___str__(self)
1355 r"""__repr__(DOFsSampler self) -> std::string"""
1356 return _IMP_kinematics.DOFsSampler___repr__(self)
1360 return _object_cast_to_DOFsSampler(o)
1363 def get_type_name(self):
1364 return self.__class__.__name__
1365 def do_show(self, out):
1368 if"IMP::kinematics" ==
"IMP":
1369 return VersionInfo(self.__module__,
1376 return _object_cast_to_DOFsSampler(o)
1378 def __disown__(self):
1380 _IMP_kinematics.disown_DOFsSampler(self)
1381 return weakref.proxy(self)
1384 r"""do_destroy(DOFsSampler self)"""
1385 return _IMP_kinematics.DOFsSampler_do_destroy(self)
1388 _IMP_kinematics.DOFsSampler_swigregister(DOFsSampler)
1389 class FibrilSampler(DOFsSampler):
1390 r"""Proxy of C++ IMP::kinematics::FibrilSampler class."""
1392 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1394 def __init__(self, trans_joint, dihedral_joints, dofs):
1395 r"""__init__(FibrilSampler self, IMP::kinematics::TransformationJoints trans_joint, IMP::kinematics::DihedralAngleRevoluteJoints dihedral_joints, IMP::kinematics::DOFs dofs) -> FibrilSampler"""
1396 _IMP_kinematics.FibrilSampler_swiginit(self, _IMP_kinematics.new_FibrilSampler(trans_joint, dihedral_joints, dofs))
1398 def apply_floats(self, values):
1399 r"""apply_floats(FibrilSampler self, IMP::Floats const & values)"""
1400 return _IMP_kinematics.FibrilSampler_apply_floats(self, values)
1402 def get_dihedral_joints(self):
1403 r"""get_dihedral_joints(FibrilSampler self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1404 return _IMP_kinematics.FibrilSampler_get_dihedral_joints(self)
1406 def get_transformation_joint(self):
1407 r"""get_transformation_joint(FibrilSampler self) -> IMP::kinematics::TransformationJoints"""
1408 return _IMP_kinematics.FibrilSampler_get_transformation_joint(self)
1411 r"""__str__(FibrilSampler self) -> std::string"""
1412 return _IMP_kinematics.FibrilSampler___str__(self)
1415 r"""__repr__(FibrilSampler self) -> std::string"""
1416 return _IMP_kinematics.FibrilSampler___repr__(self)
1420 return _object_cast_to_FibrilSampler(o)
1422 __swig_destroy__ = _IMP_kinematics.delete_FibrilSampler
1425 _IMP_kinematics.FibrilSampler_swigregister(FibrilSampler)
1426 class UniformBackboneSampler(DOFsSampler):
1427 r"""Proxy of C++ IMP::kinematics::UniformBackboneSampler class."""
1429 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1431 def __init__(self, joints, dofs):
1432 r"""__init__(UniformBackboneSampler self, IMP::kinematics::DihedralAngleRevoluteJoints joints, IMP::kinematics::DOFs dofs) -> UniformBackboneSampler"""
1433 _IMP_kinematics.UniformBackboneSampler_swiginit(self, _IMP_kinematics.new_UniformBackboneSampler(joints, dofs))
1435 def apply_floats(self, values):
1436 r"""apply_floats(UniformBackboneSampler self, IMP::Floats const & values)"""
1437 return _IMP_kinematics.UniformBackboneSampler_apply_floats(self, values)
1439 def get_joints(self):
1440 r"""get_joints(UniformBackboneSampler self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1441 return _IMP_kinematics.UniformBackboneSampler_get_joints(self)
1444 r"""__str__(UniformBackboneSampler self) -> std::string"""
1445 return _IMP_kinematics.UniformBackboneSampler___str__(self)
1448 r"""__repr__(UniformBackboneSampler self) -> std::string"""
1449 return _IMP_kinematics.UniformBackboneSampler___repr__(self)
1453 return _object_cast_to_UniformBackboneSampler(o)
1455 __swig_destroy__ = _IMP_kinematics.delete_UniformBackboneSampler
1458 _IMP_kinematics.UniformBackboneSampler_swigregister(UniformBackboneSampler)
1459 PHI = _IMP_kinematics.PHI
1461 PSI = _IMP_kinematics.PSI
1463 CHI = _IMP_kinematics.CHI
1465 CHI1 = _IMP_kinematics.CHI1
1467 CHI2 = _IMP_kinematics.CHI2
1469 CHI3 = _IMP_kinematics.CHI3
1471 CHI4 = _IMP_kinematics.CHI4
1473 CHI5 = _IMP_kinematics.CHI5
1475 OTHER = _IMP_kinematics.OTHER
1477 OTHER2 = _IMP_kinematics.OTHER2
1479 OTHER3 = _IMP_kinematics.OTHER3
1481 OTHER4 = _IMP_kinematics.OTHER4
1483 OTHER5 = _IMP_kinematics.OTHER5
1485 TOTAL = _IMP_kinematics.TOTAL
1488 r"""Proxy of C++ IMP::kinematics::ProteinKinematics class."""
1490 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1492 def __init__(self, *args):
1494 __init__(ProteinKinematics self, Hierarchy mhd, bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1495 __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, IMP::ParticleIndexQuads const custom_dihedral_angles, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1496 __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & custom_dihedral_atoms, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1497 __init__(ProteinKinematics self, Hierarchy mhd, IMP::atom::Residues const & flexible_residues, IMP::ParticleIndexQuads const custom_dihedral_angles, std::vector< IMP::kinematics::ProteinAngleType,std::allocator< IMP::kinematics::ProteinAngleType > > const & custom_dihedral_angle_types, IMP::atom::Atoms open_loop_bond_atoms=IMP::atom::Atoms(), bool flexible_backbone=True, bool flexible_side_chains=False) -> ProteinKinematics
1499 _IMP_kinematics.ProteinKinematics_swiginit(self, _IMP_kinematics.new_ProteinKinematics(*args))
1501 def get_phi(self, r):
1502 r"""get_phi(ProteinKinematics self, Residue r) -> double"""
1503 return _IMP_kinematics.ProteinKinematics_get_phi(self, r)
1505 def get_psi(self, r):
1506 r"""get_psi(ProteinKinematics self, Residue r) -> double"""
1507 return _IMP_kinematics.ProteinKinematics_get_psi(self, r)
1509 def get_joints(self):
1510 r"""get_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1511 return _IMP_kinematics.ProteinKinematics_get_joints(self)
1513 def get_loop_joints(self):
1514 r"""get_loop_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1515 return _IMP_kinematics.ProteinKinematics_get_loop_joints(self)
1517 def get_ordered_joints(self):
1518 r"""get_ordered_joints(ProteinKinematics self) -> IMP::kinematics::DihedralAngleRevoluteJoints"""
1519 return _IMP_kinematics.ProteinKinematics_get_ordered_joints(self)
1521 def get_kinematic_forest(self):
1522 r"""get_kinematic_forest(ProteinKinematics self) -> KinematicForest"""
1523 return _IMP_kinematics.ProteinKinematics_get_kinematic_forest(self)
1525 def get_rigid_bodies(self):
1526 r"""get_rigid_bodies(ProteinKinematics self) -> IMP::core::RigidBodies"""
1527 return _IMP_kinematics.ProteinKinematics_get_rigid_bodies(self)
1529 def set_phi(self, r, angle):
1530 r"""set_phi(ProteinKinematics self, Residue r, double angle)"""
1531 return _IMP_kinematics.ProteinKinematics_set_phi(self, r, angle)
1533 def set_psi(self, r, angle):
1534 r"""set_psi(ProteinKinematics self, Residue r, double angle)"""
1535 return _IMP_kinematics.ProteinKinematics_set_psi(self, r, angle)
1538 r"""get_version_info(ProteinKinematics self) -> VersionInfo"""
1539 return _IMP_kinematics.ProteinKinematics_get_version_info(self)
1540 __swig_destroy__ = _IMP_kinematics.delete_ProteinKinematics
1542 def build_topology_graph(self):
1543 r"""build_topology_graph(ProteinKinematics self)"""
1544 return _IMP_kinematics.ProteinKinematics_build_topology_graph(self)
1546 def order_rigid_bodies(self, dihedral_angles, phi_angles, psi_angles, chi1_angles, chi2_angles, chi3_angles, chi4_angles, chi5_angles, open_loop_bond_atoms):
1547 r"""order_rigid_bodies(ProteinKinematics self, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & phi_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & psi_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi1_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi2_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi3_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi4_angles, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & chi5_angles, IMP::atom::Atoms open_loop_bond_atoms)"""
1548 return _IMP_kinematics.ProteinKinematics_order_rigid_bodies(self, dihedral_angles, phi_angles, psi_angles, chi1_angles, chi2_angles, chi3_angles, chi4_angles, chi5_angles, open_loop_bond_atoms)
1550 def mark_rotatable_angles(self, dihedral_angles):
1551 r"""mark_rotatable_angles(ProteinKinematics self, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles)"""
1552 return _IMP_kinematics.ProteinKinematics_mark_rotatable_angles(self, dihedral_angles)
1554 def mark_rotatable_angle(self, dihedral_angle):
1555 r"""mark_rotatable_angle(ProteinKinematics self, std::vector< IMP::atom::Atom,std::allocator< IMP::atom::Atom > > const & dihedral_angle)"""
1556 return _IMP_kinematics.ProteinKinematics_mark_rotatable_angle(self, dihedral_angle)
1558 def build_rigid_bodies(self):
1559 r"""build_rigid_bodies(ProteinKinematics self)"""
1560 return _IMP_kinematics.ProteinKinematics_build_rigid_bodies(self)
1562 def add_dihedral_joints(self, residues, angle_type, dihedral_angles):
1563 r"""add_dihedral_joints(ProteinKinematics self, std::vector< IMP::atom::Residue,std::allocator< IMP::atom::Residue > > const & residues, IMP::kinematics::ProteinAngleType angle_type, std::vector< IMP::atom::Atoms,std::allocator< IMP::atom::Atoms > > const & dihedral_angles)"""
1564 return _IMP_kinematics.ProteinKinematics_add_dihedral_joints(self, residues, angle_type, dihedral_angles)
1566 def add_dihedral_joint(self, r, angle_type, atoms):
1567 r"""add_dihedral_joint(ProteinKinematics self, Residue r, IMP::kinematics::ProteinAngleType angle_type, IMP::atom::Atoms const & atoms)"""
1568 return _IMP_kinematics.ProteinKinematics_add_dihedral_joint(self, r, angle_type, atoms)
1570 def open_loop(self, open_loop_bond_atoms):
1571 r"""open_loop(ProteinKinematics self, IMP::atom::Atoms open_loop_bond_atoms)"""
1572 return _IMP_kinematics.ProteinKinematics_open_loop(self, open_loop_bond_atoms)
1574 def get_phi_joint(self, r):
1575 r"""get_phi_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1576 return _IMP_kinematics.ProteinKinematics_get_phi_joint(self, r)
1578 def get_psi_joint(self, r):
1579 r"""get_psi_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1580 return _IMP_kinematics.ProteinKinematics_get_psi_joint(self, r)
1582 def get_other_joint(self, r):
1583 r"""get_other_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1584 return _IMP_kinematics.ProteinKinematics_get_other_joint(self, r)
1586 def get_chi1_joint(self, r):
1587 r"""get_chi1_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1588 return _IMP_kinematics.ProteinKinematics_get_chi1_joint(self, r)
1590 def get_chi2_joint(self, r):
1591 r"""get_chi2_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1592 return _IMP_kinematics.ProteinKinematics_get_chi2_joint(self, r)
1594 def get_chi3_joint(self, r):
1595 r"""get_chi3_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1596 return _IMP_kinematics.ProteinKinematics_get_chi3_joint(self, r)
1598 def get_chi4_joint(self, r):
1599 r"""get_chi4_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1600 return _IMP_kinematics.ProteinKinematics_get_chi4_joint(self, r)
1602 def get_chi5_joint(self, r):
1603 r"""get_chi5_joint(ProteinKinematics self, Residue r) -> DihedralAngleRevoluteJoint"""
1604 return _IMP_kinematics.ProteinKinematics_get_chi5_joint(self, r)
1606 def get_joint(self, r, angle):
1607 r"""get_joint(ProteinKinematics self, Residue r, IMP::kinematics::ProteinAngleType angle) -> DihedralAngleRevoluteJoint"""
1608 return _IMP_kinematics.ProteinKinematics_get_joint(self, r, angle)
1611 r"""__str__(ProteinKinematics self) -> std::string"""
1612 return _IMP_kinematics.ProteinKinematics___str__(self)
1615 r"""__repr__(ProteinKinematics self) -> std::string"""
1616 return _IMP_kinematics.ProteinKinematics___repr__(self)
1620 return _object_cast_to_ProteinKinematics(o)
1624 _IMP_kinematics.ProteinKinematics_swigregister(ProteinKinematics)
1626 r"""Proxy of C++ IMP::kinematics::LocalPlanner class."""
1628 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1630 def __init__(self, *args, **kwargs):
1631 raise AttributeError(
"No constructor defined - class is abstract")
1634 r"""get_version_info(LocalPlanner self) -> VersionInfo"""
1635 return _IMP_kinematics.LocalPlanner_get_version_info(self)
1636 __swig_destroy__ = _IMP_kinematics.delete_LocalPlanner
1638 def plan(self, q_near, q_rand, sf):
1639 r"""plan(LocalPlanner self, DOFValues q_near, DOFValues q_rand, ScoringFunction sf) -> std::vector< IMP::kinematics::DOFValues,std::allocator< IMP::kinematics::DOFValues > >"""
1640 return _IMP_kinematics.LocalPlanner_plan(self, q_near, q_rand, sf)
1642 def is_valid(self, values, sf):
1643 r"""is_valid(LocalPlanner self, DOFValues values, ScoringFunction sf) -> bool"""
1644 return _IMP_kinematics.LocalPlanner_is_valid(self, values, sf)
1647 r"""__str__(LocalPlanner self) -> std::string"""
1648 return _IMP_kinematics.LocalPlanner___str__(self)
1651 r"""__repr__(LocalPlanner self) -> std::string"""
1652 return _IMP_kinematics.LocalPlanner___repr__(self)
1656 return _object_cast_to_LocalPlanner(o)
1660 _IMP_kinematics.LocalPlanner_swigregister(LocalPlanner)
1661 class PathLocalPlanner(LocalPlanner):
1662 r"""Proxy of C++ IMP::kinematics::PathLocalPlanner class."""
1664 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1666 def __init__(self, model, dofs_sampler, directional_dof, save_step_interval=1):
1667 r"""__init__(PathLocalPlanner self, Model model, DOFsSampler dofs_sampler, DirectionalDOF directional_dof, int save_step_interval=1) -> PathLocalPlanner"""
1668 _IMP_kinematics.PathLocalPlanner_swiginit(self, _IMP_kinematics.new_PathLocalPlanner(model, dofs_sampler, directional_dof, save_step_interval))
1671 r"""__str__(PathLocalPlanner self) -> std::string"""
1672 return _IMP_kinematics.PathLocalPlanner___str__(self)
1675 r"""__repr__(PathLocalPlanner self) -> std::string"""
1676 return _IMP_kinematics.PathLocalPlanner___repr__(self)
1680 return _object_cast_to_PathLocalPlanner(o)
1682 __swig_destroy__ = _IMP_kinematics.delete_PathLocalPlanner
1685 _IMP_kinematics.PathLocalPlanner_swigregister(PathLocalPlanner)
1687 r"""Proxy of C++ IMP::kinematics::RRT class."""
1689 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1692 r"""get_version_info(RRT self) -> VersionInfo"""
1693 return _IMP_kinematics.RRT_get_version_info(self)
1694 __swig_destroy__ = _IMP_kinematics.delete_RRT
1696 def __init__(self, m, sampler, planner, cspace_dofs, iteration_number=1000, tree_size=100, number_of_sampled_dofs=0):
1697 r"""__init__(RRT self, Model m, DOFsSampler sampler, LocalPlanner planner, IMP::kinematics::DOFs const & cspace_dofs, unsigned int iteration_number=1000, unsigned int tree_size=100, unsigned int number_of_sampled_dofs=0) -> RRT"""
1698 _IMP_kinematics.RRT_swiginit(self, _IMP_kinematics.new_RRT(m, sampler, planner, cspace_dofs, iteration_number, tree_size, number_of_sampled_dofs))
1700 def do_sample(self):
1701 r"""do_sample(RRT self) -> ConfigurationSet"""
1702 return _IMP_kinematics.RRT_do_sample(self)
1704 def run(self, number_of_iterations=0):
1705 r"""run(RRT self, unsigned int number_of_iterations=0) -> bool"""
1706 return _IMP_kinematics.RRT_run(self, number_of_iterations)
1708 def get_DOFValuesList(self):
1709 r"""get_DOFValuesList(RRT self) -> IMP::kinematics::DOFValuesList"""
1710 return _IMP_kinematics.RRT_get_DOFValuesList(self)
1712 def set_number_of_iterations(self, num):
1713 r"""set_number_of_iterations(RRT self, unsigned int num)"""
1714 return _IMP_kinematics.RRT_set_number_of_iterations(self, num)
1716 def set_tree_size(self, num):
1717 r"""set_tree_size(RRT self, unsigned int num)"""
1718 return _IMP_kinematics.RRT_set_tree_size(self, num)
1720 def set_actual_tree_size(self, num):
1721 r"""set_actual_tree_size(RRT self, unsigned int num)"""
1722 return _IMP_kinematics.RRT_set_actual_tree_size(self, num)
1724 def set_number_of_collisions(self, num):
1725 r"""set_number_of_collisions(RRT self, unsigned int num)"""
1726 return _IMP_kinematics.RRT_set_number_of_collisions(self, num)
1728 def check_initial_configuration(self, sf):
1729 r"""check_initial_configuration(RRT self, ScoringFunction sf)"""
1730 return _IMP_kinematics.RRT_check_initial_configuration(self, sf)
1733 r"""__str__(RRT self) -> std::string"""
1734 return _IMP_kinematics.RRT___str__(self)
1737 r"""__repr__(RRT self) -> std::string"""
1738 return _IMP_kinematics.RRT___repr__(self)
1742 return _object_cast_to_RRT(o)
1746 _IMP_kinematics.RRT_swigregister(RRT)
1749 r"""get_module_version() -> std::string const"""
1750 return _IMP_kinematics.get_module_version()
1753 r"""get_example_path(std::string fname) -> std::string"""
1754 return _IMP_kinematics.get_example_path(fname)
1757 r"""get_data_path(std::string fname) -> std::string"""
1758 return _IMP_kinematics.get_data_path(fname)
1760 from .
import _version_check
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
Base class for all samplers.
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()
Common base class for heavy weight IMP objects.
ScoreStates maintain invariants in the Model.
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.
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.
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.