11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
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_ATOM_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_ATOM_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_atom.delete_IMP_ATOM_SwigPyIterator
78 r"""value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
79 return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
82 r"""incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
83 return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
87 return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
95 return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
99 return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
102 r"""next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
103 return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
106 r"""__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
107 return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
110 r"""previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
111 return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
115 return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
119 return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
123 return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
127 return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
131 return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
135 return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
140 __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
147 _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
154 IMP_DEBUG = _IMP_atom.IMP_DEBUG
156 IMP_RELEASE = _IMP_atom.IMP_RELEASE
158 IMP_SILENT = _IMP_atom.IMP_SILENT
160 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
162 IMP_TERSE = _IMP_atom.IMP_TERSE
164 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
166 IMP_MEMORY = _IMP_atom.IMP_MEMORY
168 IMP_NONE = _IMP_atom.IMP_NONE
170 IMP_USAGE = _IMP_atom.IMP_USAGE
172 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_atom.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_atom.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_atom.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.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_atom._ostream_write(self, osa_buf)
237 _IMP_atom._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
321 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
323 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
325 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
327 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
352 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
377 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
381 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
385 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
387 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
389 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
393 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
396 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex > class."""
398 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
399 __repr__ = _swig_repr
402 r"""__init__(HierarchyTree self) -> HierarchyTree"""
403 _IMP_atom.HierarchyTree_swiginit(self, _IMP_atom.new_HierarchyTree())
406 r"""get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
407 return _IMP_atom.HierarchyTree_get_graph(self)
410 r"""get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
411 return _IMP_atom.HierarchyTree_get_vertices(self)
413 def get_vertex_name(self, i):
414 r"""get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
415 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
417 def get_in_neighbors(self, v):
418 r"""get_in_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
419 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
421 def get_out_neighbors(self, v):
422 r"""get_out_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
423 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
426 r"""show_graphviz(HierarchyTree self, _ostream out=std::cout)"""
427 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
429 def get_graphviz_string(self):
430 r"""get_graphviz_string(HierarchyTree self) -> std::string"""
431 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
433 def add_edge(self, v0, v1):
434 r"""add_edge(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)"""
435 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
437 def add_vertex(self, l):
438 r"""add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
439 return _IMP_atom.HierarchyTree_add_vertex(self, l)
441 def remove_vertex(self, l):
442 r"""remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
443 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
444 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
447 _IMP_atom.HierarchyTree_swigregister(HierarchyTree)
449 _value_types.append(
"HierarchyTree")
453 _plural_types.append(
"PDBRecords")
454 _value_types.append(
"PDBRecord")
457 _object_types.append(
"PDBSelector")
460 def _object_cast_to_PDBSelector(o):
461 r"""_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
462 return _IMP_atom._object_cast_to_PDBSelector(o)
465 return [Angle(x)
for x
in l]
466 _plural_types.append(
"Angles")
469 _value_types.append(
"Angle")
473 return [Atom(x)
for x
in l]
474 _plural_types.append(
"Atoms")
477 _value_types.append(
"Atom")
481 return [Bond(x)
for x
in l]
482 _plural_types.append(
"Bonds")
485 _value_types.append(
"Bond")
489 return [Bonded(x)
for x
in l]
490 _plural_types.append(
"Bondeds")
493 _value_types.append(
"Bonded")
496 def CHARMMAtomList(l=[]):
497 return [CHARMMAtom(x)
for x
in l]
498 _plural_types.append(
"CHARMMAtomList")
501 _value_types.append(
"CHARMMAtom")
505 return [Chain(x)
for x
in l]
506 _plural_types.append(
"Chains")
509 _value_types.append(
"Chain")
512 def CenterOfMasses(l=[]):
513 return [CenterOfMass(x)
for x
in l]
514 _plural_types.append(
"CenterOfMasses")
517 _value_types.append(
"CenterOfMass")
521 return [Charged(x)
for x
in l]
522 _plural_types.append(
"Chargeds")
525 _value_types.append(
"Charged")
528 def Diffusions(l=[]):
529 return [Diffusion(x)
for x
in l]
530 _plural_types.append(
"Diffusions")
533 _value_types.append(
"Diffusion")
536 def RigidBodyDiffusions(l=[]):
537 return [RigidBodyDiffusion(x)
for x
in l]
538 _plural_types.append(
"RigidBodyDiffusions")
541 _value_types.append(
"RigidBodyDiffusion")
544 def TAMDParticles(l=[]):
545 return [TAMDParticle(x)
for x
in l]
546 _plural_types.append(
"TAMDParticles")
549 _value_types.append(
"TAMDParticle")
552 def TAMDCentroids(l=[]):
553 return [TAMDCentroid(x)
for x
in l]
554 _plural_types.append(
"TAMDCentroids")
557 _value_types.append(
"TAMDCentroid")
561 return [Dihedral(x)
for x
in l]
562 _plural_types.append(
"Dihedrals")
565 _value_types.append(
"Dihedral")
569 return [Domain(x)
for x
in l]
570 _plural_types.append(
"Domains")
573 _value_types.append(
"Domain")
577 return [Fragment(x)
for x
in l]
578 _plural_types.append(
"Fragments")
581 _value_types.append(
"Fragment")
584 def Hierarchies(l=[]):
585 return [Hierarchy(x)
for x
in l]
586 _plural_types.append(
"Hierarchies")
589 _value_types.append(
"Hierarchy")
592 def LennardJonesList(l=[]):
593 return [LennardJones(x)
for x
in l]
594 _plural_types.append(
"LennardJonesList")
597 _value_types.append(
"LennardJones")
601 return [Mass(x)
for x
in l]
602 _plural_types.append(
"Masses")
605 _value_types.append(
"Mass")
608 def LinearVelocities(l=[]):
609 return [LinearVelocity(x)
for x
in l]
610 _plural_types.append(
"LinearVelocities")
613 _value_types.append(
"LinearVelocity")
616 def AngularVelocities(l=[]):
617 return [AngularVelocity(x)
for x
in l]
618 _plural_types.append(
"AngularVelocities")
621 _value_types.append(
"AngularVelocity")
625 return [Molecule(x)
for x
in l]
626 _plural_types.append(
"Molecules")
629 _value_types.append(
"Molecule")
633 return [Residue(x)
for x
in l]
634 _plural_types.append(
"Residues")
637 _value_types.append(
"Residue")
640 def Representations(l=[]):
641 return [Representation(x)
for x
in l]
642 _plural_types.append(
"Representations")
645 _value_types.append(
"Representation")
649 return [State(x)
for x
in l]
650 _plural_types.append(
"States")
653 _value_types.append(
"State")
657 return [Copy(x)
for x
in l]
658 _plural_types.append(
"Copies")
661 _value_types.append(
"Copy")
664 def SecondaryStructureResidues(l=[]):
665 return [SecondaryStructureResidue(x)
for x
in l]
666 _plural_types.append(
"SecondaryStructureResidues")
669 _value_types.append(
"SecondaryStructureResidue")
672 def StructureSources(l=[]):
673 return [StructureSource(x)
for x
in l]
674 _plural_types.append(
"StructureSources")
677 _value_types.append(
"StructureSource")
680 _object_types.append(
"Simulator")
683 def _object_cast_to_Simulator(o):
684 r"""_object_cast_to_Simulator(Object o) -> Simulator"""
685 return _IMP_atom._object_cast_to_Simulator(o)
687 _object_types.append(
"ATOMPDBSelector")
690 def _object_cast_to_ATOMPDBSelector(o):
691 r"""_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
692 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
694 _object_types.append(
"AllMol2Selector")
697 def _object_cast_to_AllMol2Selector(o):
698 r"""_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
699 return _IMP_atom._object_cast_to_AllMol2Selector(o)
701 _object_types.append(
"AllPDBSelector")
704 def _object_cast_to_AllPDBSelector(o):
705 r"""_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
706 return _IMP_atom._object_cast_to_AllPDBSelector(o)
708 _object_types.append(
"AndPDBSelector")
711 def _object_cast_to_AndPDBSelector(o):
712 r"""_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
713 return _IMP_atom._object_cast_to_AndPDBSelector(o)
715 _object_types.append(
"XorPDBSelector")
718 def _object_cast_to_XorPDBSelector(o):
719 r"""_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
720 return _IMP_atom._object_cast_to_XorPDBSelector(o)
722 _object_types.append(
"ResidueTypePDBSelector")
725 def _object_cast_to_ResidueTypePDBSelector(o):
726 r"""_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
727 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
729 _object_types.append(
"AtomTypePDBSelector")
732 def _object_cast_to_AtomTypePDBSelector(o):
733 r"""_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
734 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
736 _object_types.append(
"AngleSingletonScore")
739 def _object_cast_to_AngleSingletonScore(o):
740 r"""_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
741 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
743 _object_types.append(
"BondEndpointsRefiner")
746 def _object_cast_to_BondEndpointsRefiner(o):
747 r"""_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
748 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
750 _object_types.append(
"BondPairContainer")
753 def _object_cast_to_BondPairContainer(o):
754 r"""_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
755 return _IMP_atom._object_cast_to_BondPairContainer(o)
757 _object_types.append(
"BondSingletonScore")
760 def _object_cast_to_BondSingletonScore(o):
761 r"""_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
762 return _IMP_atom._object_cast_to_BondSingletonScore(o)
764 _object_types.append(
"BondedPairFilter")
767 def _object_cast_to_BondedPairFilter(o):
768 r"""_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
769 return _IMP_atom._object_cast_to_BondedPairFilter(o)
771 _object_types.append(
"BrownianDynamics")
774 def _object_cast_to_BrownianDynamics(o):
775 r"""_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
776 return _IMP_atom._object_cast_to_BrownianDynamics(o)
778 _object_types.append(
"BrownianDynamicsTAMD")
781 def _object_cast_to_BrownianDynamicsTAMD(o):
782 r"""_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
783 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
785 _object_types.append(
"CAlphaPDBSelector")
788 def _object_cast_to_CAlphaPDBSelector(o):
789 r"""_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
790 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
792 _object_types.append(
"CBetaPDBSelector")
795 def _object_cast_to_CBetaPDBSelector(o):
796 r"""_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
797 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
799 _object_types.append(
"BackbonePDBSelector")
802 def _object_cast_to_BackbonePDBSelector(o):
803 r"""_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
804 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
806 _object_types.append(
"CHARMMParameters")
809 def _object_cast_to_CHARMMParameters(o):
810 r"""_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
811 return _IMP_atom._object_cast_to_CHARMMParameters(o)
813 _object_types.append(
"CHARMMResidueTopology")
816 def _object_cast_to_CHARMMResidueTopology(o):
817 r"""_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
818 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
820 _object_types.append(
"CHARMMSegmentTopology")
823 def _object_cast_to_CHARMMSegmentTopology(o):
824 r"""_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
825 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
827 _object_types.append(
"CHARMMStereochemistryRestraint")
830 def _object_cast_to_CHARMMStereochemistryRestraint(o):
831 r"""_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
832 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
834 _object_types.append(
"CHARMMTopology")
837 def _object_cast_to_CHARMMTopology(o):
838 r"""_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
839 return _IMP_atom._object_cast_to_CHARMMTopology(o)
841 _object_types.append(
"CPDBSelector")
844 def _object_cast_to_CPDBSelector(o):
845 r"""_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
846 return _IMP_atom._object_cast_to_CPDBSelector(o)
848 _object_types.append(
"ChainPDBSelector")
851 def _object_cast_to_ChainPDBSelector(o):
852 r"""_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
853 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
855 _object_types.append(
"CoulombPairScore")
858 def _object_cast_to_CoulombPairScore(o):
859 r"""_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
860 return _IMP_atom._object_cast_to_CoulombPairScore(o)
862 _object_types.append(
"CoverBond")
865 def _object_cast_to_CoverBond(o):
866 r"""_object_cast_to_CoverBond(Object o) -> CoverBond"""
867 return _IMP_atom._object_cast_to_CoverBond(o)
869 _object_types.append(
"DihedralSingletonScore")
872 def _object_cast_to_DihedralSingletonScore(o):
873 r"""_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
874 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
876 _object_types.append(
"DopePairScore")
879 def _object_cast_to_DopePairScore(o):
880 r"""_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
881 return _IMP_atom._object_cast_to_DopePairScore(o)
883 _object_types.append(
"LoopStatisticalPairScore")
886 def _object_cast_to_LoopStatisticalPairScore(o):
887 r"""_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
888 return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
890 _object_types.append(
"OrientedSoapPairScore")
893 def _object_cast_to_OrientedSoapPairScore(o):
894 r"""_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
895 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
897 _object_types.append(
"EzRestraint")
900 def _object_cast_to_EzRestraint(o):
901 r"""_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
902 return _IMP_atom._object_cast_to_EzRestraint(o)
904 _object_types.append(
"ForceFieldParameters")
907 def _object_cast_to_ForceFieldParameters(o):
908 r"""_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
909 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
911 _object_types.append(
"ForceSwitch")
914 def _object_cast_to_ForceSwitch(o):
915 r"""_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
916 return _IMP_atom._object_cast_to_ForceSwitch(o)
918 _object_types.append(
"HydrogenPDBSelector")
921 def _object_cast_to_HydrogenPDBSelector(o):
922 r"""_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
923 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
925 _object_types.append(
"ImproperSingletonScore")
928 def _object_cast_to_ImproperSingletonScore(o):
929 r"""_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
930 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
932 _object_types.append(
"LennardJonesPairScore")
935 def _object_cast_to_LennardJonesPairScore(o):
936 r"""_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
937 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
939 _object_types.append(
"Mol2Selector")
942 def _object_cast_to_Mol2Selector(o):
943 r"""_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
944 return _IMP_atom._object_cast_to_Mol2Selector(o)
946 _object_types.append(
"MolecularDynamics")
949 def _object_cast_to_MolecularDynamics(o):
950 r"""_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
951 return _IMP_atom._object_cast_to_MolecularDynamics(o)
953 _object_types.append(
"NPDBSelector")
956 def _object_cast_to_NPDBSelector(o):
957 r"""_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
958 return _IMP_atom._object_cast_to_NPDBSelector(o)
960 _object_types.append(
"NonAlternativePDBSelector")
963 def _object_cast_to_NonAlternativePDBSelector(o):
964 r"""_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
965 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
967 _object_types.append(
"NonHydrogenMol2Selector")
970 def _object_cast_to_NonHydrogenMol2Selector(o):
971 r"""_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
972 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
974 _object_types.append(
"NonHydrogenPDBSelector")
977 def _object_cast_to_NonHydrogenPDBSelector(o):
978 r"""_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
979 return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
981 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
984 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
985 r"""_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
986 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
988 _object_types.append(
"NonWaterPDBSelector")
991 def _object_cast_to_NonWaterPDBSelector(o):
992 r"""_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
993 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
995 _object_types.append(
"NotPDBSelector")
998 def _object_cast_to_NotPDBSelector(o):
999 r"""_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1000 return _IMP_atom._object_cast_to_NotPDBSelector(o)
1002 _object_types.append(
"OrPDBSelector")
1005 def _object_cast_to_OrPDBSelector(o):
1006 r"""_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1007 return _IMP_atom._object_cast_to_OrPDBSelector(o)
1009 _object_types.append(
"PPDBSelector")
1012 def _object_cast_to_PPDBSelector(o):
1013 r"""_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1014 return _IMP_atom._object_cast_to_PPDBSelector(o)
1016 _object_types.append(
"ProteinLigandAtomPairScore")
1019 def _object_cast_to_ProteinLigandAtomPairScore(o):
1020 r"""_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1021 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1023 _object_types.append(
"ProteinLigandRestraint")
1026 def _object_cast_to_ProteinLigandRestraint(o):
1027 r"""_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1028 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1030 _object_types.append(
"SameResiduePairFilter")
1033 def _object_cast_to_SameResiduePairFilter(o):
1034 r"""_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1035 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1037 _object_types.append(
"SoapPairFilter")
1040 def _object_cast_to_SoapPairFilter(o):
1041 r"""_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1042 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1044 _object_types.append(
"SmoothingFunction")
1047 def _object_cast_to_SmoothingFunction(o):
1048 r"""_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1049 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1051 _object_types.append(
"StereochemistryPairFilter")
1054 def _object_cast_to_StereochemistryPairFilter(o):
1055 r"""_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1056 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1058 _object_types.append(
"VelocityScalingOptimizerState")
1061 def _object_cast_to_VelocityScalingOptimizerState(o):
1062 r"""_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1063 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1065 _object_types.append(
"WaterPDBSelector")
1068 def _object_cast_to_WaterPDBSelector(o):
1069 r"""_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1070 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1072 _object_types.append(
"WritePDBOptimizerState")
1075 def _object_cast_to_WritePDBOptimizerState(o):
1076 r"""_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1077 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1080 _plural_types.append(
"AtomTypes")
1081 _value_types.append(
"AtomType")
1084 CHARMMAtomTopologies=list
1085 _plural_types.append(
"CHARMMAtomTopologies")
1086 _value_types.append(
"CHARMMAtomTopology")
1089 CHARMMBondEndpoints=list
1090 _plural_types.append(
"CHARMMBondEndpoints")
1091 _value_types.append(
"CHARMMBondEndpoint")
1094 CHARMMBondParametersList=list
1095 _plural_types.append(
"CHARMMBondParametersList")
1096 _value_types.append(
"CHARMMBondParameters")
1099 CHARMMDihedralParametersList=list
1100 _plural_types.append(
"CHARMMDihedralParametersList")
1101 _value_types.append(
"CHARMMDihedralParameters")
1104 _object_types.append(
"CHARMMIdealResidueTopology")
1107 def _object_cast_to_CHARMMIdealResidueTopology(o):
1108 r"""_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1109 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1111 CHARMMInternalCoordinates=list
1112 _plural_types.append(
"CHARMMInternalCoordinates")
1113 _value_types.append(
"CHARMMInternalCoordinate")
1116 _object_types.append(
"CHARMMPatch")
1119 def _object_cast_to_CHARMMPatch(o):
1120 r"""_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1121 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1123 _object_types.append(
"CHARMMResidueTopologyBase")
1126 def _object_cast_to_CHARMMResidueTopologyBase(o):
1127 r"""_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1128 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1131 _plural_types.append(
"ResidueTypes")
1132 _value_types.append(
"ResidueType")
1136 _plural_types.append(
"ChainTypes")
1137 _value_types.append(
"ChainType")
1141 _plural_types.append(
"Selections")
1142 _value_types.append(
"Selection")
1145 _object_types.append(
"RemoveRigidMotionOptimizerState")
1148 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1149 r"""_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1150 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1152 _object_types.append(
"BerendsenThermostatOptimizerState")
1155 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1156 r"""_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1157 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1159 _object_types.append(
"LangevinThermostatOptimizerState")
1162 def _object_cast_to_LangevinThermostatOptimizerState(o):
1163 r"""_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1164 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1166 _object_types.append(
"SelectionGeometry")
1169 def _object_cast_to_SelectionGeometry(o):
1170 r"""_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1171 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1173 _object_types.append(
"HierarchyGeometry")
1176 def _object_cast_to_HierarchyGeometry(o):
1177 r"""_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1178 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1180 _object_types.append(
"HierarchiesGeometry")
1183 def _object_cast_to_HierarchiesGeometry(o):
1184 r"""_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1185 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1187 _object_types.append(
"BondGeometry")
1190 def _object_cast_to_BondGeometry(o):
1191 r"""_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1192 return _IMP_atom._object_cast_to_BondGeometry(o)
1194 _object_types.append(
"BondsGeometry")
1197 def _object_cast_to_BondsGeometry(o):
1198 r"""_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1199 return _IMP_atom._object_cast_to_BondsGeometry(o)
1201 _object_types.append(
"CAAngleRestraint")
1204 def _object_cast_to_CAAngleRestraint(o):
1205 r"""_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1206 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1208 _object_types.append(
"CADihedralRestraint")
1211 def _object_cast_to_CADihedralRestraint(o):
1212 r"""_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1213 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1215 _object_types.append(
"HelixRestraint")
1218 def _object_cast_to_HelixRestraint(o):
1219 r"""_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1220 return _IMP_atom._object_cast_to_HelixRestraint(o)
1222 CHARMMDihedrals=list
1223 _plural_types.append(
"CHARMMDihedrals")
1224 _value_types.append(
"CHARMMDihedral")
1228 _plural_types.append(
"CHARMMBonds")
1229 _value_types.append(
"CHARMMBond")
1233 _plural_types.append(
"CHARMMAngles")
1234 _value_types.append(
"CHARMMAngle")
1237 r"""Proxy of C++ IMP::atom::Bond class."""
1239 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1241 def __init__(self, *args):
1243 __init__(Bond self) -> Bond
1244 __init__(Bond self, Model m, ParticleIndex id) -> Bond
1245 __init__(Bond self, _ParticleAdaptor d) -> Bond
1247 _IMP_atom.Bond_swiginit(self, _IMP_atom.new_Bond(*args))
1249 def show(self, *args):
1250 r"""show(Bond self, _ostream out=std::cout)"""
1251 return _IMP_atom.Bond_show(self, *args)
1254 def get_is_setup(*args):
1256 get_is_setup(_ParticleAdaptor p) -> bool
1257 get_is_setup(Model m, ParticleIndex pi) -> bool
1259 return _IMP_atom.Bond_get_is_setup(*args)
1260 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1262 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1264 SINGLE = _IMP_atom.Bond_SINGLE
1266 DOUBLE = _IMP_atom.Bond_DOUBLE
1268 TRIPLE = _IMP_atom.Bond_TRIPLE
1270 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1272 SALT = _IMP_atom.Bond_SALT
1274 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1276 AMIDE = _IMP_atom.Bond_AMIDE
1278 AROMATIC = _IMP_atom.Bond_AROMATIC
1281 def get_bonded(self, i):
1282 r"""get_bonded(Bond self, unsigned int i) -> Bonded"""
1283 return _IMP_atom.Bond_get_bonded(self, i)
1286 r"""get_type(Bond self) -> IMP::Int"""
1287 return _IMP_atom.Bond_get_type(self)
1289 def set_type(self, t):
1290 r"""set_type(Bond self, IMP::Int t)"""
1291 return _IMP_atom.Bond_set_type(self, t)
1294 r"""get_order(Bond self) -> IMP::Int"""
1295 return _IMP_atom.Bond_get_order(self)
1297 def set_order(self, t):
1298 r"""set_order(Bond self, IMP::Int t)"""
1299 return _IMP_atom.Bond_set_order(self, t)
1301 def get_length(self):
1302 r"""get_length(Bond self) -> IMP::Float"""
1303 return _IMP_atom.Bond_get_length(self)
1305 def set_length(self, t):
1306 r"""set_length(Bond self, IMP::Float t)"""
1307 return _IMP_atom.Bond_set_length(self, t)
1309 def get_stiffness(self):
1310 r"""get_stiffness(Bond self) -> IMP::Float"""
1311 return _IMP_atom.Bond_get_stiffness(self)
1313 def set_stiffness(self, t):
1314 r"""set_stiffness(Bond self, IMP::Float t)"""
1315 return _IMP_atom.Bond_set_stiffness(self, t)
1318 def get_length_key():
1319 r"""get_length_key() -> FloatKey"""
1320 return _IMP_atom.Bond_get_length_key()
1322 def add_attribute(self, *args):
1324 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1325 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1326 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1327 add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1328 add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1329 add_attribute(Bond self, StringKey a0, IMP::String a1)
1330 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1331 add_attribute(Bond self, ObjectKey a0, Object a1)
1332 add_attribute(Bond self, SparseFloatKey a0, IMP::Float a1)
1333 add_attribute(Bond self, SparseIntKey a0, IMP::Int a1)
1334 add_attribute(Bond self, SparseStringKey a0, IMP::String a1)
1335 add_attribute(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1337 return _IMP_atom.Bond_add_attribute(self, *args)
1339 def get_value(self, *args):
1341 get_value(Bond self, FloatKey a0) -> IMP::Float
1342 get_value(Bond self, IntKey a0) -> IMP::Int
1343 get_value(Bond self, FloatsKey a0) -> IMP::Floats
1344 get_value(Bond self, IntsKey a0) -> IMP::Ints
1345 get_value(Bond self, StringKey a0) -> IMP::String
1346 get_value(Bond self, ParticleIndexKey a0) -> Particle
1347 get_value(Bond self, ObjectKey a0) -> Object
1348 get_value(Bond self, SparseFloatKey a0) -> IMP::Float
1349 get_value(Bond self, SparseIntKey a0) -> IMP::Int
1350 get_value(Bond self, SparseStringKey a0) -> IMP::String
1351 get_value(Bond self, SparseParticleIndexKey a0) -> ParticleIndex
1353 return _IMP_atom.Bond_get_value(self, *args)
1355 def set_value(self, *args):
1357 set_value(Bond self, FloatKey a0, IMP::Float a1)
1358 set_value(Bond self, IntKey a0, IMP::Int a1)
1359 set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1360 set_value(Bond self, IntsKey a0, IMP::Ints a1)
1361 set_value(Bond self, StringKey a0, IMP::String a1)
1362 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1363 set_value(Bond self, ObjectKey a0, Object a1)
1364 set_value(Bond self, SparseFloatKey a0, IMP::Float a1)
1365 set_value(Bond self, SparseIntKey a0, IMP::Int a1)
1366 set_value(Bond self, SparseStringKey a0, IMP::String a1)
1367 set_value(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1369 return _IMP_atom.Bond_set_value(self, *args)
1371 def remove_attribute(self, *args):
1373 remove_attribute(Bond self, FloatKey a0)
1374 remove_attribute(Bond self, IntKey a0)
1375 remove_attribute(Bond self, FloatsKey a0)
1376 remove_attribute(Bond self, IntsKey a0)
1377 remove_attribute(Bond self, StringKey a0)
1378 remove_attribute(Bond self, ParticleIndexKey a0)
1379 remove_attribute(Bond self, ObjectKey a0)
1380 remove_attribute(Bond self, SparseFloatKey a0)
1381 remove_attribute(Bond self, SparseIntKey a0)
1382 remove_attribute(Bond self, SparseStringKey a0)
1383 remove_attribute(Bond self, SparseParticleIndexKey a0)
1385 return _IMP_atom.Bond_remove_attribute(self, *args)
1387 def has_attribute(self, *args):
1389 has_attribute(Bond self, FloatKey a0) -> bool
1390 has_attribute(Bond self, IntKey a0) -> bool
1391 has_attribute(Bond self, FloatsKey a0) -> bool
1392 has_attribute(Bond self, IntsKey a0) -> bool
1393 has_attribute(Bond self, StringKey a0) -> bool
1394 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1395 has_attribute(Bond self, ObjectKey a0) -> bool
1396 has_attribute(Bond self, SparseFloatKey a0) -> bool
1397 has_attribute(Bond self, SparseIntKey a0) -> bool
1398 has_attribute(Bond self, SparseStringKey a0) -> bool
1399 has_attribute(Bond self, SparseParticleIndexKey a0) -> bool
1401 return _IMP_atom.Bond_has_attribute(self, *args)
1403 def get_derivative(self, a0):
1404 r"""get_derivative(Bond self, FloatKey a0) -> double"""
1405 return _IMP_atom.Bond_get_derivative(self, a0)
1408 r"""get_name(Bond self) -> std::string"""
1409 return _IMP_atom.Bond_get_name(self)
1411 def clear_caches(self):
1412 r"""clear_caches(Bond self)"""
1413 return _IMP_atom.Bond_clear_caches(self)
1415 def set_name(self, a0):
1416 r"""set_name(Bond self, std::string a0)"""
1417 return _IMP_atom.Bond_set_name(self, a0)
1420 r"""set_check_level(Bond self, IMP::CheckLevel a0)"""
1421 return _IMP_atom.Bond_set_check_level(self, a0)
1423 def add_to_derivative(self, a0, a1, a2):
1424 r"""add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1425 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1427 def set_is_optimized(self, a0, a1):
1428 r"""set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1429 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1431 def get_is_optimized(self, a0):
1432 r"""get_is_optimized(Bond self, FloatKey a0) -> bool"""
1433 return _IMP_atom.Bond_get_is_optimized(self, a0)
1436 r"""get_check_level(Bond self) -> IMP::CheckLevel"""
1437 return _IMP_atom.Bond_get_check_level(self)
1439 def __eq__(self, *args):
1441 __eq__(Bond self, Bond o) -> bool
1442 __eq__(Bond self, Particle d) -> bool
1444 return _IMP_atom.Bond___eq__(self, *args)
1446 def __ne__(self, *args):
1448 __ne__(Bond self, Bond o) -> bool
1449 __ne__(Bond self, Particle d) -> bool
1451 return _IMP_atom.Bond___ne__(self, *args)
1453 def __le__(self, *args):
1455 __le__(Bond self, Bond o) -> bool
1456 __le__(Bond self, Particle d) -> bool
1458 return _IMP_atom.Bond___le__(self, *args)
1460 def __lt__(self, *args):
1462 __lt__(Bond self, Bond o) -> bool
1463 __lt__(Bond self, Particle d) -> bool
1465 return _IMP_atom.Bond___lt__(self, *args)
1467 def __ge__(self, *args):
1469 __ge__(Bond self, Bond o) -> bool
1470 __ge__(Bond self, Particle d) -> bool
1472 return _IMP_atom.Bond___ge__(self, *args)
1474 def __gt__(self, *args):
1476 __gt__(Bond self, Bond o) -> bool
1477 __gt__(Bond self, Particle d) -> bool
1479 return _IMP_atom.Bond___gt__(self, *args)
1482 r"""__hash__(Bond self) -> std::size_t"""
1483 return _IMP_atom.Bond___hash__(self)
1486 r"""__str__(Bond self) -> std::string"""
1487 return _IMP_atom.Bond___str__(self)
1490 r"""__repr__(Bond self) -> std::string"""
1491 return _IMP_atom.Bond___repr__(self)
1493 def _get_as_binary(self):
1494 r"""_get_as_binary(Bond self) -> PyObject *"""
1495 return _IMP_atom.Bond__get_as_binary(self)
1497 def _set_from_binary(self, p):
1498 r"""_set_from_binary(Bond self, PyObject * p)"""
1499 return _IMP_atom.Bond__set_from_binary(self, p)
1501 def __getstate__(self):
1502 p = self._get_as_binary()
1503 if len(self.__dict__) > 1:
1504 d = self.__dict__.copy()
1509 def __setstate__(self, p):
1510 if not hasattr(self,
'this'):
1512 if isinstance(p, tuple):
1514 self.__dict__.update(d)
1515 return self._set_from_binary(p)
1517 __swig_destroy__ = _IMP_atom.delete_Bond
1520 _IMP_atom.Bond_swigregister(Bond)
1522 r"""Proxy of C++ IMP::atom::Bonded class."""
1524 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1526 def __init__(self, *args):
1528 __init__(Bonded self) -> Bonded
1529 __init__(Bonded self, Model m, ParticleIndex id) -> Bonded
1530 __init__(Bonded self, _ParticleAdaptor d) -> Bonded
1532 _IMP_atom.Bonded_swiginit(self, _IMP_atom.new_Bonded(*args))
1534 def show(self, *args):
1535 r"""show(Bonded self, _ostream out=std::cout)"""
1536 return _IMP_atom.Bonded_show(self, *args)
1539 def setup_particle(*args):
1541 setup_particle(Model m, ParticleIndex pi) -> Bonded
1542 setup_particle(_ParticleAdaptor pa) -> Bonded
1544 return _IMP_atom.Bonded_setup_particle(*args)
1547 def get_is_setup(*args):
1549 get_is_setup(_ParticleAdaptor p) -> bool
1550 get_is_setup(Model m, ParticleIndex pi) -> bool
1552 return _IMP_atom.Bonded_get_is_setup(*args)
1554 def get_number_of_bonds(self):
1555 r"""get_number_of_bonds(Bonded self) -> unsigned int"""
1556 return _IMP_atom.Bonded_get_number_of_bonds(self)
1558 def get_bond_indexes(self):
1559 r"""get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1560 return _IMP_atom.Bonded_get_bond_indexes(self)
1563 r"""get_bond(Bonded self, unsigned int i) -> Bond"""
1564 return _IMP_atom.Bonded_get_bond(self, i)
1566 def get_bonded(self, i):
1567 r"""get_bonded(Bonded self, unsigned int i) -> Bonded"""
1568 return _IMP_atom.Bonded_get_bonded(self, i)
1570 def add_attribute(self, *args):
1572 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1573 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1574 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1575 add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1576 add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1577 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1578 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1579 add_attribute(Bonded self, ObjectKey a0, Object a1)
1580 add_attribute(Bonded self, SparseFloatKey a0, IMP::Float a1)
1581 add_attribute(Bonded self, SparseIntKey a0, IMP::Int a1)
1582 add_attribute(Bonded self, SparseStringKey a0, IMP::String a1)
1583 add_attribute(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1585 return _IMP_atom.Bonded_add_attribute(self, *args)
1587 def get_value(self, *args):
1589 get_value(Bonded self, FloatKey a0) -> IMP::Float
1590 get_value(Bonded self, IntKey a0) -> IMP::Int
1591 get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1592 get_value(Bonded self, IntsKey a0) -> IMP::Ints
1593 get_value(Bonded self, StringKey a0) -> IMP::String
1594 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1595 get_value(Bonded self, ObjectKey a0) -> Object
1596 get_value(Bonded self, SparseFloatKey a0) -> IMP::Float
1597 get_value(Bonded self, SparseIntKey a0) -> IMP::Int
1598 get_value(Bonded self, SparseStringKey a0) -> IMP::String
1599 get_value(Bonded self, SparseParticleIndexKey a0) -> ParticleIndex
1601 return _IMP_atom.Bonded_get_value(self, *args)
1603 def set_value(self, *args):
1605 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1606 set_value(Bonded self, IntKey a0, IMP::Int a1)
1607 set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1608 set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1609 set_value(Bonded self, StringKey a0, IMP::String a1)
1610 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1611 set_value(Bonded self, ObjectKey a0, Object a1)
1612 set_value(Bonded self, SparseFloatKey a0, IMP::Float a1)
1613 set_value(Bonded self, SparseIntKey a0, IMP::Int a1)
1614 set_value(Bonded self, SparseStringKey a0, IMP::String a1)
1615 set_value(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1617 return _IMP_atom.Bonded_set_value(self, *args)
1619 def remove_attribute(self, *args):
1621 remove_attribute(Bonded self, FloatKey a0)
1622 remove_attribute(Bonded self, IntKey a0)
1623 remove_attribute(Bonded self, FloatsKey a0)
1624 remove_attribute(Bonded self, IntsKey a0)
1625 remove_attribute(Bonded self, StringKey a0)
1626 remove_attribute(Bonded self, ParticleIndexKey a0)
1627 remove_attribute(Bonded self, ObjectKey a0)
1628 remove_attribute(Bonded self, SparseFloatKey a0)
1629 remove_attribute(Bonded self, SparseIntKey a0)
1630 remove_attribute(Bonded self, SparseStringKey a0)
1631 remove_attribute(Bonded self, SparseParticleIndexKey a0)
1633 return _IMP_atom.Bonded_remove_attribute(self, *args)
1635 def has_attribute(self, *args):
1637 has_attribute(Bonded self, FloatKey a0) -> bool
1638 has_attribute(Bonded self, IntKey a0) -> bool
1639 has_attribute(Bonded self, FloatsKey a0) -> bool
1640 has_attribute(Bonded self, IntsKey a0) -> bool
1641 has_attribute(Bonded self, StringKey a0) -> bool
1642 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1643 has_attribute(Bonded self, ObjectKey a0) -> bool
1644 has_attribute(Bonded self, SparseFloatKey a0) -> bool
1645 has_attribute(Bonded self, SparseIntKey a0) -> bool
1646 has_attribute(Bonded self, SparseStringKey a0) -> bool
1647 has_attribute(Bonded self, SparseParticleIndexKey a0) -> bool
1649 return _IMP_atom.Bonded_has_attribute(self, *args)
1651 def get_derivative(self, a0):
1652 r"""get_derivative(Bonded self, FloatKey a0) -> double"""
1653 return _IMP_atom.Bonded_get_derivative(self, a0)
1656 r"""get_name(Bonded self) -> std::string"""
1657 return _IMP_atom.Bonded_get_name(self)
1659 def clear_caches(self):
1660 r"""clear_caches(Bonded self)"""
1661 return _IMP_atom.Bonded_clear_caches(self)
1663 def set_name(self, a0):
1664 r"""set_name(Bonded self, std::string a0)"""
1665 return _IMP_atom.Bonded_set_name(self, a0)
1668 r"""set_check_level(Bonded self, IMP::CheckLevel a0)"""
1669 return _IMP_atom.Bonded_set_check_level(self, a0)
1671 def add_to_derivative(self, a0, a1, a2):
1672 r"""add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1673 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1675 def set_is_optimized(self, a0, a1):
1676 r"""set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1677 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1679 def get_is_optimized(self, a0):
1680 r"""get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1681 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1684 r"""get_check_level(Bonded self) -> IMP::CheckLevel"""
1685 return _IMP_atom.Bonded_get_check_level(self)
1687 def __eq__(self, *args):
1689 __eq__(Bonded self, Bonded o) -> bool
1690 __eq__(Bonded self, Particle d) -> bool
1692 return _IMP_atom.Bonded___eq__(self, *args)
1694 def __ne__(self, *args):
1696 __ne__(Bonded self, Bonded o) -> bool
1697 __ne__(Bonded self, Particle d) -> bool
1699 return _IMP_atom.Bonded___ne__(self, *args)
1701 def __le__(self, *args):
1703 __le__(Bonded self, Bonded o) -> bool
1704 __le__(Bonded self, Particle d) -> bool
1706 return _IMP_atom.Bonded___le__(self, *args)
1708 def __lt__(self, *args):
1710 __lt__(Bonded self, Bonded o) -> bool
1711 __lt__(Bonded self, Particle d) -> bool
1713 return _IMP_atom.Bonded___lt__(self, *args)
1715 def __ge__(self, *args):
1717 __ge__(Bonded self, Bonded o) -> bool
1718 __ge__(Bonded self, Particle d) -> bool
1720 return _IMP_atom.Bonded___ge__(self, *args)
1722 def __gt__(self, *args):
1724 __gt__(Bonded self, Bonded o) -> bool
1725 __gt__(Bonded self, Particle d) -> bool
1727 return _IMP_atom.Bonded___gt__(self, *args)
1730 r"""__hash__(Bonded self) -> std::size_t"""
1731 return _IMP_atom.Bonded___hash__(self)
1734 r"""__str__(Bonded self) -> std::string"""
1735 return _IMP_atom.Bonded___str__(self)
1738 r"""__repr__(Bonded self) -> std::string"""
1739 return _IMP_atom.Bonded___repr__(self)
1741 def _get_as_binary(self):
1742 r"""_get_as_binary(Bonded self) -> PyObject *"""
1743 return _IMP_atom.Bonded__get_as_binary(self)
1745 def _set_from_binary(self, p):
1746 r"""_set_from_binary(Bonded self, PyObject * p)"""
1747 return _IMP_atom.Bonded__set_from_binary(self, p)
1749 def __getstate__(self):
1750 p = self._get_as_binary()
1751 if len(self.__dict__) > 1:
1752 d = self.__dict__.copy()
1757 def __setstate__(self, p):
1758 if not hasattr(self,
'this'):
1760 if isinstance(p, tuple):
1762 self.__dict__.update(d)
1763 return self._set_from_binary(p)
1765 __swig_destroy__ = _IMP_atom.delete_Bonded
1768 _IMP_atom.Bonded_swigregister(Bonded)
1771 r"""create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond"""
1772 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1776 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1777 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1779 return _IMP_atom.create_bond(*args)
1782 r"""destroy_bond(Bond b)"""
1783 return _IMP_atom.destroy_bond(b)
1786 r"""get_bond(Bonded a, Bonded b) -> Bond"""
1787 return _IMP_atom.get_bond(a, b)
1789 r"""Proxy of C++ IMP::atom::BondGeometry class."""
1791 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1793 def __init__(self, *args):
1795 __init__(BondGeometry self, Particle p) -> BondGeometry
1796 __init__(BondGeometry self, Bond d) -> BondGeometry
1798 _IMP_atom.BondGeometry_swiginit(self, _IMP_atom.new_BondGeometry(*args))
1800 def get_version_info(self):
1801 r"""get_version_info(BondGeometry self) -> VersionInfo"""
1802 return _IMP_atom.BondGeometry_get_version_info(self)
1803 __swig_destroy__ = _IMP_atom.delete_BondGeometry
1806 r"""__str__(BondGeometry self) -> std::string"""
1807 return _IMP_atom.BondGeometry___str__(self)
1810 r"""__repr__(BondGeometry self) -> std::string"""
1811 return _IMP_atom.BondGeometry___repr__(self)
1815 return _object_cast_to_BondGeometry(o)
1819 _IMP_atom.BondGeometry_swigregister(BondGeometry)
1821 r"""Proxy of C++ IMP::atom::BondsGeometry class."""
1823 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1825 def __init__(self, sc):
1826 r"""__init__(BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1827 _IMP_atom.BondsGeometry_swiginit(self, _IMP_atom.new_BondsGeometry(sc))
1829 def get_version_info(self):
1830 r"""get_version_info(BondsGeometry self) -> VersionInfo"""
1831 return _IMP_atom.BondsGeometry_get_version_info(self)
1832 __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1835 r"""__str__(BondsGeometry self) -> std::string"""
1836 return _IMP_atom.BondsGeometry___str__(self)
1839 r"""__repr__(BondsGeometry self) -> std::string"""
1840 return _IMP_atom.BondsGeometry___repr__(self)
1844 return _object_cast_to_BondsGeometry(o)
1848 _IMP_atom.BondsGeometry_swigregister(BondsGeometry)
1850 r"""Proxy of C++ IMP::atom::Hierarchy class."""
1852 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1854 def __init__(self, *args):
1856 __init__(Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1857 __init__(Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1858 __init__(Hierarchy self) -> Hierarchy
1859 __init__(Hierarchy self, Hierarchy h) -> Hierarchy
1861 _IMP_atom.Hierarchy_swiginit(self, _IMP_atom.new_Hierarchy(*args))
1864 def setup_particle(*args):
1866 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1867 setup_particle(Particle p) -> Hierarchy
1868 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::ParticleIndexesAdaptor()) -> Hierarchy
1870 return _IMP_atom.Hierarchy_setup_particle(*args)
1873 def get_is_setup(*args):
1875 get_is_setup(Particle p) -> bool
1876 get_is_setup(Model m, ParticleIndex p) -> bool
1878 return _IMP_atom.Hierarchy_get_is_setup(*args)
1880 def get_is_valid(self, print_info=False):
1881 r"""get_is_valid(Hierarchy self, bool print_info=False) -> bool"""
1882 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1884 def add_child(self, o):
1885 r"""add_child(Hierarchy self, Hierarchy o)"""
1886 return _IMP_atom.Hierarchy_add_child(self, o)
1888 def get_child(self, i):
1889 r"""get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1890 return _IMP_atom.Hierarchy_get_child(self, i)
1892 def get_children(self):
1893 r"""get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1894 return _IMP_atom.Hierarchy_get_children(self)
1896 def get_parent(self):
1897 r"""get_parent(Hierarchy self) -> Hierarchy"""
1898 return _IMP_atom.Hierarchy_get_parent(self)
1902 r"""get_traits() -> HierarchyTraits"""
1903 return _IMP_atom.Hierarchy_get_traits()
1905 def show(self, *args):
1907 show(Hierarchy self, _ostream out, std::string delimiter)
1908 show(Hierarchy self, _ostream out=std::cout)
1910 return _IMP_atom.Hierarchy_show(self, *args)
1912 def add_attribute(self, *args):
1914 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1915 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1916 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1917 add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1918 add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1919 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1920 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1921 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1922 add_attribute(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1923 add_attribute(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1924 add_attribute(Hierarchy self, SparseStringKey a0, IMP::String a1)
1925 add_attribute(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1927 return _IMP_atom.Hierarchy_add_attribute(self, *args)
1929 def get_value(self, *args):
1931 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1932 get_value(Hierarchy self, IntKey a0) -> IMP::Int
1933 get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1934 get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1935 get_value(Hierarchy self, StringKey a0) -> IMP::String
1936 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1937 get_value(Hierarchy self, ObjectKey a0) -> Object
1938 get_value(Hierarchy self, SparseFloatKey a0) -> IMP::Float
1939 get_value(Hierarchy self, SparseIntKey a0) -> IMP::Int
1940 get_value(Hierarchy self, SparseStringKey a0) -> IMP::String
1941 get_value(Hierarchy self, SparseParticleIndexKey a0) -> ParticleIndex
1943 return _IMP_atom.Hierarchy_get_value(self, *args)
1945 def set_value(self, *args):
1947 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1948 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1949 set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1950 set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1951 set_value(Hierarchy self, StringKey a0, IMP::String a1)
1952 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1953 set_value(Hierarchy self, ObjectKey a0, Object a1)
1954 set_value(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1955 set_value(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1956 set_value(Hierarchy self, SparseStringKey a0, IMP::String a1)
1957 set_value(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1959 return _IMP_atom.Hierarchy_set_value(self, *args)
1961 def remove_attribute(self, *args):
1963 remove_attribute(Hierarchy self, FloatKey a0)
1964 remove_attribute(Hierarchy self, IntKey a0)
1965 remove_attribute(Hierarchy self, FloatsKey a0)
1966 remove_attribute(Hierarchy self, IntsKey a0)
1967 remove_attribute(Hierarchy self, StringKey a0)
1968 remove_attribute(Hierarchy self, ParticleIndexKey a0)
1969 remove_attribute(Hierarchy self, ObjectKey a0)
1970 remove_attribute(Hierarchy self, SparseFloatKey a0)
1971 remove_attribute(Hierarchy self, SparseIntKey a0)
1972 remove_attribute(Hierarchy self, SparseStringKey a0)
1973 remove_attribute(Hierarchy self, SparseParticleIndexKey a0)
1975 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1977 def has_attribute(self, *args):
1979 has_attribute(Hierarchy self, FloatKey a0) -> bool
1980 has_attribute(Hierarchy self, IntKey a0) -> bool
1981 has_attribute(Hierarchy self, FloatsKey a0) -> bool
1982 has_attribute(Hierarchy self, IntsKey a0) -> bool
1983 has_attribute(Hierarchy self, StringKey a0) -> bool
1984 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1985 has_attribute(Hierarchy self, ObjectKey a0) -> bool
1986 has_attribute(Hierarchy self, SparseFloatKey a0) -> bool
1987 has_attribute(Hierarchy self, SparseIntKey a0) -> bool
1988 has_attribute(Hierarchy self, SparseStringKey a0) -> bool
1989 has_attribute(Hierarchy self, SparseParticleIndexKey a0) -> bool
1991 return _IMP_atom.Hierarchy_has_attribute(self, *args)
1993 def get_derivative(self, a0):
1994 r"""get_derivative(Hierarchy self, FloatKey a0) -> double"""
1995 return _IMP_atom.Hierarchy_get_derivative(self, a0)
1998 r"""get_name(Hierarchy self) -> std::string"""
1999 return _IMP_atom.Hierarchy_get_name(self)
2001 def clear_caches(self):
2002 r"""clear_caches(Hierarchy self)"""
2003 return _IMP_atom.Hierarchy_clear_caches(self)
2005 def set_name(self, a0):
2006 r"""set_name(Hierarchy self, std::string a0)"""
2007 return _IMP_atom.Hierarchy_set_name(self, a0)
2010 r"""set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2011 return _IMP_atom.Hierarchy_set_check_level(self, a0)
2013 def add_to_derivative(self, a0, a1, a2):
2014 r"""add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2015 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2017 def set_is_optimized(self, a0, a1):
2018 r"""set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2019 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2021 def get_is_optimized(self, a0):
2022 r"""get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2023 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2026 r"""get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2027 return _IMP_atom.Hierarchy_get_check_level(self)
2029 def __eq__(self, *args):
2031 __eq__(Hierarchy self, Hierarchy o) -> bool
2032 __eq__(Hierarchy self, Particle d) -> bool
2034 return _IMP_atom.Hierarchy___eq__(self, *args)
2036 def __ne__(self, *args):
2038 __ne__(Hierarchy self, Hierarchy o) -> bool
2039 __ne__(Hierarchy self, Particle d) -> bool
2041 return _IMP_atom.Hierarchy___ne__(self, *args)
2043 def __le__(self, *args):
2045 __le__(Hierarchy self, Hierarchy o) -> bool
2046 __le__(Hierarchy self, Particle d) -> bool
2048 return _IMP_atom.Hierarchy___le__(self, *args)
2050 def __lt__(self, *args):
2052 __lt__(Hierarchy self, Hierarchy o) -> bool
2053 __lt__(Hierarchy self, Particle d) -> bool
2055 return _IMP_atom.Hierarchy___lt__(self, *args)
2057 def __ge__(self, *args):
2059 __ge__(Hierarchy self, Hierarchy o) -> bool
2060 __ge__(Hierarchy self, Particle d) -> bool
2062 return _IMP_atom.Hierarchy___ge__(self, *args)
2064 def __gt__(self, *args):
2066 __gt__(Hierarchy self, Hierarchy o) -> bool
2067 __gt__(Hierarchy self, Particle d) -> bool
2069 return _IMP_atom.Hierarchy___gt__(self, *args)
2072 r"""__hash__(Hierarchy self) -> std::size_t"""
2073 return _IMP_atom.Hierarchy___hash__(self)
2076 r"""__str__(Hierarchy self) -> std::string"""
2077 return _IMP_atom.Hierarchy___str__(self)
2080 r"""__repr__(Hierarchy self) -> std::string"""
2081 return _IMP_atom.Hierarchy___repr__(self)
2083 def _get_as_binary(self):
2084 r"""_get_as_binary(Hierarchy self) -> PyObject *"""
2085 return _IMP_atom.Hierarchy__get_as_binary(self)
2087 def _set_from_binary(self, p):
2088 r"""_set_from_binary(Hierarchy self, PyObject * p)"""
2089 return _IMP_atom.Hierarchy__set_from_binary(self, p)
2091 def __getstate__(self):
2092 p = self._get_as_binary()
2093 if len(self.__dict__) > 1:
2094 d = self.__dict__.copy()
2099 def __setstate__(self, p):
2100 if not hasattr(self,
'this'):
2102 if isinstance(p, tuple):
2104 self.__dict__.update(d)
2105 return self._set_from_binary(p)
2107 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2110 _IMP_atom.Hierarchy_swigregister(Hierarchy)
2111 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2113 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2115 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2117 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2119 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2121 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2123 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2125 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2127 MASS_TYPE = _IMP_atom.MASS_TYPE
2129 STATE_TYPE = _IMP_atom.STATE_TYPE
2132 def get_by_type(mhd, t):
2133 r"""get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2134 return _IMP_atom.get_by_type(mhd, t)
2136 def create_fragment(ps):
2137 r"""create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2138 return _IMP_atom.create_fragment(ps)
2140 def get_internal_bonds(mhd):
2141 r"""get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2142 return _IMP_atom.get_internal_bonds(mhd)
2145 r"""get_root(Hierarchy h) -> Hierarchy"""
2146 return _IMP_atom.get_root(h)
2149 r"""show(Hierarchy h, _ostream out=std::cout)"""
2150 return _IMP_atom.show(*args)
2154 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
2155 create_rigid_body(Hierarchy h) -> RigidBody
2157 return _IMP_atom.create_rigid_body(*args)
2160 r"""create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2161 return _IMP_atom.create_compatible_rigid_body(h, reference)
2163 def get_is_heterogen(h):
2164 r"""get_is_heterogen(Hierarchy h) -> bool"""
2165 return _IMP_atom.get_is_heterogen(h)
2168 r"""create_clone(Hierarchy d) -> Hierarchy"""
2169 return _IMP_atom.create_clone(d)
2171 def create_clone_one(d):
2172 r"""create_clone_one(Hierarchy d) -> Hierarchy"""
2173 return _IMP_atom.create_clone_one(d)
2176 r"""destroy(Hierarchy d)"""
2177 return _IMP_atom.destroy(d)
2179 def get_bounding_box(h):
2180 r"""get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2181 return _IMP_atom.get_bounding_box(h)
2183 def get_bounding_sphere(h):
2184 r"""get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2185 return _IMP_atom.get_bounding_sphere(h)
2187 r"""Proxy of C++ IMP::atom::Angle class."""
2189 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2191 def __init__(self, *args):
2193 __init__(Angle self) -> Angle
2194 __init__(Angle self, Model m, ParticleIndex id) -> Angle
2195 __init__(Angle self, _ParticleAdaptor d) -> Angle
2197 _IMP_atom.Angle_swiginit(self, _IMP_atom.new_Angle(*args))
2199 def show(self, *args):
2200 r"""show(Angle self, _ostream out=std::cout)"""
2201 return _IMP_atom.Angle_show(self, *args)
2204 def setup_particle(*args):
2206 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2207 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c) -> Angle
2209 return _IMP_atom.Angle_setup_particle(*args)
2212 def get_is_setup(*args):
2214 get_is_setup(_ParticleAdaptor p) -> bool
2215 get_is_setup(Model m, ParticleIndex pi) -> bool
2217 return _IMP_atom.Angle_get_is_setup(*args)
2219 def get_particle(self, *args):
2221 get_particle(Angle self) -> Particle
2222 get_particle(Angle self, unsigned int i) -> Particle
2224 return _IMP_atom.Angle_get_particle(self, *args)
2226 def get_ideal(self):
2227 r"""get_ideal(Angle self) -> IMP::Float"""
2228 return _IMP_atom.Angle_get_ideal(self)
2230 def set_ideal(self, t):
2231 r"""set_ideal(Angle self, IMP::Float t)"""
2232 return _IMP_atom.Angle_set_ideal(self, t)
2234 def get_stiffness(self):
2235 r"""get_stiffness(Angle self) -> IMP::Float"""
2236 return _IMP_atom.Angle_get_stiffness(self)
2238 def set_stiffness(self, t):
2239 r"""set_stiffness(Angle self, IMP::Float t)"""
2240 return _IMP_atom.Angle_set_stiffness(self, t)
2243 def get_particle_key(i):
2244 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2245 return _IMP_atom.Angle_get_particle_key(i)
2248 def get_ideal_key():
2249 r"""get_ideal_key() -> FloatKey"""
2250 return _IMP_atom.Angle_get_ideal_key()
2253 def get_stiffness_key():
2254 r"""get_stiffness_key() -> FloatKey"""
2255 return _IMP_atom.Angle_get_stiffness_key()
2257 def add_attribute(self, *args):
2259 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2260 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2261 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2262 add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2263 add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2264 add_attribute(Angle self, StringKey a0, IMP::String a1)
2265 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2266 add_attribute(Angle self, ObjectKey a0, Object a1)
2267 add_attribute(Angle self, SparseFloatKey a0, IMP::Float a1)
2268 add_attribute(Angle self, SparseIntKey a0, IMP::Int a1)
2269 add_attribute(Angle self, SparseStringKey a0, IMP::String a1)
2270 add_attribute(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2272 return _IMP_atom.Angle_add_attribute(self, *args)
2274 def get_value(self, *args):
2276 get_value(Angle self, FloatKey a0) -> IMP::Float
2277 get_value(Angle self, IntKey a0) -> IMP::Int
2278 get_value(Angle self, FloatsKey a0) -> IMP::Floats
2279 get_value(Angle self, IntsKey a0) -> IMP::Ints
2280 get_value(Angle self, StringKey a0) -> IMP::String
2281 get_value(Angle self, ParticleIndexKey a0) -> Particle
2282 get_value(Angle self, ObjectKey a0) -> Object
2283 get_value(Angle self, SparseFloatKey a0) -> IMP::Float
2284 get_value(Angle self, SparseIntKey a0) -> IMP::Int
2285 get_value(Angle self, SparseStringKey a0) -> IMP::String
2286 get_value(Angle self, SparseParticleIndexKey a0) -> ParticleIndex
2288 return _IMP_atom.Angle_get_value(self, *args)
2290 def set_value(self, *args):
2292 set_value(Angle self, FloatKey a0, IMP::Float a1)
2293 set_value(Angle self, IntKey a0, IMP::Int a1)
2294 set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2295 set_value(Angle self, IntsKey a0, IMP::Ints a1)
2296 set_value(Angle self, StringKey a0, IMP::String a1)
2297 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2298 set_value(Angle self, ObjectKey a0, Object a1)
2299 set_value(Angle self, SparseFloatKey a0, IMP::Float a1)
2300 set_value(Angle self, SparseIntKey a0, IMP::Int a1)
2301 set_value(Angle self, SparseStringKey a0, IMP::String a1)
2302 set_value(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2304 return _IMP_atom.Angle_set_value(self, *args)
2306 def remove_attribute(self, *args):
2308 remove_attribute(Angle self, FloatKey a0)
2309 remove_attribute(Angle self, IntKey a0)
2310 remove_attribute(Angle self, FloatsKey a0)
2311 remove_attribute(Angle self, IntsKey a0)
2312 remove_attribute(Angle self, StringKey a0)
2313 remove_attribute(Angle self, ParticleIndexKey a0)
2314 remove_attribute(Angle self, ObjectKey a0)
2315 remove_attribute(Angle self, SparseFloatKey a0)
2316 remove_attribute(Angle self, SparseIntKey a0)
2317 remove_attribute(Angle self, SparseStringKey a0)
2318 remove_attribute(Angle self, SparseParticleIndexKey a0)
2320 return _IMP_atom.Angle_remove_attribute(self, *args)
2322 def has_attribute(self, *args):
2324 has_attribute(Angle self, FloatKey a0) -> bool
2325 has_attribute(Angle self, IntKey a0) -> bool
2326 has_attribute(Angle self, FloatsKey a0) -> bool
2327 has_attribute(Angle self, IntsKey a0) -> bool
2328 has_attribute(Angle self, StringKey a0) -> bool
2329 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2330 has_attribute(Angle self, ObjectKey a0) -> bool
2331 has_attribute(Angle self, SparseFloatKey a0) -> bool
2332 has_attribute(Angle self, SparseIntKey a0) -> bool
2333 has_attribute(Angle self, SparseStringKey a0) -> bool
2334 has_attribute(Angle self, SparseParticleIndexKey a0) -> bool
2336 return _IMP_atom.Angle_has_attribute(self, *args)
2338 def get_derivative(self, a0):
2339 r"""get_derivative(Angle self, FloatKey a0) -> double"""
2340 return _IMP_atom.Angle_get_derivative(self, a0)
2343 r"""get_name(Angle self) -> std::string"""
2344 return _IMP_atom.Angle_get_name(self)
2346 def clear_caches(self):
2347 r"""clear_caches(Angle self)"""
2348 return _IMP_atom.Angle_clear_caches(self)
2350 def set_name(self, a0):
2351 r"""set_name(Angle self, std::string a0)"""
2352 return _IMP_atom.Angle_set_name(self, a0)
2355 r"""set_check_level(Angle self, IMP::CheckLevel a0)"""
2356 return _IMP_atom.Angle_set_check_level(self, a0)
2358 def add_to_derivative(self, a0, a1, a2):
2359 r"""add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2360 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2362 def set_is_optimized(self, a0, a1):
2363 r"""set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2364 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2366 def get_is_optimized(self, a0):
2367 r"""get_is_optimized(Angle self, FloatKey a0) -> bool"""
2368 return _IMP_atom.Angle_get_is_optimized(self, a0)
2371 r"""get_check_level(Angle self) -> IMP::CheckLevel"""
2372 return _IMP_atom.Angle_get_check_level(self)
2374 def __eq__(self, *args):
2376 __eq__(Angle self, Angle o) -> bool
2377 __eq__(Angle self, Particle d) -> bool
2379 return _IMP_atom.Angle___eq__(self, *args)
2381 def __ne__(self, *args):
2383 __ne__(Angle self, Angle o) -> bool
2384 __ne__(Angle self, Particle d) -> bool
2386 return _IMP_atom.Angle___ne__(self, *args)
2388 def __le__(self, *args):
2390 __le__(Angle self, Angle o) -> bool
2391 __le__(Angle self, Particle d) -> bool
2393 return _IMP_atom.Angle___le__(self, *args)
2395 def __lt__(self, *args):
2397 __lt__(Angle self, Angle o) -> bool
2398 __lt__(Angle self, Particle d) -> bool
2400 return _IMP_atom.Angle___lt__(self, *args)
2402 def __ge__(self, *args):
2404 __ge__(Angle self, Angle o) -> bool
2405 __ge__(Angle self, Particle d) -> bool
2407 return _IMP_atom.Angle___ge__(self, *args)
2409 def __gt__(self, *args):
2411 __gt__(Angle self, Angle o) -> bool
2412 __gt__(Angle self, Particle d) -> bool
2414 return _IMP_atom.Angle___gt__(self, *args)
2417 r"""__hash__(Angle self) -> std::size_t"""
2418 return _IMP_atom.Angle___hash__(self)
2421 r"""__str__(Angle self) -> std::string"""
2422 return _IMP_atom.Angle___str__(self)
2425 r"""__repr__(Angle self) -> std::string"""
2426 return _IMP_atom.Angle___repr__(self)
2428 def _get_as_binary(self):
2429 r"""_get_as_binary(Angle self) -> PyObject *"""
2430 return _IMP_atom.Angle__get_as_binary(self)
2432 def _set_from_binary(self, p):
2433 r"""_set_from_binary(Angle self, PyObject * p)"""
2434 return _IMP_atom.Angle__set_from_binary(self, p)
2436 def __getstate__(self):
2437 p = self._get_as_binary()
2438 if len(self.__dict__) > 1:
2439 d = self.__dict__.copy()
2444 def __setstate__(self, p):
2445 if not hasattr(self,
'this'):
2447 if isinstance(p, tuple):
2449 self.__dict__.update(d)
2450 return self._set_from_binary(p)
2452 __swig_destroy__ = _IMP_atom.delete_Angle
2455 _IMP_atom.Angle_swigregister(Angle)
2457 r"""Proxy of C++ IMP::atom::Dihedral class."""
2459 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2461 def __init__(self, *args):
2463 __init__(Dihedral self) -> Dihedral
2464 __init__(Dihedral self, Model m, ParticleIndex id) -> Dihedral
2465 __init__(Dihedral self, _ParticleAdaptor d) -> Dihedral
2467 _IMP_atom.Dihedral_swiginit(self, _IMP_atom.new_Dihedral(*args))
2469 def show(self, *args):
2470 r"""show(Dihedral self, _ostream out=std::cout)"""
2471 return _IMP_atom.Dihedral_show(self, *args)
2474 def setup_particle(*args):
2476 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2477 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2479 return _IMP_atom.Dihedral_setup_particle(*args)
2482 def get_is_setup(*args):
2484 get_is_setup(_ParticleAdaptor p) -> bool
2485 get_is_setup(Model m, ParticleIndex pi) -> bool
2487 return _IMP_atom.Dihedral_get_is_setup(*args)
2489 def get_particle(self, *args):
2491 get_particle(Dihedral self) -> Particle
2492 get_particle(Dihedral self, unsigned int i) -> Particle
2494 return _IMP_atom.Dihedral_get_particle(self, *args)
2496 def get_ideal(self):
2497 r"""get_ideal(Dihedral self) -> IMP::Float"""
2498 return _IMP_atom.Dihedral_get_ideal(self)
2500 def set_ideal(self, t):
2501 r"""set_ideal(Dihedral self, IMP::Float t)"""
2502 return _IMP_atom.Dihedral_set_ideal(self, t)
2504 def get_multiplicity(self):
2505 r"""get_multiplicity(Dihedral self) -> IMP::Int"""
2506 return _IMP_atom.Dihedral_get_multiplicity(self)
2508 def set_multiplicity(self, t):
2509 r"""set_multiplicity(Dihedral self, IMP::Int t)"""
2510 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2512 def get_stiffness(self):
2513 r"""get_stiffness(Dihedral self) -> IMP::Float"""
2514 return _IMP_atom.Dihedral_get_stiffness(self)
2516 def set_stiffness(self, t):
2517 r"""set_stiffness(Dihedral self, IMP::Float t)"""
2518 return _IMP_atom.Dihedral_set_stiffness(self, t)
2521 def get_particle_key(i):
2522 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2523 return _IMP_atom.Dihedral_get_particle_key(i)
2526 def get_ideal_key():
2527 r"""get_ideal_key() -> FloatKey"""
2528 return _IMP_atom.Dihedral_get_ideal_key()
2531 def get_multiplicity_key():
2532 r"""get_multiplicity_key() -> IntKey"""
2533 return _IMP_atom.Dihedral_get_multiplicity_key()
2536 def get_stiffness_key():
2537 r"""get_stiffness_key() -> FloatKey"""
2538 return _IMP_atom.Dihedral_get_stiffness_key()
2540 def add_attribute(self, *args):
2542 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2543 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2544 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2545 add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2546 add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2547 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2548 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2549 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2550 add_attribute(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2551 add_attribute(Dihedral self, SparseIntKey a0, IMP::Int a1)
2552 add_attribute(Dihedral self, SparseStringKey a0, IMP::String a1)
2553 add_attribute(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2555 return _IMP_atom.Dihedral_add_attribute(self, *args)
2557 def get_value(self, *args):
2559 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2560 get_value(Dihedral self, IntKey a0) -> IMP::Int
2561 get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2562 get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2563 get_value(Dihedral self, StringKey a0) -> IMP::String
2564 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2565 get_value(Dihedral self, ObjectKey a0) -> Object
2566 get_value(Dihedral self, SparseFloatKey a0) -> IMP::Float
2567 get_value(Dihedral self, SparseIntKey a0) -> IMP::Int
2568 get_value(Dihedral self, SparseStringKey a0) -> IMP::String
2569 get_value(Dihedral self, SparseParticleIndexKey a0) -> ParticleIndex
2571 return _IMP_atom.Dihedral_get_value(self, *args)
2573 def set_value(self, *args):
2575 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2576 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2577 set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2578 set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2579 set_value(Dihedral self, StringKey a0, IMP::String a1)
2580 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2581 set_value(Dihedral self, ObjectKey a0, Object a1)
2582 set_value(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2583 set_value(Dihedral self, SparseIntKey a0, IMP::Int a1)
2584 set_value(Dihedral self, SparseStringKey a0, IMP::String a1)
2585 set_value(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2587 return _IMP_atom.Dihedral_set_value(self, *args)
2589 def remove_attribute(self, *args):
2591 remove_attribute(Dihedral self, FloatKey a0)
2592 remove_attribute(Dihedral self, IntKey a0)
2593 remove_attribute(Dihedral self, FloatsKey a0)
2594 remove_attribute(Dihedral self, IntsKey a0)
2595 remove_attribute(Dihedral self, StringKey a0)
2596 remove_attribute(Dihedral self, ParticleIndexKey a0)
2597 remove_attribute(Dihedral self, ObjectKey a0)
2598 remove_attribute(Dihedral self, SparseFloatKey a0)
2599 remove_attribute(Dihedral self, SparseIntKey a0)
2600 remove_attribute(Dihedral self, SparseStringKey a0)
2601 remove_attribute(Dihedral self, SparseParticleIndexKey a0)
2603 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2605 def has_attribute(self, *args):
2607 has_attribute(Dihedral self, FloatKey a0) -> bool
2608 has_attribute(Dihedral self, IntKey a0) -> bool
2609 has_attribute(Dihedral self, FloatsKey a0) -> bool
2610 has_attribute(Dihedral self, IntsKey a0) -> bool
2611 has_attribute(Dihedral self, StringKey a0) -> bool
2612 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2613 has_attribute(Dihedral self, ObjectKey a0) -> bool
2614 has_attribute(Dihedral self, SparseFloatKey a0) -> bool
2615 has_attribute(Dihedral self, SparseIntKey a0) -> bool
2616 has_attribute(Dihedral self, SparseStringKey a0) -> bool
2617 has_attribute(Dihedral self, SparseParticleIndexKey a0) -> bool
2619 return _IMP_atom.Dihedral_has_attribute(self, *args)
2621 def get_derivative(self, a0):
2622 r"""get_derivative(Dihedral self, FloatKey a0) -> double"""
2623 return _IMP_atom.Dihedral_get_derivative(self, a0)
2626 r"""get_name(Dihedral self) -> std::string"""
2627 return _IMP_atom.Dihedral_get_name(self)
2629 def clear_caches(self):
2630 r"""clear_caches(Dihedral self)"""
2631 return _IMP_atom.Dihedral_clear_caches(self)
2633 def set_name(self, a0):
2634 r"""set_name(Dihedral self, std::string a0)"""
2635 return _IMP_atom.Dihedral_set_name(self, a0)
2638 r"""set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2639 return _IMP_atom.Dihedral_set_check_level(self, a0)
2641 def add_to_derivative(self, a0, a1, a2):
2642 r"""add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2643 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2645 def set_is_optimized(self, a0, a1):
2646 r"""set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2647 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2649 def get_is_optimized(self, a0):
2650 r"""get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2651 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2654 r"""get_check_level(Dihedral self) -> IMP::CheckLevel"""
2655 return _IMP_atom.Dihedral_get_check_level(self)
2657 def __eq__(self, *args):
2659 __eq__(Dihedral self, Dihedral o) -> bool
2660 __eq__(Dihedral self, Particle d) -> bool
2662 return _IMP_atom.Dihedral___eq__(self, *args)
2664 def __ne__(self, *args):
2666 __ne__(Dihedral self, Dihedral o) -> bool
2667 __ne__(Dihedral self, Particle d) -> bool
2669 return _IMP_atom.Dihedral___ne__(self, *args)
2671 def __le__(self, *args):
2673 __le__(Dihedral self, Dihedral o) -> bool
2674 __le__(Dihedral self, Particle d) -> bool
2676 return _IMP_atom.Dihedral___le__(self, *args)
2678 def __lt__(self, *args):
2680 __lt__(Dihedral self, Dihedral o) -> bool
2681 __lt__(Dihedral self, Particle d) -> bool
2683 return _IMP_atom.Dihedral___lt__(self, *args)
2685 def __ge__(self, *args):
2687 __ge__(Dihedral self, Dihedral o) -> bool
2688 __ge__(Dihedral self, Particle d) -> bool
2690 return _IMP_atom.Dihedral___ge__(self, *args)
2692 def __gt__(self, *args):
2694 __gt__(Dihedral self, Dihedral o) -> bool
2695 __gt__(Dihedral self, Particle d) -> bool
2697 return _IMP_atom.Dihedral___gt__(self, *args)
2700 r"""__hash__(Dihedral self) -> std::size_t"""
2701 return _IMP_atom.Dihedral___hash__(self)
2704 r"""__str__(Dihedral self) -> std::string"""
2705 return _IMP_atom.Dihedral___str__(self)
2708 r"""__repr__(Dihedral self) -> std::string"""
2709 return _IMP_atom.Dihedral___repr__(self)
2711 def _get_as_binary(self):
2712 r"""_get_as_binary(Dihedral self) -> PyObject *"""
2713 return _IMP_atom.Dihedral__get_as_binary(self)
2715 def _set_from_binary(self, p):
2716 r"""_set_from_binary(Dihedral self, PyObject * p)"""
2717 return _IMP_atom.Dihedral__set_from_binary(self, p)
2719 def __getstate__(self):
2720 p = self._get_as_binary()
2721 if len(self.__dict__) > 1:
2722 d = self.__dict__.copy()
2727 def __setstate__(self, p):
2728 if not hasattr(self,
'this'):
2730 if isinstance(p, tuple):
2732 self.__dict__.update(d)
2733 return self._set_from_binary(p)
2735 __swig_destroy__ = _IMP_atom.delete_Dihedral
2738 _IMP_atom.Dihedral_swigregister(Dihedral)
2740 r"""Proxy of C++ IMP::atom::SmoothingFunction class."""
2742 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2744 def __init__(self, *args, **kwargs):
2745 raise AttributeError(
"No constructor defined - class is abstract")
2747 def __call__(self, *args):
2749 __call__(SmoothingFunction self, double score, double distance) -> double
2750 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2752 return _IMP_atom.SmoothingFunction___call__(self, *args)
2753 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2756 r"""__str__(SmoothingFunction self) -> std::string"""
2757 return _IMP_atom.SmoothingFunction___str__(self)
2760 r"""__repr__(SmoothingFunction self) -> std::string"""
2761 return _IMP_atom.SmoothingFunction___repr__(self)
2765 return _object_cast_to_SmoothingFunction(o)
2769 _IMP_atom.SmoothingFunction_swigregister(SmoothingFunction)
2770 class ForceSwitch(SmoothingFunction):
2771 r"""Proxy of C++ IMP::atom::ForceSwitch class."""
2773 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2775 def __init__(self, min_distance, max_distance):
2776 r"""__init__(ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2777 _IMP_atom.ForceSwitch_swiginit(self, _IMP_atom.new_ForceSwitch(min_distance, max_distance))
2779 def __call__(self, *args):
2781 __call__(ForceSwitch self, double score, double distance) -> double
2782 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2784 return _IMP_atom.ForceSwitch___call__(self, *args)
2786 def get_version_info(self):
2787 r"""get_version_info(ForceSwitch self) -> VersionInfo"""
2788 return _IMP_atom.ForceSwitch_get_version_info(self)
2789 __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2792 r"""__str__(ForceSwitch self) -> std::string"""
2793 return _IMP_atom.ForceSwitch___str__(self)
2796 r"""__repr__(ForceSwitch self) -> std::string"""
2797 return _IMP_atom.ForceSwitch___repr__(self)
2801 return _object_cast_to_ForceSwitch(o)
2805 _IMP_atom.ForceSwitch_swigregister(ForceSwitch)
2807 r"""Proxy of C++ IMP::atom::AngleSingletonScore class."""
2809 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2811 def __init__(self, f):
2812 r"""__init__(AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2813 _IMP_atom.AngleSingletonScore_swiginit(self, _IMP_atom.new_AngleSingletonScore(f))
2815 def do_get_inputs(self, m, pis):
2816 r"""do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2817 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2819 def get_version_info(self):
2820 r"""get_version_info(AngleSingletonScore self) -> VersionInfo"""
2821 return _IMP_atom.AngleSingletonScore_get_version_info(self)
2822 __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2825 r"""__str__(AngleSingletonScore self) -> std::string"""
2826 return _IMP_atom.AngleSingletonScore___str__(self)
2829 r"""__repr__(AngleSingletonScore self) -> std::string"""
2830 return _IMP_atom.AngleSingletonScore___repr__(self)
2834 return _object_cast_to_AngleSingletonScore(o)
2838 _IMP_atom.AngleSingletonScore_swigregister(AngleSingletonScore)
2840 r"""Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2842 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2845 r"""__init__(BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2846 _IMP_atom.BondEndpointsRefiner_swiginit(self, _IMP_atom.new_BondEndpointsRefiner())
2848 def do_get_inputs(self, m, pis):
2849 r"""do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2850 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2852 def get_version_info(self):
2853 r"""get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2854 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2855 __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2858 r"""__str__(BondEndpointsRefiner self) -> std::string"""
2859 return _IMP_atom.BondEndpointsRefiner___str__(self)
2862 r"""__repr__(BondEndpointsRefiner self) -> std::string"""
2863 return _IMP_atom.BondEndpointsRefiner___repr__(self)
2867 return _object_cast_to_BondEndpointsRefiner(o)
2871 _IMP_atom.BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2873 r"""Proxy of C++ IMP::atom::BondPairContainer class."""
2875 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2877 def __init__(self, sc):
2878 r"""__init__(BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2879 _IMP_atom.BondPairContainer_swiginit(self, _IMP_atom.new_BondPairContainer(sc))
2881 def do_get_inputs(self):
2882 r"""do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2883 return _IMP_atom.BondPairContainer_do_get_inputs(self)
2885 def do_apply(self, sm):
2886 r"""do_apply(BondPairContainer self, PairModifier sm)"""
2887 return _IMP_atom.BondPairContainer_do_apply(self, sm)
2889 def do_apply_moved(self, sm, moved_pis, reset_pis):
2890 r"""do_apply_moved(BondPairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
2891 return _IMP_atom.BondPairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
2893 def get_version_info(self):
2894 r"""get_version_info(BondPairContainer self) -> VersionInfo"""
2895 return _IMP_atom.BondPairContainer_get_version_info(self)
2896 __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2899 r"""__str__(BondPairContainer self) -> std::string"""
2900 return _IMP_atom.BondPairContainer___str__(self)
2903 r"""__repr__(BondPairContainer self) -> std::string"""
2904 return _IMP_atom.BondPairContainer___repr__(self)
2908 return _object_cast_to_BondPairContainer(o)
2912 _IMP_atom.BondPairContainer_swigregister(BondPairContainer)
2914 r"""Proxy of C++ IMP::atom::BondSingletonScore class."""
2916 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2918 def __init__(self, f):
2919 r"""__init__(BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2920 _IMP_atom.BondSingletonScore_swiginit(self, _IMP_atom.new_BondSingletonScore(f))
2922 def get_unary_function(self):
2923 r"""get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2924 return _IMP_atom.BondSingletonScore_get_unary_function(self)
2926 def do_get_inputs(self, m, pis):
2927 r"""do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2928 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2930 def get_version_info(self):
2931 r"""get_version_info(BondSingletonScore self) -> VersionInfo"""
2932 return _IMP_atom.BondSingletonScore_get_version_info(self)
2933 __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2936 r"""__str__(BondSingletonScore self) -> std::string"""
2937 return _IMP_atom.BondSingletonScore___str__(self)
2940 r"""__repr__(BondSingletonScore self) -> std::string"""
2941 return _IMP_atom.BondSingletonScore___repr__(self)
2945 return _object_cast_to_BondSingletonScore(o)
2949 _IMP_atom.BondSingletonScore_swigregister(BondSingletonScore)
2951 r"""Proxy of C++ IMP::atom::DihedralSingletonScore class."""
2953 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2956 r"""__init__(DihedralSingletonScore self) -> DihedralSingletonScore"""
2957 _IMP_atom.DihedralSingletonScore_swiginit(self, _IMP_atom.new_DihedralSingletonScore())
2959 def do_get_inputs(self, m, pis):
2960 r"""do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2961 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
2963 def get_version_info(self):
2964 r"""get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2965 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2966 __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
2969 r"""__str__(DihedralSingletonScore self) -> std::string"""
2970 return _IMP_atom.DihedralSingletonScore___str__(self)
2973 r"""__repr__(DihedralSingletonScore self) -> std::string"""
2974 return _IMP_atom.DihedralSingletonScore___repr__(self)
2978 return _object_cast_to_DihedralSingletonScore(o)
2981 def _get_as_binary(self):
2982 r"""_get_as_binary(DihedralSingletonScore self) -> PyObject *"""
2983 return _IMP_atom.DihedralSingletonScore__get_as_binary(self)
2985 def _set_from_binary(self, p):
2986 r"""_set_from_binary(DihedralSingletonScore self, PyObject * p)"""
2987 return _IMP_atom.DihedralSingletonScore__set_from_binary(self, p)
2989 def __getstate__(self):
2990 p = self._get_as_binary()
2991 if len(self.__dict__) > 1:
2992 d = self.__dict__.copy()
2997 def __setstate__(self, p):
2998 if not hasattr(self,
'this'):
3000 if isinstance(p, tuple):
3002 self.__dict__.update(d)
3003 return self._set_from_binary(p)
3007 _IMP_atom.DihedralSingletonScore_swigregister(DihedralSingletonScore)
3009 r"""Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3011 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3013 def __init__(self, f):
3014 r"""__init__(ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3015 _IMP_atom.ImproperSingletonScore_swiginit(self, _IMP_atom.new_ImproperSingletonScore(f))
3017 def do_get_inputs(self, m, pis):
3018 r"""do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3019 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3021 def get_version_info(self):
3022 r"""get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3023 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3024 __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
3027 r"""__str__(ImproperSingletonScore self) -> std::string"""
3028 return _IMP_atom.ImproperSingletonScore___str__(self)
3031 r"""__repr__(ImproperSingletonScore self) -> std::string"""
3032 return _IMP_atom.ImproperSingletonScore___repr__(self)
3036 return _object_cast_to_ImproperSingletonScore(o)
3040 _IMP_atom.ImproperSingletonScore_swigregister(ImproperSingletonScore)
3042 r"""Proxy of C++ IMP::atom::CenterOfMass class."""
3044 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3046 def get_constraint(self):
3047 r"""get_constraint(CenterOfMass self) -> Constraint"""
3048 return _IMP_atom.CenterOfMass_get_constraint(self)
3051 r"""get_mass(CenterOfMass self) -> IMP::Float"""
3052 return _IMP_atom.CenterOfMass_get_mass(self)
3054 def get_coordinate(self, i):
3055 r"""get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3056 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3058 def get_coordinates(self):
3059 r"""get_coordinates(CenterOfMass self) -> Vector3D"""
3060 return _IMP_atom.CenterOfMass_get_coordinates(self)
3062 def __init__(self, *args):
3064 __init__(CenterOfMass self) -> CenterOfMass
3065 __init__(CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3066 __init__(CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3068 _IMP_atom.CenterOfMass_swiginit(self, _IMP_atom.new_CenterOfMass(*args))
3070 def show(self, *args):
3071 r"""show(CenterOfMass self, _ostream out=std::cout)"""
3072 return _IMP_atom.CenterOfMass_show(self, *args)
3075 def setup_particle(*args):
3077 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3078 setup_particle(_ParticleAdaptor pa, _ParticleIndexesAdaptor members) -> CenterOfMass
3079 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3080 setup_particle(_ParticleAdaptor pa, Refiner refiner) -> CenterOfMass
3082 return _IMP_atom.CenterOfMass_setup_particle(*args)
3085 def teardown_particle(com):
3086 r"""teardown_particle(CenterOfMass com)"""
3087 return _IMP_atom.CenterOfMass_teardown_particle(com)
3090 def get_is_setup(*args):
3092 get_is_setup(_ParticleAdaptor p) -> bool
3093 get_is_setup(Model m, ParticleIndex pi) -> bool
3095 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3097 def add_attribute(self, *args):
3099 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3100 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3101 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3102 add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3103 add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3104 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3105 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3106 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3107 add_attribute(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3108 add_attribute(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3109 add_attribute(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3110 add_attribute(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3112 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3114 def get_value(self, *args):
3116 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3117 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3118 get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3119 get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3120 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3121 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3122 get_value(CenterOfMass self, ObjectKey a0) -> Object
3123 get_value(CenterOfMass self, SparseFloatKey a0) -> IMP::Float
3124 get_value(CenterOfMass self, SparseIntKey a0) -> IMP::Int
3125 get_value(CenterOfMass self, SparseStringKey a0) -> IMP::String
3126 get_value(CenterOfMass self, SparseParticleIndexKey a0) -> ParticleIndex
3128 return _IMP_atom.CenterOfMass_get_value(self, *args)
3130 def set_value(self, *args):
3132 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3133 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3134 set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3135 set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3136 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3137 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3138 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3139 set_value(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3140 set_value(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3141 set_value(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3142 set_value(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3144 return _IMP_atom.CenterOfMass_set_value(self, *args)
3146 def remove_attribute(self, *args):
3148 remove_attribute(CenterOfMass self, FloatKey a0)
3149 remove_attribute(CenterOfMass self, IntKey a0)
3150 remove_attribute(CenterOfMass self, FloatsKey a0)
3151 remove_attribute(CenterOfMass self, IntsKey a0)
3152 remove_attribute(CenterOfMass self, StringKey a0)
3153 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3154 remove_attribute(CenterOfMass self, ObjectKey a0)
3155 remove_attribute(CenterOfMass self, SparseFloatKey a0)
3156 remove_attribute(CenterOfMass self, SparseIntKey a0)
3157 remove_attribute(CenterOfMass self, SparseStringKey a0)
3158 remove_attribute(CenterOfMass self, SparseParticleIndexKey a0)
3160 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3162 def has_attribute(self, *args):
3164 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3165 has_attribute(CenterOfMass self, IntKey a0) -> bool
3166 has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3167 has_attribute(CenterOfMass self, IntsKey a0) -> bool
3168 has_attribute(CenterOfMass self, StringKey a0) -> bool
3169 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3170 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3171 has_attribute(CenterOfMass self, SparseFloatKey a0) -> bool
3172 has_attribute(CenterOfMass self, SparseIntKey a0) -> bool
3173 has_attribute(CenterOfMass self, SparseStringKey a0) -> bool
3174 has_attribute(CenterOfMass self, SparseParticleIndexKey a0) -> bool
3176 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3178 def get_derivative(self, a0):
3179 r"""get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3180 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3183 r"""get_name(CenterOfMass self) -> std::string"""
3184 return _IMP_atom.CenterOfMass_get_name(self)
3186 def clear_caches(self):
3187 r"""clear_caches(CenterOfMass self)"""
3188 return _IMP_atom.CenterOfMass_clear_caches(self)
3190 def set_name(self, a0):
3191 r"""set_name(CenterOfMass self, std::string a0)"""
3192 return _IMP_atom.CenterOfMass_set_name(self, a0)
3195 r"""set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3196 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3198 def add_to_derivative(self, a0, a1, a2):
3199 r"""add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3200 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3202 def set_is_optimized(self, a0, a1):
3203 r"""set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3204 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3206 def get_is_optimized(self, a0):
3207 r"""get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3208 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3211 r"""get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3212 return _IMP_atom.CenterOfMass_get_check_level(self)
3214 def __eq__(self, *args):
3216 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3217 __eq__(CenterOfMass self, Particle d) -> bool
3219 return _IMP_atom.CenterOfMass___eq__(self, *args)
3221 def __ne__(self, *args):
3223 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3224 __ne__(CenterOfMass self, Particle d) -> bool
3226 return _IMP_atom.CenterOfMass___ne__(self, *args)
3228 def __le__(self, *args):
3230 __le__(CenterOfMass self, CenterOfMass o) -> bool
3231 __le__(CenterOfMass self, Particle d) -> bool
3233 return _IMP_atom.CenterOfMass___le__(self, *args)
3235 def __lt__(self, *args):
3237 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3238 __lt__(CenterOfMass self, Particle d) -> bool
3240 return _IMP_atom.CenterOfMass___lt__(self, *args)
3242 def __ge__(self, *args):
3244 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3245 __ge__(CenterOfMass self, Particle d) -> bool
3247 return _IMP_atom.CenterOfMass___ge__(self, *args)
3249 def __gt__(self, *args):
3251 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3252 __gt__(CenterOfMass self, Particle d) -> bool
3254 return _IMP_atom.CenterOfMass___gt__(self, *args)
3257 r"""__hash__(CenterOfMass self) -> std::size_t"""
3258 return _IMP_atom.CenterOfMass___hash__(self)
3261 r"""__str__(CenterOfMass self) -> std::string"""
3262 return _IMP_atom.CenterOfMass___str__(self)
3265 r"""__repr__(CenterOfMass self) -> std::string"""
3266 return _IMP_atom.CenterOfMass___repr__(self)
3268 def _get_as_binary(self):
3269 r"""_get_as_binary(CenterOfMass self) -> PyObject *"""
3270 return _IMP_atom.CenterOfMass__get_as_binary(self)
3272 def _set_from_binary(self, p):
3273 r"""_set_from_binary(CenterOfMass self, PyObject * p)"""
3274 return _IMP_atom.CenterOfMass__set_from_binary(self, p)
3276 def __getstate__(self):
3277 p = self._get_as_binary()
3278 if len(self.__dict__) > 1:
3279 d = self.__dict__.copy()
3284 def __setstate__(self, p):
3285 if not hasattr(self,
'this'):
3287 if isinstance(p, tuple):
3289 self.__dict__.update(d)
3290 return self._set_from_binary(p)
3292 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3295 _IMP_atom.CenterOfMass_swigregister(CenterOfMass)
3297 r"""Proxy of C++ IMP::atom::CoverBond class."""
3299 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3302 r"""__init__(CoverBond self) -> CoverBond"""
3303 _IMP_atom.CoverBond_swiginit(self, _IMP_atom.new_CoverBond())
3305 def do_get_inputs(self, m, pis):
3306 r"""do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3307 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3309 def do_get_outputs(self, m, pis):
3310 r"""do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3311 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3313 def get_version_info(self):
3314 r"""get_version_info(CoverBond self) -> VersionInfo"""
3315 return _IMP_atom.CoverBond_get_version_info(self)
3316 __swig_destroy__ = _IMP_atom.delete_CoverBond
3319 r"""__str__(CoverBond self) -> std::string"""
3320 return _IMP_atom.CoverBond___str__(self)
3323 r"""__repr__(CoverBond self) -> std::string"""
3324 return _IMP_atom.CoverBond___repr__(self)
3328 return _object_cast_to_CoverBond(o)
3332 _IMP_atom.CoverBond_swigregister(CoverBond)
3334 r"""Proxy of C++ IMP::atom::Simulator class."""
3336 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3338 def __init__(self, *args):
3339 r"""__init__(Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator"""
3340 if self.__class__ == Simulator:
3344 _IMP_atom.Simulator_swiginit(self, _IMP_atom.new_Simulator(_self, *args))
3346 if self.__class__ != Simulator:
3347 _director_objects.register(self)
3352 def simulate(self, time_in_fs):
3353 r"""simulate(Simulator self, double time_in_fs) -> double"""
3354 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3356 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3357 r"""simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3358 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3360 def get_temperature(self):
3361 r"""get_temperature(Simulator self) -> double"""
3362 return _IMP_atom.Simulator_get_temperature(self)
3364 def set_temperature(self, d):
3365 r"""set_temperature(Simulator self, double d)"""
3366 return _IMP_atom.Simulator_set_temperature(self, d)
3368 def set_maximum_time_step(self, ts):
3369 r"""set_maximum_time_step(Simulator self, double ts)"""
3370 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3372 def get_maximum_time_step(self):
3373 r"""get_maximum_time_step(Simulator self) -> double"""
3374 return _IMP_atom.Simulator_get_maximum_time_step(self)
3376 def get_last_time_step(self):
3377 r"""get_last_time_step(Simulator self) -> double"""
3378 return _IMP_atom.Simulator_get_last_time_step(self)
3380 def set_time_step(self, ts):
3381 r"""set_time_step(Simulator self, double ts)"""
3382 return _IMP_atom.Simulator_set_time_step(self, ts)
3385 r"""get_kt(Simulator self) -> double"""
3386 return _IMP_atom.Simulator_get_kt(self)
3388 def get_current_time(self):
3389 r"""get_current_time(Simulator self) -> double"""
3390 return _IMP_atom.Simulator_get_current_time(self)
3392 def set_current_time(self, ct):
3393 r"""set_current_time(Simulator self, double ct)"""
3394 return _IMP_atom.Simulator_set_current_time(self, ct)
3396 def get_simulation_particles(self):
3397 r"""get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3398 return _IMP_atom.Simulator_get_simulation_particles(self)
3400 def get_simulation_particle_indexes(self):
3401 r"""get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3402 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3403 def __get_particles(self):
return IMP._list_util.VarList(getdimfunc=self.get_number_of_particles, getfunc=self.get_particle, erasefunc=self.erase_particle, appendfunc=self.add_particle, extendfunc=self.add_particles, clearfunc=self.clear_particles, indexfunc=self._python_index_particle)
3404 def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
3405 def __del_particles(self): IMP._list_util.del_varlist(self.particles)
3406 particles = property(__get_particles, __set_particles, __del_particles, doc=
"List of ##ucnames")
3408 def remove_particle(self, d):
3409 r"""remove_particle(Simulator self, Particle d)"""
3410 return _IMP_atom.Simulator_remove_particle(self, d)
3412 def _python_index_particle(self, d, start, stop):
3413 r"""_python_index_particle(Simulator self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
3414 return _IMP_atom.Simulator__python_index_particle(self, d, start, stop)
3416 def remove_particles(self, d):
3417 r"""remove_particles(Simulator self, IMP::Particles const & d)"""
3418 return _IMP_atom.Simulator_remove_particles(self, d)
3420 def set_particles(self, ps):
3421 r"""set_particles(Simulator self, IMP::Particles const & ps)"""
3422 return _IMP_atom.Simulator_set_particles(self, ps)
3424 def set_particles_order(self, objs):
3425 r"""set_particles_order(Simulator self, IMP::Particles const & objs)"""
3426 return _IMP_atom.Simulator_set_particles_order(self, objs)
3429 r"""add_particle(Simulator self, Particle obj) -> unsigned int"""
3430 return _IMP_atom.Simulator_add_particle(self, obj)
3433 r"""add_particles(Simulator self, IMP::Particles const & objs)"""
3434 return _IMP_atom.Simulator_add_particles(self, objs)
3436 def clear_particles(self):
3437 r"""clear_particles(Simulator self)"""
3438 return _IMP_atom.Simulator_clear_particles(self)
3440 def get_number_of_particles(self):
3441 r"""get_number_of_particles(Simulator self) -> unsigned int"""
3442 return _IMP_atom.Simulator_get_number_of_particles(self)
3444 def get_has_particles(self):
3445 r"""get_has_particles(Simulator self) -> bool"""
3446 return _IMP_atom.Simulator_get_has_particles(self)
3448 def get_particle(self, i):
3449 r"""get_particle(Simulator self, unsigned int i) -> Particle"""
3450 return _IMP_atom.Simulator_get_particle(self, i)
3453 r"""get_particles(Simulator self) -> IMP::Particles"""
3454 return _IMP_atom.Simulator_get_particles(self)
3456 def erase_particle(self, i):
3457 r"""erase_particle(Simulator self, unsigned int i)"""
3458 return _IMP_atom.Simulator_erase_particle(self, i)
3460 def reserve_particles(self, sz):
3461 r"""reserve_particles(Simulator self, unsigned int sz)"""
3462 return _IMP_atom.Simulator_reserve_particles(self, sz)
3464 def do_optimize(self, max_steps):
3465 r"""do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3466 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3468 def setup(self, arg0):
3469 r"""setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3470 return _IMP_atom.Simulator_setup(self, arg0)
3472 def do_step(self, sc, dt):
3473 r"""do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3474 return _IMP_atom.Simulator_do_step(self, sc, dt)
3476 def get_is_simulation_particle(self, p):
3477 r"""get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3478 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3480 def do_simulate(self, time):
3481 r"""do_simulate(Simulator self, double time) -> double"""
3482 return _IMP_atom.Simulator_do_simulate(self, time)
3484 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3485 r"""do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3486 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3489 r"""__str__(Simulator self) -> std::string"""
3490 return _IMP_atom.Simulator___str__(self)
3493 r"""__repr__(Simulator self) -> std::string"""
3494 return _IMP_atom.Simulator___repr__(self)
3498 return _object_cast_to_Simulator(o)
3501 def get_type_name(self):
3502 return self.__class__.__name__
3503 def do_show(self, out):
3505 def get_version_info(self):
3506 if"IMP::atom" ==
"IMP":
3507 return VersionInfo(self.__module__,
3514 return _object_cast_to_Simulator(o)
3516 __swig_destroy__ = _IMP_atom.delete_Simulator
3517 def __disown__(self):
3519 _IMP_atom.disown_Simulator(self)
3520 return weakref.proxy(self)
3522 def do_destroy(self):
3523 r"""do_destroy(Simulator self)"""
3524 return _IMP_atom.Simulator_do_destroy(self)
3526 def handle_set_has_required_score_states(self, arg0):
3527 r"""handle_set_has_required_score_states(Simulator self, bool arg0)"""
3528 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3530 def do_get_inputs(self):
3531 r"""do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3532 return _IMP_atom.Simulator_do_get_inputs(self)
3534 def do_get_outputs(self):
3535 r"""do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3536 return _IMP_atom.Simulator_do_get_outputs(self)
3538 def do_get_interactions(self):
3539 r"""do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3540 return _IMP_atom.Simulator_do_get_interactions(self)
3543 _IMP_atom.Simulator_swigregister(Simulator)
3544 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3546 class BrownianDynamics(Simulator):
3547 r"""Proxy of C++ IMP::atom::BrownianDynamics class."""
3549 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3551 def __init__(self, *args):
3552 r"""__init__(BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics"""
3553 _IMP_atom.BrownianDynamics_swiginit(self, _IMP_atom.new_BrownianDynamics(*args))
3555 def set_maximum_move(self, ms_in_A):
3556 r"""set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3557 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3559 def set_use_stochastic_runge_kutta(self, tf):
3560 r"""set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3561 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3563 def get_version_info(self):
3564 r"""get_version_info(BrownianDynamics self) -> VersionInfo"""
3565 return _IMP_atom.BrownianDynamics_get_version_info(self)
3566 __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3569 r"""__str__(BrownianDynamics self) -> std::string"""
3570 return _IMP_atom.BrownianDynamics___str__(self)
3573 r"""__repr__(BrownianDynamics self) -> std::string"""
3574 return _IMP_atom.BrownianDynamics___repr__(self)
3578 return _object_cast_to_BrownianDynamics(o)
3582 _IMP_atom.BrownianDynamics_swigregister(BrownianDynamics)
3585 r"""get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3586 return _IMP_atom.get_maximum_time_step_estimate(bd)
3588 def get_harmonic_sigma(D, f):
3589 r"""get_harmonic_sigma(double D, double f) -> double"""
3590 return _IMP_atom.get_harmonic_sigma(D, f)
3591 class BrownianDynamicsTAMD(BrownianDynamics):
3592 r"""Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3594 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3596 def __init__(self, *args):
3597 r"""__init__(BrownianDynamicsTAMD self, Model m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0) -> BrownianDynamicsTAMD"""
3598 _IMP_atom.BrownianDynamicsTAMD_swiginit(self, _IMP_atom.new_BrownianDynamicsTAMD(*args))
3601 r"""__str__(BrownianDynamicsTAMD self) -> std::string"""
3602 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3605 r"""__repr__(BrownianDynamicsTAMD self) -> std::string"""
3606 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3610 return _object_cast_to_BrownianDynamicsTAMD(o)
3612 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3615 _IMP_atom.BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3617 r"""Proxy of C++ IMP::atom::Diffusion class."""
3619 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3621 def __init__(self, *args):
3623 __init__(Diffusion self) -> Diffusion
3624 __init__(Diffusion self, Model m, ParticleIndex id) -> Diffusion
3625 __init__(Diffusion self, _ParticleAdaptor d) -> Diffusion
3627 _IMP_atom.Diffusion_swiginit(self, _IMP_atom.new_Diffusion(*args))
3629 def show(self, *args):
3630 r"""show(Diffusion self, _ostream out=std::cout)"""
3631 return _IMP_atom.Diffusion_show(self, *args)
3634 def setup_particle(*args):
3636 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3637 setup_particle(_ParticleAdaptor pa, IMP::Float D) -> Diffusion
3638 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3639 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float D) -> Diffusion
3640 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3641 setup_particle(_ParticleAdaptor pa) -> Diffusion
3643 return _IMP_atom.Diffusion_setup_particle(*args)
3646 def get_is_setup(*args):
3648 get_is_setup(_ParticleAdaptor p) -> bool
3649 get_is_setup(Model m, ParticleIndex p) -> bool
3651 return _IMP_atom.Diffusion_get_is_setup(*args)
3653 def set_diffusion_coefficient(self, d):
3654 r"""set_diffusion_coefficient(Diffusion self, double d)"""
3655 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3658 r"""get_diffusion_coefficient(Diffusion self) -> double"""
3659 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3662 def get_diffusion_coefficient_key():
3663 r"""get_diffusion_coefficient_key() -> FloatKey"""
3664 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3666 def add_attribute(self, *args):
3668 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3669 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3670 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3671 add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3672 add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3673 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3674 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3675 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3676 add_attribute(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3677 add_attribute(Diffusion self, SparseIntKey a0, IMP::Int a1)
3678 add_attribute(Diffusion self, SparseStringKey a0, IMP::String a1)
3679 add_attribute(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3681 return _IMP_atom.Diffusion_add_attribute(self, *args)
3683 def get_value(self, *args):
3685 get_value(Diffusion self, FloatKey a0) -> IMP::Float
3686 get_value(Diffusion self, IntKey a0) -> IMP::Int
3687 get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3688 get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3689 get_value(Diffusion self, StringKey a0) -> IMP::String
3690 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3691 get_value(Diffusion self, ObjectKey a0) -> Object
3692 get_value(Diffusion self, SparseFloatKey a0) -> IMP::Float
3693 get_value(Diffusion self, SparseIntKey a0) -> IMP::Int
3694 get_value(Diffusion self, SparseStringKey a0) -> IMP::String
3695 get_value(Diffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3697 return _IMP_atom.Diffusion_get_value(self, *args)
3699 def set_value(self, *args):
3701 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3702 set_value(Diffusion self, IntKey a0, IMP::Int a1)
3703 set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3704 set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3705 set_value(Diffusion self, StringKey a0, IMP::String a1)
3706 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3707 set_value(Diffusion self, ObjectKey a0, Object a1)
3708 set_value(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3709 set_value(Diffusion self, SparseIntKey a0, IMP::Int a1)
3710 set_value(Diffusion self, SparseStringKey a0, IMP::String a1)
3711 set_value(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3713 return _IMP_atom.Diffusion_set_value(self, *args)
3715 def remove_attribute(self, *args):
3717 remove_attribute(Diffusion self, FloatKey a0)
3718 remove_attribute(Diffusion self, IntKey a0)
3719 remove_attribute(Diffusion self, FloatsKey a0)
3720 remove_attribute(Diffusion self, IntsKey a0)
3721 remove_attribute(Diffusion self, StringKey a0)
3722 remove_attribute(Diffusion self, ParticleIndexKey a0)
3723 remove_attribute(Diffusion self, ObjectKey a0)
3724 remove_attribute(Diffusion self, SparseFloatKey a0)
3725 remove_attribute(Diffusion self, SparseIntKey a0)
3726 remove_attribute(Diffusion self, SparseStringKey a0)
3727 remove_attribute(Diffusion self, SparseParticleIndexKey a0)
3729 return _IMP_atom.Diffusion_remove_attribute(self, *args)
3731 def has_attribute(self, *args):
3733 has_attribute(Diffusion self, FloatKey a0) -> bool
3734 has_attribute(Diffusion self, IntKey a0) -> bool
3735 has_attribute(Diffusion self, FloatsKey a0) -> bool
3736 has_attribute(Diffusion self, IntsKey a0) -> bool
3737 has_attribute(Diffusion self, StringKey a0) -> bool
3738 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3739 has_attribute(Diffusion self, ObjectKey a0) -> bool
3740 has_attribute(Diffusion self, SparseFloatKey a0) -> bool
3741 has_attribute(Diffusion self, SparseIntKey a0) -> bool
3742 has_attribute(Diffusion self, SparseStringKey a0) -> bool
3743 has_attribute(Diffusion self, SparseParticleIndexKey a0) -> bool
3745 return _IMP_atom.Diffusion_has_attribute(self, *args)
3747 def get_derivative(self, a0):
3748 r"""get_derivative(Diffusion self, FloatKey a0) -> double"""
3749 return _IMP_atom.Diffusion_get_derivative(self, a0)
3752 r"""get_name(Diffusion self) -> std::string"""
3753 return _IMP_atom.Diffusion_get_name(self)
3755 def clear_caches(self):
3756 r"""clear_caches(Diffusion self)"""
3757 return _IMP_atom.Diffusion_clear_caches(self)
3759 def set_name(self, a0):
3760 r"""set_name(Diffusion self, std::string a0)"""
3761 return _IMP_atom.Diffusion_set_name(self, a0)
3764 r"""set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3765 return _IMP_atom.Diffusion_set_check_level(self, a0)
3767 def add_to_derivative(self, a0, a1, a2):
3768 r"""add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3769 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3771 def set_is_optimized(self, a0, a1):
3772 r"""set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3773 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3775 def get_is_optimized(self, a0):
3776 r"""get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3777 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3780 r"""get_check_level(Diffusion self) -> IMP::CheckLevel"""
3781 return _IMP_atom.Diffusion_get_check_level(self)
3783 def __eq__(self, *args):
3785 __eq__(Diffusion self, Diffusion o) -> bool
3786 __eq__(Diffusion self, Particle d) -> bool
3788 return _IMP_atom.Diffusion___eq__(self, *args)
3790 def __ne__(self, *args):
3792 __ne__(Diffusion self, Diffusion o) -> bool
3793 __ne__(Diffusion self, Particle d) -> bool
3795 return _IMP_atom.Diffusion___ne__(self, *args)
3797 def __le__(self, *args):
3799 __le__(Diffusion self, Diffusion o) -> bool
3800 __le__(Diffusion self, Particle d) -> bool
3802 return _IMP_atom.Diffusion___le__(self, *args)
3804 def __lt__(self, *args):
3806 __lt__(Diffusion self, Diffusion o) -> bool
3807 __lt__(Diffusion self, Particle d) -> bool
3809 return _IMP_atom.Diffusion___lt__(self, *args)
3811 def __ge__(self, *args):
3813 __ge__(Diffusion self, Diffusion o) -> bool
3814 __ge__(Diffusion self, Particle d) -> bool
3816 return _IMP_atom.Diffusion___ge__(self, *args)
3818 def __gt__(self, *args):
3820 __gt__(Diffusion self, Diffusion o) -> bool
3821 __gt__(Diffusion self, Particle d) -> bool
3823 return _IMP_atom.Diffusion___gt__(self, *args)
3826 r"""__hash__(Diffusion self) -> std::size_t"""
3827 return _IMP_atom.Diffusion___hash__(self)
3830 r"""__str__(Diffusion self) -> std::string"""
3831 return _IMP_atom.Diffusion___str__(self)
3834 r"""__repr__(Diffusion self) -> std::string"""
3835 return _IMP_atom.Diffusion___repr__(self)
3837 def _get_as_binary(self):
3838 r"""_get_as_binary(Diffusion self) -> PyObject *"""
3839 return _IMP_atom.Diffusion__get_as_binary(self)
3841 def _set_from_binary(self, p):
3842 r"""_set_from_binary(Diffusion self, PyObject * p)"""
3843 return _IMP_atom.Diffusion__set_from_binary(self, p)
3845 def __getstate__(self):
3846 p = self._get_as_binary()
3847 if len(self.__dict__) > 1:
3848 d = self.__dict__.copy()
3853 def __setstate__(self, p):
3854 if not hasattr(self,
'this'):
3856 if isinstance(p, tuple):
3858 self.__dict__.update(d)
3859 return self._set_from_binary(p)
3861 __swig_destroy__ = _IMP_atom.delete_Diffusion
3864 _IMP_atom.Diffusion_swigregister(Diffusion)
3866 def get_diffusion_coefficient_from_cm2_per_second(din):
3867 r"""get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3868 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3869 class RigidBodyDiffusion(Diffusion):
3870 r"""Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3872 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3874 def __init__(self, *args):
3876 __init__(RigidBodyDiffusion self) -> RigidBodyDiffusion
3877 __init__(RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3878 __init__(RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3880 _IMP_atom.RigidBodyDiffusion_swiginit(self, _IMP_atom.new_RigidBodyDiffusion(*args))
3882 def show(self, *args):
3883 r"""show(RigidBodyDiffusion self, _ostream out=std::cout)"""
3884 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3887 def setup_particle(*args):
3889 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3890 setup_particle(_ParticleAdaptor pa) -> RigidBodyDiffusion
3892 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3895 r"""get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3896 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3898 def set_rotational_diffusion_coefficient(self, d):
3899 r"""set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3900 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
3903 def get_is_setup(*args):
3905 get_is_setup(_ParticleAdaptor p) -> bool
3906 get_is_setup(Model m, ParticleIndex p) -> bool
3908 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3911 def get_rotational_diffusion_coefficient_key():
3912 r"""get_rotational_diffusion_coefficient_key() -> FloatKey"""
3913 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3915 def add_attribute(self, *args):
3917 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3918 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3919 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3920 add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3921 add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3922 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3923 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3924 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3925 add_attribute(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
3926 add_attribute(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
3927 add_attribute(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
3928 add_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3930 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3932 def get_value(self, *args):
3934 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3935 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3936 get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
3937 get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
3938 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3939 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3940 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
3941 get_value(RigidBodyDiffusion self, SparseFloatKey a0) -> IMP::Float
3942 get_value(RigidBodyDiffusion self, SparseIntKey a0) -> IMP::Int
3943 get_value(RigidBodyDiffusion self, SparseStringKey a0) -> IMP::String
3944 get_value(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3946 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3948 def set_value(self, *args):
3950 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3951 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3952 set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3953 set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3954 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3955 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3956 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3957 set_value(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
3958 set_value(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
3959 set_value(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
3960 set_value(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3962 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3964 def remove_attribute(self, *args):
3966 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3967 remove_attribute(RigidBodyDiffusion self, IntKey a0)
3968 remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
3969 remove_attribute(RigidBodyDiffusion self, IntsKey a0)
3970 remove_attribute(RigidBodyDiffusion self, StringKey a0)
3971 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3972 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3973 remove_attribute(RigidBodyDiffusion self, SparseFloatKey a0)
3974 remove_attribute(RigidBodyDiffusion self, SparseIntKey a0)
3975 remove_attribute(RigidBodyDiffusion self, SparseStringKey a0)
3976 remove_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0)
3978 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3980 def has_attribute(self, *args):
3982 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3983 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3984 has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
3985 has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
3986 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3987 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3988 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3989 has_attribute(RigidBodyDiffusion self, SparseFloatKey a0) -> bool
3990 has_attribute(RigidBodyDiffusion self, SparseIntKey a0) -> bool
3991 has_attribute(RigidBodyDiffusion self, SparseStringKey a0) -> bool
3992 has_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> bool
3994 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3996 def get_derivative(self, a0):
3997 r"""get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3998 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4001 r"""get_name(RigidBodyDiffusion self) -> std::string"""
4002 return _IMP_atom.RigidBodyDiffusion_get_name(self)
4004 def clear_caches(self):
4005 r"""clear_caches(RigidBodyDiffusion self)"""
4006 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4008 def set_name(self, a0):
4009 r"""set_name(RigidBodyDiffusion self, std::string a0)"""
4010 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4013 r"""set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4014 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4016 def add_to_derivative(self, a0, a1, a2):
4017 r"""add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4018 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4020 def set_is_optimized(self, a0, a1):
4021 r"""set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4022 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4024 def get_is_optimized(self, a0):
4025 r"""get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4026 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4029 r"""get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4030 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4032 def __eq__(self, *args):
4034 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4035 __eq__(RigidBodyDiffusion self, Particle d) -> bool
4037 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4039 def __ne__(self, *args):
4041 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4042 __ne__(RigidBodyDiffusion self, Particle d) -> bool
4044 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4046 def __le__(self, *args):
4048 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4049 __le__(RigidBodyDiffusion self, Particle d) -> bool
4051 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4053 def __lt__(self, *args):
4055 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4056 __lt__(RigidBodyDiffusion self, Particle d) -> bool
4058 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4060 def __ge__(self, *args):
4062 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4063 __ge__(RigidBodyDiffusion self, Particle d) -> bool
4065 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4067 def __gt__(self, *args):
4069 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4070 __gt__(RigidBodyDiffusion self, Particle d) -> bool
4072 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4075 r"""__hash__(RigidBodyDiffusion self) -> std::size_t"""
4076 return _IMP_atom.RigidBodyDiffusion___hash__(self)
4079 r"""__str__(RigidBodyDiffusion self) -> std::string"""
4080 return _IMP_atom.RigidBodyDiffusion___str__(self)
4083 r"""__repr__(RigidBodyDiffusion self) -> std::string"""
4084 return _IMP_atom.RigidBodyDiffusion___repr__(self)
4086 def _get_as_binary(self):
4087 r"""_get_as_binary(RigidBodyDiffusion self) -> PyObject *"""
4088 return _IMP_atom.RigidBodyDiffusion__get_as_binary(self)
4090 def _set_from_binary(self, p):
4091 r"""_set_from_binary(RigidBodyDiffusion self, PyObject * p)"""
4092 return _IMP_atom.RigidBodyDiffusion__set_from_binary(self, p)
4094 def __getstate__(self):
4095 p = self._get_as_binary()
4096 if len(self.__dict__) > 1:
4097 d = self.__dict__.copy()
4102 def __setstate__(self, p):
4103 if not hasattr(self,
'this'):
4105 if isinstance(p, tuple):
4107 self.__dict__.update(d)
4108 return self._set_from_binary(p)
4110 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4113 _IMP_atom.RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4115 r"""Proxy of C++ IMP::atom::TAMDParticle class."""
4117 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4119 def __init__(self, *args):
4121 __init__(TAMDParticle self) -> TAMDParticle
4122 __init__(TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4123 __init__(TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4125 _IMP_atom.TAMDParticle_swiginit(self, _IMP_atom.new_TAMDParticle(*args))
4127 def show(self, *args):
4128 r"""show(TAMDParticle self, _ostream out=std::cout)"""
4129 return _IMP_atom.TAMDParticle_show(self, *args)
4132 def setup_particle(*args):
4134 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4135 setup_particle(_ParticleAdaptor pa, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4136 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4137 setup_particle(_ParticleAdaptor pa, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4139 return _IMP_atom.TAMDParticle_setup_particle(*args)
4142 def get_is_setup(*args):
4144 get_is_setup(_ParticleAdaptor p) -> bool
4145 get_is_setup(Model m, ParticleIndex p) -> bool
4147 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4149 def get_reference_particle_index(self):
4150 r"""get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4151 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4153 def set_temperature_scale_factor(self, tsf):
4154 r"""set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4155 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4157 def get_temperature_scale_factor(self):
4158 r"""get_temperature_scale_factor(TAMDParticle self) -> double"""
4159 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4161 def set_friction_scale_factor(self, tsf):
4162 r"""set_friction_scale_factor(TAMDParticle self, float tsf)"""
4163 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4165 def get_friction_scale_factor(self):
4166 r"""get_friction_scale_factor(TAMDParticle self) -> double"""
4167 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4169 def update_coordinates_from_ref(self):
4170 r"""update_coordinates_from_ref(TAMDParticle self)"""
4171 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4174 def get_temperature_scale_factor_key():
4175 r"""get_temperature_scale_factor_key() -> FloatKey"""
4176 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4179 def get_friction_scale_factor_key():
4180 r"""get_friction_scale_factor_key() -> FloatKey"""
4181 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4184 def get_reference_particle_index_key():
4185 r"""get_reference_particle_index_key() -> ParticleIndexKey"""
4186 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4188 def add_attribute(self, *args):
4190 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4191 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4192 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4193 add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4194 add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4195 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4196 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4197 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4198 add_attribute(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4199 add_attribute(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4200 add_attribute(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4201 add_attribute(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4203 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4205 def get_value(self, *args):
4207 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4208 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4209 get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4210 get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4211 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4212 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4213 get_value(TAMDParticle self, ObjectKey a0) -> Object
4214 get_value(TAMDParticle self, SparseFloatKey a0) -> IMP::Float
4215 get_value(TAMDParticle self, SparseIntKey a0) -> IMP::Int
4216 get_value(TAMDParticle self, SparseStringKey a0) -> IMP::String
4217 get_value(TAMDParticle self, SparseParticleIndexKey a0) -> ParticleIndex
4219 return _IMP_atom.TAMDParticle_get_value(self, *args)
4221 def set_value(self, *args):
4223 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4224 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4225 set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4226 set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4227 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4228 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4229 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4230 set_value(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4231 set_value(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4232 set_value(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4233 set_value(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4235 return _IMP_atom.TAMDParticle_set_value(self, *args)
4237 def remove_attribute(self, *args):
4239 remove_attribute(TAMDParticle self, FloatKey a0)
4240 remove_attribute(TAMDParticle self, IntKey a0)
4241 remove_attribute(TAMDParticle self, FloatsKey a0)
4242 remove_attribute(TAMDParticle self, IntsKey a0)
4243 remove_attribute(TAMDParticle self, StringKey a0)
4244 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4245 remove_attribute(TAMDParticle self, ObjectKey a0)
4246 remove_attribute(TAMDParticle self, SparseFloatKey a0)
4247 remove_attribute(TAMDParticle self, SparseIntKey a0)
4248 remove_attribute(TAMDParticle self, SparseStringKey a0)
4249 remove_attribute(TAMDParticle self, SparseParticleIndexKey a0)
4251 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4253 def has_attribute(self, *args):
4255 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4256 has_attribute(TAMDParticle self, IntKey a0) -> bool
4257 has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4258 has_attribute(TAMDParticle self, IntsKey a0) -> bool
4259 has_attribute(TAMDParticle self, StringKey a0) -> bool
4260 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4261 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4262 has_attribute(TAMDParticle self, SparseFloatKey a0) -> bool
4263 has_attribute(TAMDParticle self, SparseIntKey a0) -> bool
4264 has_attribute(TAMDParticle self, SparseStringKey a0) -> bool
4265 has_attribute(TAMDParticle self, SparseParticleIndexKey a0) -> bool
4267 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4269 def get_derivative(self, a0):
4270 r"""get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4271 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4274 r"""get_name(TAMDParticle self) -> std::string"""
4275 return _IMP_atom.TAMDParticle_get_name(self)
4277 def clear_caches(self):
4278 r"""clear_caches(TAMDParticle self)"""
4279 return _IMP_atom.TAMDParticle_clear_caches(self)
4281 def set_name(self, a0):
4282 r"""set_name(TAMDParticle self, std::string a0)"""
4283 return _IMP_atom.TAMDParticle_set_name(self, a0)
4286 r"""set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4287 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4289 def add_to_derivative(self, a0, a1, a2):
4290 r"""add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4291 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4293 def set_is_optimized(self, a0, a1):
4294 r"""set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4295 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4297 def get_is_optimized(self, a0):
4298 r"""get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4299 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4302 r"""get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4303 return _IMP_atom.TAMDParticle_get_check_level(self)
4305 def __eq__(self, *args):
4307 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4308 __eq__(TAMDParticle self, Particle d) -> bool
4310 return _IMP_atom.TAMDParticle___eq__(self, *args)
4312 def __ne__(self, *args):
4314 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4315 __ne__(TAMDParticle self, Particle d) -> bool
4317 return _IMP_atom.TAMDParticle___ne__(self, *args)
4319 def __le__(self, *args):
4321 __le__(TAMDParticle self, TAMDParticle o) -> bool
4322 __le__(TAMDParticle self, Particle d) -> bool
4324 return _IMP_atom.TAMDParticle___le__(self, *args)
4326 def __lt__(self, *args):
4328 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4329 __lt__(TAMDParticle self, Particle d) -> bool
4331 return _IMP_atom.TAMDParticle___lt__(self, *args)
4333 def __ge__(self, *args):
4335 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4336 __ge__(TAMDParticle self, Particle d) -> bool
4338 return _IMP_atom.TAMDParticle___ge__(self, *args)
4340 def __gt__(self, *args):
4342 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4343 __gt__(TAMDParticle self, Particle d) -> bool
4345 return _IMP_atom.TAMDParticle___gt__(self, *args)
4348 r"""__hash__(TAMDParticle self) -> std::size_t"""
4349 return _IMP_atom.TAMDParticle___hash__(self)
4352 r"""__str__(TAMDParticle self) -> std::string"""
4353 return _IMP_atom.TAMDParticle___str__(self)
4356 r"""__repr__(TAMDParticle self) -> std::string"""
4357 return _IMP_atom.TAMDParticle___repr__(self)
4359 def _get_as_binary(self):
4360 r"""_get_as_binary(TAMDParticle self) -> PyObject *"""
4361 return _IMP_atom.TAMDParticle__get_as_binary(self)
4363 def _set_from_binary(self, p):
4364 r"""_set_from_binary(TAMDParticle self, PyObject * p)"""
4365 return _IMP_atom.TAMDParticle__set_from_binary(self, p)
4367 def __getstate__(self):
4368 p = self._get_as_binary()
4369 if len(self.__dict__) > 1:
4370 d = self.__dict__.copy()
4375 def __setstate__(self, p):
4376 if not hasattr(self,
'this'):
4378 if isinstance(p, tuple):
4380 self.__dict__.update(d)
4381 return self._set_from_binary(p)
4383 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4386 _IMP_atom.TAMDParticle_swigregister(TAMDParticle)
4388 r"""Proxy of C++ IMP::atom::Charged class."""
4390 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4392 def __init__(self, *args):
4394 __init__(Charged self) -> Charged
4395 __init__(Charged self, Model m, ParticleIndex id) -> Charged
4396 __init__(Charged self, _ParticleAdaptor d) -> Charged
4398 _IMP_atom.Charged_swiginit(self, _IMP_atom.new_Charged(*args))
4400 def show(self, *args):
4401 r"""show(Charged self, _ostream out=std::cout)"""
4402 return _IMP_atom.Charged_show(self, *args)
4405 def setup_particle(*args):
4407 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4408 setup_particle(_ParticleAdaptor pa, IMP::Float charge) -> Charged
4409 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4410 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float charge) -> Charged
4412 return _IMP_atom.Charged_setup_particle(*args)
4414 def get_charge(self):
4415 r"""get_charge(Charged self) -> IMP::Float"""
4416 return _IMP_atom.Charged_get_charge(self)
4418 def set_charge(self, t):
4419 r"""set_charge(Charged self, IMP::Float t)"""
4420 return _IMP_atom.Charged_set_charge(self, t)
4423 def get_is_setup(*args):
4425 get_is_setup(_ParticleAdaptor p) -> bool
4426 get_is_setup(Model m, ParticleIndex pi) -> bool
4428 return _IMP_atom.Charged_get_is_setup(*args)
4431 def get_charge_key():
4432 r"""get_charge_key() -> FloatKey"""
4433 return _IMP_atom.Charged_get_charge_key()
4435 def add_attribute(self, *args):
4437 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4438 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4439 add_attribute(Charged self, IntKey a0, IMP::Int a1)
4440 add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
4441 add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
4442 add_attribute(Charged self, StringKey a0, IMP::String a1)
4443 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4444 add_attribute(Charged self, ObjectKey a0, Object a1)
4445 add_attribute(Charged self, SparseFloatKey a0, IMP::Float a1)
4446 add_attribute(Charged self, SparseIntKey a0, IMP::Int a1)
4447 add_attribute(Charged self, SparseStringKey a0, IMP::String a1)
4448 add_attribute(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4450 return _IMP_atom.Charged_add_attribute(self, *args)
4452 def get_value(self, *args):
4454 get_value(Charged self, FloatKey a0) -> IMP::Float
4455 get_value(Charged self, IntKey a0) -> IMP::Int
4456 get_value(Charged self, FloatsKey a0) -> IMP::Floats
4457 get_value(Charged self, IntsKey a0) -> IMP::Ints
4458 get_value(Charged self, StringKey a0) -> IMP::String
4459 get_value(Charged self, ParticleIndexKey a0) -> Particle
4460 get_value(Charged self, ObjectKey a0) -> Object
4461 get_value(Charged self, SparseFloatKey a0) -> IMP::Float
4462 get_value(Charged self, SparseIntKey a0) -> IMP::Int
4463 get_value(Charged self, SparseStringKey a0) -> IMP::String
4464 get_value(Charged self, SparseParticleIndexKey a0) -> ParticleIndex
4466 return _IMP_atom.Charged_get_value(self, *args)
4468 def set_value(self, *args):
4470 set_value(Charged self, FloatKey a0, IMP::Float a1)
4471 set_value(Charged self, IntKey a0, IMP::Int a1)
4472 set_value(Charged self, FloatsKey a0, IMP::Floats a1)
4473 set_value(Charged self, IntsKey a0, IMP::Ints a1)
4474 set_value(Charged self, StringKey a0, IMP::String a1)
4475 set_value(Charged self, ParticleIndexKey a0, Particle a1)
4476 set_value(Charged self, ObjectKey a0, Object a1)
4477 set_value(Charged self, SparseFloatKey a0, IMP::Float a1)
4478 set_value(Charged self, SparseIntKey a0, IMP::Int a1)
4479 set_value(Charged self, SparseStringKey a0, IMP::String a1)
4480 set_value(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4482 return _IMP_atom.Charged_set_value(self, *args)
4484 def remove_attribute(self, *args):
4486 remove_attribute(Charged self, FloatKey a0)
4487 remove_attribute(Charged self, IntKey a0)
4488 remove_attribute(Charged self, FloatsKey a0)
4489 remove_attribute(Charged self, IntsKey a0)
4490 remove_attribute(Charged self, StringKey a0)
4491 remove_attribute(Charged self, ParticleIndexKey a0)
4492 remove_attribute(Charged self, ObjectKey a0)
4493 remove_attribute(Charged self, SparseFloatKey a0)
4494 remove_attribute(Charged self, SparseIntKey a0)
4495 remove_attribute(Charged self, SparseStringKey a0)
4496 remove_attribute(Charged self, SparseParticleIndexKey a0)
4498 return _IMP_atom.Charged_remove_attribute(self, *args)
4500 def has_attribute(self, *args):
4502 has_attribute(Charged self, FloatKey a0) -> bool
4503 has_attribute(Charged self, IntKey a0) -> bool
4504 has_attribute(Charged self, FloatsKey a0) -> bool
4505 has_attribute(Charged self, IntsKey a0) -> bool
4506 has_attribute(Charged self, StringKey a0) -> bool
4507 has_attribute(Charged self, ParticleIndexKey a0) -> bool
4508 has_attribute(Charged self, ObjectKey a0) -> bool
4509 has_attribute(Charged self, SparseFloatKey a0) -> bool
4510 has_attribute(Charged self, SparseIntKey a0) -> bool
4511 has_attribute(Charged self, SparseStringKey a0) -> bool
4512 has_attribute(Charged self, SparseParticleIndexKey a0) -> bool
4514 return _IMP_atom.Charged_has_attribute(self, *args)
4516 def get_derivative(self, a0):
4517 r"""get_derivative(Charged self, FloatKey a0) -> double"""
4518 return _IMP_atom.Charged_get_derivative(self, a0)
4521 r"""get_name(Charged self) -> std::string"""
4522 return _IMP_atom.Charged_get_name(self)
4524 def clear_caches(self):
4525 r"""clear_caches(Charged self)"""
4526 return _IMP_atom.Charged_clear_caches(self)
4528 def set_name(self, a0):
4529 r"""set_name(Charged self, std::string a0)"""
4530 return _IMP_atom.Charged_set_name(self, a0)
4533 r"""set_check_level(Charged self, IMP::CheckLevel a0)"""
4534 return _IMP_atom.Charged_set_check_level(self, a0)
4536 def add_to_derivative(self, a0, a1, a2):
4537 r"""add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4538 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4540 def set_is_optimized(self, a0, a1):
4541 r"""set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4542 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4544 def get_is_optimized(self, a0):
4545 r"""get_is_optimized(Charged self, FloatKey a0) -> bool"""
4546 return _IMP_atom.Charged_get_is_optimized(self, a0)
4549 r"""get_check_level(Charged self) -> IMP::CheckLevel"""
4550 return _IMP_atom.Charged_get_check_level(self)
4552 def __eq__(self, *args):
4554 __eq__(Charged self, Charged o) -> bool
4555 __eq__(Charged self, Particle d) -> bool
4557 return _IMP_atom.Charged___eq__(self, *args)
4559 def __ne__(self, *args):
4561 __ne__(Charged self, Charged o) -> bool
4562 __ne__(Charged self, Particle d) -> bool
4564 return _IMP_atom.Charged___ne__(self, *args)
4566 def __le__(self, *args):
4568 __le__(Charged self, Charged o) -> bool
4569 __le__(Charged self, Particle d) -> bool
4571 return _IMP_atom.Charged___le__(self, *args)
4573 def __lt__(self, *args):
4575 __lt__(Charged self, Charged o) -> bool
4576 __lt__(Charged self, Particle d) -> bool
4578 return _IMP_atom.Charged___lt__(self, *args)
4580 def __ge__(self, *args):
4582 __ge__(Charged self, Charged o) -> bool
4583 __ge__(Charged self, Particle d) -> bool
4585 return _IMP_atom.Charged___ge__(self, *args)
4587 def __gt__(self, *args):
4589 __gt__(Charged self, Charged o) -> bool
4590 __gt__(Charged self, Particle d) -> bool
4592 return _IMP_atom.Charged___gt__(self, *args)
4595 r"""__hash__(Charged self) -> std::size_t"""
4596 return _IMP_atom.Charged___hash__(self)
4599 r"""__str__(Charged self) -> std::string"""
4600 return _IMP_atom.Charged___str__(self)
4603 r"""__repr__(Charged self) -> std::string"""
4604 return _IMP_atom.Charged___repr__(self)
4606 def _get_as_binary(self):
4607 r"""_get_as_binary(Charged self) -> PyObject *"""
4608 return _IMP_atom.Charged__get_as_binary(self)
4610 def _set_from_binary(self, p):
4611 r"""_set_from_binary(Charged self, PyObject * p)"""
4612 return _IMP_atom.Charged__set_from_binary(self, p)
4614 def __getstate__(self):
4615 p = self._get_as_binary()
4616 if len(self.__dict__) > 1:
4617 d = self.__dict__.copy()
4622 def __setstate__(self, p):
4623 if not hasattr(self,
'this'):
4625 if isinstance(p, tuple):
4627 self.__dict__.update(d)
4628 return self._set_from_binary(p)
4630 __swig_destroy__ = _IMP_atom.delete_Charged
4633 _IMP_atom.Charged_swigregister(Charged)
4635 r"""Proxy of C++ IMP::atom::CoulombPairScore class."""
4637 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4639 def __init__(self, f):
4640 r"""__init__(CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4641 _IMP_atom.CoulombPairScore_swiginit(self, _IMP_atom.new_CoulombPairScore(f))
4643 def set_relative_dielectric(self, relative_dielectric):
4644 r"""set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4645 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
4647 def get_relative_dielectric(self):
4648 r"""get_relative_dielectric(CoulombPairScore self) -> double"""
4649 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4651 def do_get_inputs(self, m, pis):
4652 r"""do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4653 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
4655 def get_version_info(self):
4656 r"""get_version_info(CoulombPairScore self) -> VersionInfo"""
4657 return _IMP_atom.CoulombPairScore_get_version_info(self)
4658 __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4661 r"""__str__(CoulombPairScore self) -> std::string"""
4662 return _IMP_atom.CoulombPairScore___str__(self)
4665 r"""__repr__(CoulombPairScore self) -> std::string"""
4666 return _IMP_atom.CoulombPairScore___repr__(self)
4670 return _object_cast_to_CoulombPairScore(o)
4674 _IMP_atom.CoulombPairScore_swigregister(CoulombPairScore)
4675 class Domain(Hierarchy):
4676 r"""Proxy of C++ IMP::atom::Domain class."""
4678 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4680 def set_index_range(self, ir):
4681 r"""set_index_range(Domain self, IMP::IntRange ir)"""
4682 return _IMP_atom.Domain_set_index_range(self, ir)
4684 def get_index_range(self):
4685 r"""get_index_range(Domain self) -> IMP::IntRange"""
4686 return _IMP_atom.Domain_get_index_range(self)
4688 def __init__(self, *args):
4690 __init__(Domain self) -> Domain
4691 __init__(Domain self, Model m, ParticleIndex id) -> Domain
4692 __init__(Domain self, _ParticleAdaptor d) -> Domain
4694 _IMP_atom.Domain_swiginit(self, _IMP_atom.new_Domain(*args))
4697 def get_is_setup(*args):
4699 get_is_setup(Model m, ParticleIndex pi) -> bool
4700 get_is_setup(_ParticleAdaptor p) -> bool
4702 return _IMP_atom.Domain_get_is_setup(*args)
4704 def show(self, *args):
4705 r"""show(Domain self, _ostream out=std::cout)"""
4706 return _IMP_atom.Domain_show(self, *args)
4709 def setup_particle(*args):
4711 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
4712 setup_particle(_ParticleAdaptor pa, Domain other) -> Domain
4713 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
4714 setup_particle(_ParticleAdaptor pa, IMP::IntRange residues) -> Domain
4716 return _IMP_atom.Domain_setup_particle(*args)
4718 def add_attribute(self, *args):
4720 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4721 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4722 add_attribute(Domain self, IntKey a0, IMP::Int a1)
4723 add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
4724 add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
4725 add_attribute(Domain self, StringKey a0, IMP::String a1)
4726 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4727 add_attribute(Domain self, ObjectKey a0, Object a1)
4728 add_attribute(Domain self, SparseFloatKey a0, IMP::Float a1)
4729 add_attribute(Domain self, SparseIntKey a0, IMP::Int a1)
4730 add_attribute(Domain self, SparseStringKey a0, IMP::String a1)
4731 add_attribute(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4733 return _IMP_atom.Domain_add_attribute(self, *args)
4735 def get_value(self, *args):
4737 get_value(Domain self, FloatKey a0) -> IMP::Float
4738 get_value(Domain self, IntKey a0) -> IMP::Int
4739 get_value(Domain self, FloatsKey a0) -> IMP::Floats
4740 get_value(Domain self, IntsKey a0) -> IMP::Ints
4741 get_value(Domain self, StringKey a0) -> IMP::String
4742 get_value(Domain self, ParticleIndexKey a0) -> Particle
4743 get_value(Domain self, ObjectKey a0) -> Object
4744 get_value(Domain self, SparseFloatKey a0) -> IMP::Float
4745 get_value(Domain self, SparseIntKey a0) -> IMP::Int
4746 get_value(Domain self, SparseStringKey a0) -> IMP::String
4747 get_value(Domain self, SparseParticleIndexKey a0) -> ParticleIndex
4749 return _IMP_atom.Domain_get_value(self, *args)
4751 def set_value(self, *args):
4753 set_value(Domain self, FloatKey a0, IMP::Float a1)
4754 set_value(Domain self, IntKey a0, IMP::Int a1)
4755 set_value(Domain self, FloatsKey a0, IMP::Floats a1)
4756 set_value(Domain self, IntsKey a0, IMP::Ints a1)
4757 set_value(Domain self, StringKey a0, IMP::String a1)
4758 set_value(Domain self, ParticleIndexKey a0, Particle a1)
4759 set_value(Domain self, ObjectKey a0, Object a1)
4760 set_value(Domain self, SparseFloatKey a0, IMP::Float a1)
4761 set_value(Domain self, SparseIntKey a0, IMP::Int a1)
4762 set_value(Domain self, SparseStringKey a0, IMP::String a1)
4763 set_value(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4765 return _IMP_atom.Domain_set_value(self, *args)
4767 def remove_attribute(self, *args):
4769 remove_attribute(Domain self, FloatKey a0)
4770 remove_attribute(Domain self, IntKey a0)
4771 remove_attribute(Domain self, FloatsKey a0)
4772 remove_attribute(Domain self, IntsKey a0)
4773 remove_attribute(Domain self, StringKey a0)
4774 remove_attribute(Domain self, ParticleIndexKey a0)
4775 remove_attribute(Domain self, ObjectKey a0)
4776 remove_attribute(Domain self, SparseFloatKey a0)
4777 remove_attribute(Domain self, SparseIntKey a0)
4778 remove_attribute(Domain self, SparseStringKey a0)
4779 remove_attribute(Domain self, SparseParticleIndexKey a0)
4781 return _IMP_atom.Domain_remove_attribute(self, *args)
4783 def has_attribute(self, *args):
4785 has_attribute(Domain self, FloatKey a0) -> bool
4786 has_attribute(Domain self, IntKey a0) -> bool
4787 has_attribute(Domain self, FloatsKey a0) -> bool
4788 has_attribute(Domain self, IntsKey a0) -> bool
4789 has_attribute(Domain self, StringKey a0) -> bool
4790 has_attribute(Domain self, ParticleIndexKey a0) -> bool
4791 has_attribute(Domain self, ObjectKey a0) -> bool
4792 has_attribute(Domain self, SparseFloatKey a0) -> bool
4793 has_attribute(Domain self, SparseIntKey a0) -> bool
4794 has_attribute(Domain self, SparseStringKey a0) -> bool
4795 has_attribute(Domain self, SparseParticleIndexKey a0) -> bool
4797 return _IMP_atom.Domain_has_attribute(self, *args)
4799 def get_derivative(self, a0):
4800 r"""get_derivative(Domain self, FloatKey a0) -> double"""
4801 return _IMP_atom.Domain_get_derivative(self, a0)
4804 r"""get_name(Domain self) -> std::string"""
4805 return _IMP_atom.Domain_get_name(self)
4807 def clear_caches(self):
4808 r"""clear_caches(Domain self)"""
4809 return _IMP_atom.Domain_clear_caches(self)
4811 def set_name(self, a0):
4812 r"""set_name(Domain self, std::string a0)"""
4813 return _IMP_atom.Domain_set_name(self, a0)
4816 r"""set_check_level(Domain self, IMP::CheckLevel a0)"""
4817 return _IMP_atom.Domain_set_check_level(self, a0)
4819 def add_to_derivative(self, a0, a1, a2):
4820 r"""add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4821 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
4823 def set_is_optimized(self, a0, a1):
4824 r"""set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4825 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
4827 def get_is_optimized(self, a0):
4828 r"""get_is_optimized(Domain self, FloatKey a0) -> bool"""
4829 return _IMP_atom.Domain_get_is_optimized(self, a0)
4832 r"""get_check_level(Domain self) -> IMP::CheckLevel"""
4833 return _IMP_atom.Domain_get_check_level(self)
4835 def __eq__(self, *args):
4837 __eq__(Domain self, Domain o) -> bool
4838 __eq__(Domain self, Particle d) -> bool
4840 return _IMP_atom.Domain___eq__(self, *args)
4842 def __ne__(self, *args):
4844 __ne__(Domain self, Domain o) -> bool
4845 __ne__(Domain self, Particle d) -> bool
4847 return _IMP_atom.Domain___ne__(self, *args)
4849 def __le__(self, *args):
4851 __le__(Domain self, Domain o) -> bool
4852 __le__(Domain self, Particle d) -> bool
4854 return _IMP_atom.Domain___le__(self, *args)
4856 def __lt__(self, *args):
4858 __lt__(Domain self, Domain o) -> bool
4859 __lt__(Domain self, Particle d) -> bool
4861 return _IMP_atom.Domain___lt__(self, *args)
4863 def __ge__(self, *args):
4865 __ge__(Domain self, Domain o) -> bool
4866 __ge__(Domain self, Particle d) -> bool
4868 return _IMP_atom.Domain___ge__(self, *args)
4870 def __gt__(self, *args):
4872 __gt__(Domain self, Domain o) -> bool
4873 __gt__(Domain self, Particle d) -> bool
4875 return _IMP_atom.Domain___gt__(self, *args)
4878 r"""__hash__(Domain self) -> std::size_t"""
4879 return _IMP_atom.Domain___hash__(self)
4882 r"""__str__(Domain self) -> std::string"""
4883 return _IMP_atom.Domain___str__(self)
4886 r"""__repr__(Domain self) -> std::string"""
4887 return _IMP_atom.Domain___repr__(self)
4889 def _get_as_binary(self):
4890 r"""_get_as_binary(Domain self) -> PyObject *"""
4891 return _IMP_atom.Domain__get_as_binary(self)
4893 def _set_from_binary(self, p):
4894 r"""_set_from_binary(Domain self, PyObject * p)"""
4895 return _IMP_atom.Domain__set_from_binary(self, p)
4897 def __getstate__(self):
4898 p = self._get_as_binary()
4899 if len(self.__dict__) > 1:
4900 d = self.__dict__.copy()
4905 def __setstate__(self, p):
4906 if not hasattr(self,
'this'):
4908 if isinstance(p, tuple):
4910 self.__dict__.update(d)
4911 return self._set_from_binary(p)
4913 __swig_destroy__ = _IMP_atom.delete_Domain
4916 _IMP_atom.Domain_swigregister(Domain)
4918 r"""Proxy of C++ IMP::atom::LennardJones class."""
4920 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4922 def __init__(self, *args):
4924 __init__(LennardJones self) -> LennardJones
4925 __init__(LennardJones self, Model m, ParticleIndex id) -> LennardJones
4926 __init__(LennardJones self, _ParticleAdaptor d) -> LennardJones
4928 _IMP_atom.LennardJones_swiginit(self, _IMP_atom.new_LennardJones(*args))
4930 def show(self, *args):
4931 r"""show(LennardJones self, _ostream out=std::cout)"""
4932 return _IMP_atom.LennardJones_show(self, *args)
4935 def setup_particle(*args):
4937 setup_particle(Model m, ParticleIndex pi) -> LennardJones
4938 setup_particle(_ParticleAdaptor pa) -> LennardJones
4939 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4940 setup_particle(_ParticleAdaptor pa, IMP::Float well_depth) -> LennardJones
4942 return _IMP_atom.LennardJones_setup_particle(*args)
4944 def get_well_depth(self):
4945 r"""get_well_depth(LennardJones self) -> IMP::Float"""
4946 return _IMP_atom.LennardJones_get_well_depth(self)
4948 def set_well_depth(self, well_depth):
4949 r"""set_well_depth(LennardJones self, IMP::Float well_depth)"""
4950 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
4953 def get_is_setup(*args):
4955 get_is_setup(_ParticleAdaptor p) -> bool
4956 get_is_setup(Model m, ParticleIndex pi) -> bool
4958 return _IMP_atom.LennardJones_get_is_setup(*args)
4961 def get_well_depth_key():
4962 r"""get_well_depth_key() -> FloatKey"""
4963 return _IMP_atom.LennardJones_get_well_depth_key()
4965 def add_attribute(self, *args):
4967 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
4968 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
4969 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
4970 add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
4971 add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
4972 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
4973 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
4974 add_attribute(LennardJones self, ObjectKey a0, Object a1)
4975 add_attribute(LennardJones self, SparseFloatKey a0, IMP::Float a1)
4976 add_attribute(LennardJones self, SparseIntKey a0, IMP::Int a1)
4977 add_attribute(LennardJones self, SparseStringKey a0, IMP::String a1)
4978 add_attribute(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
4980 return _IMP_atom.LennardJones_add_attribute(self, *args)
4982 def get_value(self, *args):
4984 get_value(LennardJones self, FloatKey a0) -> IMP::Float
4985 get_value(LennardJones self, IntKey a0) -> IMP::Int
4986 get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
4987 get_value(LennardJones self, IntsKey a0) -> IMP::Ints
4988 get_value(LennardJones self, StringKey a0) -> IMP::String
4989 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
4990 get_value(LennardJones self, ObjectKey a0) -> Object
4991 get_value(LennardJones self, SparseFloatKey a0) -> IMP::Float
4992 get_value(LennardJones self, SparseIntKey a0) -> IMP::Int
4993 get_value(LennardJones self, SparseStringKey a0) -> IMP::String
4994 get_value(LennardJones self, SparseParticleIndexKey a0) -> ParticleIndex
4996 return _IMP_atom.LennardJones_get_value(self, *args)
4998 def set_value(self, *args):
5000 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5001 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5002 set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5003 set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5004 set_value(LennardJones self, StringKey a0, IMP::String a1)
5005 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5006 set_value(LennardJones self, ObjectKey a0, Object a1)
5007 set_value(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5008 set_value(LennardJones self, SparseIntKey a0, IMP::Int a1)
5009 set_value(LennardJones self, SparseStringKey a0, IMP::String a1)
5010 set_value(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5012 return _IMP_atom.LennardJones_set_value(self, *args)
5014 def remove_attribute(self, *args):
5016 remove_attribute(LennardJones self, FloatKey a0)
5017 remove_attribute(LennardJones self, IntKey a0)
5018 remove_attribute(LennardJones self, FloatsKey a0)
5019 remove_attribute(LennardJones self, IntsKey a0)
5020 remove_attribute(LennardJones self, StringKey a0)
5021 remove_attribute(LennardJones self, ParticleIndexKey a0)
5022 remove_attribute(LennardJones self, ObjectKey a0)
5023 remove_attribute(LennardJones self, SparseFloatKey a0)
5024 remove_attribute(LennardJones self, SparseIntKey a0)
5025 remove_attribute(LennardJones self, SparseStringKey a0)
5026 remove_attribute(LennardJones self, SparseParticleIndexKey a0)
5028 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5030 def has_attribute(self, *args):
5032 has_attribute(LennardJones self, FloatKey a0) -> bool
5033 has_attribute(LennardJones self, IntKey a0) -> bool
5034 has_attribute(LennardJones self, FloatsKey a0) -> bool
5035 has_attribute(LennardJones self, IntsKey a0) -> bool
5036 has_attribute(LennardJones self, StringKey a0) -> bool
5037 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5038 has_attribute(LennardJones self, ObjectKey a0) -> bool
5039 has_attribute(LennardJones self, SparseFloatKey a0) -> bool
5040 has_attribute(LennardJones self, SparseIntKey a0) -> bool
5041 has_attribute(LennardJones self, SparseStringKey a0) -> bool
5042 has_attribute(LennardJones self, SparseParticleIndexKey a0) -> bool
5044 return _IMP_atom.LennardJones_has_attribute(self, *args)
5046 def get_derivative(self, a0):
5047 r"""get_derivative(LennardJones self, FloatKey a0) -> double"""
5048 return _IMP_atom.LennardJones_get_derivative(self, a0)
5051 r"""get_name(LennardJones self) -> std::string"""
5052 return _IMP_atom.LennardJones_get_name(self)
5054 def clear_caches(self):
5055 r"""clear_caches(LennardJones self)"""
5056 return _IMP_atom.LennardJones_clear_caches(self)
5058 def set_name(self, a0):
5059 r"""set_name(LennardJones self, std::string a0)"""
5060 return _IMP_atom.LennardJones_set_name(self, a0)
5063 r"""set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5064 return _IMP_atom.LennardJones_set_check_level(self, a0)
5066 def add_to_derivative(self, a0, a1, a2):
5067 r"""add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5068 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5070 def set_is_optimized(self, a0, a1):
5071 r"""set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5072 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5074 def get_is_optimized(self, a0):
5075 r"""get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5076 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5079 r"""get_check_level(LennardJones self) -> IMP::CheckLevel"""
5080 return _IMP_atom.LennardJones_get_check_level(self)
5082 def __eq__(self, *args):
5084 __eq__(LennardJones self, LennardJones o) -> bool
5085 __eq__(LennardJones self, Particle d) -> bool
5087 return _IMP_atom.LennardJones___eq__(self, *args)
5089 def __ne__(self, *args):
5091 __ne__(LennardJones self, LennardJones o) -> bool
5092 __ne__(LennardJones self, Particle d) -> bool
5094 return _IMP_atom.LennardJones___ne__(self, *args)
5096 def __le__(self, *args):
5098 __le__(LennardJones self, LennardJones o) -> bool
5099 __le__(LennardJones self, Particle d) -> bool
5101 return _IMP_atom.LennardJones___le__(self, *args)
5103 def __lt__(self, *args):
5105 __lt__(LennardJones self, LennardJones o) -> bool
5106 __lt__(LennardJones self, Particle d) -> bool
5108 return _IMP_atom.LennardJones___lt__(self, *args)
5110 def __ge__(self, *args):
5112 __ge__(LennardJones self, LennardJones o) -> bool
5113 __ge__(LennardJones self, Particle d) -> bool
5115 return _IMP_atom.LennardJones___ge__(self, *args)
5117 def __gt__(self, *args):
5119 __gt__(LennardJones self, LennardJones o) -> bool
5120 __gt__(LennardJones self, Particle d) -> bool
5122 return _IMP_atom.LennardJones___gt__(self, *args)
5125 r"""__hash__(LennardJones self) -> std::size_t"""
5126 return _IMP_atom.LennardJones___hash__(self)
5129 r"""__str__(LennardJones self) -> std::string"""
5130 return _IMP_atom.LennardJones___str__(self)
5133 r"""__repr__(LennardJones self) -> std::string"""
5134 return _IMP_atom.LennardJones___repr__(self)
5136 def _get_as_binary(self):
5137 r"""_get_as_binary(LennardJones self) -> PyObject *"""
5138 return _IMP_atom.LennardJones__get_as_binary(self)
5140 def _set_from_binary(self, p):
5141 r"""_set_from_binary(LennardJones self, PyObject * p)"""
5142 return _IMP_atom.LennardJones__set_from_binary(self, p)
5144 def __getstate__(self):
5145 p = self._get_as_binary()
5146 if len(self.__dict__) > 1:
5147 d = self.__dict__.copy()
5152 def __setstate__(self, p):
5153 if not hasattr(self,
'this'):
5155 if isinstance(p, tuple):
5157 self.__dict__.update(d)
5158 return self._set_from_binary(p)
5160 __swig_destroy__ = _IMP_atom.delete_LennardJones
5163 _IMP_atom.LennardJones_swigregister(LennardJones)
5165 r"""Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5167 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5169 def __init__(self, f):
5170 r"""__init__(LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5171 _IMP_atom.LennardJonesPairScore_swiginit(self, _IMP_atom.new_LennardJonesPairScore(f))
5173 def set_repulsive_weight(self, repulsive_weight):
5174 r"""set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5175 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5177 def get_repulsive_weight(self):
5178 r"""get_repulsive_weight(LennardJonesPairScore self) -> double"""
5179 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5181 def set_attractive_weight(self, attractive_weight):
5182 r"""set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5183 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5185 def get_attractive_weight(self):
5186 r"""get_attractive_weight(LennardJonesPairScore self) -> double"""
5187 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5189 def do_get_inputs(self, m, pis):
5190 r"""do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5191 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5193 def get_version_info(self):
5194 r"""get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5195 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5196 __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
5199 r"""__str__(LennardJonesPairScore self) -> std::string"""
5200 return _IMP_atom.LennardJonesPairScore___str__(self)
5203 r"""__repr__(LennardJonesPairScore self) -> std::string"""
5204 return _IMP_atom.LennardJonesPairScore___repr__(self)
5208 return _object_cast_to_LennardJonesPairScore(o)
5212 _IMP_atom.LennardJonesPairScore_swigregister(LennardJonesPairScore)
5214 r"""Proxy of C++ IMP::atom::LinearVelocity class."""
5216 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5218 def __init__(self, *args):
5220 __init__(LinearVelocity self) -> LinearVelocity
5221 __init__(LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5222 __init__(LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5224 _IMP_atom.LinearVelocity_swiginit(self, _IMP_atom.new_LinearVelocity(*args))
5227 def get_is_setup(*args):
5229 get_is_setup(Model m, ParticleIndex pi) -> bool
5230 get_is_setup(_ParticleAdaptor p) -> bool
5232 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5234 def show(self, *args):
5235 r"""show(LinearVelocity self, _ostream out=std::cout)"""
5236 return _IMP_atom.LinearVelocity_show(self, *args)
5239 def setup_particle(*args):
5241 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5242 setup_particle(_ParticleAdaptor pa) -> LinearVelocity
5243 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5244 setup_particle(_ParticleAdaptor pa, Vector3D v) -> LinearVelocity
5246 return _IMP_atom.LinearVelocity_setup_particle(*args)
5248 def set_velocity(self, v):
5249 r"""set_velocity(LinearVelocity self, Vector3D v)"""
5250 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5252 def get_velocity(self):
5253 r"""get_velocity(LinearVelocity self) -> Vector3D"""
5254 return _IMP_atom.LinearVelocity_get_velocity(self)
5256 def add_attribute(self, *args):
5258 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5259 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5260 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5261 add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5262 add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5263 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5264 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5265 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5266 add_attribute(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5267 add_attribute(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5268 add_attribute(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5269 add_attribute(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5271 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5273 def get_value(self, *args):
5275 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5276 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5277 get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5278 get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5279 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5280 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5281 get_value(LinearVelocity self, ObjectKey a0) -> Object
5282 get_value(LinearVelocity self, SparseFloatKey a0) -> IMP::Float
5283 get_value(LinearVelocity self, SparseIntKey a0) -> IMP::Int
5284 get_value(LinearVelocity self, SparseStringKey a0) -> IMP::String
5285 get_value(LinearVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5287 return _IMP_atom.LinearVelocity_get_value(self, *args)
5289 def set_value(self, *args):
5291 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5292 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5293 set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5294 set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5295 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5296 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5297 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5298 set_value(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5299 set_value(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5300 set_value(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5301 set_value(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5303 return _IMP_atom.LinearVelocity_set_value(self, *args)
5305 def remove_attribute(self, *args):
5307 remove_attribute(LinearVelocity self, FloatKey a0)
5308 remove_attribute(LinearVelocity self, IntKey a0)
5309 remove_attribute(LinearVelocity self, FloatsKey a0)
5310 remove_attribute(LinearVelocity self, IntsKey a0)
5311 remove_attribute(LinearVelocity self, StringKey a0)
5312 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5313 remove_attribute(LinearVelocity self, ObjectKey a0)
5314 remove_attribute(LinearVelocity self, SparseFloatKey a0)
5315 remove_attribute(LinearVelocity self, SparseIntKey a0)
5316 remove_attribute(LinearVelocity self, SparseStringKey a0)
5317 remove_attribute(LinearVelocity self, SparseParticleIndexKey a0)
5319 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5321 def has_attribute(self, *args):
5323 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5324 has_attribute(LinearVelocity self, IntKey a0) -> bool
5325 has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5326 has_attribute(LinearVelocity self, IntsKey a0) -> bool
5327 has_attribute(LinearVelocity self, StringKey a0) -> bool
5328 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5329 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5330 has_attribute(LinearVelocity self, SparseFloatKey a0) -> bool
5331 has_attribute(LinearVelocity self, SparseIntKey a0) -> bool
5332 has_attribute(LinearVelocity self, SparseStringKey a0) -> bool
5333 has_attribute(LinearVelocity self, SparseParticleIndexKey a0) -> bool
5335 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5337 def get_derivative(self, a0):
5338 r"""get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5339 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5342 r"""get_name(LinearVelocity self) -> std::string"""
5343 return _IMP_atom.LinearVelocity_get_name(self)
5345 def clear_caches(self):
5346 r"""clear_caches(LinearVelocity self)"""
5347 return _IMP_atom.LinearVelocity_clear_caches(self)
5349 def set_name(self, a0):
5350 r"""set_name(LinearVelocity self, std::string a0)"""
5351 return _IMP_atom.LinearVelocity_set_name(self, a0)
5354 r"""set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5355 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5357 def add_to_derivative(self, a0, a1, a2):
5358 r"""add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5359 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5361 def set_is_optimized(self, a0, a1):
5362 r"""set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5363 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5365 def get_is_optimized(self, a0):
5366 r"""get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5367 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5370 r"""get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5371 return _IMP_atom.LinearVelocity_get_check_level(self)
5373 def __eq__(self, *args):
5375 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5376 __eq__(LinearVelocity self, Particle d) -> bool
5378 return _IMP_atom.LinearVelocity___eq__(self, *args)
5380 def __ne__(self, *args):
5382 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5383 __ne__(LinearVelocity self, Particle d) -> bool
5385 return _IMP_atom.LinearVelocity___ne__(self, *args)
5387 def __le__(self, *args):
5389 __le__(LinearVelocity self, LinearVelocity o) -> bool
5390 __le__(LinearVelocity self, Particle d) -> bool
5392 return _IMP_atom.LinearVelocity___le__(self, *args)
5394 def __lt__(self, *args):
5396 __lt__(LinearVelocity self, LinearVelocity o) -> bool
5397 __lt__(LinearVelocity self, Particle d) -> bool
5399 return _IMP_atom.LinearVelocity___lt__(self, *args)
5401 def __ge__(self, *args):
5403 __ge__(LinearVelocity self, LinearVelocity o) -> bool
5404 __ge__(LinearVelocity self, Particle d) -> bool
5406 return _IMP_atom.LinearVelocity___ge__(self, *args)
5408 def __gt__(self, *args):
5410 __gt__(LinearVelocity self, LinearVelocity o) -> bool
5411 __gt__(LinearVelocity self, Particle d) -> bool
5413 return _IMP_atom.LinearVelocity___gt__(self, *args)
5416 r"""__hash__(LinearVelocity self) -> std::size_t"""
5417 return _IMP_atom.LinearVelocity___hash__(self)
5420 r"""__str__(LinearVelocity self) -> std::string"""
5421 return _IMP_atom.LinearVelocity___str__(self)
5424 r"""__repr__(LinearVelocity self) -> std::string"""
5425 return _IMP_atom.LinearVelocity___repr__(self)
5427 def _get_as_binary(self):
5428 r"""_get_as_binary(LinearVelocity self) -> PyObject *"""
5429 return _IMP_atom.LinearVelocity__get_as_binary(self)
5431 def _set_from_binary(self, p):
5432 r"""_set_from_binary(LinearVelocity self, PyObject * p)"""
5433 return _IMP_atom.LinearVelocity__set_from_binary(self, p)
5435 def __getstate__(self):
5436 p = self._get_as_binary()
5437 if len(self.__dict__) > 1:
5438 d = self.__dict__.copy()
5443 def __setstate__(self, p):
5444 if not hasattr(self,
'this'):
5446 if isinstance(p, tuple):
5448 self.__dict__.update(d)
5449 return self._set_from_binary(p)
5451 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5454 _IMP_atom.LinearVelocity_swigregister(LinearVelocity)
5456 r"""Proxy of C++ IMP::atom::AngularVelocity class."""
5458 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5460 def __init__(self, *args):
5462 __init__(AngularVelocity self) -> AngularVelocity
5463 __init__(AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5464 __init__(AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5466 _IMP_atom.AngularVelocity_swiginit(self, _IMP_atom.new_AngularVelocity(*args))
5469 def get_is_setup(*args):
5471 get_is_setup(Model m, ParticleIndex pi) -> bool
5472 get_is_setup(_ParticleAdaptor p) -> bool
5474 return _IMP_atom.AngularVelocity_get_is_setup(*args)
5476 def show(self, *args):
5477 r"""show(AngularVelocity self, _ostream out=std::cout)"""
5478 return _IMP_atom.AngularVelocity_show(self, *args)
5481 def setup_particle(*args):
5483 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5484 setup_particle(_ParticleAdaptor pa) -> AngularVelocity
5485 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5486 setup_particle(_ParticleAdaptor pa, Vector4D v) -> AngularVelocity
5488 return _IMP_atom.AngularVelocity_setup_particle(*args)
5490 def set_velocity(self, v):
5491 r"""set_velocity(AngularVelocity self, Vector4D v)"""
5492 return _IMP_atom.AngularVelocity_set_velocity(self, v)
5494 def get_velocity(self):
5495 r"""get_velocity(AngularVelocity self) -> Vector4D"""
5496 return _IMP_atom.AngularVelocity_get_velocity(self)
5498 def add_attribute(self, *args):
5500 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5501 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5502 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5503 add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5504 add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5505 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5506 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5507 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5508 add_attribute(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5509 add_attribute(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5510 add_attribute(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5511 add_attribute(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5513 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5515 def get_value(self, *args):
5517 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5518 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5519 get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
5520 get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
5521 get_value(AngularVelocity self, StringKey a0) -> IMP::String
5522 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5523 get_value(AngularVelocity self, ObjectKey a0) -> Object
5524 get_value(AngularVelocity self, SparseFloatKey a0) -> IMP::Float
5525 get_value(AngularVelocity self, SparseIntKey a0) -> IMP::Int
5526 get_value(AngularVelocity self, SparseStringKey a0) -> IMP::String
5527 get_value(AngularVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5529 return _IMP_atom.AngularVelocity_get_value(self, *args)
5531 def set_value(self, *args):
5533 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5534 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5535 set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5536 set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5537 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5538 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5539 set_value(AngularVelocity self, ObjectKey a0, Object a1)
5540 set_value(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5541 set_value(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5542 set_value(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5543 set_value(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5545 return _IMP_atom.AngularVelocity_set_value(self, *args)
5547 def remove_attribute(self, *args):
5549 remove_attribute(AngularVelocity self, FloatKey a0)
5550 remove_attribute(AngularVelocity self, IntKey a0)
5551 remove_attribute(AngularVelocity self, FloatsKey a0)
5552 remove_attribute(AngularVelocity self, IntsKey a0)
5553 remove_attribute(AngularVelocity self, StringKey a0)
5554 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5555 remove_attribute(AngularVelocity self, ObjectKey a0)
5556 remove_attribute(AngularVelocity self, SparseFloatKey a0)
5557 remove_attribute(AngularVelocity self, SparseIntKey a0)
5558 remove_attribute(AngularVelocity self, SparseStringKey a0)
5559 remove_attribute(AngularVelocity self, SparseParticleIndexKey a0)
5561 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5563 def has_attribute(self, *args):
5565 has_attribute(AngularVelocity self, FloatKey a0) -> bool
5566 has_attribute(AngularVelocity self, IntKey a0) -> bool
5567 has_attribute(AngularVelocity self, FloatsKey a0) -> bool
5568 has_attribute(AngularVelocity self, IntsKey a0) -> bool
5569 has_attribute(AngularVelocity self, StringKey a0) -> bool
5570 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
5571 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
5572 has_attribute(AngularVelocity self, SparseFloatKey a0) -> bool
5573 has_attribute(AngularVelocity self, SparseIntKey a0) -> bool
5574 has_attribute(AngularVelocity self, SparseStringKey a0) -> bool
5575 has_attribute(AngularVelocity self, SparseParticleIndexKey a0) -> bool
5577 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
5579 def get_derivative(self, a0):
5580 r"""get_derivative(AngularVelocity self, FloatKey a0) -> double"""
5581 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
5584 r"""get_name(AngularVelocity self) -> std::string"""
5585 return _IMP_atom.AngularVelocity_get_name(self)
5587 def clear_caches(self):
5588 r"""clear_caches(AngularVelocity self)"""
5589 return _IMP_atom.AngularVelocity_clear_caches(self)
5591 def set_name(self, a0):
5592 r"""set_name(AngularVelocity self, std::string a0)"""
5593 return _IMP_atom.AngularVelocity_set_name(self, a0)
5596 r"""set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
5597 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
5599 def add_to_derivative(self, a0, a1, a2):
5600 r"""add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5601 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
5603 def set_is_optimized(self, a0, a1):
5604 r"""set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
5605 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
5607 def get_is_optimized(self, a0):
5608 r"""get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
5609 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
5612 r"""get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
5613 return _IMP_atom.AngularVelocity_get_check_level(self)
5615 def __eq__(self, *args):
5617 __eq__(AngularVelocity self, AngularVelocity o) -> bool
5618 __eq__(AngularVelocity self, Particle d) -> bool
5620 return _IMP_atom.AngularVelocity___eq__(self, *args)
5622 def __ne__(self, *args):
5624 __ne__(AngularVelocity self, AngularVelocity o) -> bool
5625 __ne__(AngularVelocity self, Particle d) -> bool
5627 return _IMP_atom.AngularVelocity___ne__(self, *args)
5629 def __le__(self, *args):
5631 __le__(AngularVelocity self, AngularVelocity o) -> bool
5632 __le__(AngularVelocity self, Particle d) -> bool
5634 return _IMP_atom.AngularVelocity___le__(self, *args)
5636 def __lt__(self, *args):
5638 __lt__(AngularVelocity self, AngularVelocity o) -> bool
5639 __lt__(AngularVelocity self, Particle d) -> bool
5641 return _IMP_atom.AngularVelocity___lt__(self, *args)
5643 def __ge__(self, *args):
5645 __ge__(AngularVelocity self, AngularVelocity o) -> bool
5646 __ge__(AngularVelocity self, Particle d) -> bool
5648 return _IMP_atom.AngularVelocity___ge__(self, *args)
5650 def __gt__(self, *args):
5652 __gt__(AngularVelocity self, AngularVelocity o) -> bool
5653 __gt__(AngularVelocity self, Particle d) -> bool
5655 return _IMP_atom.AngularVelocity___gt__(self, *args)
5658 r"""__hash__(AngularVelocity self) -> std::size_t"""
5659 return _IMP_atom.AngularVelocity___hash__(self)
5662 r"""__str__(AngularVelocity self) -> std::string"""
5663 return _IMP_atom.AngularVelocity___str__(self)
5666 r"""__repr__(AngularVelocity self) -> std::string"""
5667 return _IMP_atom.AngularVelocity___repr__(self)
5669 def _get_as_binary(self):
5670 r"""_get_as_binary(AngularVelocity self) -> PyObject *"""
5671 return _IMP_atom.AngularVelocity__get_as_binary(self)
5673 def _set_from_binary(self, p):
5674 r"""_set_from_binary(AngularVelocity self, PyObject * p)"""
5675 return _IMP_atom.AngularVelocity__set_from_binary(self, p)
5677 def __getstate__(self):
5678 p = self._get_as_binary()
5679 if len(self.__dict__) > 1:
5680 d = self.__dict__.copy()
5685 def __setstate__(self, p):
5686 if not hasattr(self,
'this'):
5688 if isinstance(p, tuple):
5690 self.__dict__.update(d)
5691 return self._set_from_binary(p)
5693 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
5696 _IMP_atom.AngularVelocity_swigregister(AngularVelocity)
5697 class MolecularDynamics(Simulator):
5698 r"""Proxy of C++ IMP::atom::MolecularDynamics class."""
5700 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5702 def __init__(self, m):
5703 r"""__init__(MolecularDynamics self, Model m) -> MolecularDynamics"""
5704 _IMP_atom.MolecularDynamics_swiginit(self, _IMP_atom.new_MolecularDynamics(m))
5706 def get_kinetic_energy(self):
5707 r"""get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
5708 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
5710 def get_kinetic_temperature(self, ekinetic):
5711 r"""get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
5712 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
5714 def set_velocity_cap(self, velocity_cap):
5715 r"""set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
5716 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
5718 def assign_velocities(self, temperature):
5719 r"""assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
5720 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
5722 def setup(self, ps):
5723 r"""setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
5724 return _IMP_atom.MolecularDynamics_setup(self, ps)
5726 def do_step(self, sc, dt):
5727 r"""do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
5728 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
5730 def get_is_simulation_particle(self, p):
5731 r"""get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
5732 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
5734 def get_version_info(self):
5735 r"""get_version_info(MolecularDynamics self) -> VersionInfo"""
5736 return _IMP_atom.MolecularDynamics_get_version_info(self)
5737 __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
5740 r"""__str__(MolecularDynamics self) -> std::string"""
5741 return _IMP_atom.MolecularDynamics___str__(self)
5744 r"""__repr__(MolecularDynamics self) -> std::string"""
5745 return _IMP_atom.MolecularDynamics___repr__(self)
5749 return _object_cast_to_MolecularDynamics(o)
5753 _IMP_atom.MolecularDynamics_swigregister(MolecularDynamics)
5755 r"""Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
5757 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5759 def __init__(self, m, pis, temperature):
5760 r"""__init__(VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
5761 _IMP_atom.VelocityScalingOptimizerState_swiginit(self, _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature))
5763 def set_particles(self, pis):
5764 r"""set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
5765 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
5767 def set_temperature(self, temperature):
5768 r"""set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
5769 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
5771 def rescale_velocities(self):
5772 r"""rescale_velocities(VelocityScalingOptimizerState self)"""
5773 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
5775 def get_version_info(self):
5776 r"""get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
5777 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
5778 __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
5781 r"""__str__(VelocityScalingOptimizerState self) -> std::string"""
5782 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
5785 r"""__repr__(VelocityScalingOptimizerState self) -> std::string"""
5786 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
5790 return _object_cast_to_VelocityScalingOptimizerState(o)
5794 _IMP_atom.VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
5795 class Fragment(Hierarchy):
5796 r"""Proxy of C++ IMP::atom::Fragment class."""
5798 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5800 def set_residue_indexes(self, o):
5801 r"""set_residue_indexes(Fragment self, IMP::Ints o)"""
5802 return _IMP_atom.Fragment_set_residue_indexes(self, o)
5804 def get_residue_indexes(self):
5805 r"""get_residue_indexes(Fragment self) -> IMP::Ints"""
5806 return _IMP_atom.Fragment_get_residue_indexes(self)
5808 def get_contains_residue(self, rindex):
5809 r"""get_contains_residue(Fragment self, int rindex) -> bool"""
5810 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
5812 def get_contains_any_sorted_residue(self, rinds):
5813 r"""get_contains_any_sorted_residue(Fragment self, IMP::Ints const & rinds) -> bool"""
5814 return _IMP_atom.Fragment_get_contains_any_sorted_residue(self, rinds)
5816 def __init__(self, *args):
5818 __init__(Fragment self) -> Fragment
5819 __init__(Fragment self, Model m, ParticleIndex id) -> Fragment
5820 __init__(Fragment self, _ParticleAdaptor d) -> Fragment
5822 _IMP_atom.Fragment_swiginit(self, _IMP_atom.new_Fragment(*args))
5825 def get_is_setup(*args):
5827 get_is_setup(Model m, ParticleIndex pi) -> bool
5828 get_is_setup(_ParticleAdaptor p) -> bool
5830 return _IMP_atom.Fragment_get_is_setup(*args)
5832 def show(self, *args):
5833 r"""show(Fragment self, _ostream out=std::cout)"""
5834 return _IMP_atom.Fragment_show(self, *args)
5837 def setup_particle(*args):
5839 setup_particle(Model m, ParticleIndex pi) -> Fragment
5840 setup_particle(_ParticleAdaptor pa) -> Fragment
5841 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
5842 setup_particle(_ParticleAdaptor pa, Fragment other) -> Fragment
5843 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
5844 setup_particle(_ParticleAdaptor pa, IMP::Ints residue_indexes) -> Fragment
5846 return _IMP_atom.Fragment_setup_particle(*args)
5848 def add_attribute(self, *args):
5850 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
5851 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
5852 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
5853 add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
5854 add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
5855 add_attribute(Fragment self, StringKey a0, IMP::String a1)
5856 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
5857 add_attribute(Fragment self, ObjectKey a0, Object a1)
5858 add_attribute(Fragment self, SparseFloatKey a0, IMP::Float a1)
5859 add_attribute(Fragment self, SparseIntKey a0, IMP::Int a1)
5860 add_attribute(Fragment self, SparseStringKey a0, IMP::String a1)
5861 add_attribute(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
5863 return _IMP_atom.Fragment_add_attribute(self, *args)
5865 def get_value(self, *args):
5867 get_value(Fragment self, FloatKey a0) -> IMP::Float
5868 get_value(Fragment self, IntKey a0) -> IMP::Int
5869 get_value(Fragment self, FloatsKey a0) -> IMP::Floats
5870 get_value(Fragment self, IntsKey a0) -> IMP::Ints
5871 get_value(Fragment self, StringKey a0) -> IMP::String
5872 get_value(Fragment self, ParticleIndexKey a0) -> Particle
5873 get_value(Fragment self, ObjectKey a0) -> Object
5874 get_value(Fragment self, SparseFloatKey a0) -> IMP::Float
5875 get_value(Fragment self, SparseIntKey a0) -> IMP::Int
5876 get_value(Fragment self, SparseStringKey a0) -> IMP::String
5877 get_value(Fragment self, SparseParticleIndexKey a0) -> ParticleIndex
5879 return _IMP_atom.Fragment_get_value(self, *args)
5881 def set_value(self, *args):
5883 set_value(Fragment self, FloatKey a0, IMP::Float a1)
5884 set_value(Fragment self, IntKey a0, IMP::Int a1)
5885 set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
5886 set_value(Fragment self, IntsKey a0, IMP::Ints a1)
5887 set_value(Fragment self, StringKey a0, IMP::String a1)
5888 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
5889 set_value(Fragment self, ObjectKey a0, Object a1)
5890 set_value(Fragment self, SparseFloatKey a0, IMP::Float a1)
5891 set_value(Fragment self, SparseIntKey a0, IMP::Int a1)
5892 set_value(Fragment self, SparseStringKey a0, IMP::String a1)
5893 set_value(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
5895 return _IMP_atom.Fragment_set_value(self, *args)
5897 def remove_attribute(self, *args):
5899 remove_attribute(Fragment self, FloatKey a0)
5900 remove_attribute(Fragment self, IntKey a0)
5901 remove_attribute(Fragment self, FloatsKey a0)
5902 remove_attribute(Fragment self, IntsKey a0)
5903 remove_attribute(Fragment self, StringKey a0)
5904 remove_attribute(Fragment self, ParticleIndexKey a0)
5905 remove_attribute(Fragment self, ObjectKey a0)
5906 remove_attribute(Fragment self, SparseFloatKey a0)
5907 remove_attribute(Fragment self, SparseIntKey a0)
5908 remove_attribute(Fragment self, SparseStringKey a0)
5909 remove_attribute(Fragment self, SparseParticleIndexKey a0)
5911 return _IMP_atom.Fragment_remove_attribute(self, *args)
5913 def has_attribute(self, *args):
5915 has_attribute(Fragment self, FloatKey a0) -> bool
5916 has_attribute(Fragment self, IntKey a0) -> bool
5917 has_attribute(Fragment self, FloatsKey a0) -> bool
5918 has_attribute(Fragment self, IntsKey a0) -> bool
5919 has_attribute(Fragment self, StringKey a0) -> bool
5920 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
5921 has_attribute(Fragment self, ObjectKey a0) -> bool
5922 has_attribute(Fragment self, SparseFloatKey a0) -> bool
5923 has_attribute(Fragment self, SparseIntKey a0) -> bool
5924 has_attribute(Fragment self, SparseStringKey a0) -> bool
5925 has_attribute(Fragment self, SparseParticleIndexKey a0) -> bool
5927 return _IMP_atom.Fragment_has_attribute(self, *args)
5929 def get_derivative(self, a0):
5930 r"""get_derivative(Fragment self, FloatKey a0) -> double"""
5931 return _IMP_atom.Fragment_get_derivative(self, a0)
5934 r"""get_name(Fragment self) -> std::string"""
5935 return _IMP_atom.Fragment_get_name(self)
5937 def clear_caches(self):
5938 r"""clear_caches(Fragment self)"""
5939 return _IMP_atom.Fragment_clear_caches(self)
5941 def set_name(self, a0):
5942 r"""set_name(Fragment self, std::string a0)"""
5943 return _IMP_atom.Fragment_set_name(self, a0)
5946 r"""set_check_level(Fragment self, IMP::CheckLevel a0)"""
5947 return _IMP_atom.Fragment_set_check_level(self, a0)
5949 def add_to_derivative(self, a0, a1, a2):
5950 r"""add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5951 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
5953 def set_is_optimized(self, a0, a1):
5954 r"""set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
5955 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
5957 def get_is_optimized(self, a0):
5958 r"""get_is_optimized(Fragment self, FloatKey a0) -> bool"""
5959 return _IMP_atom.Fragment_get_is_optimized(self, a0)
5962 r"""get_check_level(Fragment self) -> IMP::CheckLevel"""
5963 return _IMP_atom.Fragment_get_check_level(self)
5965 def __eq__(self, *args):
5967 __eq__(Fragment self, Fragment o) -> bool
5968 __eq__(Fragment self, Particle d) -> bool
5970 return _IMP_atom.Fragment___eq__(self, *args)
5972 def __ne__(self, *args):
5974 __ne__(Fragment self, Fragment o) -> bool
5975 __ne__(Fragment self, Particle d) -> bool
5977 return _IMP_atom.Fragment___ne__(self, *args)
5979 def __le__(self, *args):
5981 __le__(Fragment self, Fragment o) -> bool
5982 __le__(Fragment self, Particle d) -> bool
5984 return _IMP_atom.Fragment___le__(self, *args)
5986 def __lt__(self, *args):
5988 __lt__(Fragment self, Fragment o) -> bool
5989 __lt__(Fragment self, Particle d) -> bool
5991 return _IMP_atom.Fragment___lt__(self, *args)
5993 def __ge__(self, *args):
5995 __ge__(Fragment self, Fragment o) -> bool
5996 __ge__(Fragment self, Particle d) -> bool
5998 return _IMP_atom.Fragment___ge__(self, *args)
6000 def __gt__(self, *args):
6002 __gt__(Fragment self, Fragment o) -> bool
6003 __gt__(Fragment self, Particle d) -> bool
6005 return _IMP_atom.Fragment___gt__(self, *args)
6008 r"""__hash__(Fragment self) -> std::size_t"""
6009 return _IMP_atom.Fragment___hash__(self)
6012 r"""__str__(Fragment self) -> std::string"""
6013 return _IMP_atom.Fragment___str__(self)
6016 r"""__repr__(Fragment self) -> std::string"""
6017 return _IMP_atom.Fragment___repr__(self)
6019 def _get_as_binary(self):
6020 r"""_get_as_binary(Fragment self) -> PyObject *"""
6021 return _IMP_atom.Fragment__get_as_binary(self)
6023 def _set_from_binary(self, p):
6024 r"""_set_from_binary(Fragment self, PyObject * p)"""
6025 return _IMP_atom.Fragment__set_from_binary(self, p)
6027 def __getstate__(self):
6028 p = self._get_as_binary()
6029 if len(self.__dict__) > 1:
6030 d = self.__dict__.copy()
6035 def __setstate__(self, p):
6036 if not hasattr(self,
'this'):
6038 if isinstance(p, tuple):
6040 self.__dict__.update(d)
6041 return self._set_from_binary(p)
6043 __swig_destroy__ = _IMP_atom.delete_Fragment
6046 _IMP_atom.Fragment_swigregister(Fragment)
6048 r"""Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6050 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6053 r"""__init__(StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6054 _IMP_atom.StereochemistryPairFilter_swiginit(self, _IMP_atom.new_StereochemistryPairFilter())
6056 def set_bonds(self, bonds):
6057 r"""set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6058 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6060 def set_angles(self, angles):
6061 r"""set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6062 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6064 def set_dihedrals(self, dihedrals):
6065 r"""set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6066 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6068 def do_get_inputs(self, m, pis):
6069 r"""do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6070 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6072 def get_value(self, *args):
6074 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6075 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6077 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6079 def get_value_index(self, *args):
6081 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6082 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6084 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6086 def get_version_info(self):
6087 r"""get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6088 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6089 __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
6092 r"""__str__(StereochemistryPairFilter self) -> std::string"""
6093 return _IMP_atom.StereochemistryPairFilter___str__(self)
6096 r"""__repr__(StereochemistryPairFilter self) -> std::string"""
6097 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6101 return _object_cast_to_StereochemistryPairFilter(o)
6105 _IMP_atom.StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6107 r"""Proxy of C++ IMP::atom::SoapPairFilter class."""
6109 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6111 def __init__(self, library):
6112 r"""__init__(SoapPairFilter self, std::string library) -> SoapPairFilter"""
6113 _IMP_atom.SoapPairFilter_swiginit(self, _IMP_atom.new_SoapPairFilter(library))
6115 def do_get_inputs(self, m, pis):
6116 r"""do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6117 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6119 def get_value(self, *args):
6121 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6122 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6124 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6126 def get_value_index(self, *args):
6128 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6129 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6131 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6133 def get_version_info(self):
6134 r"""get_version_info(SoapPairFilter self) -> VersionInfo"""
6135 return _IMP_atom.SoapPairFilter_get_version_info(self)
6136 __swig_destroy__ = _IMP_atom.delete_SoapPairFilter
6139 r"""__str__(SoapPairFilter self) -> std::string"""
6140 return _IMP_atom.SoapPairFilter___str__(self)
6143 r"""__repr__(SoapPairFilter self) -> std::string"""
6144 return _IMP_atom.SoapPairFilter___repr__(self)
6148 return _object_cast_to_SoapPairFilter(o)
6152 _IMP_atom.SoapPairFilter_swigregister(SoapPairFilter)
6154 r"""Proxy of C++ IMP::atom::Mass class."""
6156 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6159 r"""get_mass(Mass self) -> IMP::Float"""
6160 return _IMP_atom.Mass_get_mass(self)
6162 def set_mass(self, d):
6163 r"""set_mass(Mass self, IMP::Float d)"""
6164 return _IMP_atom.Mass_set_mass(self, d)
6166 def __init__(self, *args):
6168 __init__(Mass self) -> Mass
6169 __init__(Mass self, Model m, ParticleIndex id) -> Mass
6170 __init__(Mass self, _ParticleAdaptor d) -> Mass
6172 _IMP_atom.Mass_swiginit(self, _IMP_atom.new_Mass(*args))
6175 def get_is_setup(*args):
6177 get_is_setup(Model m, ParticleIndex pi) -> bool
6178 get_is_setup(_ParticleAdaptor p) -> bool
6180 return _IMP_atom.Mass_get_is_setup(*args)
6182 def show(self, *args):
6183 r"""show(Mass self, _ostream out=std::cout)"""
6184 return _IMP_atom.Mass_show(self, *args)
6187 def setup_particle(*args):
6189 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6190 setup_particle(_ParticleAdaptor pa, IMP::Float mass) -> Mass
6191 setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6192 setup_particle(_ParticleAdaptor pa, Mass other) -> Mass
6194 return _IMP_atom.Mass_setup_particle(*args)
6198 r"""get_mass_key() -> FloatKey"""
6199 return _IMP_atom.Mass_get_mass_key()
6201 def add_attribute(self, *args):
6203 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6204 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6205 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6206 add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6207 add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6208 add_attribute(Mass self, StringKey a0, IMP::String a1)
6209 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6210 add_attribute(Mass self, ObjectKey a0, Object a1)
6211 add_attribute(Mass self, SparseFloatKey a0, IMP::Float a1)
6212 add_attribute(Mass self, SparseIntKey a0, IMP::Int a1)
6213 add_attribute(Mass self, SparseStringKey a0, IMP::String a1)
6214 add_attribute(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6216 return _IMP_atom.Mass_add_attribute(self, *args)
6218 def get_value(self, *args):
6220 get_value(Mass self, FloatKey a0) -> IMP::Float
6221 get_value(Mass self, IntKey a0) -> IMP::Int
6222 get_value(Mass self, FloatsKey a0) -> IMP::Floats
6223 get_value(Mass self, IntsKey a0) -> IMP::Ints
6224 get_value(Mass self, StringKey a0) -> IMP::String
6225 get_value(Mass self, ParticleIndexKey a0) -> Particle
6226 get_value(Mass self, ObjectKey a0) -> Object
6227 get_value(Mass self, SparseFloatKey a0) -> IMP::Float
6228 get_value(Mass self, SparseIntKey a0) -> IMP::Int
6229 get_value(Mass self, SparseStringKey a0) -> IMP::String
6230 get_value(Mass self, SparseParticleIndexKey a0) -> ParticleIndex
6232 return _IMP_atom.Mass_get_value(self, *args)
6234 def set_value(self, *args):
6236 set_value(Mass self, FloatKey a0, IMP::Float a1)
6237 set_value(Mass self, IntKey a0, IMP::Int a1)
6238 set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6239 set_value(Mass self, IntsKey a0, IMP::Ints a1)
6240 set_value(Mass self, StringKey a0, IMP::String a1)
6241 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6242 set_value(Mass self, ObjectKey a0, Object a1)
6243 set_value(Mass self, SparseFloatKey a0, IMP::Float a1)
6244 set_value(Mass self, SparseIntKey a0, IMP::Int a1)
6245 set_value(Mass self, SparseStringKey a0, IMP::String a1)
6246 set_value(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6248 return _IMP_atom.Mass_set_value(self, *args)
6250 def remove_attribute(self, *args):
6252 remove_attribute(Mass self, FloatKey a0)
6253 remove_attribute(Mass self, IntKey a0)
6254 remove_attribute(Mass self, FloatsKey a0)
6255 remove_attribute(Mass self, IntsKey a0)
6256 remove_attribute(Mass self, StringKey a0)
6257 remove_attribute(Mass self, ParticleIndexKey a0)
6258 remove_attribute(Mass self, ObjectKey a0)
6259 remove_attribute(Mass self, SparseFloatKey a0)
6260 remove_attribute(Mass self, SparseIntKey a0)
6261 remove_attribute(Mass self, SparseStringKey a0)
6262 remove_attribute(Mass self, SparseParticleIndexKey a0)
6264 return _IMP_atom.Mass_remove_attribute(self, *args)
6266 def has_attribute(self, *args):
6268 has_attribute(Mass self, FloatKey a0) -> bool
6269 has_attribute(Mass self, IntKey a0) -> bool
6270 has_attribute(Mass self, FloatsKey a0) -> bool
6271 has_attribute(Mass self, IntsKey a0) -> bool
6272 has_attribute(Mass self, StringKey a0) -> bool
6273 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6274 has_attribute(Mass self, ObjectKey a0) -> bool
6275 has_attribute(Mass self, SparseFloatKey a0) -> bool
6276 has_attribute(Mass self, SparseIntKey a0) -> bool
6277 has_attribute(Mass self, SparseStringKey a0) -> bool
6278 has_attribute(Mass self, SparseParticleIndexKey a0) -> bool
6280 return _IMP_atom.Mass_has_attribute(self, *args)
6282 def get_derivative(self, a0):
6283 r"""get_derivative(Mass self, FloatKey a0) -> double"""
6284 return _IMP_atom.Mass_get_derivative(self, a0)
6287 r"""get_name(Mass self) -> std::string"""
6288 return _IMP_atom.Mass_get_name(self)
6290 def clear_caches(self):
6291 r"""clear_caches(Mass self)"""
6292 return _IMP_atom.Mass_clear_caches(self)
6294 def set_name(self, a0):
6295 r"""set_name(Mass self, std::string a0)"""
6296 return _IMP_atom.Mass_set_name(self, a0)
6299 r"""set_check_level(Mass self, IMP::CheckLevel a0)"""
6300 return _IMP_atom.Mass_set_check_level(self, a0)
6302 def add_to_derivative(self, a0, a1, a2):
6303 r"""add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6304 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6306 def set_is_optimized(self, a0, a1):
6307 r"""set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6308 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6310 def get_is_optimized(self, a0):
6311 r"""get_is_optimized(Mass self, FloatKey a0) -> bool"""
6312 return _IMP_atom.Mass_get_is_optimized(self, a0)
6315 r"""get_check_level(Mass self) -> IMP::CheckLevel"""
6316 return _IMP_atom.Mass_get_check_level(self)
6318 def __eq__(self, *args):
6320 __eq__(Mass self, Mass o) -> bool
6321 __eq__(Mass self, Particle d) -> bool
6323 return _IMP_atom.Mass___eq__(self, *args)
6325 def __ne__(self, *args):
6327 __ne__(Mass self, Mass o) -> bool
6328 __ne__(Mass self, Particle d) -> bool
6330 return _IMP_atom.Mass___ne__(self, *args)
6332 def __le__(self, *args):
6334 __le__(Mass self, Mass o) -> bool
6335 __le__(Mass self, Particle d) -> bool
6337 return _IMP_atom.Mass___le__(self, *args)
6339 def __lt__(self, *args):
6341 __lt__(Mass self, Mass o) -> bool
6342 __lt__(Mass self, Particle d) -> bool
6344 return _IMP_atom.Mass___lt__(self, *args)
6346 def __ge__(self, *args):
6348 __ge__(Mass self, Mass o) -> bool
6349 __ge__(Mass self, Particle d) -> bool
6351 return _IMP_atom.Mass___ge__(self, *args)
6353 def __gt__(self, *args):
6355 __gt__(Mass self, Mass o) -> bool
6356 __gt__(Mass self, Particle d) -> bool
6358 return _IMP_atom.Mass___gt__(self, *args)
6361 r"""__hash__(Mass self) -> std::size_t"""
6362 return _IMP_atom.Mass___hash__(self)
6365 r"""__str__(Mass self) -> std::string"""
6366 return _IMP_atom.Mass___str__(self)
6369 r"""__repr__(Mass self) -> std::string"""
6370 return _IMP_atom.Mass___repr__(self)
6372 def _get_as_binary(self):
6373 r"""_get_as_binary(Mass self) -> PyObject *"""
6374 return _IMP_atom.Mass__get_as_binary(self)
6376 def _set_from_binary(self, p):
6377 r"""_set_from_binary(Mass self, PyObject * p)"""
6378 return _IMP_atom.Mass__set_from_binary(self, p)
6380 def __getstate__(self):
6381 p = self._get_as_binary()
6382 if len(self.__dict__) > 1:
6383 d = self.__dict__.copy()
6388 def __setstate__(self, p):
6389 if not hasattr(self,
'this'):
6391 if isinstance(p, tuple):
6393 self.__dict__.update(d)
6394 return self._set_from_binary(p)
6396 __swig_destroy__ = _IMP_atom.delete_Mass
6399 _IMP_atom.Mass_swigregister(Mass)
6401 r"""Proxy of C++ IMP::atom::BondedPairFilter class."""
6403 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6406 r"""__init__(BondedPairFilter self) -> BondedPairFilter"""
6407 _IMP_atom.BondedPairFilter_swiginit(self, _IMP_atom.new_BondedPairFilter())
6409 def do_get_inputs(self, m, pis):
6410 r"""do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6411 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6413 def get_value(self, *args):
6415 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6416 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6418 return _IMP_atom.BondedPairFilter_get_value(self, *args)
6420 def get_value_index(self, *args):
6422 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6423 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6425 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6427 def get_version_info(self):
6428 r"""get_version_info(BondedPairFilter self) -> VersionInfo"""
6429 return _IMP_atom.BondedPairFilter_get_version_info(self)
6430 __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
6433 r"""__str__(BondedPairFilter self) -> std::string"""
6434 return _IMP_atom.BondedPairFilter___str__(self)
6437 r"""__repr__(BondedPairFilter self) -> std::string"""
6438 return _IMP_atom.BondedPairFilter___repr__(self)
6442 return _object_cast_to_BondedPairFilter(o)
6446 _IMP_atom.BondedPairFilter_swigregister(BondedPairFilter)
6448 r"""Proxy of C++ IMP::atom::Mol2Selector class."""
6450 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6452 def __init__(self, *args, **kwargs):
6453 raise AttributeError(
"No constructor defined - class is abstract")
6455 def get_is_selected(self, atom_line):
6456 r"""get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6457 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6458 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6461 r"""__str__(Mol2Selector self) -> std::string"""
6462 return _IMP_atom.Mol2Selector___str__(self)
6465 r"""__repr__(Mol2Selector self) -> std::string"""
6466 return _IMP_atom.Mol2Selector___repr__(self)
6470 return _object_cast_to_Mol2Selector(o)
6474 _IMP_atom.Mol2Selector_swigregister(Mol2Selector)
6475 class AllMol2Selector(Mol2Selector):
6476 r"""Proxy of C++ IMP::atom::AllMol2Selector class."""
6478 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6481 r"""__str__(AllMol2Selector self) -> std::string"""
6482 return _IMP_atom.AllMol2Selector___str__(self)
6485 r"""__repr__(AllMol2Selector self) -> std::string"""
6486 return _IMP_atom.AllMol2Selector___repr__(self)
6490 return _object_cast_to_AllMol2Selector(o)
6494 r"""__init__(AllMol2Selector self) -> AllMol2Selector"""
6495 _IMP_atom.AllMol2Selector_swiginit(self, _IMP_atom.new_AllMol2Selector())
6496 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6499 _IMP_atom.AllMol2Selector_swigregister(AllMol2Selector)
6500 class NonHydrogenMol2Selector(Mol2Selector):
6501 r"""Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6503 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6506 r"""__str__(NonHydrogenMol2Selector self) -> std::string"""
6507 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6510 r"""__repr__(NonHydrogenMol2Selector self) -> std::string"""
6511 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6515 return _object_cast_to_NonHydrogenMol2Selector(o)
6519 r"""__init__(NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6520 _IMP_atom.NonHydrogenMol2Selector_swiginit(self, _IMP_atom.new_NonHydrogenMol2Selector())
6521 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6524 _IMP_atom.NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
6526 def read_mol2(mol2_file, model, mol2sel=None):
6527 r"""read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy"""
6528 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
6531 r"""write_mol2(Hierarchy rhd, TextOutput file_name)"""
6532 return _IMP_atom.write_mol2(rhd, file_name)
6534 r"""Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
6536 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6538 def __init__(self, *args):
6540 __init__(SecondaryStructureResidue self) -> SecondaryStructureResidue
6541 __init__(SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
6542 __init__(SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
6544 _IMP_atom.SecondaryStructureResidue_swiginit(self, _IMP_atom.new_SecondaryStructureResidue(*args))
6546 def show(self, *args):
6547 r"""show(SecondaryStructureResidue self, _ostream out=std::cout)"""
6548 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
6551 def setup_particle(*args):
6553 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6554 setup_particle(_ParticleAdaptor pa, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6555 setup_particle(Particle res_p) -> SecondaryStructureResidue
6557 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
6560 def get_is_setup(*args):
6562 get_is_setup(_ParticleAdaptor p) -> bool
6563 get_is_setup(Model m, ParticleIndex pi) -> bool
6565 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
6567 def get_particle(self):
6568 r"""get_particle(SecondaryStructureResidue self) -> Particle"""
6569 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
6571 def get_all_probabilities(self):
6572 r"""get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
6573 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
6575 def get_prob_helix(self):
6576 r"""get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
6577 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
6579 def set_prob_helix(self, t):
6580 r"""set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
6581 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
6583 def get_prob_strand(self):
6584 r"""get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
6585 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
6587 def set_prob_strand(self, t):
6588 r"""set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
6589 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
6591 def get_prob_coil(self):
6592 r"""get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
6593 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
6595 def set_prob_coil(self, t):
6596 r"""set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
6597 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
6600 def get_prob_helix_key():
6601 r"""get_prob_helix_key() -> FloatKey"""
6602 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
6605 def get_prob_strand_key():
6606 r"""get_prob_strand_key() -> FloatKey"""
6607 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
6610 def get_prob_coil_key():
6611 r"""get_prob_coil_key() -> FloatKey"""
6612 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
6614 def add_attribute(self, *args):
6616 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
6617 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6618 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6619 add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6620 add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6621 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6622 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6623 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6624 add_attribute(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
6625 add_attribute(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
6626 add_attribute(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
6627 add_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
6629 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
6631 def get_value(self, *args):
6633 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
6634 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
6635 get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
6636 get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
6637 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
6638 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
6639 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
6640 get_value(SecondaryStructureResidue self, SparseFloatKey a0) -> IMP::Float
6641 get_value(SecondaryStructureResidue self, SparseIntKey a0) -> IMP::Int
6642 get_value(SecondaryStructureResidue self, SparseStringKey a0) -> IMP::String
6643 get_value(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> ParticleIndex
6645 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
6647 def set_value(self, *args):
6649 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6650 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6651 set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6652 set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6653 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6654 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6655 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6656 set_value(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
6657 set_value(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
6658 set_value(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
6659 set_value(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
6661 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
6663 def remove_attribute(self, *args):
6665 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
6666 remove_attribute(SecondaryStructureResidue self, IntKey a0)
6667 remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
6668 remove_attribute(SecondaryStructureResidue self, IntsKey a0)
6669 remove_attribute(SecondaryStructureResidue self, StringKey a0)
6670 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
6671 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
6672 remove_attribute(SecondaryStructureResidue self, SparseFloatKey a0)
6673 remove_attribute(SecondaryStructureResidue self, SparseIntKey a0)
6674 remove_attribute(SecondaryStructureResidue self, SparseStringKey a0)
6675 remove_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0)
6677 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
6679 def has_attribute(self, *args):
6681 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
6682 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
6683 has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
6684 has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
6685 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
6686 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
6687 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
6688 has_attribute(SecondaryStructureResidue self, SparseFloatKey a0) -> bool
6689 has_attribute(SecondaryStructureResidue self, SparseIntKey a0) -> bool
6690 has_attribute(SecondaryStructureResidue self, SparseStringKey a0) -> bool
6691 has_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> bool
6693 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
6695 def get_derivative(self, a0):
6696 r"""get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
6697 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
6700 r"""get_name(SecondaryStructureResidue self) -> std::string"""
6701 return _IMP_atom.SecondaryStructureResidue_get_name(self)
6703 def clear_caches(self):
6704 r"""clear_caches(SecondaryStructureResidue self)"""
6705 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
6707 def set_name(self, a0):
6708 r"""set_name(SecondaryStructureResidue self, std::string a0)"""
6709 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
6712 r"""set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
6713 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
6715 def add_to_derivative(self, a0, a1, a2):
6716 r"""add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6717 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
6719 def set_is_optimized(self, a0, a1):
6720 r"""set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
6721 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
6723 def get_is_optimized(self, a0):
6724 r"""get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
6725 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
6728 r"""get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
6729 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
6731 def __eq__(self, *args):
6733 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6734 __eq__(SecondaryStructureResidue self, Particle d) -> bool
6736 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
6738 def __ne__(self, *args):
6740 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6741 __ne__(SecondaryStructureResidue self, Particle d) -> bool
6743 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
6745 def __le__(self, *args):
6747 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6748 __le__(SecondaryStructureResidue self, Particle d) -> bool
6750 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
6752 def __lt__(self, *args):
6754 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6755 __lt__(SecondaryStructureResidue self, Particle d) -> bool
6757 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
6759 def __ge__(self, *args):
6761 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6762 __ge__(SecondaryStructureResidue self, Particle d) -> bool
6764 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
6766 def __gt__(self, *args):
6768 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6769 __gt__(SecondaryStructureResidue self, Particle d) -> bool
6771 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
6774 r"""__hash__(SecondaryStructureResidue self) -> std::size_t"""
6775 return _IMP_atom.SecondaryStructureResidue___hash__(self)
6778 r"""__str__(SecondaryStructureResidue self) -> std::string"""
6779 return _IMP_atom.SecondaryStructureResidue___str__(self)
6782 r"""__repr__(SecondaryStructureResidue self) -> std::string"""
6783 return _IMP_atom.SecondaryStructureResidue___repr__(self)
6785 def _get_as_binary(self):
6786 r"""_get_as_binary(SecondaryStructureResidue self) -> PyObject *"""
6787 return _IMP_atom.SecondaryStructureResidue__get_as_binary(self)
6789 def _set_from_binary(self, p):
6790 r"""_set_from_binary(SecondaryStructureResidue self, PyObject * p)"""
6791 return _IMP_atom.SecondaryStructureResidue__set_from_binary(self, p)
6793 def __getstate__(self):
6794 p = self._get_as_binary()
6795 if len(self.__dict__) > 1:
6796 d = self.__dict__.copy()
6801 def __setstate__(self, p):
6802 if not hasattr(self,
'this'):
6804 if isinstance(p, tuple):
6806 self.__dict__.update(d)
6807 return self._set_from_binary(p)
6809 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
6812 _IMP_atom.SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
6815 r"""setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue"""
6816 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
6819 r"""setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues"""
6820 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
6823 r"""get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
6824 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
6826 def read_psipred(*args):
6828 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
6829 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
6831 return _IMP_atom.read_psipred(*args)
6833 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Dope > class."""
6835 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6836 __repr__ = _swig_repr
6838 def __init__(self, *args):
6840 __init__(_ADopeBase self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
6841 __init__(_ADopeBase self) -> _ADopeBase
6843 _IMP_atom._ADopeBase_swiginit(self, _IMP_atom.new__ADopeBase(*args))
6845 def do_get_inputs(self, m, pis):
6846 r"""do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6847 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
6849 def get_score_functor(self):
6850 r"""get_score_functor(_ADopeBase self) -> Dope"""
6851 return _IMP_atom._ADopeBase_get_score_functor(self)
6853 def get_version_info(self):
6854 r"""get_version_info(_ADopeBase self) -> VersionInfo"""
6855 return _IMP_atom._ADopeBase_get_version_info(self)
6856 __swig_destroy__ = _IMP_atom.delete__ADopeBase
6859 _IMP_atom._ADopeBase_swigregister(_ADopeBase)
6861 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > > class."""
6863 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6864 __repr__ = _swig_repr
6866 def __init__(self, *args):
6868 __init__(_BDopeBase self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _BDopeBase
6869 __init__(_BDopeBase self) -> _BDopeBase
6871 _IMP_atom._BDopeBase_swiginit(self, _IMP_atom.new__BDopeBase(*args))
6873 def do_get_inputs(self, m, pis):
6874 r"""do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6875 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
6877 def get_score_functor(self):
6878 r"""get_score_functor(_BDopeBase self) -> _DopeBase"""
6879 return _IMP_atom._BDopeBase_get_score_functor(self)
6881 def get_version_info(self):
6882 r"""get_version_info(_BDopeBase self) -> VersionInfo"""
6883 return _IMP_atom._BDopeBase_get_version_info(self)
6884 __swig_destroy__ = _IMP_atom.delete__BDopeBase
6887 _IMP_atom._BDopeBase_swigregister(_BDopeBase)
6889 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::LoopStatistical > class."""
6891 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6892 __repr__ = _swig_repr
6894 def __init__(self, *args):
6896 __init__(_ALoopStatisticalBase self, LoopStatistical t0, std::string name="FunctorDistancePairScore %1%") -> _ALoopStatisticalBase
6897 __init__(_ALoopStatisticalBase self) -> _ALoopStatisticalBase
6899 _IMP_atom._ALoopStatisticalBase_swiginit(self, _IMP_atom.new__ALoopStatisticalBase(*args))
6901 def do_get_inputs(self, m, pis):
6902 r"""do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6903 return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
6905 def get_score_functor(self):
6906 r"""get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
6907 return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
6909 def get_version_info(self):
6910 r"""get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
6911 return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
6912 __swig_destroy__ = _IMP_atom.delete__ALoopStatisticalBase
6915 _IMP_atom._ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
6917 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > > class."""
6919 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6920 __repr__ = _swig_repr
6922 def __init__(self, *args):
6924 __init__(_BLoopStatisticalBase self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _BLoopStatisticalBase
6925 __init__(_BLoopStatisticalBase self) -> _BLoopStatisticalBase
6927 _IMP_atom._BLoopStatisticalBase_swiginit(self, _IMP_atom.new__BLoopStatisticalBase(*args))
6929 def do_get_inputs(self, m, pis):
6930 r"""do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6931 return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
6933 def get_score_functor(self):
6934 r"""get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
6935 return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
6937 def get_version_info(self):
6938 r"""get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
6939 return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
6940 __swig_destroy__ = _IMP_atom.delete__BLoopStatisticalBase
6943 _IMP_atom._BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
6945 r"""Proxy of C++ IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap > class."""
6947 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6948 __repr__ = _swig_repr
6950 def __init__(self, *args):
6951 r"""__init__(_OrientedSoapBase self, IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name="FunctorDistancePairScoreWithCache %1%") -> _OrientedSoapBase"""
6952 _IMP_atom._OrientedSoapBase_swiginit(self, _IMP_atom.new__OrientedSoapBase(*args))
6954 def do_get_inputs(self, m, pis):
6955 r"""do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6956 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
6958 def get_score_functor(self):
6959 r"""get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
6960 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
6962 def get_version_info(self):
6963 r"""get_version_info(_OrientedSoapBase self) -> VersionInfo"""
6964 return _IMP_atom._OrientedSoapBase_get_version_info(self)
6965 __swig_destroy__ = _IMP_atom.delete__OrientedSoapBase
6968 _IMP_atom._OrientedSoapBase_swigregister(_OrientedSoapBase)
6970 r"""Proxy of C++ IMP::score_functor::DistancePairScore< score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > > class."""
6972 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6973 __repr__ = _swig_repr
6975 def __init__(self, *args):
6977 __init__(_SPSFTB self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _SPSFTB
6978 __init__(_SPSFTB self) -> _SPSFTB
6980 _IMP_atom._SPSFTB_swiginit(self, _IMP_atom.new__SPSFTB(*args))
6982 def do_get_inputs(self, m, pis):
6983 r"""do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6984 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
6986 def get_score_functor(self):
6987 r"""get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
6988 return _IMP_atom._SPSFTB_get_score_functor(self)
6990 def get_version_info(self):
6991 r"""get_version_info(_SPSFTB self) -> VersionInfo"""
6992 return _IMP_atom._SPSFTB_get_version_info(self)
6993 __swig_destroy__ = _IMP_atom.delete__SPSFTB
6996 _IMP_atom._SPSFTB_swigregister(_SPSFTB)
6997 class _SPSTF(_SPSFTB):
6998 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType,true,false > class."""
7000 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7001 __repr__ = _swig_repr
7003 def __init__(self, *args):
7005 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7006 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7008 _IMP_atom._SPSTF_swiginit(self, _IMP_atom.new__SPSTF(*args))
7009 __swig_destroy__ = _IMP_atom.delete__SPSTF
7012 _IMP_atom._SPSTF_swigregister(_SPSTF)
7013 class _SPSFT(_BDopeBase):
7014 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::DopeType,false,true > class."""
7016 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7017 __repr__ = _swig_repr
7019 def __init__(self, *args):
7021 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7022 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7024 _IMP_atom._SPSFT_swiginit(self, _IMP_atom.new__SPSFT(*args))
7025 __swig_destroy__ = _IMP_atom.delete__SPSFT
7028 _IMP_atom._SPSFT_swigregister(_SPSFT)
7029 class _SPSFTL(_BLoopStatisticalBase):
7030 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType,false,true > class."""
7032 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7033 __repr__ = _swig_repr
7035 def __init__(self, *args):
7037 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7038 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7040 _IMP_atom._SPSFTL_swiginit(self, _IMP_atom.new__SPSFTL(*args))
7041 __swig_destroy__ = _IMP_atom.delete__SPSFTL
7044 _IMP_atom._SPSFTL_swigregister(_SPSFTL)
7045 class ProteinLigandAtomPairScore(_SPSTF):
7046 r"""Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7048 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7050 def __init__(self, *args):
7052 __init__(ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
7053 __init__(ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7055 _IMP_atom.ProteinLigandAtomPairScore_swiginit(self, _IMP_atom.new_ProteinLigandAtomPairScore(*args))
7057 def get_maximum_distance(self):
7058 r"""get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7059 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7062 r"""__str__(ProteinLigandAtomPairScore self) -> std::string"""
7063 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7066 r"""__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7067 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7071 return _object_cast_to_ProteinLigandAtomPairScore(o)
7073 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7076 _IMP_atom.ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7078 r"""Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7080 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7082 def __init__(self, *args):
7084 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
7085 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7087 _IMP_atom.ProteinLigandRestraint_swiginit(self, _IMP_atom.new_ProteinLigandRestraint(*args))
7090 r"""__str__(ProteinLigandRestraint self) -> std::string"""
7091 return _IMP_atom.ProteinLigandRestraint___str__(self)
7094 r"""__repr__(ProteinLigandRestraint self) -> std::string"""
7095 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7099 return _object_cast_to_ProteinLigandRestraint(o)
7101 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7104 _IMP_atom.ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7107 r"""add_protein_ligand_score_data(Hierarchy h)"""
7108 return _IMP_atom.add_protein_ligand_score_data(h)
7109 class AtomType(IMP._Value):
7110 r"""Proxy of C++ IMP::Key< 8974343 > class."""
7112 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7114 def __init__(self, *args):
7116 __init__(AtomType self) -> AtomType
7117 __init__(AtomType self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7118 __init__(AtomType self, unsigned int i) -> AtomType
7120 _IMP_atom.AtomType_swiginit(self, _IMP_atom.new_AtomType(*args))
7124 r"""add_key(std::string sc) -> unsigned int"""
7125 return _IMP_atom.AtomType_add_key(sc)
7128 def get_key_exists(sc):
7129 r"""get_key_exists(std::string sc) -> bool"""
7130 return _IMP_atom.AtomType_get_key_exists(sc)
7132 def get_string(self):
7133 r"""get_string(AtomType self) -> std::string const"""
7134 return _IMP_atom.AtomType_get_string(self)
7136 def __cmp__(self, o):
7137 r"""__cmp__(AtomType self, AtomType o) -> int"""
7138 return _IMP_atom.AtomType___cmp__(self, o)
7140 def __eq__(self, o):
7141 r"""__eq__(AtomType self, AtomType o) -> bool"""
7142 return _IMP_atom.AtomType___eq__(self, o)
7144 def __ne__(self, o):
7145 r"""__ne__(AtomType self, AtomType o) -> bool"""
7146 return _IMP_atom.AtomType___ne__(self, o)
7148 def __lt__(self, o):
7149 r"""__lt__(AtomType self, AtomType o) -> bool"""
7150 return _IMP_atom.AtomType___lt__(self, o)
7152 def __gt__(self, o):
7153 r"""__gt__(AtomType self, AtomType o) -> bool"""
7154 return _IMP_atom.AtomType___gt__(self, o)
7156 def __ge__(self, o):
7157 r"""__ge__(AtomType self, AtomType o) -> bool"""
7158 return _IMP_atom.AtomType___ge__(self, o)
7160 def __le__(self, o):
7161 r"""__le__(AtomType self, AtomType o) -> bool"""
7162 return _IMP_atom.AtomType___le__(self, o)
7165 r"""__hash__(AtomType self) -> std::size_t"""
7166 return _IMP_atom.AtomType___hash__(self)
7168 def show(self, *args):
7169 r"""show(AtomType self, _ostream out=std::cout)"""
7170 return _IMP_atom.AtomType_show(self, *args)
7173 def add_alias(old_key, new_name):
7174 r"""add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7175 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7178 def get_number_of_keys():
7179 r"""get_number_of_keys() -> unsigned int"""
7180 return _IMP_atom.AtomType_get_number_of_keys()
7183 r"""get_index(AtomType self) -> unsigned int"""
7184 return _IMP_atom.AtomType_get_index(self)
7188 r"""show_all(_ostream out)"""
7189 return _IMP_atom.AtomType_show_all(out)
7192 def get_all_strings():
7193 r"""get_all_strings() -> IMP::Vector< std::string >"""
7194 return _IMP_atom.AtomType_get_all_strings()
7197 def get_number_unique():
7198 r"""get_number_unique() -> unsigned int"""
7199 return _IMP_atom.AtomType_get_number_unique()
7202 r"""__str__(AtomType self) -> std::string"""
7203 return _IMP_atom.AtomType___str__(self)
7206 r"""__repr__(AtomType self) -> std::string"""
7207 return _IMP_atom.AtomType___repr__(self)
7208 __swig_destroy__ = _IMP_atom.delete_AtomType
7211 _IMP_atom.AtomType_swigregister(AtomType)
7212 class ResidueType(IMP._Value):
7213 r"""Proxy of C++ IMP::Key< 90784334 > class."""
7215 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7217 def __init__(self, *args):
7219 __init__(ResidueType self) -> ResidueType
7220 __init__(ResidueType self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7221 __init__(ResidueType self, unsigned int i) -> ResidueType
7223 _IMP_atom.ResidueType_swiginit(self, _IMP_atom.new_ResidueType(*args))
7227 r"""add_key(std::string sc) -> unsigned int"""
7228 return _IMP_atom.ResidueType_add_key(sc)
7231 def get_key_exists(sc):
7232 r"""get_key_exists(std::string sc) -> bool"""
7233 return _IMP_atom.ResidueType_get_key_exists(sc)
7235 def get_string(self):
7236 r"""get_string(ResidueType self) -> std::string const"""
7237 return _IMP_atom.ResidueType_get_string(self)
7239 def __cmp__(self, o):
7240 r"""__cmp__(ResidueType self, ResidueType o) -> int"""
7241 return _IMP_atom.ResidueType___cmp__(self, o)
7243 def __eq__(self, o):
7244 r"""__eq__(ResidueType self, ResidueType o) -> bool"""
7245 return _IMP_atom.ResidueType___eq__(self, o)
7247 def __ne__(self, o):
7248 r"""__ne__(ResidueType self, ResidueType o) -> bool"""
7249 return _IMP_atom.ResidueType___ne__(self, o)
7251 def __lt__(self, o):
7252 r"""__lt__(ResidueType self, ResidueType o) -> bool"""
7253 return _IMP_atom.ResidueType___lt__(self, o)
7255 def __gt__(self, o):
7256 r"""__gt__(ResidueType self, ResidueType o) -> bool"""
7257 return _IMP_atom.ResidueType___gt__(self, o)
7259 def __ge__(self, o):
7260 r"""__ge__(ResidueType self, ResidueType o) -> bool"""
7261 return _IMP_atom.ResidueType___ge__(self, o)
7263 def __le__(self, o):
7264 r"""__le__(ResidueType self, ResidueType o) -> bool"""
7265 return _IMP_atom.ResidueType___le__(self, o)
7268 r"""__hash__(ResidueType self) -> std::size_t"""
7269 return _IMP_atom.ResidueType___hash__(self)
7271 def show(self, *args):
7272 r"""show(ResidueType self, _ostream out=std::cout)"""
7273 return _IMP_atom.ResidueType_show(self, *args)
7276 def add_alias(old_key, new_name):
7277 r"""add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7278 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7281 def get_number_of_keys():
7282 r"""get_number_of_keys() -> unsigned int"""
7283 return _IMP_atom.ResidueType_get_number_of_keys()
7286 r"""get_index(ResidueType self) -> unsigned int"""
7287 return _IMP_atom.ResidueType_get_index(self)
7291 r"""show_all(_ostream out)"""
7292 return _IMP_atom.ResidueType_show_all(out)
7295 def get_all_strings():
7296 r"""get_all_strings() -> IMP::Vector< std::string >"""
7297 return _IMP_atom.ResidueType_get_all_strings()
7300 def get_number_unique():
7301 r"""get_number_unique() -> unsigned int"""
7302 return _IMP_atom.ResidueType_get_number_unique()
7305 r"""__str__(ResidueType self) -> std::string"""
7306 return _IMP_atom.ResidueType___str__(self)
7309 r"""__repr__(ResidueType self) -> std::string"""
7310 return _IMP_atom.ResidueType___repr__(self)
7311 __swig_destroy__ = _IMP_atom.delete_ResidueType
7314 _IMP_atom.ResidueType_swigregister(ResidueType)
7315 class ChainType(IMP._Value):
7316 r"""Proxy of C++ IMP::Key< 90784336 > class."""
7318 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7320 def __init__(self, *args):
7322 __init__(ChainType self) -> ChainType
7323 __init__(ChainType self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
7324 __init__(ChainType self, unsigned int i) -> ChainType
7326 _IMP_atom.ChainType_swiginit(self, _IMP_atom.new_ChainType(*args))
7330 r"""add_key(std::string sc) -> unsigned int"""
7331 return _IMP_atom.ChainType_add_key(sc)
7334 def get_key_exists(sc):
7335 r"""get_key_exists(std::string sc) -> bool"""
7336 return _IMP_atom.ChainType_get_key_exists(sc)
7338 def get_string(self):
7339 r"""get_string(ChainType self) -> std::string const"""
7340 return _IMP_atom.ChainType_get_string(self)
7342 def __cmp__(self, o):
7343 r"""__cmp__(ChainType self, ChainType o) -> int"""
7344 return _IMP_atom.ChainType___cmp__(self, o)
7346 def __eq__(self, o):
7347 r"""__eq__(ChainType self, ChainType o) -> bool"""
7348 return _IMP_atom.ChainType___eq__(self, o)
7350 def __ne__(self, o):
7351 r"""__ne__(ChainType self, ChainType o) -> bool"""
7352 return _IMP_atom.ChainType___ne__(self, o)
7354 def __lt__(self, o):
7355 r"""__lt__(ChainType self, ChainType o) -> bool"""
7356 return _IMP_atom.ChainType___lt__(self, o)
7358 def __gt__(self, o):
7359 r"""__gt__(ChainType self, ChainType o) -> bool"""
7360 return _IMP_atom.ChainType___gt__(self, o)
7362 def __ge__(self, o):
7363 r"""__ge__(ChainType self, ChainType o) -> bool"""
7364 return _IMP_atom.ChainType___ge__(self, o)
7366 def __le__(self, o):
7367 r"""__le__(ChainType self, ChainType o) -> bool"""
7368 return _IMP_atom.ChainType___le__(self, o)
7371 r"""__hash__(ChainType self) -> std::size_t"""
7372 return _IMP_atom.ChainType___hash__(self)
7374 def show(self, *args):
7375 r"""show(ChainType self, _ostream out=std::cout)"""
7376 return _IMP_atom.ChainType_show(self, *args)
7379 def add_alias(old_key, new_name):
7380 r"""add_alias(ChainType old_key, std::string new_name) -> ChainType"""
7381 return _IMP_atom.ChainType_add_alias(old_key, new_name)
7384 def get_number_of_keys():
7385 r"""get_number_of_keys() -> unsigned int"""
7386 return _IMP_atom.ChainType_get_number_of_keys()
7389 r"""get_index(ChainType self) -> unsigned int"""
7390 return _IMP_atom.ChainType_get_index(self)
7394 r"""show_all(_ostream out)"""
7395 return _IMP_atom.ChainType_show_all(out)
7398 def get_all_strings():
7399 r"""get_all_strings() -> IMP::Vector< std::string >"""
7400 return _IMP_atom.ChainType_get_all_strings()
7403 def get_number_unique():
7404 r"""get_number_unique() -> unsigned int"""
7405 return _IMP_atom.ChainType_get_number_unique()
7408 r"""__str__(ChainType self) -> std::string"""
7409 return _IMP_atom.ChainType___str__(self)
7412 r"""__repr__(ChainType self) -> std::string"""
7413 return _IMP_atom.ChainType___repr__(self)
7414 __swig_destroy__ = _IMP_atom.delete_ChainType
7417 _IMP_atom.ChainType_swigregister(ChainType)
7418 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
7636 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
7640 r"""hash_value(IMP::atom::Element e) -> size_t"""
7641 return _IMP_atom.hash_value(e)
7642 class ElementTable(object):
7643 r"""Proxy of C++ IMP::atom::ElementTable class."""
7645 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7646 __repr__ = _swig_repr
7649 r"""__init__(ElementTable self) -> ElementTable"""
7650 _IMP_atom.ElementTable_swiginit(self, _IMP_atom.new_ElementTable())
7652 def get_element(self, s):
7653 r"""get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
7654 return _IMP_atom.ElementTable_get_element(self, s)
7656 def get_name(self, e):
7657 r"""get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
7658 return _IMP_atom.ElementTable_get_name(self, e)
7661 r"""get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
7662 return _IMP_atom.ElementTable_get_mass(self, e)
7663 __swig_destroy__ = _IMP_atom.delete_ElementTable
7666 _IMP_atom.ElementTable_swigregister(ElementTable)
7668 def get_element_table():
7669 r"""get_element_table() -> ElementTable"""
7670 return _IMP_atom.get_element_table()
7671 class Atom(Hierarchy):
7672 r"""Proxy of C++ IMP::atom::Atom class."""
7674 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7676 def __init__(self, *args):
7678 __init__(Atom self) -> Atom
7679 __init__(Atom self, Model m, ParticleIndex id) -> Atom
7680 __init__(Atom self, _ParticleAdaptor d) -> Atom
7682 _IMP_atom.Atom_swiginit(self, _IMP_atom.new_Atom(*args))
7684 def show(self, *args):
7685 r"""show(Atom self, _ostream out=std::cout)"""
7686 return _IMP_atom.Atom_show(self, *args)
7689 def setup_particle(*args):
7691 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
7692 setup_particle(_ParticleAdaptor pa, Atom other) -> Atom
7693 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
7694 setup_particle(_ParticleAdaptor pa, AtomType atom_type) -> Atom
7696 return _IMP_atom.Atom_setup_particle(*args)
7699 def get_is_setup(*args):
7701 get_is_setup(_ParticleAdaptor p) -> bool
7702 get_is_setup(Model m, ParticleIndex pi) -> bool
7704 return _IMP_atom.Atom_get_is_setup(*args)
7706 def get_atom_type(self):
7707 r"""get_atom_type(Atom self) -> AtomType"""
7708 return _IMP_atom.Atom_get_atom_type(self)
7710 def set_atom_type(self, t):
7711 r"""set_atom_type(Atom self, AtomType t)"""
7712 return _IMP_atom.Atom_set_atom_type(self, t)
7714 def get_element(self):
7715 r"""get_element(Atom self) -> IMP::atom::Element"""
7716 return _IMP_atom.Atom_get_element(self)
7718 def set_element(self, e):
7719 r"""set_element(Atom self, IMP::atom::Element e)"""
7720 return _IMP_atom.Atom_set_element(self, e)
7722 def get_occupancy(self):
7723 r"""get_occupancy(Atom self) -> double"""
7724 return _IMP_atom.Atom_get_occupancy(self)
7726 def set_occupancy(self, occupancy):
7727 r"""set_occupancy(Atom self, double occupancy)"""
7728 return _IMP_atom.Atom_set_occupancy(self, occupancy)
7730 def get_temperature_factor(self):
7731 r"""get_temperature_factor(Atom self) -> double"""
7732 return _IMP_atom.Atom_get_temperature_factor(self)
7734 def set_temperature_factor(self, tempFactor):
7735 r"""set_temperature_factor(Atom self, double tempFactor)"""
7736 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
7738 def get_input_index(self):
7739 r"""get_input_index(Atom self) -> IMP::Int"""
7740 return _IMP_atom.Atom_get_input_index(self)
7742 def set_input_index(self, t):
7743 r"""set_input_index(Atom self, IMP::Int t)"""
7744 return _IMP_atom.Atom_set_input_index(self, t)
7747 def get_atom_type_key():
7748 r"""get_atom_type_key() -> IntKey"""
7749 return _IMP_atom.Atom_get_atom_type_key()
7752 def get_element_key():
7753 r"""get_element_key() -> IntKey"""
7754 return _IMP_atom.Atom_get_element_key()
7757 def get_input_index_key():
7758 r"""get_input_index_key() -> IntKey"""
7759 return _IMP_atom.Atom_get_input_index_key()
7762 def get_occupancy_key():
7763 r"""get_occupancy_key() -> FloatKey"""
7764 return _IMP_atom.Atom_get_occupancy_key()
7767 def get_temperature_factor_key():
7768 r"""get_temperature_factor_key() -> FloatKey"""
7769 return _IMP_atom.Atom_get_temperature_factor_key()
7771 def add_attribute(self, *args):
7773 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
7774 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
7775 add_attribute(Atom self, IntKey a0, IMP::Int a1)
7776 add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
7777 add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
7778 add_attribute(Atom self, StringKey a0, IMP::String a1)
7779 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
7780 add_attribute(Atom self, ObjectKey a0, Object a1)
7781 add_attribute(Atom self, SparseFloatKey a0, IMP::Float a1)
7782 add_attribute(Atom self, SparseIntKey a0, IMP::Int a1)
7783 add_attribute(Atom self, SparseStringKey a0, IMP::String a1)
7784 add_attribute(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
7786 return _IMP_atom.Atom_add_attribute(self, *args)
7788 def get_value(self, *args):
7790 get_value(Atom self, FloatKey a0) -> IMP::Float
7791 get_value(Atom self, IntKey a0) -> IMP::Int
7792 get_value(Atom self, FloatsKey a0) -> IMP::Floats
7793 get_value(Atom self, IntsKey a0) -> IMP::Ints
7794 get_value(Atom self, StringKey a0) -> IMP::String
7795 get_value(Atom self, ParticleIndexKey a0) -> Particle
7796 get_value(Atom self, ObjectKey a0) -> Object
7797 get_value(Atom self, SparseFloatKey a0) -> IMP::Float
7798 get_value(Atom self, SparseIntKey a0) -> IMP::Int
7799 get_value(Atom self, SparseStringKey a0) -> IMP::String
7800 get_value(Atom self, SparseParticleIndexKey a0) -> ParticleIndex
7802 return _IMP_atom.Atom_get_value(self, *args)
7804 def set_value(self, *args):
7806 set_value(Atom self, FloatKey a0, IMP::Float a1)
7807 set_value(Atom self, IntKey a0, IMP::Int a1)
7808 set_value(Atom self, FloatsKey a0, IMP::Floats a1)
7809 set_value(Atom self, IntsKey a0, IMP::Ints a1)
7810 set_value(Atom self, StringKey a0, IMP::String a1)
7811 set_value(Atom self, ParticleIndexKey a0, Particle a1)
7812 set_value(Atom self, ObjectKey a0, Object a1)
7813 set_value(Atom self, SparseFloatKey a0, IMP::Float a1)
7814 set_value(Atom self, SparseIntKey a0, IMP::Int a1)
7815 set_value(Atom self, SparseStringKey a0, IMP::String a1)
7816 set_value(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
7818 return _IMP_atom.Atom_set_value(self, *args)
7820 def remove_attribute(self, *args):
7822 remove_attribute(Atom self, FloatKey a0)
7823 remove_attribute(Atom self, IntKey a0)
7824 remove_attribute(Atom self, FloatsKey a0)
7825 remove_attribute(Atom self, IntsKey a0)
7826 remove_attribute(Atom self, StringKey a0)
7827 remove_attribute(Atom self, ParticleIndexKey a0)
7828 remove_attribute(Atom self, ObjectKey a0)
7829 remove_attribute(Atom self, SparseFloatKey a0)
7830 remove_attribute(Atom self, SparseIntKey a0)
7831 remove_attribute(Atom self, SparseStringKey a0)
7832 remove_attribute(Atom self, SparseParticleIndexKey a0)
7834 return _IMP_atom.Atom_remove_attribute(self, *args)
7836 def has_attribute(self, *args):
7838 has_attribute(Atom self, FloatKey a0) -> bool
7839 has_attribute(Atom self, IntKey a0) -> bool
7840 has_attribute(Atom self, FloatsKey a0) -> bool
7841 has_attribute(Atom self, IntsKey a0) -> bool
7842 has_attribute(Atom self, StringKey a0) -> bool
7843 has_attribute(Atom self, ParticleIndexKey a0) -> bool
7844 has_attribute(Atom self, ObjectKey a0) -> bool
7845 has_attribute(Atom self, SparseFloatKey a0) -> bool
7846 has_attribute(Atom self, SparseIntKey a0) -> bool
7847 has_attribute(Atom self, SparseStringKey a0) -> bool
7848 has_attribute(Atom self, SparseParticleIndexKey a0) -> bool
7850 return _IMP_atom.Atom_has_attribute(self, *args)
7852 def get_derivative(self, a0):
7853 r"""get_derivative(Atom self, FloatKey a0) -> double"""
7854 return _IMP_atom.Atom_get_derivative(self, a0)
7857 r"""get_name(Atom self) -> std::string"""
7858 return _IMP_atom.Atom_get_name(self)
7860 def clear_caches(self):
7861 r"""clear_caches(Atom self)"""
7862 return _IMP_atom.Atom_clear_caches(self)
7864 def set_name(self, a0):
7865 r"""set_name(Atom self, std::string a0)"""
7866 return _IMP_atom.Atom_set_name(self, a0)
7869 r"""set_check_level(Atom self, IMP::CheckLevel a0)"""
7870 return _IMP_atom.Atom_set_check_level(self, a0)
7872 def add_to_derivative(self, a0, a1, a2):
7873 r"""add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7874 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
7876 def set_is_optimized(self, a0, a1):
7877 r"""set_is_optimized(Atom self, FloatKey a0, bool a1)"""
7878 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
7880 def get_is_optimized(self, a0):
7881 r"""get_is_optimized(Atom self, FloatKey a0) -> bool"""
7882 return _IMP_atom.Atom_get_is_optimized(self, a0)
7885 r"""get_check_level(Atom self) -> IMP::CheckLevel"""
7886 return _IMP_atom.Atom_get_check_level(self)
7888 def __eq__(self, *args):
7890 __eq__(Atom self, Atom o) -> bool
7891 __eq__(Atom self, Particle d) -> bool
7893 return _IMP_atom.Atom___eq__(self, *args)
7895 def __ne__(self, *args):
7897 __ne__(Atom self, Atom o) -> bool
7898 __ne__(Atom self, Particle d) -> bool
7900 return _IMP_atom.Atom___ne__(self, *args)
7902 def __le__(self, *args):
7904 __le__(Atom self, Atom o) -> bool
7905 __le__(Atom self, Particle d) -> bool
7907 return _IMP_atom.Atom___le__(self, *args)
7909 def __lt__(self, *args):
7911 __lt__(Atom self, Atom o) -> bool
7912 __lt__(Atom self, Particle d) -> bool
7914 return _IMP_atom.Atom___lt__(self, *args)
7916 def __ge__(self, *args):
7918 __ge__(Atom self, Atom o) -> bool
7919 __ge__(Atom self, Particle d) -> bool
7921 return _IMP_atom.Atom___ge__(self, *args)
7923 def __gt__(self, *args):
7925 __gt__(Atom self, Atom o) -> bool
7926 __gt__(Atom self, Particle d) -> bool
7928 return _IMP_atom.Atom___gt__(self, *args)
7931 r"""__hash__(Atom self) -> std::size_t"""
7932 return _IMP_atom.Atom___hash__(self)
7935 r"""__str__(Atom self) -> std::string"""
7936 return _IMP_atom.Atom___str__(self)
7939 r"""__repr__(Atom self) -> std::string"""
7940 return _IMP_atom.Atom___repr__(self)
7942 def _get_as_binary(self):
7943 r"""_get_as_binary(Atom self) -> PyObject *"""
7944 return _IMP_atom.Atom__get_as_binary(self)
7946 def _set_from_binary(self, p):
7947 r"""_set_from_binary(Atom self, PyObject * p)"""
7948 return _IMP_atom.Atom__set_from_binary(self, p)
7950 def __getstate__(self):
7951 p = self._get_as_binary()
7952 if len(self.__dict__) > 1:
7953 d = self.__dict__.copy()
7958 def __setstate__(self, p):
7959 if not hasattr(self,
'this'):
7961 if isinstance(p, tuple):
7963 self.__dict__.update(d)
7964 return self._set_from_binary(p)
7966 __swig_destroy__ = _IMP_atom.delete_Atom
7969 _IMP_atom.Atom_swigregister(Atom)
7970 cvar = _IMP_atom.cvar
7971 AT_UNKNOWN = cvar.AT_UNKNOWN
7981 AT_HA1 = cvar.AT_HA1
7982 AT_HA2 = cvar.AT_HA2
7983 AT_HA3 = cvar.AT_HA3
7986 AT_HB1 = cvar.AT_HB1
7987 AT_HB2 = cvar.AT_HB2
7988 AT_HB3 = cvar.AT_HB3
7989 AT_OXT = cvar.AT_OXT
7990 AT_CH3 = cvar.AT_CH3
7993 AT_CG1 = cvar.AT_CG1
7994 AT_CG2 = cvar.AT_CG2
7996 AT_HG1 = cvar.AT_HG1
7997 AT_HG2 = cvar.AT_HG2
7998 AT_HG3 = cvar.AT_HG3
7999 AT_HG11 = cvar.AT_HG11
8000 AT_HG21 = cvar.AT_HG21
8001 AT_HG31 = cvar.AT_HG31
8002 AT_HG12 = cvar.AT_HG12
8003 AT_HG13 = cvar.AT_HG13
8004 AT_HG22 = cvar.AT_HG22
8005 AT_HG23 = cvar.AT_HG23
8006 AT_HG32 = cvar.AT_HG32
8008 AT_OG1 = cvar.AT_OG1
8011 AT_CD1 = cvar.AT_CD1
8012 AT_CD2 = cvar.AT_CD2
8014 AT_HD1 = cvar.AT_HD1
8015 AT_HD2 = cvar.AT_HD2
8016 AT_HD3 = cvar.AT_HD3
8017 AT_HD11 = cvar.AT_HD11
8018 AT_HD21 = cvar.AT_HD21
8019 AT_HD31 = cvar.AT_HD31
8020 AT_HD12 = cvar.AT_HD12
8021 AT_HD13 = cvar.AT_HD13
8022 AT_HD22 = cvar.AT_HD22
8023 AT_HD23 = cvar.AT_HD23
8024 AT_HD32 = cvar.AT_HD32
8026 AT_OD1 = cvar.AT_OD1
8027 AT_OD2 = cvar.AT_OD2
8028 AT_ND1 = cvar.AT_ND1
8029 AT_ND2 = cvar.AT_ND2
8031 AT_CE1 = cvar.AT_CE1
8032 AT_CE2 = cvar.AT_CE2
8033 AT_CE3 = cvar.AT_CE3
8035 AT_HE1 = cvar.AT_HE1
8036 AT_HE2 = cvar.AT_HE2
8037 AT_HE3 = cvar.AT_HE3
8038 AT_HE21 = cvar.AT_HE21
8039 AT_HE22 = cvar.AT_HE22
8040 AT_OE1 = cvar.AT_OE1
8041 AT_OE2 = cvar.AT_OE2
8043 AT_NE1 = cvar.AT_NE1
8044 AT_NE2 = cvar.AT_NE2
8046 AT_CZ2 = cvar.AT_CZ2
8047 AT_CZ3 = cvar.AT_CZ3
8050 AT_HZ1 = cvar.AT_HZ1
8051 AT_HZ2 = cvar.AT_HZ2
8052 AT_HZ3 = cvar.AT_HZ3
8053 AT_CH2 = cvar.AT_CH2
8054 AT_NH1 = cvar.AT_NH1
8055 AT_NH2 = cvar.AT_NH2
8058 AT_HH11 = cvar.AT_HH11
8059 AT_HH21 = cvar.AT_HH21
8060 AT_HH2 = cvar.AT_HH2
8061 AT_HH12 = cvar.AT_HH12
8062 AT_HH22 = cvar.AT_HH22
8063 AT_HH13 = cvar.AT_HH13
8064 AT_HH23 = cvar.AT_HH23
8065 AT_HH33 = cvar.AT_HH33
8067 AT_OP1 = cvar.AT_OP1
8068 AT_OP2 = cvar.AT_OP2
8069 AT_OP3 = cvar.AT_OP3
8070 AT_O5p = cvar.AT_O5p
8071 AT_C5p = cvar.AT_C5p
8072 AT_H5p = cvar.AT_H5p
8073 AT_H5pp = cvar.AT_H5pp
8074 AT_C4p = cvar.AT_C4p
8075 AT_H4p = cvar.AT_H4p
8076 AT_O4p = cvar.AT_O4p
8077 AT_C1p = cvar.AT_C1p
8078 AT_H1p = cvar.AT_H1p
8079 AT_C3p = cvar.AT_C3p
8080 AT_H3p = cvar.AT_H3p
8081 AT_O3p = cvar.AT_O3p
8082 AT_C2p = cvar.AT_C2p
8083 AT_H2p = cvar.AT_H2p
8084 AT_H2pp = cvar.AT_H2pp
8085 AT_O2p = cvar.AT_O2p
8086 AT_HO2p = cvar.AT_HO2p
8098 AT_H61 = cvar.AT_H61
8099 AT_H62 = cvar.AT_H62
8103 AT_H21 = cvar.AT_H21
8104 AT_H22 = cvar.AT_H22
8109 AT_H41 = cvar.AT_H41
8110 AT_H42 = cvar.AT_H42
8113 AT_H71 = cvar.AT_H71
8114 AT_H72 = cvar.AT_H72
8115 AT_H73 = cvar.AT_H73
8116 AT_O1A = cvar.AT_O1A
8117 AT_O2A = cvar.AT_O2A
8118 AT_O3A = cvar.AT_O3A
8119 AT_O1B = cvar.AT_O1B
8120 AT_O2B = cvar.AT_O2B
8121 AT_O3B = cvar.AT_O3B
8122 AT_CAY = cvar.AT_CAY
8125 AT_CAT = cvar.AT_CAT
8130 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8131 get_residue(Atom d, bool nothrow=False) -> Residue
8133 return _IMP_atom.get_residue(*args)
8136 r"""get_atom(Residue rd, AtomType at) -> Atom"""
8137 return _IMP_atom.get_atom(rd, at)
8140 r"""add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8141 return _IMP_atom.add_atom_type(name, e)
8143 def get_element_for_atom_type(at):
8144 r"""get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8145 return _IMP_atom.get_element_for_atom_type(at)
8148 r"""get_atom_type_exists(std::string name) -> bool"""
8149 return _IMP_atom.get_atom_type_exists(name)
8150 class Residue(Hierarchy):
8151 r"""Proxy of C++ IMP::atom::Residue class."""
8153 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8155 def __init__(self, *args):
8157 __init__(Residue self) -> Residue
8158 __init__(Residue self, Model m, ParticleIndex id) -> Residue
8159 __init__(Residue self, _ParticleAdaptor d) -> Residue
8161 _IMP_atom.Residue_swiginit(self, _IMP_atom.new_Residue(*args))
8163 def show(self, *args):
8164 r"""show(Residue self, _ostream out=std::cout)"""
8165 return _IMP_atom.Residue_show(self, *args)
8168 def setup_particle(*args):
8170 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8171 setup_particle(_ParticleAdaptor pa, ResidueType t, int index, int insertion_code) -> Residue
8172 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8173 setup_particle(_ParticleAdaptor pa, ResidueType t, int index) -> Residue
8174 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8175 setup_particle(_ParticleAdaptor pa, ResidueType t) -> Residue
8176 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8177 setup_particle(_ParticleAdaptor pa, Residue other) -> Residue
8179 return _IMP_atom.Residue_setup_particle(*args)
8182 def get_is_setup(*args):
8184 get_is_setup(_ParticleAdaptor p) -> bool
8185 get_is_setup(Model m, ParticleIndex pi) -> bool
8187 return _IMP_atom.Residue_get_is_setup(*args)
8189 def get_residue_type(self):
8190 r"""get_residue_type(Residue self) -> ResidueType"""
8191 return _IMP_atom.Residue_get_residue_type(self)
8193 def set_residue_type(self, t):
8194 r"""set_residue_type(Residue self, ResidueType t)"""
8195 return _IMP_atom.Residue_set_residue_type(self, t)
8197 def get_is_protein(self):
8198 r"""get_is_protein(Residue self) -> bool"""
8199 return _IMP_atom.Residue_get_is_protein(self)
8201 def get_is_dna(self):
8202 r"""get_is_dna(Residue self) -> bool"""
8203 return _IMP_atom.Residue_get_is_dna(self)
8205 def get_is_rna(self):
8206 r"""get_is_rna(Residue self) -> bool"""
8207 return _IMP_atom.Residue_get_is_rna(self)
8210 r"""get_index(Residue self) -> IMP::Int"""
8211 return _IMP_atom.Residue_get_index(self)
8213 def set_index(self, t):
8214 r"""set_index(Residue self, IMP::Int t)"""
8215 return _IMP_atom.Residue_set_index(self, t)
8217 def get_insertion_code(self):
8218 r"""get_insertion_code(Residue self) -> char"""
8219 return _IMP_atom.Residue_get_insertion_code(self)
8221 def set_insertion_code(self, insertion_code):
8222 r"""set_insertion_code(Residue self, char insertion_code)"""
8223 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8226 def get_index_key():
8227 r"""get_index_key() -> IntKey"""
8228 return _IMP_atom.Residue_get_index_key()
8231 def get_residue_type_key():
8232 r"""get_residue_type_key() -> IntKey"""
8233 return _IMP_atom.Residue_get_residue_type_key()
8236 def get_insertion_code_key():
8237 r"""get_insertion_code_key() -> IntKey"""
8238 return _IMP_atom.Residue_get_insertion_code_key()
8241 def get_type_changed_key():
8242 r"""get_type_changed_key() -> TriggerKey"""
8243 return _IMP_atom.Residue_get_type_changed_key()
8245 def add_attribute(self, *args):
8247 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8248 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8249 add_attribute(Residue self, IntKey a0, IMP::Int a1)
8250 add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
8251 add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
8252 add_attribute(Residue self, StringKey a0, IMP::String a1)
8253 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8254 add_attribute(Residue self, ObjectKey a0, Object a1)
8255 add_attribute(Residue self, SparseFloatKey a0, IMP::Float a1)
8256 add_attribute(Residue self, SparseIntKey a0, IMP::Int a1)
8257 add_attribute(Residue self, SparseStringKey a0, IMP::String a1)
8258 add_attribute(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8260 return _IMP_atom.Residue_add_attribute(self, *args)
8262 def get_value(self, *args):
8264 get_value(Residue self, FloatKey a0) -> IMP::Float
8265 get_value(Residue self, IntKey a0) -> IMP::Int
8266 get_value(Residue self, FloatsKey a0) -> IMP::Floats
8267 get_value(Residue self, IntsKey a0) -> IMP::Ints
8268 get_value(Residue self, StringKey a0) -> IMP::String
8269 get_value(Residue self, ParticleIndexKey a0) -> Particle
8270 get_value(Residue self, ObjectKey a0) -> Object
8271 get_value(Residue self, SparseFloatKey a0) -> IMP::Float
8272 get_value(Residue self, SparseIntKey a0) -> IMP::Int
8273 get_value(Residue self, SparseStringKey a0) -> IMP::String
8274 get_value(Residue self, SparseParticleIndexKey a0) -> ParticleIndex
8276 return _IMP_atom.Residue_get_value(self, *args)
8278 def set_value(self, *args):
8280 set_value(Residue self, FloatKey a0, IMP::Float a1)
8281 set_value(Residue self, IntKey a0, IMP::Int a1)
8282 set_value(Residue self, FloatsKey a0, IMP::Floats a1)
8283 set_value(Residue self, IntsKey a0, IMP::Ints a1)
8284 set_value(Residue self, StringKey a0, IMP::String a1)
8285 set_value(Residue self, ParticleIndexKey a0, Particle a1)
8286 set_value(Residue self, ObjectKey a0, Object a1)
8287 set_value(Residue self, SparseFloatKey a0, IMP::Float a1)
8288 set_value(Residue self, SparseIntKey a0, IMP::Int a1)
8289 set_value(Residue self, SparseStringKey a0, IMP::String a1)
8290 set_value(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8292 return _IMP_atom.Residue_set_value(self, *args)
8294 def remove_attribute(self, *args):
8296 remove_attribute(Residue self, FloatKey a0)
8297 remove_attribute(Residue self, IntKey a0)
8298 remove_attribute(Residue self, FloatsKey a0)
8299 remove_attribute(Residue self, IntsKey a0)
8300 remove_attribute(Residue self, StringKey a0)
8301 remove_attribute(Residue self, ParticleIndexKey a0)
8302 remove_attribute(Residue self, ObjectKey a0)
8303 remove_attribute(Residue self, SparseFloatKey a0)
8304 remove_attribute(Residue self, SparseIntKey a0)
8305 remove_attribute(Residue self, SparseStringKey a0)
8306 remove_attribute(Residue self, SparseParticleIndexKey a0)
8308 return _IMP_atom.Residue_remove_attribute(self, *args)
8310 def has_attribute(self, *args):
8312 has_attribute(Residue self, FloatKey a0) -> bool
8313 has_attribute(Residue self, IntKey a0) -> bool
8314 has_attribute(Residue self, FloatsKey a0) -> bool
8315 has_attribute(Residue self, IntsKey a0) -> bool
8316 has_attribute(Residue self, StringKey a0) -> bool
8317 has_attribute(Residue self, ParticleIndexKey a0) -> bool
8318 has_attribute(Residue self, ObjectKey a0) -> bool
8319 has_attribute(Residue self, SparseFloatKey a0) -> bool
8320 has_attribute(Residue self, SparseIntKey a0) -> bool
8321 has_attribute(Residue self, SparseStringKey a0) -> bool
8322 has_attribute(Residue self, SparseParticleIndexKey a0) -> bool
8324 return _IMP_atom.Residue_has_attribute(self, *args)
8326 def get_derivative(self, a0):
8327 r"""get_derivative(Residue self, FloatKey a0) -> double"""
8328 return _IMP_atom.Residue_get_derivative(self, a0)
8331 r"""get_name(Residue self) -> std::string"""
8332 return _IMP_atom.Residue_get_name(self)
8334 def clear_caches(self):
8335 r"""clear_caches(Residue self)"""
8336 return _IMP_atom.Residue_clear_caches(self)
8338 def set_name(self, a0):
8339 r"""set_name(Residue self, std::string a0)"""
8340 return _IMP_atom.Residue_set_name(self, a0)
8343 r"""set_check_level(Residue self, IMP::CheckLevel a0)"""
8344 return _IMP_atom.Residue_set_check_level(self, a0)
8346 def add_to_derivative(self, a0, a1, a2):
8347 r"""add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8348 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8350 def set_is_optimized(self, a0, a1):
8351 r"""set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8352 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8354 def get_is_optimized(self, a0):
8355 r"""get_is_optimized(Residue self, FloatKey a0) -> bool"""
8356 return _IMP_atom.Residue_get_is_optimized(self, a0)
8359 r"""get_check_level(Residue self) -> IMP::CheckLevel"""
8360 return _IMP_atom.Residue_get_check_level(self)
8362 def __eq__(self, *args):
8364 __eq__(Residue self, Residue o) -> bool
8365 __eq__(Residue self, Particle d) -> bool
8367 return _IMP_atom.Residue___eq__(self, *args)
8369 def __ne__(self, *args):
8371 __ne__(Residue self, Residue o) -> bool
8372 __ne__(Residue self, Particle d) -> bool
8374 return _IMP_atom.Residue___ne__(self, *args)
8376 def __le__(self, *args):
8378 __le__(Residue self, Residue o) -> bool
8379 __le__(Residue self, Particle d) -> bool
8381 return _IMP_atom.Residue___le__(self, *args)
8383 def __lt__(self, *args):
8385 __lt__(Residue self, Residue o) -> bool
8386 __lt__(Residue self, Particle d) -> bool
8388 return _IMP_atom.Residue___lt__(self, *args)
8390 def __ge__(self, *args):
8392 __ge__(Residue self, Residue o) -> bool
8393 __ge__(Residue self, Particle d) -> bool
8395 return _IMP_atom.Residue___ge__(self, *args)
8397 def __gt__(self, *args):
8399 __gt__(Residue self, Residue o) -> bool
8400 __gt__(Residue self, Particle d) -> bool
8402 return _IMP_atom.Residue___gt__(self, *args)
8405 r"""__hash__(Residue self) -> std::size_t"""
8406 return _IMP_atom.Residue___hash__(self)
8409 r"""__str__(Residue self) -> std::string"""
8410 return _IMP_atom.Residue___str__(self)
8413 r"""__repr__(Residue self) -> std::string"""
8414 return _IMP_atom.Residue___repr__(self)
8416 def _get_as_binary(self):
8417 r"""_get_as_binary(Residue self) -> PyObject *"""
8418 return _IMP_atom.Residue__get_as_binary(self)
8420 def _set_from_binary(self, p):
8421 r"""_set_from_binary(Residue self, PyObject * p)"""
8422 return _IMP_atom.Residue__set_from_binary(self, p)
8424 def __getstate__(self):
8425 p = self._get_as_binary()
8426 if len(self.__dict__) > 1:
8427 d = self.__dict__.copy()
8432 def __setstate__(self, p):
8433 if not hasattr(self,
'this'):
8435 if isinstance(p, tuple):
8437 self.__dict__.update(d)
8438 return self._set_from_binary(p)
8440 __swig_destroy__ = _IMP_atom.delete_Residue
8443 _IMP_atom.Residue_swigregister(Residue)
8484 r"""get_next_residue(Residue rd) -> Hierarchy"""
8485 return _IMP_atom.get_next_residue(rd)
8488 r"""get_previous_residue(Residue rd) -> Hierarchy"""
8489 return _IMP_atom.get_previous_residue(rd)
8492 r"""get_one_letter_code(ResidueType c) -> char"""
8493 return _IMP_atom.get_one_letter_code(c)
8494 BALLS = _IMP_atom.BALLS
8496 DENSITIES = _IMP_atom.DENSITIES
8498 class Representation(Hierarchy):
8499 r"""Proxy of C++ IMP::atom::Representation class."""
8501 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8504 def setup_particle(*args):
8506 setup_particle(Model m, ParticleIndex pi) -> Representation
8507 setup_particle(_ParticleAdaptor pa) -> Representation
8508 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
8509 setup_particle(_ParticleAdaptor pa, double resolution) -> Representation
8510 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
8511 setup_particle(_ParticleAdaptor pa, Representation other) -> Representation
8513 return _IMP_atom.Representation_setup_particle(*args)
8515 def __init__(self, *args):
8517 __init__(Representation self) -> Representation
8518 __init__(Representation self, Model m, ParticleIndex id) -> Representation
8519 __init__(Representation self, _ParticleAdaptor d) -> Representation
8521 _IMP_atom.Representation_swiginit(self, _IMP_atom.new_Representation(*args))
8523 def show(self, *args):
8524 r"""show(Representation self, _ostream out=std::cout)"""
8525 return _IMP_atom.Representation_show(self, *args)
8528 def get_is_setup(*args):
8530 get_is_setup(_ParticleAdaptor p) -> bool
8531 get_is_setup(Model m, ParticleIndex pi) -> bool
8533 return _IMP_atom.Representation_get_is_setup(*args)
8536 r"""get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy"""
8537 return _IMP_atom.Representation_get_representation(self, *args)
8539 def get_representations(self, *args):
8540 r"""get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies"""
8541 return _IMP_atom.Representation_get_representations(self, *args)
8543 def add_representation(self, *args):
8544 r"""add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)"""
8545 return _IMP_atom.Representation_add_representation(self, *args)
8547 def get_resolutions(self, *args):
8548 r"""get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats"""
8549 return _IMP_atom.Representation_get_resolutions(self, *args)
8551 def remove_representation(self, rep):
8552 r"""remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
8553 return _IMP_atom.Representation_remove_representation(self, rep)
8555 def update_parents(self):
8556 r"""update_parents(Representation self)"""
8557 return _IMP_atom.Representation_update_parents(self)
8559 def add_attribute(self, *args):
8561 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
8562 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
8563 add_attribute(Representation self, IntKey a0, IMP::Int a1)
8564 add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
8565 add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
8566 add_attribute(Representation self, StringKey a0, IMP::String a1)
8567 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
8568 add_attribute(Representation self, ObjectKey a0, Object a1)
8569 add_attribute(Representation self, SparseFloatKey a0, IMP::Float a1)
8570 add_attribute(Representation self, SparseIntKey a0, IMP::Int a1)
8571 add_attribute(Representation self, SparseStringKey a0, IMP::String a1)
8572 add_attribute(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
8574 return _IMP_atom.Representation_add_attribute(self, *args)
8576 def get_value(self, *args):
8578 get_value(Representation self, FloatKey a0) -> IMP::Float
8579 get_value(Representation self, IntKey a0) -> IMP::Int
8580 get_value(Representation self, FloatsKey a0) -> IMP::Floats
8581 get_value(Representation self, IntsKey a0) -> IMP::Ints
8582 get_value(Representation self, StringKey a0) -> IMP::String
8583 get_value(Representation self, ParticleIndexKey a0) -> Particle
8584 get_value(Representation self, ObjectKey a0) -> Object
8585 get_value(Representation self, SparseFloatKey a0) -> IMP::Float
8586 get_value(Representation self, SparseIntKey a0) -> IMP::Int
8587 get_value(Representation self, SparseStringKey a0) -> IMP::String
8588 get_value(Representation self, SparseParticleIndexKey a0) -> ParticleIndex
8590 return _IMP_atom.Representation_get_value(self, *args)
8592 def set_value(self, *args):
8594 set_value(Representation self, FloatKey a0, IMP::Float a1)
8595 set_value(Representation self, IntKey a0, IMP::Int a1)
8596 set_value(Representation self, FloatsKey a0, IMP::Floats a1)
8597 set_value(Representation self, IntsKey a0, IMP::Ints a1)
8598 set_value(Representation self, StringKey a0, IMP::String a1)
8599 set_value(Representation self, ParticleIndexKey a0, Particle a1)
8600 set_value(Representation self, ObjectKey a0, Object a1)
8601 set_value(Representation self, SparseFloatKey a0, IMP::Float a1)
8602 set_value(Representation self, SparseIntKey a0, IMP::Int a1)
8603 set_value(Representation self, SparseStringKey a0, IMP::String a1)
8604 set_value(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
8606 return _IMP_atom.Representation_set_value(self, *args)
8608 def remove_attribute(self, *args):
8610 remove_attribute(Representation self, FloatKey a0)
8611 remove_attribute(Representation self, IntKey a0)
8612 remove_attribute(Representation self, FloatsKey a0)
8613 remove_attribute(Representation self, IntsKey a0)
8614 remove_attribute(Representation self, StringKey a0)
8615 remove_attribute(Representation self, ParticleIndexKey a0)
8616 remove_attribute(Representation self, ObjectKey a0)
8617 remove_attribute(Representation self, SparseFloatKey a0)
8618 remove_attribute(Representation self, SparseIntKey a0)
8619 remove_attribute(Representation self, SparseStringKey a0)
8620 remove_attribute(Representation self, SparseParticleIndexKey a0)
8622 return _IMP_atom.Representation_remove_attribute(self, *args)
8624 def has_attribute(self, *args):
8626 has_attribute(Representation self, FloatKey a0) -> bool
8627 has_attribute(Representation self, IntKey a0) -> bool
8628 has_attribute(Representation self, FloatsKey a0) -> bool
8629 has_attribute(Representation self, IntsKey a0) -> bool
8630 has_attribute(Representation self, StringKey a0) -> bool
8631 has_attribute(Representation self, ParticleIndexKey a0) -> bool
8632 has_attribute(Representation self, ObjectKey a0) -> bool
8633 has_attribute(Representation self, SparseFloatKey a0) -> bool
8634 has_attribute(Representation self, SparseIntKey a0) -> bool
8635 has_attribute(Representation self, SparseStringKey a0) -> bool
8636 has_attribute(Representation self, SparseParticleIndexKey a0) -> bool
8638 return _IMP_atom.Representation_has_attribute(self, *args)
8640 def get_derivative(self, a0):
8641 r"""get_derivative(Representation self, FloatKey a0) -> double"""
8642 return _IMP_atom.Representation_get_derivative(self, a0)
8645 r"""get_name(Representation self) -> std::string"""
8646 return _IMP_atom.Representation_get_name(self)
8648 def clear_caches(self):
8649 r"""clear_caches(Representation self)"""
8650 return _IMP_atom.Representation_clear_caches(self)
8652 def set_name(self, a0):
8653 r"""set_name(Representation self, std::string a0)"""
8654 return _IMP_atom.Representation_set_name(self, a0)
8657 r"""set_check_level(Representation self, IMP::CheckLevel a0)"""
8658 return _IMP_atom.Representation_set_check_level(self, a0)
8660 def add_to_derivative(self, a0, a1, a2):
8661 r"""add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8662 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
8664 def set_is_optimized(self, a0, a1):
8665 r"""set_is_optimized(Representation self, FloatKey a0, bool a1)"""
8666 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
8668 def get_is_optimized(self, a0):
8669 r"""get_is_optimized(Representation self, FloatKey a0) -> bool"""
8670 return _IMP_atom.Representation_get_is_optimized(self, a0)
8673 r"""get_check_level(Representation self) -> IMP::CheckLevel"""
8674 return _IMP_atom.Representation_get_check_level(self)
8676 def __eq__(self, *args):
8678 __eq__(Representation self, Representation o) -> bool
8679 __eq__(Representation self, Particle d) -> bool
8681 return _IMP_atom.Representation___eq__(self, *args)
8683 def __ne__(self, *args):
8685 __ne__(Representation self, Representation o) -> bool
8686 __ne__(Representation self, Particle d) -> bool
8688 return _IMP_atom.Representation___ne__(self, *args)
8690 def __le__(self, *args):
8692 __le__(Representation self, Representation o) -> bool
8693 __le__(Representation self, Particle d) -> bool
8695 return _IMP_atom.Representation___le__(self, *args)
8697 def __lt__(self, *args):
8699 __lt__(Representation self, Representation o) -> bool
8700 __lt__(Representation self, Particle d) -> bool
8702 return _IMP_atom.Representation___lt__(self, *args)
8704 def __ge__(self, *args):
8706 __ge__(Representation self, Representation o) -> bool
8707 __ge__(Representation self, Particle d) -> bool
8709 return _IMP_atom.Representation___ge__(self, *args)
8711 def __gt__(self, *args):
8713 __gt__(Representation self, Representation o) -> bool
8714 __gt__(Representation self, Particle d) -> bool
8716 return _IMP_atom.Representation___gt__(self, *args)
8719 r"""__hash__(Representation self) -> std::size_t"""
8720 return _IMP_atom.Representation___hash__(self)
8723 r"""__str__(Representation self) -> std::string"""
8724 return _IMP_atom.Representation___str__(self)
8727 r"""__repr__(Representation self) -> std::string"""
8728 return _IMP_atom.Representation___repr__(self)
8730 def _get_as_binary(self):
8731 r"""_get_as_binary(Representation self) -> PyObject *"""
8732 return _IMP_atom.Representation__get_as_binary(self)
8734 def _set_from_binary(self, p):
8735 r"""_set_from_binary(Representation self, PyObject * p)"""
8736 return _IMP_atom.Representation__set_from_binary(self, p)
8738 def __getstate__(self):
8739 p = self._get_as_binary()
8740 if len(self.__dict__) > 1:
8741 d = self.__dict__.copy()
8746 def __setstate__(self, p):
8747 if not hasattr(self,
'this'):
8749 if isinstance(p, tuple):
8751 self.__dict__.update(d)
8752 return self._set_from_binary(p)
8754 __swig_destroy__ = _IMP_atom.delete_Representation
8757 _IMP_atom.Representation_swigregister(Representation)
8758 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
8763 get_resolution(Model m, ParticleIndex pi) -> double
8764 get_resolution(Hierarchy h) -> double
8766 return _IMP_atom.get_resolution(*args)
8769 r"""get_representation(Hierarchy h, bool nothrow=False) -> Representation"""
8770 return _IMP_atom.get_representation(h, nothrow)
8773 r"""show_with_representations(Hierarchy h, _ostream out=std::cout)"""
8774 return _IMP_atom.show_with_representations(*args)
8775 class State(Hierarchy):
8776 r"""Proxy of C++ IMP::atom::State class."""
8778 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8781 def setup_particle(*args):
8783 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
8784 setup_particle(_ParticleAdaptor pa, unsigned int index) -> State
8785 setup_particle(Model m, ParticleIndex pi, State other) -> State
8786 setup_particle(_ParticleAdaptor pa, State other) -> State
8788 return _IMP_atom.State_setup_particle(*args)
8790 def __init__(self, *args):
8792 __init__(State self) -> State
8793 __init__(State self, Model m, ParticleIndex id) -> State
8794 __init__(State self, _ParticleAdaptor d) -> State
8796 _IMP_atom.State_swiginit(self, _IMP_atom.new_State(*args))
8798 def show(self, *args):
8799 r"""show(State self, _ostream out=std::cout)"""
8800 return _IMP_atom.State_show(self, *args)
8803 def get_is_setup(*args):
8805 get_is_setup(_ParticleAdaptor p) -> bool
8806 get_is_setup(Model m, ParticleIndex pi) -> bool
8808 return _IMP_atom.State_get_is_setup(*args)
8811 r"""get_state_index(State self) -> unsigned int"""
8812 return _IMP_atom.State_get_state_index(self)
8814 def add_attribute(self, *args):
8816 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
8817 add_attribute(State self, FloatKey a0, IMP::Float a1)
8818 add_attribute(State self, IntKey a0, IMP::Int a1)
8819 add_attribute(State self, FloatsKey a0, IMP::Floats a1)
8820 add_attribute(State self, IntsKey a0, IMP::Ints a1)
8821 add_attribute(State self, StringKey a0, IMP::String a1)
8822 add_attribute(State self, ParticleIndexKey a0, Particle a1)
8823 add_attribute(State self, ObjectKey a0, Object a1)
8824 add_attribute(State self, SparseFloatKey a0, IMP::Float a1)
8825 add_attribute(State self, SparseIntKey a0, IMP::Int a1)
8826 add_attribute(State self, SparseStringKey a0, IMP::String a1)
8827 add_attribute(State self, SparseParticleIndexKey a0, ParticleIndex a1)
8829 return _IMP_atom.State_add_attribute(self, *args)
8831 def get_value(self, *args):
8833 get_value(State self, FloatKey a0) -> IMP::Float
8834 get_value(State self, IntKey a0) -> IMP::Int
8835 get_value(State self, FloatsKey a0) -> IMP::Floats
8836 get_value(State self, IntsKey a0) -> IMP::Ints
8837 get_value(State self, StringKey a0) -> IMP::String
8838 get_value(State self, ParticleIndexKey a0) -> Particle
8839 get_value(State self, ObjectKey a0) -> Object
8840 get_value(State self, SparseFloatKey a0) -> IMP::Float
8841 get_value(State self, SparseIntKey a0) -> IMP::Int
8842 get_value(State self, SparseStringKey a0) -> IMP::String
8843 get_value(State self, SparseParticleIndexKey a0) -> ParticleIndex
8845 return _IMP_atom.State_get_value(self, *args)
8847 def set_value(self, *args):
8849 set_value(State self, FloatKey a0, IMP::Float a1)
8850 set_value(State self, IntKey a0, IMP::Int a1)
8851 set_value(State self, FloatsKey a0, IMP::Floats a1)
8852 set_value(State self, IntsKey a0, IMP::Ints a1)
8853 set_value(State self, StringKey a0, IMP::String a1)
8854 set_value(State self, ParticleIndexKey a0, Particle a1)
8855 set_value(State self, ObjectKey a0, Object a1)
8856 set_value(State self, SparseFloatKey a0, IMP::Float a1)
8857 set_value(State self, SparseIntKey a0, IMP::Int a1)
8858 set_value(State self, SparseStringKey a0, IMP::String a1)
8859 set_value(State self, SparseParticleIndexKey a0, ParticleIndex a1)
8861 return _IMP_atom.State_set_value(self, *args)
8863 def remove_attribute(self, *args):
8865 remove_attribute(State self, FloatKey a0)
8866 remove_attribute(State self, IntKey a0)
8867 remove_attribute(State self, FloatsKey a0)
8868 remove_attribute(State self, IntsKey a0)
8869 remove_attribute(State self, StringKey a0)
8870 remove_attribute(State self, ParticleIndexKey a0)
8871 remove_attribute(State self, ObjectKey a0)
8872 remove_attribute(State self, SparseFloatKey a0)
8873 remove_attribute(State self, SparseIntKey a0)
8874 remove_attribute(State self, SparseStringKey a0)
8875 remove_attribute(State self, SparseParticleIndexKey a0)
8877 return _IMP_atom.State_remove_attribute(self, *args)
8879 def has_attribute(self, *args):
8881 has_attribute(State self, FloatKey a0) -> bool
8882 has_attribute(State self, IntKey a0) -> bool
8883 has_attribute(State self, FloatsKey a0) -> bool
8884 has_attribute(State self, IntsKey a0) -> bool
8885 has_attribute(State self, StringKey a0) -> bool
8886 has_attribute(State self, ParticleIndexKey a0) -> bool
8887 has_attribute(State self, ObjectKey a0) -> bool
8888 has_attribute(State self, SparseFloatKey a0) -> bool
8889 has_attribute(State self, SparseIntKey a0) -> bool
8890 has_attribute(State self, SparseStringKey a0) -> bool
8891 has_attribute(State self, SparseParticleIndexKey a0) -> bool
8893 return _IMP_atom.State_has_attribute(self, *args)
8895 def get_derivative(self, a0):
8896 r"""get_derivative(State self, FloatKey a0) -> double"""
8897 return _IMP_atom.State_get_derivative(self, a0)
8900 r"""get_name(State self) -> std::string"""
8901 return _IMP_atom.State_get_name(self)
8903 def clear_caches(self):
8904 r"""clear_caches(State self)"""
8905 return _IMP_atom.State_clear_caches(self)
8907 def set_name(self, a0):
8908 r"""set_name(State self, std::string a0)"""
8909 return _IMP_atom.State_set_name(self, a0)
8912 r"""set_check_level(State self, IMP::CheckLevel a0)"""
8913 return _IMP_atom.State_set_check_level(self, a0)
8915 def add_to_derivative(self, a0, a1, a2):
8916 r"""add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8917 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
8919 def set_is_optimized(self, a0, a1):
8920 r"""set_is_optimized(State self, FloatKey a0, bool a1)"""
8921 return _IMP_atom.State_set_is_optimized(self, a0, a1)
8923 def get_is_optimized(self, a0):
8924 r"""get_is_optimized(State self, FloatKey a0) -> bool"""
8925 return _IMP_atom.State_get_is_optimized(self, a0)
8928 r"""get_check_level(State self) -> IMP::CheckLevel"""
8929 return _IMP_atom.State_get_check_level(self)
8931 def __eq__(self, *args):
8933 __eq__(State self, State o) -> bool
8934 __eq__(State self, Particle d) -> bool
8936 return _IMP_atom.State___eq__(self, *args)
8938 def __ne__(self, *args):
8940 __ne__(State self, State o) -> bool
8941 __ne__(State self, Particle d) -> bool
8943 return _IMP_atom.State___ne__(self, *args)
8945 def __le__(self, *args):
8947 __le__(State self, State o) -> bool
8948 __le__(State self, Particle d) -> bool
8950 return _IMP_atom.State___le__(self, *args)
8952 def __lt__(self, *args):
8954 __lt__(State self, State o) -> bool
8955 __lt__(State self, Particle d) -> bool
8957 return _IMP_atom.State___lt__(self, *args)
8959 def __ge__(self, *args):
8961 __ge__(State self, State o) -> bool
8962 __ge__(State self, Particle d) -> bool
8964 return _IMP_atom.State___ge__(self, *args)
8966 def __gt__(self, *args):
8968 __gt__(State self, State o) -> bool
8969 __gt__(State self, Particle d) -> bool
8971 return _IMP_atom.State___gt__(self, *args)
8974 r"""__hash__(State self) -> std::size_t"""
8975 return _IMP_atom.State___hash__(self)
8978 r"""__str__(State self) -> std::string"""
8979 return _IMP_atom.State___str__(self)
8982 r"""__repr__(State self) -> std::string"""
8983 return _IMP_atom.State___repr__(self)
8985 def _get_as_binary(self):
8986 r"""_get_as_binary(State self) -> PyObject *"""
8987 return _IMP_atom.State__get_as_binary(self)
8989 def _set_from_binary(self, p):
8990 r"""_set_from_binary(State self, PyObject * p)"""
8991 return _IMP_atom.State__set_from_binary(self, p)
8993 def __getstate__(self):
8994 p = self._get_as_binary()
8995 if len(self.__dict__) > 1:
8996 d = self.__dict__.copy()
9001 def __setstate__(self, p):
9002 if not hasattr(self,
'this'):
9004 if isinstance(p, tuple):
9006 self.__dict__.update(d)
9007 return self._set_from_binary(p)
9009 __swig_destroy__ = _IMP_atom.delete_State
9012 _IMP_atom.State_swigregister(State)
9015 r"""get_state_index(Hierarchy h) -> int"""
9016 return _IMP_atom.get_state_index(h)
9019 r"""get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9020 return _IMP_atom.get_phi_dihedral_atoms(rd)
9023 r"""get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9024 return _IMP_atom.get_psi_dihedral_atoms(rd)
9027 r"""get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9028 return _IMP_atom.get_omega_dihedral_atoms(rd)
9031 r"""get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
9032 return _IMP_atom.get_chi_dihedral_atom_types(rt)
9035 r"""get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
9036 return _IMP_atom.get_chi_dihedral_atoms(rd)
9039 r"""get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
9040 return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
9041 class Molecule(Hierarchy):
9042 r"""Proxy of C++ IMP::atom::Molecule class."""
9044 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9046 def __init__(self, *args):
9048 __init__(Molecule self) -> Molecule
9049 __init__(Molecule self, Model m, ParticleIndex id) -> Molecule
9050 __init__(Molecule self, _ParticleAdaptor d) -> Molecule
9052 _IMP_atom.Molecule_swiginit(self, _IMP_atom.new_Molecule(*args))
9054 def show(self, *args):
9055 r"""show(Molecule self, _ostream out=std::cout)"""
9056 return _IMP_atom.Molecule_show(self, *args)
9059 def setup_particle(*args):
9061 setup_particle(Model m, ParticleIndex pi) -> Molecule
9062 setup_particle(_ParticleAdaptor pa) -> Molecule
9063 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9064 setup_particle(_ParticleAdaptor pa, Molecule other) -> Molecule
9066 return _IMP_atom.Molecule_setup_particle(*args)
9069 def get_is_setup(*args):
9071 get_is_setup(_ParticleAdaptor p) -> bool
9072 get_is_setup(Model m, ParticleIndex pi) -> bool
9074 return _IMP_atom.Molecule_get_is_setup(*args)
9076 def add_attribute(self, *args):
9078 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9079 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9080 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9081 add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
9082 add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
9083 add_attribute(Molecule self, StringKey a0, IMP::String a1)
9084 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9085 add_attribute(Molecule self, ObjectKey a0, Object a1)
9086 add_attribute(Molecule self, SparseFloatKey a0, IMP::Float a1)
9087 add_attribute(Molecule self, SparseIntKey a0, IMP::Int a1)
9088 add_attribute(Molecule self, SparseStringKey a0, IMP::String a1)
9089 add_attribute(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9091 return _IMP_atom.Molecule_add_attribute(self, *args)
9093 def get_value(self, *args):
9095 get_value(Molecule self, FloatKey a0) -> IMP::Float
9096 get_value(Molecule self, IntKey a0) -> IMP::Int
9097 get_value(Molecule self, FloatsKey a0) -> IMP::Floats
9098 get_value(Molecule self, IntsKey a0) -> IMP::Ints
9099 get_value(Molecule self, StringKey a0) -> IMP::String
9100 get_value(Molecule self, ParticleIndexKey a0) -> Particle
9101 get_value(Molecule self, ObjectKey a0) -> Object
9102 get_value(Molecule self, SparseFloatKey a0) -> IMP::Float
9103 get_value(Molecule self, SparseIntKey a0) -> IMP::Int
9104 get_value(Molecule self, SparseStringKey a0) -> IMP::String
9105 get_value(Molecule self, SparseParticleIndexKey a0) -> ParticleIndex
9107 return _IMP_atom.Molecule_get_value(self, *args)
9109 def set_value(self, *args):
9111 set_value(Molecule self, FloatKey a0, IMP::Float a1)
9112 set_value(Molecule self, IntKey a0, IMP::Int a1)
9113 set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
9114 set_value(Molecule self, IntsKey a0, IMP::Ints a1)
9115 set_value(Molecule self, StringKey a0, IMP::String a1)
9116 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9117 set_value(Molecule self, ObjectKey a0, Object a1)
9118 set_value(Molecule self, SparseFloatKey a0, IMP::Float a1)
9119 set_value(Molecule self, SparseIntKey a0, IMP::Int a1)
9120 set_value(Molecule self, SparseStringKey a0, IMP::String a1)
9121 set_value(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9123 return _IMP_atom.Molecule_set_value(self, *args)
9125 def remove_attribute(self, *args):
9127 remove_attribute(Molecule self, FloatKey a0)
9128 remove_attribute(Molecule self, IntKey a0)
9129 remove_attribute(Molecule self, FloatsKey a0)
9130 remove_attribute(Molecule self, IntsKey a0)
9131 remove_attribute(Molecule self, StringKey a0)
9132 remove_attribute(Molecule self, ParticleIndexKey a0)
9133 remove_attribute(Molecule self, ObjectKey a0)
9134 remove_attribute(Molecule self, SparseFloatKey a0)
9135 remove_attribute(Molecule self, SparseIntKey a0)
9136 remove_attribute(Molecule self, SparseStringKey a0)
9137 remove_attribute(Molecule self, SparseParticleIndexKey a0)
9139 return _IMP_atom.Molecule_remove_attribute(self, *args)
9141 def has_attribute(self, *args):
9143 has_attribute(Molecule self, FloatKey a0) -> bool
9144 has_attribute(Molecule self, IntKey a0) -> bool
9145 has_attribute(Molecule self, FloatsKey a0) -> bool
9146 has_attribute(Molecule self, IntsKey a0) -> bool
9147 has_attribute(Molecule self, StringKey a0) -> bool
9148 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9149 has_attribute(Molecule self, ObjectKey a0) -> bool
9150 has_attribute(Molecule self, SparseFloatKey a0) -> bool
9151 has_attribute(Molecule self, SparseIntKey a0) -> bool
9152 has_attribute(Molecule self, SparseStringKey a0) -> bool
9153 has_attribute(Molecule self, SparseParticleIndexKey a0) -> bool
9155 return _IMP_atom.Molecule_has_attribute(self, *args)
9157 def get_derivative(self, a0):
9158 r"""get_derivative(Molecule self, FloatKey a0) -> double"""
9159 return _IMP_atom.Molecule_get_derivative(self, a0)
9162 r"""get_name(Molecule self) -> std::string"""
9163 return _IMP_atom.Molecule_get_name(self)
9165 def clear_caches(self):
9166 r"""clear_caches(Molecule self)"""
9167 return _IMP_atom.Molecule_clear_caches(self)
9169 def set_name(self, a0):
9170 r"""set_name(Molecule self, std::string a0)"""
9171 return _IMP_atom.Molecule_set_name(self, a0)
9174 r"""set_check_level(Molecule self, IMP::CheckLevel a0)"""
9175 return _IMP_atom.Molecule_set_check_level(self, a0)
9177 def add_to_derivative(self, a0, a1, a2):
9178 r"""add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9179 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9181 def set_is_optimized(self, a0, a1):
9182 r"""set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9183 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9185 def get_is_optimized(self, a0):
9186 r"""get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9187 return _IMP_atom.Molecule_get_is_optimized(self, a0)
9190 r"""get_check_level(Molecule self) -> IMP::CheckLevel"""
9191 return _IMP_atom.Molecule_get_check_level(self)
9193 def __eq__(self, *args):
9195 __eq__(Molecule self, Molecule o) -> bool
9196 __eq__(Molecule self, Particle d) -> bool
9198 return _IMP_atom.Molecule___eq__(self, *args)
9200 def __ne__(self, *args):
9202 __ne__(Molecule self, Molecule o) -> bool
9203 __ne__(Molecule self, Particle d) -> bool
9205 return _IMP_atom.Molecule___ne__(self, *args)
9207 def __le__(self, *args):
9209 __le__(Molecule self, Molecule o) -> bool
9210 __le__(Molecule self, Particle d) -> bool
9212 return _IMP_atom.Molecule___le__(self, *args)
9214 def __lt__(self, *args):
9216 __lt__(Molecule self, Molecule o) -> bool
9217 __lt__(Molecule self, Particle d) -> bool
9219 return _IMP_atom.Molecule___lt__(self, *args)
9221 def __ge__(self, *args):
9223 __ge__(Molecule self, Molecule o) -> bool
9224 __ge__(Molecule self, Particle d) -> bool
9226 return _IMP_atom.Molecule___ge__(self, *args)
9228 def __gt__(self, *args):
9230 __gt__(Molecule self, Molecule o) -> bool
9231 __gt__(Molecule self, Particle d) -> bool
9233 return _IMP_atom.Molecule___gt__(self, *args)
9236 r"""__hash__(Molecule self) -> std::size_t"""
9237 return _IMP_atom.Molecule___hash__(self)
9240 r"""__str__(Molecule self) -> std::string"""
9241 return _IMP_atom.Molecule___str__(self)
9244 r"""__repr__(Molecule self) -> std::string"""
9245 return _IMP_atom.Molecule___repr__(self)
9247 def _get_as_binary(self):
9248 r"""_get_as_binary(Molecule self) -> PyObject *"""
9249 return _IMP_atom.Molecule__get_as_binary(self)
9251 def _set_from_binary(self, p):
9252 r"""_set_from_binary(Molecule self, PyObject * p)"""
9253 return _IMP_atom.Molecule__set_from_binary(self, p)
9255 def __getstate__(self):
9256 p = self._get_as_binary()
9257 if len(self.__dict__) > 1:
9258 d = self.__dict__.copy()
9263 def __setstate__(self, p):
9264 if not hasattr(self,
'this'):
9266 if isinstance(p, tuple):
9268 self.__dict__.update(d)
9269 return self._set_from_binary(p)
9271 __swig_destroy__ = _IMP_atom.delete_Molecule
9274 _IMP_atom.Molecule_swigregister(Molecule)
9277 r"""get_molecule_name(Hierarchy h) -> std::string"""
9278 return _IMP_atom.get_molecule_name(h)
9279 class Copy(Molecule):
9280 r"""Proxy of C++ IMP::atom::Copy class."""
9282 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9285 def get_copy_index_key():
9286 r"""get_copy_index_key() -> IntKey"""
9287 return _IMP_atom.Copy_get_copy_index_key()
9289 def __init__(self, *args):
9291 __init__(Copy self) -> Copy
9292 __init__(Copy self, Model m, ParticleIndex id) -> Copy
9293 __init__(Copy self, _ParticleAdaptor d) -> Copy
9295 _IMP_atom.Copy_swiginit(self, _IMP_atom.new_Copy(*args))
9297 def show(self, *args):
9298 r"""show(Copy self, _ostream out=std::cout)"""
9299 return _IMP_atom.Copy_show(self, *args)
9302 def setup_particle(*args):
9304 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9305 setup_particle(_ParticleAdaptor pa, IMP::Int number) -> Copy
9307 return _IMP_atom.Copy_setup_particle(*args)
9310 def get_is_setup(*args):
9312 get_is_setup(_ParticleAdaptor p) -> bool
9313 get_is_setup(Model m, ParticleIndex pi) -> bool
9315 return _IMP_atom.Copy_get_is_setup(*args)
9318 r"""get_copy_index(Copy self) -> int"""
9319 return _IMP_atom.Copy_get_copy_index(self)
9321 def add_attribute(self, *args):
9323 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9324 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9325 add_attribute(Copy self, IntKey a0, IMP::Int a1)
9326 add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
9327 add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
9328 add_attribute(Copy self, StringKey a0, IMP::String a1)
9329 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9330 add_attribute(Copy self, ObjectKey a0, Object a1)
9331 add_attribute(Copy self, SparseFloatKey a0, IMP::Float a1)
9332 add_attribute(Copy self, SparseIntKey a0, IMP::Int a1)
9333 add_attribute(Copy self, SparseStringKey a0, IMP::String a1)
9334 add_attribute(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9336 return _IMP_atom.Copy_add_attribute(self, *args)
9338 def get_value(self, *args):
9340 get_value(Copy self, FloatKey a0) -> IMP::Float
9341 get_value(Copy self, IntKey a0) -> IMP::Int
9342 get_value(Copy self, FloatsKey a0) -> IMP::Floats
9343 get_value(Copy self, IntsKey a0) -> IMP::Ints
9344 get_value(Copy self, StringKey a0) -> IMP::String
9345 get_value(Copy self, ParticleIndexKey a0) -> Particle
9346 get_value(Copy self, ObjectKey a0) -> Object
9347 get_value(Copy self, SparseFloatKey a0) -> IMP::Float
9348 get_value(Copy self, SparseIntKey a0) -> IMP::Int
9349 get_value(Copy self, SparseStringKey a0) -> IMP::String
9350 get_value(Copy self, SparseParticleIndexKey a0) -> ParticleIndex
9352 return _IMP_atom.Copy_get_value(self, *args)
9354 def set_value(self, *args):
9356 set_value(Copy self, FloatKey a0, IMP::Float a1)
9357 set_value(Copy self, IntKey a0, IMP::Int a1)
9358 set_value(Copy self, FloatsKey a0, IMP::Floats a1)
9359 set_value(Copy self, IntsKey a0, IMP::Ints a1)
9360 set_value(Copy self, StringKey a0, IMP::String a1)
9361 set_value(Copy self, ParticleIndexKey a0, Particle a1)
9362 set_value(Copy self, ObjectKey a0, Object a1)
9363 set_value(Copy self, SparseFloatKey a0, IMP::Float a1)
9364 set_value(Copy self, SparseIntKey a0, IMP::Int a1)
9365 set_value(Copy self, SparseStringKey a0, IMP::String a1)
9366 set_value(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9368 return _IMP_atom.Copy_set_value(self, *args)
9370 def remove_attribute(self, *args):
9372 remove_attribute(Copy self, FloatKey a0)
9373 remove_attribute(Copy self, IntKey a0)
9374 remove_attribute(Copy self, FloatsKey a0)
9375 remove_attribute(Copy self, IntsKey a0)
9376 remove_attribute(Copy self, StringKey a0)
9377 remove_attribute(Copy self, ParticleIndexKey a0)
9378 remove_attribute(Copy self, ObjectKey a0)
9379 remove_attribute(Copy self, SparseFloatKey a0)
9380 remove_attribute(Copy self, SparseIntKey a0)
9381 remove_attribute(Copy self, SparseStringKey a0)
9382 remove_attribute(Copy self, SparseParticleIndexKey a0)
9384 return _IMP_atom.Copy_remove_attribute(self, *args)
9386 def has_attribute(self, *args):
9388 has_attribute(Copy self, FloatKey a0) -> bool
9389 has_attribute(Copy self, IntKey a0) -> bool
9390 has_attribute(Copy self, FloatsKey a0) -> bool
9391 has_attribute(Copy self, IntsKey a0) -> bool
9392 has_attribute(Copy self, StringKey a0) -> bool
9393 has_attribute(Copy self, ParticleIndexKey a0) -> bool
9394 has_attribute(Copy self, ObjectKey a0) -> bool
9395 has_attribute(Copy self, SparseFloatKey a0) -> bool
9396 has_attribute(Copy self, SparseIntKey a0) -> bool
9397 has_attribute(Copy self, SparseStringKey a0) -> bool
9398 has_attribute(Copy self, SparseParticleIndexKey a0) -> bool
9400 return _IMP_atom.Copy_has_attribute(self, *args)
9402 def get_derivative(self, a0):
9403 r"""get_derivative(Copy self, FloatKey a0) -> double"""
9404 return _IMP_atom.Copy_get_derivative(self, a0)
9407 r"""get_name(Copy self) -> std::string"""
9408 return _IMP_atom.Copy_get_name(self)
9410 def clear_caches(self):
9411 r"""clear_caches(Copy self)"""
9412 return _IMP_atom.Copy_clear_caches(self)
9414 def set_name(self, a0):
9415 r"""set_name(Copy self, std::string a0)"""
9416 return _IMP_atom.Copy_set_name(self, a0)
9419 r"""set_check_level(Copy self, IMP::CheckLevel a0)"""
9420 return _IMP_atom.Copy_set_check_level(self, a0)
9422 def add_to_derivative(self, a0, a1, a2):
9423 r"""add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9424 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9426 def set_is_optimized(self, a0, a1):
9427 r"""set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9428 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9430 def get_is_optimized(self, a0):
9431 r"""get_is_optimized(Copy self, FloatKey a0) -> bool"""
9432 return _IMP_atom.Copy_get_is_optimized(self, a0)
9435 r"""get_check_level(Copy self) -> IMP::CheckLevel"""
9436 return _IMP_atom.Copy_get_check_level(self)
9438 def __eq__(self, *args):
9440 __eq__(Copy self, Copy o) -> bool
9441 __eq__(Copy self, Particle d) -> bool
9443 return _IMP_atom.Copy___eq__(self, *args)
9445 def __ne__(self, *args):
9447 __ne__(Copy self, Copy o) -> bool
9448 __ne__(Copy self, Particle d) -> bool
9450 return _IMP_atom.Copy___ne__(self, *args)
9452 def __le__(self, *args):
9454 __le__(Copy self, Copy o) -> bool
9455 __le__(Copy self, Particle d) -> bool
9457 return _IMP_atom.Copy___le__(self, *args)
9459 def __lt__(self, *args):
9461 __lt__(Copy self, Copy o) -> bool
9462 __lt__(Copy self, Particle d) -> bool
9464 return _IMP_atom.Copy___lt__(self, *args)
9466 def __ge__(self, *args):
9468 __ge__(Copy self, Copy o) -> bool
9469 __ge__(Copy self, Particle d) -> bool
9471 return _IMP_atom.Copy___ge__(self, *args)
9473 def __gt__(self, *args):
9475 __gt__(Copy self, Copy o) -> bool
9476 __gt__(Copy self, Particle d) -> bool
9478 return _IMP_atom.Copy___gt__(self, *args)
9481 r"""__hash__(Copy self) -> std::size_t"""
9482 return _IMP_atom.Copy___hash__(self)
9485 r"""__str__(Copy self) -> std::string"""
9486 return _IMP_atom.Copy___str__(self)
9489 r"""__repr__(Copy self) -> std::string"""
9490 return _IMP_atom.Copy___repr__(self)
9492 def _get_as_binary(self):
9493 r"""_get_as_binary(Copy self) -> PyObject *"""
9494 return _IMP_atom.Copy__get_as_binary(self)
9496 def _set_from_binary(self, p):
9497 r"""_set_from_binary(Copy self, PyObject * p)"""
9498 return _IMP_atom.Copy__set_from_binary(self, p)
9500 def __getstate__(self):
9501 p = self._get_as_binary()
9502 if len(self.__dict__) > 1:
9503 d = self.__dict__.copy()
9508 def __setstate__(self, p):
9509 if not hasattr(self,
'this'):
9511 if isinstance(p, tuple):
9513 self.__dict__.update(d)
9514 return self._set_from_binary(p)
9516 __swig_destroy__ = _IMP_atom.delete_Copy
9519 _IMP_atom.Copy_swigregister(Copy)
9522 r"""get_copy_index(Hierarchy h) -> int"""
9523 return _IMP_atom.get_copy_index(h)
9524 class Chain(Hierarchy):
9525 r"""Proxy of C++ IMP::atom::Chain class."""
9527 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9529 def __init__(self, *args):
9531 __init__(Chain self) -> Chain
9532 __init__(Chain self, Model m, ParticleIndex id) -> Chain
9533 __init__(Chain self, _ParticleAdaptor d) -> Chain
9535 _IMP_atom.Chain_swiginit(self, _IMP_atom.new_Chain(*args))
9537 def show(self, *args):
9538 r"""show(Chain self, _ostream out=std::cout)"""
9539 return _IMP_atom.Chain_show(self, *args)
9542 def setup_particle(*args):
9544 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
9545 setup_particle(_ParticleAdaptor pa, std::string id) -> Chain
9546 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
9547 setup_particle(_ParticleAdaptor pa, char id) -> Chain
9548 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
9549 setup_particle(_ParticleAdaptor pa, Chain other) -> Chain
9551 return _IMP_atom.Chain_setup_particle(*args)
9554 def get_is_setup(*args):
9556 get_is_setup(_ParticleAdaptor p) -> bool
9557 get_is_setup(Model m, ParticleIndex pi) -> bool
9559 return _IMP_atom.Chain_get_is_setup(*args)
9562 r"""get_id(Chain self) -> std::string"""
9563 return _IMP_atom.Chain_get_id(self)
9565 def set_id(self, c):
9566 r"""set_id(Chain self, std::string c)"""
9567 return _IMP_atom.Chain_set_id(self, c)
9569 def get_sequence(self):
9570 r"""get_sequence(Chain self) -> std::string"""
9571 return _IMP_atom.Chain_get_sequence(self)
9573 def set_sequence(self, sequence):
9574 r"""set_sequence(Chain self, std::string sequence)"""
9575 return _IMP_atom.Chain_set_sequence(self, sequence)
9577 def get_sequence_offset(self):
9578 r"""get_sequence_offset(Chain self) -> int"""
9579 return _IMP_atom.Chain_get_sequence_offset(self)
9581 def set_sequence_offset(self, offset):
9582 r"""set_sequence_offset(Chain self, int offset)"""
9583 return _IMP_atom.Chain_set_sequence_offset(self, offset)
9585 def get_uniprot_accession(self):
9586 r"""get_uniprot_accession(Chain self) -> std::string"""
9587 return _IMP_atom.Chain_get_uniprot_accession(self)
9589 def set_uniprot_accession(self, accession):
9590 r"""set_uniprot_accession(Chain self, std::string accession)"""
9591 return _IMP_atom.Chain_set_uniprot_accession(self, accession)
9593 def get_chain_type(self):
9594 r"""get_chain_type(Chain self) -> ChainType"""
9595 return _IMP_atom.Chain_get_chain_type(self)
9597 def set_chain_type(self, t):
9598 r"""set_chain_type(Chain self, ChainType t)"""
9599 return _IMP_atom.Chain_set_chain_type(self, t)
9603 r"""get_id_key() -> SparseStringKey"""
9604 return _IMP_atom.Chain_get_id_key()
9607 def get_sequence_key():
9608 r"""get_sequence_key() -> SparseStringKey"""
9609 return _IMP_atom.Chain_get_sequence_key()
9612 def get_sequence_offset_key():
9613 r"""get_sequence_offset_key() -> SparseIntKey"""
9614 return _IMP_atom.Chain_get_sequence_offset_key()
9617 def get_uniprot_accession_key():
9618 r"""get_uniprot_accession_key() -> SparseStringKey"""
9619 return _IMP_atom.Chain_get_uniprot_accession_key()
9622 def get_chain_type_key():
9623 r"""get_chain_type_key() -> SparseIntKey"""
9624 return _IMP_atom.Chain_get_chain_type_key()
9626 def add_attribute(self, *args):
9628 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
9629 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
9630 add_attribute(Chain self, IntKey a0, IMP::Int a1)
9631 add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
9632 add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
9633 add_attribute(Chain self, StringKey a0, IMP::String a1)
9634 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
9635 add_attribute(Chain self, ObjectKey a0, Object a1)
9636 add_attribute(Chain self, SparseFloatKey a0, IMP::Float a1)
9637 add_attribute(Chain self, SparseIntKey a0, IMP::Int a1)
9638 add_attribute(Chain self, SparseStringKey a0, IMP::String a1)
9639 add_attribute(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
9641 return _IMP_atom.Chain_add_attribute(self, *args)
9643 def get_value(self, *args):
9645 get_value(Chain self, FloatKey a0) -> IMP::Float
9646 get_value(Chain self, IntKey a0) -> IMP::Int
9647 get_value(Chain self, FloatsKey a0) -> IMP::Floats
9648 get_value(Chain self, IntsKey a0) -> IMP::Ints
9649 get_value(Chain self, StringKey a0) -> IMP::String
9650 get_value(Chain self, ParticleIndexKey a0) -> Particle
9651 get_value(Chain self, ObjectKey a0) -> Object
9652 get_value(Chain self, SparseFloatKey a0) -> IMP::Float
9653 get_value(Chain self, SparseIntKey a0) -> IMP::Int
9654 get_value(Chain self, SparseStringKey a0) -> IMP::String
9655 get_value(Chain self, SparseParticleIndexKey a0) -> ParticleIndex
9657 return _IMP_atom.Chain_get_value(self, *args)
9659 def set_value(self, *args):
9661 set_value(Chain self, FloatKey a0, IMP::Float a1)
9662 set_value(Chain self, IntKey a0, IMP::Int a1)
9663 set_value(Chain self, FloatsKey a0, IMP::Floats a1)
9664 set_value(Chain self, IntsKey a0, IMP::Ints a1)
9665 set_value(Chain self, StringKey a0, IMP::String a1)
9666 set_value(Chain self, ParticleIndexKey a0, Particle a1)
9667 set_value(Chain self, ObjectKey a0, Object a1)
9668 set_value(Chain self, SparseFloatKey a0, IMP::Float a1)
9669 set_value(Chain self, SparseIntKey a0, IMP::Int a1)
9670 set_value(Chain self, SparseStringKey a0, IMP::String a1)
9671 set_value(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
9673 return _IMP_atom.Chain_set_value(self, *args)
9675 def remove_attribute(self, *args):
9677 remove_attribute(Chain self, FloatKey a0)
9678 remove_attribute(Chain self, IntKey a0)
9679 remove_attribute(Chain self, FloatsKey a0)
9680 remove_attribute(Chain self, IntsKey a0)
9681 remove_attribute(Chain self, StringKey a0)
9682 remove_attribute(Chain self, ParticleIndexKey a0)
9683 remove_attribute(Chain self, ObjectKey a0)
9684 remove_attribute(Chain self, SparseFloatKey a0)
9685 remove_attribute(Chain self, SparseIntKey a0)
9686 remove_attribute(Chain self, SparseStringKey a0)
9687 remove_attribute(Chain self, SparseParticleIndexKey a0)
9689 return _IMP_atom.Chain_remove_attribute(self, *args)
9691 def has_attribute(self, *args):
9693 has_attribute(Chain self, FloatKey a0) -> bool
9694 has_attribute(Chain self, IntKey a0) -> bool
9695 has_attribute(Chain self, FloatsKey a0) -> bool
9696 has_attribute(Chain self, IntsKey a0) -> bool
9697 has_attribute(Chain self, StringKey a0) -> bool
9698 has_attribute(Chain self, ParticleIndexKey a0) -> bool
9699 has_attribute(Chain self, ObjectKey a0) -> bool
9700 has_attribute(Chain self, SparseFloatKey a0) -> bool
9701 has_attribute(Chain self, SparseIntKey a0) -> bool
9702 has_attribute(Chain self, SparseStringKey a0) -> bool
9703 has_attribute(Chain self, SparseParticleIndexKey a0) -> bool
9705 return _IMP_atom.Chain_has_attribute(self, *args)
9707 def get_derivative(self, a0):
9708 r"""get_derivative(Chain self, FloatKey a0) -> double"""
9709 return _IMP_atom.Chain_get_derivative(self, a0)
9712 r"""get_name(Chain self) -> std::string"""
9713 return _IMP_atom.Chain_get_name(self)
9715 def clear_caches(self):
9716 r"""clear_caches(Chain self)"""
9717 return _IMP_atom.Chain_clear_caches(self)
9719 def set_name(self, a0):
9720 r"""set_name(Chain self, std::string a0)"""
9721 return _IMP_atom.Chain_set_name(self, a0)
9724 r"""set_check_level(Chain self, IMP::CheckLevel a0)"""
9725 return _IMP_atom.Chain_set_check_level(self, a0)
9727 def add_to_derivative(self, a0, a1, a2):
9728 r"""add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9729 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
9731 def set_is_optimized(self, a0, a1):
9732 r"""set_is_optimized(Chain self, FloatKey a0, bool a1)"""
9733 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
9735 def get_is_optimized(self, a0):
9736 r"""get_is_optimized(Chain self, FloatKey a0) -> bool"""
9737 return _IMP_atom.Chain_get_is_optimized(self, a0)
9740 r"""get_check_level(Chain self) -> IMP::CheckLevel"""
9741 return _IMP_atom.Chain_get_check_level(self)
9743 def __eq__(self, *args):
9745 __eq__(Chain self, Chain o) -> bool
9746 __eq__(Chain self, Particle d) -> bool
9748 return _IMP_atom.Chain___eq__(self, *args)
9750 def __ne__(self, *args):
9752 __ne__(Chain self, Chain o) -> bool
9753 __ne__(Chain self, Particle d) -> bool
9755 return _IMP_atom.Chain___ne__(self, *args)
9757 def __le__(self, *args):
9759 __le__(Chain self, Chain o) -> bool
9760 __le__(Chain self, Particle d) -> bool
9762 return _IMP_atom.Chain___le__(self, *args)
9764 def __lt__(self, *args):
9766 __lt__(Chain self, Chain o) -> bool
9767 __lt__(Chain self, Particle d) -> bool
9769 return _IMP_atom.Chain___lt__(self, *args)
9771 def __ge__(self, *args):
9773 __ge__(Chain self, Chain o) -> bool
9774 __ge__(Chain self, Particle d) -> bool
9776 return _IMP_atom.Chain___ge__(self, *args)
9778 def __gt__(self, *args):
9780 __gt__(Chain self, Chain o) -> bool
9781 __gt__(Chain self, Particle d) -> bool
9783 return _IMP_atom.Chain___gt__(self, *args)
9786 r"""__hash__(Chain self) -> std::size_t"""
9787 return _IMP_atom.Chain___hash__(self)
9790 r"""__str__(Chain self) -> std::string"""
9791 return _IMP_atom.Chain___str__(self)
9794 r"""__repr__(Chain self) -> std::string"""
9795 return _IMP_atom.Chain___repr__(self)
9797 def _get_as_binary(self):
9798 r"""_get_as_binary(Chain self) -> PyObject *"""
9799 return _IMP_atom.Chain__get_as_binary(self)
9801 def _set_from_binary(self, p):
9802 r"""_set_from_binary(Chain self, PyObject * p)"""
9803 return _IMP_atom.Chain__set_from_binary(self, p)
9805 def __getstate__(self):
9806 p = self._get_as_binary()
9807 if len(self.__dict__) > 1:
9808 d = self.__dict__.copy()
9813 def __setstate__(self, p):
9814 if not hasattr(self,
'this'):
9816 if isinstance(p, tuple):
9818 self.__dict__.update(d)
9819 return self._set_from_binary(p)
9821 __swig_destroy__ = _IMP_atom.delete_Chain
9824 _IMP_atom.Chain_swigregister(Chain)
9825 UnknownChainType = cvar.UnknownChainType
9826 DPolypeptide = cvar.DPolypeptide
9827 LPolypeptide = cvar.LPolypeptide
9828 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
9829 Polyribonucleotide = cvar.Polyribonucleotide
9830 DPolysaccharide = cvar.DPolysaccharide
9831 LPolysaccharide = cvar.LPolysaccharide
9832 Protein = cvar.Protein
9838 r"""get_chain(Hierarchy h) -> Chain"""
9839 return _IMP_atom.get_chain(h)
9842 r"""get_chain_id(Hierarchy h) -> std::string"""
9843 return _IMP_atom.get_chain_id(h)
9844 class Selection(IMP._ParticleIndexesAdaptor):
9845 r"""Proxy of C++ IMP::atom::Selection class."""
9847 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9848 NONE = _IMP_atom.Selection_NONE
9850 C = _IMP_atom.Selection_C
9852 N = _IMP_atom.Selection_N
9855 def __init__(self, *args):
9857 __init__(Selection self) -> Selection
9858 __init__(Selection self, Hierarchy h) -> Selection
9859 __init__(Selection self, Particle h) -> Selection
9860 __init__(Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
9861 __init__(Selection self, IMP::ParticlesTemp const & h) -> Selection
9863 _IMP_atom.Selection_swiginit(self, _IMP_atom.new_Selection(*args))
9866 r"""create_clone(Selection self) -> Selection"""
9867 return _IMP_atom.Selection_create_clone(self)
9869 def get_hierarchies(self):
9870 r"""get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
9871 return _IMP_atom.Selection_get_hierarchies(self)
9873 def set_molecules(self, mols):
9874 r"""set_molecules(Selection self, IMP::Strings mols)"""
9875 return _IMP_atom.Selection_set_molecules(self, mols)
9877 def set_resolution(self, r):
9878 r"""set_resolution(Selection self, double r)"""
9879 return _IMP_atom.Selection_set_resolution(self, r)
9881 def set_representation_type(self, t):
9882 r"""set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
9883 return _IMP_atom.Selection_set_representation_type(self, t)
9885 def set_state_index(self, state):
9886 r"""set_state_index(Selection self, int state)"""
9887 return _IMP_atom.Selection_set_state_index(self, state)
9889 def set_state_indexes(self, states):
9890 r"""set_state_indexes(Selection self, IMP::Ints states)"""
9891 return _IMP_atom.Selection_set_state_indexes(self, states)
9893 def set_terminus(self, t):
9894 r"""set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
9895 return _IMP_atom.Selection_set_terminus(self, t)
9897 def set_element(self, e):
9898 r"""set_element(Selection self, IMP::atom::Element e)"""
9899 return _IMP_atom.Selection_set_element(self, e)
9901 def set_chain_ids(self, chains):
9902 r"""set_chain_ids(Selection self, IMP::Strings chains)"""
9903 return _IMP_atom.Selection_set_chain_ids(self, chains)
9905 def set_chains(self, chains):
9906 r"""set_chains(Selection self, IMP::Strings chains)"""
9907 return _IMP_atom.Selection_set_chains(self, chains)
9909 def set_residue_indexes(self, indexes):
9910 r"""set_residue_indexes(Selection self, IMP::Ints indexes)"""
9911 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
9913 def set_atom_types(self, types):
9914 r"""set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
9915 return _IMP_atom.Selection_set_atom_types(self, types)
9917 def set_residue_types(self, types):
9918 r"""set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
9919 return _IMP_atom.Selection_set_residue_types(self, types)
9921 def set_domains(self, names):
9922 r"""set_domains(Selection self, IMP::Strings names)"""
9923 return _IMP_atom.Selection_set_domains(self, names)
9925 def set_molecule(self, mol):
9926 r"""set_molecule(Selection self, std::string mol)"""
9927 return _IMP_atom.Selection_set_molecule(self, mol)
9929 def set_chain_id(self, c):
9930 r"""set_chain_id(Selection self, std::string c)"""
9931 return _IMP_atom.Selection_set_chain_id(self, c)
9933 def set_chain(self, c):
9934 r"""set_chain(Selection self, std::string c)"""
9935 return _IMP_atom.Selection_set_chain(self, c)
9937 def set_residue_index(self, i):
9938 r"""set_residue_index(Selection self, int i)"""
9939 return _IMP_atom.Selection_set_residue_index(self, i)
9941 def set_atom_type(self, types):
9942 r"""set_atom_type(Selection self, AtomType types)"""
9943 return _IMP_atom.Selection_set_atom_type(self, types)
9945 def set_residue_type(self, type):
9946 r"""set_residue_type(Selection self, ResidueType type)"""
9947 return _IMP_atom.Selection_set_residue_type(self, type)
9949 def set_domain(self, name):
9950 r"""set_domain(Selection self, std::string name)"""
9951 return _IMP_atom.Selection_set_domain(self, name)
9953 def set_copy_index(self, copy):
9954 r"""set_copy_index(Selection self, unsigned int copy)"""
9955 return _IMP_atom.Selection_set_copy_index(self, copy)
9957 def set_copy_indexes(self, copies):
9958 r"""set_copy_indexes(Selection self, IMP::Ints copies)"""
9959 return _IMP_atom.Selection_set_copy_indexes(self, copies)
9961 def set_particle_type(self, t):
9962 r"""set_particle_type(Selection self, ParticleType t)"""
9963 return _IMP_atom.Selection_set_particle_type(self, t)
9965 def set_particle_types(self, t):
9966 r"""set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
9967 return _IMP_atom.Selection_set_particle_types(self, t)
9969 def set_hierarchy_types(self, types):
9970 r"""set_hierarchy_types(Selection self, IMP::Ints types)"""
9971 return _IMP_atom.Selection_set_hierarchy_types(self, types)
9973 def set_intersection(self, s):
9974 r"""set_intersection(Selection self, Selection s)"""
9975 return _IMP_atom.Selection_set_intersection(self, s)
9977 def set_union(self, s):
9978 r"""set_union(Selection self, Selection s)"""
9979 return _IMP_atom.Selection_set_union(self, s)
9981 def set_symmetric_difference(self, s):
9982 r"""set_symmetric_difference(Selection self, Selection s)"""
9983 return _IMP_atom.Selection_set_symmetric_difference(self, s)
9985 def set_difference(self, s):
9986 r"""set_difference(Selection self, Selection s)"""
9987 return _IMP_atom.Selection_set_difference(self, s)
9989 def get_selected_particles(self, with_representation=True):
9990 r"""get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp"""
9991 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
9993 def get_selected_particle_indexes(self, with_representation=True):
9994 r"""get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes"""
9995 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
9997 def show(self, *args):
9998 r"""show(Selection self, _ostream out=std::cout)"""
9999 return _IMP_atom.Selection_show(self, *args)
10002 r"""__str__(Selection self) -> std::string"""
10003 return _IMP_atom.Selection___str__(self)
10005 def __repr__(self):
10006 r"""__repr__(Selection self) -> std::string"""
10007 return _IMP_atom.Selection___repr__(self)
10009 def __init__(self, hierarchy=None,
10010 hierarchies=
None, **params):
10011 if hierarchy
and hierarchies:
10012 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
10014 this = _IMP_atom.new_Selection(hierarchy)
10015 try: self.this.append(this)
10016 except: self.this = this
10018 this = _IMP_atom.new_Selection(hierarchies)
10019 try: self.this.append(this)
10020 except: self.this = this
10022 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
10023 for k
in params.keys():
10024 eval(
"self.set_%s(params[k])"%k)
10026 def union(self, s):
10027 news = self.create_clone()
10028 news.union_update(s)
10030 def intersection(self, s):
10031 news = self.create_clone()
10032 news.intersection_update(s)
10034 def symmetric_difference(self, s):
10035 news = self.create_clone()
10036 news.symmetric_difference_update(s)
10038 def difference(self, s):
10039 news = self.create_clone()
10040 news.difference_update(s)
10042 def union_update(self, s):
10045 def intersection_update(self, s):
10046 self.set_intersection(s)
10048 def symmetric_difference_update(self, s):
10049 self.set_symmetric_difference(s)
10051 def difference_update(self, s):
10052 self.set_difference(s)
10055 __and__ = intersection
10056 __xor__ = symmetric_difference
10057 __sub__ = difference
10058 __ior__ = union_update
10059 __iand__ = intersection_update
10060 __ixor__ = symmetric_difference_update
10061 __isub__ = difference_update
10063 __swig_destroy__ = _IMP_atom.delete_Selection
10066 _IMP_atom.Selection_swigregister(Selection)
10069 r"""create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint"""
10070 return _IMP_atom.create_distance_restraint(*args)
10074 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
10075 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10077 return _IMP_atom.create_connectivity_restraint(*args)
10081 create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
10082 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10084 return _IMP_atom.create_internal_connectivity_restraint(*args)
10087 r"""create_cover(Selection s, std::string name=std::string()) -> XYZR"""
10088 return _IMP_atom.create_cover(*args)
10092 get_mass(ResidueType c) -> double
10093 get_mass(Selection s) -> double
10095 return _IMP_atom.get_mass(*args)
10098 r"""get_volume(Selection s) -> double"""
10099 return _IMP_atom.get_volume(s)
10102 r"""get_surface_area(Selection s) -> double"""
10103 return _IMP_atom.get_surface_area(s)
10107 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10108 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10109 get_leaves(Selection h) -> IMP::atom::Hierarchies
10111 return _IMP_atom.get_leaves(*args)
10113 r"""Proxy of C++ IMP::atom::SelectionGeometry class."""
10115 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10117 def __init__(self, *args):
10118 r"""__init__(SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry"""
10119 _IMP_atom.SelectionGeometry_swiginit(self, _IMP_atom.new_SelectionGeometry(*args))
10121 def get_version_info(self):
10122 r"""get_version_info(SelectionGeometry self) -> VersionInfo"""
10123 return _IMP_atom.SelectionGeometry_get_version_info(self)
10124 __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
10127 r"""__str__(SelectionGeometry self) -> std::string"""
10128 return _IMP_atom.SelectionGeometry___str__(self)
10130 def __repr__(self):
10131 r"""__repr__(SelectionGeometry self) -> std::string"""
10132 return _IMP_atom.SelectionGeometry___repr__(self)
10136 return _object_cast_to_SelectionGeometry(o)
10140 _IMP_atom.SelectionGeometry_swigregister(SelectionGeometry)
10144 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10145 get_rmsd(Selection s0, Selection s1) -> double
10147 return _IMP_atom.get_rmsd(*args)
10151 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10152 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10154 return _IMP_atom.get_rmsd_transforming_first(*args)
10157 r"""get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10158 return _IMP_atom.get_placement_score(source, target)
10161 r"""get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> IMP::FloatPair"""
10162 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10165 r"""get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> double"""
10166 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10170 get_radius_of_gyration(Selection s) -> double
10171 get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10173 return _IMP_atom.get_radius_of_gyration(*args)
10175 r"""Proxy of C++ IMP::atom::ForceFieldParameters class."""
10177 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10179 def __init__(self):
10180 r"""__init__(ForceFieldParameters self) -> ForceFieldParameters"""
10181 _IMP_atom.ForceFieldParameters_swiginit(self, _IMP_atom.new_ForceFieldParameters())
10183 def get_radius(self, atom):
10184 r"""get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10185 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10187 def get_epsilon(self, atom):
10188 r"""get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10189 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10192 r"""add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=IMP::FloatKey("radius"))"""
10193 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10195 def add_well_depths(self, mhd):
10196 r"""add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10197 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10200 r"""add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10201 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10202 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10205 r"""__str__(ForceFieldParameters self) -> std::string"""
10206 return _IMP_atom.ForceFieldParameters___str__(self)
10208 def __repr__(self):
10209 r"""__repr__(ForceFieldParameters self) -> std::string"""
10210 return _IMP_atom.ForceFieldParameters___repr__(self)
10214 return _object_cast_to_ForceFieldParameters(o)
10218 _IMP_atom.ForceFieldParameters_swigregister(ForceFieldParameters)
10219 class CHARMMAtomTopology(object):
10220 r"""Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10222 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10224 def __init__(self, *args):
10226 __init__(CHARMMAtomTopology self) -> CHARMMAtomTopology
10227 __init__(CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10228 __init__(CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10230 _IMP_atom.CHARMMAtomTopology_swiginit(self, _IMP_atom.new_CHARMMAtomTopology(*args))
10232 def get_name(self):
10233 r"""get_name(CHARMMAtomTopology self) -> std::string"""
10234 return _IMP_atom.CHARMMAtomTopology_get_name(self)
10236 def get_charmm_type(self):
10237 r"""get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10238 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10240 def get_charge(self):
10241 r"""get_charge(CHARMMAtomTopology self) -> double"""
10242 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10244 def set_charmm_type(self, charmm_type):
10245 r"""set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10246 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10248 def set_charge(self, charge):
10249 r"""set_charge(CHARMMAtomTopology self, double charge)"""
10250 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10252 def show(self, *args):
10253 r"""show(CHARMMAtomTopology self, _ostream out=std::cout)"""
10254 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10257 r"""__str__(CHARMMAtomTopology self) -> std::string"""
10258 return _IMP_atom.CHARMMAtomTopology___str__(self)
10260 def __repr__(self):
10261 r"""__repr__(CHARMMAtomTopology self) -> std::string"""
10262 return _IMP_atom.CHARMMAtomTopology___repr__(self)
10264 def _get_as_binary(self):
10265 r"""_get_as_binary(CHARMMAtomTopology self) -> PyObject *"""
10266 return _IMP_atom.CHARMMAtomTopology__get_as_binary(self)
10268 def _set_from_binary(self, p):
10269 r"""_set_from_binary(CHARMMAtomTopology self, PyObject * p)"""
10270 return _IMP_atom.CHARMMAtomTopology__set_from_binary(self, p)
10272 def __getstate__(self):
10273 p = self._get_as_binary()
10274 if len(self.__dict__) > 1:
10275 d = self.__dict__.copy()
10280 def __setstate__(self, p):
10281 if not hasattr(self,
'this'):
10283 if isinstance(p, tuple):
10285 self.__dict__.update(d)
10286 return self._set_from_binary(p)
10288 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10291 _IMP_atom.CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10292 class CHARMMBondEndpoint(object):
10293 r"""Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10295 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10297 def __init__(self, atom_name, residue=None):
10298 r"""__init__(CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint"""
10299 _IMP_atom.CHARMMBondEndpoint_swiginit(self, _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue))
10301 def get_atom_name(self):
10302 r"""get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10303 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10305 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10306 r"""get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue, std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom"""
10307 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10309 def show(self, *args):
10310 r"""show(CHARMMBondEndpoint self, _ostream out=std::cout)"""
10311 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10314 r"""__str__(CHARMMBondEndpoint self) -> std::string"""
10315 return _IMP_atom.CHARMMBondEndpoint___str__(self)
10317 def __repr__(self):
10318 r"""__repr__(CHARMMBondEndpoint self) -> std::string"""
10319 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10320 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10323 _IMP_atom.CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10324 class CHARMMDihedral(object):
10325 r"""Proxy of C++ IMP::atom::CHARMMConnection< 4 > class."""
10327 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10328 __repr__ = _swig_repr
10330 def __init__(self, atoms):
10331 r"""__init__(CHARMMDihedral self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10332 _IMP_atom.CHARMMDihedral_swiginit(self, _IMP_atom.new_CHARMMDihedral(atoms))
10334 def get_endpoint(self, i):
10335 r"""get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10336 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10338 def get_contains_atom(self, name):
10339 r"""get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10340 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10342 def show(self, *args):
10343 r"""show(CHARMMDihedral self, _ostream out=std::cout)"""
10344 return _IMP_atom.CHARMMDihedral_show(self, *args)
10345 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10348 _IMP_atom.CHARMMDihedral_swigregister(CHARMMDihedral)
10349 class CHARMMInternalCoordinate(CHARMMDihedral):
10350 r"""Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10352 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10354 def __init__(self, *args):
10356 __init__(CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10357 __init__(CHARMMInternalCoordinate self, IMP::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10359 _IMP_atom.CHARMMInternalCoordinate_swiginit(self, _IMP_atom.new_CHARMMInternalCoordinate(*args))
10361 def get_first_distance(self):
10362 r"""get_first_distance(CHARMMInternalCoordinate self) -> float"""
10363 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10365 def get_second_distance(self):
10366 r"""get_second_distance(CHARMMInternalCoordinate self) -> float"""
10367 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10369 def get_first_angle(self):
10370 r"""get_first_angle(CHARMMInternalCoordinate self) -> float"""
10371 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10373 def get_second_angle(self):
10374 r"""get_second_angle(CHARMMInternalCoordinate self) -> float"""
10375 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10378 r"""get_dihedral(CHARMMInternalCoordinate self) -> float"""
10379 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10381 def get_improper(self):
10382 r"""get_improper(CHARMMInternalCoordinate self) -> bool"""
10383 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10385 def show(self, *args):
10386 r"""show(CHARMMInternalCoordinate self, _ostream out=std::cout)"""
10387 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10390 r"""__str__(CHARMMInternalCoordinate self) -> std::string"""
10391 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10393 def __repr__(self):
10394 r"""__repr__(CHARMMInternalCoordinate self) -> std::string"""
10395 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10396 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10399 _IMP_atom.CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10400 class CHARMMResidueTopologyBase(
IMP.Object):
10401 r"""Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10403 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10405 def __init__(self, *args, **kwargs):
10406 raise AttributeError(
"No constructor defined")
10408 def get_type(self):
10409 r"""get_type(CHARMMResidueTopologyBase self) -> std::string"""
10410 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10412 def get_number_of_atoms(self):
10413 r"""get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10414 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10416 def add_atom(self, atom):
10417 r"""add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10418 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10422 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10423 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10424 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10426 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10428 def get_number_of_bonds(self):
10429 r"""get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10430 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10432 def add_bond(self, bond):
10433 r"""add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
10434 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10436 def get_number_of_angles(self):
10437 r"""get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10438 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10440 def add_angle(self, bond):
10441 r"""add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
10442 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10444 def get_number_of_dihedrals(self):
10445 r"""get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10446 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10448 def add_dihedral(self, bond):
10449 r"""add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10450 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10452 def get_number_of_impropers(self):
10453 r"""get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10454 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10456 def add_improper(self, bond):
10457 r"""add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10458 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10460 def get_number_of_internal_coordinates(self):
10461 r"""get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
10462 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
10464 def add_internal_coordinate(self, ic):
10465 r"""add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
10466 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
10468 def get_internal_coordinate(self, index):
10469 r"""get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
10470 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
10473 r"""get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
10474 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
10477 r"""get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
10478 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
10481 r"""get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10482 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
10484 def get_improper(self, index):
10485 r"""get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10486 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
10488 def get_version_info(self):
10489 r"""get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
10490 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
10491 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
10494 r"""__str__(CHARMMResidueTopologyBase self) -> std::string"""
10495 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
10497 def __repr__(self):
10498 r"""__repr__(CHARMMResidueTopologyBase self) -> std::string"""
10499 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
10503 return _object_cast_to_CHARMMResidueTopologyBase(o)
10507 _IMP_atom.CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
10508 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
10509 r"""Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
10511 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10513 def __init__(self, *args):
10515 __init__(CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
10516 __init__(CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
10518 _IMP_atom.CHARMMIdealResidueTopology_swiginit(self, _IMP_atom.new_CHARMMIdealResidueTopology(*args))
10520 def remove_atom(self, name):
10521 r"""remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
10522 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
10524 def set_default_first_patch(self, patch):
10525 r"""set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10526 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
10528 def set_default_last_patch(self, patch):
10529 r"""set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10530 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
10532 def get_default_first_patch(self):
10533 r"""get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
10534 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
10536 def get_default_last_patch(self):
10537 r"""get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
10538 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
10539 __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
10542 r"""__str__(CHARMMIdealResidueTopology self) -> std::string"""
10543 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
10545 def __repr__(self):
10546 r"""__repr__(CHARMMIdealResidueTopology self) -> std::string"""
10547 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
10551 return _object_cast_to_CHARMMIdealResidueTopology(o)
10555 _IMP_atom.CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
10556 class CHARMMPatch(CHARMMResidueTopologyBase):
10557 r"""Proxy of C++ IMP::atom::CHARMMPatch class."""
10559 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10561 def __init__(self, type):
10562 r"""__init__(CHARMMPatch self, std::string type) -> CHARMMPatch"""
10563 _IMP_atom.CHARMMPatch_swiginit(self, _IMP_atom.new_CHARMMPatch(type))
10565 def add_removed_atom(self, name):
10566 r"""add_removed_atom(CHARMMPatch self, std::string name)"""
10567 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
10569 def get_number_of_removed_atoms(self):
10570 r"""get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
10571 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
10573 def get_removed_atom(self, i):
10574 r"""get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
10575 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
10577 def apply(self, *args):
10579 apply(CHARMMPatch self, CHARMMResidueTopology res)
10580 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
10582 return _IMP_atom.CHARMMPatch_apply(self, *args)
10583 __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
10586 r"""__str__(CHARMMPatch self) -> std::string"""
10587 return _IMP_atom.CHARMMPatch___str__(self)
10589 def __repr__(self):
10590 r"""__repr__(CHARMMPatch self) -> std::string"""
10591 return _IMP_atom.CHARMMPatch___repr__(self)
10595 return _object_cast_to_CHARMMPatch(o)
10599 _IMP_atom.CHARMMPatch_swigregister(CHARMMPatch)
10600 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
10601 r"""Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
10603 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10605 def __init__(self, *args):
10607 __init__(CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
10608 __init__(CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
10610 _IMP_atom.CHARMMResidueTopology_swiginit(self, _IMP_atom.new_CHARMMResidueTopology(*args))
10612 def get_patched(self):
10613 r"""get_patched(CHARMMResidueTopology self) -> bool"""
10614 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
10616 def set_patched(self, patched):
10617 r"""set_patched(CHARMMResidueTopology self, bool patched)"""
10618 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
10619 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
10622 r"""__str__(CHARMMResidueTopology self) -> std::string"""
10623 return _IMP_atom.CHARMMResidueTopology___str__(self)
10625 def __repr__(self):
10626 r"""__repr__(CHARMMResidueTopology self) -> std::string"""
10627 return _IMP_atom.CHARMMResidueTopology___repr__(self)
10631 return _object_cast_to_CHARMMResidueTopology(o)
10635 _IMP_atom.CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
10636 class CHARMMAtom(Atom):
10637 r"""Proxy of C++ IMP::atom::CHARMMAtom class."""
10639 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10641 def __init__(self, *args):
10643 __init__(CHARMMAtom self) -> CHARMMAtom
10644 __init__(CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
10645 __init__(CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
10647 _IMP_atom.CHARMMAtom_swiginit(self, _IMP_atom.new_CHARMMAtom(*args))
10649 def show(self, *args):
10650 r"""show(CHARMMAtom self, _ostream out=std::cout)"""
10651 return _IMP_atom.CHARMMAtom_show(self, *args)
10654 def setup_particle(*args):
10656 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
10657 setup_particle(_ParticleAdaptor pa, IMP::String charmm_type) -> CHARMMAtom
10659 return _IMP_atom.CHARMMAtom_setup_particle(*args)
10661 def get_charmm_type(self):
10662 r"""get_charmm_type(CHARMMAtom self) -> IMP::String"""
10663 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
10665 def set_charmm_type(self, t):
10666 r"""set_charmm_type(CHARMMAtom self, IMP::String t)"""
10667 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
10670 def get_is_setup(*args):
10672 get_is_setup(_ParticleAdaptor p) -> bool
10673 get_is_setup(Model m, ParticleIndex pi) -> bool
10675 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
10678 def get_charmm_type_key():
10679 r"""get_charmm_type_key() -> StringKey"""
10680 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
10682 def add_attribute(self, *args):
10684 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
10685 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10686 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
10687 add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10688 add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10689 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
10690 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10691 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
10692 add_attribute(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
10693 add_attribute(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
10694 add_attribute(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
10695 add_attribute(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
10697 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
10699 def get_value(self, *args):
10701 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
10702 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
10703 get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
10704 get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
10705 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
10706 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
10707 get_value(CHARMMAtom self, ObjectKey a0) -> Object
10708 get_value(CHARMMAtom self, SparseFloatKey a0) -> IMP::Float
10709 get_value(CHARMMAtom self, SparseIntKey a0) -> IMP::Int
10710 get_value(CHARMMAtom self, SparseStringKey a0) -> IMP::String
10711 get_value(CHARMMAtom self, SparseParticleIndexKey a0) -> ParticleIndex
10713 return _IMP_atom.CHARMMAtom_get_value(self, *args)
10715 def set_value(self, *args):
10717 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10718 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
10719 set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10720 set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10721 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
10722 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10723 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
10724 set_value(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
10725 set_value(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
10726 set_value(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
10727 set_value(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
10729 return _IMP_atom.CHARMMAtom_set_value(self, *args)
10731 def remove_attribute(self, *args):
10733 remove_attribute(CHARMMAtom self, FloatKey a0)
10734 remove_attribute(CHARMMAtom self, IntKey a0)
10735 remove_attribute(CHARMMAtom self, FloatsKey a0)
10736 remove_attribute(CHARMMAtom self, IntsKey a0)
10737 remove_attribute(CHARMMAtom self, StringKey a0)
10738 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
10739 remove_attribute(CHARMMAtom self, ObjectKey a0)
10740 remove_attribute(CHARMMAtom self, SparseFloatKey a0)
10741 remove_attribute(CHARMMAtom self, SparseIntKey a0)
10742 remove_attribute(CHARMMAtom self, SparseStringKey a0)
10743 remove_attribute(CHARMMAtom self, SparseParticleIndexKey a0)
10745 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
10747 def has_attribute(self, *args):
10749 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
10750 has_attribute(CHARMMAtom self, IntKey a0) -> bool
10751 has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
10752 has_attribute(CHARMMAtom self, IntsKey a0) -> bool
10753 has_attribute(CHARMMAtom self, StringKey a0) -> bool
10754 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
10755 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
10756 has_attribute(CHARMMAtom self, SparseFloatKey a0) -> bool
10757 has_attribute(CHARMMAtom self, SparseIntKey a0) -> bool
10758 has_attribute(CHARMMAtom self, SparseStringKey a0) -> bool
10759 has_attribute(CHARMMAtom self, SparseParticleIndexKey a0) -> bool
10761 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
10763 def get_derivative(self, a0):
10764 r"""get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
10765 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
10767 def get_name(self):
10768 r"""get_name(CHARMMAtom self) -> std::string"""
10769 return _IMP_atom.CHARMMAtom_get_name(self)
10771 def clear_caches(self):
10772 r"""clear_caches(CHARMMAtom self)"""
10773 return _IMP_atom.CHARMMAtom_clear_caches(self)
10775 def set_name(self, a0):
10776 r"""set_name(CHARMMAtom self, std::string a0)"""
10777 return _IMP_atom.CHARMMAtom_set_name(self, a0)
10780 r"""set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
10781 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
10783 def add_to_derivative(self, a0, a1, a2):
10784 r"""add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10785 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
10787 def set_is_optimized(self, a0, a1):
10788 r"""set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
10789 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
10791 def get_is_optimized(self, a0):
10792 r"""get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
10793 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
10796 r"""get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
10797 return _IMP_atom.CHARMMAtom_get_check_level(self)
10799 def __eq__(self, *args):
10801 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
10802 __eq__(CHARMMAtom self, Particle d) -> bool
10804 return _IMP_atom.CHARMMAtom___eq__(self, *args)
10806 def __ne__(self, *args):
10808 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
10809 __ne__(CHARMMAtom self, Particle d) -> bool
10811 return _IMP_atom.CHARMMAtom___ne__(self, *args)
10813 def __le__(self, *args):
10815 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
10816 __le__(CHARMMAtom self, Particle d) -> bool
10818 return _IMP_atom.CHARMMAtom___le__(self, *args)
10820 def __lt__(self, *args):
10822 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
10823 __lt__(CHARMMAtom self, Particle d) -> bool
10825 return _IMP_atom.CHARMMAtom___lt__(self, *args)
10827 def __ge__(self, *args):
10829 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
10830 __ge__(CHARMMAtom self, Particle d) -> bool
10832 return _IMP_atom.CHARMMAtom___ge__(self, *args)
10834 def __gt__(self, *args):
10836 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
10837 __gt__(CHARMMAtom self, Particle d) -> bool
10839 return _IMP_atom.CHARMMAtom___gt__(self, *args)
10841 def __hash__(self):
10842 r"""__hash__(CHARMMAtom self) -> std::size_t"""
10843 return _IMP_atom.CHARMMAtom___hash__(self)
10846 r"""__str__(CHARMMAtom self) -> std::string"""
10847 return _IMP_atom.CHARMMAtom___str__(self)
10849 def __repr__(self):
10850 r"""__repr__(CHARMMAtom self) -> std::string"""
10851 return _IMP_atom.CHARMMAtom___repr__(self)
10853 def _get_as_binary(self):
10854 r"""_get_as_binary(CHARMMAtom self) -> PyObject *"""
10855 return _IMP_atom.CHARMMAtom__get_as_binary(self)
10857 def _set_from_binary(self, p):
10858 r"""_set_from_binary(CHARMMAtom self, PyObject * p)"""
10859 return _IMP_atom.CHARMMAtom__set_from_binary(self, p)
10861 def __getstate__(self):
10862 p = self._get_as_binary()
10863 if len(self.__dict__) > 1:
10864 d = self.__dict__.copy()
10869 def __setstate__(self, p):
10870 if not hasattr(self,
'this'):
10872 if isinstance(p, tuple):
10874 self.__dict__.update(d)
10875 return self._set_from_binary(p)
10877 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
10880 _IMP_atom.CHARMMAtom_swigregister(CHARMMAtom)
10883 r"""get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
10884 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
10887 r"""remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
10888 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
10889 class CHARMMBondParameters(object):
10890 r"""Proxy of C++ IMP::atom::CHARMMBondParameters class."""
10892 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10893 force_constant = property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set, doc=
r"""force_constant : double""")
10894 ideal = property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set, doc=
r"""ideal : double""")
10896 def __init__(self):
10897 r"""__init__(CHARMMBondParameters self) -> CHARMMBondParameters"""
10898 _IMP_atom.CHARMMBondParameters_swiginit(self, _IMP_atom.new_CHARMMBondParameters())
10900 def show(self, *args):
10901 r"""show(CHARMMBondParameters self, _ostream out=std::cout)"""
10902 return _IMP_atom.CHARMMBondParameters_show(self, *args)
10905 r"""__str__(CHARMMBondParameters self) -> std::string"""
10906 return _IMP_atom.CHARMMBondParameters___str__(self)
10908 def __repr__(self):
10909 r"""__repr__(CHARMMBondParameters self) -> std::string"""
10910 return _IMP_atom.CHARMMBondParameters___repr__(self)
10912 def _get_as_binary(self):
10913 r"""_get_as_binary(CHARMMBondParameters self) -> PyObject *"""
10914 return _IMP_atom.CHARMMBondParameters__get_as_binary(self)
10916 def _set_from_binary(self, p):
10917 r"""_set_from_binary(CHARMMBondParameters self, PyObject * p)"""
10918 return _IMP_atom.CHARMMBondParameters__set_from_binary(self, p)
10920 def __getstate__(self):
10921 p = self._get_as_binary()
10922 if len(self.__dict__) > 1:
10923 d = self.__dict__.copy()
10928 def __setstate__(self, p):
10929 if not hasattr(self,
'this'):
10931 if isinstance(p, tuple):
10933 self.__dict__.update(d)
10934 return self._set_from_binary(p)
10936 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
10939 _IMP_atom.CHARMMBondParameters_swigregister(CHARMMBondParameters)
10940 class CHARMMDihedralParameters(object):
10941 r"""Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
10943 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10944 force_constant = property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set, doc=
r"""force_constant : double""")
10945 multiplicity = property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set, doc=
r"""multiplicity : int""")
10946 ideal = property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set, doc=
r"""ideal : double""")
10948 def __init__(self):
10949 r"""__init__(CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
10950 _IMP_atom.CHARMMDihedralParameters_swiginit(self, _IMP_atom.new_CHARMMDihedralParameters())
10952 def show(self, *args):
10953 r"""show(CHARMMDihedralParameters self, _ostream out=std::cout)"""
10954 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
10957 r"""__str__(CHARMMDihedralParameters self) -> std::string"""
10958 return _IMP_atom.CHARMMDihedralParameters___str__(self)
10960 def __repr__(self):
10961 r"""__repr__(CHARMMDihedralParameters self) -> std::string"""
10962 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
10964 def _get_as_binary(self):
10965 r"""_get_as_binary(CHARMMDihedralParameters self) -> PyObject *"""
10966 return _IMP_atom.CHARMMDihedralParameters__get_as_binary(self)
10968 def _set_from_binary(self, p):
10969 r"""_set_from_binary(CHARMMDihedralParameters self, PyObject * p)"""
10970 return _IMP_atom.CHARMMDihedralParameters__set_from_binary(self, p)
10972 def __getstate__(self):
10973 p = self._get_as_binary()
10974 if len(self.__dict__) > 1:
10975 d = self.__dict__.copy()
10980 def __setstate__(self, p):
10981 if not hasattr(self,
'this'):
10983 if isinstance(p, tuple):
10985 self.__dict__.update(d)
10986 return self._set_from_binary(p)
10988 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
10991 _IMP_atom.CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
10992 class CHARMMParameters(ForceFieldParameters):
10993 r"""Proxy of C++ IMP::atom::CHARMMParameters class."""
10995 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10997 def __init__(self, *args):
10998 r"""__init__(CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters"""
10999 _IMP_atom.CHARMMParameters_swiginit(self, _IMP_atom.new_CHARMMParameters(*args))
11001 def add_residue_topology(self, res):
11002 r"""add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11003 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11005 def get_residue_topology(self, type):
11006 r"""get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11007 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11009 def add_patch(self, patch):
11010 r"""add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11011 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11013 def get_patch(self, name):
11014 r"""get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11015 return _IMP_atom.CHARMMParameters_get_patch(self, name)
11017 def create_topology(self, hierarchy):
11018 r"""create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11019 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11021 def get_bond_parameters(self, type1, type2):
11022 r"""get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11023 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11025 def get_angle_parameters(self, type1, type2, type3):
11026 r"""get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11027 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11029 def get_dihedral_parameters(self, type1, type2, type3, type4):
11030 r"""get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11031 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11033 def get_improper_parameters(self, type1, type2, type3, type4):
11034 r"""get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11035 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11037 def create_angles(self, bonds):
11038 r"""create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11039 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11041 def create_dihedrals(self, bonds):
11042 r"""create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11043 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11045 def get_version_info(self):
11046 r"""get_version_info(CHARMMParameters self) -> VersionInfo"""
11047 return _IMP_atom.CHARMMParameters_get_version_info(self)
11048 __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
11051 r"""__str__(CHARMMParameters self) -> std::string"""
11052 return _IMP_atom.CHARMMParameters___str__(self)
11054 def __repr__(self):
11055 r"""__repr__(CHARMMParameters self) -> std::string"""
11056 return _IMP_atom.CHARMMParameters___repr__(self)
11060 return _object_cast_to_CHARMMParameters(o)
11064 _IMP_atom.CHARMMParameters_swigregister(CHARMMParameters)
11067 r"""get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11068 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11071 r"""get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11072 return _IMP_atom.get_all_atom_CHARMM_parameters()
11074 r"""Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11076 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11077 def __get_residues(self):
return IMP._list_util.VarList(getdimfunc=self.get_number_of_residues, getfunc=self.get_residue, erasefunc=self.erase_residue, appendfunc=self.add_residue, extendfunc=self.add_residues, clearfunc=self.clear_residues, indexfunc=self._python_index_residue)
11078 def __set_residues(self, obj): IMP._list_util.set_varlist(self.residues, obj)
11079 def __del_residues(self): IMP._list_util.del_varlist(self.residues)
11080 residues = property(__get_residues, __set_residues, __del_residues, doc=
"List of ##ucnames")
11082 def remove_residue(self, d):
11083 r"""remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11084 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11086 def _python_index_residue(self, d, start, stop):
11087 r"""_python_index_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11088 return _IMP_atom.CHARMMSegmentTopology__python_index_residue(self, d, start, stop)
11090 def remove_residues(self, d):
11091 r"""remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11092 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11094 def set_residues(self, ps):
11095 r"""set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11096 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11098 def set_residues_order(self, objs):
11099 r"""set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11100 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11102 def add_residue(self, obj):
11103 r"""add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11104 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11106 def add_residues(self, objs):
11107 r"""add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11108 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11110 def clear_residues(self):
11111 r"""clear_residues(CHARMMSegmentTopology self)"""
11112 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11114 def get_number_of_residues(self):
11115 r"""get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11116 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11118 def get_has_residues(self):
11119 r"""get_has_residues(CHARMMSegmentTopology self) -> bool"""
11120 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11123 r"""get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11124 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11126 def get_residues(self):
11127 r"""get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11128 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11130 def erase_residue(self, i):
11131 r"""erase_residue(CHARMMSegmentTopology self, unsigned int i)"""
11132 return _IMP_atom.CHARMMSegmentTopology_erase_residue(self, i)
11134 def reserve_residues(self, sz):
11135 r"""reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11136 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11138 def get_version_info(self):
11139 r"""get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11140 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11141 __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
11143 def __init__(self, *args):
11144 r"""__init__(CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology"""
11145 _IMP_atom.CHARMMSegmentTopology_swiginit(self, _IMP_atom.new_CHARMMSegmentTopology(*args))
11147 def apply_default_patches(self, ff):
11148 r"""apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11149 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11152 r"""__str__(CHARMMSegmentTopology self) -> std::string"""
11153 return _IMP_atom.CHARMMSegmentTopology___str__(self)
11155 def __repr__(self):
11156 r"""__repr__(CHARMMSegmentTopology self) -> std::string"""
11157 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11161 return _object_cast_to_CHARMMSegmentTopology(o)
11165 _IMP_atom.CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11167 r"""Proxy of C++ IMP::atom::CHARMMTopology class."""
11169 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11171 def __init__(self, *args):
11172 r"""__init__(CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology"""
11173 _IMP_atom.CHARMMTopology_swiginit(self, _IMP_atom.new_CHARMMTopology(*args))
11175 def get_parameters(self):
11176 r"""get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11177 return _IMP_atom.CHARMMTopology_get_parameters(self)
11179 def add_sequence(self, sequence):
11180 r"""add_sequence(CHARMMTopology self, std::string sequence)"""
11181 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11183 def apply_default_patches(self):
11184 r"""apply_default_patches(CHARMMTopology self)"""
11185 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11187 def create_hierarchy(self, model):
11188 r"""create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11189 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11191 def add_atom_types(self, hierarchy):
11192 r"""add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11193 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11195 def add_coordinates(self, hierarchy):
11196 r"""add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11197 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11199 def add_missing_atoms(self, hierarchy):
11200 r"""add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11201 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11203 def setup_hierarchy(self, hierarchy):
11204 r"""setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11205 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11207 def add_charges(self, hierarchy):
11208 r"""add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11209 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11212 r"""add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11213 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11215 def add_dihedrals(self, hierarchy):
11216 r"""add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11217 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11219 def add_impropers(self, hierarchy):
11220 r"""add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11221 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11222 def __get_segments(self):
return IMP._list_util.VarList(getdimfunc=self.get_number_of_segments, getfunc=self.get_segment, erasefunc=self.erase_segment, appendfunc=self.add_segment, extendfunc=self.add_segments, clearfunc=self.clear_segments, indexfunc=self._python_index_segment)
11223 def __set_segments(self, obj): IMP._list_util.set_varlist(self.segments, obj)
11224 def __del_segments(self): IMP._list_util.del_varlist(self.segments)
11225 segments = property(__get_segments, __set_segments, __del_segments, doc=
"List of ##ucnames")
11227 def remove_segment(self, d):
11228 r"""remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11229 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11231 def _python_index_segment(self, d, start, stop):
11232 r"""_python_index_segment(CHARMMTopology self, CHARMMSegmentTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11233 return _IMP_atom.CHARMMTopology__python_index_segment(self, d, start, stop)
11235 def remove_segments(self, d):
11236 r"""remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11237 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11239 def set_segments(self, ps):
11240 r"""set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11241 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11243 def set_segments_order(self, objs):
11244 r"""set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11245 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11247 def add_segment(self, obj):
11248 r"""add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11249 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11251 def add_segments(self, objs):
11252 r"""add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11253 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11255 def clear_segments(self):
11256 r"""clear_segments(CHARMMTopology self)"""
11257 return _IMP_atom.CHARMMTopology_clear_segments(self)
11259 def get_number_of_segments(self):
11260 r"""get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11261 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11263 def get_has_segments(self):
11264 r"""get_has_segments(CHARMMTopology self) -> bool"""
11265 return _IMP_atom.CHARMMTopology_get_has_segments(self)
11268 r"""get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11269 return _IMP_atom.CHARMMTopology_get_segment(self, i)
11271 def get_segments(self):
11272 r"""get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11273 return _IMP_atom.CHARMMTopology_get_segments(self)
11275 def erase_segment(self, i):
11276 r"""erase_segment(CHARMMTopology self, unsigned int i)"""
11277 return _IMP_atom.CHARMMTopology_erase_segment(self, i)
11279 def reserve_segments(self, sz):
11280 r"""reserve_segments(CHARMMTopology self, unsigned int sz)"""
11281 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11283 def get_version_info(self):
11284 r"""get_version_info(CHARMMTopology self) -> VersionInfo"""
11285 return _IMP_atom.CHARMMTopology_get_version_info(self)
11286 __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
11289 r"""__str__(CHARMMTopology self) -> std::string"""
11290 return _IMP_atom.CHARMMTopology___str__(self)
11292 def __repr__(self):
11293 r"""__repr__(CHARMMTopology self) -> std::string"""
11294 return _IMP_atom.CHARMMTopology___repr__(self)
11298 return _object_cast_to_CHARMMTopology(o)
11302 _IMP_atom.CHARMMTopology_swigregister(CHARMMTopology)
11304 r"""Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11306 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11308 def __init__(self, *args):
11310 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11311 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11313 _IMP_atom.CHARMMStereochemistryRestraint_swiginit(self, _IMP_atom.new_CHARMMStereochemistryRestraint(*args))
11315 def get_pair_filter(self):
11316 r"""get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11317 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11319 def get_full_pair_filter(self):
11320 r"""get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11321 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11323 def do_get_inputs(self):
11324 r"""do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11325 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11327 def get_version_info(self):
11328 r"""get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11329 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11330 __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
11333 r"""__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11334 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11336 def __repr__(self):
11337 r"""__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11338 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11342 return _object_cast_to_CHARMMStereochemistryRestraint(o)
11346 _IMP_atom.CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11349 r"""add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())"""
11350 return _IMP_atom.add_bonds(*args)
11353 r"""add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(), FloatKey radius_key=IMP::FloatKey("radius"))"""
11354 return _IMP_atom.add_radii(*args)
11355 ALBER = _IMP_atom.ALBER
11357 HARPAZ = _IMP_atom.HARPAZ
11359 ANDERSSON = _IMP_atom.ANDERSSON
11361 TSAI = _IMP_atom.TSAI
11363 QUILLIN = _IMP_atom.QUILLIN
11365 SQUIRE = _IMP_atom.SQUIRE
11369 r"""get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11370 return _IMP_atom.get_protein_density_from_reference(densityReference)
11373 r"""get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11374 return _IMP_atom.get_volume_from_mass(*args)
11377 r"""get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11378 return _IMP_atom.get_mass_from_volume(*args)
11381 r"""get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11382 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11385 r"""get_volume_from_residue_type(ResidueType rt) -> double"""
11386 return _IMP_atom.get_volume_from_residue_type(rt)
11389 r"""get_molarity(double n, double volume) -> double"""
11390 return _IMP_atom.get_molarity(n, volume)
11392 def get_kd(na, nb, nab, volume):
11393 r"""get_kd(double na, double nb, double nab, double volume) -> double"""
11394 return _IMP_atom.get_kd(na, nb, nab, volume)
11397 r"""get_einstein_diffusion_coefficient(double r, double temp=-1) -> double"""
11398 return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
11401 r"""get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double"""
11402 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
11406 get_diffusion_length(double D, double t) -> double
11407 get_diffusion_length(double D, double force, double t, double temp=-1) -> double
11409 return _IMP_atom.get_diffusion_length(*args)
11412 r"""get_diffusion_angle(double D, double dtfs) -> double"""
11413 return _IMP_atom.get_diffusion_angle(D, dtfs)
11417 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
11418 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
11420 return _IMP_atom.get_diffusion_coefficient(*args)
11423 r"""get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
11424 return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
11426 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11427 r"""get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11428 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11431 r"""get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11432 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11435 r"""get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11436 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11438 r"""Proxy of C++ IMP::atom::EzRestraint class."""
11440 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11442 def __init__(self, m, ps):
11443 r"""__init__(EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11444 _IMP_atom.EzRestraint_swiginit(self, _IMP_atom.new_EzRestraint(m, ps))
11446 def get_version_info(self):
11447 r"""get_version_info(EzRestraint self) -> VersionInfo"""
11448 return _IMP_atom.EzRestraint_get_version_info(self)
11449 __swig_destroy__ = _IMP_atom.delete_EzRestraint
11452 r"""__str__(EzRestraint self) -> std::string"""
11453 return _IMP_atom.EzRestraint___str__(self)
11455 def __repr__(self):
11456 r"""__repr__(EzRestraint self) -> std::string"""
11457 return _IMP_atom.EzRestraint___repr__(self)
11461 return _object_cast_to_EzRestraint(o)
11465 _IMP_atom.EzRestraint_swigregister(EzRestraint)
11469 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1, bool ismol=True) -> Hierarchy
11470 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
11472 return _IMP_atom.create_protein(*args)
11476 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
11477 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
11479 return _IMP_atom.create_simplified_along_backbone(*args)
11482 r"""create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11483 return _IMP_atom.create_simplified_from_volume(h, resolution)
11486 r"""create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11487 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
11489 def get_residue_indexes(h):
11490 r"""get_residue_indexes(Hierarchy h) -> IMP::Ints"""
11491 return _IMP_atom.get_residue_indexes(h)
11493 def get_residue_type(*args):
11495 get_residue_type(char c) -> ResidueType
11496 get_residue_type(Hierarchy h) -> ResidueType
11498 return _IMP_atom.get_residue_type(*args)
11500 def get_atom_type(h):
11501 r"""get_atom_type(Hierarchy h) -> AtomType"""
11502 return _IMP_atom.get_atom_type(h)
11504 def get_domain_name(h):
11505 r"""get_domain_name(Hierarchy h) -> std::string"""
11506 return _IMP_atom.get_domain_name(h)
11510 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
11511 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
11513 return _IMP_atom.create_excluded_volume_restraint(*args)
11517 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
11518 setup_as_approximation(Hierarchy h, double resolution=-1)
11520 return _IMP_atom.setup_as_approximation(*args)
11521 class _HierarchyTreeVertexIndex(object):
11522 r"""Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
11524 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11525 __repr__ = _swig_repr
11527 def __init__(self):
11528 r"""__init__(_HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
11529 _IMP_atom._HierarchyTreeVertexIndex_swiginit(self, _IMP_atom.new__HierarchyTreeVertexIndex())
11530 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
11533 _IMP_atom._HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
11535 def show_as_graphviz(name, out):
11536 r"""show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
11537 return _IMP_atom.show_as_graphviz(name, out)
11539 def get_vertex_index(g):
11540 r"""get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
11541 return _IMP_atom.get_vertex_index(g)
11544 r"""get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
11545 return _IMP_atom.get_hierarchy_tree(h)
11547 r"""Proxy of C++ IMP::atom::HierarchyGeometry class."""
11549 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11551 def __init__(self, d, resolution=0):
11552 r"""__init__(HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry"""
11553 _IMP_atom.HierarchyGeometry_swiginit(self, _IMP_atom.new_HierarchyGeometry(d, resolution))
11555 def get_version_info(self):
11556 r"""get_version_info(HierarchyGeometry self) -> VersionInfo"""
11557 return _IMP_atom.HierarchyGeometry_get_version_info(self)
11558 __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
11561 r"""__str__(HierarchyGeometry self) -> std::string"""
11562 return _IMP_atom.HierarchyGeometry___str__(self)
11564 def __repr__(self):
11565 r"""__repr__(HierarchyGeometry self) -> std::string"""
11566 return _IMP_atom.HierarchyGeometry___repr__(self)
11570 return _object_cast_to_HierarchyGeometry(o)
11574 _IMP_atom.HierarchyGeometry_swigregister(HierarchyGeometry)
11576 r"""Proxy of C++ IMP::atom::HierarchiesGeometry class."""
11578 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11580 def __init__(self, sc, resolution=-1):
11581 r"""__init__(HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry"""
11582 _IMP_atom.HierarchiesGeometry_swiginit(self, _IMP_atom.new_HierarchiesGeometry(sc, resolution))
11584 def get_version_info(self):
11585 r"""get_version_info(HierarchiesGeometry self) -> VersionInfo"""
11586 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
11587 __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
11590 r"""__str__(HierarchiesGeometry self) -> std::string"""
11591 return _IMP_atom.HierarchiesGeometry___str__(self)
11593 def __repr__(self):
11594 r"""__repr__(HierarchiesGeometry self) -> std::string"""
11595 return _IMP_atom.HierarchiesGeometry___repr__(self)
11599 return _object_cast_to_HierarchiesGeometry(o)
11603 _IMP_atom.HierarchiesGeometry_swigregister(HierarchiesGeometry)
11607 transform(Hierarchy h, Transformation3D tr)
11608 transform(Hierarchy h, Transformation3D tr)
11610 return _IMP_atom.transform(*args)
11611 class DopePairScore(_ADopeBase):
11612 r"""Proxy of C++ IMP::atom::DopePairScore class."""
11614 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11616 def __init__(self, *args):
11618 __init__(DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
11619 __init__(DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
11621 _IMP_atom.DopePairScore_swiginit(self, _IMP_atom.new_DopePairScore(*args))
11624 r"""__str__(DopePairScore self) -> std::string"""
11625 return _IMP_atom.DopePairScore___str__(self)
11627 def __repr__(self):
11628 r"""__repr__(DopePairScore self) -> std::string"""
11629 return _IMP_atom.DopePairScore___repr__(self)
11633 return _object_cast_to_DopePairScore(o)
11635 __swig_destroy__ = _IMP_atom.delete_DopePairScore
11638 _IMP_atom.DopePairScore_swigregister(DopePairScore)
11641 r"""add_dope_score_data(Hierarchy h)"""
11642 return _IMP_atom.add_dope_score_data(h)
11643 class LoopStatisticalPairScore(_ALoopStatisticalBase):
11644 r"""Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
11646 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11648 def __init__(self, *args):
11650 __init__(LoopStatisticalPairScore self, double threshold=std::numeric_limits< double >::max()) -> LoopStatisticalPairScore
11651 __init__(LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
11653 _IMP_atom.LoopStatisticalPairScore_swiginit(self, _IMP_atom.new_LoopStatisticalPairScore(*args))
11656 r"""__str__(LoopStatisticalPairScore self) -> std::string"""
11657 return _IMP_atom.LoopStatisticalPairScore___str__(self)
11659 def __repr__(self):
11660 r"""__repr__(LoopStatisticalPairScore self) -> std::string"""
11661 return _IMP_atom.LoopStatisticalPairScore___repr__(self)
11665 return _object_cast_to_LoopStatisticalPairScore(o)
11667 __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
11670 _IMP_atom.LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
11673 r"""add_loop_statistical_score_data(Hierarchy h)"""
11674 return _IMP_atom.add_loop_statistical_score_data(h)
11675 class OrientedSoapPairScore(_OrientedSoapBase):
11676 r"""Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
11678 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11680 def __init__(self, library):
11681 r"""__init__(OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
11682 _IMP_atom.OrientedSoapPairScore_swiginit(self, _IMP_atom.new_OrientedSoapPairScore(library))
11684 def get_pair_filter(self):
11685 r"""get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
11686 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
11689 r"""__str__(OrientedSoapPairScore self) -> std::string"""
11690 return _IMP_atom.OrientedSoapPairScore___str__(self)
11692 def __repr__(self):
11693 r"""__repr__(OrientedSoapPairScore self) -> std::string"""
11694 return _IMP_atom.OrientedSoapPairScore___repr__(self)
11698 return _object_cast_to_OrientedSoapPairScore(o)
11700 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
11703 _IMP_atom.OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
11705 r"""Proxy of C++ IMP::atom::SameResiduePairFilter class."""
11707 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11709 def __init__(self):
11710 r"""__init__(SameResiduePairFilter self) -> SameResiduePairFilter"""
11711 _IMP_atom.SameResiduePairFilter_swiginit(self, _IMP_atom.new_SameResiduePairFilter())
11713 def do_get_inputs(self, m, pis):
11714 r"""do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
11715 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
11717 def get_value(self, *args):
11719 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
11720 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
11722 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
11724 def get_value_index(self, *args):
11726 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
11727 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
11729 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
11731 def get_version_info(self):
11732 r"""get_version_info(SameResiduePairFilter self) -> VersionInfo"""
11733 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
11734 __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
11737 r"""__str__(SameResiduePairFilter self) -> std::string"""
11738 return _IMP_atom.SameResiduePairFilter___str__(self)
11740 def __repr__(self):
11741 r"""__repr__(SameResiduePairFilter self) -> std::string"""
11742 return _IMP_atom.SameResiduePairFilter___repr__(self)
11746 return _object_cast_to_SameResiduePairFilter(o)
11750 _IMP_atom.SameResiduePairFilter_swigregister(SameResiduePairFilter)
11752 r"""Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
11754 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11756 def __init__(self, m, pis):
11757 r"""__init__(RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
11758 _IMP_atom.RemoveRigidMotionOptimizerState_swiginit(self, _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis))
11760 def set_particles(self, pis):
11761 r"""set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
11762 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
11764 def remove_rigid_motion(self):
11765 r"""remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
11766 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
11768 def get_version_info(self):
11769 r"""get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
11770 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
11771 __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
11774 r"""__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
11775 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
11777 def __repr__(self):
11778 r"""__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
11779 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
11783 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
11787 _IMP_atom.RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
11789 r"""Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
11791 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11793 def __init__(self, pis, temperature, tau):
11794 r"""__init__(BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
11795 _IMP_atom.BerendsenThermostatOptimizerState_swiginit(self, _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau))
11797 def set_particles(self, pis):
11798 r"""set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
11799 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
11801 def get_temperature(self):
11802 r"""get_temperature(BerendsenThermostatOptimizerState self) -> double"""
11803 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
11806 r"""get_tau(BerendsenThermostatOptimizerState self) -> double"""
11807 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
11809 def set_temperature(self, temperature):
11810 r"""set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
11811 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
11813 def set_tau(self, tau):
11814 r"""set_tau(BerendsenThermostatOptimizerState self, double tau)"""
11815 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
11817 def rescale_velocities(self):
11818 r"""rescale_velocities(BerendsenThermostatOptimizerState self)"""
11819 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
11821 def get_version_info(self):
11822 r"""get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
11823 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
11824 __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
11827 r"""__str__(BerendsenThermostatOptimizerState self) -> std::string"""
11828 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
11830 def __repr__(self):
11831 r"""__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
11832 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
11836 return _object_cast_to_BerendsenThermostatOptimizerState(o)
11840 _IMP_atom.BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
11842 r"""Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
11844 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11846 def __init__(self, m, pis, temperature, gamma):
11847 r"""__init__(LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
11848 _IMP_atom.LangevinThermostatOptimizerState_swiginit(self, _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma))
11850 def set_particles(self, pis):
11851 r"""set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
11852 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
11854 def get_temperature(self):
11855 r"""get_temperature(LangevinThermostatOptimizerState self) -> double"""
11856 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
11858 def get_gamma(self):
11859 r"""get_gamma(LangevinThermostatOptimizerState self) -> double"""
11860 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
11862 def set_temperature(self, temperature):
11863 r"""set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
11864 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
11866 def set_gamma(self, gamma):
11867 r"""set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
11868 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
11870 def rescale_velocities(self):
11871 r"""rescale_velocities(LangevinThermostatOptimizerState self)"""
11872 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
11874 def get_version_info(self):
11875 r"""get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
11876 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
11877 __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
11880 r"""__str__(LangevinThermostatOptimizerState self) -> std::string"""
11881 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
11883 def __repr__(self):
11884 r"""__repr__(LangevinThermostatOptimizerState self) -> std::string"""
11885 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
11889 return _object_cast_to_LangevinThermostatOptimizerState(o)
11893 _IMP_atom.LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
11894 class PDBRecord(IMP._Value):
11895 r"""Proxy of C++ IMP::atom::PDBRecord class."""
11897 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11899 def __init__(self):
11900 r"""__init__(PDBRecord self) -> PDBRecord"""
11901 _IMP_atom.PDBRecord_swiginit(self, _IMP_atom.new_PDBRecord())
11903 def get_alt_loc_indicator(self):
11904 r"""get_alt_loc_indicator(PDBRecord self) -> std::string"""
11905 return _IMP_atom.PDBRecord_get_alt_loc_indicator(self)
11907 def get_is_atom(self):
11908 r"""get_is_atom(PDBRecord self) -> bool"""
11909 return _IMP_atom.PDBRecord_get_is_atom(self)
11911 def get_trimmed_atom_name(self):
11912 r"""get_trimmed_atom_name(PDBRecord self) -> std::string"""
11913 return _IMP_atom.PDBRecord_get_trimmed_atom_name(self)
11915 def get_padded_atom_name(self):
11916 r"""get_padded_atom_name(PDBRecord self) -> std::string"""
11917 return _IMP_atom.PDBRecord_get_padded_atom_name(self)
11919 def get_residue_name(self):
11920 r"""get_residue_name(PDBRecord self) -> std::string"""
11921 return _IMP_atom.PDBRecord_get_residue_name(self)
11924 r"""get_chain_id(PDBRecord self) -> std::string"""
11925 return _IMP_atom.PDBRecord_get_chain_id(self)
11927 def get_element(self):
11928 r"""get_element(PDBRecord self) -> std::string"""
11929 return _IMP_atom.PDBRecord_get_element(self)
11931 def show(self, *args):
11932 r"""show(PDBRecord self, _ostream out=std::cout)"""
11933 return _IMP_atom.PDBRecord_show(self, *args)
11936 r"""__str__(PDBRecord self) -> std::string"""
11937 return _IMP_atom.PDBRecord___str__(self)
11939 def __repr__(self):
11940 r"""__repr__(PDBRecord self) -> std::string"""
11941 return _IMP_atom.PDBRecord___repr__(self)
11942 __swig_destroy__ = _IMP_atom.delete_PDBRecord
11945 _IMP_atom.PDBRecord_swigregister(PDBRecord)
11947 r"""Proxy of C++ IMP::atom::PDBSelector class."""
11949 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11951 def __init__(self, name):
11952 r"""__init__(PDBSelector self, std::string name) -> PDBSelector"""
11953 if self.__class__ == PDBSelector:
11957 _IMP_atom.PDBSelector_swiginit(self, _IMP_atom.new_PDBSelector(_self, name))
11959 if self.__class__ != PDBSelector:
11960 _director_objects.register(self)
11965 def get_is_selected(self, record):
11966 r"""get_is_selected(PDBSelector self, PDBRecord record) -> bool"""
11967 return _IMP_atom.PDBSelector_get_is_selected(self, record)
11968 __swig_destroy__ = _IMP_atom.delete_PDBSelector
11971 r"""__str__(PDBSelector self) -> std::string"""
11972 return _IMP_atom.PDBSelector___str__(self)
11974 def __repr__(self):
11975 r"""__repr__(PDBSelector self) -> std::string"""
11976 return _IMP_atom.PDBSelector___repr__(self)
11980 return _object_cast_to_PDBSelector(o)
11983 def get_type_name(self):
11984 return self.__class__.__name__
11985 def do_show(self, out):
11987 def get_version_info(self):
11988 if"IMP::atom" ==
"IMP":
11989 return VersionInfo(self.__module__,
11996 return _object_cast_to_PDBSelector(o)
11999 def __and__(self, s):
12000 return AndPDBSelector(self, s)
12001 def __or__(self, s):
12002 return OrPDBSelector(self, s)
12003 def __xor__(self, s):
12004 return XorPDBSelector(self, s)
12005 def __invert__(self):
12006 return NotPDBSelector(self)
12007 def __sub__(self, s):
12008 return AndPDBSelector(self, NotPDBSelector(s))
12010 def __disown__(self):
12012 _IMP_atom.disown_PDBSelector(self)
12013 return weakref.proxy(self)
12015 def do_destroy(self):
12016 r"""do_destroy(PDBSelector self)"""
12017 return _IMP_atom.PDBSelector_do_destroy(self)
12020 _IMP_atom.PDBSelector_swigregister(PDBSelector)
12021 class NonAlternativePDBSelector(PDBSelector):
12022 r"""Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12024 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12026 def __init__(self, *args):
12027 r"""__init__(NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector"""
12028 _IMP_atom.NonAlternativePDBSelector_swiginit(self, _IMP_atom.new_NonAlternativePDBSelector(*args))
12030 def get_version_info(self):
12031 r"""get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12032 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12033 __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
12036 r"""__str__(NonAlternativePDBSelector self) -> std::string"""
12037 return _IMP_atom.NonAlternativePDBSelector___str__(self)
12039 def __repr__(self):
12040 r"""__repr__(NonAlternativePDBSelector self) -> std::string"""
12041 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12045 return _object_cast_to_NonAlternativePDBSelector(o)
12049 _IMP_atom.NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12050 class ATOMPDBSelector(NonAlternativePDBSelector):
12051 r"""Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12053 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12055 def __init__(self, *args):
12056 r"""__init__(ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector"""
12057 _IMP_atom.ATOMPDBSelector_swiginit(self, _IMP_atom.new_ATOMPDBSelector(*args))
12058 __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
12061 r"""__str__(ATOMPDBSelector self) -> std::string"""
12062 return _IMP_atom.ATOMPDBSelector___str__(self)
12064 def __repr__(self):
12065 r"""__repr__(ATOMPDBSelector self) -> std::string"""
12066 return _IMP_atom.ATOMPDBSelector___repr__(self)
12070 return _object_cast_to_ATOMPDBSelector(o)
12074 _IMP_atom.ATOMPDBSelector_swigregister(ATOMPDBSelector)
12075 class CAlphaPDBSelector(NonAlternativePDBSelector):
12076 r"""Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12078 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12080 def __init__(self, *args):
12081 r"""__init__(CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector"""
12082 _IMP_atom.CAlphaPDBSelector_swiginit(self, _IMP_atom.new_CAlphaPDBSelector(*args))
12083 __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
12086 r"""__str__(CAlphaPDBSelector self) -> std::string"""
12087 return _IMP_atom.CAlphaPDBSelector___str__(self)
12089 def __repr__(self):
12090 r"""__repr__(CAlphaPDBSelector self) -> std::string"""
12091 return _IMP_atom.CAlphaPDBSelector___repr__(self)
12095 return _object_cast_to_CAlphaPDBSelector(o)
12099 _IMP_atom.CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12100 class CBetaPDBSelector(NonAlternativePDBSelector):
12101 r"""Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12103 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12105 def __init__(self, *args):
12106 r"""__init__(CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector"""
12107 _IMP_atom.CBetaPDBSelector_swiginit(self, _IMP_atom.new_CBetaPDBSelector(*args))
12108 __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
12111 r"""__str__(CBetaPDBSelector self) -> std::string"""
12112 return _IMP_atom.CBetaPDBSelector___str__(self)
12114 def __repr__(self):
12115 r"""__repr__(CBetaPDBSelector self) -> std::string"""
12116 return _IMP_atom.CBetaPDBSelector___repr__(self)
12120 return _object_cast_to_CBetaPDBSelector(o)
12124 _IMP_atom.CBetaPDBSelector_swigregister(CBetaPDBSelector)
12125 class AtomTypePDBSelector(PDBSelector):
12126 r"""Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12128 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12130 def __init__(self, *args):
12131 r"""__init__(AtomTypePDBSelector self, IMP::Strings atom_types, std::string name="AtomTypePDBSelector%1%") -> AtomTypePDBSelector"""
12132 _IMP_atom.AtomTypePDBSelector_swiginit(self, _IMP_atom.new_AtomTypePDBSelector(*args))
12134 def get_version_info(self):
12135 r"""get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12136 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12137 __swig_destroy__ = _IMP_atom.delete_AtomTypePDBSelector
12140 r"""__str__(AtomTypePDBSelector self) -> std::string"""
12141 return _IMP_atom.AtomTypePDBSelector___str__(self)
12143 def __repr__(self):
12144 r"""__repr__(AtomTypePDBSelector self) -> std::string"""
12145 return _IMP_atom.AtomTypePDBSelector___repr__(self)
12149 return _object_cast_to_AtomTypePDBSelector(o)
12153 _IMP_atom.AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12154 class ResidueTypePDBSelector(PDBSelector):
12155 r"""Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12157 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12159 def __init__(self, *args):
12160 r"""__init__(ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name="ResidueTypePDBSelector%1%") -> ResidueTypePDBSelector"""
12161 _IMP_atom.ResidueTypePDBSelector_swiginit(self, _IMP_atom.new_ResidueTypePDBSelector(*args))
12163 def get_version_info(self):
12164 r"""get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12165 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12166 __swig_destroy__ = _IMP_atom.delete_ResidueTypePDBSelector
12169 r"""__str__(ResidueTypePDBSelector self) -> std::string"""
12170 return _IMP_atom.ResidueTypePDBSelector___str__(self)
12172 def __repr__(self):
12173 r"""__repr__(ResidueTypePDBSelector self) -> std::string"""
12174 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12178 return _object_cast_to_ResidueTypePDBSelector(o)
12182 _IMP_atom.ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12183 class CPDBSelector(NonAlternativePDBSelector):
12184 r"""Proxy of C++ IMP::atom::CPDBSelector class."""
12186 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12188 def __init__(self, *args):
12189 r"""__init__(CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector"""
12190 _IMP_atom.CPDBSelector_swiginit(self, _IMP_atom.new_CPDBSelector(*args))
12191 __swig_destroy__ = _IMP_atom.delete_CPDBSelector
12194 r"""__str__(CPDBSelector self) -> std::string"""
12195 return _IMP_atom.CPDBSelector___str__(self)
12197 def __repr__(self):
12198 r"""__repr__(CPDBSelector self) -> std::string"""
12199 return _IMP_atom.CPDBSelector___repr__(self)
12203 return _object_cast_to_CPDBSelector(o)
12207 _IMP_atom.CPDBSelector_swigregister(CPDBSelector)
12208 class NPDBSelector(NonAlternativePDBSelector):
12209 r"""Proxy of C++ IMP::atom::NPDBSelector class."""
12211 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12213 def __init__(self, *args):
12214 r"""__init__(NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector"""
12215 _IMP_atom.NPDBSelector_swiginit(self, _IMP_atom.new_NPDBSelector(*args))
12216 __swig_destroy__ = _IMP_atom.delete_NPDBSelector
12219 r"""__str__(NPDBSelector self) -> std::string"""
12220 return _IMP_atom.NPDBSelector___str__(self)
12222 def __repr__(self):
12223 r"""__repr__(NPDBSelector self) -> std::string"""
12224 return _IMP_atom.NPDBSelector___repr__(self)
12228 return _object_cast_to_NPDBSelector(o)
12232 _IMP_atom.NPDBSelector_swigregister(NPDBSelector)
12233 class AllPDBSelector(PDBSelector):
12234 r"""Proxy of C++ IMP::atom::AllPDBSelector class."""
12236 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12238 def __init__(self, *args):
12239 r"""__init__(AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector"""
12240 _IMP_atom.AllPDBSelector_swiginit(self, _IMP_atom.new_AllPDBSelector(*args))
12242 def get_version_info(self):
12243 r"""get_version_info(AllPDBSelector self) -> VersionInfo"""
12244 return _IMP_atom.AllPDBSelector_get_version_info(self)
12245 __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
12248 r"""__str__(AllPDBSelector self) -> std::string"""
12249 return _IMP_atom.AllPDBSelector___str__(self)
12251 def __repr__(self):
12252 r"""__repr__(AllPDBSelector self) -> std::string"""
12253 return _IMP_atom.AllPDBSelector___repr__(self)
12257 return _object_cast_to_AllPDBSelector(o)
12261 _IMP_atom.AllPDBSelector_swigregister(AllPDBSelector)
12262 class ChainPDBSelector(NonAlternativePDBSelector):
12263 r"""Proxy of C++ IMP::atom::ChainPDBSelector class."""
12265 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12266 __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
12268 def __init__(self, *args):
12270 __init__(ChainPDBSelector self, IMP::Strings chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
12271 __init__(ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector
12273 _IMP_atom.ChainPDBSelector_swiginit(self, _IMP_atom.new_ChainPDBSelector(*args))
12276 r"""__str__(ChainPDBSelector self) -> std::string"""
12277 return _IMP_atom.ChainPDBSelector___str__(self)
12279 def __repr__(self):
12280 r"""__repr__(ChainPDBSelector self) -> std::string"""
12281 return _IMP_atom.ChainPDBSelector___repr__(self)
12285 return _object_cast_to_ChainPDBSelector(o)
12289 _IMP_atom.ChainPDBSelector_swigregister(ChainPDBSelector)
12290 class WaterPDBSelector(NonAlternativePDBSelector):
12291 r"""Proxy of C++ IMP::atom::WaterPDBSelector class."""
12293 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12295 def __init__(self, *args):
12296 r"""__init__(WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector"""
12297 _IMP_atom.WaterPDBSelector_swiginit(self, _IMP_atom.new_WaterPDBSelector(*args))
12298 __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
12301 r"""__str__(WaterPDBSelector self) -> std::string"""
12302 return _IMP_atom.WaterPDBSelector___str__(self)
12304 def __repr__(self):
12305 r"""__repr__(WaterPDBSelector self) -> std::string"""
12306 return _IMP_atom.WaterPDBSelector___repr__(self)
12310 return _object_cast_to_WaterPDBSelector(o)
12314 _IMP_atom.WaterPDBSelector_swigregister(WaterPDBSelector)
12315 class HydrogenPDBSelector(NonAlternativePDBSelector):
12316 r"""Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12318 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12320 def __init__(self, *args):
12321 r"""__init__(HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector"""
12322 _IMP_atom.HydrogenPDBSelector_swiginit(self, _IMP_atom.new_HydrogenPDBSelector(*args))
12323 __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
12326 r"""__str__(HydrogenPDBSelector self) -> std::string"""
12327 return _IMP_atom.HydrogenPDBSelector___str__(self)
12329 def __repr__(self):
12330 r"""__repr__(HydrogenPDBSelector self) -> std::string"""
12331 return _IMP_atom.HydrogenPDBSelector___repr__(self)
12335 return _object_cast_to_HydrogenPDBSelector(o)
12339 _IMP_atom.HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12340 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12341 r"""Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12343 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12344 __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
12346 def __init__(self, *args):
12348 __init__(NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12349 __init__(NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12351 _IMP_atom.NonWaterNonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args))
12354 r"""__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12355 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12357 def __repr__(self):
12358 r"""__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12359 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12363 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12367 _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12368 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12369 r"""Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12371 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12372 __swig_destroy__ = _IMP_atom.delete_NonHydrogenPDBSelector
12374 def __init__(self, *args):
12376 __init__(NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12377 __init__(NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12379 _IMP_atom.NonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonHydrogenPDBSelector(*args))
12382 r"""__str__(NonHydrogenPDBSelector self) -> std::string"""
12383 return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12385 def __repr__(self):
12386 r"""__repr__(NonHydrogenPDBSelector self) -> std::string"""
12387 return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12391 return _object_cast_to_NonHydrogenPDBSelector(o)
12395 _IMP_atom.NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12396 class NonWaterPDBSelector(NonAlternativePDBSelector):
12397 r"""Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12399 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12400 __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
12402 def __init__(self, *args):
12404 __init__(NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12405 __init__(NonWaterPDBSelector self) -> NonWaterPDBSelector
12407 _IMP_atom.NonWaterPDBSelector_swiginit(self, _IMP_atom.new_NonWaterPDBSelector(*args))
12410 r"""__str__(NonWaterPDBSelector self) -> std::string"""
12411 return _IMP_atom.NonWaterPDBSelector___str__(self)
12413 def __repr__(self):
12414 r"""__repr__(NonWaterPDBSelector self) -> std::string"""
12415 return _IMP_atom.NonWaterPDBSelector___repr__(self)
12419 return _object_cast_to_NonWaterPDBSelector(o)
12423 _IMP_atom.NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12424 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12425 r"""Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12427 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12429 def __init__(self, *args):
12430 r"""__init__(BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector"""
12431 _IMP_atom.BackbonePDBSelector_swiginit(self, _IMP_atom.new_BackbonePDBSelector(*args))
12432 __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
12435 r"""__str__(BackbonePDBSelector self) -> std::string"""
12436 return _IMP_atom.BackbonePDBSelector___str__(self)
12438 def __repr__(self):
12439 r"""__repr__(BackbonePDBSelector self) -> std::string"""
12440 return _IMP_atom.BackbonePDBSelector___repr__(self)
12444 return _object_cast_to_BackbonePDBSelector(o)
12448 _IMP_atom.BackbonePDBSelector_swigregister(BackbonePDBSelector)
12449 class PPDBSelector(NonAlternativePDBSelector):
12450 r"""Proxy of C++ IMP::atom::PPDBSelector class."""
12452 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12454 def __init__(self, *args):
12455 r"""__init__(PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector"""
12456 _IMP_atom.PPDBSelector_swiginit(self, _IMP_atom.new_PPDBSelector(*args))
12457 __swig_destroy__ = _IMP_atom.delete_PPDBSelector
12460 r"""__str__(PPDBSelector self) -> std::string"""
12461 return _IMP_atom.PPDBSelector___str__(self)
12463 def __repr__(self):
12464 r"""__repr__(PPDBSelector self) -> std::string"""
12465 return _IMP_atom.PPDBSelector___repr__(self)
12469 return _object_cast_to_PPDBSelector(o)
12473 _IMP_atom.PPDBSelector_swigregister(PPDBSelector)
12474 class AndPDBSelector(PDBSelector):
12475 r"""Proxy of C++ IMP::atom::AndPDBSelector class."""
12477 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12479 def get_version_info(self):
12480 r"""get_version_info(AndPDBSelector self) -> VersionInfo"""
12481 return _IMP_atom.AndPDBSelector_get_version_info(self)
12482 __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
12484 def __init__(self, a, b):
12485 r"""__init__(AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
12486 _IMP_atom.AndPDBSelector_swiginit(self, _IMP_atom.new_AndPDBSelector(a, b))
12489 r"""__str__(AndPDBSelector self) -> std::string"""
12490 return _IMP_atom.AndPDBSelector___str__(self)
12492 def __repr__(self):
12493 r"""__repr__(AndPDBSelector self) -> std::string"""
12494 return _IMP_atom.AndPDBSelector___repr__(self)
12498 return _object_cast_to_AndPDBSelector(o)
12502 _IMP_atom.AndPDBSelector_swigregister(AndPDBSelector)
12503 class OrPDBSelector(PDBSelector):
12504 r"""Proxy of C++ IMP::atom::OrPDBSelector class."""
12506 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12508 def get_version_info(self):
12509 r"""get_version_info(OrPDBSelector self) -> VersionInfo"""
12510 return _IMP_atom.OrPDBSelector_get_version_info(self)
12511 __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
12513 def __init__(self, a, b):
12514 r"""__init__(OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
12515 _IMP_atom.OrPDBSelector_swiginit(self, _IMP_atom.new_OrPDBSelector(a, b))
12518 r"""__str__(OrPDBSelector self) -> std::string"""
12519 return _IMP_atom.OrPDBSelector___str__(self)
12521 def __repr__(self):
12522 r"""__repr__(OrPDBSelector self) -> std::string"""
12523 return _IMP_atom.OrPDBSelector___repr__(self)
12527 return _object_cast_to_OrPDBSelector(o)
12531 _IMP_atom.OrPDBSelector_swigregister(OrPDBSelector)
12532 class XorPDBSelector(PDBSelector):
12533 r"""Proxy of C++ IMP::atom::XorPDBSelector class."""
12535 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12537 def get_version_info(self):
12538 r"""get_version_info(XorPDBSelector self) -> VersionInfo"""
12539 return _IMP_atom.XorPDBSelector_get_version_info(self)
12540 __swig_destroy__ = _IMP_atom.delete_XorPDBSelector
12542 def __init__(self, a, b):
12543 r"""__init__(XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
12544 _IMP_atom.XorPDBSelector_swiginit(self, _IMP_atom.new_XorPDBSelector(a, b))
12547 r"""__str__(XorPDBSelector self) -> std::string"""
12548 return _IMP_atom.XorPDBSelector___str__(self)
12550 def __repr__(self):
12551 r"""__repr__(XorPDBSelector self) -> std::string"""
12552 return _IMP_atom.XorPDBSelector___repr__(self)
12556 return _object_cast_to_XorPDBSelector(o)
12560 _IMP_atom.XorPDBSelector_swigregister(XorPDBSelector)
12561 class NotPDBSelector(PDBSelector):
12562 r"""Proxy of C++ IMP::atom::NotPDBSelector class."""
12564 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12566 def get_version_info(self):
12567 r"""get_version_info(NotPDBSelector self) -> VersionInfo"""
12568 return _IMP_atom.NotPDBSelector_get_version_info(self)
12569 __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
12571 def __init__(self, a):
12572 r"""__init__(NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
12573 _IMP_atom.NotPDBSelector_swiginit(self, _IMP_atom.new_NotPDBSelector(a))
12576 r"""__str__(NotPDBSelector self) -> std::string"""
12577 return _IMP_atom.NotPDBSelector___str__(self)
12579 def __repr__(self):
12580 r"""__repr__(NotPDBSelector self) -> std::string"""
12581 return _IMP_atom.NotPDBSelector___repr__(self)
12585 return _object_cast_to_NotPDBSelector(o)
12589 _IMP_atom.NotPDBSelector_swigregister(NotPDBSelector)
12591 def get_default_pdb_selector():
12592 r"""get_default_pdb_selector() -> PDBSelector"""
12593 return _IMP_atom.get_default_pdb_selector()
12597 read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool no_radii=False) -> Hierarchy
12598 read_pdb(TextInput input, int model, Hierarchy h)
12600 return _IMP_atom.read_pdb(*args)
12603 r"""read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12604 return _IMP_atom.read_multimodel_pdb(*args)
12607 r"""write_pdb(Selection mhd, TextOutput out, unsigned int model=1)"""
12608 return _IMP_atom.write_pdb(mhd, out, model)
12611 r"""write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)"""
12612 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
12615 r"""write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
12616 return _IMP_atom.write_multimodel_pdb(mhd, out)
12618 def get_pdb_string(*args):
12619 r"""get_pdb_string(Vector3D v, int index=-1, AtomType at=AT_CA, ResidueType rt=ALA, char chain=' ', int res_index=1, char res_icode=' ', double occupancy=1.00, double tempFactor=0.00, IMP::atom::Element e=C) -> std::string"""
12620 return _IMP_atom.get_pdb_string(*args)
12622 def get_pdb_conect_record_string(arg1, arg2):
12623 r"""get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
12624 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
12626 r"""Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
12628 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12630 def __init__(self, *args):
12632 __init__(WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
12633 __init__(WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
12634 __init__(WritePDBOptimizerState self) -> WritePDBOptimizerState
12636 _IMP_atom.WritePDBOptimizerState_swiginit(self, _IMP_atom.new_WritePDBOptimizerState(*args))
12638 def get_version_info(self):
12639 r"""get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
12640 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
12641 __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
12644 r"""__str__(WritePDBOptimizerState self) -> std::string"""
12645 return _IMP_atom.WritePDBOptimizerState___str__(self)
12647 def __repr__(self):
12648 r"""__repr__(WritePDBOptimizerState self) -> std::string"""
12649 return _IMP_atom.WritePDBOptimizerState___repr__(self)
12653 return _object_cast_to_WritePDBOptimizerState(o)
12656 def _get_as_binary(self):
12657 r"""_get_as_binary(WritePDBOptimizerState self) -> PyObject *"""
12658 return _IMP_atom.WritePDBOptimizerState__get_as_binary(self)
12660 def _set_from_binary(self, p):
12661 r"""_set_from_binary(WritePDBOptimizerState self, PyObject * p)"""
12662 return _IMP_atom.WritePDBOptimizerState__set_from_binary(self, p)
12664 def __getstate__(self):
12665 p = self._get_as_binary()
12666 if len(self.__dict__) > 1:
12667 d = self.__dict__.copy()
12672 def __setstate__(self, p):
12673 if not hasattr(self,
'this'):
12675 if isinstance(p, tuple):
12677 self.__dict__.update(d)
12678 return self._set_from_binary(p)
12682 _IMP_atom.WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
12685 r"""read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12686 return _IMP_atom.read_multimodel_mmcif(*args)
12689 r"""read_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
12690 return _IMP_atom.read_mmcif(*args)
12693 r"""read_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
12694 return _IMP_atom.read_pdb_or_mmcif(*args)
12697 r"""read_multimodel_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12698 return _IMP_atom.read_multimodel_pdb_or_mmcif(*args)
12701 r"""get_kt(double T) -> double"""
12702 return _IMP_atom.get_kt(T)
12704 r"""Proxy of C++ IMP::atom::CAAngleRestraint class."""
12706 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12708 def __init__(self, m, p1, p2, p3, phi0, score):
12709 r"""__init__(CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
12710 _IMP_atom.CAAngleRestraint_swiginit(self, _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score))
12712 def do_get_inputs(self):
12713 r"""do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
12714 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
12716 def get_version_info(self):
12717 r"""get_version_info(CAAngleRestraint self) -> VersionInfo"""
12718 return _IMP_atom.CAAngleRestraint_get_version_info(self)
12719 __swig_destroy__ = _IMP_atom.delete_CAAngleRestraint
12722 r"""__str__(CAAngleRestraint self) -> std::string"""
12723 return _IMP_atom.CAAngleRestraint___str__(self)
12725 def __repr__(self):
12726 r"""__repr__(CAAngleRestraint self) -> std::string"""
12727 return _IMP_atom.CAAngleRestraint___repr__(self)
12731 return _object_cast_to_CAAngleRestraint(o)
12735 _IMP_atom.CAAngleRestraint_swigregister(CAAngleRestraint)
12737 r"""Proxy of C++ IMP::atom::CADihedralRestraint class."""
12739 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12741 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
12742 r"""__init__(CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
12743 _IMP_atom.CADihedralRestraint_swiginit(self, _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score))
12745 def do_get_inputs(self):
12746 r"""do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
12747 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
12749 def get_version_info(self):
12750 r"""get_version_info(CADihedralRestraint self) -> VersionInfo"""
12751 return _IMP_atom.CADihedralRestraint_get_version_info(self)
12752 __swig_destroy__ = _IMP_atom.delete_CADihedralRestraint
12755 r"""__str__(CADihedralRestraint self) -> std::string"""
12756 return _IMP_atom.CADihedralRestraint___str__(self)
12758 def __repr__(self):
12759 r"""__repr__(CADihedralRestraint self) -> std::string"""
12760 return _IMP_atom.CADihedralRestraint___repr__(self)
12764 return _object_cast_to_CADihedralRestraint(o)
12768 _IMP_atom.CADihedralRestraint_swigregister(CADihedralRestraint)
12770 r"""Proxy of C++ IMP::atom::StructureSource class."""
12772 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12774 def get_source_id(self):
12775 r"""get_source_id(StructureSource self) -> std::string"""
12776 return _IMP_atom.StructureSource_get_source_id(self)
12778 def get_source_chain_id(self):
12779 r"""get_source_chain_id(StructureSource self) -> std::string"""
12780 return _IMP_atom.StructureSource_get_source_chain_id(self)
12782 def set_source_id(self, source_id):
12783 r"""set_source_id(StructureSource self, std::string source_id)"""
12784 return _IMP_atom.StructureSource_set_source_id(self, source_id)
12786 def set_source_chain_id(self, source_chain_id):
12787 r"""set_source_chain_id(StructureSource self, std::string source_chain_id)"""
12788 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
12790 def __init__(self, *args):
12792 __init__(StructureSource self) -> StructureSource
12793 __init__(StructureSource self, Model m, ParticleIndex id) -> StructureSource
12794 __init__(StructureSource self, _ParticleAdaptor d) -> StructureSource
12796 _IMP_atom.StructureSource_swiginit(self, _IMP_atom.new_StructureSource(*args))
12799 def get_is_setup(*args):
12801 get_is_setup(Model m, ParticleIndex pi) -> bool
12802 get_is_setup(_ParticleAdaptor p) -> bool
12804 return _IMP_atom.StructureSource_get_is_setup(*args)
12806 def show(self, *args):
12807 r"""show(StructureSource self, _ostream out=std::cout)"""
12808 return _IMP_atom.StructureSource_show(self, *args)
12811 def setup_particle(*args):
12813 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
12814 setup_particle(_ParticleAdaptor pa, std::string source_id, std::string source_chain_id) -> StructureSource
12816 return _IMP_atom.StructureSource_setup_particle(*args)
12818 def add_attribute(self, *args):
12820 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
12821 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
12822 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
12823 add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
12824 add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
12825 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
12826 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
12827 add_attribute(StructureSource self, ObjectKey a0, Object a1)
12828 add_attribute(StructureSource self, SparseFloatKey a0, IMP::Float a1)
12829 add_attribute(StructureSource self, SparseIntKey a0, IMP::Int a1)
12830 add_attribute(StructureSource self, SparseStringKey a0, IMP::String a1)
12831 add_attribute(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
12833 return _IMP_atom.StructureSource_add_attribute(self, *args)
12835 def get_value(self, *args):
12837 get_value(StructureSource self, FloatKey a0) -> IMP::Float
12838 get_value(StructureSource self, IntKey a0) -> IMP::Int
12839 get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
12840 get_value(StructureSource self, IntsKey a0) -> IMP::Ints
12841 get_value(StructureSource self, StringKey a0) -> IMP::String
12842 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
12843 get_value(StructureSource self, ObjectKey a0) -> Object
12844 get_value(StructureSource self, SparseFloatKey a0) -> IMP::Float
12845 get_value(StructureSource self, SparseIntKey a0) -> IMP::Int
12846 get_value(StructureSource self, SparseStringKey a0) -> IMP::String
12847 get_value(StructureSource self, SparseParticleIndexKey a0) -> ParticleIndex
12849 return _IMP_atom.StructureSource_get_value(self, *args)
12851 def set_value(self, *args):
12853 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
12854 set_value(StructureSource self, IntKey a0, IMP::Int a1)
12855 set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
12856 set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
12857 set_value(StructureSource self, StringKey a0, IMP::String a1)
12858 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
12859 set_value(StructureSource self, ObjectKey a0, Object a1)
12860 set_value(StructureSource self, SparseFloatKey a0, IMP::Float a1)
12861 set_value(StructureSource self, SparseIntKey a0, IMP::Int a1)
12862 set_value(StructureSource self, SparseStringKey a0, IMP::String a1)
12863 set_value(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
12865 return _IMP_atom.StructureSource_set_value(self, *args)
12867 def remove_attribute(self, *args):
12869 remove_attribute(StructureSource self, FloatKey a0)
12870 remove_attribute(StructureSource self, IntKey a0)
12871 remove_attribute(StructureSource self, FloatsKey a0)
12872 remove_attribute(StructureSource self, IntsKey a0)
12873 remove_attribute(StructureSource self, StringKey a0)
12874 remove_attribute(StructureSource self, ParticleIndexKey a0)
12875 remove_attribute(StructureSource self, ObjectKey a0)
12876 remove_attribute(StructureSource self, SparseFloatKey a0)
12877 remove_attribute(StructureSource self, SparseIntKey a0)
12878 remove_attribute(StructureSource self, SparseStringKey a0)
12879 remove_attribute(StructureSource self, SparseParticleIndexKey a0)
12881 return _IMP_atom.StructureSource_remove_attribute(self, *args)
12883 def has_attribute(self, *args):
12885 has_attribute(StructureSource self, FloatKey a0) -> bool
12886 has_attribute(StructureSource self, IntKey a0) -> bool
12887 has_attribute(StructureSource self, FloatsKey a0) -> bool
12888 has_attribute(StructureSource self, IntsKey a0) -> bool
12889 has_attribute(StructureSource self, StringKey a0) -> bool
12890 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
12891 has_attribute(StructureSource self, ObjectKey a0) -> bool
12892 has_attribute(StructureSource self, SparseFloatKey a0) -> bool
12893 has_attribute(StructureSource self, SparseIntKey a0) -> bool
12894 has_attribute(StructureSource self, SparseStringKey a0) -> bool
12895 has_attribute(StructureSource self, SparseParticleIndexKey a0) -> bool
12897 return _IMP_atom.StructureSource_has_attribute(self, *args)
12899 def get_derivative(self, a0):
12900 r"""get_derivative(StructureSource self, FloatKey a0) -> double"""
12901 return _IMP_atom.StructureSource_get_derivative(self, a0)
12903 def get_name(self):
12904 r"""get_name(StructureSource self) -> std::string"""
12905 return _IMP_atom.StructureSource_get_name(self)
12907 def clear_caches(self):
12908 r"""clear_caches(StructureSource self)"""
12909 return _IMP_atom.StructureSource_clear_caches(self)
12911 def set_name(self, a0):
12912 r"""set_name(StructureSource self, std::string a0)"""
12913 return _IMP_atom.StructureSource_set_name(self, a0)
12916 r"""set_check_level(StructureSource self, IMP::CheckLevel a0)"""
12917 return _IMP_atom.StructureSource_set_check_level(self, a0)
12919 def add_to_derivative(self, a0, a1, a2):
12920 r"""add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
12921 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
12923 def set_is_optimized(self, a0, a1):
12924 r"""set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
12925 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
12927 def get_is_optimized(self, a0):
12928 r"""get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
12929 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
12932 r"""get_check_level(StructureSource self) -> IMP::CheckLevel"""
12933 return _IMP_atom.StructureSource_get_check_level(self)
12935 def __eq__(self, *args):
12937 __eq__(StructureSource self, StructureSource o) -> bool
12938 __eq__(StructureSource self, Particle d) -> bool
12940 return _IMP_atom.StructureSource___eq__(self, *args)
12942 def __ne__(self, *args):
12944 __ne__(StructureSource self, StructureSource o) -> bool
12945 __ne__(StructureSource self, Particle d) -> bool
12947 return _IMP_atom.StructureSource___ne__(self, *args)
12949 def __le__(self, *args):
12951 __le__(StructureSource self, StructureSource o) -> bool
12952 __le__(StructureSource self, Particle d) -> bool
12954 return _IMP_atom.StructureSource___le__(self, *args)
12956 def __lt__(self, *args):
12958 __lt__(StructureSource self, StructureSource o) -> bool
12959 __lt__(StructureSource self, Particle d) -> bool
12961 return _IMP_atom.StructureSource___lt__(self, *args)
12963 def __ge__(self, *args):
12965 __ge__(StructureSource self, StructureSource o) -> bool
12966 __ge__(StructureSource self, Particle d) -> bool
12968 return _IMP_atom.StructureSource___ge__(self, *args)
12970 def __gt__(self, *args):
12972 __gt__(StructureSource self, StructureSource o) -> bool
12973 __gt__(StructureSource self, Particle d) -> bool
12975 return _IMP_atom.StructureSource___gt__(self, *args)
12977 def __hash__(self):
12978 r"""__hash__(StructureSource self) -> std::size_t"""
12979 return _IMP_atom.StructureSource___hash__(self)
12982 r"""__str__(StructureSource self) -> std::string"""
12983 return _IMP_atom.StructureSource___str__(self)
12985 def __repr__(self):
12986 r"""__repr__(StructureSource self) -> std::string"""
12987 return _IMP_atom.StructureSource___repr__(self)
12989 def _get_as_binary(self):
12990 r"""_get_as_binary(StructureSource self) -> PyObject *"""
12991 return _IMP_atom.StructureSource__get_as_binary(self)
12993 def _set_from_binary(self, p):
12994 r"""_set_from_binary(StructureSource self, PyObject * p)"""
12995 return _IMP_atom.StructureSource__set_from_binary(self, p)
12997 def __getstate__(self):
12998 p = self._get_as_binary()
12999 if len(self.__dict__) > 1:
13000 d = self.__dict__.copy()
13005 def __setstate__(self, p):
13006 if not hasattr(self,
'this'):
13008 if isinstance(p, tuple):
13010 self.__dict__.update(d)
13011 return self._set_from_binary(p)
13013 __swig_destroy__ = _IMP_atom.delete_StructureSource
13016 _IMP_atom.StructureSource_swigregister(StructureSource)
13018 def __lshift__(*args):
13020 __lshift__(_ostream out, Bonded n) -> _ostream
13021 __lshift__(_ostream out, Bond n) -> _ostream
13022 __lshift__(_ostream out, Hierarchy n) -> _ostream
13023 __lshift__(_ostream out, Angle n) -> _ostream
13024 __lshift__(_ostream out, Dihedral n) -> _ostream
13025 __lshift__(_ostream out, CenterOfMass n) -> _ostream
13026 __lshift__(_ostream out, Diffusion n) -> _ostream
13027 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13028 __lshift__(_ostream out, TAMDParticle n) -> _ostream
13029 __lshift__(_ostream out, Charged n) -> _ostream
13030 __lshift__(_ostream out, Domain n) -> _ostream
13031 __lshift__(_ostream out, LennardJones n) -> _ostream
13032 __lshift__(_ostream out, Fragment n) -> _ostream
13033 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13034 __lshift__(_ostream out, Atom n) -> _ostream
13035 __lshift__(_ostream out, Residue n) -> _ostream
13036 __lshift__(_ostream out, Representation n) -> _ostream
13037 __lshift__(_ostream out, State n) -> _ostream
13038 __lshift__(_ostream out, Molecule n) -> _ostream
13039 __lshift__(_ostream out, Copy n) -> _ostream
13040 __lshift__(_ostream out, Chain n) -> _ostream
13041 __lshift__(_ostream out, StructureSource n) -> _ostream
13043 return _IMP_atom.__lshift__(*args)
13045 r"""Proxy of C++ IMP::atom::HelixRestraint class."""
13047 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13049 def __init__(self, rs, ideal=True):
13050 r"""__init__(HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint"""
13051 _IMP_atom.HelixRestraint_swiginit(self, _IMP_atom.new_HelixRestraint(rs, ideal))
13053 def get_number_of_bonds(self):
13054 r"""get_number_of_bonds(HelixRestraint self) -> int"""
13055 return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13057 def get_number_of_dihedrals(self):
13058 r"""get_number_of_dihedrals(HelixRestraint self) -> int"""
13059 return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13061 def do_get_inputs(self):
13062 r"""do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13063 return _IMP_atom.HelixRestraint_do_get_inputs(self)
13065 def get_version_info(self):
13066 r"""get_version_info(HelixRestraint self) -> VersionInfo"""
13067 return _IMP_atom.HelixRestraint_get_version_info(self)
13068 __swig_destroy__ = _IMP_atom.delete_HelixRestraint
13071 r"""__str__(HelixRestraint self) -> std::string"""
13072 return _IMP_atom.HelixRestraint___str__(self)
13074 def __repr__(self):
13075 r"""__repr__(HelixRestraint self) -> std::string"""
13076 return _IMP_atom.HelixRestraint___repr__(self)
13080 return _object_cast_to_HelixRestraint(o)
13084 _IMP_atom.HelixRestraint_swigregister(HelixRestraint)
13087 r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
13088 return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
13091 r"""show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream"""
13092 return _IMP_atom.show_molecular_hierarchy(*args)
13093 class CHARMMBond(object):
13094 r"""Proxy of C++ IMP::atom::CHARMMConnection< 2 > class."""
13096 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13097 __repr__ = _swig_repr
13099 def __init__(self, atoms):
13100 r"""__init__(CHARMMBond self, IMP::Strings const & atoms) -> CHARMMBond"""
13101 _IMP_atom.CHARMMBond_swiginit(self, _IMP_atom.new_CHARMMBond(atoms))
13103 def get_endpoint(self, i):
13104 r"""get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13105 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13107 def get_contains_atom(self, name):
13108 r"""get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13109 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13111 def show(self, *args):
13112 r"""show(CHARMMBond self, _ostream out=std::cout)"""
13113 return _IMP_atom.CHARMMBond_show(self, *args)
13114 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13117 _IMP_atom.CHARMMBond_swigregister(CHARMMBond)
13118 class CHARMMAngle(object):
13119 r"""Proxy of C++ IMP::atom::CHARMMConnection< 3 > class."""
13121 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13122 __repr__ = _swig_repr
13124 def __init__(self, atoms):
13125 r"""__init__(CHARMMAngle self, IMP::Strings const & atoms) -> CHARMMAngle"""
13126 _IMP_atom.CHARMMAngle_swiginit(self, _IMP_atom.new_CHARMMAngle(atoms))
13128 def get_endpoint(self, i):
13129 r"""get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13130 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13132 def get_contains_atom(self, name):
13133 r"""get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13134 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13136 def show(self, *args):
13137 r"""show(CHARMMAngle self, _ostream out=std::cout)"""
13138 return _IMP_atom.CHARMMAngle_show(self, *args)
13139 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13142 _IMP_atom.CHARMMAngle_swigregister(CHARMMAngle)
13144 def _get_native_overlap_cpp(m1, m2, threshold):
13145 r"""_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13146 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13148 def _get_drmsd_cpp(m0, m1):
13149 r"""_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13150 return _IMP_atom._get_drmsd_cpp(m0, m1)
13152 def _get_drmsd_Q_cpp(m0, m1, threshold):
13153 r"""_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13154 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13156 def _get_drms_cpp(m1, m2):
13157 r"""_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13158 return _IMP_atom._get_drms_cpp(m1, m2)
13160 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13161 r"""_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, IMP::IntRanges const & ranges) -> double"""
13162 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13165 va= [IMP.algebra.get_vector(x)
for x
in a]
13166 vb= [IMP.algebra.get_vector(x)
for x
in b]
13167 return _get_native_overlap_cpp(va, vb, d)
13170 va= [IMP.algebra.get_vector(x)
for x
in a]
13171 vb= [IMP.algebra.get_vector(x)
for x
in b]
13172 return _get_drmsd_cpp(va, vb)
13175 va= [IMP.algebra.get_vector(x)
for x
in a]
13176 vb= [IMP.algebra.get_vector(x)
for x
in b]
13177 return _get_drms_cpp(va, vb)
13180 va= [IMP.algebra.get_vector(x)
for x
in a]
13181 vb= [IMP.algebra.get_vector(x)
for x
in b]
13182 return _get_drmsd_Q_cpp(va, vb, t)
13185 va= [IMP.algebra.get_vector(x)
for x
in a]
13186 vb= [IMP.algebra.get_vector(x)
for x
in b]
13188 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13193 r"""get_module_version() -> std::string const"""
13194 return _IMP_atom.get_module_version()
13197 r"""get_example_path(std::string fname) -> std::string"""
13198 return _IMP_atom.get_example_path(fname)
13201 r"""get_data_path(std::string fname) -> std::string"""
13202 return _IMP_atom.get_data_path(fname)
13204 from .
import _version_check
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Hierarchy read_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB or mmCIF file.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
double get_einstein_rotational_diffusion_coefficient(double r, double temp=-1)
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the mmCIF file.
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
CheckLevel get_check_level()
Get the current audit mode.
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square)
Convert spring constant from kcal/mol/A^2 to femtonewton/A.
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Add vdW radius from given force field.
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
ParticleIndexQuads get_chi_dihedral_particle_indexes(Residue rd)
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
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.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
double get_kd(double na, double nb, double nab, double volume)
double get_diffusion_angle(double D, double dtfs)
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &orientations, double dt)
Base class for all optimizers.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
A decorator for a particle with x,y,z coordinates.
void add_loop_statistical_score_data(atom::Hierarchy h)
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
Hierarchies read_multimodel_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB or mmCIF file.
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom)
Convert force from kcal/mol/A to femtonewtons.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
Add bonds using definitions from given force field parameters.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
double get_diffusion_length(double D, double t)
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
A decorator for a particle with x,y,z coordinates and a radius.