14 from sys
import version_info
as _swig_python_version_info
18 import builtins
as __builtin__
24 strthis =
"proxy of " + self.this.__repr__()
25 except __builtin__.Exception:
27 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
30 def _swig_setattr_nondynamic_instance_variable(set):
31 def set_instance_attr(self, name, value):
33 set(self, name, value)
34 elif name ==
"thisown":
36 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
37 set(self, name, value)
39 raise AttributeError(
"You cannot add instance attributes to %s" % self)
40 return set_instance_attr
43 def _swig_setattr_nondynamic_class_variable(set):
44 def set_class_attr(cls, name, value):
45 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
48 raise AttributeError(
"You cannot add class attributes to %s" % cls)
52 def _swig_add_metaclass(metaclass):
53 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
59 class _SwigNonDynamicMeta(type):
60 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
66 class IMP_ATOM_SwigPyIterator(object):
67 r"""Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
69 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
71 def __init__(self, *args, **kwargs):
72 raise AttributeError(
"No constructor defined - class is abstract")
74 __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
77 r"""value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
78 return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
81 r"""incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
82 return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
85 r"""decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
86 return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
88 def distance(self, x):
89 r"""distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
90 return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
93 r"""equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
94 return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
97 r"""copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
98 return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
101 r"""next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
102 return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
105 r"""__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
106 return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
109 r"""previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
110 return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
112 def advance(self, n):
113 r"""advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
114 return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
117 r"""__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
118 return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
121 r"""__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
122 return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
124 def __iadd__(self, n):
125 r"""__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
126 return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
128 def __isub__(self, n):
129 r"""__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
130 return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
132 def __add__(self, n):
133 r"""__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
134 return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
136 def __sub__(self, *args):
138 __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
139 __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
141 return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
146 _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
153 IMP_DEBUG = _IMP_atom.IMP_DEBUG
155 IMP_RELEASE = _IMP_atom.IMP_RELEASE
157 IMP_SILENT = _IMP_atom.IMP_SILENT
159 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
161 IMP_TERSE = _IMP_atom.IMP_TERSE
163 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
165 IMP_MEMORY = _IMP_atom.IMP_MEMORY
167 IMP_NONE = _IMP_atom.IMP_NONE
169 IMP_USAGE = _IMP_atom.IMP_USAGE
171 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_atom.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_atom.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_atom.IMP_COMPILER_HAS_THREE_WAY
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
185 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
187 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
189 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
197 class _DirectorObjects:
198 """@internal Simple class to keep references to director objects
199 to prevent premature deletion."""
202 def register(self, obj):
203 """Take a reference to a director object; will only work for
204 refcounted C++ classes"""
205 if hasattr(obj,
'get_ref_count'):
206 self._objects.append(obj)
208 """Only drop our reference and allow cleanup by Python if no other
209 Python references exist (we hold 3 references: one in self._objects,
210 one in x, and one in the argument list for getrefcount) *and* no
211 other C++ references exist (the Python object always holds one)"""
212 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
213 or x.get_ref_count() > 1]
217 def get_object_count(self):
218 """Get number of director objects (useful for testing only)"""
219 return len(self._objects)
220 _director_objects = _DirectorObjects()
222 class _ostream(object):
223 r"""Proxy of C++ std::ostream class."""
225 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
227 def __init__(self, *args, **kwargs):
228 raise AttributeError(
"No constructor defined")
229 __repr__ = _swig_repr
231 def write(self, osa_buf):
232 r"""write(_ostream self, char const * osa_buf)"""
233 return _IMP_atom._ostream_write(self, osa_buf)
236 _IMP_atom._ostream_swigregister(_ostream)
237 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
240 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
248 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
250 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
265 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
267 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
269 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
272 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
274 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
280 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
284 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
286 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
289 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
301 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
303 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
308 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
310 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
312 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
314 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
318 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
320 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
322 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
324 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
326 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
329 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
335 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
337 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
345 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
351 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
353 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
355 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
359 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
362 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
364 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
368 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
370 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
372 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
374 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
376 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
378 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
380 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
382 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
384 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
386 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
388 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
390 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
392 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
395 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex > class."""
397 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
398 __repr__ = _swig_repr
401 r"""__init__(HierarchyTree self) -> HierarchyTree"""
402 _IMP_atom.HierarchyTree_swiginit(self, _IMP_atom.new_HierarchyTree())
405 r"""get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
406 return _IMP_atom.HierarchyTree_get_graph(self)
409 r"""get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
410 return _IMP_atom.HierarchyTree_get_vertices(self)
412 def get_vertex_name(self, i):
413 r"""get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
414 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
416 def get_in_neighbors(self, v):
417 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"""
418 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
420 def get_out_neighbors(self, v):
421 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"""
422 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
425 r"""show_graphviz(HierarchyTree self, _ostream out=std::cout)"""
426 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
428 def get_graphviz_string(self):
429 r"""get_graphviz_string(HierarchyTree self) -> std::string"""
430 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
432 def add_edge(self, v0, v1):
433 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)"""
434 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
436 def add_vertex(self, l):
437 r"""add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
438 return _IMP_atom.HierarchyTree_add_vertex(self, l)
440 def remove_vertex(self, l):
441 r"""remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
442 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
443 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
446 _IMP_atom.HierarchyTree_swigregister(HierarchyTree)
448 _value_types.append(
"HierarchyTree")
452 _plural_types.append(
"PDBRecords")
453 _value_types.append(
"PDBRecord")
456 _object_types.append(
"LennardJonesType")
459 def _object_cast_to_LennardJonesType(o):
460 r"""_object_cast_to_LennardJonesType(Object o) -> LennardJonesType"""
461 return _IMP_atom._object_cast_to_LennardJonesType(o)
463 _object_types.append(
"PDBSelector")
466 def _object_cast_to_PDBSelector(o):
467 r"""_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
468 return _IMP_atom._object_cast_to_PDBSelector(o)
471 return [Angle(x)
for x
in l]
472 _plural_types.append(
"Angles")
475 _value_types.append(
"Angle")
479 return [Atom(x)
for x
in l]
480 _plural_types.append(
"Atoms")
483 _value_types.append(
"Atom")
487 return [Bond(x)
for x
in l]
488 _plural_types.append(
"Bonds")
491 _value_types.append(
"Bond")
495 return [Bonded(x)
for x
in l]
496 _plural_types.append(
"Bondeds")
499 _value_types.append(
"Bonded")
502 def CHARMMAtomList(l=[]):
503 return [CHARMMAtom(x)
for x
in l]
504 _plural_types.append(
"CHARMMAtomList")
507 _value_types.append(
"CHARMMAtom")
511 return [Chain(x)
for x
in l]
512 _plural_types.append(
"Chains")
515 _value_types.append(
"Chain")
518 def CenterOfMasses(l=[]):
519 return [CenterOfMass(x)
for x
in l]
520 _plural_types.append(
"CenterOfMasses")
523 _value_types.append(
"CenterOfMass")
527 return [Charged(x)
for x
in l]
528 _plural_types.append(
"Chargeds")
531 _value_types.append(
"Charged")
534 def Diffusions(l=[]):
535 return [Diffusion(x)
for x
in l]
536 _plural_types.append(
"Diffusions")
539 _value_types.append(
"Diffusion")
542 def RigidBodyDiffusions(l=[]):
543 return [RigidBodyDiffusion(x)
for x
in l]
544 _plural_types.append(
"RigidBodyDiffusions")
547 _value_types.append(
"RigidBodyDiffusion")
550 def TAMDParticles(l=[]):
551 return [TAMDParticle(x)
for x
in l]
552 _plural_types.append(
"TAMDParticles")
555 _value_types.append(
"TAMDParticle")
558 def TAMDCentroids(l=[]):
559 return [TAMDCentroid(x)
for x
in l]
560 _plural_types.append(
"TAMDCentroids")
563 _value_types.append(
"TAMDCentroid")
567 return [Dihedral(x)
for x
in l]
568 _plural_types.append(
"Dihedrals")
571 _value_types.append(
"Dihedral")
575 return [Domain(x)
for x
in l]
576 _plural_types.append(
"Domains")
579 _value_types.append(
"Domain")
583 return [Fragment(x)
for x
in l]
584 _plural_types.append(
"Fragments")
587 _value_types.append(
"Fragment")
590 def Hierarchies(l=[]):
591 return [Hierarchy(x)
for x
in l]
592 _plural_types.append(
"Hierarchies")
595 _value_types.append(
"Hierarchy")
598 def LennardJonesList(l=[]):
599 return [LennardJones(x)
for x
in l]
600 _plural_types.append(
"LennardJonesList")
603 _value_types.append(
"LennardJones")
606 def LennardJonesTypeds(l=[]):
607 return [LennardJonesTyped(x)
for x
in l]
608 _plural_types.append(
"LennardJonesTypeds")
611 _value_types.append(
"LennardJonesTyped")
615 return [Mass(x)
for x
in l]
616 _plural_types.append(
"Masses")
619 _value_types.append(
"Mass")
622 def LinearVelocities(l=[]):
623 return [LinearVelocity(x)
for x
in l]
624 _plural_types.append(
"LinearVelocities")
627 _value_types.append(
"LinearVelocity")
630 def AngularVelocities(l=[]):
631 return [AngularVelocity(x)
for x
in l]
632 _plural_types.append(
"AngularVelocities")
635 _value_types.append(
"AngularVelocity")
639 return [Molecule(x)
for x
in l]
640 _plural_types.append(
"Molecules")
643 _value_types.append(
"Molecule")
647 return [Residue(x)
for x
in l]
648 _plural_types.append(
"Residues")
651 _value_types.append(
"Residue")
654 def Representations(l=[]):
655 return [Representation(x)
for x
in l]
656 _plural_types.append(
"Representations")
659 _value_types.append(
"Representation")
663 return [State(x)
for x
in l]
664 _plural_types.append(
"States")
667 _value_types.append(
"State")
671 return [Copy(x)
for x
in l]
672 _plural_types.append(
"Copies")
675 _value_types.append(
"Copy")
678 def SecondaryStructureResidues(l=[]):
679 return [SecondaryStructureResidue(x)
for x
in l]
680 _plural_types.append(
"SecondaryStructureResidues")
683 _value_types.append(
"SecondaryStructureResidue")
686 def StructureSources(l=[]):
687 return [StructureSource(x)
for x
in l]
688 _plural_types.append(
"StructureSources")
691 _value_types.append(
"StructureSource")
694 _object_types.append(
"Simulator")
697 def _object_cast_to_Simulator(o):
698 r"""_object_cast_to_Simulator(Object o) -> Simulator"""
699 return _IMP_atom._object_cast_to_Simulator(o)
701 _object_types.append(
"ATOMPDBSelector")
704 def _object_cast_to_ATOMPDBSelector(o):
705 r"""_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
706 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
708 _object_types.append(
"AllMol2Selector")
711 def _object_cast_to_AllMol2Selector(o):
712 r"""_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
713 return _IMP_atom._object_cast_to_AllMol2Selector(o)
715 _object_types.append(
"AllPDBSelector")
718 def _object_cast_to_AllPDBSelector(o):
719 r"""_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
720 return _IMP_atom._object_cast_to_AllPDBSelector(o)
722 _object_types.append(
"AndPDBSelector")
725 def _object_cast_to_AndPDBSelector(o):
726 r"""_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
727 return _IMP_atom._object_cast_to_AndPDBSelector(o)
729 _object_types.append(
"XorPDBSelector")
732 def _object_cast_to_XorPDBSelector(o):
733 r"""_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
734 return _IMP_atom._object_cast_to_XorPDBSelector(o)
736 _object_types.append(
"ResidueTypePDBSelector")
739 def _object_cast_to_ResidueTypePDBSelector(o):
740 r"""_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
741 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
743 _object_types.append(
"AtomTypePDBSelector")
746 def _object_cast_to_AtomTypePDBSelector(o):
747 r"""_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
748 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
750 _object_types.append(
"AngleSingletonScore")
753 def _object_cast_to_AngleSingletonScore(o):
754 r"""_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
755 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
757 _object_types.append(
"BondEndpointsRefiner")
760 def _object_cast_to_BondEndpointsRefiner(o):
761 r"""_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
762 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
764 _object_types.append(
"BondPairContainer")
767 def _object_cast_to_BondPairContainer(o):
768 r"""_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
769 return _IMP_atom._object_cast_to_BondPairContainer(o)
771 _object_types.append(
"BondSingletonScore")
774 def _object_cast_to_BondSingletonScore(o):
775 r"""_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
776 return _IMP_atom._object_cast_to_BondSingletonScore(o)
778 _object_types.append(
"BondedPairFilter")
781 def _object_cast_to_BondedPairFilter(o):
782 r"""_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
783 return _IMP_atom._object_cast_to_BondedPairFilter(o)
785 _object_types.append(
"BrownianDynamics")
788 def _object_cast_to_BrownianDynamics(o):
789 r"""_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
790 return _IMP_atom._object_cast_to_BrownianDynamics(o)
792 _object_types.append(
"BrownianDynamicsTAMD")
795 def _object_cast_to_BrownianDynamicsTAMD(o):
796 r"""_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
797 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
799 _object_types.append(
"CAlphaPDBSelector")
802 def _object_cast_to_CAlphaPDBSelector(o):
803 r"""_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
804 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
806 _object_types.append(
"CBetaPDBSelector")
809 def _object_cast_to_CBetaPDBSelector(o):
810 r"""_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
811 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
813 _object_types.append(
"BackbonePDBSelector")
816 def _object_cast_to_BackbonePDBSelector(o):
817 r"""_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
818 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
820 _object_types.append(
"CHARMMParameters")
823 def _object_cast_to_CHARMMParameters(o):
824 r"""_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
825 return _IMP_atom._object_cast_to_CHARMMParameters(o)
827 _object_types.append(
"CHARMMResidueTopology")
830 def _object_cast_to_CHARMMResidueTopology(o):
831 r"""_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
832 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
834 _object_types.append(
"CHARMMSegmentTopology")
837 def _object_cast_to_CHARMMSegmentTopology(o):
838 r"""_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
839 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
841 _object_types.append(
"CHARMMStereochemistryRestraint")
844 def _object_cast_to_CHARMMStereochemistryRestraint(o):
845 r"""_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
846 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
848 _object_types.append(
"CHARMMTopology")
851 def _object_cast_to_CHARMMTopology(o):
852 r"""_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
853 return _IMP_atom._object_cast_to_CHARMMTopology(o)
855 _object_types.append(
"CPDBSelector")
858 def _object_cast_to_CPDBSelector(o):
859 r"""_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
860 return _IMP_atom._object_cast_to_CPDBSelector(o)
862 _object_types.append(
"ChainPDBSelector")
865 def _object_cast_to_ChainPDBSelector(o):
866 r"""_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
867 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
869 _object_types.append(
"CoulombPairScore")
872 def _object_cast_to_CoulombPairScore(o):
873 r"""_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
874 return _IMP_atom._object_cast_to_CoulombPairScore(o)
876 _object_types.append(
"CoverBond")
879 def _object_cast_to_CoverBond(o):
880 r"""_object_cast_to_CoverBond(Object o) -> CoverBond"""
881 return _IMP_atom._object_cast_to_CoverBond(o)
883 _object_types.append(
"DihedralSingletonScore")
886 def _object_cast_to_DihedralSingletonScore(o):
887 r"""_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
888 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
890 _object_types.append(
"DopePairScore")
893 def _object_cast_to_DopePairScore(o):
894 r"""_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
895 return _IMP_atom._object_cast_to_DopePairScore(o)
897 _object_types.append(
"LoopStatisticalPairScore")
900 def _object_cast_to_LoopStatisticalPairScore(o):
901 r"""_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
902 return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
904 _object_types.append(
"OrientedSoapPairScore")
907 def _object_cast_to_OrientedSoapPairScore(o):
908 r"""_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
909 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
911 _object_types.append(
"EzRestraint")
914 def _object_cast_to_EzRestraint(o):
915 r"""_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
916 return _IMP_atom._object_cast_to_EzRestraint(o)
918 _object_types.append(
"ForceFieldParameters")
921 def _object_cast_to_ForceFieldParameters(o):
922 r"""_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
923 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
925 _object_types.append(
"ForceSwitch")
928 def _object_cast_to_ForceSwitch(o):
929 r"""_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
930 return _IMP_atom._object_cast_to_ForceSwitch(o)
932 _object_types.append(
"HydrogenPDBSelector")
935 def _object_cast_to_HydrogenPDBSelector(o):
936 r"""_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
937 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
939 _object_types.append(
"ImproperSingletonScore")
942 def _object_cast_to_ImproperSingletonScore(o):
943 r"""_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
944 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
946 _object_types.append(
"LennardJonesPairScore")
949 def _object_cast_to_LennardJonesPairScore(o):
950 r"""_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
951 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
953 _object_types.append(
"_LennardJonesTypedPairScore")
956 def _object_cast_to__LennardJonesTypedPairScore(o):
957 r"""_object_cast_to__LennardJonesTypedPairScore(Object o) -> _LennardJonesTypedPairScore"""
958 return _IMP_atom._object_cast_to__LennardJonesTypedPairScore(o)
960 _object_types.append(
"_SwitchedLennardJonesTypedPairScore")
963 def _object_cast_to__SwitchedLennardJonesTypedPairScore(o):
964 r"""_object_cast_to__SwitchedLennardJonesTypedPairScore(Object o) -> _SwitchedLennardJonesTypedPairScore"""
965 return _IMP_atom._object_cast_to__SwitchedLennardJonesTypedPairScore(o)
967 _object_types.append(
"Mol2Selector")
970 def _object_cast_to_Mol2Selector(o):
971 r"""_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
972 return _IMP_atom._object_cast_to_Mol2Selector(o)
974 _object_types.append(
"MolecularDynamics")
977 def _object_cast_to_MolecularDynamics(o):
978 r"""_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
979 return _IMP_atom._object_cast_to_MolecularDynamics(o)
981 _object_types.append(
"NPDBSelector")
984 def _object_cast_to_NPDBSelector(o):
985 r"""_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
986 return _IMP_atom._object_cast_to_NPDBSelector(o)
988 _object_types.append(
"NonAlternativePDBSelector")
991 def _object_cast_to_NonAlternativePDBSelector(o):
992 r"""_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
993 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
995 _object_types.append(
"NonHydrogenMol2Selector")
998 def _object_cast_to_NonHydrogenMol2Selector(o):
999 r"""_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
1000 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
1002 _object_types.append(
"NonHydrogenPDBSelector")
1005 def _object_cast_to_NonHydrogenPDBSelector(o):
1006 r"""_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
1007 return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
1009 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
1012 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
1013 r"""_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
1014 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
1016 _object_types.append(
"NonWaterPDBSelector")
1019 def _object_cast_to_NonWaterPDBSelector(o):
1020 r"""_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
1021 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
1023 _object_types.append(
"NotPDBSelector")
1026 def _object_cast_to_NotPDBSelector(o):
1027 r"""_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1028 return _IMP_atom._object_cast_to_NotPDBSelector(o)
1030 _object_types.append(
"OrPDBSelector")
1033 def _object_cast_to_OrPDBSelector(o):
1034 r"""_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1035 return _IMP_atom._object_cast_to_OrPDBSelector(o)
1037 _object_types.append(
"PPDBSelector")
1040 def _object_cast_to_PPDBSelector(o):
1041 r"""_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1042 return _IMP_atom._object_cast_to_PPDBSelector(o)
1044 _object_types.append(
"ProteinLigandAtomPairScore")
1047 def _object_cast_to_ProteinLigandAtomPairScore(o):
1048 r"""_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1049 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1051 _object_types.append(
"ProteinLigandRestraint")
1054 def _object_cast_to_ProteinLigandRestraint(o):
1055 r"""_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1056 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1058 _object_types.append(
"SameResiduePairFilter")
1061 def _object_cast_to_SameResiduePairFilter(o):
1062 r"""_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1063 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1065 _object_types.append(
"SoapPairFilter")
1068 def _object_cast_to_SoapPairFilter(o):
1069 r"""_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1070 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1072 _object_types.append(
"SmoothingFunction")
1075 def _object_cast_to_SmoothingFunction(o):
1076 r"""_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1077 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1079 _object_types.append(
"StereochemistryPairFilter")
1082 def _object_cast_to_StereochemistryPairFilter(o):
1083 r"""_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1084 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1086 _object_types.append(
"VelocityScalingOptimizerState")
1089 def _object_cast_to_VelocityScalingOptimizerState(o):
1090 r"""_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1091 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1093 _object_types.append(
"WaterPDBSelector")
1096 def _object_cast_to_WaterPDBSelector(o):
1097 r"""_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1098 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1100 _object_types.append(
"WritePDBOptimizerState")
1103 def _object_cast_to_WritePDBOptimizerState(o):
1104 r"""_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1105 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1108 _plural_types.append(
"AtomTypes")
1109 _value_types.append(
"AtomType")
1112 CHARMMAtomTopologies=list
1113 _plural_types.append(
"CHARMMAtomTopologies")
1114 _value_types.append(
"CHARMMAtomTopology")
1117 CHARMMBondEndpoints=list
1118 _plural_types.append(
"CHARMMBondEndpoints")
1119 _value_types.append(
"CHARMMBondEndpoint")
1122 CHARMMBondParametersList=list
1123 _plural_types.append(
"CHARMMBondParametersList")
1124 _value_types.append(
"CHARMMBondParameters")
1127 CHARMMDihedralParametersList=list
1128 _plural_types.append(
"CHARMMDihedralParametersList")
1129 _value_types.append(
"CHARMMDihedralParameters")
1132 _object_types.append(
"CHARMMIdealResidueTopology")
1135 def _object_cast_to_CHARMMIdealResidueTopology(o):
1136 r"""_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1137 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1139 CHARMMInternalCoordinates=list
1140 _plural_types.append(
"CHARMMInternalCoordinates")
1141 _value_types.append(
"CHARMMInternalCoordinate")
1144 _object_types.append(
"CHARMMPatch")
1147 def _object_cast_to_CHARMMPatch(o):
1148 r"""_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1149 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1151 _object_types.append(
"CHARMMResidueTopologyBase")
1154 def _object_cast_to_CHARMMResidueTopologyBase(o):
1155 r"""_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1156 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1159 _plural_types.append(
"ResidueTypes")
1160 _value_types.append(
"ResidueType")
1164 _plural_types.append(
"ChainTypes")
1165 _value_types.append(
"ChainType")
1169 _plural_types.append(
"Selections")
1170 _value_types.append(
"Selection")
1173 _object_types.append(
"RemoveRigidMotionOptimizerState")
1176 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1177 r"""_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1178 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1180 _object_types.append(
"BerendsenThermostatOptimizerState")
1183 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1184 r"""_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1185 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1187 _object_types.append(
"LangevinThermostatOptimizerState")
1190 def _object_cast_to_LangevinThermostatOptimizerState(o):
1191 r"""_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1192 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1194 _object_types.append(
"SelectionGeometry")
1197 def _object_cast_to_SelectionGeometry(o):
1198 r"""_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1199 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1201 _object_types.append(
"HierarchyGeometry")
1204 def _object_cast_to_HierarchyGeometry(o):
1205 r"""_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1206 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1208 _object_types.append(
"HierarchiesGeometry")
1211 def _object_cast_to_HierarchiesGeometry(o):
1212 r"""_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1213 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1215 _object_types.append(
"BondGeometry")
1218 def _object_cast_to_BondGeometry(o):
1219 r"""_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1220 return _IMP_atom._object_cast_to_BondGeometry(o)
1222 _object_types.append(
"BondsGeometry")
1225 def _object_cast_to_BondsGeometry(o):
1226 r"""_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1227 return _IMP_atom._object_cast_to_BondsGeometry(o)
1229 _object_types.append(
"CAAngleRestraint")
1232 def _object_cast_to_CAAngleRestraint(o):
1233 r"""_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1234 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1236 _object_types.append(
"CADihedralRestraint")
1239 def _object_cast_to_CADihedralRestraint(o):
1240 r"""_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1241 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1243 _object_types.append(
"HelixRestraint")
1246 def _object_cast_to_HelixRestraint(o):
1247 r"""_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1248 return _IMP_atom._object_cast_to_HelixRestraint(o)
1250 CHARMMDihedrals=list
1251 _plural_types.append(
"CHARMMDihedrals")
1252 _value_types.append(
"CHARMMDihedral")
1256 _plural_types.append(
"CHARMMBonds")
1257 _value_types.append(
"CHARMMBond")
1261 _plural_types.append(
"CHARMMAngles")
1262 _value_types.append(
"CHARMMAngle")
1265 r"""Proxy of C++ IMP::atom::Bond class."""
1267 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1269 def __init__(self, *args):
1271 __init__(Bond self) -> Bond
1272 __init__(Bond self, Model m, ParticleIndex id) -> Bond
1273 __init__(Bond self, _ParticleAdaptor d) -> Bond
1275 _IMP_atom.Bond_swiginit(self, _IMP_atom.new_Bond(*args))
1277 def show(self, *args):
1278 r"""show(Bond self, _ostream out=std::cout)"""
1279 return _IMP_atom.Bond_show(self, *args)
1282 def get_is_setup(*args):
1284 get_is_setup(_ParticleAdaptor p) -> bool
1285 get_is_setup(Model m, ParticleIndex pi) -> bool
1287 return _IMP_atom.Bond_get_is_setup(*args)
1288 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1290 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1292 SINGLE = _IMP_atom.Bond_SINGLE
1294 DOUBLE = _IMP_atom.Bond_DOUBLE
1296 TRIPLE = _IMP_atom.Bond_TRIPLE
1298 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1300 SALT = _IMP_atom.Bond_SALT
1302 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1304 AMIDE = _IMP_atom.Bond_AMIDE
1306 AROMATIC = _IMP_atom.Bond_AROMATIC
1309 def get_bonded(self, i):
1310 r"""get_bonded(Bond self, unsigned int i) -> Bonded"""
1311 return _IMP_atom.Bond_get_bonded(self, i)
1314 r"""get_type(Bond self) -> IMP::Int"""
1315 return _IMP_atom.Bond_get_type(self)
1317 def set_type(self, t):
1318 r"""set_type(Bond self, IMP::Int t)"""
1319 return _IMP_atom.Bond_set_type(self, t)
1322 r"""get_order(Bond self) -> IMP::Int"""
1323 return _IMP_atom.Bond_get_order(self)
1325 def set_order(self, t):
1326 r"""set_order(Bond self, IMP::Int t)"""
1327 return _IMP_atom.Bond_set_order(self, t)
1329 def get_length(self):
1330 r"""get_length(Bond self) -> IMP::Float"""
1331 return _IMP_atom.Bond_get_length(self)
1333 def set_length(self, t):
1334 r"""set_length(Bond self, IMP::Float t)"""
1335 return _IMP_atom.Bond_set_length(self, t)
1337 def get_stiffness(self):
1338 r"""get_stiffness(Bond self) -> IMP::Float"""
1339 return _IMP_atom.Bond_get_stiffness(self)
1341 def set_stiffness(self, t):
1342 r"""set_stiffness(Bond self, IMP::Float t)"""
1343 return _IMP_atom.Bond_set_stiffness(self, t)
1346 def get_length_key():
1347 r"""get_length_key() -> FloatKey"""
1348 return _IMP_atom.Bond_get_length_key()
1350 def add_attribute(self, *args):
1352 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1353 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1354 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1355 add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1356 add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1357 add_attribute(Bond self, StringKey a0, IMP::String a1)
1358 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1359 add_attribute(Bond self, ObjectKey a0, Object a1)
1360 add_attribute(Bond self, SparseFloatKey a0, IMP::Float a1)
1361 add_attribute(Bond self, SparseIntKey a0, IMP::Int a1)
1362 add_attribute(Bond self, SparseStringKey a0, IMP::String a1)
1363 add_attribute(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1365 return _IMP_atom.Bond_add_attribute(self, *args)
1367 def get_value(self, *args):
1369 get_value(Bond self, FloatKey a0) -> IMP::Float
1370 get_value(Bond self, IntKey a0) -> IMP::Int
1371 get_value(Bond self, FloatsKey a0) -> IMP::Floats
1372 get_value(Bond self, IntsKey a0) -> IMP::Ints
1373 get_value(Bond self, StringKey a0) -> IMP::String
1374 get_value(Bond self, ParticleIndexKey a0) -> Particle
1375 get_value(Bond self, ObjectKey a0) -> Object
1376 get_value(Bond self, SparseFloatKey a0) -> IMP::Float
1377 get_value(Bond self, SparseIntKey a0) -> IMP::Int
1378 get_value(Bond self, SparseStringKey a0) -> IMP::String
1379 get_value(Bond self, SparseParticleIndexKey a0) -> ParticleIndex
1381 return _IMP_atom.Bond_get_value(self, *args)
1383 def set_value(self, *args):
1385 set_value(Bond self, FloatKey a0, IMP::Float a1)
1386 set_value(Bond self, IntKey a0, IMP::Int a1)
1387 set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1388 set_value(Bond self, IntsKey a0, IMP::Ints a1)
1389 set_value(Bond self, StringKey a0, IMP::String a1)
1390 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1391 set_value(Bond self, ObjectKey a0, Object a1)
1392 set_value(Bond self, SparseFloatKey a0, IMP::Float a1)
1393 set_value(Bond self, SparseIntKey a0, IMP::Int a1)
1394 set_value(Bond self, SparseStringKey a0, IMP::String a1)
1395 set_value(Bond self, SparseParticleIndexKey a0, ParticleIndex a1)
1397 return _IMP_atom.Bond_set_value(self, *args)
1399 def remove_attribute(self, *args):
1401 remove_attribute(Bond self, FloatKey a0)
1402 remove_attribute(Bond self, IntKey a0)
1403 remove_attribute(Bond self, FloatsKey a0)
1404 remove_attribute(Bond self, IntsKey a0)
1405 remove_attribute(Bond self, StringKey a0)
1406 remove_attribute(Bond self, ParticleIndexKey a0)
1407 remove_attribute(Bond self, ObjectKey a0)
1408 remove_attribute(Bond self, SparseFloatKey a0)
1409 remove_attribute(Bond self, SparseIntKey a0)
1410 remove_attribute(Bond self, SparseStringKey a0)
1411 remove_attribute(Bond self, SparseParticleIndexKey a0)
1413 return _IMP_atom.Bond_remove_attribute(self, *args)
1415 def has_attribute(self, *args):
1417 has_attribute(Bond self, FloatKey a0) -> bool
1418 has_attribute(Bond self, IntKey a0) -> bool
1419 has_attribute(Bond self, FloatsKey a0) -> bool
1420 has_attribute(Bond self, IntsKey a0) -> bool
1421 has_attribute(Bond self, StringKey a0) -> bool
1422 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1423 has_attribute(Bond self, ObjectKey a0) -> bool
1424 has_attribute(Bond self, SparseFloatKey a0) -> bool
1425 has_attribute(Bond self, SparseIntKey a0) -> bool
1426 has_attribute(Bond self, SparseStringKey a0) -> bool
1427 has_attribute(Bond self, SparseParticleIndexKey a0) -> bool
1429 return _IMP_atom.Bond_has_attribute(self, *args)
1431 def get_derivative(self, a0):
1432 r"""get_derivative(Bond self, FloatKey a0) -> double"""
1433 return _IMP_atom.Bond_get_derivative(self, a0)
1436 r"""get_name(Bond self) -> std::string"""
1437 return _IMP_atom.Bond_get_name(self)
1439 def clear_caches(self):
1440 r"""clear_caches(Bond self)"""
1441 return _IMP_atom.Bond_clear_caches(self)
1443 def set_name(self, a0):
1444 r"""set_name(Bond self, std::string a0)"""
1445 return _IMP_atom.Bond_set_name(self, a0)
1448 r"""set_check_level(Bond self, IMP::CheckLevel a0)"""
1449 return _IMP_atom.Bond_set_check_level(self, a0)
1451 def add_to_derivative(self, a0, a1, a2):
1452 r"""add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1453 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1455 def set_is_optimized(self, a0, a1):
1456 r"""set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1457 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1459 def get_is_optimized(self, a0):
1460 r"""get_is_optimized(Bond self, FloatKey a0) -> bool"""
1461 return _IMP_atom.Bond_get_is_optimized(self, a0)
1464 r"""get_check_level(Bond self) -> IMP::CheckLevel"""
1465 return _IMP_atom.Bond_get_check_level(self)
1467 def __eq__(self, *args):
1469 __eq__(Bond self, Bond o) -> bool
1470 __eq__(Bond self, Particle d) -> bool
1472 return _IMP_atom.Bond___eq__(self, *args)
1474 def __ne__(self, *args):
1476 __ne__(Bond self, Bond o) -> bool
1477 __ne__(Bond self, Particle d) -> bool
1479 return _IMP_atom.Bond___ne__(self, *args)
1481 def __le__(self, *args):
1483 __le__(Bond self, Bond o) -> bool
1484 __le__(Bond self, Particle d) -> bool
1486 return _IMP_atom.Bond___le__(self, *args)
1488 def __lt__(self, *args):
1490 __lt__(Bond self, Bond o) -> bool
1491 __lt__(Bond self, Particle d) -> bool
1493 return _IMP_atom.Bond___lt__(self, *args)
1495 def __ge__(self, *args):
1497 __ge__(Bond self, Bond o) -> bool
1498 __ge__(Bond self, Particle d) -> bool
1500 return _IMP_atom.Bond___ge__(self, *args)
1502 def __gt__(self, *args):
1504 __gt__(Bond self, Bond o) -> bool
1505 __gt__(Bond self, Particle d) -> bool
1507 return _IMP_atom.Bond___gt__(self, *args)
1510 r"""__hash__(Bond self) -> std::size_t"""
1511 return _IMP_atom.Bond___hash__(self)
1514 r"""__str__(Bond self) -> std::string"""
1515 return _IMP_atom.Bond___str__(self)
1518 r"""__repr__(Bond self) -> std::string"""
1519 return _IMP_atom.Bond___repr__(self)
1521 def _get_as_binary(self):
1522 r"""_get_as_binary(Bond self) -> PyObject *"""
1523 return _IMP_atom.Bond__get_as_binary(self)
1525 def _set_from_binary(self, p):
1526 r"""_set_from_binary(Bond self, PyObject * p)"""
1527 return _IMP_atom.Bond__set_from_binary(self, p)
1529 def __getstate__(self):
1530 p = self._get_as_binary()
1531 if len(self.__dict__) > 1:
1532 d = self.__dict__.copy()
1537 def __setstate__(self, p):
1538 if not hasattr(self,
'this'):
1540 if isinstance(p, tuple):
1542 self.__dict__.update(d)
1543 return self._set_from_binary(p)
1545 __swig_destroy__ = _IMP_atom.delete_Bond
1548 _IMP_atom.Bond_swigregister(Bond)
1550 r"""Proxy of C++ IMP::atom::Bonded class."""
1552 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1554 def __init__(self, *args):
1556 __init__(Bonded self) -> Bonded
1557 __init__(Bonded self, Model m, ParticleIndex id) -> Bonded
1558 __init__(Bonded self, _ParticleAdaptor d) -> Bonded
1560 _IMP_atom.Bonded_swiginit(self, _IMP_atom.new_Bonded(*args))
1562 def show(self, *args):
1563 r"""show(Bonded self, _ostream out=std::cout)"""
1564 return _IMP_atom.Bonded_show(self, *args)
1567 def setup_particle(*args):
1569 setup_particle(Model m, ParticleIndex pi) -> Bonded
1570 setup_particle(_ParticleAdaptor pa) -> Bonded
1572 return _IMP_atom.Bonded_setup_particle(*args)
1575 def get_is_setup(*args):
1577 get_is_setup(_ParticleAdaptor p) -> bool
1578 get_is_setup(Model m, ParticleIndex pi) -> bool
1580 return _IMP_atom.Bonded_get_is_setup(*args)
1582 def get_number_of_bonds(self):
1583 r"""get_number_of_bonds(Bonded self) -> unsigned int"""
1584 return _IMP_atom.Bonded_get_number_of_bonds(self)
1586 def get_bond_indexes(self):
1587 r"""get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1588 return _IMP_atom.Bonded_get_bond_indexes(self)
1591 r"""get_bond(Bonded self, unsigned int i) -> Bond"""
1592 return _IMP_atom.Bonded_get_bond(self, i)
1594 def get_bonded(self, i):
1595 r"""get_bonded(Bonded self, unsigned int i) -> Bonded"""
1596 return _IMP_atom.Bonded_get_bonded(self, i)
1598 def add_attribute(self, *args):
1600 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1601 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1602 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1603 add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1604 add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1605 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1606 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1607 add_attribute(Bonded self, ObjectKey a0, Object a1)
1608 add_attribute(Bonded self, SparseFloatKey a0, IMP::Float a1)
1609 add_attribute(Bonded self, SparseIntKey a0, IMP::Int a1)
1610 add_attribute(Bonded self, SparseStringKey a0, IMP::String a1)
1611 add_attribute(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1613 return _IMP_atom.Bonded_add_attribute(self, *args)
1615 def get_value(self, *args):
1617 get_value(Bonded self, FloatKey a0) -> IMP::Float
1618 get_value(Bonded self, IntKey a0) -> IMP::Int
1619 get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1620 get_value(Bonded self, IntsKey a0) -> IMP::Ints
1621 get_value(Bonded self, StringKey a0) -> IMP::String
1622 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1623 get_value(Bonded self, ObjectKey a0) -> Object
1624 get_value(Bonded self, SparseFloatKey a0) -> IMP::Float
1625 get_value(Bonded self, SparseIntKey a0) -> IMP::Int
1626 get_value(Bonded self, SparseStringKey a0) -> IMP::String
1627 get_value(Bonded self, SparseParticleIndexKey a0) -> ParticleIndex
1629 return _IMP_atom.Bonded_get_value(self, *args)
1631 def set_value(self, *args):
1633 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1634 set_value(Bonded self, IntKey a0, IMP::Int a1)
1635 set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1636 set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1637 set_value(Bonded self, StringKey a0, IMP::String a1)
1638 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1639 set_value(Bonded self, ObjectKey a0, Object a1)
1640 set_value(Bonded self, SparseFloatKey a0, IMP::Float a1)
1641 set_value(Bonded self, SparseIntKey a0, IMP::Int a1)
1642 set_value(Bonded self, SparseStringKey a0, IMP::String a1)
1643 set_value(Bonded self, SparseParticleIndexKey a0, ParticleIndex a1)
1645 return _IMP_atom.Bonded_set_value(self, *args)
1647 def remove_attribute(self, *args):
1649 remove_attribute(Bonded self, FloatKey a0)
1650 remove_attribute(Bonded self, IntKey a0)
1651 remove_attribute(Bonded self, FloatsKey a0)
1652 remove_attribute(Bonded self, IntsKey a0)
1653 remove_attribute(Bonded self, StringKey a0)
1654 remove_attribute(Bonded self, ParticleIndexKey a0)
1655 remove_attribute(Bonded self, ObjectKey a0)
1656 remove_attribute(Bonded self, SparseFloatKey a0)
1657 remove_attribute(Bonded self, SparseIntKey a0)
1658 remove_attribute(Bonded self, SparseStringKey a0)
1659 remove_attribute(Bonded self, SparseParticleIndexKey a0)
1661 return _IMP_atom.Bonded_remove_attribute(self, *args)
1663 def has_attribute(self, *args):
1665 has_attribute(Bonded self, FloatKey a0) -> bool
1666 has_attribute(Bonded self, IntKey a0) -> bool
1667 has_attribute(Bonded self, FloatsKey a0) -> bool
1668 has_attribute(Bonded self, IntsKey a0) -> bool
1669 has_attribute(Bonded self, StringKey a0) -> bool
1670 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1671 has_attribute(Bonded self, ObjectKey a0) -> bool
1672 has_attribute(Bonded self, SparseFloatKey a0) -> bool
1673 has_attribute(Bonded self, SparseIntKey a0) -> bool
1674 has_attribute(Bonded self, SparseStringKey a0) -> bool
1675 has_attribute(Bonded self, SparseParticleIndexKey a0) -> bool
1677 return _IMP_atom.Bonded_has_attribute(self, *args)
1679 def get_derivative(self, a0):
1680 r"""get_derivative(Bonded self, FloatKey a0) -> double"""
1681 return _IMP_atom.Bonded_get_derivative(self, a0)
1684 r"""get_name(Bonded self) -> std::string"""
1685 return _IMP_atom.Bonded_get_name(self)
1687 def clear_caches(self):
1688 r"""clear_caches(Bonded self)"""
1689 return _IMP_atom.Bonded_clear_caches(self)
1691 def set_name(self, a0):
1692 r"""set_name(Bonded self, std::string a0)"""
1693 return _IMP_atom.Bonded_set_name(self, a0)
1696 r"""set_check_level(Bonded self, IMP::CheckLevel a0)"""
1697 return _IMP_atom.Bonded_set_check_level(self, a0)
1699 def add_to_derivative(self, a0, a1, a2):
1700 r"""add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1701 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1703 def set_is_optimized(self, a0, a1):
1704 r"""set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1705 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1707 def get_is_optimized(self, a0):
1708 r"""get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1709 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1712 r"""get_check_level(Bonded self) -> IMP::CheckLevel"""
1713 return _IMP_atom.Bonded_get_check_level(self)
1715 def __eq__(self, *args):
1717 __eq__(Bonded self, Bonded o) -> bool
1718 __eq__(Bonded self, Particle d) -> bool
1720 return _IMP_atom.Bonded___eq__(self, *args)
1722 def __ne__(self, *args):
1724 __ne__(Bonded self, Bonded o) -> bool
1725 __ne__(Bonded self, Particle d) -> bool
1727 return _IMP_atom.Bonded___ne__(self, *args)
1729 def __le__(self, *args):
1731 __le__(Bonded self, Bonded o) -> bool
1732 __le__(Bonded self, Particle d) -> bool
1734 return _IMP_atom.Bonded___le__(self, *args)
1736 def __lt__(self, *args):
1738 __lt__(Bonded self, Bonded o) -> bool
1739 __lt__(Bonded self, Particle d) -> bool
1741 return _IMP_atom.Bonded___lt__(self, *args)
1743 def __ge__(self, *args):
1745 __ge__(Bonded self, Bonded o) -> bool
1746 __ge__(Bonded self, Particle d) -> bool
1748 return _IMP_atom.Bonded___ge__(self, *args)
1750 def __gt__(self, *args):
1752 __gt__(Bonded self, Bonded o) -> bool
1753 __gt__(Bonded self, Particle d) -> bool
1755 return _IMP_atom.Bonded___gt__(self, *args)
1758 r"""__hash__(Bonded self) -> std::size_t"""
1759 return _IMP_atom.Bonded___hash__(self)
1762 r"""__str__(Bonded self) -> std::string"""
1763 return _IMP_atom.Bonded___str__(self)
1766 r"""__repr__(Bonded self) -> std::string"""
1767 return _IMP_atom.Bonded___repr__(self)
1769 def _get_as_binary(self):
1770 r"""_get_as_binary(Bonded self) -> PyObject *"""
1771 return _IMP_atom.Bonded__get_as_binary(self)
1773 def _set_from_binary(self, p):
1774 r"""_set_from_binary(Bonded self, PyObject * p)"""
1775 return _IMP_atom.Bonded__set_from_binary(self, p)
1777 def __getstate__(self):
1778 p = self._get_as_binary()
1779 if len(self.__dict__) > 1:
1780 d = self.__dict__.copy()
1785 def __setstate__(self, p):
1786 if not hasattr(self,
'this'):
1788 if isinstance(p, tuple):
1790 self.__dict__.update(d)
1791 return self._set_from_binary(p)
1793 __swig_destroy__ = _IMP_atom.delete_Bonded
1796 _IMP_atom.Bonded_swigregister(Bonded)
1799 r"""create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond"""
1800 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1804 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1805 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1807 return _IMP_atom.create_bond(*args)
1810 r"""destroy_bond(Bond b)"""
1811 return _IMP_atom.destroy_bond(b)
1814 r"""get_bond(Bonded a, Bonded b) -> Bond"""
1815 return _IMP_atom.get_bond(a, b)
1817 r"""Proxy of C++ IMP::atom::BondGeometry class."""
1819 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1821 def __init__(self, *args):
1823 __init__(BondGeometry self, Particle p) -> BondGeometry
1824 __init__(BondGeometry self, Bond d) -> BondGeometry
1826 _IMP_atom.BondGeometry_swiginit(self, _IMP_atom.new_BondGeometry(*args))
1828 def get_version_info(self):
1829 r"""get_version_info(BondGeometry self) -> VersionInfo"""
1830 return _IMP_atom.BondGeometry_get_version_info(self)
1831 __swig_destroy__ = _IMP_atom.delete_BondGeometry
1834 r"""__str__(BondGeometry self) -> std::string"""
1835 return _IMP_atom.BondGeometry___str__(self)
1838 r"""__repr__(BondGeometry self) -> std::string"""
1839 return _IMP_atom.BondGeometry___repr__(self)
1843 return _object_cast_to_BondGeometry(o)
1847 _IMP_atom.BondGeometry_swigregister(BondGeometry)
1849 r"""Proxy of C++ IMP::atom::BondsGeometry class."""
1851 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1853 def __init__(self, sc):
1854 r"""__init__(BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1855 _IMP_atom.BondsGeometry_swiginit(self, _IMP_atom.new_BondsGeometry(sc))
1857 def get_version_info(self):
1858 r"""get_version_info(BondsGeometry self) -> VersionInfo"""
1859 return _IMP_atom.BondsGeometry_get_version_info(self)
1860 __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1863 r"""__str__(BondsGeometry self) -> std::string"""
1864 return _IMP_atom.BondsGeometry___str__(self)
1867 r"""__repr__(BondsGeometry self) -> std::string"""
1868 return _IMP_atom.BondsGeometry___repr__(self)
1872 return _object_cast_to_BondsGeometry(o)
1876 _IMP_atom.BondsGeometry_swigregister(BondsGeometry)
1878 r"""Proxy of C++ IMP::atom::Hierarchy class."""
1880 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1882 def __init__(self, *args):
1884 __init__(Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1885 __init__(Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1886 __init__(Hierarchy self) -> Hierarchy
1887 __init__(Hierarchy self, Hierarchy h) -> Hierarchy
1889 _IMP_atom.Hierarchy_swiginit(self, _IMP_atom.new_Hierarchy(*args))
1892 def setup_particle(*args):
1894 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1895 setup_particle(Particle p) -> Hierarchy
1896 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::ParticleIndexesAdaptor()) -> Hierarchy
1898 return _IMP_atom.Hierarchy_setup_particle(*args)
1901 def get_is_setup(*args):
1903 get_is_setup(Particle p) -> bool
1904 get_is_setup(Model m, ParticleIndex p) -> bool
1906 return _IMP_atom.Hierarchy_get_is_setup(*args)
1908 def get_is_valid(self, print_info=False):
1909 r"""get_is_valid(Hierarchy self, bool print_info=False) -> bool"""
1910 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1912 def add_child(self, o):
1913 r"""add_child(Hierarchy self, Hierarchy o)"""
1914 return _IMP_atom.Hierarchy_add_child(self, o)
1916 def get_child(self, i):
1917 r"""get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1918 return _IMP_atom.Hierarchy_get_child(self, i)
1920 def get_children(self):
1921 r"""get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1922 return _IMP_atom.Hierarchy_get_children(self)
1924 def get_parent(self):
1925 r"""get_parent(Hierarchy self) -> Hierarchy"""
1926 return _IMP_atom.Hierarchy_get_parent(self)
1930 r"""get_traits() -> HierarchyTraits"""
1931 return _IMP_atom.Hierarchy_get_traits()
1933 def show(self, *args):
1935 show(Hierarchy self, _ostream out, std::string delimiter)
1936 show(Hierarchy self, _ostream out=std::cout)
1938 return _IMP_atom.Hierarchy_show(self, *args)
1940 def add_attribute(self, *args):
1942 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1943 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1944 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1945 add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1946 add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1947 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1948 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1949 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1950 add_attribute(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1951 add_attribute(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1952 add_attribute(Hierarchy self, SparseStringKey a0, IMP::String a1)
1953 add_attribute(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1955 return _IMP_atom.Hierarchy_add_attribute(self, *args)
1957 def get_value(self, *args):
1959 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1960 get_value(Hierarchy self, IntKey a0) -> IMP::Int
1961 get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1962 get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1963 get_value(Hierarchy self, StringKey a0) -> IMP::String
1964 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1965 get_value(Hierarchy self, ObjectKey a0) -> Object
1966 get_value(Hierarchy self, SparseFloatKey a0) -> IMP::Float
1967 get_value(Hierarchy self, SparseIntKey a0) -> IMP::Int
1968 get_value(Hierarchy self, SparseStringKey a0) -> IMP::String
1969 get_value(Hierarchy self, SparseParticleIndexKey a0) -> ParticleIndex
1971 return _IMP_atom.Hierarchy_get_value(self, *args)
1973 def set_value(self, *args):
1975 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1976 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1977 set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1978 set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1979 set_value(Hierarchy self, StringKey a0, IMP::String a1)
1980 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1981 set_value(Hierarchy self, ObjectKey a0, Object a1)
1982 set_value(Hierarchy self, SparseFloatKey a0, IMP::Float a1)
1983 set_value(Hierarchy self, SparseIntKey a0, IMP::Int a1)
1984 set_value(Hierarchy self, SparseStringKey a0, IMP::String a1)
1985 set_value(Hierarchy self, SparseParticleIndexKey a0, ParticleIndex a1)
1987 return _IMP_atom.Hierarchy_set_value(self, *args)
1989 def remove_attribute(self, *args):
1991 remove_attribute(Hierarchy self, FloatKey a0)
1992 remove_attribute(Hierarchy self, IntKey a0)
1993 remove_attribute(Hierarchy self, FloatsKey a0)
1994 remove_attribute(Hierarchy self, IntsKey a0)
1995 remove_attribute(Hierarchy self, StringKey a0)
1996 remove_attribute(Hierarchy self, ParticleIndexKey a0)
1997 remove_attribute(Hierarchy self, ObjectKey a0)
1998 remove_attribute(Hierarchy self, SparseFloatKey a0)
1999 remove_attribute(Hierarchy self, SparseIntKey a0)
2000 remove_attribute(Hierarchy self, SparseStringKey a0)
2001 remove_attribute(Hierarchy self, SparseParticleIndexKey a0)
2003 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
2005 def has_attribute(self, *args):
2007 has_attribute(Hierarchy self, FloatKey a0) -> bool
2008 has_attribute(Hierarchy self, IntKey a0) -> bool
2009 has_attribute(Hierarchy self, FloatsKey a0) -> bool
2010 has_attribute(Hierarchy self, IntsKey a0) -> bool
2011 has_attribute(Hierarchy self, StringKey a0) -> bool
2012 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2013 has_attribute(Hierarchy self, ObjectKey a0) -> bool
2014 has_attribute(Hierarchy self, SparseFloatKey a0) -> bool
2015 has_attribute(Hierarchy self, SparseIntKey a0) -> bool
2016 has_attribute(Hierarchy self, SparseStringKey a0) -> bool
2017 has_attribute(Hierarchy self, SparseParticleIndexKey a0) -> bool
2019 return _IMP_atom.Hierarchy_has_attribute(self, *args)
2021 def get_derivative(self, a0):
2022 r"""get_derivative(Hierarchy self, FloatKey a0) -> double"""
2023 return _IMP_atom.Hierarchy_get_derivative(self, a0)
2026 r"""get_name(Hierarchy self) -> std::string"""
2027 return _IMP_atom.Hierarchy_get_name(self)
2029 def clear_caches(self):
2030 r"""clear_caches(Hierarchy self)"""
2031 return _IMP_atom.Hierarchy_clear_caches(self)
2033 def set_name(self, a0):
2034 r"""set_name(Hierarchy self, std::string a0)"""
2035 return _IMP_atom.Hierarchy_set_name(self, a0)
2038 r"""set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2039 return _IMP_atom.Hierarchy_set_check_level(self, a0)
2041 def add_to_derivative(self, a0, a1, a2):
2042 r"""add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2043 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2045 def set_is_optimized(self, a0, a1):
2046 r"""set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2047 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2049 def get_is_optimized(self, a0):
2050 r"""get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2051 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2054 r"""get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2055 return _IMP_atom.Hierarchy_get_check_level(self)
2057 def __eq__(self, *args):
2059 __eq__(Hierarchy self, Hierarchy o) -> bool
2060 __eq__(Hierarchy self, Particle d) -> bool
2062 return _IMP_atom.Hierarchy___eq__(self, *args)
2064 def __ne__(self, *args):
2066 __ne__(Hierarchy self, Hierarchy o) -> bool
2067 __ne__(Hierarchy self, Particle d) -> bool
2069 return _IMP_atom.Hierarchy___ne__(self, *args)
2071 def __le__(self, *args):
2073 __le__(Hierarchy self, Hierarchy o) -> bool
2074 __le__(Hierarchy self, Particle d) -> bool
2076 return _IMP_atom.Hierarchy___le__(self, *args)
2078 def __lt__(self, *args):
2080 __lt__(Hierarchy self, Hierarchy o) -> bool
2081 __lt__(Hierarchy self, Particle d) -> bool
2083 return _IMP_atom.Hierarchy___lt__(self, *args)
2085 def __ge__(self, *args):
2087 __ge__(Hierarchy self, Hierarchy o) -> bool
2088 __ge__(Hierarchy self, Particle d) -> bool
2090 return _IMP_atom.Hierarchy___ge__(self, *args)
2092 def __gt__(self, *args):
2094 __gt__(Hierarchy self, Hierarchy o) -> bool
2095 __gt__(Hierarchy self, Particle d) -> bool
2097 return _IMP_atom.Hierarchy___gt__(self, *args)
2100 r"""__hash__(Hierarchy self) -> std::size_t"""
2101 return _IMP_atom.Hierarchy___hash__(self)
2104 r"""__str__(Hierarchy self) -> std::string"""
2105 return _IMP_atom.Hierarchy___str__(self)
2108 r"""__repr__(Hierarchy self) -> std::string"""
2109 return _IMP_atom.Hierarchy___repr__(self)
2111 def _get_as_binary(self):
2112 r"""_get_as_binary(Hierarchy self) -> PyObject *"""
2113 return _IMP_atom.Hierarchy__get_as_binary(self)
2115 def _set_from_binary(self, p):
2116 r"""_set_from_binary(Hierarchy self, PyObject * p)"""
2117 return _IMP_atom.Hierarchy__set_from_binary(self, p)
2119 def __getstate__(self):
2120 p = self._get_as_binary()
2121 if len(self.__dict__) > 1:
2122 d = self.__dict__.copy()
2127 def __setstate__(self, p):
2128 if not hasattr(self,
'this'):
2130 if isinstance(p, tuple):
2132 self.__dict__.update(d)
2133 return self._set_from_binary(p)
2135 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2138 _IMP_atom.Hierarchy_swigregister(Hierarchy)
2139 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2141 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2143 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2145 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2147 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2149 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2151 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2153 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2155 MASS_TYPE = _IMP_atom.MASS_TYPE
2157 STATE_TYPE = _IMP_atom.STATE_TYPE
2160 def get_by_type(mhd, t):
2161 r"""get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2162 return _IMP_atom.get_by_type(mhd, t)
2164 def create_fragment(ps):
2165 r"""create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2166 return _IMP_atom.create_fragment(ps)
2168 def get_internal_bonds(mhd, with_representations=False):
2169 r"""get_internal_bonds(Hierarchy mhd, bool with_representations=False) -> IMP::atom::Bonds"""
2170 return _IMP_atom.get_internal_bonds(mhd, with_representations)
2173 r"""get_root(Hierarchy h) -> Hierarchy"""
2174 return _IMP_atom.get_root(h)
2177 r"""show(Hierarchy h, _ostream out=std::cout)"""
2178 return _IMP_atom.show(*args)
2182 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
2183 create_rigid_body(Hierarchy h) -> RigidBody
2185 return _IMP_atom.create_rigid_body(*args)
2188 r"""create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2189 return _IMP_atom.create_compatible_rigid_body(h, reference)
2191 def get_is_heterogen(h):
2192 r"""get_is_heterogen(Hierarchy h) -> bool"""
2193 return _IMP_atom.get_is_heterogen(h)
2196 r"""create_clone(Hierarchy d) -> Hierarchy"""
2197 return _IMP_atom.create_clone(d)
2199 def create_clone_one(d):
2200 r"""create_clone_one(Hierarchy d) -> Hierarchy"""
2201 return _IMP_atom.create_clone_one(d)
2204 r"""destroy(Hierarchy d)"""
2205 return _IMP_atom.destroy(d)
2207 def get_bounding_box(h):
2208 r"""get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2209 return _IMP_atom.get_bounding_box(h)
2211 def get_bounding_sphere(h):
2212 r"""get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2213 return _IMP_atom.get_bounding_sphere(h)
2215 r"""Proxy of C++ IMP::atom::Angle class."""
2217 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2219 def __init__(self, *args):
2221 __init__(Angle self) -> Angle
2222 __init__(Angle self, Model m, ParticleIndex id) -> Angle
2223 __init__(Angle self, _ParticleAdaptor d) -> Angle
2225 _IMP_atom.Angle_swiginit(self, _IMP_atom.new_Angle(*args))
2227 def show(self, *args):
2228 r"""show(Angle self, _ostream out=std::cout)"""
2229 return _IMP_atom.Angle_show(self, *args)
2232 def setup_particle(*args):
2234 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2235 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c) -> Angle
2237 return _IMP_atom.Angle_setup_particle(*args)
2240 def get_is_setup(*args):
2242 get_is_setup(_ParticleAdaptor p) -> bool
2243 get_is_setup(Model m, ParticleIndex pi) -> bool
2245 return _IMP_atom.Angle_get_is_setup(*args)
2247 def get_particle(self, *args):
2249 get_particle(Angle self) -> Particle
2250 get_particle(Angle self, unsigned int i) -> Particle
2252 return _IMP_atom.Angle_get_particle(self, *args)
2254 def get_ideal(self):
2255 r"""get_ideal(Angle self) -> IMP::Float"""
2256 return _IMP_atom.Angle_get_ideal(self)
2258 def set_ideal(self, t):
2259 r"""set_ideal(Angle self, IMP::Float t)"""
2260 return _IMP_atom.Angle_set_ideal(self, t)
2262 def get_stiffness(self):
2263 r"""get_stiffness(Angle self) -> IMP::Float"""
2264 return _IMP_atom.Angle_get_stiffness(self)
2266 def set_stiffness(self, t):
2267 r"""set_stiffness(Angle self, IMP::Float t)"""
2268 return _IMP_atom.Angle_set_stiffness(self, t)
2271 def get_particle_key(i):
2272 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2273 return _IMP_atom.Angle_get_particle_key(i)
2276 def get_ideal_key():
2277 r"""get_ideal_key() -> FloatKey"""
2278 return _IMP_atom.Angle_get_ideal_key()
2281 def get_stiffness_key():
2282 r"""get_stiffness_key() -> FloatKey"""
2283 return _IMP_atom.Angle_get_stiffness_key()
2285 def add_attribute(self, *args):
2287 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2288 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2289 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2290 add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2291 add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2292 add_attribute(Angle self, StringKey a0, IMP::String a1)
2293 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2294 add_attribute(Angle self, ObjectKey a0, Object a1)
2295 add_attribute(Angle self, SparseFloatKey a0, IMP::Float a1)
2296 add_attribute(Angle self, SparseIntKey a0, IMP::Int a1)
2297 add_attribute(Angle self, SparseStringKey a0, IMP::String a1)
2298 add_attribute(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2300 return _IMP_atom.Angle_add_attribute(self, *args)
2302 def get_value(self, *args):
2304 get_value(Angle self, FloatKey a0) -> IMP::Float
2305 get_value(Angle self, IntKey a0) -> IMP::Int
2306 get_value(Angle self, FloatsKey a0) -> IMP::Floats
2307 get_value(Angle self, IntsKey a0) -> IMP::Ints
2308 get_value(Angle self, StringKey a0) -> IMP::String
2309 get_value(Angle self, ParticleIndexKey a0) -> Particle
2310 get_value(Angle self, ObjectKey a0) -> Object
2311 get_value(Angle self, SparseFloatKey a0) -> IMP::Float
2312 get_value(Angle self, SparseIntKey a0) -> IMP::Int
2313 get_value(Angle self, SparseStringKey a0) -> IMP::String
2314 get_value(Angle self, SparseParticleIndexKey a0) -> ParticleIndex
2316 return _IMP_atom.Angle_get_value(self, *args)
2318 def set_value(self, *args):
2320 set_value(Angle self, FloatKey a0, IMP::Float a1)
2321 set_value(Angle self, IntKey a0, IMP::Int a1)
2322 set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2323 set_value(Angle self, IntsKey a0, IMP::Ints a1)
2324 set_value(Angle self, StringKey a0, IMP::String a1)
2325 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2326 set_value(Angle self, ObjectKey a0, Object a1)
2327 set_value(Angle self, SparseFloatKey a0, IMP::Float a1)
2328 set_value(Angle self, SparseIntKey a0, IMP::Int a1)
2329 set_value(Angle self, SparseStringKey a0, IMP::String a1)
2330 set_value(Angle self, SparseParticleIndexKey a0, ParticleIndex a1)
2332 return _IMP_atom.Angle_set_value(self, *args)
2334 def remove_attribute(self, *args):
2336 remove_attribute(Angle self, FloatKey a0)
2337 remove_attribute(Angle self, IntKey a0)
2338 remove_attribute(Angle self, FloatsKey a0)
2339 remove_attribute(Angle self, IntsKey a0)
2340 remove_attribute(Angle self, StringKey a0)
2341 remove_attribute(Angle self, ParticleIndexKey a0)
2342 remove_attribute(Angle self, ObjectKey a0)
2343 remove_attribute(Angle self, SparseFloatKey a0)
2344 remove_attribute(Angle self, SparseIntKey a0)
2345 remove_attribute(Angle self, SparseStringKey a0)
2346 remove_attribute(Angle self, SparseParticleIndexKey a0)
2348 return _IMP_atom.Angle_remove_attribute(self, *args)
2350 def has_attribute(self, *args):
2352 has_attribute(Angle self, FloatKey a0) -> bool
2353 has_attribute(Angle self, IntKey a0) -> bool
2354 has_attribute(Angle self, FloatsKey a0) -> bool
2355 has_attribute(Angle self, IntsKey a0) -> bool
2356 has_attribute(Angle self, StringKey a0) -> bool
2357 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2358 has_attribute(Angle self, ObjectKey a0) -> bool
2359 has_attribute(Angle self, SparseFloatKey a0) -> bool
2360 has_attribute(Angle self, SparseIntKey a0) -> bool
2361 has_attribute(Angle self, SparseStringKey a0) -> bool
2362 has_attribute(Angle self, SparseParticleIndexKey a0) -> bool
2364 return _IMP_atom.Angle_has_attribute(self, *args)
2366 def get_derivative(self, a0):
2367 r"""get_derivative(Angle self, FloatKey a0) -> double"""
2368 return _IMP_atom.Angle_get_derivative(self, a0)
2371 r"""get_name(Angle self) -> std::string"""
2372 return _IMP_atom.Angle_get_name(self)
2374 def clear_caches(self):
2375 r"""clear_caches(Angle self)"""
2376 return _IMP_atom.Angle_clear_caches(self)
2378 def set_name(self, a0):
2379 r"""set_name(Angle self, std::string a0)"""
2380 return _IMP_atom.Angle_set_name(self, a0)
2383 r"""set_check_level(Angle self, IMP::CheckLevel a0)"""
2384 return _IMP_atom.Angle_set_check_level(self, a0)
2386 def add_to_derivative(self, a0, a1, a2):
2387 r"""add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2388 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2390 def set_is_optimized(self, a0, a1):
2391 r"""set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2392 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2394 def get_is_optimized(self, a0):
2395 r"""get_is_optimized(Angle self, FloatKey a0) -> bool"""
2396 return _IMP_atom.Angle_get_is_optimized(self, a0)
2399 r"""get_check_level(Angle self) -> IMP::CheckLevel"""
2400 return _IMP_atom.Angle_get_check_level(self)
2402 def __eq__(self, *args):
2404 __eq__(Angle self, Angle o) -> bool
2405 __eq__(Angle self, Particle d) -> bool
2407 return _IMP_atom.Angle___eq__(self, *args)
2409 def __ne__(self, *args):
2411 __ne__(Angle self, Angle o) -> bool
2412 __ne__(Angle self, Particle d) -> bool
2414 return _IMP_atom.Angle___ne__(self, *args)
2416 def __le__(self, *args):
2418 __le__(Angle self, Angle o) -> bool
2419 __le__(Angle self, Particle d) -> bool
2421 return _IMP_atom.Angle___le__(self, *args)
2423 def __lt__(self, *args):
2425 __lt__(Angle self, Angle o) -> bool
2426 __lt__(Angle self, Particle d) -> bool
2428 return _IMP_atom.Angle___lt__(self, *args)
2430 def __ge__(self, *args):
2432 __ge__(Angle self, Angle o) -> bool
2433 __ge__(Angle self, Particle d) -> bool
2435 return _IMP_atom.Angle___ge__(self, *args)
2437 def __gt__(self, *args):
2439 __gt__(Angle self, Angle o) -> bool
2440 __gt__(Angle self, Particle d) -> bool
2442 return _IMP_atom.Angle___gt__(self, *args)
2445 r"""__hash__(Angle self) -> std::size_t"""
2446 return _IMP_atom.Angle___hash__(self)
2449 r"""__str__(Angle self) -> std::string"""
2450 return _IMP_atom.Angle___str__(self)
2453 r"""__repr__(Angle self) -> std::string"""
2454 return _IMP_atom.Angle___repr__(self)
2456 def _get_as_binary(self):
2457 r"""_get_as_binary(Angle self) -> PyObject *"""
2458 return _IMP_atom.Angle__get_as_binary(self)
2460 def _set_from_binary(self, p):
2461 r"""_set_from_binary(Angle self, PyObject * p)"""
2462 return _IMP_atom.Angle__set_from_binary(self, p)
2464 def __getstate__(self):
2465 p = self._get_as_binary()
2466 if len(self.__dict__) > 1:
2467 d = self.__dict__.copy()
2472 def __setstate__(self, p):
2473 if not hasattr(self,
'this'):
2475 if isinstance(p, tuple):
2477 self.__dict__.update(d)
2478 return self._set_from_binary(p)
2480 __swig_destroy__ = _IMP_atom.delete_Angle
2483 _IMP_atom.Angle_swigregister(Angle)
2485 r"""Proxy of C++ IMP::atom::Dihedral class."""
2487 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2489 def __init__(self, *args):
2491 __init__(Dihedral self) -> Dihedral
2492 __init__(Dihedral self, Model m, ParticleIndex id) -> Dihedral
2493 __init__(Dihedral self, _ParticleAdaptor d) -> Dihedral
2495 _IMP_atom.Dihedral_swiginit(self, _IMP_atom.new_Dihedral(*args))
2497 def show(self, *args):
2498 r"""show(Dihedral self, _ostream out=std::cout)"""
2499 return _IMP_atom.Dihedral_show(self, *args)
2502 def setup_particle(*args):
2504 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2505 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2507 return _IMP_atom.Dihedral_setup_particle(*args)
2510 def get_is_setup(*args):
2512 get_is_setup(_ParticleAdaptor p) -> bool
2513 get_is_setup(Model m, ParticleIndex pi) -> bool
2515 return _IMP_atom.Dihedral_get_is_setup(*args)
2517 def get_particle(self, *args):
2519 get_particle(Dihedral self) -> Particle
2520 get_particle(Dihedral self, unsigned int i) -> Particle
2522 return _IMP_atom.Dihedral_get_particle(self, *args)
2524 def get_ideal(self):
2525 r"""get_ideal(Dihedral self) -> IMP::Float"""
2526 return _IMP_atom.Dihedral_get_ideal(self)
2528 def set_ideal(self, t):
2529 r"""set_ideal(Dihedral self, IMP::Float t)"""
2530 return _IMP_atom.Dihedral_set_ideal(self, t)
2532 def get_multiplicity(self):
2533 r"""get_multiplicity(Dihedral self) -> IMP::Int"""
2534 return _IMP_atom.Dihedral_get_multiplicity(self)
2536 def set_multiplicity(self, t):
2537 r"""set_multiplicity(Dihedral self, IMP::Int t)"""
2538 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2540 def get_stiffness(self):
2541 r"""get_stiffness(Dihedral self) -> IMP::Float"""
2542 return _IMP_atom.Dihedral_get_stiffness(self)
2544 def set_stiffness(self, t):
2545 r"""set_stiffness(Dihedral self, IMP::Float t)"""
2546 return _IMP_atom.Dihedral_set_stiffness(self, t)
2549 def get_particle_key(i):
2550 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2551 return _IMP_atom.Dihedral_get_particle_key(i)
2554 def get_ideal_key():
2555 r"""get_ideal_key() -> FloatKey"""
2556 return _IMP_atom.Dihedral_get_ideal_key()
2559 def get_multiplicity_key():
2560 r"""get_multiplicity_key() -> IntKey"""
2561 return _IMP_atom.Dihedral_get_multiplicity_key()
2564 def get_stiffness_key():
2565 r"""get_stiffness_key() -> FloatKey"""
2566 return _IMP_atom.Dihedral_get_stiffness_key()
2568 def add_attribute(self, *args):
2570 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2571 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2572 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2573 add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2574 add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2575 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2576 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2577 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2578 add_attribute(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2579 add_attribute(Dihedral self, SparseIntKey a0, IMP::Int a1)
2580 add_attribute(Dihedral self, SparseStringKey a0, IMP::String a1)
2581 add_attribute(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2583 return _IMP_atom.Dihedral_add_attribute(self, *args)
2585 def get_value(self, *args):
2587 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2588 get_value(Dihedral self, IntKey a0) -> IMP::Int
2589 get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2590 get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2591 get_value(Dihedral self, StringKey a0) -> IMP::String
2592 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2593 get_value(Dihedral self, ObjectKey a0) -> Object
2594 get_value(Dihedral self, SparseFloatKey a0) -> IMP::Float
2595 get_value(Dihedral self, SparseIntKey a0) -> IMP::Int
2596 get_value(Dihedral self, SparseStringKey a0) -> IMP::String
2597 get_value(Dihedral self, SparseParticleIndexKey a0) -> ParticleIndex
2599 return _IMP_atom.Dihedral_get_value(self, *args)
2601 def set_value(self, *args):
2603 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2604 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2605 set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2606 set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2607 set_value(Dihedral self, StringKey a0, IMP::String a1)
2608 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2609 set_value(Dihedral self, ObjectKey a0, Object a1)
2610 set_value(Dihedral self, SparseFloatKey a0, IMP::Float a1)
2611 set_value(Dihedral self, SparseIntKey a0, IMP::Int a1)
2612 set_value(Dihedral self, SparseStringKey a0, IMP::String a1)
2613 set_value(Dihedral self, SparseParticleIndexKey a0, ParticleIndex a1)
2615 return _IMP_atom.Dihedral_set_value(self, *args)
2617 def remove_attribute(self, *args):
2619 remove_attribute(Dihedral self, FloatKey a0)
2620 remove_attribute(Dihedral self, IntKey a0)
2621 remove_attribute(Dihedral self, FloatsKey a0)
2622 remove_attribute(Dihedral self, IntsKey a0)
2623 remove_attribute(Dihedral self, StringKey a0)
2624 remove_attribute(Dihedral self, ParticleIndexKey a0)
2625 remove_attribute(Dihedral self, ObjectKey a0)
2626 remove_attribute(Dihedral self, SparseFloatKey a0)
2627 remove_attribute(Dihedral self, SparseIntKey a0)
2628 remove_attribute(Dihedral self, SparseStringKey a0)
2629 remove_attribute(Dihedral self, SparseParticleIndexKey a0)
2631 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2633 def has_attribute(self, *args):
2635 has_attribute(Dihedral self, FloatKey a0) -> bool
2636 has_attribute(Dihedral self, IntKey a0) -> bool
2637 has_attribute(Dihedral self, FloatsKey a0) -> bool
2638 has_attribute(Dihedral self, IntsKey a0) -> bool
2639 has_attribute(Dihedral self, StringKey a0) -> bool
2640 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2641 has_attribute(Dihedral self, ObjectKey a0) -> bool
2642 has_attribute(Dihedral self, SparseFloatKey a0) -> bool
2643 has_attribute(Dihedral self, SparseIntKey a0) -> bool
2644 has_attribute(Dihedral self, SparseStringKey a0) -> bool
2645 has_attribute(Dihedral self, SparseParticleIndexKey a0) -> bool
2647 return _IMP_atom.Dihedral_has_attribute(self, *args)
2649 def get_derivative(self, a0):
2650 r"""get_derivative(Dihedral self, FloatKey a0) -> double"""
2651 return _IMP_atom.Dihedral_get_derivative(self, a0)
2654 r"""get_name(Dihedral self) -> std::string"""
2655 return _IMP_atom.Dihedral_get_name(self)
2657 def clear_caches(self):
2658 r"""clear_caches(Dihedral self)"""
2659 return _IMP_atom.Dihedral_clear_caches(self)
2661 def set_name(self, a0):
2662 r"""set_name(Dihedral self, std::string a0)"""
2663 return _IMP_atom.Dihedral_set_name(self, a0)
2666 r"""set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2667 return _IMP_atom.Dihedral_set_check_level(self, a0)
2669 def add_to_derivative(self, a0, a1, a2):
2670 r"""add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2671 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2673 def set_is_optimized(self, a0, a1):
2674 r"""set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2675 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2677 def get_is_optimized(self, a0):
2678 r"""get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2679 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2682 r"""get_check_level(Dihedral self) -> IMP::CheckLevel"""
2683 return _IMP_atom.Dihedral_get_check_level(self)
2685 def __eq__(self, *args):
2687 __eq__(Dihedral self, Dihedral o) -> bool
2688 __eq__(Dihedral self, Particle d) -> bool
2690 return _IMP_atom.Dihedral___eq__(self, *args)
2692 def __ne__(self, *args):
2694 __ne__(Dihedral self, Dihedral o) -> bool
2695 __ne__(Dihedral self, Particle d) -> bool
2697 return _IMP_atom.Dihedral___ne__(self, *args)
2699 def __le__(self, *args):
2701 __le__(Dihedral self, Dihedral o) -> bool
2702 __le__(Dihedral self, Particle d) -> bool
2704 return _IMP_atom.Dihedral___le__(self, *args)
2706 def __lt__(self, *args):
2708 __lt__(Dihedral self, Dihedral o) -> bool
2709 __lt__(Dihedral self, Particle d) -> bool
2711 return _IMP_atom.Dihedral___lt__(self, *args)
2713 def __ge__(self, *args):
2715 __ge__(Dihedral self, Dihedral o) -> bool
2716 __ge__(Dihedral self, Particle d) -> bool
2718 return _IMP_atom.Dihedral___ge__(self, *args)
2720 def __gt__(self, *args):
2722 __gt__(Dihedral self, Dihedral o) -> bool
2723 __gt__(Dihedral self, Particle d) -> bool
2725 return _IMP_atom.Dihedral___gt__(self, *args)
2728 r"""__hash__(Dihedral self) -> std::size_t"""
2729 return _IMP_atom.Dihedral___hash__(self)
2732 r"""__str__(Dihedral self) -> std::string"""
2733 return _IMP_atom.Dihedral___str__(self)
2736 r"""__repr__(Dihedral self) -> std::string"""
2737 return _IMP_atom.Dihedral___repr__(self)
2739 def _get_as_binary(self):
2740 r"""_get_as_binary(Dihedral self) -> PyObject *"""
2741 return _IMP_atom.Dihedral__get_as_binary(self)
2743 def _set_from_binary(self, p):
2744 r"""_set_from_binary(Dihedral self, PyObject * p)"""
2745 return _IMP_atom.Dihedral__set_from_binary(self, p)
2747 def __getstate__(self):
2748 p = self._get_as_binary()
2749 if len(self.__dict__) > 1:
2750 d = self.__dict__.copy()
2755 def __setstate__(self, p):
2756 if not hasattr(self,
'this'):
2758 if isinstance(p, tuple):
2760 self.__dict__.update(d)
2761 return self._set_from_binary(p)
2763 __swig_destroy__ = _IMP_atom.delete_Dihedral
2766 _IMP_atom.Dihedral_swigregister(Dihedral)
2768 r"""Proxy of C++ IMP::atom::SmoothingFunction class."""
2770 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2772 def __init__(self, *args, **kwargs):
2773 raise AttributeError(
"No constructor defined - class is abstract")
2775 def __call__(self, *args):
2777 __call__(SmoothingFunction self, double score, double distance) -> double
2778 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2780 return _IMP_atom.SmoothingFunction___call__(self, *args)
2781 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2784 r"""__str__(SmoothingFunction self) -> std::string"""
2785 return _IMP_atom.SmoothingFunction___str__(self)
2788 r"""__repr__(SmoothingFunction self) -> std::string"""
2789 return _IMP_atom.SmoothingFunction___repr__(self)
2793 return _object_cast_to_SmoothingFunction(o)
2797 _IMP_atom.SmoothingFunction_swigregister(SmoothingFunction)
2798 class ForceSwitch(SmoothingFunction):
2799 r"""Proxy of C++ IMP::atom::ForceSwitch class."""
2801 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2803 def __init__(self, min_distance, max_distance):
2804 r"""__init__(ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2805 _IMP_atom.ForceSwitch_swiginit(self, _IMP_atom.new_ForceSwitch(min_distance, max_distance))
2807 def __call__(self, *args):
2809 __call__(ForceSwitch self, double score, double distance) -> double
2810 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2812 return _IMP_atom.ForceSwitch___call__(self, *args)
2814 def get_version_info(self):
2815 r"""get_version_info(ForceSwitch self) -> VersionInfo"""
2816 return _IMP_atom.ForceSwitch_get_version_info(self)
2817 __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2820 r"""__str__(ForceSwitch self) -> std::string"""
2821 return _IMP_atom.ForceSwitch___str__(self)
2824 r"""__repr__(ForceSwitch self) -> std::string"""
2825 return _IMP_atom.ForceSwitch___repr__(self)
2829 return _object_cast_to_ForceSwitch(o)
2833 _IMP_atom.ForceSwitch_swigregister(ForceSwitch)
2835 r"""Proxy of C++ IMP::atom::AngleSingletonScore class."""
2837 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2839 def __init__(self, f):
2840 r"""__init__(AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2841 _IMP_atom.AngleSingletonScore_swiginit(self, _IMP_atom.new_AngleSingletonScore(f))
2843 def do_get_inputs(self, m, pis):
2844 r"""do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2845 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2847 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
2848 r"""evaluate_indexes(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2849 return _IMP_atom.AngleSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
2851 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
2852 r"""evaluate_indexes_scores(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2853 return _IMP_atom.AngleSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
2855 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
2856 r"""evaluate_indexes_delta(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2857 return _IMP_atom.AngleSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
2859 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
2860 r"""evaluate_if_good_indexes(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2861 return _IMP_atom.AngleSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
2863 def get_version_info(self):
2864 r"""get_version_info(AngleSingletonScore self) -> VersionInfo"""
2865 return _IMP_atom.AngleSingletonScore_get_version_info(self)
2866 __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2869 r"""__str__(AngleSingletonScore self) -> std::string"""
2870 return _IMP_atom.AngleSingletonScore___str__(self)
2873 r"""__repr__(AngleSingletonScore self) -> std::string"""
2874 return _IMP_atom.AngleSingletonScore___repr__(self)
2878 return _object_cast_to_AngleSingletonScore(o)
2882 _IMP_atom.AngleSingletonScore_swigregister(AngleSingletonScore)
2884 r"""Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2886 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2889 r"""__init__(BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2890 _IMP_atom.BondEndpointsRefiner_swiginit(self, _IMP_atom.new_BondEndpointsRefiner())
2892 def do_get_inputs(self, m, pis):
2893 r"""do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2894 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2896 def get_version_info(self):
2897 r"""get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2898 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2899 __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2902 r"""__str__(BondEndpointsRefiner self) -> std::string"""
2903 return _IMP_atom.BondEndpointsRefiner___str__(self)
2906 r"""__repr__(BondEndpointsRefiner self) -> std::string"""
2907 return _IMP_atom.BondEndpointsRefiner___repr__(self)
2911 return _object_cast_to_BondEndpointsRefiner(o)
2915 _IMP_atom.BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2917 r"""Proxy of C++ IMP::atom::BondPairContainer class."""
2919 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2921 def __init__(self, sc):
2922 r"""__init__(BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2923 _IMP_atom.BondPairContainer_swiginit(self, _IMP_atom.new_BondPairContainer(sc))
2925 def do_get_inputs(self):
2926 r"""do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2927 return _IMP_atom.BondPairContainer_do_get_inputs(self)
2929 def do_apply(self, sm):
2930 r"""do_apply(BondPairContainer self, PairModifier sm)"""
2931 return _IMP_atom.BondPairContainer_do_apply(self, sm)
2933 def do_apply_moved(self, sm, moved_pis, reset_pis):
2934 r"""do_apply_moved(BondPairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
2935 return _IMP_atom.BondPairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
2937 def get_version_info(self):
2938 r"""get_version_info(BondPairContainer self) -> VersionInfo"""
2939 return _IMP_atom.BondPairContainer_get_version_info(self)
2940 __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2943 r"""__str__(BondPairContainer self) -> std::string"""
2944 return _IMP_atom.BondPairContainer___str__(self)
2947 r"""__repr__(BondPairContainer self) -> std::string"""
2948 return _IMP_atom.BondPairContainer___repr__(self)
2952 return _object_cast_to_BondPairContainer(o)
2956 _IMP_atom.BondPairContainer_swigregister(BondPairContainer)
2958 r"""Proxy of C++ IMP::atom::BondSingletonScore class."""
2960 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2962 def __init__(self, f):
2963 r"""__init__(BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2964 _IMP_atom.BondSingletonScore_swiginit(self, _IMP_atom.new_BondSingletonScore(f))
2966 def get_unary_function(self):
2967 r"""get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2968 return _IMP_atom.BondSingletonScore_get_unary_function(self)
2970 def do_get_inputs(self, m, pis):
2971 r"""do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2972 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2974 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
2975 r"""evaluate_indexes(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2976 return _IMP_atom.BondSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
2978 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
2979 r"""evaluate_indexes_scores(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2980 return _IMP_atom.BondSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
2982 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
2983 r"""evaluate_indexes_delta(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
2984 return _IMP_atom.BondSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
2986 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
2987 r"""evaluate_if_good_indexes(BondSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
2988 return _IMP_atom.BondSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
2990 def get_version_info(self):
2991 r"""get_version_info(BondSingletonScore self) -> VersionInfo"""
2992 return _IMP_atom.BondSingletonScore_get_version_info(self)
2993 __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2996 r"""__str__(BondSingletonScore self) -> std::string"""
2997 return _IMP_atom.BondSingletonScore___str__(self)
3000 r"""__repr__(BondSingletonScore self) -> std::string"""
3001 return _IMP_atom.BondSingletonScore___repr__(self)
3005 return _object_cast_to_BondSingletonScore(o)
3009 _IMP_atom.BondSingletonScore_swigregister(BondSingletonScore)
3011 r"""Proxy of C++ IMP::atom::DihedralSingletonScore class."""
3013 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3016 r"""__init__(DihedralSingletonScore self) -> DihedralSingletonScore"""
3017 _IMP_atom.DihedralSingletonScore_swiginit(self, _IMP_atom.new_DihedralSingletonScore())
3019 def do_get_inputs(self, m, pis):
3020 r"""do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3021 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3023 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
3024 r"""evaluate_indexes(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3025 return _IMP_atom.DihedralSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
3027 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
3028 r"""evaluate_indexes_scores(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3029 return _IMP_atom.DihedralSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
3031 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
3032 r"""evaluate_indexes_delta(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3033 return _IMP_atom.DihedralSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
3035 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
3036 r"""evaluate_if_good_indexes(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3037 return _IMP_atom.DihedralSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
3039 def get_version_info(self):
3040 r"""get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3041 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3042 __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
3045 r"""__str__(DihedralSingletonScore self) -> std::string"""
3046 return _IMP_atom.DihedralSingletonScore___str__(self)
3049 r"""__repr__(DihedralSingletonScore self) -> std::string"""
3050 return _IMP_atom.DihedralSingletonScore___repr__(self)
3054 return _object_cast_to_DihedralSingletonScore(o)
3057 def _get_as_binary(self):
3058 r"""_get_as_binary(DihedralSingletonScore self) -> PyObject *"""
3059 return _IMP_atom.DihedralSingletonScore__get_as_binary(self)
3061 def _set_from_binary(self, p):
3062 r"""_set_from_binary(DihedralSingletonScore self, PyObject * p)"""
3063 return _IMP_atom.DihedralSingletonScore__set_from_binary(self, p)
3065 def __getstate__(self):
3066 p = self._get_as_binary()
3067 if len(self.__dict__) > 1:
3068 d = self.__dict__.copy()
3073 def __setstate__(self, p):
3074 if not hasattr(self,
'this'):
3076 if isinstance(p, tuple):
3078 self.__dict__.update(d)
3079 return self._set_from_binary(p)
3083 _IMP_atom.DihedralSingletonScore_swigregister(DihedralSingletonScore)
3085 r"""Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3087 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3089 def __init__(self, f):
3090 r"""__init__(ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3091 _IMP_atom.ImproperSingletonScore_swiginit(self, _IMP_atom.new_ImproperSingletonScore(f))
3093 def do_get_inputs(self, m, pis):
3094 r"""do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3095 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3097 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
3098 r"""evaluate_indexes(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3099 return _IMP_atom.ImproperSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
3101 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
3102 r"""evaluate_indexes_scores(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3103 return _IMP_atom.ImproperSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
3105 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
3106 r"""evaluate_indexes_delta(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
3107 return _IMP_atom.ImproperSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
3109 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
3110 r"""evaluate_if_good_indexes(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
3111 return _IMP_atom.ImproperSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
3113 def get_version_info(self):
3114 r"""get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3115 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3116 __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
3119 r"""__str__(ImproperSingletonScore self) -> std::string"""
3120 return _IMP_atom.ImproperSingletonScore___str__(self)
3123 r"""__repr__(ImproperSingletonScore self) -> std::string"""
3124 return _IMP_atom.ImproperSingletonScore___repr__(self)
3128 return _object_cast_to_ImproperSingletonScore(o)
3132 _IMP_atom.ImproperSingletonScore_swigregister(ImproperSingletonScore)
3134 r"""Proxy of C++ IMP::atom::CenterOfMass class."""
3136 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3138 def get_constraint(self):
3139 r"""get_constraint(CenterOfMass self) -> Constraint"""
3140 return _IMP_atom.CenterOfMass_get_constraint(self)
3143 r"""get_mass(CenterOfMass self) -> IMP::Float"""
3144 return _IMP_atom.CenterOfMass_get_mass(self)
3146 def get_coordinate(self, i):
3147 r"""get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3148 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3150 def get_coordinates(self):
3151 r"""get_coordinates(CenterOfMass self) -> Vector3D"""
3152 return _IMP_atom.CenterOfMass_get_coordinates(self)
3154 def __init__(self, *args):
3156 __init__(CenterOfMass self) -> CenterOfMass
3157 __init__(CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3158 __init__(CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3160 _IMP_atom.CenterOfMass_swiginit(self, _IMP_atom.new_CenterOfMass(*args))
3162 def show(self, *args):
3163 r"""show(CenterOfMass self, _ostream out=std::cout)"""
3164 return _IMP_atom.CenterOfMass_show(self, *args)
3167 def setup_particle(*args):
3169 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3170 setup_particle(_ParticleAdaptor pa, _ParticleIndexesAdaptor members) -> CenterOfMass
3171 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3172 setup_particle(_ParticleAdaptor pa, Refiner refiner) -> CenterOfMass
3174 return _IMP_atom.CenterOfMass_setup_particle(*args)
3177 def teardown_particle(com):
3178 r"""teardown_particle(CenterOfMass com)"""
3179 return _IMP_atom.CenterOfMass_teardown_particle(com)
3182 def get_is_setup(*args):
3184 get_is_setup(_ParticleAdaptor p) -> bool
3185 get_is_setup(Model m, ParticleIndex pi) -> bool
3187 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3189 def add_attribute(self, *args):
3191 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3192 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3193 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3194 add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3195 add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3196 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3197 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3198 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3199 add_attribute(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3200 add_attribute(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3201 add_attribute(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3202 add_attribute(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3204 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3206 def get_value(self, *args):
3208 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3209 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3210 get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3211 get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3212 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3213 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3214 get_value(CenterOfMass self, ObjectKey a0) -> Object
3215 get_value(CenterOfMass self, SparseFloatKey a0) -> IMP::Float
3216 get_value(CenterOfMass self, SparseIntKey a0) -> IMP::Int
3217 get_value(CenterOfMass self, SparseStringKey a0) -> IMP::String
3218 get_value(CenterOfMass self, SparseParticleIndexKey a0) -> ParticleIndex
3220 return _IMP_atom.CenterOfMass_get_value(self, *args)
3222 def set_value(self, *args):
3224 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3225 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3226 set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3227 set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3228 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3229 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3230 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3231 set_value(CenterOfMass self, SparseFloatKey a0, IMP::Float a1)
3232 set_value(CenterOfMass self, SparseIntKey a0, IMP::Int a1)
3233 set_value(CenterOfMass self, SparseStringKey a0, IMP::String a1)
3234 set_value(CenterOfMass self, SparseParticleIndexKey a0, ParticleIndex a1)
3236 return _IMP_atom.CenterOfMass_set_value(self, *args)
3238 def remove_attribute(self, *args):
3240 remove_attribute(CenterOfMass self, FloatKey a0)
3241 remove_attribute(CenterOfMass self, IntKey a0)
3242 remove_attribute(CenterOfMass self, FloatsKey a0)
3243 remove_attribute(CenterOfMass self, IntsKey a0)
3244 remove_attribute(CenterOfMass self, StringKey a0)
3245 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3246 remove_attribute(CenterOfMass self, ObjectKey a0)
3247 remove_attribute(CenterOfMass self, SparseFloatKey a0)
3248 remove_attribute(CenterOfMass self, SparseIntKey a0)
3249 remove_attribute(CenterOfMass self, SparseStringKey a0)
3250 remove_attribute(CenterOfMass self, SparseParticleIndexKey a0)
3252 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3254 def has_attribute(self, *args):
3256 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3257 has_attribute(CenterOfMass self, IntKey a0) -> bool
3258 has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3259 has_attribute(CenterOfMass self, IntsKey a0) -> bool
3260 has_attribute(CenterOfMass self, StringKey a0) -> bool
3261 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3262 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3263 has_attribute(CenterOfMass self, SparseFloatKey a0) -> bool
3264 has_attribute(CenterOfMass self, SparseIntKey a0) -> bool
3265 has_attribute(CenterOfMass self, SparseStringKey a0) -> bool
3266 has_attribute(CenterOfMass self, SparseParticleIndexKey a0) -> bool
3268 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3270 def get_derivative(self, a0):
3271 r"""get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3272 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3275 r"""get_name(CenterOfMass self) -> std::string"""
3276 return _IMP_atom.CenterOfMass_get_name(self)
3278 def clear_caches(self):
3279 r"""clear_caches(CenterOfMass self)"""
3280 return _IMP_atom.CenterOfMass_clear_caches(self)
3282 def set_name(self, a0):
3283 r"""set_name(CenterOfMass self, std::string a0)"""
3284 return _IMP_atom.CenterOfMass_set_name(self, a0)
3287 r"""set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3288 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3290 def add_to_derivative(self, a0, a1, a2):
3291 r"""add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3292 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3294 def set_is_optimized(self, a0, a1):
3295 r"""set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3296 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3298 def get_is_optimized(self, a0):
3299 r"""get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3300 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3303 r"""get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3304 return _IMP_atom.CenterOfMass_get_check_level(self)
3306 def __eq__(self, *args):
3308 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3309 __eq__(CenterOfMass self, Particle d) -> bool
3311 return _IMP_atom.CenterOfMass___eq__(self, *args)
3313 def __ne__(self, *args):
3315 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3316 __ne__(CenterOfMass self, Particle d) -> bool
3318 return _IMP_atom.CenterOfMass___ne__(self, *args)
3320 def __le__(self, *args):
3322 __le__(CenterOfMass self, CenterOfMass o) -> bool
3323 __le__(CenterOfMass self, Particle d) -> bool
3325 return _IMP_atom.CenterOfMass___le__(self, *args)
3327 def __lt__(self, *args):
3329 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3330 __lt__(CenterOfMass self, Particle d) -> bool
3332 return _IMP_atom.CenterOfMass___lt__(self, *args)
3334 def __ge__(self, *args):
3336 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3337 __ge__(CenterOfMass self, Particle d) -> bool
3339 return _IMP_atom.CenterOfMass___ge__(self, *args)
3341 def __gt__(self, *args):
3343 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3344 __gt__(CenterOfMass self, Particle d) -> bool
3346 return _IMP_atom.CenterOfMass___gt__(self, *args)
3349 r"""__hash__(CenterOfMass self) -> std::size_t"""
3350 return _IMP_atom.CenterOfMass___hash__(self)
3353 r"""__str__(CenterOfMass self) -> std::string"""
3354 return _IMP_atom.CenterOfMass___str__(self)
3357 r"""__repr__(CenterOfMass self) -> std::string"""
3358 return _IMP_atom.CenterOfMass___repr__(self)
3360 def _get_as_binary(self):
3361 r"""_get_as_binary(CenterOfMass self) -> PyObject *"""
3362 return _IMP_atom.CenterOfMass__get_as_binary(self)
3364 def _set_from_binary(self, p):
3365 r"""_set_from_binary(CenterOfMass self, PyObject * p)"""
3366 return _IMP_atom.CenterOfMass__set_from_binary(self, p)
3368 def __getstate__(self):
3369 p = self._get_as_binary()
3370 if len(self.__dict__) > 1:
3371 d = self.__dict__.copy()
3376 def __setstate__(self, p):
3377 if not hasattr(self,
'this'):
3379 if isinstance(p, tuple):
3381 self.__dict__.update(d)
3382 return self._set_from_binary(p)
3384 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3387 _IMP_atom.CenterOfMass_swigregister(CenterOfMass)
3389 r"""Proxy of C++ IMP::atom::CoverBond class."""
3391 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3394 r"""__init__(CoverBond self) -> CoverBond"""
3395 _IMP_atom.CoverBond_swiginit(self, _IMP_atom.new_CoverBond())
3397 def do_get_inputs(self, m, pis):
3398 r"""do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3399 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3401 def do_get_outputs(self, m, pis):
3402 r"""do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3403 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3405 def get_version_info(self):
3406 r"""get_version_info(CoverBond self) -> VersionInfo"""
3407 return _IMP_atom.CoverBond_get_version_info(self)
3408 __swig_destroy__ = _IMP_atom.delete_CoverBond
3411 r"""__str__(CoverBond self) -> std::string"""
3412 return _IMP_atom.CoverBond___str__(self)
3415 r"""__repr__(CoverBond self) -> std::string"""
3416 return _IMP_atom.CoverBond___repr__(self)
3420 return _object_cast_to_CoverBond(o)
3424 _IMP_atom.CoverBond_swigregister(CoverBond)
3426 r"""Proxy of C++ IMP::atom::Simulator class."""
3428 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3430 def __init__(self, *args):
3431 r"""__init__(Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator"""
3432 if self.__class__ == Simulator:
3436 _IMP_atom.Simulator_swiginit(self, _IMP_atom.new_Simulator(_self, *args))
3438 if self.__class__ != Simulator:
3439 _director_objects.register(self)
3444 def simulate(self, time_in_fs):
3445 r"""simulate(Simulator self, double time_in_fs) -> double"""
3446 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3448 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3449 r"""simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3450 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3452 def get_temperature(self):
3453 r"""get_temperature(Simulator self) -> double"""
3454 return _IMP_atom.Simulator_get_temperature(self)
3456 def set_temperature(self, d):
3457 r"""set_temperature(Simulator self, double d)"""
3458 return _IMP_atom.Simulator_set_temperature(self, d)
3460 def set_maximum_time_step(self, ts):
3461 r"""set_maximum_time_step(Simulator self, double ts)"""
3462 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3464 def get_maximum_time_step(self):
3465 r"""get_maximum_time_step(Simulator self) -> double"""
3466 return _IMP_atom.Simulator_get_maximum_time_step(self)
3468 def get_last_time_step(self):
3469 r"""get_last_time_step(Simulator self) -> double"""
3470 return _IMP_atom.Simulator_get_last_time_step(self)
3472 def set_time_step(self, ts):
3473 r"""set_time_step(Simulator self, double ts)"""
3474 return _IMP_atom.Simulator_set_time_step(self, ts)
3477 r"""get_kt(Simulator self) -> double"""
3478 return _IMP_atom.Simulator_get_kt(self)
3480 def get_current_time(self):
3481 r"""get_current_time(Simulator self) -> double"""
3482 return _IMP_atom.Simulator_get_current_time(self)
3484 def set_current_time(self, ct):
3485 r"""set_current_time(Simulator self, double ct)"""
3486 return _IMP_atom.Simulator_set_current_time(self, ct)
3488 def get_simulation_particles(self):
3489 r"""get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3490 return _IMP_atom.Simulator_get_simulation_particles(self)
3492 def get_simulation_particle_indexes(self):
3493 r"""get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3494 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3495 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)
3496 def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
3497 def __del_particles(self): IMP._list_util.del_varlist(self.particles)
3498 particles = property(__get_particles, __set_particles, __del_particles, doc=
"List of ##ucnames")
3500 def remove_particle(self, d):
3501 r"""remove_particle(Simulator self, Particle d)"""
3502 return _IMP_atom.Simulator_remove_particle(self, d)
3504 def _python_index_particle(self, d, start, stop):
3505 r"""_python_index_particle(Simulator self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
3506 return _IMP_atom.Simulator__python_index_particle(self, d, start, stop)
3508 def remove_particles(self, d):
3509 r"""remove_particles(Simulator self, IMP::Particles const & d)"""
3510 return _IMP_atom.Simulator_remove_particles(self, d)
3512 def set_particles(self, ps):
3513 r"""set_particles(Simulator self, IMP::Particles const & ps)"""
3514 return _IMP_atom.Simulator_set_particles(self, ps)
3516 def set_particles_order(self, objs):
3517 r"""set_particles_order(Simulator self, IMP::Particles const & objs)"""
3518 return _IMP_atom.Simulator_set_particles_order(self, objs)
3521 r"""add_particle(Simulator self, Particle obj) -> unsigned int"""
3522 return _IMP_atom.Simulator_add_particle(self, obj)
3525 r"""add_particles(Simulator self, IMP::Particles const & objs)"""
3526 return _IMP_atom.Simulator_add_particles(self, objs)
3528 def clear_particles(self):
3529 r"""clear_particles(Simulator self)"""
3530 return _IMP_atom.Simulator_clear_particles(self)
3532 def get_number_of_particles(self):
3533 r"""get_number_of_particles(Simulator self) -> unsigned int"""
3534 return _IMP_atom.Simulator_get_number_of_particles(self)
3536 def get_has_particles(self):
3537 r"""get_has_particles(Simulator self) -> bool"""
3538 return _IMP_atom.Simulator_get_has_particles(self)
3540 def get_particle(self, i):
3541 r"""get_particle(Simulator self, unsigned int i) -> Particle"""
3542 return _IMP_atom.Simulator_get_particle(self, i)
3545 r"""get_particles(Simulator self) -> IMP::Particles"""
3546 return _IMP_atom.Simulator_get_particles(self)
3548 def erase_particle(self, i):
3549 r"""erase_particle(Simulator self, unsigned int i)"""
3550 return _IMP_atom.Simulator_erase_particle(self, i)
3552 def reserve_particles(self, sz):
3553 r"""reserve_particles(Simulator self, unsigned int sz)"""
3554 return _IMP_atom.Simulator_reserve_particles(self, sz)
3556 def do_optimize(self, max_steps):
3557 r"""do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3558 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3560 def setup(self, arg0):
3561 r"""setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3562 return _IMP_atom.Simulator_setup(self, arg0)
3564 def do_step(self, sc, dt):
3565 r"""do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3566 return _IMP_atom.Simulator_do_step(self, sc, dt)
3568 def get_is_simulation_particle(self, p):
3569 r"""get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3570 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3572 def do_simulate(self, time):
3573 r"""do_simulate(Simulator self, double time) -> double"""
3574 return _IMP_atom.Simulator_do_simulate(self, time)
3576 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3577 r"""do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3578 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3581 r"""__str__(Simulator self) -> std::string"""
3582 return _IMP_atom.Simulator___str__(self)
3585 r"""__repr__(Simulator self) -> std::string"""
3586 return _IMP_atom.Simulator___repr__(self)
3590 return _object_cast_to_Simulator(o)
3593 def get_type_name(self):
3594 return self.__class__.__name__
3595 def do_show(self, out):
3597 def get_version_info(self):
3598 if"IMP::atom" ==
"IMP":
3599 return VersionInfo(self.__module__,
3606 return _object_cast_to_Simulator(o)
3608 __swig_destroy__ = _IMP_atom.delete_Simulator
3609 def __disown__(self):
3611 _IMP_atom.disown_Simulator(self)
3612 return weakref.proxy(self)
3614 def do_destroy(self):
3615 r"""do_destroy(Simulator self)"""
3616 return _IMP_atom.Simulator_do_destroy(self)
3618 def handle_set_has_required_score_states(self, arg0):
3619 r"""handle_set_has_required_score_states(Simulator self, bool arg0)"""
3620 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3622 def do_get_inputs(self):
3623 r"""do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3624 return _IMP_atom.Simulator_do_get_inputs(self)
3626 def do_get_outputs(self):
3627 r"""do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3628 return _IMP_atom.Simulator_do_get_outputs(self)
3630 def do_get_interactions(self):
3631 r"""do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3632 return _IMP_atom.Simulator_do_get_interactions(self)
3635 _IMP_atom.Simulator_swigregister(Simulator)
3636 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3638 class BrownianDynamics(Simulator):
3639 r"""Proxy of C++ IMP::atom::BrownianDynamics class."""
3641 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3643 def __init__(self, *args):
3644 r"""__init__(BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics"""
3645 _IMP_atom.BrownianDynamics_swiginit(self, _IMP_atom.new_BrownianDynamics(*args))
3647 def set_maximum_move(self, ms_in_A):
3648 r"""set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3649 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3651 def set_use_stochastic_runge_kutta(self, tf):
3652 r"""set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3653 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3655 def get_version_info(self):
3656 r"""get_version_info(BrownianDynamics self) -> VersionInfo"""
3657 return _IMP_atom.BrownianDynamics_get_version_info(self)
3658 __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3661 r"""__str__(BrownianDynamics self) -> std::string"""
3662 return _IMP_atom.BrownianDynamics___str__(self)
3665 r"""__repr__(BrownianDynamics self) -> std::string"""
3666 return _IMP_atom.BrownianDynamics___repr__(self)
3670 return _object_cast_to_BrownianDynamics(o)
3674 _IMP_atom.BrownianDynamics_swigregister(BrownianDynamics)
3677 r"""get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3678 return _IMP_atom.get_maximum_time_step_estimate(bd)
3680 def get_harmonic_sigma(D, f):
3681 r"""get_harmonic_sigma(double D, double f) -> double"""
3682 return _IMP_atom.get_harmonic_sigma(D, f)
3683 class BrownianDynamicsTAMD(BrownianDynamics):
3684 r"""Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3686 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3688 def __init__(self, *args):
3689 r"""__init__(BrownianDynamicsTAMD self, Model m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0) -> BrownianDynamicsTAMD"""
3690 _IMP_atom.BrownianDynamicsTAMD_swiginit(self, _IMP_atom.new_BrownianDynamicsTAMD(*args))
3693 r"""__str__(BrownianDynamicsTAMD self) -> std::string"""
3694 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3697 r"""__repr__(BrownianDynamicsTAMD self) -> std::string"""
3698 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3702 return _object_cast_to_BrownianDynamicsTAMD(o)
3704 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3707 _IMP_atom.BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3709 r"""Proxy of C++ IMP::atom::Diffusion class."""
3711 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3713 def __init__(self, *args):
3715 __init__(Diffusion self) -> Diffusion
3716 __init__(Diffusion self, Model m, ParticleIndex id) -> Diffusion
3717 __init__(Diffusion self, _ParticleAdaptor d) -> Diffusion
3719 _IMP_atom.Diffusion_swiginit(self, _IMP_atom.new_Diffusion(*args))
3721 def show(self, *args):
3722 r"""show(Diffusion self, _ostream out=std::cout)"""
3723 return _IMP_atom.Diffusion_show(self, *args)
3726 def setup_particle(*args):
3728 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3729 setup_particle(_ParticleAdaptor pa, IMP::Float D) -> Diffusion
3730 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3731 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float D) -> Diffusion
3732 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3733 setup_particle(_ParticleAdaptor pa) -> Diffusion
3735 return _IMP_atom.Diffusion_setup_particle(*args)
3738 def get_is_setup(*args):
3740 get_is_setup(_ParticleAdaptor p) -> bool
3741 get_is_setup(Model m, ParticleIndex p) -> bool
3743 return _IMP_atom.Diffusion_get_is_setup(*args)
3745 def set_diffusion_coefficient(self, d):
3746 r"""set_diffusion_coefficient(Diffusion self, double d)"""
3747 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3750 r"""get_diffusion_coefficient(Diffusion self) -> double"""
3751 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3754 def get_diffusion_coefficient_key():
3755 r"""get_diffusion_coefficient_key() -> FloatKey"""
3756 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3758 def add_attribute(self, *args):
3760 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3761 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3762 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3763 add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3764 add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3765 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3766 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3767 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3768 add_attribute(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3769 add_attribute(Diffusion self, SparseIntKey a0, IMP::Int a1)
3770 add_attribute(Diffusion self, SparseStringKey a0, IMP::String a1)
3771 add_attribute(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3773 return _IMP_atom.Diffusion_add_attribute(self, *args)
3775 def get_value(self, *args):
3777 get_value(Diffusion self, FloatKey a0) -> IMP::Float
3778 get_value(Diffusion self, IntKey a0) -> IMP::Int
3779 get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3780 get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3781 get_value(Diffusion self, StringKey a0) -> IMP::String
3782 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3783 get_value(Diffusion self, ObjectKey a0) -> Object
3784 get_value(Diffusion self, SparseFloatKey a0) -> IMP::Float
3785 get_value(Diffusion self, SparseIntKey a0) -> IMP::Int
3786 get_value(Diffusion self, SparseStringKey a0) -> IMP::String
3787 get_value(Diffusion self, SparseParticleIndexKey a0) -> ParticleIndex
3789 return _IMP_atom.Diffusion_get_value(self, *args)
3791 def set_value(self, *args):
3793 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3794 set_value(Diffusion self, IntKey a0, IMP::Int a1)
3795 set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3796 set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3797 set_value(Diffusion self, StringKey a0, IMP::String a1)
3798 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3799 set_value(Diffusion self, ObjectKey a0, Object a1)
3800 set_value(Diffusion self, SparseFloatKey a0, IMP::Float a1)
3801 set_value(Diffusion self, SparseIntKey a0, IMP::Int a1)
3802 set_value(Diffusion self, SparseStringKey a0, IMP::String a1)
3803 set_value(Diffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
3805 return _IMP_atom.Diffusion_set_value(self, *args)
3807 def remove_attribute(self, *args):
3809 remove_attribute(Diffusion self, FloatKey a0)
3810 remove_attribute(Diffusion self, IntKey a0)
3811 remove_attribute(Diffusion self, FloatsKey a0)
3812 remove_attribute(Diffusion self, IntsKey a0)
3813 remove_attribute(Diffusion self, StringKey a0)
3814 remove_attribute(Diffusion self, ParticleIndexKey a0)
3815 remove_attribute(Diffusion self, ObjectKey a0)
3816 remove_attribute(Diffusion self, SparseFloatKey a0)
3817 remove_attribute(Diffusion self, SparseIntKey a0)
3818 remove_attribute(Diffusion self, SparseStringKey a0)
3819 remove_attribute(Diffusion self, SparseParticleIndexKey a0)
3821 return _IMP_atom.Diffusion_remove_attribute(self, *args)
3823 def has_attribute(self, *args):
3825 has_attribute(Diffusion self, FloatKey a0) -> bool
3826 has_attribute(Diffusion self, IntKey a0) -> bool
3827 has_attribute(Diffusion self, FloatsKey a0) -> bool
3828 has_attribute(Diffusion self, IntsKey a0) -> bool
3829 has_attribute(Diffusion self, StringKey a0) -> bool
3830 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3831 has_attribute(Diffusion self, ObjectKey a0) -> bool
3832 has_attribute(Diffusion self, SparseFloatKey a0) -> bool
3833 has_attribute(Diffusion self, SparseIntKey a0) -> bool
3834 has_attribute(Diffusion self, SparseStringKey a0) -> bool
3835 has_attribute(Diffusion self, SparseParticleIndexKey a0) -> bool
3837 return _IMP_atom.Diffusion_has_attribute(self, *args)
3839 def get_derivative(self, a0):
3840 r"""get_derivative(Diffusion self, FloatKey a0) -> double"""
3841 return _IMP_atom.Diffusion_get_derivative(self, a0)
3844 r"""get_name(Diffusion self) -> std::string"""
3845 return _IMP_atom.Diffusion_get_name(self)
3847 def clear_caches(self):
3848 r"""clear_caches(Diffusion self)"""
3849 return _IMP_atom.Diffusion_clear_caches(self)
3851 def set_name(self, a0):
3852 r"""set_name(Diffusion self, std::string a0)"""
3853 return _IMP_atom.Diffusion_set_name(self, a0)
3856 r"""set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3857 return _IMP_atom.Diffusion_set_check_level(self, a0)
3859 def add_to_derivative(self, a0, a1, a2):
3860 r"""add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3861 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3863 def set_is_optimized(self, a0, a1):
3864 r"""set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3865 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3867 def get_is_optimized(self, a0):
3868 r"""get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3869 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3872 r"""get_check_level(Diffusion self) -> IMP::CheckLevel"""
3873 return _IMP_atom.Diffusion_get_check_level(self)
3875 def __eq__(self, *args):
3877 __eq__(Diffusion self, Diffusion o) -> bool
3878 __eq__(Diffusion self, Particle d) -> bool
3880 return _IMP_atom.Diffusion___eq__(self, *args)
3882 def __ne__(self, *args):
3884 __ne__(Diffusion self, Diffusion o) -> bool
3885 __ne__(Diffusion self, Particle d) -> bool
3887 return _IMP_atom.Diffusion___ne__(self, *args)
3889 def __le__(self, *args):
3891 __le__(Diffusion self, Diffusion o) -> bool
3892 __le__(Diffusion self, Particle d) -> bool
3894 return _IMP_atom.Diffusion___le__(self, *args)
3896 def __lt__(self, *args):
3898 __lt__(Diffusion self, Diffusion o) -> bool
3899 __lt__(Diffusion self, Particle d) -> bool
3901 return _IMP_atom.Diffusion___lt__(self, *args)
3903 def __ge__(self, *args):
3905 __ge__(Diffusion self, Diffusion o) -> bool
3906 __ge__(Diffusion self, Particle d) -> bool
3908 return _IMP_atom.Diffusion___ge__(self, *args)
3910 def __gt__(self, *args):
3912 __gt__(Diffusion self, Diffusion o) -> bool
3913 __gt__(Diffusion self, Particle d) -> bool
3915 return _IMP_atom.Diffusion___gt__(self, *args)
3918 r"""__hash__(Diffusion self) -> std::size_t"""
3919 return _IMP_atom.Diffusion___hash__(self)
3922 r"""__str__(Diffusion self) -> std::string"""
3923 return _IMP_atom.Diffusion___str__(self)
3926 r"""__repr__(Diffusion self) -> std::string"""
3927 return _IMP_atom.Diffusion___repr__(self)
3929 def _get_as_binary(self):
3930 r"""_get_as_binary(Diffusion self) -> PyObject *"""
3931 return _IMP_atom.Diffusion__get_as_binary(self)
3933 def _set_from_binary(self, p):
3934 r"""_set_from_binary(Diffusion self, PyObject * p)"""
3935 return _IMP_atom.Diffusion__set_from_binary(self, p)
3937 def __getstate__(self):
3938 p = self._get_as_binary()
3939 if len(self.__dict__) > 1:
3940 d = self.__dict__.copy()
3945 def __setstate__(self, p):
3946 if not hasattr(self,
'this'):
3948 if isinstance(p, tuple):
3950 self.__dict__.update(d)
3951 return self._set_from_binary(p)
3953 __swig_destroy__ = _IMP_atom.delete_Diffusion
3956 _IMP_atom.Diffusion_swigregister(Diffusion)
3958 def get_diffusion_coefficient_from_cm2_per_second(din):
3959 r"""get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3960 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3961 class RigidBodyDiffusion(Diffusion):
3962 r"""Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3964 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3966 def __init__(self, *args):
3968 __init__(RigidBodyDiffusion self) -> RigidBodyDiffusion
3969 __init__(RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3970 __init__(RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3972 _IMP_atom.RigidBodyDiffusion_swiginit(self, _IMP_atom.new_RigidBodyDiffusion(*args))
3974 def show(self, *args):
3975 r"""show(RigidBodyDiffusion self, _ostream out=std::cout)"""
3976 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3979 def setup_particle(*args):
3981 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3982 setup_particle(_ParticleAdaptor pa) -> RigidBodyDiffusion
3984 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3987 r"""get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3988 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3990 def set_rotational_diffusion_coefficient(self, d):
3991 r"""set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3992 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
3995 def get_is_setup(*args):
3997 get_is_setup(_ParticleAdaptor p) -> bool
3998 get_is_setup(Model m, ParticleIndex p) -> bool
4000 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4003 def get_rotational_diffusion_coefficient_key():
4004 r"""get_rotational_diffusion_coefficient_key() -> FloatKey"""
4005 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4007 def add_attribute(self, *args):
4009 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4010 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4011 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4012 add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4013 add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4014 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4015 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4016 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4017 add_attribute(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
4018 add_attribute(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
4019 add_attribute(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
4020 add_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
4022 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4024 def get_value(self, *args):
4026 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4027 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4028 get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
4029 get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
4030 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4031 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4032 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4033 get_value(RigidBodyDiffusion self, SparseFloatKey a0) -> IMP::Float
4034 get_value(RigidBodyDiffusion self, SparseIntKey a0) -> IMP::Int
4035 get_value(RigidBodyDiffusion self, SparseStringKey a0) -> IMP::String
4036 get_value(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> ParticleIndex
4038 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4040 def set_value(self, *args):
4042 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4043 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4044 set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4045 set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4046 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4047 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4048 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4049 set_value(RigidBodyDiffusion self, SparseFloatKey a0, IMP::Float a1)
4050 set_value(RigidBodyDiffusion self, SparseIntKey a0, IMP::Int a1)
4051 set_value(RigidBodyDiffusion self, SparseStringKey a0, IMP::String a1)
4052 set_value(RigidBodyDiffusion self, SparseParticleIndexKey a0, ParticleIndex a1)
4054 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4056 def remove_attribute(self, *args):
4058 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4059 remove_attribute(RigidBodyDiffusion self, IntKey a0)
4060 remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
4061 remove_attribute(RigidBodyDiffusion self, IntsKey a0)
4062 remove_attribute(RigidBodyDiffusion self, StringKey a0)
4063 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4064 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4065 remove_attribute(RigidBodyDiffusion self, SparseFloatKey a0)
4066 remove_attribute(RigidBodyDiffusion self, SparseIntKey a0)
4067 remove_attribute(RigidBodyDiffusion self, SparseStringKey a0)
4068 remove_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0)
4070 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4072 def has_attribute(self, *args):
4074 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4075 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4076 has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
4077 has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
4078 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4079 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4080 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4081 has_attribute(RigidBodyDiffusion self, SparseFloatKey a0) -> bool
4082 has_attribute(RigidBodyDiffusion self, SparseIntKey a0) -> bool
4083 has_attribute(RigidBodyDiffusion self, SparseStringKey a0) -> bool
4084 has_attribute(RigidBodyDiffusion self, SparseParticleIndexKey a0) -> bool
4086 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4088 def get_derivative(self, a0):
4089 r"""get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4090 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4093 r"""get_name(RigidBodyDiffusion self) -> std::string"""
4094 return _IMP_atom.RigidBodyDiffusion_get_name(self)
4096 def clear_caches(self):
4097 r"""clear_caches(RigidBodyDiffusion self)"""
4098 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4100 def set_name(self, a0):
4101 r"""set_name(RigidBodyDiffusion self, std::string a0)"""
4102 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4105 r"""set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4106 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4108 def add_to_derivative(self, a0, a1, a2):
4109 r"""add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4110 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4112 def set_is_optimized(self, a0, a1):
4113 r"""set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4114 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4116 def get_is_optimized(self, a0):
4117 r"""get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4118 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4121 r"""get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4122 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4124 def __eq__(self, *args):
4126 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4127 __eq__(RigidBodyDiffusion self, Particle d) -> bool
4129 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4131 def __ne__(self, *args):
4133 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4134 __ne__(RigidBodyDiffusion self, Particle d) -> bool
4136 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4138 def __le__(self, *args):
4140 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4141 __le__(RigidBodyDiffusion self, Particle d) -> bool
4143 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4145 def __lt__(self, *args):
4147 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4148 __lt__(RigidBodyDiffusion self, Particle d) -> bool
4150 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4152 def __ge__(self, *args):
4154 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4155 __ge__(RigidBodyDiffusion self, Particle d) -> bool
4157 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4159 def __gt__(self, *args):
4161 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4162 __gt__(RigidBodyDiffusion self, Particle d) -> bool
4164 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4167 r"""__hash__(RigidBodyDiffusion self) -> std::size_t"""
4168 return _IMP_atom.RigidBodyDiffusion___hash__(self)
4171 r"""__str__(RigidBodyDiffusion self) -> std::string"""
4172 return _IMP_atom.RigidBodyDiffusion___str__(self)
4175 r"""__repr__(RigidBodyDiffusion self) -> std::string"""
4176 return _IMP_atom.RigidBodyDiffusion___repr__(self)
4178 def _get_as_binary(self):
4179 r"""_get_as_binary(RigidBodyDiffusion self) -> PyObject *"""
4180 return _IMP_atom.RigidBodyDiffusion__get_as_binary(self)
4182 def _set_from_binary(self, p):
4183 r"""_set_from_binary(RigidBodyDiffusion self, PyObject * p)"""
4184 return _IMP_atom.RigidBodyDiffusion__set_from_binary(self, p)
4186 def __getstate__(self):
4187 p = self._get_as_binary()
4188 if len(self.__dict__) > 1:
4189 d = self.__dict__.copy()
4194 def __setstate__(self, p):
4195 if not hasattr(self,
'this'):
4197 if isinstance(p, tuple):
4199 self.__dict__.update(d)
4200 return self._set_from_binary(p)
4202 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4205 _IMP_atom.RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4207 r"""Proxy of C++ IMP::atom::TAMDParticle class."""
4209 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4211 def __init__(self, *args):
4213 __init__(TAMDParticle self) -> TAMDParticle
4214 __init__(TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4215 __init__(TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4217 _IMP_atom.TAMDParticle_swiginit(self, _IMP_atom.new_TAMDParticle(*args))
4219 def show(self, *args):
4220 r"""show(TAMDParticle self, _ostream out=std::cout)"""
4221 return _IMP_atom.TAMDParticle_show(self, *args)
4224 def setup_particle(*args):
4226 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4227 setup_particle(_ParticleAdaptor pa, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4228 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4229 setup_particle(_ParticleAdaptor pa, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4231 return _IMP_atom.TAMDParticle_setup_particle(*args)
4234 def get_is_setup(*args):
4236 get_is_setup(_ParticleAdaptor p) -> bool
4237 get_is_setup(Model m, ParticleIndex p) -> bool
4239 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4241 def get_reference_particle_index(self):
4242 r"""get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4243 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4245 def set_temperature_scale_factor(self, tsf):
4246 r"""set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4247 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4249 def get_temperature_scale_factor(self):
4250 r"""get_temperature_scale_factor(TAMDParticle self) -> double"""
4251 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4253 def set_friction_scale_factor(self, tsf):
4254 r"""set_friction_scale_factor(TAMDParticle self, float tsf)"""
4255 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4257 def get_friction_scale_factor(self):
4258 r"""get_friction_scale_factor(TAMDParticle self) -> double"""
4259 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4261 def update_coordinates_from_ref(self):
4262 r"""update_coordinates_from_ref(TAMDParticle self)"""
4263 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4266 def get_temperature_scale_factor_key():
4267 r"""get_temperature_scale_factor_key() -> FloatKey"""
4268 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4271 def get_friction_scale_factor_key():
4272 r"""get_friction_scale_factor_key() -> FloatKey"""
4273 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4276 def get_reference_particle_index_key():
4277 r"""get_reference_particle_index_key() -> ParticleIndexKey"""
4278 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4280 def add_attribute(self, *args):
4282 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4283 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4284 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4285 add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4286 add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4287 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4288 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4289 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4290 add_attribute(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4291 add_attribute(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4292 add_attribute(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4293 add_attribute(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4295 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4297 def get_value(self, *args):
4299 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4300 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4301 get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4302 get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4303 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4304 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4305 get_value(TAMDParticle self, ObjectKey a0) -> Object
4306 get_value(TAMDParticle self, SparseFloatKey a0) -> IMP::Float
4307 get_value(TAMDParticle self, SparseIntKey a0) -> IMP::Int
4308 get_value(TAMDParticle self, SparseStringKey a0) -> IMP::String
4309 get_value(TAMDParticle self, SparseParticleIndexKey a0) -> ParticleIndex
4311 return _IMP_atom.TAMDParticle_get_value(self, *args)
4313 def set_value(self, *args):
4315 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4316 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4317 set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4318 set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4319 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4320 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4321 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4322 set_value(TAMDParticle self, SparseFloatKey a0, IMP::Float a1)
4323 set_value(TAMDParticle self, SparseIntKey a0, IMP::Int a1)
4324 set_value(TAMDParticle self, SparseStringKey a0, IMP::String a1)
4325 set_value(TAMDParticle self, SparseParticleIndexKey a0, ParticleIndex a1)
4327 return _IMP_atom.TAMDParticle_set_value(self, *args)
4329 def remove_attribute(self, *args):
4331 remove_attribute(TAMDParticle self, FloatKey a0)
4332 remove_attribute(TAMDParticle self, IntKey a0)
4333 remove_attribute(TAMDParticle self, FloatsKey a0)
4334 remove_attribute(TAMDParticle self, IntsKey a0)
4335 remove_attribute(TAMDParticle self, StringKey a0)
4336 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4337 remove_attribute(TAMDParticle self, ObjectKey a0)
4338 remove_attribute(TAMDParticle self, SparseFloatKey a0)
4339 remove_attribute(TAMDParticle self, SparseIntKey a0)
4340 remove_attribute(TAMDParticle self, SparseStringKey a0)
4341 remove_attribute(TAMDParticle self, SparseParticleIndexKey a0)
4343 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4345 def has_attribute(self, *args):
4347 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4348 has_attribute(TAMDParticle self, IntKey a0) -> bool
4349 has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4350 has_attribute(TAMDParticle self, IntsKey a0) -> bool
4351 has_attribute(TAMDParticle self, StringKey a0) -> bool
4352 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4353 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4354 has_attribute(TAMDParticle self, SparseFloatKey a0) -> bool
4355 has_attribute(TAMDParticle self, SparseIntKey a0) -> bool
4356 has_attribute(TAMDParticle self, SparseStringKey a0) -> bool
4357 has_attribute(TAMDParticle self, SparseParticleIndexKey a0) -> bool
4359 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4361 def get_derivative(self, a0):
4362 r"""get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4363 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4366 r"""get_name(TAMDParticle self) -> std::string"""
4367 return _IMP_atom.TAMDParticle_get_name(self)
4369 def clear_caches(self):
4370 r"""clear_caches(TAMDParticle self)"""
4371 return _IMP_atom.TAMDParticle_clear_caches(self)
4373 def set_name(self, a0):
4374 r"""set_name(TAMDParticle self, std::string a0)"""
4375 return _IMP_atom.TAMDParticle_set_name(self, a0)
4378 r"""set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4379 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4381 def add_to_derivative(self, a0, a1, a2):
4382 r"""add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4383 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4385 def set_is_optimized(self, a0, a1):
4386 r"""set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4387 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4389 def get_is_optimized(self, a0):
4390 r"""get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4391 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4394 r"""get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4395 return _IMP_atom.TAMDParticle_get_check_level(self)
4397 def __eq__(self, *args):
4399 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4400 __eq__(TAMDParticle self, Particle d) -> bool
4402 return _IMP_atom.TAMDParticle___eq__(self, *args)
4404 def __ne__(self, *args):
4406 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4407 __ne__(TAMDParticle self, Particle d) -> bool
4409 return _IMP_atom.TAMDParticle___ne__(self, *args)
4411 def __le__(self, *args):
4413 __le__(TAMDParticle self, TAMDParticle o) -> bool
4414 __le__(TAMDParticle self, Particle d) -> bool
4416 return _IMP_atom.TAMDParticle___le__(self, *args)
4418 def __lt__(self, *args):
4420 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4421 __lt__(TAMDParticle self, Particle d) -> bool
4423 return _IMP_atom.TAMDParticle___lt__(self, *args)
4425 def __ge__(self, *args):
4427 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4428 __ge__(TAMDParticle self, Particle d) -> bool
4430 return _IMP_atom.TAMDParticle___ge__(self, *args)
4432 def __gt__(self, *args):
4434 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4435 __gt__(TAMDParticle self, Particle d) -> bool
4437 return _IMP_atom.TAMDParticle___gt__(self, *args)
4440 r"""__hash__(TAMDParticle self) -> std::size_t"""
4441 return _IMP_atom.TAMDParticle___hash__(self)
4444 r"""__str__(TAMDParticle self) -> std::string"""
4445 return _IMP_atom.TAMDParticle___str__(self)
4448 r"""__repr__(TAMDParticle self) -> std::string"""
4449 return _IMP_atom.TAMDParticle___repr__(self)
4451 def _get_as_binary(self):
4452 r"""_get_as_binary(TAMDParticle self) -> PyObject *"""
4453 return _IMP_atom.TAMDParticle__get_as_binary(self)
4455 def _set_from_binary(self, p):
4456 r"""_set_from_binary(TAMDParticle self, PyObject * p)"""
4457 return _IMP_atom.TAMDParticle__set_from_binary(self, p)
4459 def __getstate__(self):
4460 p = self._get_as_binary()
4461 if len(self.__dict__) > 1:
4462 d = self.__dict__.copy()
4467 def __setstate__(self, p):
4468 if not hasattr(self,
'this'):
4470 if isinstance(p, tuple):
4472 self.__dict__.update(d)
4473 return self._set_from_binary(p)
4475 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4478 _IMP_atom.TAMDParticle_swigregister(TAMDParticle)
4480 r"""Proxy of C++ IMP::atom::Charged class."""
4482 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4484 def __init__(self, *args):
4486 __init__(Charged self) -> Charged
4487 __init__(Charged self, Model m, ParticleIndex id) -> Charged
4488 __init__(Charged self, _ParticleAdaptor d) -> Charged
4490 _IMP_atom.Charged_swiginit(self, _IMP_atom.new_Charged(*args))
4492 def show(self, *args):
4493 r"""show(Charged self, _ostream out=std::cout)"""
4494 return _IMP_atom.Charged_show(self, *args)
4497 def setup_particle(*args):
4499 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4500 setup_particle(_ParticleAdaptor pa, IMP::Float charge) -> Charged
4501 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4502 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float charge) -> Charged
4504 return _IMP_atom.Charged_setup_particle(*args)
4506 def get_charge(self):
4507 r"""get_charge(Charged self) -> IMP::Float"""
4508 return _IMP_atom.Charged_get_charge(self)
4510 def set_charge(self, t):
4511 r"""set_charge(Charged self, IMP::Float t)"""
4512 return _IMP_atom.Charged_set_charge(self, t)
4515 def get_is_setup(*args):
4517 get_is_setup(_ParticleAdaptor p) -> bool
4518 get_is_setup(Model m, ParticleIndex pi) -> bool
4520 return _IMP_atom.Charged_get_is_setup(*args)
4523 def get_charge_key():
4524 r"""get_charge_key() -> FloatKey"""
4525 return _IMP_atom.Charged_get_charge_key()
4527 def add_attribute(self, *args):
4529 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4530 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4531 add_attribute(Charged self, IntKey a0, IMP::Int a1)
4532 add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
4533 add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
4534 add_attribute(Charged self, StringKey a0, IMP::String a1)
4535 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4536 add_attribute(Charged self, ObjectKey a0, Object a1)
4537 add_attribute(Charged self, SparseFloatKey a0, IMP::Float a1)
4538 add_attribute(Charged self, SparseIntKey a0, IMP::Int a1)
4539 add_attribute(Charged self, SparseStringKey a0, IMP::String a1)
4540 add_attribute(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4542 return _IMP_atom.Charged_add_attribute(self, *args)
4544 def get_value(self, *args):
4546 get_value(Charged self, FloatKey a0) -> IMP::Float
4547 get_value(Charged self, IntKey a0) -> IMP::Int
4548 get_value(Charged self, FloatsKey a0) -> IMP::Floats
4549 get_value(Charged self, IntsKey a0) -> IMP::Ints
4550 get_value(Charged self, StringKey a0) -> IMP::String
4551 get_value(Charged self, ParticleIndexKey a0) -> Particle
4552 get_value(Charged self, ObjectKey a0) -> Object
4553 get_value(Charged self, SparseFloatKey a0) -> IMP::Float
4554 get_value(Charged self, SparseIntKey a0) -> IMP::Int
4555 get_value(Charged self, SparseStringKey a0) -> IMP::String
4556 get_value(Charged self, SparseParticleIndexKey a0) -> ParticleIndex
4558 return _IMP_atom.Charged_get_value(self, *args)
4560 def set_value(self, *args):
4562 set_value(Charged self, FloatKey a0, IMP::Float a1)
4563 set_value(Charged self, IntKey a0, IMP::Int a1)
4564 set_value(Charged self, FloatsKey a0, IMP::Floats a1)
4565 set_value(Charged self, IntsKey a0, IMP::Ints a1)
4566 set_value(Charged self, StringKey a0, IMP::String a1)
4567 set_value(Charged self, ParticleIndexKey a0, Particle a1)
4568 set_value(Charged self, ObjectKey a0, Object a1)
4569 set_value(Charged self, SparseFloatKey a0, IMP::Float a1)
4570 set_value(Charged self, SparseIntKey a0, IMP::Int a1)
4571 set_value(Charged self, SparseStringKey a0, IMP::String a1)
4572 set_value(Charged self, SparseParticleIndexKey a0, ParticleIndex a1)
4574 return _IMP_atom.Charged_set_value(self, *args)
4576 def remove_attribute(self, *args):
4578 remove_attribute(Charged self, FloatKey a0)
4579 remove_attribute(Charged self, IntKey a0)
4580 remove_attribute(Charged self, FloatsKey a0)
4581 remove_attribute(Charged self, IntsKey a0)
4582 remove_attribute(Charged self, StringKey a0)
4583 remove_attribute(Charged self, ParticleIndexKey a0)
4584 remove_attribute(Charged self, ObjectKey a0)
4585 remove_attribute(Charged self, SparseFloatKey a0)
4586 remove_attribute(Charged self, SparseIntKey a0)
4587 remove_attribute(Charged self, SparseStringKey a0)
4588 remove_attribute(Charged self, SparseParticleIndexKey a0)
4590 return _IMP_atom.Charged_remove_attribute(self, *args)
4592 def has_attribute(self, *args):
4594 has_attribute(Charged self, FloatKey a0) -> bool
4595 has_attribute(Charged self, IntKey a0) -> bool
4596 has_attribute(Charged self, FloatsKey a0) -> bool
4597 has_attribute(Charged self, IntsKey a0) -> bool
4598 has_attribute(Charged self, StringKey a0) -> bool
4599 has_attribute(Charged self, ParticleIndexKey a0) -> bool
4600 has_attribute(Charged self, ObjectKey a0) -> bool
4601 has_attribute(Charged self, SparseFloatKey a0) -> bool
4602 has_attribute(Charged self, SparseIntKey a0) -> bool
4603 has_attribute(Charged self, SparseStringKey a0) -> bool
4604 has_attribute(Charged self, SparseParticleIndexKey a0) -> bool
4606 return _IMP_atom.Charged_has_attribute(self, *args)
4608 def get_derivative(self, a0):
4609 r"""get_derivative(Charged self, FloatKey a0) -> double"""
4610 return _IMP_atom.Charged_get_derivative(self, a0)
4613 r"""get_name(Charged self) -> std::string"""
4614 return _IMP_atom.Charged_get_name(self)
4616 def clear_caches(self):
4617 r"""clear_caches(Charged self)"""
4618 return _IMP_atom.Charged_clear_caches(self)
4620 def set_name(self, a0):
4621 r"""set_name(Charged self, std::string a0)"""
4622 return _IMP_atom.Charged_set_name(self, a0)
4625 r"""set_check_level(Charged self, IMP::CheckLevel a0)"""
4626 return _IMP_atom.Charged_set_check_level(self, a0)
4628 def add_to_derivative(self, a0, a1, a2):
4629 r"""add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4630 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4632 def set_is_optimized(self, a0, a1):
4633 r"""set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4634 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4636 def get_is_optimized(self, a0):
4637 r"""get_is_optimized(Charged self, FloatKey a0) -> bool"""
4638 return _IMP_atom.Charged_get_is_optimized(self, a0)
4641 r"""get_check_level(Charged self) -> IMP::CheckLevel"""
4642 return _IMP_atom.Charged_get_check_level(self)
4644 def __eq__(self, *args):
4646 __eq__(Charged self, Charged o) -> bool
4647 __eq__(Charged self, Particle d) -> bool
4649 return _IMP_atom.Charged___eq__(self, *args)
4651 def __ne__(self, *args):
4653 __ne__(Charged self, Charged o) -> bool
4654 __ne__(Charged self, Particle d) -> bool
4656 return _IMP_atom.Charged___ne__(self, *args)
4658 def __le__(self, *args):
4660 __le__(Charged self, Charged o) -> bool
4661 __le__(Charged self, Particle d) -> bool
4663 return _IMP_atom.Charged___le__(self, *args)
4665 def __lt__(self, *args):
4667 __lt__(Charged self, Charged o) -> bool
4668 __lt__(Charged self, Particle d) -> bool
4670 return _IMP_atom.Charged___lt__(self, *args)
4672 def __ge__(self, *args):
4674 __ge__(Charged self, Charged o) -> bool
4675 __ge__(Charged self, Particle d) -> bool
4677 return _IMP_atom.Charged___ge__(self, *args)
4679 def __gt__(self, *args):
4681 __gt__(Charged self, Charged o) -> bool
4682 __gt__(Charged self, Particle d) -> bool
4684 return _IMP_atom.Charged___gt__(self, *args)
4687 r"""__hash__(Charged self) -> std::size_t"""
4688 return _IMP_atom.Charged___hash__(self)
4691 r"""__str__(Charged self) -> std::string"""
4692 return _IMP_atom.Charged___str__(self)
4695 r"""__repr__(Charged self) -> std::string"""
4696 return _IMP_atom.Charged___repr__(self)
4698 def _get_as_binary(self):
4699 r"""_get_as_binary(Charged self) -> PyObject *"""
4700 return _IMP_atom.Charged__get_as_binary(self)
4702 def _set_from_binary(self, p):
4703 r"""_set_from_binary(Charged self, PyObject * p)"""
4704 return _IMP_atom.Charged__set_from_binary(self, p)
4706 def __getstate__(self):
4707 p = self._get_as_binary()
4708 if len(self.__dict__) > 1:
4709 d = self.__dict__.copy()
4714 def __setstate__(self, p):
4715 if not hasattr(self,
'this'):
4717 if isinstance(p, tuple):
4719 self.__dict__.update(d)
4720 return self._set_from_binary(p)
4722 __swig_destroy__ = _IMP_atom.delete_Charged
4725 _IMP_atom.Charged_swigregister(Charged)
4727 r"""Proxy of C++ IMP::atom::CoulombPairScore class."""
4729 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4731 def __init__(self, f):
4732 r"""__init__(CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4733 _IMP_atom.CoulombPairScore_swiginit(self, _IMP_atom.new_CoulombPairScore(f))
4735 def set_relative_dielectric(self, relative_dielectric):
4736 r"""set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4737 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
4739 def get_relative_dielectric(self):
4740 r"""get_relative_dielectric(CoulombPairScore self) -> double"""
4741 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4743 def do_get_inputs(self, m, pis):
4744 r"""do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4745 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
4747 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
4748 r"""evaluate_indexes(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
4749 return _IMP_atom.CoulombPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
4751 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
4752 r"""evaluate_indexes_scores(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
4753 return _IMP_atom.CoulombPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
4755 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
4756 r"""evaluate_indexes_delta(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
4757 return _IMP_atom.CoulombPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
4759 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
4760 r"""evaluate_if_good_indexes(CoulombPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
4761 return _IMP_atom.CoulombPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
4763 def get_version_info(self):
4764 r"""get_version_info(CoulombPairScore self) -> VersionInfo"""
4765 return _IMP_atom.CoulombPairScore_get_version_info(self)
4766 __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4769 r"""__str__(CoulombPairScore self) -> std::string"""
4770 return _IMP_atom.CoulombPairScore___str__(self)
4773 r"""__repr__(CoulombPairScore self) -> std::string"""
4774 return _IMP_atom.CoulombPairScore___repr__(self)
4778 return _object_cast_to_CoulombPairScore(o)
4782 _IMP_atom.CoulombPairScore_swigregister(CoulombPairScore)
4783 class Domain(Hierarchy):
4784 r"""Proxy of C++ IMP::atom::Domain class."""
4786 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4788 def set_index_range(self, ir):
4789 r"""set_index_range(Domain self, IMP::IntRange ir)"""
4790 return _IMP_atom.Domain_set_index_range(self, ir)
4792 def get_index_range(self):
4793 r"""get_index_range(Domain self) -> IMP::IntRange"""
4794 return _IMP_atom.Domain_get_index_range(self)
4796 def __init__(self, *args):
4798 __init__(Domain self) -> Domain
4799 __init__(Domain self, Model m, ParticleIndex id) -> Domain
4800 __init__(Domain self, _ParticleAdaptor d) -> Domain
4802 _IMP_atom.Domain_swiginit(self, _IMP_atom.new_Domain(*args))
4805 def get_is_setup(*args):
4807 get_is_setup(Model m, ParticleIndex pi) -> bool
4808 get_is_setup(_ParticleAdaptor p) -> bool
4810 return _IMP_atom.Domain_get_is_setup(*args)
4812 def show(self, *args):
4813 r"""show(Domain self, _ostream out=std::cout)"""
4814 return _IMP_atom.Domain_show(self, *args)
4817 def setup_particle(*args):
4819 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
4820 setup_particle(_ParticleAdaptor pa, Domain other) -> Domain
4821 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
4822 setup_particle(_ParticleAdaptor pa, IMP::IntRange residues) -> Domain
4824 return _IMP_atom.Domain_setup_particle(*args)
4826 def add_attribute(self, *args):
4828 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4829 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4830 add_attribute(Domain self, IntKey a0, IMP::Int a1)
4831 add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
4832 add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
4833 add_attribute(Domain self, StringKey a0, IMP::String a1)
4834 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4835 add_attribute(Domain self, ObjectKey a0, Object a1)
4836 add_attribute(Domain self, SparseFloatKey a0, IMP::Float a1)
4837 add_attribute(Domain self, SparseIntKey a0, IMP::Int a1)
4838 add_attribute(Domain self, SparseStringKey a0, IMP::String a1)
4839 add_attribute(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4841 return _IMP_atom.Domain_add_attribute(self, *args)
4843 def get_value(self, *args):
4845 get_value(Domain self, FloatKey a0) -> IMP::Float
4846 get_value(Domain self, IntKey a0) -> IMP::Int
4847 get_value(Domain self, FloatsKey a0) -> IMP::Floats
4848 get_value(Domain self, IntsKey a0) -> IMP::Ints
4849 get_value(Domain self, StringKey a0) -> IMP::String
4850 get_value(Domain self, ParticleIndexKey a0) -> Particle
4851 get_value(Domain self, ObjectKey a0) -> Object
4852 get_value(Domain self, SparseFloatKey a0) -> IMP::Float
4853 get_value(Domain self, SparseIntKey a0) -> IMP::Int
4854 get_value(Domain self, SparseStringKey a0) -> IMP::String
4855 get_value(Domain self, SparseParticleIndexKey a0) -> ParticleIndex
4857 return _IMP_atom.Domain_get_value(self, *args)
4859 def set_value(self, *args):
4861 set_value(Domain self, FloatKey a0, IMP::Float a1)
4862 set_value(Domain self, IntKey a0, IMP::Int a1)
4863 set_value(Domain self, FloatsKey a0, IMP::Floats a1)
4864 set_value(Domain self, IntsKey a0, IMP::Ints a1)
4865 set_value(Domain self, StringKey a0, IMP::String a1)
4866 set_value(Domain self, ParticleIndexKey a0, Particle a1)
4867 set_value(Domain self, ObjectKey a0, Object a1)
4868 set_value(Domain self, SparseFloatKey a0, IMP::Float a1)
4869 set_value(Domain self, SparseIntKey a0, IMP::Int a1)
4870 set_value(Domain self, SparseStringKey a0, IMP::String a1)
4871 set_value(Domain self, SparseParticleIndexKey a0, ParticleIndex a1)
4873 return _IMP_atom.Domain_set_value(self, *args)
4875 def remove_attribute(self, *args):
4877 remove_attribute(Domain self, FloatKey a0)
4878 remove_attribute(Domain self, IntKey a0)
4879 remove_attribute(Domain self, FloatsKey a0)
4880 remove_attribute(Domain self, IntsKey a0)
4881 remove_attribute(Domain self, StringKey a0)
4882 remove_attribute(Domain self, ParticleIndexKey a0)
4883 remove_attribute(Domain self, ObjectKey a0)
4884 remove_attribute(Domain self, SparseFloatKey a0)
4885 remove_attribute(Domain self, SparseIntKey a0)
4886 remove_attribute(Domain self, SparseStringKey a0)
4887 remove_attribute(Domain self, SparseParticleIndexKey a0)
4889 return _IMP_atom.Domain_remove_attribute(self, *args)
4891 def has_attribute(self, *args):
4893 has_attribute(Domain self, FloatKey a0) -> bool
4894 has_attribute(Domain self, IntKey a0) -> bool
4895 has_attribute(Domain self, FloatsKey a0) -> bool
4896 has_attribute(Domain self, IntsKey a0) -> bool
4897 has_attribute(Domain self, StringKey a0) -> bool
4898 has_attribute(Domain self, ParticleIndexKey a0) -> bool
4899 has_attribute(Domain self, ObjectKey a0) -> bool
4900 has_attribute(Domain self, SparseFloatKey a0) -> bool
4901 has_attribute(Domain self, SparseIntKey a0) -> bool
4902 has_attribute(Domain self, SparseStringKey a0) -> bool
4903 has_attribute(Domain self, SparseParticleIndexKey a0) -> bool
4905 return _IMP_atom.Domain_has_attribute(self, *args)
4907 def get_derivative(self, a0):
4908 r"""get_derivative(Domain self, FloatKey a0) -> double"""
4909 return _IMP_atom.Domain_get_derivative(self, a0)
4912 r"""get_name(Domain self) -> std::string"""
4913 return _IMP_atom.Domain_get_name(self)
4915 def clear_caches(self):
4916 r"""clear_caches(Domain self)"""
4917 return _IMP_atom.Domain_clear_caches(self)
4919 def set_name(self, a0):
4920 r"""set_name(Domain self, std::string a0)"""
4921 return _IMP_atom.Domain_set_name(self, a0)
4924 r"""set_check_level(Domain self, IMP::CheckLevel a0)"""
4925 return _IMP_atom.Domain_set_check_level(self, a0)
4927 def add_to_derivative(self, a0, a1, a2):
4928 r"""add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4929 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
4931 def set_is_optimized(self, a0, a1):
4932 r"""set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4933 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
4935 def get_is_optimized(self, a0):
4936 r"""get_is_optimized(Domain self, FloatKey a0) -> bool"""
4937 return _IMP_atom.Domain_get_is_optimized(self, a0)
4940 r"""get_check_level(Domain self) -> IMP::CheckLevel"""
4941 return _IMP_atom.Domain_get_check_level(self)
4943 def __eq__(self, *args):
4945 __eq__(Domain self, Domain o) -> bool
4946 __eq__(Domain self, Particle d) -> bool
4948 return _IMP_atom.Domain___eq__(self, *args)
4950 def __ne__(self, *args):
4952 __ne__(Domain self, Domain o) -> bool
4953 __ne__(Domain self, Particle d) -> bool
4955 return _IMP_atom.Domain___ne__(self, *args)
4957 def __le__(self, *args):
4959 __le__(Domain self, Domain o) -> bool
4960 __le__(Domain self, Particle d) -> bool
4962 return _IMP_atom.Domain___le__(self, *args)
4964 def __lt__(self, *args):
4966 __lt__(Domain self, Domain o) -> bool
4967 __lt__(Domain self, Particle d) -> bool
4969 return _IMP_atom.Domain___lt__(self, *args)
4971 def __ge__(self, *args):
4973 __ge__(Domain self, Domain o) -> bool
4974 __ge__(Domain self, Particle d) -> bool
4976 return _IMP_atom.Domain___ge__(self, *args)
4978 def __gt__(self, *args):
4980 __gt__(Domain self, Domain o) -> bool
4981 __gt__(Domain self, Particle d) -> bool
4983 return _IMP_atom.Domain___gt__(self, *args)
4986 r"""__hash__(Domain self) -> std::size_t"""
4987 return _IMP_atom.Domain___hash__(self)
4990 r"""__str__(Domain self) -> std::string"""
4991 return _IMP_atom.Domain___str__(self)
4994 r"""__repr__(Domain self) -> std::string"""
4995 return _IMP_atom.Domain___repr__(self)
4997 def _get_as_binary(self):
4998 r"""_get_as_binary(Domain self) -> PyObject *"""
4999 return _IMP_atom.Domain__get_as_binary(self)
5001 def _set_from_binary(self, p):
5002 r"""_set_from_binary(Domain self, PyObject * p)"""
5003 return _IMP_atom.Domain__set_from_binary(self, p)
5005 def __getstate__(self):
5006 p = self._get_as_binary()
5007 if len(self.__dict__) > 1:
5008 d = self.__dict__.copy()
5013 def __setstate__(self, p):
5014 if not hasattr(self,
'this'):
5016 if isinstance(p, tuple):
5018 self.__dict__.update(d)
5019 return self._set_from_binary(p)
5021 __swig_destroy__ = _IMP_atom.delete_Domain
5024 _IMP_atom.Domain_swigregister(Domain)
5026 r"""Proxy of C++ IMP::atom::LennardJones class."""
5028 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5030 def __init__(self, *args):
5032 __init__(LennardJones self) -> LennardJones
5033 __init__(LennardJones self, Model m, ParticleIndex id) -> LennardJones
5034 __init__(LennardJones self, _ParticleAdaptor d) -> LennardJones
5036 _IMP_atom.LennardJones_swiginit(self, _IMP_atom.new_LennardJones(*args))
5038 def show(self, *args):
5039 r"""show(LennardJones self, _ostream out=std::cout)"""
5040 return _IMP_atom.LennardJones_show(self, *args)
5043 def setup_particle(*args):
5045 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5046 setup_particle(_ParticleAdaptor pa) -> LennardJones
5047 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5048 setup_particle(_ParticleAdaptor pa, IMP::Float well_depth) -> LennardJones
5050 return _IMP_atom.LennardJones_setup_particle(*args)
5052 def get_well_depth(self):
5053 r"""get_well_depth(LennardJones self) -> IMP::Float"""
5054 return _IMP_atom.LennardJones_get_well_depth(self)
5056 def set_well_depth(self, well_depth):
5057 r"""set_well_depth(LennardJones self, IMP::Float well_depth)"""
5058 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5061 def get_is_setup(*args):
5063 get_is_setup(_ParticleAdaptor p) -> bool
5064 get_is_setup(Model m, ParticleIndex pi) -> bool
5066 return _IMP_atom.LennardJones_get_is_setup(*args)
5069 def get_well_depth_key():
5070 r"""get_well_depth_key() -> FloatKey"""
5071 return _IMP_atom.LennardJones_get_well_depth_key()
5073 def add_attribute(self, *args):
5075 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5076 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5077 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5078 add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
5079 add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
5080 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5081 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5082 add_attribute(LennardJones self, ObjectKey a0, Object a1)
5083 add_attribute(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5084 add_attribute(LennardJones self, SparseIntKey a0, IMP::Int a1)
5085 add_attribute(LennardJones self, SparseStringKey a0, IMP::String a1)
5086 add_attribute(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5088 return _IMP_atom.LennardJones_add_attribute(self, *args)
5090 def get_value(self, *args):
5092 get_value(LennardJones self, FloatKey a0) -> IMP::Float
5093 get_value(LennardJones self, IntKey a0) -> IMP::Int
5094 get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
5095 get_value(LennardJones self, IntsKey a0) -> IMP::Ints
5096 get_value(LennardJones self, StringKey a0) -> IMP::String
5097 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5098 get_value(LennardJones self, ObjectKey a0) -> Object
5099 get_value(LennardJones self, SparseFloatKey a0) -> IMP::Float
5100 get_value(LennardJones self, SparseIntKey a0) -> IMP::Int
5101 get_value(LennardJones self, SparseStringKey a0) -> IMP::String
5102 get_value(LennardJones self, SparseParticleIndexKey a0) -> ParticleIndex
5104 return _IMP_atom.LennardJones_get_value(self, *args)
5106 def set_value(self, *args):
5108 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5109 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5110 set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5111 set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5112 set_value(LennardJones self, StringKey a0, IMP::String a1)
5113 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5114 set_value(LennardJones self, ObjectKey a0, Object a1)
5115 set_value(LennardJones self, SparseFloatKey a0, IMP::Float a1)
5116 set_value(LennardJones self, SparseIntKey a0, IMP::Int a1)
5117 set_value(LennardJones self, SparseStringKey a0, IMP::String a1)
5118 set_value(LennardJones self, SparseParticleIndexKey a0, ParticleIndex a1)
5120 return _IMP_atom.LennardJones_set_value(self, *args)
5122 def remove_attribute(self, *args):
5124 remove_attribute(LennardJones self, FloatKey a0)
5125 remove_attribute(LennardJones self, IntKey a0)
5126 remove_attribute(LennardJones self, FloatsKey a0)
5127 remove_attribute(LennardJones self, IntsKey a0)
5128 remove_attribute(LennardJones self, StringKey a0)
5129 remove_attribute(LennardJones self, ParticleIndexKey a0)
5130 remove_attribute(LennardJones self, ObjectKey a0)
5131 remove_attribute(LennardJones self, SparseFloatKey a0)
5132 remove_attribute(LennardJones self, SparseIntKey a0)
5133 remove_attribute(LennardJones self, SparseStringKey a0)
5134 remove_attribute(LennardJones self, SparseParticleIndexKey a0)
5136 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5138 def has_attribute(self, *args):
5140 has_attribute(LennardJones self, FloatKey a0) -> bool
5141 has_attribute(LennardJones self, IntKey a0) -> bool
5142 has_attribute(LennardJones self, FloatsKey a0) -> bool
5143 has_attribute(LennardJones self, IntsKey a0) -> bool
5144 has_attribute(LennardJones self, StringKey a0) -> bool
5145 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5146 has_attribute(LennardJones self, ObjectKey a0) -> bool
5147 has_attribute(LennardJones self, SparseFloatKey a0) -> bool
5148 has_attribute(LennardJones self, SparseIntKey a0) -> bool
5149 has_attribute(LennardJones self, SparseStringKey a0) -> bool
5150 has_attribute(LennardJones self, SparseParticleIndexKey a0) -> bool
5152 return _IMP_atom.LennardJones_has_attribute(self, *args)
5154 def get_derivative(self, a0):
5155 r"""get_derivative(LennardJones self, FloatKey a0) -> double"""
5156 return _IMP_atom.LennardJones_get_derivative(self, a0)
5159 r"""get_name(LennardJones self) -> std::string"""
5160 return _IMP_atom.LennardJones_get_name(self)
5162 def clear_caches(self):
5163 r"""clear_caches(LennardJones self)"""
5164 return _IMP_atom.LennardJones_clear_caches(self)
5166 def set_name(self, a0):
5167 r"""set_name(LennardJones self, std::string a0)"""
5168 return _IMP_atom.LennardJones_set_name(self, a0)
5171 r"""set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5172 return _IMP_atom.LennardJones_set_check_level(self, a0)
5174 def add_to_derivative(self, a0, a1, a2):
5175 r"""add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5176 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5178 def set_is_optimized(self, a0, a1):
5179 r"""set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5180 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5182 def get_is_optimized(self, a0):
5183 r"""get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5184 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5187 r"""get_check_level(LennardJones self) -> IMP::CheckLevel"""
5188 return _IMP_atom.LennardJones_get_check_level(self)
5190 def __eq__(self, *args):
5192 __eq__(LennardJones self, LennardJones o) -> bool
5193 __eq__(LennardJones self, Particle d) -> bool
5195 return _IMP_atom.LennardJones___eq__(self, *args)
5197 def __ne__(self, *args):
5199 __ne__(LennardJones self, LennardJones o) -> bool
5200 __ne__(LennardJones self, Particle d) -> bool
5202 return _IMP_atom.LennardJones___ne__(self, *args)
5204 def __le__(self, *args):
5206 __le__(LennardJones self, LennardJones o) -> bool
5207 __le__(LennardJones self, Particle d) -> bool
5209 return _IMP_atom.LennardJones___le__(self, *args)
5211 def __lt__(self, *args):
5213 __lt__(LennardJones self, LennardJones o) -> bool
5214 __lt__(LennardJones self, Particle d) -> bool
5216 return _IMP_atom.LennardJones___lt__(self, *args)
5218 def __ge__(self, *args):
5220 __ge__(LennardJones self, LennardJones o) -> bool
5221 __ge__(LennardJones self, Particle d) -> bool
5223 return _IMP_atom.LennardJones___ge__(self, *args)
5225 def __gt__(self, *args):
5227 __gt__(LennardJones self, LennardJones o) -> bool
5228 __gt__(LennardJones self, Particle d) -> bool
5230 return _IMP_atom.LennardJones___gt__(self, *args)
5233 r"""__hash__(LennardJones self) -> std::size_t"""
5234 return _IMP_atom.LennardJones___hash__(self)
5237 r"""__str__(LennardJones self) -> std::string"""
5238 return _IMP_atom.LennardJones___str__(self)
5241 r"""__repr__(LennardJones self) -> std::string"""
5242 return _IMP_atom.LennardJones___repr__(self)
5244 def _get_as_binary(self):
5245 r"""_get_as_binary(LennardJones self) -> PyObject *"""
5246 return _IMP_atom.LennardJones__get_as_binary(self)
5248 def _set_from_binary(self, p):
5249 r"""_set_from_binary(LennardJones self, PyObject * p)"""
5250 return _IMP_atom.LennardJones__set_from_binary(self, p)
5252 def __getstate__(self):
5253 p = self._get_as_binary()
5254 if len(self.__dict__) > 1:
5255 d = self.__dict__.copy()
5260 def __setstate__(self, p):
5261 if not hasattr(self,
'this'):
5263 if isinstance(p, tuple):
5265 self.__dict__.update(d)
5266 return self._set_from_binary(p)
5268 __swig_destroy__ = _IMP_atom.delete_LennardJones
5271 _IMP_atom.LennardJones_swigregister(LennardJones)
5273 r"""Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5275 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5277 def __init__(self, f):
5278 r"""__init__(LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5279 _IMP_atom.LennardJonesPairScore_swiginit(self, _IMP_atom.new_LennardJonesPairScore(f))
5281 def set_repulsive_weight(self, repulsive_weight):
5282 r"""set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5283 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5285 def get_repulsive_weight(self):
5286 r"""get_repulsive_weight(LennardJonesPairScore self) -> double"""
5287 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5289 def set_attractive_weight(self, attractive_weight):
5290 r"""set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5291 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5293 def get_attractive_weight(self):
5294 r"""get_attractive_weight(LennardJonesPairScore self) -> double"""
5295 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5297 def do_get_inputs(self, m, pis):
5298 r"""do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5299 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5301 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
5302 r"""evaluate_indexes(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
5303 return _IMP_atom.LennardJonesPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
5305 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
5306 r"""evaluate_indexes_scores(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
5307 return _IMP_atom.LennardJonesPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
5309 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
5310 r"""evaluate_indexes_delta(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
5311 return _IMP_atom.LennardJonesPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
5313 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
5314 r"""evaluate_if_good_indexes(LennardJonesPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
5315 return _IMP_atom.LennardJonesPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
5317 def get_version_info(self):
5318 r"""get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5319 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5320 __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
5323 r"""__str__(LennardJonesPairScore self) -> std::string"""
5324 return _IMP_atom.LennardJonesPairScore___str__(self)
5327 r"""__repr__(LennardJonesPairScore self) -> std::string"""
5328 return _IMP_atom.LennardJonesPairScore___repr__(self)
5332 return _object_cast_to_LennardJonesPairScore(o)
5336 _IMP_atom.LennardJonesPairScore_swigregister(LennardJonesPairScore)
5338 r"""Proxy of C++ IMP::atom::LennardJonesType class."""
5340 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5342 def __init__(self, *args):
5343 r"""__init__(LennardJonesType self, double well_depth, double radius, std::string name="LennardJonesType%1%") -> LennardJonesType"""
5344 _IMP_atom.LennardJonesType_swiginit(self, _IMP_atom.new_LennardJonesType(*args))
5346 def get_well_depth(self):
5347 r"""get_well_depth(LennardJonesType self) -> double"""
5348 return _IMP_atom.LennardJonesType_get_well_depth(self)
5350 def set_well_depth(self, d):
5351 r"""set_well_depth(LennardJonesType self, double d)"""
5352 return _IMP_atom.LennardJonesType_set_well_depth(self, d)
5354 def get_radius(self):
5355 r"""get_radius(LennardJonesType self) -> double"""
5356 return _IMP_atom.LennardJonesType_get_radius(self)
5358 def set_radius(self, r):
5359 r"""set_radius(LennardJonesType self, double r)"""
5360 return _IMP_atom.LennardJonesType_set_radius(self, r)
5363 r"""get_index(LennardJonesType self) -> int"""
5364 return _IMP_atom.LennardJonesType_get_index(self)
5366 def get_version_info(self):
5367 r"""get_version_info(LennardJonesType self) -> VersionInfo"""
5368 return _IMP_atom.LennardJonesType_get_version_info(self)
5369 __swig_destroy__ = _IMP_atom.delete_LennardJonesType
5372 r"""__str__(LennardJonesType self) -> std::string"""
5373 return _IMP_atom.LennardJonesType___str__(self)
5376 r"""__repr__(LennardJonesType self) -> std::string"""
5377 return _IMP_atom.LennardJonesType___repr__(self)
5381 return _object_cast_to_LennardJonesType(o)
5385 _IMP_atom.LennardJonesType_swigregister(LennardJonesType)
5387 r"""Proxy of C++ IMP::atom::LennardJonesTyped class."""
5389 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5391 def __init__(self, *args):
5393 __init__(LennardJonesTyped self) -> LennardJonesTyped
5394 __init__(LennardJonesTyped self, Model m, ParticleIndex id) -> LennardJonesTyped
5395 __init__(LennardJonesTyped self, _ParticleAdaptor d) -> LennardJonesTyped
5397 _IMP_atom.LennardJonesTyped_swiginit(self, _IMP_atom.new_LennardJonesTyped(*args))
5399 def show(self, *args):
5400 r"""show(LennardJonesTyped self, _ostream out=std::cout)"""
5401 return _IMP_atom.LennardJonesTyped_show(self, *args)
5404 def setup_particle(*args):
5406 setup_particle(Model m, ParticleIndex pi, LennardJonesType type) -> LennardJonesTyped
5407 setup_particle(_ParticleAdaptor pa, LennardJonesType type) -> LennardJonesTyped
5409 return _IMP_atom.LennardJonesTyped_setup_particle(*args)
5412 def get_is_setup(*args):
5414 get_is_setup(_ParticleAdaptor p) -> bool
5415 get_is_setup(Model m, ParticleIndex pi) -> bool
5417 return _IMP_atom.LennardJonesTyped_get_is_setup(*args)
5419 def set_type(self, type):
5420 r"""set_type(LennardJonesTyped self, LennardJonesType type)"""
5421 return _IMP_atom.LennardJonesTyped_set_type(self, type)
5424 r"""get_type(LennardJonesTyped self) -> LennardJonesType"""
5425 return _IMP_atom.LennardJonesTyped_get_type(self)
5428 r"""get_index(LennardJonesTyped self) -> int"""
5429 return _IMP_atom.LennardJonesTyped_get_index(self)
5431 def get_well_depth(self):
5432 r"""get_well_depth(LennardJonesTyped self) -> double"""
5433 return _IMP_atom.LennardJonesTyped_get_well_depth(self)
5435 def get_radius(self):
5436 r"""get_radius(LennardJonesTyped self) -> double"""
5437 return _IMP_atom.LennardJonesTyped_get_radius(self)
5441 r"""get_type_key() -> IntKey"""
5442 return _IMP_atom.LennardJonesTyped_get_type_key()
5444 def add_attribute(self, *args):
5446 add_attribute(LennardJonesTyped self, FloatKey k, IMP::Float v, bool opt)
5447 add_attribute(LennardJonesTyped self, FloatKey a0, IMP::Float a1)
5448 add_attribute(LennardJonesTyped self, IntKey a0, IMP::Int a1)
5449 add_attribute(LennardJonesTyped self, FloatsKey a0, IMP::Floats a1)
5450 add_attribute(LennardJonesTyped self, IntsKey a0, IMP::Ints a1)
5451 add_attribute(LennardJonesTyped self, StringKey a0, IMP::String a1)
5452 add_attribute(LennardJonesTyped self, ParticleIndexKey a0, Particle a1)
5453 add_attribute(LennardJonesTyped self, ObjectKey a0, Object a1)
5454 add_attribute(LennardJonesTyped self, SparseFloatKey a0, IMP::Float a1)
5455 add_attribute(LennardJonesTyped self, SparseIntKey a0, IMP::Int a1)
5456 add_attribute(LennardJonesTyped self, SparseStringKey a0, IMP::String a1)
5457 add_attribute(LennardJonesTyped self, SparseParticleIndexKey a0, ParticleIndex a1)
5459 return _IMP_atom.LennardJonesTyped_add_attribute(self, *args)
5461 def get_value(self, *args):
5463 get_value(LennardJonesTyped self, FloatKey a0) -> IMP::Float
5464 get_value(LennardJonesTyped self, IntKey a0) -> IMP::Int
5465 get_value(LennardJonesTyped self, FloatsKey a0) -> IMP::Floats
5466 get_value(LennardJonesTyped self, IntsKey a0) -> IMP::Ints
5467 get_value(LennardJonesTyped self, StringKey a0) -> IMP::String
5468 get_value(LennardJonesTyped self, ParticleIndexKey a0) -> Particle
5469 get_value(LennardJonesTyped self, ObjectKey a0) -> Object
5470 get_value(LennardJonesTyped self, SparseFloatKey a0) -> IMP::Float
5471 get_value(LennardJonesTyped self, SparseIntKey a0) -> IMP::Int
5472 get_value(LennardJonesTyped self, SparseStringKey a0) -> IMP::String
5473 get_value(LennardJonesTyped self, SparseParticleIndexKey a0) -> ParticleIndex
5475 return _IMP_atom.LennardJonesTyped_get_value(self, *args)
5477 def set_value(self, *args):
5479 set_value(LennardJonesTyped self, FloatKey a0, IMP::Float a1)
5480 set_value(LennardJonesTyped self, IntKey a0, IMP::Int a1)
5481 set_value(LennardJonesTyped self, FloatsKey a0, IMP::Floats a1)
5482 set_value(LennardJonesTyped self, IntsKey a0, IMP::Ints a1)
5483 set_value(LennardJonesTyped self, StringKey a0, IMP::String a1)
5484 set_value(LennardJonesTyped self, ParticleIndexKey a0, Particle a1)
5485 set_value(LennardJonesTyped self, ObjectKey a0, Object a1)
5486 set_value(LennardJonesTyped self, SparseFloatKey a0, IMP::Float a1)
5487 set_value(LennardJonesTyped self, SparseIntKey a0, IMP::Int a1)
5488 set_value(LennardJonesTyped self, SparseStringKey a0, IMP::String a1)
5489 set_value(LennardJonesTyped self, SparseParticleIndexKey a0, ParticleIndex a1)
5491 return _IMP_atom.LennardJonesTyped_set_value(self, *args)
5493 def remove_attribute(self, *args):
5495 remove_attribute(LennardJonesTyped self, FloatKey a0)
5496 remove_attribute(LennardJonesTyped self, IntKey a0)
5497 remove_attribute(LennardJonesTyped self, FloatsKey a0)
5498 remove_attribute(LennardJonesTyped self, IntsKey a0)
5499 remove_attribute(LennardJonesTyped self, StringKey a0)
5500 remove_attribute(LennardJonesTyped self, ParticleIndexKey a0)
5501 remove_attribute(LennardJonesTyped self, ObjectKey a0)
5502 remove_attribute(LennardJonesTyped self, SparseFloatKey a0)
5503 remove_attribute(LennardJonesTyped self, SparseIntKey a0)
5504 remove_attribute(LennardJonesTyped self, SparseStringKey a0)
5505 remove_attribute(LennardJonesTyped self, SparseParticleIndexKey a0)
5507 return _IMP_atom.LennardJonesTyped_remove_attribute(self, *args)
5509 def has_attribute(self, *args):
5511 has_attribute(LennardJonesTyped self, FloatKey a0) -> bool
5512 has_attribute(LennardJonesTyped self, IntKey a0) -> bool
5513 has_attribute(LennardJonesTyped self, FloatsKey a0) -> bool
5514 has_attribute(LennardJonesTyped self, IntsKey a0) -> bool
5515 has_attribute(LennardJonesTyped self, StringKey a0) -> bool
5516 has_attribute(LennardJonesTyped self, ParticleIndexKey a0) -> bool
5517 has_attribute(LennardJonesTyped self, ObjectKey a0) -> bool
5518 has_attribute(LennardJonesTyped self, SparseFloatKey a0) -> bool
5519 has_attribute(LennardJonesTyped self, SparseIntKey a0) -> bool
5520 has_attribute(LennardJonesTyped self, SparseStringKey a0) -> bool
5521 has_attribute(LennardJonesTyped self, SparseParticleIndexKey a0) -> bool
5523 return _IMP_atom.LennardJonesTyped_has_attribute(self, *args)
5525 def get_derivative(self, a0):
5526 r"""get_derivative(LennardJonesTyped self, FloatKey a0) -> double"""
5527 return _IMP_atom.LennardJonesTyped_get_derivative(self, a0)
5530 r"""get_name(LennardJonesTyped self) -> std::string"""
5531 return _IMP_atom.LennardJonesTyped_get_name(self)
5533 def clear_caches(self):
5534 r"""clear_caches(LennardJonesTyped self)"""
5535 return _IMP_atom.LennardJonesTyped_clear_caches(self)
5537 def set_name(self, a0):
5538 r"""set_name(LennardJonesTyped self, std::string a0)"""
5539 return _IMP_atom.LennardJonesTyped_set_name(self, a0)
5542 r"""set_check_level(LennardJonesTyped self, IMP::CheckLevel a0)"""
5543 return _IMP_atom.LennardJonesTyped_set_check_level(self, a0)
5545 def add_to_derivative(self, a0, a1, a2):
5546 r"""add_to_derivative(LennardJonesTyped self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5547 return _IMP_atom.LennardJonesTyped_add_to_derivative(self, a0, a1, a2)
5549 def set_is_optimized(self, a0, a1):
5550 r"""set_is_optimized(LennardJonesTyped self, FloatKey a0, bool a1)"""
5551 return _IMP_atom.LennardJonesTyped_set_is_optimized(self, a0, a1)
5553 def get_is_optimized(self, a0):
5554 r"""get_is_optimized(LennardJonesTyped self, FloatKey a0) -> bool"""
5555 return _IMP_atom.LennardJonesTyped_get_is_optimized(self, a0)
5558 r"""get_check_level(LennardJonesTyped self) -> IMP::CheckLevel"""
5559 return _IMP_atom.LennardJonesTyped_get_check_level(self)
5561 def __eq__(self, *args):
5563 __eq__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5564 __eq__(LennardJonesTyped self, Particle d) -> bool
5566 return _IMP_atom.LennardJonesTyped___eq__(self, *args)
5568 def __ne__(self, *args):
5570 __ne__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5571 __ne__(LennardJonesTyped self, Particle d) -> bool
5573 return _IMP_atom.LennardJonesTyped___ne__(self, *args)
5575 def __le__(self, *args):
5577 __le__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5578 __le__(LennardJonesTyped self, Particle d) -> bool
5580 return _IMP_atom.LennardJonesTyped___le__(self, *args)
5582 def __lt__(self, *args):
5584 __lt__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5585 __lt__(LennardJonesTyped self, Particle d) -> bool
5587 return _IMP_atom.LennardJonesTyped___lt__(self, *args)
5589 def __ge__(self, *args):
5591 __ge__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5592 __ge__(LennardJonesTyped self, Particle d) -> bool
5594 return _IMP_atom.LennardJonesTyped___ge__(self, *args)
5596 def __gt__(self, *args):
5598 __gt__(LennardJonesTyped self, LennardJonesTyped o) -> bool
5599 __gt__(LennardJonesTyped self, Particle d) -> bool
5601 return _IMP_atom.LennardJonesTyped___gt__(self, *args)
5604 r"""__hash__(LennardJonesTyped self) -> std::size_t"""
5605 return _IMP_atom.LennardJonesTyped___hash__(self)
5608 r"""__str__(LennardJonesTyped self) -> std::string"""
5609 return _IMP_atom.LennardJonesTyped___str__(self)
5612 r"""__repr__(LennardJonesTyped self) -> std::string"""
5613 return _IMP_atom.LennardJonesTyped___repr__(self)
5615 def _get_as_binary(self):
5616 r"""_get_as_binary(LennardJonesTyped self) -> PyObject *"""
5617 return _IMP_atom.LennardJonesTyped__get_as_binary(self)
5619 def _set_from_binary(self, p):
5620 r"""_set_from_binary(LennardJonesTyped self, PyObject * p)"""
5621 return _IMP_atom.LennardJonesTyped__set_from_binary(self, p)
5623 def __getstate__(self):
5624 p = self._get_as_binary()
5625 if len(self.__dict__) > 1:
5626 d = self.__dict__.copy()
5631 def __setstate__(self, p):
5632 if not hasattr(self,
'this'):
5634 if isinstance(p, tuple):
5636 self.__dict__.update(d)
5637 return self._set_from_binary(p)
5639 __swig_destroy__ = _IMP_atom.delete_LennardJonesTyped
5642 _IMP_atom.LennardJonesTyped_swigregister(LennardJonesTyped)
5644 r"""Proxy of C++ IMP::atom::LinearVelocity class."""
5646 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5648 def __init__(self, *args):
5650 __init__(LinearVelocity self) -> LinearVelocity
5651 __init__(LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5652 __init__(LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5654 _IMP_atom.LinearVelocity_swiginit(self, _IMP_atom.new_LinearVelocity(*args))
5657 def get_is_setup(*args):
5659 get_is_setup(Model m, ParticleIndex pi) -> bool
5660 get_is_setup(_ParticleAdaptor p) -> bool
5662 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5664 def show(self, *args):
5665 r"""show(LinearVelocity self, _ostream out=std::cout)"""
5666 return _IMP_atom.LinearVelocity_show(self, *args)
5669 def setup_particle(*args):
5671 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5672 setup_particle(_ParticleAdaptor pa) -> LinearVelocity
5673 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5674 setup_particle(_ParticleAdaptor pa, Vector3D v) -> LinearVelocity
5676 return _IMP_atom.LinearVelocity_setup_particle(*args)
5678 def set_velocity(self, v):
5679 r"""set_velocity(LinearVelocity self, Vector3D v)"""
5680 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5682 def get_velocity(self):
5683 r"""get_velocity(LinearVelocity self) -> Vector3D"""
5684 return _IMP_atom.LinearVelocity_get_velocity(self)
5686 def add_attribute(self, *args):
5688 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5689 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5690 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5691 add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5692 add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5693 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5694 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5695 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5696 add_attribute(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5697 add_attribute(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5698 add_attribute(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5699 add_attribute(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5701 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5703 def get_value(self, *args):
5705 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5706 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5707 get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5708 get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5709 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5710 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5711 get_value(LinearVelocity self, ObjectKey a0) -> Object
5712 get_value(LinearVelocity self, SparseFloatKey a0) -> IMP::Float
5713 get_value(LinearVelocity self, SparseIntKey a0) -> IMP::Int
5714 get_value(LinearVelocity self, SparseStringKey a0) -> IMP::String
5715 get_value(LinearVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5717 return _IMP_atom.LinearVelocity_get_value(self, *args)
5719 def set_value(self, *args):
5721 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5722 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5723 set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5724 set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5725 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5726 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5727 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5728 set_value(LinearVelocity self, SparseFloatKey a0, IMP::Float a1)
5729 set_value(LinearVelocity self, SparseIntKey a0, IMP::Int a1)
5730 set_value(LinearVelocity self, SparseStringKey a0, IMP::String a1)
5731 set_value(LinearVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5733 return _IMP_atom.LinearVelocity_set_value(self, *args)
5735 def remove_attribute(self, *args):
5737 remove_attribute(LinearVelocity self, FloatKey a0)
5738 remove_attribute(LinearVelocity self, IntKey a0)
5739 remove_attribute(LinearVelocity self, FloatsKey a0)
5740 remove_attribute(LinearVelocity self, IntsKey a0)
5741 remove_attribute(LinearVelocity self, StringKey a0)
5742 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5743 remove_attribute(LinearVelocity self, ObjectKey a0)
5744 remove_attribute(LinearVelocity self, SparseFloatKey a0)
5745 remove_attribute(LinearVelocity self, SparseIntKey a0)
5746 remove_attribute(LinearVelocity self, SparseStringKey a0)
5747 remove_attribute(LinearVelocity self, SparseParticleIndexKey a0)
5749 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5751 def has_attribute(self, *args):
5753 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5754 has_attribute(LinearVelocity self, IntKey a0) -> bool
5755 has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5756 has_attribute(LinearVelocity self, IntsKey a0) -> bool
5757 has_attribute(LinearVelocity self, StringKey a0) -> bool
5758 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5759 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5760 has_attribute(LinearVelocity self, SparseFloatKey a0) -> bool
5761 has_attribute(LinearVelocity self, SparseIntKey a0) -> bool
5762 has_attribute(LinearVelocity self, SparseStringKey a0) -> bool
5763 has_attribute(LinearVelocity self, SparseParticleIndexKey a0) -> bool
5765 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5767 def get_derivative(self, a0):
5768 r"""get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5769 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5772 r"""get_name(LinearVelocity self) -> std::string"""
5773 return _IMP_atom.LinearVelocity_get_name(self)
5775 def clear_caches(self):
5776 r"""clear_caches(LinearVelocity self)"""
5777 return _IMP_atom.LinearVelocity_clear_caches(self)
5779 def set_name(self, a0):
5780 r"""set_name(LinearVelocity self, std::string a0)"""
5781 return _IMP_atom.LinearVelocity_set_name(self, a0)
5784 r"""set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5785 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5787 def add_to_derivative(self, a0, a1, a2):
5788 r"""add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5789 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5791 def set_is_optimized(self, a0, a1):
5792 r"""set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5793 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5795 def get_is_optimized(self, a0):
5796 r"""get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5797 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5800 r"""get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5801 return _IMP_atom.LinearVelocity_get_check_level(self)
5803 def __eq__(self, *args):
5805 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5806 __eq__(LinearVelocity self, Particle d) -> bool
5808 return _IMP_atom.LinearVelocity___eq__(self, *args)
5810 def __ne__(self, *args):
5812 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5813 __ne__(LinearVelocity self, Particle d) -> bool
5815 return _IMP_atom.LinearVelocity___ne__(self, *args)
5817 def __le__(self, *args):
5819 __le__(LinearVelocity self, LinearVelocity o) -> bool
5820 __le__(LinearVelocity self, Particle d) -> bool
5822 return _IMP_atom.LinearVelocity___le__(self, *args)
5824 def __lt__(self, *args):
5826 __lt__(LinearVelocity self, LinearVelocity o) -> bool
5827 __lt__(LinearVelocity self, Particle d) -> bool
5829 return _IMP_atom.LinearVelocity___lt__(self, *args)
5831 def __ge__(self, *args):
5833 __ge__(LinearVelocity self, LinearVelocity o) -> bool
5834 __ge__(LinearVelocity self, Particle d) -> bool
5836 return _IMP_atom.LinearVelocity___ge__(self, *args)
5838 def __gt__(self, *args):
5840 __gt__(LinearVelocity self, LinearVelocity o) -> bool
5841 __gt__(LinearVelocity self, Particle d) -> bool
5843 return _IMP_atom.LinearVelocity___gt__(self, *args)
5846 r"""__hash__(LinearVelocity self) -> std::size_t"""
5847 return _IMP_atom.LinearVelocity___hash__(self)
5850 r"""__str__(LinearVelocity self) -> std::string"""
5851 return _IMP_atom.LinearVelocity___str__(self)
5854 r"""__repr__(LinearVelocity self) -> std::string"""
5855 return _IMP_atom.LinearVelocity___repr__(self)
5857 def _get_as_binary(self):
5858 r"""_get_as_binary(LinearVelocity self) -> PyObject *"""
5859 return _IMP_atom.LinearVelocity__get_as_binary(self)
5861 def _set_from_binary(self, p):
5862 r"""_set_from_binary(LinearVelocity self, PyObject * p)"""
5863 return _IMP_atom.LinearVelocity__set_from_binary(self, p)
5865 def __getstate__(self):
5866 p = self._get_as_binary()
5867 if len(self.__dict__) > 1:
5868 d = self.__dict__.copy()
5873 def __setstate__(self, p):
5874 if not hasattr(self,
'this'):
5876 if isinstance(p, tuple):
5878 self.__dict__.update(d)
5879 return self._set_from_binary(p)
5881 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5884 _IMP_atom.LinearVelocity_swigregister(LinearVelocity)
5886 r"""Proxy of C++ IMP::atom::AngularVelocity class."""
5888 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5890 def __init__(self, *args):
5892 __init__(AngularVelocity self) -> AngularVelocity
5893 __init__(AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5894 __init__(AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5896 _IMP_atom.AngularVelocity_swiginit(self, _IMP_atom.new_AngularVelocity(*args))
5899 def get_is_setup(*args):
5901 get_is_setup(Model m, ParticleIndex pi) -> bool
5902 get_is_setup(_ParticleAdaptor p) -> bool
5904 return _IMP_atom.AngularVelocity_get_is_setup(*args)
5906 def show(self, *args):
5907 r"""show(AngularVelocity self, _ostream out=std::cout)"""
5908 return _IMP_atom.AngularVelocity_show(self, *args)
5911 def setup_particle(*args):
5913 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5914 setup_particle(_ParticleAdaptor pa) -> AngularVelocity
5915 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5916 setup_particle(_ParticleAdaptor pa, Vector4D v) -> AngularVelocity
5918 return _IMP_atom.AngularVelocity_setup_particle(*args)
5920 def set_velocity(self, v):
5921 r"""set_velocity(AngularVelocity self, Vector4D v)"""
5922 return _IMP_atom.AngularVelocity_set_velocity(self, v)
5924 def get_velocity(self):
5925 r"""get_velocity(AngularVelocity self) -> Vector4D"""
5926 return _IMP_atom.AngularVelocity_get_velocity(self)
5928 def add_attribute(self, *args):
5930 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5931 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5932 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5933 add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5934 add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5935 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5936 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5937 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5938 add_attribute(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5939 add_attribute(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5940 add_attribute(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5941 add_attribute(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5943 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5945 def get_value(self, *args):
5947 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5948 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5949 get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
5950 get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
5951 get_value(AngularVelocity self, StringKey a0) -> IMP::String
5952 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5953 get_value(AngularVelocity self, ObjectKey a0) -> Object
5954 get_value(AngularVelocity self, SparseFloatKey a0) -> IMP::Float
5955 get_value(AngularVelocity self, SparseIntKey a0) -> IMP::Int
5956 get_value(AngularVelocity self, SparseStringKey a0) -> IMP::String
5957 get_value(AngularVelocity self, SparseParticleIndexKey a0) -> ParticleIndex
5959 return _IMP_atom.AngularVelocity_get_value(self, *args)
5961 def set_value(self, *args):
5963 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5964 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5965 set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5966 set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5967 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5968 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5969 set_value(AngularVelocity self, ObjectKey a0, Object a1)
5970 set_value(AngularVelocity self, SparseFloatKey a0, IMP::Float a1)
5971 set_value(AngularVelocity self, SparseIntKey a0, IMP::Int a1)
5972 set_value(AngularVelocity self, SparseStringKey a0, IMP::String a1)
5973 set_value(AngularVelocity self, SparseParticleIndexKey a0, ParticleIndex a1)
5975 return _IMP_atom.AngularVelocity_set_value(self, *args)
5977 def remove_attribute(self, *args):
5979 remove_attribute(AngularVelocity self, FloatKey a0)
5980 remove_attribute(AngularVelocity self, IntKey a0)
5981 remove_attribute(AngularVelocity self, FloatsKey a0)
5982 remove_attribute(AngularVelocity self, IntsKey a0)
5983 remove_attribute(AngularVelocity self, StringKey a0)
5984 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5985 remove_attribute(AngularVelocity self, ObjectKey a0)
5986 remove_attribute(AngularVelocity self, SparseFloatKey a0)
5987 remove_attribute(AngularVelocity self, SparseIntKey a0)
5988 remove_attribute(AngularVelocity self, SparseStringKey a0)
5989 remove_attribute(AngularVelocity self, SparseParticleIndexKey a0)
5991 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5993 def has_attribute(self, *args):
5995 has_attribute(AngularVelocity self, FloatKey a0) -> bool
5996 has_attribute(AngularVelocity self, IntKey a0) -> bool
5997 has_attribute(AngularVelocity self, FloatsKey a0) -> bool
5998 has_attribute(AngularVelocity self, IntsKey a0) -> bool
5999 has_attribute(AngularVelocity self, StringKey a0) -> bool
6000 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6001 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6002 has_attribute(AngularVelocity self, SparseFloatKey a0) -> bool
6003 has_attribute(AngularVelocity self, SparseIntKey a0) -> bool
6004 has_attribute(AngularVelocity self, SparseStringKey a0) -> bool
6005 has_attribute(AngularVelocity self, SparseParticleIndexKey a0) -> bool
6007 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6009 def get_derivative(self, a0):
6010 r"""get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6011 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6014 r"""get_name(AngularVelocity self) -> std::string"""
6015 return _IMP_atom.AngularVelocity_get_name(self)
6017 def clear_caches(self):
6018 r"""clear_caches(AngularVelocity self)"""
6019 return _IMP_atom.AngularVelocity_clear_caches(self)
6021 def set_name(self, a0):
6022 r"""set_name(AngularVelocity self, std::string a0)"""
6023 return _IMP_atom.AngularVelocity_set_name(self, a0)
6026 r"""set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6027 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6029 def add_to_derivative(self, a0, a1, a2):
6030 r"""add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6031 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6033 def set_is_optimized(self, a0, a1):
6034 r"""set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6035 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6037 def get_is_optimized(self, a0):
6038 r"""get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6039 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6042 r"""get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6043 return _IMP_atom.AngularVelocity_get_check_level(self)
6045 def __eq__(self, *args):
6047 __eq__(AngularVelocity self, AngularVelocity o) -> bool
6048 __eq__(AngularVelocity self, Particle d) -> bool
6050 return _IMP_atom.AngularVelocity___eq__(self, *args)
6052 def __ne__(self, *args):
6054 __ne__(AngularVelocity self, AngularVelocity o) -> bool
6055 __ne__(AngularVelocity self, Particle d) -> bool
6057 return _IMP_atom.AngularVelocity___ne__(self, *args)
6059 def __le__(self, *args):
6061 __le__(AngularVelocity self, AngularVelocity o) -> bool
6062 __le__(AngularVelocity self, Particle d) -> bool
6064 return _IMP_atom.AngularVelocity___le__(self, *args)
6066 def __lt__(self, *args):
6068 __lt__(AngularVelocity self, AngularVelocity o) -> bool
6069 __lt__(AngularVelocity self, Particle d) -> bool
6071 return _IMP_atom.AngularVelocity___lt__(self, *args)
6073 def __ge__(self, *args):
6075 __ge__(AngularVelocity self, AngularVelocity o) -> bool
6076 __ge__(AngularVelocity self, Particle d) -> bool
6078 return _IMP_atom.AngularVelocity___ge__(self, *args)
6080 def __gt__(self, *args):
6082 __gt__(AngularVelocity self, AngularVelocity o) -> bool
6083 __gt__(AngularVelocity self, Particle d) -> bool
6085 return _IMP_atom.AngularVelocity___gt__(self, *args)
6088 r"""__hash__(AngularVelocity self) -> std::size_t"""
6089 return _IMP_atom.AngularVelocity___hash__(self)
6092 r"""__str__(AngularVelocity self) -> std::string"""
6093 return _IMP_atom.AngularVelocity___str__(self)
6096 r"""__repr__(AngularVelocity self) -> std::string"""
6097 return _IMP_atom.AngularVelocity___repr__(self)
6099 def _get_as_binary(self):
6100 r"""_get_as_binary(AngularVelocity self) -> PyObject *"""
6101 return _IMP_atom.AngularVelocity__get_as_binary(self)
6103 def _set_from_binary(self, p):
6104 r"""_set_from_binary(AngularVelocity self, PyObject * p)"""
6105 return _IMP_atom.AngularVelocity__set_from_binary(self, p)
6107 def __getstate__(self):
6108 p = self._get_as_binary()
6109 if len(self.__dict__) > 1:
6110 d = self.__dict__.copy()
6115 def __setstate__(self, p):
6116 if not hasattr(self,
'this'):
6118 if isinstance(p, tuple):
6120 self.__dict__.update(d)
6121 return self._set_from_binary(p)
6123 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6126 _IMP_atom.AngularVelocity_swigregister(AngularVelocity)
6127 class MolecularDynamics(Simulator):
6128 r"""Proxy of C++ IMP::atom::MolecularDynamics class."""
6130 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6132 def __init__(self, m):
6133 r"""__init__(MolecularDynamics self, Model m) -> MolecularDynamics"""
6134 _IMP_atom.MolecularDynamics_swiginit(self, _IMP_atom.new_MolecularDynamics(m))
6136 def get_kinetic_energy(self):
6137 r"""get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6138 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6140 def get_kinetic_temperature(self, ekinetic):
6141 r"""get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6142 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6144 def set_velocity_cap(self, velocity_cap):
6145 r"""set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6146 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6148 def assign_velocities(self, temperature):
6149 r"""assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6150 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6152 def setup(self, ps):
6153 r"""setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6154 return _IMP_atom.MolecularDynamics_setup(self, ps)
6156 def do_step(self, sc, dt):
6157 r"""do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6158 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6160 def get_is_simulation_particle(self, p):
6161 r"""get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6162 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6164 def get_version_info(self):
6165 r"""get_version_info(MolecularDynamics self) -> VersionInfo"""
6166 return _IMP_atom.MolecularDynamics_get_version_info(self)
6167 __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
6170 r"""__str__(MolecularDynamics self) -> std::string"""
6171 return _IMP_atom.MolecularDynamics___str__(self)
6174 r"""__repr__(MolecularDynamics self) -> std::string"""
6175 return _IMP_atom.MolecularDynamics___repr__(self)
6179 return _object_cast_to_MolecularDynamics(o)
6183 _IMP_atom.MolecularDynamics_swigregister(MolecularDynamics)
6185 r"""Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6187 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6189 def __init__(self, m, pis, temperature):
6190 r"""__init__(VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6191 _IMP_atom.VelocityScalingOptimizerState_swiginit(self, _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature))
6193 def set_particles(self, pis):
6194 r"""set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6195 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6197 def set_temperature(self, temperature):
6198 r"""set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6199 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6201 def rescale_velocities(self):
6202 r"""rescale_velocities(VelocityScalingOptimizerState self)"""
6203 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6205 def get_version_info(self):
6206 r"""get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6207 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6208 __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
6211 r"""__str__(VelocityScalingOptimizerState self) -> std::string"""
6212 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6215 r"""__repr__(VelocityScalingOptimizerState self) -> std::string"""
6216 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6220 return _object_cast_to_VelocityScalingOptimizerState(o)
6224 _IMP_atom.VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6225 class Fragment(Hierarchy):
6226 r"""Proxy of C++ IMP::atom::Fragment class."""
6228 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6230 def set_residue_indexes(self, o):
6231 r"""set_residue_indexes(Fragment self, IMP::Ints o)"""
6232 return _IMP_atom.Fragment_set_residue_indexes(self, o)
6234 def get_residue_indexes(self):
6235 r"""get_residue_indexes(Fragment self) -> IMP::Ints"""
6236 return _IMP_atom.Fragment_get_residue_indexes(self)
6238 def get_contains_residue(self, rindex):
6239 r"""get_contains_residue(Fragment self, int rindex) -> bool"""
6240 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6242 def get_contains_any_sorted_residue(self, rinds):
6243 r"""get_contains_any_sorted_residue(Fragment self, IMP::Ints const & rinds) -> bool"""
6244 return _IMP_atom.Fragment_get_contains_any_sorted_residue(self, rinds)
6246 def __init__(self, *args):
6248 __init__(Fragment self) -> Fragment
6249 __init__(Fragment self, Model m, ParticleIndex id) -> Fragment
6250 __init__(Fragment self, _ParticleAdaptor d) -> Fragment
6252 _IMP_atom.Fragment_swiginit(self, _IMP_atom.new_Fragment(*args))
6255 def get_is_setup(*args):
6257 get_is_setup(Model m, ParticleIndex pi) -> bool
6258 get_is_setup(_ParticleAdaptor p) -> bool
6260 return _IMP_atom.Fragment_get_is_setup(*args)
6262 def show(self, *args):
6263 r"""show(Fragment self, _ostream out=std::cout)"""
6264 return _IMP_atom.Fragment_show(self, *args)
6267 def setup_particle(*args):
6269 setup_particle(Model m, ParticleIndex pi) -> Fragment
6270 setup_particle(_ParticleAdaptor pa) -> Fragment
6271 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6272 setup_particle(_ParticleAdaptor pa, Fragment other) -> Fragment
6273 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6274 setup_particle(_ParticleAdaptor pa, IMP::Ints residue_indexes) -> Fragment
6276 return _IMP_atom.Fragment_setup_particle(*args)
6278 def add_attribute(self, *args):
6280 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6281 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6282 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6283 add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
6284 add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
6285 add_attribute(Fragment self, StringKey a0, IMP::String a1)
6286 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6287 add_attribute(Fragment self, ObjectKey a0, Object a1)
6288 add_attribute(Fragment self, SparseFloatKey a0, IMP::Float a1)
6289 add_attribute(Fragment self, SparseIntKey a0, IMP::Int a1)
6290 add_attribute(Fragment self, SparseStringKey a0, IMP::String a1)
6291 add_attribute(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
6293 return _IMP_atom.Fragment_add_attribute(self, *args)
6295 def get_value(self, *args):
6297 get_value(Fragment self, FloatKey a0) -> IMP::Float
6298 get_value(Fragment self, IntKey a0) -> IMP::Int
6299 get_value(Fragment self, FloatsKey a0) -> IMP::Floats
6300 get_value(Fragment self, IntsKey a0) -> IMP::Ints
6301 get_value(Fragment self, StringKey a0) -> IMP::String
6302 get_value(Fragment self, ParticleIndexKey a0) -> Particle
6303 get_value(Fragment self, ObjectKey a0) -> Object
6304 get_value(Fragment self, SparseFloatKey a0) -> IMP::Float
6305 get_value(Fragment self, SparseIntKey a0) -> IMP::Int
6306 get_value(Fragment self, SparseStringKey a0) -> IMP::String
6307 get_value(Fragment self, SparseParticleIndexKey a0) -> ParticleIndex
6309 return _IMP_atom.Fragment_get_value(self, *args)
6311 def set_value(self, *args):
6313 set_value(Fragment self, FloatKey a0, IMP::Float a1)
6314 set_value(Fragment self, IntKey a0, IMP::Int a1)
6315 set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
6316 set_value(Fragment self, IntsKey a0, IMP::Ints a1)
6317 set_value(Fragment self, StringKey a0, IMP::String a1)
6318 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6319 set_value(Fragment self, ObjectKey a0, Object a1)
6320 set_value(Fragment self, SparseFloatKey a0, IMP::Float a1)
6321 set_value(Fragment self, SparseIntKey a0, IMP::Int a1)
6322 set_value(Fragment self, SparseStringKey a0, IMP::String a1)
6323 set_value(Fragment self, SparseParticleIndexKey a0, ParticleIndex a1)
6325 return _IMP_atom.Fragment_set_value(self, *args)
6327 def remove_attribute(self, *args):
6329 remove_attribute(Fragment self, FloatKey a0)
6330 remove_attribute(Fragment self, IntKey a0)
6331 remove_attribute(Fragment self, FloatsKey a0)
6332 remove_attribute(Fragment self, IntsKey a0)
6333 remove_attribute(Fragment self, StringKey a0)
6334 remove_attribute(Fragment self, ParticleIndexKey a0)
6335 remove_attribute(Fragment self, ObjectKey a0)
6336 remove_attribute(Fragment self, SparseFloatKey a0)
6337 remove_attribute(Fragment self, SparseIntKey a0)
6338 remove_attribute(Fragment self, SparseStringKey a0)
6339 remove_attribute(Fragment self, SparseParticleIndexKey a0)
6341 return _IMP_atom.Fragment_remove_attribute(self, *args)
6343 def has_attribute(self, *args):
6345 has_attribute(Fragment self, FloatKey a0) -> bool
6346 has_attribute(Fragment self, IntKey a0) -> bool
6347 has_attribute(Fragment self, FloatsKey a0) -> bool
6348 has_attribute(Fragment self, IntsKey a0) -> bool
6349 has_attribute(Fragment self, StringKey a0) -> bool
6350 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6351 has_attribute(Fragment self, ObjectKey a0) -> bool
6352 has_attribute(Fragment self, SparseFloatKey a0) -> bool
6353 has_attribute(Fragment self, SparseIntKey a0) -> bool
6354 has_attribute(Fragment self, SparseStringKey a0) -> bool
6355 has_attribute(Fragment self, SparseParticleIndexKey a0) -> bool
6357 return _IMP_atom.Fragment_has_attribute(self, *args)
6359 def get_derivative(self, a0):
6360 r"""get_derivative(Fragment self, FloatKey a0) -> double"""
6361 return _IMP_atom.Fragment_get_derivative(self, a0)
6364 r"""get_name(Fragment self) -> std::string"""
6365 return _IMP_atom.Fragment_get_name(self)
6367 def clear_caches(self):
6368 r"""clear_caches(Fragment self)"""
6369 return _IMP_atom.Fragment_clear_caches(self)
6371 def set_name(self, a0):
6372 r"""set_name(Fragment self, std::string a0)"""
6373 return _IMP_atom.Fragment_set_name(self, a0)
6376 r"""set_check_level(Fragment self, IMP::CheckLevel a0)"""
6377 return _IMP_atom.Fragment_set_check_level(self, a0)
6379 def add_to_derivative(self, a0, a1, a2):
6380 r"""add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6381 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6383 def set_is_optimized(self, a0, a1):
6384 r"""set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6385 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6387 def get_is_optimized(self, a0):
6388 r"""get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6389 return _IMP_atom.Fragment_get_is_optimized(self, a0)
6392 r"""get_check_level(Fragment self) -> IMP::CheckLevel"""
6393 return _IMP_atom.Fragment_get_check_level(self)
6395 def __eq__(self, *args):
6397 __eq__(Fragment self, Fragment o) -> bool
6398 __eq__(Fragment self, Particle d) -> bool
6400 return _IMP_atom.Fragment___eq__(self, *args)
6402 def __ne__(self, *args):
6404 __ne__(Fragment self, Fragment o) -> bool
6405 __ne__(Fragment self, Particle d) -> bool
6407 return _IMP_atom.Fragment___ne__(self, *args)
6409 def __le__(self, *args):
6411 __le__(Fragment self, Fragment o) -> bool
6412 __le__(Fragment self, Particle d) -> bool
6414 return _IMP_atom.Fragment___le__(self, *args)
6416 def __lt__(self, *args):
6418 __lt__(Fragment self, Fragment o) -> bool
6419 __lt__(Fragment self, Particle d) -> bool
6421 return _IMP_atom.Fragment___lt__(self, *args)
6423 def __ge__(self, *args):
6425 __ge__(Fragment self, Fragment o) -> bool
6426 __ge__(Fragment self, Particle d) -> bool
6428 return _IMP_atom.Fragment___ge__(self, *args)
6430 def __gt__(self, *args):
6432 __gt__(Fragment self, Fragment o) -> bool
6433 __gt__(Fragment self, Particle d) -> bool
6435 return _IMP_atom.Fragment___gt__(self, *args)
6438 r"""__hash__(Fragment self) -> std::size_t"""
6439 return _IMP_atom.Fragment___hash__(self)
6442 r"""__str__(Fragment self) -> std::string"""
6443 return _IMP_atom.Fragment___str__(self)
6446 r"""__repr__(Fragment self) -> std::string"""
6447 return _IMP_atom.Fragment___repr__(self)
6449 def _get_as_binary(self):
6450 r"""_get_as_binary(Fragment self) -> PyObject *"""
6451 return _IMP_atom.Fragment__get_as_binary(self)
6453 def _set_from_binary(self, p):
6454 r"""_set_from_binary(Fragment self, PyObject * p)"""
6455 return _IMP_atom.Fragment__set_from_binary(self, p)
6457 def __getstate__(self):
6458 p = self._get_as_binary()
6459 if len(self.__dict__) > 1:
6460 d = self.__dict__.copy()
6465 def __setstate__(self, p):
6466 if not hasattr(self,
'this'):
6468 if isinstance(p, tuple):
6470 self.__dict__.update(d)
6471 return self._set_from_binary(p)
6473 __swig_destroy__ = _IMP_atom.delete_Fragment
6476 _IMP_atom.Fragment_swigregister(Fragment)
6478 r"""Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6480 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6483 r"""__init__(StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6484 _IMP_atom.StereochemistryPairFilter_swiginit(self, _IMP_atom.new_StereochemistryPairFilter())
6486 def set_bonds(self, bonds):
6487 r"""set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6488 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6490 def set_angles(self, angles):
6491 r"""set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6492 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6494 def set_dihedrals(self, dihedrals):
6495 r"""set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6496 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6498 def do_get_inputs(self, m, pis):
6499 r"""do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6500 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6502 def get_value(self, *args):
6504 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6505 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6507 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6509 def get_value_index(self, *args):
6511 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6512 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6514 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6516 def get_version_info(self):
6517 r"""get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6518 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6519 __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
6522 r"""__str__(StereochemistryPairFilter self) -> std::string"""
6523 return _IMP_atom.StereochemistryPairFilter___str__(self)
6526 r"""__repr__(StereochemistryPairFilter self) -> std::string"""
6527 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6531 return _object_cast_to_StereochemistryPairFilter(o)
6535 _IMP_atom.StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6537 r"""Proxy of C++ IMP::atom::SoapPairFilter class."""
6539 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6541 def __init__(self, library):
6542 r"""__init__(SoapPairFilter self, std::string library) -> SoapPairFilter"""
6543 _IMP_atom.SoapPairFilter_swiginit(self, _IMP_atom.new_SoapPairFilter(library))
6545 def do_get_inputs(self, m, pis):
6546 r"""do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6547 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6549 def get_value(self, *args):
6551 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6552 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6554 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6556 def get_value_index(self, *args):
6558 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6559 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6561 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6563 def get_version_info(self):
6564 r"""get_version_info(SoapPairFilter self) -> VersionInfo"""
6565 return _IMP_atom.SoapPairFilter_get_version_info(self)
6566 __swig_destroy__ = _IMP_atom.delete_SoapPairFilter
6569 r"""__str__(SoapPairFilter self) -> std::string"""
6570 return _IMP_atom.SoapPairFilter___str__(self)
6573 r"""__repr__(SoapPairFilter self) -> std::string"""
6574 return _IMP_atom.SoapPairFilter___repr__(self)
6578 return _object_cast_to_SoapPairFilter(o)
6582 _IMP_atom.SoapPairFilter_swigregister(SoapPairFilter)
6584 r"""Proxy of C++ IMP::atom::Mass class."""
6586 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6589 r"""get_mass(Mass self) -> IMP::Float"""
6590 return _IMP_atom.Mass_get_mass(self)
6592 def set_mass(self, d):
6593 r"""set_mass(Mass self, IMP::Float d)"""
6594 return _IMP_atom.Mass_set_mass(self, d)
6596 def __init__(self, *args):
6598 __init__(Mass self) -> Mass
6599 __init__(Mass self, Model m, ParticleIndex id) -> Mass
6600 __init__(Mass self, _ParticleAdaptor d) -> Mass
6602 _IMP_atom.Mass_swiginit(self, _IMP_atom.new_Mass(*args))
6605 def get_is_setup(*args):
6607 get_is_setup(Model m, ParticleIndex pi) -> bool
6608 get_is_setup(_ParticleAdaptor p) -> bool
6610 return _IMP_atom.Mass_get_is_setup(*args)
6612 def show(self, *args):
6613 r"""show(Mass self, _ostream out=std::cout)"""
6614 return _IMP_atom.Mass_show(self, *args)
6617 def setup_particle(*args):
6619 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6620 setup_particle(_ParticleAdaptor pa, IMP::Float mass) -> Mass
6621 setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6622 setup_particle(_ParticleAdaptor pa, Mass other) -> Mass
6624 return _IMP_atom.Mass_setup_particle(*args)
6628 r"""get_mass_key() -> FloatKey"""
6629 return _IMP_atom.Mass_get_mass_key()
6631 def add_attribute(self, *args):
6633 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6634 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6635 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6636 add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6637 add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6638 add_attribute(Mass self, StringKey a0, IMP::String a1)
6639 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6640 add_attribute(Mass self, ObjectKey a0, Object a1)
6641 add_attribute(Mass self, SparseFloatKey a0, IMP::Float a1)
6642 add_attribute(Mass self, SparseIntKey a0, IMP::Int a1)
6643 add_attribute(Mass self, SparseStringKey a0, IMP::String a1)
6644 add_attribute(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6646 return _IMP_atom.Mass_add_attribute(self, *args)
6648 def get_value(self, *args):
6650 get_value(Mass self, FloatKey a0) -> IMP::Float
6651 get_value(Mass self, IntKey a0) -> IMP::Int
6652 get_value(Mass self, FloatsKey a0) -> IMP::Floats
6653 get_value(Mass self, IntsKey a0) -> IMP::Ints
6654 get_value(Mass self, StringKey a0) -> IMP::String
6655 get_value(Mass self, ParticleIndexKey a0) -> Particle
6656 get_value(Mass self, ObjectKey a0) -> Object
6657 get_value(Mass self, SparseFloatKey a0) -> IMP::Float
6658 get_value(Mass self, SparseIntKey a0) -> IMP::Int
6659 get_value(Mass self, SparseStringKey a0) -> IMP::String
6660 get_value(Mass self, SparseParticleIndexKey a0) -> ParticleIndex
6662 return _IMP_atom.Mass_get_value(self, *args)
6664 def set_value(self, *args):
6666 set_value(Mass self, FloatKey a0, IMP::Float a1)
6667 set_value(Mass self, IntKey a0, IMP::Int a1)
6668 set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6669 set_value(Mass self, IntsKey a0, IMP::Ints a1)
6670 set_value(Mass self, StringKey a0, IMP::String a1)
6671 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6672 set_value(Mass self, ObjectKey a0, Object a1)
6673 set_value(Mass self, SparseFloatKey a0, IMP::Float a1)
6674 set_value(Mass self, SparseIntKey a0, IMP::Int a1)
6675 set_value(Mass self, SparseStringKey a0, IMP::String a1)
6676 set_value(Mass self, SparseParticleIndexKey a0, ParticleIndex a1)
6678 return _IMP_atom.Mass_set_value(self, *args)
6680 def remove_attribute(self, *args):
6682 remove_attribute(Mass self, FloatKey a0)
6683 remove_attribute(Mass self, IntKey a0)
6684 remove_attribute(Mass self, FloatsKey a0)
6685 remove_attribute(Mass self, IntsKey a0)
6686 remove_attribute(Mass self, StringKey a0)
6687 remove_attribute(Mass self, ParticleIndexKey a0)
6688 remove_attribute(Mass self, ObjectKey a0)
6689 remove_attribute(Mass self, SparseFloatKey a0)
6690 remove_attribute(Mass self, SparseIntKey a0)
6691 remove_attribute(Mass self, SparseStringKey a0)
6692 remove_attribute(Mass self, SparseParticleIndexKey a0)
6694 return _IMP_atom.Mass_remove_attribute(self, *args)
6696 def has_attribute(self, *args):
6698 has_attribute(Mass self, FloatKey a0) -> bool
6699 has_attribute(Mass self, IntKey a0) -> bool
6700 has_attribute(Mass self, FloatsKey a0) -> bool
6701 has_attribute(Mass self, IntsKey a0) -> bool
6702 has_attribute(Mass self, StringKey a0) -> bool
6703 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6704 has_attribute(Mass self, ObjectKey a0) -> bool
6705 has_attribute(Mass self, SparseFloatKey a0) -> bool
6706 has_attribute(Mass self, SparseIntKey a0) -> bool
6707 has_attribute(Mass self, SparseStringKey a0) -> bool
6708 has_attribute(Mass self, SparseParticleIndexKey a0) -> bool
6710 return _IMP_atom.Mass_has_attribute(self, *args)
6712 def get_derivative(self, a0):
6713 r"""get_derivative(Mass self, FloatKey a0) -> double"""
6714 return _IMP_atom.Mass_get_derivative(self, a0)
6717 r"""get_name(Mass self) -> std::string"""
6718 return _IMP_atom.Mass_get_name(self)
6720 def clear_caches(self):
6721 r"""clear_caches(Mass self)"""
6722 return _IMP_atom.Mass_clear_caches(self)
6724 def set_name(self, a0):
6725 r"""set_name(Mass self, std::string a0)"""
6726 return _IMP_atom.Mass_set_name(self, a0)
6729 r"""set_check_level(Mass self, IMP::CheckLevel a0)"""
6730 return _IMP_atom.Mass_set_check_level(self, a0)
6732 def add_to_derivative(self, a0, a1, a2):
6733 r"""add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6734 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6736 def set_is_optimized(self, a0, a1):
6737 r"""set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6738 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6740 def get_is_optimized(self, a0):
6741 r"""get_is_optimized(Mass self, FloatKey a0) -> bool"""
6742 return _IMP_atom.Mass_get_is_optimized(self, a0)
6745 r"""get_check_level(Mass self) -> IMP::CheckLevel"""
6746 return _IMP_atom.Mass_get_check_level(self)
6748 def __eq__(self, *args):
6750 __eq__(Mass self, Mass o) -> bool
6751 __eq__(Mass self, Particle d) -> bool
6753 return _IMP_atom.Mass___eq__(self, *args)
6755 def __ne__(self, *args):
6757 __ne__(Mass self, Mass o) -> bool
6758 __ne__(Mass self, Particle d) -> bool
6760 return _IMP_atom.Mass___ne__(self, *args)
6762 def __le__(self, *args):
6764 __le__(Mass self, Mass o) -> bool
6765 __le__(Mass self, Particle d) -> bool
6767 return _IMP_atom.Mass___le__(self, *args)
6769 def __lt__(self, *args):
6771 __lt__(Mass self, Mass o) -> bool
6772 __lt__(Mass self, Particle d) -> bool
6774 return _IMP_atom.Mass___lt__(self, *args)
6776 def __ge__(self, *args):
6778 __ge__(Mass self, Mass o) -> bool
6779 __ge__(Mass self, Particle d) -> bool
6781 return _IMP_atom.Mass___ge__(self, *args)
6783 def __gt__(self, *args):
6785 __gt__(Mass self, Mass o) -> bool
6786 __gt__(Mass self, Particle d) -> bool
6788 return _IMP_atom.Mass___gt__(self, *args)
6791 r"""__hash__(Mass self) -> std::size_t"""
6792 return _IMP_atom.Mass___hash__(self)
6795 r"""__str__(Mass self) -> std::string"""
6796 return _IMP_atom.Mass___str__(self)
6799 r"""__repr__(Mass self) -> std::string"""
6800 return _IMP_atom.Mass___repr__(self)
6802 def _get_as_binary(self):
6803 r"""_get_as_binary(Mass self) -> PyObject *"""
6804 return _IMP_atom.Mass__get_as_binary(self)
6806 def _set_from_binary(self, p):
6807 r"""_set_from_binary(Mass self, PyObject * p)"""
6808 return _IMP_atom.Mass__set_from_binary(self, p)
6810 def __getstate__(self):
6811 p = self._get_as_binary()
6812 if len(self.__dict__) > 1:
6813 d = self.__dict__.copy()
6818 def __setstate__(self, p):
6819 if not hasattr(self,
'this'):
6821 if isinstance(p, tuple):
6823 self.__dict__.update(d)
6824 return self._set_from_binary(p)
6826 __swig_destroy__ = _IMP_atom.delete_Mass
6829 _IMP_atom.Mass_swigregister(Mass)
6831 r"""Proxy of C++ IMP::atom::BondedPairFilter class."""
6833 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6836 r"""__init__(BondedPairFilter self) -> BondedPairFilter"""
6837 _IMP_atom.BondedPairFilter_swiginit(self, _IMP_atom.new_BondedPairFilter())
6839 def do_get_inputs(self, m, pis):
6840 r"""do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6841 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6843 def get_value(self, *args):
6845 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6846 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6848 return _IMP_atom.BondedPairFilter_get_value(self, *args)
6850 def get_value_index(self, *args):
6852 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6853 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6855 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6857 def get_version_info(self):
6858 r"""get_version_info(BondedPairFilter self) -> VersionInfo"""
6859 return _IMP_atom.BondedPairFilter_get_version_info(self)
6860 __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
6863 r"""__str__(BondedPairFilter self) -> std::string"""
6864 return _IMP_atom.BondedPairFilter___str__(self)
6867 r"""__repr__(BondedPairFilter self) -> std::string"""
6868 return _IMP_atom.BondedPairFilter___repr__(self)
6872 return _object_cast_to_BondedPairFilter(o)
6876 _IMP_atom.BondedPairFilter_swigregister(BondedPairFilter)
6878 r"""Proxy of C++ IMP::atom::Mol2Selector class."""
6880 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6882 def __init__(self, *args, **kwargs):
6883 raise AttributeError(
"No constructor defined - class is abstract")
6885 def get_is_selected(self, atom_line):
6886 r"""get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6887 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6888 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6891 r"""__str__(Mol2Selector self) -> std::string"""
6892 return _IMP_atom.Mol2Selector___str__(self)
6895 r"""__repr__(Mol2Selector self) -> std::string"""
6896 return _IMP_atom.Mol2Selector___repr__(self)
6900 return _object_cast_to_Mol2Selector(o)
6904 _IMP_atom.Mol2Selector_swigregister(Mol2Selector)
6905 class AllMol2Selector(Mol2Selector):
6906 r"""Proxy of C++ IMP::atom::AllMol2Selector class."""
6908 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6911 r"""__str__(AllMol2Selector self) -> std::string"""
6912 return _IMP_atom.AllMol2Selector___str__(self)
6915 r"""__repr__(AllMol2Selector self) -> std::string"""
6916 return _IMP_atom.AllMol2Selector___repr__(self)
6920 return _object_cast_to_AllMol2Selector(o)
6924 r"""__init__(AllMol2Selector self) -> AllMol2Selector"""
6925 _IMP_atom.AllMol2Selector_swiginit(self, _IMP_atom.new_AllMol2Selector())
6926 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6929 _IMP_atom.AllMol2Selector_swigregister(AllMol2Selector)
6930 class NonHydrogenMol2Selector(Mol2Selector):
6931 r"""Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6933 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6936 r"""__str__(NonHydrogenMol2Selector self) -> std::string"""
6937 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6940 r"""__repr__(NonHydrogenMol2Selector self) -> std::string"""
6941 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6945 return _object_cast_to_NonHydrogenMol2Selector(o)
6949 r"""__init__(NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6950 _IMP_atom.NonHydrogenMol2Selector_swiginit(self, _IMP_atom.new_NonHydrogenMol2Selector())
6951 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6954 _IMP_atom.NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
6956 def read_mol2(mol2_file, model, mol2sel=None):
6957 r"""read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy"""
6958 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
6961 r"""write_mol2(Hierarchy rhd, TextOutput file_name)"""
6962 return _IMP_atom.write_mol2(rhd, file_name)
6964 r"""Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
6966 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6968 def __init__(self, *args):
6970 __init__(SecondaryStructureResidue self) -> SecondaryStructureResidue
6971 __init__(SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
6972 __init__(SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
6974 _IMP_atom.SecondaryStructureResidue_swiginit(self, _IMP_atom.new_SecondaryStructureResidue(*args))
6976 def show(self, *args):
6977 r"""show(SecondaryStructureResidue self, _ostream out=std::cout)"""
6978 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
6981 def setup_particle(*args):
6983 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6984 setup_particle(_ParticleAdaptor pa, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6985 setup_particle(Particle res_p) -> SecondaryStructureResidue
6987 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
6990 def get_is_setup(*args):
6992 get_is_setup(_ParticleAdaptor p) -> bool
6993 get_is_setup(Model m, ParticleIndex pi) -> bool
6995 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
6997 def get_particle(self):
6998 r"""get_particle(SecondaryStructureResidue self) -> Particle"""
6999 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7001 def get_all_probabilities(self):
7002 r"""get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7003 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7005 def get_prob_helix(self):
7006 r"""get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7007 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7009 def set_prob_helix(self, t):
7010 r"""set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7011 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7013 def get_prob_strand(self):
7014 r"""get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7015 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7017 def set_prob_strand(self, t):
7018 r"""set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7019 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7021 def get_prob_coil(self):
7022 r"""get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7023 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7025 def set_prob_coil(self, t):
7026 r"""set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7027 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7030 def get_prob_helix_key():
7031 r"""get_prob_helix_key() -> FloatKey"""
7032 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7035 def get_prob_strand_key():
7036 r"""get_prob_strand_key() -> FloatKey"""
7037 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7040 def get_prob_coil_key():
7041 r"""get_prob_coil_key() -> FloatKey"""
7042 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7044 def add_attribute(self, *args):
7046 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7047 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7048 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7049 add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7050 add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7051 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7052 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7053 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7054 add_attribute(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
7055 add_attribute(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
7056 add_attribute(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
7057 add_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
7059 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7061 def get_value(self, *args):
7063 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7064 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7065 get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
7066 get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
7067 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7068 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7069 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7070 get_value(SecondaryStructureResidue self, SparseFloatKey a0) -> IMP::Float
7071 get_value(SecondaryStructureResidue self, SparseIntKey a0) -> IMP::Int
7072 get_value(SecondaryStructureResidue self, SparseStringKey a0) -> IMP::String
7073 get_value(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> ParticleIndex
7075 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7077 def set_value(self, *args):
7079 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7080 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7081 set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7082 set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7083 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7084 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7085 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7086 set_value(SecondaryStructureResidue self, SparseFloatKey a0, IMP::Float a1)
7087 set_value(SecondaryStructureResidue self, SparseIntKey a0, IMP::Int a1)
7088 set_value(SecondaryStructureResidue self, SparseStringKey a0, IMP::String a1)
7089 set_value(SecondaryStructureResidue self, SparseParticleIndexKey a0, ParticleIndex a1)
7091 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7093 def remove_attribute(self, *args):
7095 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7096 remove_attribute(SecondaryStructureResidue self, IntKey a0)
7097 remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
7098 remove_attribute(SecondaryStructureResidue self, IntsKey a0)
7099 remove_attribute(SecondaryStructureResidue self, StringKey a0)
7100 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7101 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7102 remove_attribute(SecondaryStructureResidue self, SparseFloatKey a0)
7103 remove_attribute(SecondaryStructureResidue self, SparseIntKey a0)
7104 remove_attribute(SecondaryStructureResidue self, SparseStringKey a0)
7105 remove_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0)
7107 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7109 def has_attribute(self, *args):
7111 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7112 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7113 has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
7114 has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
7115 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7116 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7117 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7118 has_attribute(SecondaryStructureResidue self, SparseFloatKey a0) -> bool
7119 has_attribute(SecondaryStructureResidue self, SparseIntKey a0) -> bool
7120 has_attribute(SecondaryStructureResidue self, SparseStringKey a0) -> bool
7121 has_attribute(SecondaryStructureResidue self, SparseParticleIndexKey a0) -> bool
7123 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7125 def get_derivative(self, a0):
7126 r"""get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7127 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7130 r"""get_name(SecondaryStructureResidue self) -> std::string"""
7131 return _IMP_atom.SecondaryStructureResidue_get_name(self)
7133 def clear_caches(self):
7134 r"""clear_caches(SecondaryStructureResidue self)"""
7135 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7137 def set_name(self, a0):
7138 r"""set_name(SecondaryStructureResidue self, std::string a0)"""
7139 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7142 r"""set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7143 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7145 def add_to_derivative(self, a0, a1, a2):
7146 r"""add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7147 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7149 def set_is_optimized(self, a0, a1):
7150 r"""set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7151 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7153 def get_is_optimized(self, a0):
7154 r"""get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7155 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7158 r"""get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7159 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7161 def __eq__(self, *args):
7163 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7164 __eq__(SecondaryStructureResidue self, Particle d) -> bool
7166 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7168 def __ne__(self, *args):
7170 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7171 __ne__(SecondaryStructureResidue self, Particle d) -> bool
7173 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7175 def __le__(self, *args):
7177 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7178 __le__(SecondaryStructureResidue self, Particle d) -> bool
7180 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7182 def __lt__(self, *args):
7184 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7185 __lt__(SecondaryStructureResidue self, Particle d) -> bool
7187 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7189 def __ge__(self, *args):
7191 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7192 __ge__(SecondaryStructureResidue self, Particle d) -> bool
7194 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7196 def __gt__(self, *args):
7198 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7199 __gt__(SecondaryStructureResidue self, Particle d) -> bool
7201 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7204 r"""__hash__(SecondaryStructureResidue self) -> std::size_t"""
7205 return _IMP_atom.SecondaryStructureResidue___hash__(self)
7208 r"""__str__(SecondaryStructureResidue self) -> std::string"""
7209 return _IMP_atom.SecondaryStructureResidue___str__(self)
7212 r"""__repr__(SecondaryStructureResidue self) -> std::string"""
7213 return _IMP_atom.SecondaryStructureResidue___repr__(self)
7215 def _get_as_binary(self):
7216 r"""_get_as_binary(SecondaryStructureResidue self) -> PyObject *"""
7217 return _IMP_atom.SecondaryStructureResidue__get_as_binary(self)
7219 def _set_from_binary(self, p):
7220 r"""_set_from_binary(SecondaryStructureResidue self, PyObject * p)"""
7221 return _IMP_atom.SecondaryStructureResidue__set_from_binary(self, p)
7223 def __getstate__(self):
7224 p = self._get_as_binary()
7225 if len(self.__dict__) > 1:
7226 d = self.__dict__.copy()
7231 def __setstate__(self, p):
7232 if not hasattr(self,
'this'):
7234 if isinstance(p, tuple):
7236 self.__dict__.update(d)
7237 return self._set_from_binary(p)
7239 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7242 _IMP_atom.SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7245 r"""setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue"""
7246 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7249 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"""
7250 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7253 r"""get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7254 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7256 def read_psipred(*args):
7258 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7259 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7261 return _IMP_atom.read_psipred(*args)
7263 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Dope > class."""
7265 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7266 __repr__ = _swig_repr
7268 def __init__(self, *args):
7270 __init__(_ADopeBase self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
7271 __init__(_ADopeBase self) -> _ADopeBase
7273 _IMP_atom._ADopeBase_swiginit(self, _IMP_atom.new__ADopeBase(*args))
7275 def do_get_inputs(self, m, pis):
7276 r"""do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7277 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7279 def get_score_functor(self):
7280 r"""get_score_functor(_ADopeBase self) -> Dope"""
7281 return _IMP_atom._ADopeBase_get_score_functor(self)
7283 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7284 r"""evaluate_indexes(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7285 return _IMP_atom._ADopeBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7287 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7288 r"""evaluate_indexes_scores(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7289 return _IMP_atom._ADopeBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7291 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7292 r"""evaluate_indexes_delta(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7293 return _IMP_atom._ADopeBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7295 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7296 r"""evaluate_if_good_indexes(_ADopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7297 return _IMP_atom._ADopeBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7299 def get_version_info(self):
7300 r"""get_version_info(_ADopeBase self) -> VersionInfo"""
7301 return _IMP_atom._ADopeBase_get_version_info(self)
7302 __swig_destroy__ = _IMP_atom.delete__ADopeBase
7305 _IMP_atom._ADopeBase_swigregister(_ADopeBase)
7307 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > > class."""
7309 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7310 __repr__ = _swig_repr
7312 def __init__(self, *args):
7314 __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
7315 __init__(_BDopeBase self) -> _BDopeBase
7317 _IMP_atom._BDopeBase_swiginit(self, _IMP_atom.new__BDopeBase(*args))
7319 def do_get_inputs(self, m, pis):
7320 r"""do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7321 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7323 def get_score_functor(self):
7324 r"""get_score_functor(_BDopeBase self) -> _DopeBase"""
7325 return _IMP_atom._BDopeBase_get_score_functor(self)
7327 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7328 r"""evaluate_indexes(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7329 return _IMP_atom._BDopeBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7331 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7332 r"""evaluate_indexes_scores(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7333 return _IMP_atom._BDopeBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7335 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7336 r"""evaluate_indexes_delta(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7337 return _IMP_atom._BDopeBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7339 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7340 r"""evaluate_if_good_indexes(_BDopeBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7341 return _IMP_atom._BDopeBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7343 def get_version_info(self):
7344 r"""get_version_info(_BDopeBase self) -> VersionInfo"""
7345 return _IMP_atom._BDopeBase_get_version_info(self)
7346 __swig_destroy__ = _IMP_atom.delete__BDopeBase
7349 _IMP_atom._BDopeBase_swigregister(_BDopeBase)
7351 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::LoopStatistical > class."""
7353 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7354 __repr__ = _swig_repr
7356 def __init__(self, *args):
7358 __init__(_ALoopStatisticalBase self, LoopStatistical t0, std::string name="FunctorDistancePairScore %1%") -> _ALoopStatisticalBase
7359 __init__(_ALoopStatisticalBase self) -> _ALoopStatisticalBase
7361 _IMP_atom._ALoopStatisticalBase_swiginit(self, _IMP_atom.new__ALoopStatisticalBase(*args))
7363 def do_get_inputs(self, m, pis):
7364 r"""do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7365 return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
7367 def get_score_functor(self):
7368 r"""get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
7369 return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
7371 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7372 r"""evaluate_indexes(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7373 return _IMP_atom._ALoopStatisticalBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7375 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7376 r"""evaluate_indexes_scores(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7377 return _IMP_atom._ALoopStatisticalBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7379 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7380 r"""evaluate_indexes_delta(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7381 return _IMP_atom._ALoopStatisticalBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7383 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7384 r"""evaluate_if_good_indexes(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7385 return _IMP_atom._ALoopStatisticalBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7387 def get_version_info(self):
7388 r"""get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
7389 return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
7390 __swig_destroy__ = _IMP_atom.delete__ALoopStatisticalBase
7393 _IMP_atom._ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
7395 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > > class."""
7397 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7398 __repr__ = _swig_repr
7400 def __init__(self, *args):
7402 __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
7403 __init__(_BLoopStatisticalBase self) -> _BLoopStatisticalBase
7405 _IMP_atom._BLoopStatisticalBase_swiginit(self, _IMP_atom.new__BLoopStatisticalBase(*args))
7407 def do_get_inputs(self, m, pis):
7408 r"""do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7409 return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
7411 def get_score_functor(self):
7412 r"""get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
7413 return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
7415 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7416 r"""evaluate_indexes(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7417 return _IMP_atom._BLoopStatisticalBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7419 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7420 r"""evaluate_indexes_scores(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7421 return _IMP_atom._BLoopStatisticalBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7423 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7424 r"""evaluate_indexes_delta(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7425 return _IMP_atom._BLoopStatisticalBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7427 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7428 r"""evaluate_if_good_indexes(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7429 return _IMP_atom._BLoopStatisticalBase_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7431 def get_version_info(self):
7432 r"""get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
7433 return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
7434 __swig_destroy__ = _IMP_atom.delete__BLoopStatisticalBase
7437 _IMP_atom._BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
7439 r"""Proxy of C++ IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap > class."""
7441 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7442 __repr__ = _swig_repr
7444 def __init__(self, *args):
7445 r"""__init__(_OrientedSoapBase self, IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name="FunctorDistancePairScoreWithCache %1%") -> _OrientedSoapBase"""
7446 _IMP_atom._OrientedSoapBase_swiginit(self, _IMP_atom.new__OrientedSoapBase(*args))
7448 def do_get_inputs(self, m, pis):
7449 r"""do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7450 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7452 def get_score_functor(self):
7453 r"""get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7454 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7456 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7457 r"""evaluate_indexes(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7458 return _IMP_atom._OrientedSoapBase_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7460 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7461 r"""evaluate_indexes_scores(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7462 return _IMP_atom._OrientedSoapBase_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7464 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7465 r"""evaluate_indexes_delta(_OrientedSoapBase self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7466 return _IMP_atom._OrientedSoapBase_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7468 def get_version_info(self):
7469 r"""get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7470 return _IMP_atom._OrientedSoapBase_get_version_info(self)
7471 __swig_destroy__ = _IMP_atom.delete__OrientedSoapBase
7474 _IMP_atom._OrientedSoapBase_swigregister(_OrientedSoapBase)
7476 r"""Proxy of C++ IMP::score_functor::DistancePairScore< score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > > class."""
7478 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7479 __repr__ = _swig_repr
7481 def __init__(self, *args):
7483 __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
7484 __init__(_SPSFTB self) -> _SPSFTB
7486 _IMP_atom._SPSFTB_swiginit(self, _IMP_atom.new__SPSFTB(*args))
7488 def do_get_inputs(self, m, pis):
7489 r"""do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7490 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7492 def get_score_functor(self):
7493 r"""get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7494 return _IMP_atom._SPSFTB_get_score_functor(self)
7496 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
7497 r"""evaluate_indexes(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7498 return _IMP_atom._SPSFTB_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
7500 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7501 r"""evaluate_indexes_scores(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7502 return _IMP_atom._SPSFTB_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
7504 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
7505 r"""evaluate_indexes_delta(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7506 return _IMP_atom._SPSFTB_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
7508 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7509 r"""evaluate_if_good_indexes(_SPSFTB self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7510 return _IMP_atom._SPSFTB_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
7512 def get_version_info(self):
7513 r"""get_version_info(_SPSFTB self) -> VersionInfo"""
7514 return _IMP_atom._SPSFTB_get_version_info(self)
7515 __swig_destroy__ = _IMP_atom.delete__SPSFTB
7518 _IMP_atom._SPSFTB_swigregister(_SPSFTB)
7519 class _SPSTF(_SPSFTB):
7520 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType,true,false > class."""
7522 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7523 __repr__ = _swig_repr
7525 def __init__(self, *args):
7527 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7528 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7530 _IMP_atom._SPSTF_swiginit(self, _IMP_atom.new__SPSTF(*args))
7531 __swig_destroy__ = _IMP_atom.delete__SPSTF
7534 _IMP_atom._SPSTF_swigregister(_SPSTF)
7535 class _SPSFT(_BDopeBase):
7536 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::DopeType,false,true > class."""
7538 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7539 __repr__ = _swig_repr
7541 def __init__(self, *args):
7543 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7544 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7546 _IMP_atom._SPSFT_swiginit(self, _IMP_atom.new__SPSFT(*args))
7547 __swig_destroy__ = _IMP_atom.delete__SPSFT
7550 _IMP_atom._SPSFT_swigregister(_SPSFT)
7551 class _SPSFTL(_BLoopStatisticalBase):
7552 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType,false,true > class."""
7554 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7555 __repr__ = _swig_repr
7557 def __init__(self, *args):
7559 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7560 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7562 _IMP_atom._SPSFTL_swiginit(self, _IMP_atom.new__SPSFTL(*args))
7563 __swig_destroy__ = _IMP_atom.delete__SPSFTL
7566 _IMP_atom._SPSFTL_swigregister(_SPSFTL)
7567 class ProteinLigandAtomPairScore(_SPSTF):
7568 r"""Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7570 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7572 def __init__(self, *args):
7574 __init__(ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
7575 __init__(ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7577 _IMP_atom.ProteinLigandAtomPairScore_swiginit(self, _IMP_atom.new_ProteinLigandAtomPairScore(*args))
7579 def get_maximum_distance(self):
7580 r"""get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7581 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7584 r"""__str__(ProteinLigandAtomPairScore self) -> std::string"""
7585 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7588 r"""__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7589 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7593 return _object_cast_to_ProteinLigandAtomPairScore(o)
7595 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7598 _IMP_atom.ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7600 r"""Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7602 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7604 def __init__(self, *args):
7606 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
7607 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7609 _IMP_atom.ProteinLigandRestraint_swiginit(self, _IMP_atom.new_ProteinLigandRestraint(*args))
7612 r"""__str__(ProteinLigandRestraint self) -> std::string"""
7613 return _IMP_atom.ProteinLigandRestraint___str__(self)
7616 r"""__repr__(ProteinLigandRestraint self) -> std::string"""
7617 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7621 return _object_cast_to_ProteinLigandRestraint(o)
7623 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7626 _IMP_atom.ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7629 r"""add_protein_ligand_score_data(Hierarchy h)"""
7630 return _IMP_atom.add_protein_ligand_score_data(h)
7631 class AtomType(IMP._Value):
7632 r"""Proxy of C++ IMP::Key< 8974343 > class."""
7634 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7636 def __init__(self, *args):
7638 __init__(AtomType self) -> AtomType
7639 __init__(AtomType self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7640 __init__(AtomType self, unsigned int i) -> AtomType
7642 _IMP_atom.AtomType_swiginit(self, _IMP_atom.new_AtomType(*args))
7646 r"""add_key(std::string sc) -> unsigned int"""
7647 return _IMP_atom.AtomType_add_key(sc)
7650 def get_key_exists(sc):
7651 r"""get_key_exists(std::string sc) -> bool"""
7652 return _IMP_atom.AtomType_get_key_exists(sc)
7654 def get_string(self):
7655 r"""get_string(AtomType self) -> std::string const"""
7656 return _IMP_atom.AtomType_get_string(self)
7658 def __cmp__(self, o):
7659 r"""__cmp__(AtomType self, AtomType o) -> int"""
7660 return _IMP_atom.AtomType___cmp__(self, o)
7662 def __eq__(self, o):
7663 r"""__eq__(AtomType self, AtomType o) -> bool"""
7664 return _IMP_atom.AtomType___eq__(self, o)
7666 def __ne__(self, o):
7667 r"""__ne__(AtomType self, AtomType o) -> bool"""
7668 return _IMP_atom.AtomType___ne__(self, o)
7670 def __lt__(self, o):
7671 r"""__lt__(AtomType self, AtomType o) -> bool"""
7672 return _IMP_atom.AtomType___lt__(self, o)
7674 def __gt__(self, o):
7675 r"""__gt__(AtomType self, AtomType o) -> bool"""
7676 return _IMP_atom.AtomType___gt__(self, o)
7678 def __ge__(self, o):
7679 r"""__ge__(AtomType self, AtomType o) -> bool"""
7680 return _IMP_atom.AtomType___ge__(self, o)
7682 def __le__(self, o):
7683 r"""__le__(AtomType self, AtomType o) -> bool"""
7684 return _IMP_atom.AtomType___le__(self, o)
7687 r"""__hash__(AtomType self) -> std::size_t"""
7688 return _IMP_atom.AtomType___hash__(self)
7690 def show(self, *args):
7691 r"""show(AtomType self, _ostream out=std::cout)"""
7692 return _IMP_atom.AtomType_show(self, *args)
7695 def add_alias(old_key, new_name):
7696 r"""add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7697 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7700 def get_number_of_keys():
7701 r"""get_number_of_keys() -> unsigned int"""
7702 return _IMP_atom.AtomType_get_number_of_keys()
7705 r"""get_index(AtomType self) -> unsigned int"""
7706 return _IMP_atom.AtomType_get_index(self)
7710 r"""show_all(_ostream out)"""
7711 return _IMP_atom.AtomType_show_all(out)
7714 def get_all_strings():
7715 r"""get_all_strings() -> IMP::Vector< std::string >"""
7716 return _IMP_atom.AtomType_get_all_strings()
7719 def get_number_unique():
7720 r"""get_number_unique() -> unsigned int"""
7721 return _IMP_atom.AtomType_get_number_unique()
7724 r"""__str__(AtomType self) -> std::string"""
7725 return _IMP_atom.AtomType___str__(self)
7728 r"""__repr__(AtomType self) -> std::string"""
7729 return _IMP_atom.AtomType___repr__(self)
7730 __swig_destroy__ = _IMP_atom.delete_AtomType
7733 _IMP_atom.AtomType_swigregister(AtomType)
7734 class ResidueType(IMP._Value):
7735 r"""Proxy of C++ IMP::Key< 90784334 > class."""
7737 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7739 def __init__(self, *args):
7741 __init__(ResidueType self) -> ResidueType
7742 __init__(ResidueType self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7743 __init__(ResidueType self, unsigned int i) -> ResidueType
7745 _IMP_atom.ResidueType_swiginit(self, _IMP_atom.new_ResidueType(*args))
7749 r"""add_key(std::string sc) -> unsigned int"""
7750 return _IMP_atom.ResidueType_add_key(sc)
7753 def get_key_exists(sc):
7754 r"""get_key_exists(std::string sc) -> bool"""
7755 return _IMP_atom.ResidueType_get_key_exists(sc)
7757 def get_string(self):
7758 r"""get_string(ResidueType self) -> std::string const"""
7759 return _IMP_atom.ResidueType_get_string(self)
7761 def __cmp__(self, o):
7762 r"""__cmp__(ResidueType self, ResidueType o) -> int"""
7763 return _IMP_atom.ResidueType___cmp__(self, o)
7765 def __eq__(self, o):
7766 r"""__eq__(ResidueType self, ResidueType o) -> bool"""
7767 return _IMP_atom.ResidueType___eq__(self, o)
7769 def __ne__(self, o):
7770 r"""__ne__(ResidueType self, ResidueType o) -> bool"""
7771 return _IMP_atom.ResidueType___ne__(self, o)
7773 def __lt__(self, o):
7774 r"""__lt__(ResidueType self, ResidueType o) -> bool"""
7775 return _IMP_atom.ResidueType___lt__(self, o)
7777 def __gt__(self, o):
7778 r"""__gt__(ResidueType self, ResidueType o) -> bool"""
7779 return _IMP_atom.ResidueType___gt__(self, o)
7781 def __ge__(self, o):
7782 r"""__ge__(ResidueType self, ResidueType o) -> bool"""
7783 return _IMP_atom.ResidueType___ge__(self, o)
7785 def __le__(self, o):
7786 r"""__le__(ResidueType self, ResidueType o) -> bool"""
7787 return _IMP_atom.ResidueType___le__(self, o)
7790 r"""__hash__(ResidueType self) -> std::size_t"""
7791 return _IMP_atom.ResidueType___hash__(self)
7793 def show(self, *args):
7794 r"""show(ResidueType self, _ostream out=std::cout)"""
7795 return _IMP_atom.ResidueType_show(self, *args)
7798 def add_alias(old_key, new_name):
7799 r"""add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7800 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7803 def get_number_of_keys():
7804 r"""get_number_of_keys() -> unsigned int"""
7805 return _IMP_atom.ResidueType_get_number_of_keys()
7808 r"""get_index(ResidueType self) -> unsigned int"""
7809 return _IMP_atom.ResidueType_get_index(self)
7813 r"""show_all(_ostream out)"""
7814 return _IMP_atom.ResidueType_show_all(out)
7817 def get_all_strings():
7818 r"""get_all_strings() -> IMP::Vector< std::string >"""
7819 return _IMP_atom.ResidueType_get_all_strings()
7822 def get_number_unique():
7823 r"""get_number_unique() -> unsigned int"""
7824 return _IMP_atom.ResidueType_get_number_unique()
7827 r"""__str__(ResidueType self) -> std::string"""
7828 return _IMP_atom.ResidueType___str__(self)
7831 r"""__repr__(ResidueType self) -> std::string"""
7832 return _IMP_atom.ResidueType___repr__(self)
7833 __swig_destroy__ = _IMP_atom.delete_ResidueType
7836 _IMP_atom.ResidueType_swigregister(ResidueType)
7837 class ChainType(IMP._Value):
7838 r"""Proxy of C++ IMP::Key< 90784336 > class."""
7840 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7842 def __init__(self, *args):
7844 __init__(ChainType self) -> ChainType
7845 __init__(ChainType self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
7846 __init__(ChainType self, unsigned int i) -> ChainType
7848 _IMP_atom.ChainType_swiginit(self, _IMP_atom.new_ChainType(*args))
7852 r"""add_key(std::string sc) -> unsigned int"""
7853 return _IMP_atom.ChainType_add_key(sc)
7856 def get_key_exists(sc):
7857 r"""get_key_exists(std::string sc) -> bool"""
7858 return _IMP_atom.ChainType_get_key_exists(sc)
7860 def get_string(self):
7861 r"""get_string(ChainType self) -> std::string const"""
7862 return _IMP_atom.ChainType_get_string(self)
7864 def __cmp__(self, o):
7865 r"""__cmp__(ChainType self, ChainType o) -> int"""
7866 return _IMP_atom.ChainType___cmp__(self, o)
7868 def __eq__(self, o):
7869 r"""__eq__(ChainType self, ChainType o) -> bool"""
7870 return _IMP_atom.ChainType___eq__(self, o)
7872 def __ne__(self, o):
7873 r"""__ne__(ChainType self, ChainType o) -> bool"""
7874 return _IMP_atom.ChainType___ne__(self, o)
7876 def __lt__(self, o):
7877 r"""__lt__(ChainType self, ChainType o) -> bool"""
7878 return _IMP_atom.ChainType___lt__(self, o)
7880 def __gt__(self, o):
7881 r"""__gt__(ChainType self, ChainType o) -> bool"""
7882 return _IMP_atom.ChainType___gt__(self, o)
7884 def __ge__(self, o):
7885 r"""__ge__(ChainType self, ChainType o) -> bool"""
7886 return _IMP_atom.ChainType___ge__(self, o)
7888 def __le__(self, o):
7889 r"""__le__(ChainType self, ChainType o) -> bool"""
7890 return _IMP_atom.ChainType___le__(self, o)
7893 r"""__hash__(ChainType self) -> std::size_t"""
7894 return _IMP_atom.ChainType___hash__(self)
7896 def show(self, *args):
7897 r"""show(ChainType self, _ostream out=std::cout)"""
7898 return _IMP_atom.ChainType_show(self, *args)
7901 def add_alias(old_key, new_name):
7902 r"""add_alias(ChainType old_key, std::string new_name) -> ChainType"""
7903 return _IMP_atom.ChainType_add_alias(old_key, new_name)
7906 def get_number_of_keys():
7907 r"""get_number_of_keys() -> unsigned int"""
7908 return _IMP_atom.ChainType_get_number_of_keys()
7911 r"""get_index(ChainType self) -> unsigned int"""
7912 return _IMP_atom.ChainType_get_index(self)
7916 r"""show_all(_ostream out)"""
7917 return _IMP_atom.ChainType_show_all(out)
7920 def get_all_strings():
7921 r"""get_all_strings() -> IMP::Vector< std::string >"""
7922 return _IMP_atom.ChainType_get_all_strings()
7925 def get_number_unique():
7926 r"""get_number_unique() -> unsigned int"""
7927 return _IMP_atom.ChainType_get_number_unique()
7930 r"""__str__(ChainType self) -> std::string"""
7931 return _IMP_atom.ChainType___str__(self)
7934 r"""__repr__(ChainType self) -> std::string"""
7935 return _IMP_atom.ChainType___repr__(self)
7936 __swig_destroy__ = _IMP_atom.delete_ChainType
7939 _IMP_atom.ChainType_swigregister(ChainType)
7940 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8158 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8162 r"""hash_value(IMP::atom::Element e) -> size_t"""
8163 return _IMP_atom.hash_value(e)
8164 class ElementTable(object):
8165 r"""Proxy of C++ IMP::atom::ElementTable class."""
8167 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8168 __repr__ = _swig_repr
8171 r"""__init__(ElementTable self) -> ElementTable"""
8172 _IMP_atom.ElementTable_swiginit(self, _IMP_atom.new_ElementTable())
8174 def get_element(self, s):
8175 r"""get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8176 return _IMP_atom.ElementTable_get_element(self, s)
8178 def get_name(self, e):
8179 r"""get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8180 return _IMP_atom.ElementTable_get_name(self, e)
8183 r"""get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8184 return _IMP_atom.ElementTable_get_mass(self, e)
8185 __swig_destroy__ = _IMP_atom.delete_ElementTable
8188 _IMP_atom.ElementTable_swigregister(ElementTable)
8190 def get_element_table():
8191 r"""get_element_table() -> ElementTable"""
8192 return _IMP_atom.get_element_table()
8193 class Atom(Hierarchy):
8194 r"""Proxy of C++ IMP::atom::Atom class."""
8196 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8198 def __init__(self, *args):
8200 __init__(Atom self) -> Atom
8201 __init__(Atom self, Model m, ParticleIndex id) -> Atom
8202 __init__(Atom self, _ParticleAdaptor d) -> Atom
8204 _IMP_atom.Atom_swiginit(self, _IMP_atom.new_Atom(*args))
8206 def show(self, *args):
8207 r"""show(Atom self, _ostream out=std::cout)"""
8208 return _IMP_atom.Atom_show(self, *args)
8211 def setup_particle(*args):
8213 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8214 setup_particle(_ParticleAdaptor pa, Atom other) -> Atom
8215 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8216 setup_particle(_ParticleAdaptor pa, AtomType atom_type) -> Atom
8218 return _IMP_atom.Atom_setup_particle(*args)
8221 def get_is_setup(*args):
8223 get_is_setup(_ParticleAdaptor p) -> bool
8224 get_is_setup(Model m, ParticleIndex pi) -> bool
8226 return _IMP_atom.Atom_get_is_setup(*args)
8228 def get_atom_type(self):
8229 r"""get_atom_type(Atom self) -> AtomType"""
8230 return _IMP_atom.Atom_get_atom_type(self)
8232 def set_atom_type(self, t):
8233 r"""set_atom_type(Atom self, AtomType t)"""
8234 return _IMP_atom.Atom_set_atom_type(self, t)
8236 def get_element(self):
8237 r"""get_element(Atom self) -> IMP::atom::Element"""
8238 return _IMP_atom.Atom_get_element(self)
8240 def set_element(self, e):
8241 r"""set_element(Atom self, IMP::atom::Element e)"""
8242 return _IMP_atom.Atom_set_element(self, e)
8244 def get_occupancy(self):
8245 r"""get_occupancy(Atom self) -> double"""
8246 return _IMP_atom.Atom_get_occupancy(self)
8248 def set_occupancy(self, occupancy):
8249 r"""set_occupancy(Atom self, double occupancy)"""
8250 return _IMP_atom.Atom_set_occupancy(self, occupancy)
8252 def get_temperature_factor(self):
8253 r"""get_temperature_factor(Atom self) -> double"""
8254 return _IMP_atom.Atom_get_temperature_factor(self)
8256 def set_temperature_factor(self, tempFactor):
8257 r"""set_temperature_factor(Atom self, double tempFactor)"""
8258 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8260 def get_input_index(self):
8261 r"""get_input_index(Atom self) -> IMP::Int"""
8262 return _IMP_atom.Atom_get_input_index(self)
8264 def set_input_index(self, t):
8265 r"""set_input_index(Atom self, IMP::Int t)"""
8266 return _IMP_atom.Atom_set_input_index(self, t)
8269 def get_atom_type_key():
8270 r"""get_atom_type_key() -> IntKey"""
8271 return _IMP_atom.Atom_get_atom_type_key()
8274 def get_element_key():
8275 r"""get_element_key() -> IntKey"""
8276 return _IMP_atom.Atom_get_element_key()
8279 def get_input_index_key():
8280 r"""get_input_index_key() -> IntKey"""
8281 return _IMP_atom.Atom_get_input_index_key()
8284 def get_occupancy_key():
8285 r"""get_occupancy_key() -> FloatKey"""
8286 return _IMP_atom.Atom_get_occupancy_key()
8289 def get_temperature_factor_key():
8290 r"""get_temperature_factor_key() -> FloatKey"""
8291 return _IMP_atom.Atom_get_temperature_factor_key()
8293 def add_attribute(self, *args):
8295 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8296 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8297 add_attribute(Atom self, IntKey a0, IMP::Int a1)
8298 add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
8299 add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
8300 add_attribute(Atom self, StringKey a0, IMP::String a1)
8301 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8302 add_attribute(Atom self, ObjectKey a0, Object a1)
8303 add_attribute(Atom self, SparseFloatKey a0, IMP::Float a1)
8304 add_attribute(Atom self, SparseIntKey a0, IMP::Int a1)
8305 add_attribute(Atom self, SparseStringKey a0, IMP::String a1)
8306 add_attribute(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
8308 return _IMP_atom.Atom_add_attribute(self, *args)
8310 def get_value(self, *args):
8312 get_value(Atom self, FloatKey a0) -> IMP::Float
8313 get_value(Atom self, IntKey a0) -> IMP::Int
8314 get_value(Atom self, FloatsKey a0) -> IMP::Floats
8315 get_value(Atom self, IntsKey a0) -> IMP::Ints
8316 get_value(Atom self, StringKey a0) -> IMP::String
8317 get_value(Atom self, ParticleIndexKey a0) -> Particle
8318 get_value(Atom self, ObjectKey a0) -> Object
8319 get_value(Atom self, SparseFloatKey a0) -> IMP::Float
8320 get_value(Atom self, SparseIntKey a0) -> IMP::Int
8321 get_value(Atom self, SparseStringKey a0) -> IMP::String
8322 get_value(Atom self, SparseParticleIndexKey a0) -> ParticleIndex
8324 return _IMP_atom.Atom_get_value(self, *args)
8326 def set_value(self, *args):
8328 set_value(Atom self, FloatKey a0, IMP::Float a1)
8329 set_value(Atom self, IntKey a0, IMP::Int a1)
8330 set_value(Atom self, FloatsKey a0, IMP::Floats a1)
8331 set_value(Atom self, IntsKey a0, IMP::Ints a1)
8332 set_value(Atom self, StringKey a0, IMP::String a1)
8333 set_value(Atom self, ParticleIndexKey a0, Particle a1)
8334 set_value(Atom self, ObjectKey a0, Object a1)
8335 set_value(Atom self, SparseFloatKey a0, IMP::Float a1)
8336 set_value(Atom self, SparseIntKey a0, IMP::Int a1)
8337 set_value(Atom self, SparseStringKey a0, IMP::String a1)
8338 set_value(Atom self, SparseParticleIndexKey a0, ParticleIndex a1)
8340 return _IMP_atom.Atom_set_value(self, *args)
8342 def remove_attribute(self, *args):
8344 remove_attribute(Atom self, FloatKey a0)
8345 remove_attribute(Atom self, IntKey a0)
8346 remove_attribute(Atom self, FloatsKey a0)
8347 remove_attribute(Atom self, IntsKey a0)
8348 remove_attribute(Atom self, StringKey a0)
8349 remove_attribute(Atom self, ParticleIndexKey a0)
8350 remove_attribute(Atom self, ObjectKey a0)
8351 remove_attribute(Atom self, SparseFloatKey a0)
8352 remove_attribute(Atom self, SparseIntKey a0)
8353 remove_attribute(Atom self, SparseStringKey a0)
8354 remove_attribute(Atom self, SparseParticleIndexKey a0)
8356 return _IMP_atom.Atom_remove_attribute(self, *args)
8358 def has_attribute(self, *args):
8360 has_attribute(Atom self, FloatKey a0) -> bool
8361 has_attribute(Atom self, IntKey a0) -> bool
8362 has_attribute(Atom self, FloatsKey a0) -> bool
8363 has_attribute(Atom self, IntsKey a0) -> bool
8364 has_attribute(Atom self, StringKey a0) -> bool
8365 has_attribute(Atom self, ParticleIndexKey a0) -> bool
8366 has_attribute(Atom self, ObjectKey a0) -> bool
8367 has_attribute(Atom self, SparseFloatKey a0) -> bool
8368 has_attribute(Atom self, SparseIntKey a0) -> bool
8369 has_attribute(Atom self, SparseStringKey a0) -> bool
8370 has_attribute(Atom self, SparseParticleIndexKey a0) -> bool
8372 return _IMP_atom.Atom_has_attribute(self, *args)
8374 def get_derivative(self, a0):
8375 r"""get_derivative(Atom self, FloatKey a0) -> double"""
8376 return _IMP_atom.Atom_get_derivative(self, a0)
8379 r"""get_name(Atom self) -> std::string"""
8380 return _IMP_atom.Atom_get_name(self)
8382 def clear_caches(self):
8383 r"""clear_caches(Atom self)"""
8384 return _IMP_atom.Atom_clear_caches(self)
8386 def set_name(self, a0):
8387 r"""set_name(Atom self, std::string a0)"""
8388 return _IMP_atom.Atom_set_name(self, a0)
8391 r"""set_check_level(Atom self, IMP::CheckLevel a0)"""
8392 return _IMP_atom.Atom_set_check_level(self, a0)
8394 def add_to_derivative(self, a0, a1, a2):
8395 r"""add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8396 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8398 def set_is_optimized(self, a0, a1):
8399 r"""set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8400 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8402 def get_is_optimized(self, a0):
8403 r"""get_is_optimized(Atom self, FloatKey a0) -> bool"""
8404 return _IMP_atom.Atom_get_is_optimized(self, a0)
8407 r"""get_check_level(Atom self) -> IMP::CheckLevel"""
8408 return _IMP_atom.Atom_get_check_level(self)
8410 def __eq__(self, *args):
8412 __eq__(Atom self, Atom o) -> bool
8413 __eq__(Atom self, Particle d) -> bool
8415 return _IMP_atom.Atom___eq__(self, *args)
8417 def __ne__(self, *args):
8419 __ne__(Atom self, Atom o) -> bool
8420 __ne__(Atom self, Particle d) -> bool
8422 return _IMP_atom.Atom___ne__(self, *args)
8424 def __le__(self, *args):
8426 __le__(Atom self, Atom o) -> bool
8427 __le__(Atom self, Particle d) -> bool
8429 return _IMP_atom.Atom___le__(self, *args)
8431 def __lt__(self, *args):
8433 __lt__(Atom self, Atom o) -> bool
8434 __lt__(Atom self, Particle d) -> bool
8436 return _IMP_atom.Atom___lt__(self, *args)
8438 def __ge__(self, *args):
8440 __ge__(Atom self, Atom o) -> bool
8441 __ge__(Atom self, Particle d) -> bool
8443 return _IMP_atom.Atom___ge__(self, *args)
8445 def __gt__(self, *args):
8447 __gt__(Atom self, Atom o) -> bool
8448 __gt__(Atom self, Particle d) -> bool
8450 return _IMP_atom.Atom___gt__(self, *args)
8453 r"""__hash__(Atom self) -> std::size_t"""
8454 return _IMP_atom.Atom___hash__(self)
8457 r"""__str__(Atom self) -> std::string"""
8458 return _IMP_atom.Atom___str__(self)
8461 r"""__repr__(Atom self) -> std::string"""
8462 return _IMP_atom.Atom___repr__(self)
8464 def _get_as_binary(self):
8465 r"""_get_as_binary(Atom self) -> PyObject *"""
8466 return _IMP_atom.Atom__get_as_binary(self)
8468 def _set_from_binary(self, p):
8469 r"""_set_from_binary(Atom self, PyObject * p)"""
8470 return _IMP_atom.Atom__set_from_binary(self, p)
8472 def __getstate__(self):
8473 p = self._get_as_binary()
8474 if len(self.__dict__) > 1:
8475 d = self.__dict__.copy()
8480 def __setstate__(self, p):
8481 if not hasattr(self,
'this'):
8483 if isinstance(p, tuple):
8485 self.__dict__.update(d)
8486 return self._set_from_binary(p)
8488 __swig_destroy__ = _IMP_atom.delete_Atom
8491 _IMP_atom.Atom_swigregister(Atom)
8492 cvar = _IMP_atom.cvar
8493 AT_UNKNOWN = cvar.AT_UNKNOWN
8503 AT_HA1 = cvar.AT_HA1
8504 AT_HA2 = cvar.AT_HA2
8505 AT_HA3 = cvar.AT_HA3
8508 AT_HB1 = cvar.AT_HB1
8509 AT_HB2 = cvar.AT_HB2
8510 AT_HB3 = cvar.AT_HB3
8511 AT_OXT = cvar.AT_OXT
8512 AT_CH3 = cvar.AT_CH3
8515 AT_CG1 = cvar.AT_CG1
8516 AT_CG2 = cvar.AT_CG2
8518 AT_HG1 = cvar.AT_HG1
8519 AT_HG2 = cvar.AT_HG2
8520 AT_HG3 = cvar.AT_HG3
8521 AT_HG11 = cvar.AT_HG11
8522 AT_HG21 = cvar.AT_HG21
8523 AT_HG31 = cvar.AT_HG31
8524 AT_HG12 = cvar.AT_HG12
8525 AT_HG13 = cvar.AT_HG13
8526 AT_HG22 = cvar.AT_HG22
8527 AT_HG23 = cvar.AT_HG23
8528 AT_HG32 = cvar.AT_HG32
8530 AT_OG1 = cvar.AT_OG1
8533 AT_CD1 = cvar.AT_CD1
8534 AT_CD2 = cvar.AT_CD2
8536 AT_HD1 = cvar.AT_HD1
8537 AT_HD2 = cvar.AT_HD2
8538 AT_HD3 = cvar.AT_HD3
8539 AT_HD11 = cvar.AT_HD11
8540 AT_HD21 = cvar.AT_HD21
8541 AT_HD31 = cvar.AT_HD31
8542 AT_HD12 = cvar.AT_HD12
8543 AT_HD13 = cvar.AT_HD13
8544 AT_HD22 = cvar.AT_HD22
8545 AT_HD23 = cvar.AT_HD23
8546 AT_HD32 = cvar.AT_HD32
8548 AT_OD1 = cvar.AT_OD1
8549 AT_OD2 = cvar.AT_OD2
8550 AT_ND1 = cvar.AT_ND1
8551 AT_ND2 = cvar.AT_ND2
8553 AT_CE1 = cvar.AT_CE1
8554 AT_CE2 = cvar.AT_CE2
8555 AT_CE3 = cvar.AT_CE3
8557 AT_HE1 = cvar.AT_HE1
8558 AT_HE2 = cvar.AT_HE2
8559 AT_HE3 = cvar.AT_HE3
8560 AT_HE21 = cvar.AT_HE21
8561 AT_HE22 = cvar.AT_HE22
8562 AT_OE1 = cvar.AT_OE1
8563 AT_OE2 = cvar.AT_OE2
8565 AT_NE1 = cvar.AT_NE1
8566 AT_NE2 = cvar.AT_NE2
8568 AT_CZ2 = cvar.AT_CZ2
8569 AT_CZ3 = cvar.AT_CZ3
8572 AT_HZ1 = cvar.AT_HZ1
8573 AT_HZ2 = cvar.AT_HZ2
8574 AT_HZ3 = cvar.AT_HZ3
8575 AT_CH2 = cvar.AT_CH2
8576 AT_NH1 = cvar.AT_NH1
8577 AT_NH2 = cvar.AT_NH2
8580 AT_HH11 = cvar.AT_HH11
8581 AT_HH21 = cvar.AT_HH21
8582 AT_HH2 = cvar.AT_HH2
8583 AT_HH12 = cvar.AT_HH12
8584 AT_HH22 = cvar.AT_HH22
8585 AT_HH13 = cvar.AT_HH13
8586 AT_HH23 = cvar.AT_HH23
8587 AT_HH33 = cvar.AT_HH33
8589 AT_OP1 = cvar.AT_OP1
8590 AT_OP2 = cvar.AT_OP2
8591 AT_OP3 = cvar.AT_OP3
8592 AT_O5p = cvar.AT_O5p
8593 AT_C5p = cvar.AT_C5p
8594 AT_H5p = cvar.AT_H5p
8595 AT_H5pp = cvar.AT_H5pp
8596 AT_C4p = cvar.AT_C4p
8597 AT_H4p = cvar.AT_H4p
8598 AT_O4p = cvar.AT_O4p
8599 AT_C1p = cvar.AT_C1p
8600 AT_H1p = cvar.AT_H1p
8601 AT_C3p = cvar.AT_C3p
8602 AT_H3p = cvar.AT_H3p
8603 AT_O3p = cvar.AT_O3p
8604 AT_C2p = cvar.AT_C2p
8605 AT_H2p = cvar.AT_H2p
8606 AT_H2pp = cvar.AT_H2pp
8607 AT_O2p = cvar.AT_O2p
8608 AT_HO2p = cvar.AT_HO2p
8620 AT_H61 = cvar.AT_H61
8621 AT_H62 = cvar.AT_H62
8625 AT_H21 = cvar.AT_H21
8626 AT_H22 = cvar.AT_H22
8631 AT_H41 = cvar.AT_H41
8632 AT_H42 = cvar.AT_H42
8635 AT_H71 = cvar.AT_H71
8636 AT_H72 = cvar.AT_H72
8637 AT_H73 = cvar.AT_H73
8638 AT_O1A = cvar.AT_O1A
8639 AT_O2A = cvar.AT_O2A
8640 AT_O3A = cvar.AT_O3A
8641 AT_O1B = cvar.AT_O1B
8642 AT_O2B = cvar.AT_O2B
8643 AT_O3B = cvar.AT_O3B
8644 AT_CAY = cvar.AT_CAY
8647 AT_CAT = cvar.AT_CAT
8652 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8653 get_residue(Atom d, bool nothrow=False) -> Residue
8655 return _IMP_atom.get_residue(*args)
8658 r"""get_atom(Residue rd, AtomType at) -> Atom"""
8659 return _IMP_atom.get_atom(rd, at)
8662 r"""add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8663 return _IMP_atom.add_atom_type(name, e)
8665 def get_element_for_atom_type(at):
8666 r"""get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8667 return _IMP_atom.get_element_for_atom_type(at)
8670 r"""get_atom_type_exists(std::string name) -> bool"""
8671 return _IMP_atom.get_atom_type_exists(name)
8672 class Residue(Hierarchy):
8673 r"""Proxy of C++ IMP::atom::Residue class."""
8675 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8677 def __init__(self, *args):
8679 __init__(Residue self) -> Residue
8680 __init__(Residue self, Model m, ParticleIndex id) -> Residue
8681 __init__(Residue self, _ParticleAdaptor d) -> Residue
8683 _IMP_atom.Residue_swiginit(self, _IMP_atom.new_Residue(*args))
8685 def show(self, *args):
8686 r"""show(Residue self, _ostream out=std::cout)"""
8687 return _IMP_atom.Residue_show(self, *args)
8690 def setup_particle(*args):
8692 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8693 setup_particle(_ParticleAdaptor pa, ResidueType t, int index, int insertion_code) -> Residue
8694 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8695 setup_particle(_ParticleAdaptor pa, ResidueType t, int index) -> Residue
8696 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8697 setup_particle(_ParticleAdaptor pa, ResidueType t) -> Residue
8698 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8699 setup_particle(_ParticleAdaptor pa, Residue other) -> Residue
8701 return _IMP_atom.Residue_setup_particle(*args)
8704 def get_is_setup(*args):
8706 get_is_setup(_ParticleAdaptor p) -> bool
8707 get_is_setup(Model m, ParticleIndex pi) -> bool
8709 return _IMP_atom.Residue_get_is_setup(*args)
8711 def get_residue_type(self):
8712 r"""get_residue_type(Residue self) -> ResidueType"""
8713 return _IMP_atom.Residue_get_residue_type(self)
8715 def set_residue_type(self, t):
8716 r"""set_residue_type(Residue self, ResidueType t)"""
8717 return _IMP_atom.Residue_set_residue_type(self, t)
8719 def get_is_protein(self):
8720 r"""get_is_protein(Residue self) -> bool"""
8721 return _IMP_atom.Residue_get_is_protein(self)
8723 def get_is_dna(self):
8724 r"""get_is_dna(Residue self) -> bool"""
8725 return _IMP_atom.Residue_get_is_dna(self)
8727 def get_is_rna(self):
8728 r"""get_is_rna(Residue self) -> bool"""
8729 return _IMP_atom.Residue_get_is_rna(self)
8732 r"""get_index(Residue self) -> IMP::Int"""
8733 return _IMP_atom.Residue_get_index(self)
8735 def set_index(self, t):
8736 r"""set_index(Residue self, IMP::Int t)"""
8737 return _IMP_atom.Residue_set_index(self, t)
8739 def get_insertion_code(self):
8740 r"""get_insertion_code(Residue self) -> char"""
8741 return _IMP_atom.Residue_get_insertion_code(self)
8743 def set_insertion_code(self, insertion_code):
8744 r"""set_insertion_code(Residue self, char insertion_code)"""
8745 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8748 def get_index_key():
8749 r"""get_index_key() -> IntKey"""
8750 return _IMP_atom.Residue_get_index_key()
8753 def get_residue_type_key():
8754 r"""get_residue_type_key() -> IntKey"""
8755 return _IMP_atom.Residue_get_residue_type_key()
8758 def get_insertion_code_key():
8759 r"""get_insertion_code_key() -> IntKey"""
8760 return _IMP_atom.Residue_get_insertion_code_key()
8763 def get_type_changed_key():
8764 r"""get_type_changed_key() -> TriggerKey"""
8765 return _IMP_atom.Residue_get_type_changed_key()
8767 def add_attribute(self, *args):
8769 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8770 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8771 add_attribute(Residue self, IntKey a0, IMP::Int a1)
8772 add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
8773 add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
8774 add_attribute(Residue self, StringKey a0, IMP::String a1)
8775 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8776 add_attribute(Residue self, ObjectKey a0, Object a1)
8777 add_attribute(Residue self, SparseFloatKey a0, IMP::Float a1)
8778 add_attribute(Residue self, SparseIntKey a0, IMP::Int a1)
8779 add_attribute(Residue self, SparseStringKey a0, IMP::String a1)
8780 add_attribute(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8782 return _IMP_atom.Residue_add_attribute(self, *args)
8784 def get_value(self, *args):
8786 get_value(Residue self, FloatKey a0) -> IMP::Float
8787 get_value(Residue self, IntKey a0) -> IMP::Int
8788 get_value(Residue self, FloatsKey a0) -> IMP::Floats
8789 get_value(Residue self, IntsKey a0) -> IMP::Ints
8790 get_value(Residue self, StringKey a0) -> IMP::String
8791 get_value(Residue self, ParticleIndexKey a0) -> Particle
8792 get_value(Residue self, ObjectKey a0) -> Object
8793 get_value(Residue self, SparseFloatKey a0) -> IMP::Float
8794 get_value(Residue self, SparseIntKey a0) -> IMP::Int
8795 get_value(Residue self, SparseStringKey a0) -> IMP::String
8796 get_value(Residue self, SparseParticleIndexKey a0) -> ParticleIndex
8798 return _IMP_atom.Residue_get_value(self, *args)
8800 def set_value(self, *args):
8802 set_value(Residue self, FloatKey a0, IMP::Float a1)
8803 set_value(Residue self, IntKey a0, IMP::Int a1)
8804 set_value(Residue self, FloatsKey a0, IMP::Floats a1)
8805 set_value(Residue self, IntsKey a0, IMP::Ints a1)
8806 set_value(Residue self, StringKey a0, IMP::String a1)
8807 set_value(Residue self, ParticleIndexKey a0, Particle a1)
8808 set_value(Residue self, ObjectKey a0, Object a1)
8809 set_value(Residue self, SparseFloatKey a0, IMP::Float a1)
8810 set_value(Residue self, SparseIntKey a0, IMP::Int a1)
8811 set_value(Residue self, SparseStringKey a0, IMP::String a1)
8812 set_value(Residue self, SparseParticleIndexKey a0, ParticleIndex a1)
8814 return _IMP_atom.Residue_set_value(self, *args)
8816 def remove_attribute(self, *args):
8818 remove_attribute(Residue self, FloatKey a0)
8819 remove_attribute(Residue self, IntKey a0)
8820 remove_attribute(Residue self, FloatsKey a0)
8821 remove_attribute(Residue self, IntsKey a0)
8822 remove_attribute(Residue self, StringKey a0)
8823 remove_attribute(Residue self, ParticleIndexKey a0)
8824 remove_attribute(Residue self, ObjectKey a0)
8825 remove_attribute(Residue self, SparseFloatKey a0)
8826 remove_attribute(Residue self, SparseIntKey a0)
8827 remove_attribute(Residue self, SparseStringKey a0)
8828 remove_attribute(Residue self, SparseParticleIndexKey a0)
8830 return _IMP_atom.Residue_remove_attribute(self, *args)
8832 def has_attribute(self, *args):
8834 has_attribute(Residue self, FloatKey a0) -> bool
8835 has_attribute(Residue self, IntKey a0) -> bool
8836 has_attribute(Residue self, FloatsKey a0) -> bool
8837 has_attribute(Residue self, IntsKey a0) -> bool
8838 has_attribute(Residue self, StringKey a0) -> bool
8839 has_attribute(Residue self, ParticleIndexKey a0) -> bool
8840 has_attribute(Residue self, ObjectKey a0) -> bool
8841 has_attribute(Residue self, SparseFloatKey a0) -> bool
8842 has_attribute(Residue self, SparseIntKey a0) -> bool
8843 has_attribute(Residue self, SparseStringKey a0) -> bool
8844 has_attribute(Residue self, SparseParticleIndexKey a0) -> bool
8846 return _IMP_atom.Residue_has_attribute(self, *args)
8848 def get_derivative(self, a0):
8849 r"""get_derivative(Residue self, FloatKey a0) -> double"""
8850 return _IMP_atom.Residue_get_derivative(self, a0)
8853 r"""get_name(Residue self) -> std::string"""
8854 return _IMP_atom.Residue_get_name(self)
8856 def clear_caches(self):
8857 r"""clear_caches(Residue self)"""
8858 return _IMP_atom.Residue_clear_caches(self)
8860 def set_name(self, a0):
8861 r"""set_name(Residue self, std::string a0)"""
8862 return _IMP_atom.Residue_set_name(self, a0)
8865 r"""set_check_level(Residue self, IMP::CheckLevel a0)"""
8866 return _IMP_atom.Residue_set_check_level(self, a0)
8868 def add_to_derivative(self, a0, a1, a2):
8869 r"""add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8870 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8872 def set_is_optimized(self, a0, a1):
8873 r"""set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8874 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8876 def get_is_optimized(self, a0):
8877 r"""get_is_optimized(Residue self, FloatKey a0) -> bool"""
8878 return _IMP_atom.Residue_get_is_optimized(self, a0)
8881 r"""get_check_level(Residue self) -> IMP::CheckLevel"""
8882 return _IMP_atom.Residue_get_check_level(self)
8884 def __eq__(self, *args):
8886 __eq__(Residue self, Residue o) -> bool
8887 __eq__(Residue self, Particle d) -> bool
8889 return _IMP_atom.Residue___eq__(self, *args)
8891 def __ne__(self, *args):
8893 __ne__(Residue self, Residue o) -> bool
8894 __ne__(Residue self, Particle d) -> bool
8896 return _IMP_atom.Residue___ne__(self, *args)
8898 def __le__(self, *args):
8900 __le__(Residue self, Residue o) -> bool
8901 __le__(Residue self, Particle d) -> bool
8903 return _IMP_atom.Residue___le__(self, *args)
8905 def __lt__(self, *args):
8907 __lt__(Residue self, Residue o) -> bool
8908 __lt__(Residue self, Particle d) -> bool
8910 return _IMP_atom.Residue___lt__(self, *args)
8912 def __ge__(self, *args):
8914 __ge__(Residue self, Residue o) -> bool
8915 __ge__(Residue self, Particle d) -> bool
8917 return _IMP_atom.Residue___ge__(self, *args)
8919 def __gt__(self, *args):
8921 __gt__(Residue self, Residue o) -> bool
8922 __gt__(Residue self, Particle d) -> bool
8924 return _IMP_atom.Residue___gt__(self, *args)
8927 r"""__hash__(Residue self) -> std::size_t"""
8928 return _IMP_atom.Residue___hash__(self)
8931 r"""__str__(Residue self) -> std::string"""
8932 return _IMP_atom.Residue___str__(self)
8935 r"""__repr__(Residue self) -> std::string"""
8936 return _IMP_atom.Residue___repr__(self)
8938 def _get_as_binary(self):
8939 r"""_get_as_binary(Residue self) -> PyObject *"""
8940 return _IMP_atom.Residue__get_as_binary(self)
8942 def _set_from_binary(self, p):
8943 r"""_set_from_binary(Residue self, PyObject * p)"""
8944 return _IMP_atom.Residue__set_from_binary(self, p)
8946 def __getstate__(self):
8947 p = self._get_as_binary()
8948 if len(self.__dict__) > 1:
8949 d = self.__dict__.copy()
8954 def __setstate__(self, p):
8955 if not hasattr(self,
'this'):
8957 if isinstance(p, tuple):
8959 self.__dict__.update(d)
8960 return self._set_from_binary(p)
8962 __swig_destroy__ = _IMP_atom.delete_Residue
8965 _IMP_atom.Residue_swigregister(Residue)
9006 r"""get_next_residue(Residue rd) -> Hierarchy"""
9007 return _IMP_atom.get_next_residue(rd)
9010 r"""get_previous_residue(Residue rd) -> Hierarchy"""
9011 return _IMP_atom.get_previous_residue(rd)
9014 r"""get_one_letter_code(ResidueType c) -> char"""
9015 return _IMP_atom.get_one_letter_code(c)
9016 BALLS = _IMP_atom.BALLS
9018 DENSITIES = _IMP_atom.DENSITIES
9020 class Representation(Hierarchy):
9021 r"""Proxy of C++ IMP::atom::Representation class."""
9023 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9026 def setup_particle(*args):
9028 setup_particle(Model m, ParticleIndex pi) -> Representation
9029 setup_particle(_ParticleAdaptor pa) -> Representation
9030 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9031 setup_particle(_ParticleAdaptor pa, double resolution) -> Representation
9032 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9033 setup_particle(_ParticleAdaptor pa, Representation other) -> Representation
9035 return _IMP_atom.Representation_setup_particle(*args)
9037 def __init__(self, *args):
9039 __init__(Representation self) -> Representation
9040 __init__(Representation self, Model m, ParticleIndex id) -> Representation
9041 __init__(Representation self, _ParticleAdaptor d) -> Representation
9043 _IMP_atom.Representation_swiginit(self, _IMP_atom.new_Representation(*args))
9045 def show(self, *args):
9046 r"""show(Representation self, _ostream out=std::cout)"""
9047 return _IMP_atom.Representation_show(self, *args)
9050 def get_is_setup(*args):
9052 get_is_setup(_ParticleAdaptor p) -> bool
9053 get_is_setup(Model m, ParticleIndex pi) -> bool
9055 return _IMP_atom.Representation_get_is_setup(*args)
9058 r"""get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy"""
9059 return _IMP_atom.Representation_get_representation(self, *args)
9061 def get_representations(self, *args):
9062 r"""get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies"""
9063 return _IMP_atom.Representation_get_representations(self, *args)
9065 def add_representation(self, *args):
9066 r"""add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)"""
9067 return _IMP_atom.Representation_add_representation(self, *args)
9069 def get_resolutions(self, *args):
9070 r"""get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats"""
9071 return _IMP_atom.Representation_get_resolutions(self, *args)
9073 def remove_representation(self, rep):
9074 r"""remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
9075 return _IMP_atom.Representation_remove_representation(self, rep)
9077 def update_parents(self):
9078 r"""update_parents(Representation self)"""
9079 return _IMP_atom.Representation_update_parents(self)
9081 def add_attribute(self, *args):
9083 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9084 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9085 add_attribute(Representation self, IntKey a0, IMP::Int a1)
9086 add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
9087 add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
9088 add_attribute(Representation self, StringKey a0, IMP::String a1)
9089 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9090 add_attribute(Representation self, ObjectKey a0, Object a1)
9091 add_attribute(Representation self, SparseFloatKey a0, IMP::Float a1)
9092 add_attribute(Representation self, SparseIntKey a0, IMP::Int a1)
9093 add_attribute(Representation self, SparseStringKey a0, IMP::String a1)
9094 add_attribute(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
9096 return _IMP_atom.Representation_add_attribute(self, *args)
9098 def get_value(self, *args):
9100 get_value(Representation self, FloatKey a0) -> IMP::Float
9101 get_value(Representation self, IntKey a0) -> IMP::Int
9102 get_value(Representation self, FloatsKey a0) -> IMP::Floats
9103 get_value(Representation self, IntsKey a0) -> IMP::Ints
9104 get_value(Representation self, StringKey a0) -> IMP::String
9105 get_value(Representation self, ParticleIndexKey a0) -> Particle
9106 get_value(Representation self, ObjectKey a0) -> Object
9107 get_value(Representation self, SparseFloatKey a0) -> IMP::Float
9108 get_value(Representation self, SparseIntKey a0) -> IMP::Int
9109 get_value(Representation self, SparseStringKey a0) -> IMP::String
9110 get_value(Representation self, SparseParticleIndexKey a0) -> ParticleIndex
9112 return _IMP_atom.Representation_get_value(self, *args)
9114 def set_value(self, *args):
9116 set_value(Representation self, FloatKey a0, IMP::Float a1)
9117 set_value(Representation self, IntKey a0, IMP::Int a1)
9118 set_value(Representation self, FloatsKey a0, IMP::Floats a1)
9119 set_value(Representation self, IntsKey a0, IMP::Ints a1)
9120 set_value(Representation self, StringKey a0, IMP::String a1)
9121 set_value(Representation self, ParticleIndexKey a0, Particle a1)
9122 set_value(Representation self, ObjectKey a0, Object a1)
9123 set_value(Representation self, SparseFloatKey a0, IMP::Float a1)
9124 set_value(Representation self, SparseIntKey a0, IMP::Int a1)
9125 set_value(Representation self, SparseStringKey a0, IMP::String a1)
9126 set_value(Representation self, SparseParticleIndexKey a0, ParticleIndex a1)
9128 return _IMP_atom.Representation_set_value(self, *args)
9130 def remove_attribute(self, *args):
9132 remove_attribute(Representation self, FloatKey a0)
9133 remove_attribute(Representation self, IntKey a0)
9134 remove_attribute(Representation self, FloatsKey a0)
9135 remove_attribute(Representation self, IntsKey a0)
9136 remove_attribute(Representation self, StringKey a0)
9137 remove_attribute(Representation self, ParticleIndexKey a0)
9138 remove_attribute(Representation self, ObjectKey a0)
9139 remove_attribute(Representation self, SparseFloatKey a0)
9140 remove_attribute(Representation self, SparseIntKey a0)
9141 remove_attribute(Representation self, SparseStringKey a0)
9142 remove_attribute(Representation self, SparseParticleIndexKey a0)
9144 return _IMP_atom.Representation_remove_attribute(self, *args)
9146 def has_attribute(self, *args):
9148 has_attribute(Representation self, FloatKey a0) -> bool
9149 has_attribute(Representation self, IntKey a0) -> bool
9150 has_attribute(Representation self, FloatsKey a0) -> bool
9151 has_attribute(Representation self, IntsKey a0) -> bool
9152 has_attribute(Representation self, StringKey a0) -> bool
9153 has_attribute(Representation self, ParticleIndexKey a0) -> bool
9154 has_attribute(Representation self, ObjectKey a0) -> bool
9155 has_attribute(Representation self, SparseFloatKey a0) -> bool
9156 has_attribute(Representation self, SparseIntKey a0) -> bool
9157 has_attribute(Representation self, SparseStringKey a0) -> bool
9158 has_attribute(Representation self, SparseParticleIndexKey a0) -> bool
9160 return _IMP_atom.Representation_has_attribute(self, *args)
9162 def get_derivative(self, a0):
9163 r"""get_derivative(Representation self, FloatKey a0) -> double"""
9164 return _IMP_atom.Representation_get_derivative(self, a0)
9167 r"""get_name(Representation self) -> std::string"""
9168 return _IMP_atom.Representation_get_name(self)
9170 def clear_caches(self):
9171 r"""clear_caches(Representation self)"""
9172 return _IMP_atom.Representation_clear_caches(self)
9174 def set_name(self, a0):
9175 r"""set_name(Representation self, std::string a0)"""
9176 return _IMP_atom.Representation_set_name(self, a0)
9179 r"""set_check_level(Representation self, IMP::CheckLevel a0)"""
9180 return _IMP_atom.Representation_set_check_level(self, a0)
9182 def add_to_derivative(self, a0, a1, a2):
9183 r"""add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9184 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9186 def set_is_optimized(self, a0, a1):
9187 r"""set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9188 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9190 def get_is_optimized(self, a0):
9191 r"""get_is_optimized(Representation self, FloatKey a0) -> bool"""
9192 return _IMP_atom.Representation_get_is_optimized(self, a0)
9195 r"""get_check_level(Representation self) -> IMP::CheckLevel"""
9196 return _IMP_atom.Representation_get_check_level(self)
9198 def __eq__(self, *args):
9200 __eq__(Representation self, Representation o) -> bool
9201 __eq__(Representation self, Particle d) -> bool
9203 return _IMP_atom.Representation___eq__(self, *args)
9205 def __ne__(self, *args):
9207 __ne__(Representation self, Representation o) -> bool
9208 __ne__(Representation self, Particle d) -> bool
9210 return _IMP_atom.Representation___ne__(self, *args)
9212 def __le__(self, *args):
9214 __le__(Representation self, Representation o) -> bool
9215 __le__(Representation self, Particle d) -> bool
9217 return _IMP_atom.Representation___le__(self, *args)
9219 def __lt__(self, *args):
9221 __lt__(Representation self, Representation o) -> bool
9222 __lt__(Representation self, Particle d) -> bool
9224 return _IMP_atom.Representation___lt__(self, *args)
9226 def __ge__(self, *args):
9228 __ge__(Representation self, Representation o) -> bool
9229 __ge__(Representation self, Particle d) -> bool
9231 return _IMP_atom.Representation___ge__(self, *args)
9233 def __gt__(self, *args):
9235 __gt__(Representation self, Representation o) -> bool
9236 __gt__(Representation self, Particle d) -> bool
9238 return _IMP_atom.Representation___gt__(self, *args)
9241 r"""__hash__(Representation self) -> std::size_t"""
9242 return _IMP_atom.Representation___hash__(self)
9245 r"""__str__(Representation self) -> std::string"""
9246 return _IMP_atom.Representation___str__(self)
9249 r"""__repr__(Representation self) -> std::string"""
9250 return _IMP_atom.Representation___repr__(self)
9252 def _get_as_binary(self):
9253 r"""_get_as_binary(Representation self) -> PyObject *"""
9254 return _IMP_atom.Representation__get_as_binary(self)
9256 def _set_from_binary(self, p):
9257 r"""_set_from_binary(Representation self, PyObject * p)"""
9258 return _IMP_atom.Representation__set_from_binary(self, p)
9260 def __getstate__(self):
9261 p = self._get_as_binary()
9262 if len(self.__dict__) > 1:
9263 d = self.__dict__.copy()
9268 def __setstate__(self, p):
9269 if not hasattr(self,
'this'):
9271 if isinstance(p, tuple):
9273 self.__dict__.update(d)
9274 return self._set_from_binary(p)
9276 __swig_destroy__ = _IMP_atom.delete_Representation
9279 _IMP_atom.Representation_swigregister(Representation)
9280 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9285 get_resolution(Model m, ParticleIndex pi) -> double
9286 get_resolution(Hierarchy h) -> double
9288 return _IMP_atom.get_resolution(*args)
9291 r"""get_representation(Hierarchy h, bool nothrow=False) -> Representation"""
9292 return _IMP_atom.get_representation(h, nothrow)
9295 r"""show_with_representations(Hierarchy h, _ostream out=std::cout)"""
9296 return _IMP_atom.show_with_representations(*args)
9297 class State(Hierarchy):
9298 r"""Proxy of C++ IMP::atom::State class."""
9300 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9303 def setup_particle(*args):
9305 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9306 setup_particle(_ParticleAdaptor pa, unsigned int index) -> State
9307 setup_particle(Model m, ParticleIndex pi, State other) -> State
9308 setup_particle(_ParticleAdaptor pa, State other) -> State
9310 return _IMP_atom.State_setup_particle(*args)
9312 def __init__(self, *args):
9314 __init__(State self) -> State
9315 __init__(State self, Model m, ParticleIndex id) -> State
9316 __init__(State self, _ParticleAdaptor d) -> State
9318 _IMP_atom.State_swiginit(self, _IMP_atom.new_State(*args))
9320 def show(self, *args):
9321 r"""show(State self, _ostream out=std::cout)"""
9322 return _IMP_atom.State_show(self, *args)
9325 def get_is_setup(*args):
9327 get_is_setup(_ParticleAdaptor p) -> bool
9328 get_is_setup(Model m, ParticleIndex pi) -> bool
9330 return _IMP_atom.State_get_is_setup(*args)
9333 r"""get_state_index(State self) -> unsigned int"""
9334 return _IMP_atom.State_get_state_index(self)
9336 def add_attribute(self, *args):
9338 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9339 add_attribute(State self, FloatKey a0, IMP::Float a1)
9340 add_attribute(State self, IntKey a0, IMP::Int a1)
9341 add_attribute(State self, FloatsKey a0, IMP::Floats a1)
9342 add_attribute(State self, IntsKey a0, IMP::Ints a1)
9343 add_attribute(State self, StringKey a0, IMP::String a1)
9344 add_attribute(State self, ParticleIndexKey a0, Particle a1)
9345 add_attribute(State self, ObjectKey a0, Object a1)
9346 add_attribute(State self, SparseFloatKey a0, IMP::Float a1)
9347 add_attribute(State self, SparseIntKey a0, IMP::Int a1)
9348 add_attribute(State self, SparseStringKey a0, IMP::String a1)
9349 add_attribute(State self, SparseParticleIndexKey a0, ParticleIndex a1)
9351 return _IMP_atom.State_add_attribute(self, *args)
9353 def get_value(self, *args):
9355 get_value(State self, FloatKey a0) -> IMP::Float
9356 get_value(State self, IntKey a0) -> IMP::Int
9357 get_value(State self, FloatsKey a0) -> IMP::Floats
9358 get_value(State self, IntsKey a0) -> IMP::Ints
9359 get_value(State self, StringKey a0) -> IMP::String
9360 get_value(State self, ParticleIndexKey a0) -> Particle
9361 get_value(State self, ObjectKey a0) -> Object
9362 get_value(State self, SparseFloatKey a0) -> IMP::Float
9363 get_value(State self, SparseIntKey a0) -> IMP::Int
9364 get_value(State self, SparseStringKey a0) -> IMP::String
9365 get_value(State self, SparseParticleIndexKey a0) -> ParticleIndex
9367 return _IMP_atom.State_get_value(self, *args)
9369 def set_value(self, *args):
9371 set_value(State self, FloatKey a0, IMP::Float a1)
9372 set_value(State self, IntKey a0, IMP::Int a1)
9373 set_value(State self, FloatsKey a0, IMP::Floats a1)
9374 set_value(State self, IntsKey a0, IMP::Ints a1)
9375 set_value(State self, StringKey a0, IMP::String a1)
9376 set_value(State self, ParticleIndexKey a0, Particle a1)
9377 set_value(State self, ObjectKey a0, Object a1)
9378 set_value(State self, SparseFloatKey a0, IMP::Float a1)
9379 set_value(State self, SparseIntKey a0, IMP::Int a1)
9380 set_value(State self, SparseStringKey a0, IMP::String a1)
9381 set_value(State self, SparseParticleIndexKey a0, ParticleIndex a1)
9383 return _IMP_atom.State_set_value(self, *args)
9385 def remove_attribute(self, *args):
9387 remove_attribute(State self, FloatKey a0)
9388 remove_attribute(State self, IntKey a0)
9389 remove_attribute(State self, FloatsKey a0)
9390 remove_attribute(State self, IntsKey a0)
9391 remove_attribute(State self, StringKey a0)
9392 remove_attribute(State self, ParticleIndexKey a0)
9393 remove_attribute(State self, ObjectKey a0)
9394 remove_attribute(State self, SparseFloatKey a0)
9395 remove_attribute(State self, SparseIntKey a0)
9396 remove_attribute(State self, SparseStringKey a0)
9397 remove_attribute(State self, SparseParticleIndexKey a0)
9399 return _IMP_atom.State_remove_attribute(self, *args)
9401 def has_attribute(self, *args):
9403 has_attribute(State self, FloatKey a0) -> bool
9404 has_attribute(State self, IntKey a0) -> bool
9405 has_attribute(State self, FloatsKey a0) -> bool
9406 has_attribute(State self, IntsKey a0) -> bool
9407 has_attribute(State self, StringKey a0) -> bool
9408 has_attribute(State self, ParticleIndexKey a0) -> bool
9409 has_attribute(State self, ObjectKey a0) -> bool
9410 has_attribute(State self, SparseFloatKey a0) -> bool
9411 has_attribute(State self, SparseIntKey a0) -> bool
9412 has_attribute(State self, SparseStringKey a0) -> bool
9413 has_attribute(State self, SparseParticleIndexKey a0) -> bool
9415 return _IMP_atom.State_has_attribute(self, *args)
9417 def get_derivative(self, a0):
9418 r"""get_derivative(State self, FloatKey a0) -> double"""
9419 return _IMP_atom.State_get_derivative(self, a0)
9422 r"""get_name(State self) -> std::string"""
9423 return _IMP_atom.State_get_name(self)
9425 def clear_caches(self):
9426 r"""clear_caches(State self)"""
9427 return _IMP_atom.State_clear_caches(self)
9429 def set_name(self, a0):
9430 r"""set_name(State self, std::string a0)"""
9431 return _IMP_atom.State_set_name(self, a0)
9434 r"""set_check_level(State self, IMP::CheckLevel a0)"""
9435 return _IMP_atom.State_set_check_level(self, a0)
9437 def add_to_derivative(self, a0, a1, a2):
9438 r"""add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9439 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9441 def set_is_optimized(self, a0, a1):
9442 r"""set_is_optimized(State self, FloatKey a0, bool a1)"""
9443 return _IMP_atom.State_set_is_optimized(self, a0, a1)
9445 def get_is_optimized(self, a0):
9446 r"""get_is_optimized(State self, FloatKey a0) -> bool"""
9447 return _IMP_atom.State_get_is_optimized(self, a0)
9450 r"""get_check_level(State self) -> IMP::CheckLevel"""
9451 return _IMP_atom.State_get_check_level(self)
9453 def __eq__(self, *args):
9455 __eq__(State self, State o) -> bool
9456 __eq__(State self, Particle d) -> bool
9458 return _IMP_atom.State___eq__(self, *args)
9460 def __ne__(self, *args):
9462 __ne__(State self, State o) -> bool
9463 __ne__(State self, Particle d) -> bool
9465 return _IMP_atom.State___ne__(self, *args)
9467 def __le__(self, *args):
9469 __le__(State self, State o) -> bool
9470 __le__(State self, Particle d) -> bool
9472 return _IMP_atom.State___le__(self, *args)
9474 def __lt__(self, *args):
9476 __lt__(State self, State o) -> bool
9477 __lt__(State self, Particle d) -> bool
9479 return _IMP_atom.State___lt__(self, *args)
9481 def __ge__(self, *args):
9483 __ge__(State self, State o) -> bool
9484 __ge__(State self, Particle d) -> bool
9486 return _IMP_atom.State___ge__(self, *args)
9488 def __gt__(self, *args):
9490 __gt__(State self, State o) -> bool
9491 __gt__(State self, Particle d) -> bool
9493 return _IMP_atom.State___gt__(self, *args)
9496 r"""__hash__(State self) -> std::size_t"""
9497 return _IMP_atom.State___hash__(self)
9500 r"""__str__(State self) -> std::string"""
9501 return _IMP_atom.State___str__(self)
9504 r"""__repr__(State self) -> std::string"""
9505 return _IMP_atom.State___repr__(self)
9507 def _get_as_binary(self):
9508 r"""_get_as_binary(State self) -> PyObject *"""
9509 return _IMP_atom.State__get_as_binary(self)
9511 def _set_from_binary(self, p):
9512 r"""_set_from_binary(State self, PyObject * p)"""
9513 return _IMP_atom.State__set_from_binary(self, p)
9515 def __getstate__(self):
9516 p = self._get_as_binary()
9517 if len(self.__dict__) > 1:
9518 d = self.__dict__.copy()
9523 def __setstate__(self, p):
9524 if not hasattr(self,
'this'):
9526 if isinstance(p, tuple):
9528 self.__dict__.update(d)
9529 return self._set_from_binary(p)
9531 __swig_destroy__ = _IMP_atom.delete_State
9534 _IMP_atom.State_swigregister(State)
9537 r"""get_state_index(Hierarchy h) -> int"""
9538 return _IMP_atom.get_state_index(h)
9541 r"""get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9542 return _IMP_atom.get_phi_dihedral_atoms(rd)
9545 r"""get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9546 return _IMP_atom.get_psi_dihedral_atoms(rd)
9549 r"""get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9550 return _IMP_atom.get_omega_dihedral_atoms(rd)
9553 r"""get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
9554 return _IMP_atom.get_chi_dihedral_atom_types(rt)
9557 r"""get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
9558 return _IMP_atom.get_chi_dihedral_atoms(rd)
9561 r"""get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
9562 return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
9563 class Molecule(Hierarchy):
9564 r"""Proxy of C++ IMP::atom::Molecule class."""
9566 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9568 def __init__(self, *args):
9570 __init__(Molecule self) -> Molecule
9571 __init__(Molecule self, Model m, ParticleIndex id) -> Molecule
9572 __init__(Molecule self, _ParticleAdaptor d) -> Molecule
9574 _IMP_atom.Molecule_swiginit(self, _IMP_atom.new_Molecule(*args))
9576 def show(self, *args):
9577 r"""show(Molecule self, _ostream out=std::cout)"""
9578 return _IMP_atom.Molecule_show(self, *args)
9581 def setup_particle(*args):
9583 setup_particle(Model m, ParticleIndex pi) -> Molecule
9584 setup_particle(_ParticleAdaptor pa) -> Molecule
9585 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9586 setup_particle(_ParticleAdaptor pa, Molecule other) -> Molecule
9588 return _IMP_atom.Molecule_setup_particle(*args)
9591 def get_is_setup(*args):
9593 get_is_setup(_ParticleAdaptor p) -> bool
9594 get_is_setup(Model m, ParticleIndex pi) -> bool
9596 return _IMP_atom.Molecule_get_is_setup(*args)
9598 def add_attribute(self, *args):
9600 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9601 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9602 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9603 add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
9604 add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
9605 add_attribute(Molecule self, StringKey a0, IMP::String a1)
9606 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9607 add_attribute(Molecule self, ObjectKey a0, Object a1)
9608 add_attribute(Molecule self, SparseFloatKey a0, IMP::Float a1)
9609 add_attribute(Molecule self, SparseIntKey a0, IMP::Int a1)
9610 add_attribute(Molecule self, SparseStringKey a0, IMP::String a1)
9611 add_attribute(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9613 return _IMP_atom.Molecule_add_attribute(self, *args)
9615 def get_value(self, *args):
9617 get_value(Molecule self, FloatKey a0) -> IMP::Float
9618 get_value(Molecule self, IntKey a0) -> IMP::Int
9619 get_value(Molecule self, FloatsKey a0) -> IMP::Floats
9620 get_value(Molecule self, IntsKey a0) -> IMP::Ints
9621 get_value(Molecule self, StringKey a0) -> IMP::String
9622 get_value(Molecule self, ParticleIndexKey a0) -> Particle
9623 get_value(Molecule self, ObjectKey a0) -> Object
9624 get_value(Molecule self, SparseFloatKey a0) -> IMP::Float
9625 get_value(Molecule self, SparseIntKey a0) -> IMP::Int
9626 get_value(Molecule self, SparseStringKey a0) -> IMP::String
9627 get_value(Molecule self, SparseParticleIndexKey a0) -> ParticleIndex
9629 return _IMP_atom.Molecule_get_value(self, *args)
9631 def set_value(self, *args):
9633 set_value(Molecule self, FloatKey a0, IMP::Float a1)
9634 set_value(Molecule self, IntKey a0, IMP::Int a1)
9635 set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
9636 set_value(Molecule self, IntsKey a0, IMP::Ints a1)
9637 set_value(Molecule self, StringKey a0, IMP::String a1)
9638 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9639 set_value(Molecule self, ObjectKey a0, Object a1)
9640 set_value(Molecule self, SparseFloatKey a0, IMP::Float a1)
9641 set_value(Molecule self, SparseIntKey a0, IMP::Int a1)
9642 set_value(Molecule self, SparseStringKey a0, IMP::String a1)
9643 set_value(Molecule self, SparseParticleIndexKey a0, ParticleIndex a1)
9645 return _IMP_atom.Molecule_set_value(self, *args)
9647 def remove_attribute(self, *args):
9649 remove_attribute(Molecule self, FloatKey a0)
9650 remove_attribute(Molecule self, IntKey a0)
9651 remove_attribute(Molecule self, FloatsKey a0)
9652 remove_attribute(Molecule self, IntsKey a0)
9653 remove_attribute(Molecule self, StringKey a0)
9654 remove_attribute(Molecule self, ParticleIndexKey a0)
9655 remove_attribute(Molecule self, ObjectKey a0)
9656 remove_attribute(Molecule self, SparseFloatKey a0)
9657 remove_attribute(Molecule self, SparseIntKey a0)
9658 remove_attribute(Molecule self, SparseStringKey a0)
9659 remove_attribute(Molecule self, SparseParticleIndexKey a0)
9661 return _IMP_atom.Molecule_remove_attribute(self, *args)
9663 def has_attribute(self, *args):
9665 has_attribute(Molecule self, FloatKey a0) -> bool
9666 has_attribute(Molecule self, IntKey a0) -> bool
9667 has_attribute(Molecule self, FloatsKey a0) -> bool
9668 has_attribute(Molecule self, IntsKey a0) -> bool
9669 has_attribute(Molecule self, StringKey a0) -> bool
9670 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9671 has_attribute(Molecule self, ObjectKey a0) -> bool
9672 has_attribute(Molecule self, SparseFloatKey a0) -> bool
9673 has_attribute(Molecule self, SparseIntKey a0) -> bool
9674 has_attribute(Molecule self, SparseStringKey a0) -> bool
9675 has_attribute(Molecule self, SparseParticleIndexKey a0) -> bool
9677 return _IMP_atom.Molecule_has_attribute(self, *args)
9679 def get_derivative(self, a0):
9680 r"""get_derivative(Molecule self, FloatKey a0) -> double"""
9681 return _IMP_atom.Molecule_get_derivative(self, a0)
9684 r"""get_name(Molecule self) -> std::string"""
9685 return _IMP_atom.Molecule_get_name(self)
9687 def clear_caches(self):
9688 r"""clear_caches(Molecule self)"""
9689 return _IMP_atom.Molecule_clear_caches(self)
9691 def set_name(self, a0):
9692 r"""set_name(Molecule self, std::string a0)"""
9693 return _IMP_atom.Molecule_set_name(self, a0)
9696 r"""set_check_level(Molecule self, IMP::CheckLevel a0)"""
9697 return _IMP_atom.Molecule_set_check_level(self, a0)
9699 def add_to_derivative(self, a0, a1, a2):
9700 r"""add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9701 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9703 def set_is_optimized(self, a0, a1):
9704 r"""set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9705 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9707 def get_is_optimized(self, a0):
9708 r"""get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9709 return _IMP_atom.Molecule_get_is_optimized(self, a0)
9712 r"""get_check_level(Molecule self) -> IMP::CheckLevel"""
9713 return _IMP_atom.Molecule_get_check_level(self)
9715 def __eq__(self, *args):
9717 __eq__(Molecule self, Molecule o) -> bool
9718 __eq__(Molecule self, Particle d) -> bool
9720 return _IMP_atom.Molecule___eq__(self, *args)
9722 def __ne__(self, *args):
9724 __ne__(Molecule self, Molecule o) -> bool
9725 __ne__(Molecule self, Particle d) -> bool
9727 return _IMP_atom.Molecule___ne__(self, *args)
9729 def __le__(self, *args):
9731 __le__(Molecule self, Molecule o) -> bool
9732 __le__(Molecule self, Particle d) -> bool
9734 return _IMP_atom.Molecule___le__(self, *args)
9736 def __lt__(self, *args):
9738 __lt__(Molecule self, Molecule o) -> bool
9739 __lt__(Molecule self, Particle d) -> bool
9741 return _IMP_atom.Molecule___lt__(self, *args)
9743 def __ge__(self, *args):
9745 __ge__(Molecule self, Molecule o) -> bool
9746 __ge__(Molecule self, Particle d) -> bool
9748 return _IMP_atom.Molecule___ge__(self, *args)
9750 def __gt__(self, *args):
9752 __gt__(Molecule self, Molecule o) -> bool
9753 __gt__(Molecule self, Particle d) -> bool
9755 return _IMP_atom.Molecule___gt__(self, *args)
9758 r"""__hash__(Molecule self) -> std::size_t"""
9759 return _IMP_atom.Molecule___hash__(self)
9762 r"""__str__(Molecule self) -> std::string"""
9763 return _IMP_atom.Molecule___str__(self)
9766 r"""__repr__(Molecule self) -> std::string"""
9767 return _IMP_atom.Molecule___repr__(self)
9769 def _get_as_binary(self):
9770 r"""_get_as_binary(Molecule self) -> PyObject *"""
9771 return _IMP_atom.Molecule__get_as_binary(self)
9773 def _set_from_binary(self, p):
9774 r"""_set_from_binary(Molecule self, PyObject * p)"""
9775 return _IMP_atom.Molecule__set_from_binary(self, p)
9777 def __getstate__(self):
9778 p = self._get_as_binary()
9779 if len(self.__dict__) > 1:
9780 d = self.__dict__.copy()
9785 def __setstate__(self, p):
9786 if not hasattr(self,
'this'):
9788 if isinstance(p, tuple):
9790 self.__dict__.update(d)
9791 return self._set_from_binary(p)
9793 __swig_destroy__ = _IMP_atom.delete_Molecule
9796 _IMP_atom.Molecule_swigregister(Molecule)
9799 r"""get_molecule_name(Hierarchy h) -> std::string"""
9800 return _IMP_atom.get_molecule_name(h)
9801 class Copy(Molecule):
9802 r"""Proxy of C++ IMP::atom::Copy class."""
9804 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9807 def get_copy_index_key():
9808 r"""get_copy_index_key() -> IntKey"""
9809 return _IMP_atom.Copy_get_copy_index_key()
9811 def __init__(self, *args):
9813 __init__(Copy self) -> Copy
9814 __init__(Copy self, Model m, ParticleIndex id) -> Copy
9815 __init__(Copy self, _ParticleAdaptor d) -> Copy
9817 _IMP_atom.Copy_swiginit(self, _IMP_atom.new_Copy(*args))
9819 def show(self, *args):
9820 r"""show(Copy self, _ostream out=std::cout)"""
9821 return _IMP_atom.Copy_show(self, *args)
9824 def setup_particle(*args):
9826 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9827 setup_particle(_ParticleAdaptor pa, IMP::Int number) -> Copy
9829 return _IMP_atom.Copy_setup_particle(*args)
9832 def get_is_setup(*args):
9834 get_is_setup(_ParticleAdaptor p) -> bool
9835 get_is_setup(Model m, ParticleIndex pi) -> bool
9837 return _IMP_atom.Copy_get_is_setup(*args)
9840 r"""get_copy_index(Copy self) -> int"""
9841 return _IMP_atom.Copy_get_copy_index(self)
9843 def add_attribute(self, *args):
9845 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9846 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9847 add_attribute(Copy self, IntKey a0, IMP::Int a1)
9848 add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
9849 add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
9850 add_attribute(Copy self, StringKey a0, IMP::String a1)
9851 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9852 add_attribute(Copy self, ObjectKey a0, Object a1)
9853 add_attribute(Copy self, SparseFloatKey a0, IMP::Float a1)
9854 add_attribute(Copy self, SparseIntKey a0, IMP::Int a1)
9855 add_attribute(Copy self, SparseStringKey a0, IMP::String a1)
9856 add_attribute(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9858 return _IMP_atom.Copy_add_attribute(self, *args)
9860 def get_value(self, *args):
9862 get_value(Copy self, FloatKey a0) -> IMP::Float
9863 get_value(Copy self, IntKey a0) -> IMP::Int
9864 get_value(Copy self, FloatsKey a0) -> IMP::Floats
9865 get_value(Copy self, IntsKey a0) -> IMP::Ints
9866 get_value(Copy self, StringKey a0) -> IMP::String
9867 get_value(Copy self, ParticleIndexKey a0) -> Particle
9868 get_value(Copy self, ObjectKey a0) -> Object
9869 get_value(Copy self, SparseFloatKey a0) -> IMP::Float
9870 get_value(Copy self, SparseIntKey a0) -> IMP::Int
9871 get_value(Copy self, SparseStringKey a0) -> IMP::String
9872 get_value(Copy self, SparseParticleIndexKey a0) -> ParticleIndex
9874 return _IMP_atom.Copy_get_value(self, *args)
9876 def set_value(self, *args):
9878 set_value(Copy self, FloatKey a0, IMP::Float a1)
9879 set_value(Copy self, IntKey a0, IMP::Int a1)
9880 set_value(Copy self, FloatsKey a0, IMP::Floats a1)
9881 set_value(Copy self, IntsKey a0, IMP::Ints a1)
9882 set_value(Copy self, StringKey a0, IMP::String a1)
9883 set_value(Copy self, ParticleIndexKey a0, Particle a1)
9884 set_value(Copy self, ObjectKey a0, Object a1)
9885 set_value(Copy self, SparseFloatKey a0, IMP::Float a1)
9886 set_value(Copy self, SparseIntKey a0, IMP::Int a1)
9887 set_value(Copy self, SparseStringKey a0, IMP::String a1)
9888 set_value(Copy self, SparseParticleIndexKey a0, ParticleIndex a1)
9890 return _IMP_atom.Copy_set_value(self, *args)
9892 def remove_attribute(self, *args):
9894 remove_attribute(Copy self, FloatKey a0)
9895 remove_attribute(Copy self, IntKey a0)
9896 remove_attribute(Copy self, FloatsKey a0)
9897 remove_attribute(Copy self, IntsKey a0)
9898 remove_attribute(Copy self, StringKey a0)
9899 remove_attribute(Copy self, ParticleIndexKey a0)
9900 remove_attribute(Copy self, ObjectKey a0)
9901 remove_attribute(Copy self, SparseFloatKey a0)
9902 remove_attribute(Copy self, SparseIntKey a0)
9903 remove_attribute(Copy self, SparseStringKey a0)
9904 remove_attribute(Copy self, SparseParticleIndexKey a0)
9906 return _IMP_atom.Copy_remove_attribute(self, *args)
9908 def has_attribute(self, *args):
9910 has_attribute(Copy self, FloatKey a0) -> bool
9911 has_attribute(Copy self, IntKey a0) -> bool
9912 has_attribute(Copy self, FloatsKey a0) -> bool
9913 has_attribute(Copy self, IntsKey a0) -> bool
9914 has_attribute(Copy self, StringKey a0) -> bool
9915 has_attribute(Copy self, ParticleIndexKey a0) -> bool
9916 has_attribute(Copy self, ObjectKey a0) -> bool
9917 has_attribute(Copy self, SparseFloatKey a0) -> bool
9918 has_attribute(Copy self, SparseIntKey a0) -> bool
9919 has_attribute(Copy self, SparseStringKey a0) -> bool
9920 has_attribute(Copy self, SparseParticleIndexKey a0) -> bool
9922 return _IMP_atom.Copy_has_attribute(self, *args)
9924 def get_derivative(self, a0):
9925 r"""get_derivative(Copy self, FloatKey a0) -> double"""
9926 return _IMP_atom.Copy_get_derivative(self, a0)
9929 r"""get_name(Copy self) -> std::string"""
9930 return _IMP_atom.Copy_get_name(self)
9932 def clear_caches(self):
9933 r"""clear_caches(Copy self)"""
9934 return _IMP_atom.Copy_clear_caches(self)
9936 def set_name(self, a0):
9937 r"""set_name(Copy self, std::string a0)"""
9938 return _IMP_atom.Copy_set_name(self, a0)
9941 r"""set_check_level(Copy self, IMP::CheckLevel a0)"""
9942 return _IMP_atom.Copy_set_check_level(self, a0)
9944 def add_to_derivative(self, a0, a1, a2):
9945 r"""add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9946 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9948 def set_is_optimized(self, a0, a1):
9949 r"""set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9950 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9952 def get_is_optimized(self, a0):
9953 r"""get_is_optimized(Copy self, FloatKey a0) -> bool"""
9954 return _IMP_atom.Copy_get_is_optimized(self, a0)
9957 r"""get_check_level(Copy self) -> IMP::CheckLevel"""
9958 return _IMP_atom.Copy_get_check_level(self)
9960 def __eq__(self, *args):
9962 __eq__(Copy self, Copy o) -> bool
9963 __eq__(Copy self, Particle d) -> bool
9965 return _IMP_atom.Copy___eq__(self, *args)
9967 def __ne__(self, *args):
9969 __ne__(Copy self, Copy o) -> bool
9970 __ne__(Copy self, Particle d) -> bool
9972 return _IMP_atom.Copy___ne__(self, *args)
9974 def __le__(self, *args):
9976 __le__(Copy self, Copy o) -> bool
9977 __le__(Copy self, Particle d) -> bool
9979 return _IMP_atom.Copy___le__(self, *args)
9981 def __lt__(self, *args):
9983 __lt__(Copy self, Copy o) -> bool
9984 __lt__(Copy self, Particle d) -> bool
9986 return _IMP_atom.Copy___lt__(self, *args)
9988 def __ge__(self, *args):
9990 __ge__(Copy self, Copy o) -> bool
9991 __ge__(Copy self, Particle d) -> bool
9993 return _IMP_atom.Copy___ge__(self, *args)
9995 def __gt__(self, *args):
9997 __gt__(Copy self, Copy o) -> bool
9998 __gt__(Copy self, Particle d) -> bool
10000 return _IMP_atom.Copy___gt__(self, *args)
10002 def __hash__(self):
10003 r"""__hash__(Copy self) -> std::size_t"""
10004 return _IMP_atom.Copy___hash__(self)
10007 r"""__str__(Copy self) -> std::string"""
10008 return _IMP_atom.Copy___str__(self)
10010 def __repr__(self):
10011 r"""__repr__(Copy self) -> std::string"""
10012 return _IMP_atom.Copy___repr__(self)
10014 def _get_as_binary(self):
10015 r"""_get_as_binary(Copy self) -> PyObject *"""
10016 return _IMP_atom.Copy__get_as_binary(self)
10018 def _set_from_binary(self, p):
10019 r"""_set_from_binary(Copy self, PyObject * p)"""
10020 return _IMP_atom.Copy__set_from_binary(self, p)
10022 def __getstate__(self):
10023 p = self._get_as_binary()
10024 if len(self.__dict__) > 1:
10025 d = self.__dict__.copy()
10030 def __setstate__(self, p):
10031 if not hasattr(self,
'this'):
10033 if isinstance(p, tuple):
10035 self.__dict__.update(d)
10036 return self._set_from_binary(p)
10038 __swig_destroy__ = _IMP_atom.delete_Copy
10041 _IMP_atom.Copy_swigregister(Copy)
10044 r"""get_copy_index(Hierarchy h) -> int"""
10045 return _IMP_atom.get_copy_index(h)
10046 class Chain(Hierarchy):
10047 r"""Proxy of C++ IMP::atom::Chain class."""
10049 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10051 def __init__(self, *args):
10053 __init__(Chain self) -> Chain
10054 __init__(Chain self, Model m, ParticleIndex id) -> Chain
10055 __init__(Chain self, _ParticleAdaptor d) -> Chain
10057 _IMP_atom.Chain_swiginit(self, _IMP_atom.new_Chain(*args))
10059 def show(self, *args):
10060 r"""show(Chain self, _ostream out=std::cout)"""
10061 return _IMP_atom.Chain_show(self, *args)
10064 def setup_particle(*args):
10066 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
10067 setup_particle(_ParticleAdaptor pa, std::string id) -> Chain
10068 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
10069 setup_particle(_ParticleAdaptor pa, char id) -> Chain
10070 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
10071 setup_particle(_ParticleAdaptor pa, Chain other) -> Chain
10073 return _IMP_atom.Chain_setup_particle(*args)
10076 def get_is_setup(*args):
10078 get_is_setup(_ParticleAdaptor p) -> bool
10079 get_is_setup(Model m, ParticleIndex pi) -> bool
10081 return _IMP_atom.Chain_get_is_setup(*args)
10084 r"""get_id(Chain self) -> std::string"""
10085 return _IMP_atom.Chain_get_id(self)
10087 def set_id(self, c):
10088 r"""set_id(Chain self, std::string c)"""
10089 return _IMP_atom.Chain_set_id(self, c)
10091 def get_label_asym_id(self):
10092 r"""get_label_asym_id(Chain self) -> std::string"""
10093 return _IMP_atom.Chain_get_label_asym_id(self)
10095 def set_label_asym_id(self, c):
10096 r"""set_label_asym_id(Chain self, std::string c)"""
10097 return _IMP_atom.Chain_set_label_asym_id(self, c)
10099 def get_sequence(self):
10100 r"""get_sequence(Chain self) -> std::string"""
10101 return _IMP_atom.Chain_get_sequence(self)
10103 def set_sequence(self, sequence):
10104 r"""set_sequence(Chain self, std::string sequence)"""
10105 return _IMP_atom.Chain_set_sequence(self, sequence)
10107 def get_sequence_offset(self):
10108 r"""get_sequence_offset(Chain self) -> int"""
10109 return _IMP_atom.Chain_get_sequence_offset(self)
10111 def set_sequence_offset(self, offset):
10112 r"""set_sequence_offset(Chain self, int offset)"""
10113 return _IMP_atom.Chain_set_sequence_offset(self, offset)
10115 def get_uniprot_accession(self):
10116 r"""get_uniprot_accession(Chain self) -> std::string"""
10117 return _IMP_atom.Chain_get_uniprot_accession(self)
10119 def set_uniprot_accession(self, accession):
10120 r"""set_uniprot_accession(Chain self, std::string accession)"""
10121 return _IMP_atom.Chain_set_uniprot_accession(self, accession)
10123 def get_chain_type(self):
10124 r"""get_chain_type(Chain self) -> ChainType"""
10125 return _IMP_atom.Chain_get_chain_type(self)
10127 def set_chain_type(self, t):
10128 r"""set_chain_type(Chain self, ChainType t)"""
10129 return _IMP_atom.Chain_set_chain_type(self, t)
10133 r"""get_id_key() -> SparseStringKey"""
10134 return _IMP_atom.Chain_get_id_key()
10137 def get_label_asym_id_key():
10138 r"""get_label_asym_id_key() -> SparseStringKey"""
10139 return _IMP_atom.Chain_get_label_asym_id_key()
10142 def get_sequence_key():
10143 r"""get_sequence_key() -> SparseStringKey"""
10144 return _IMP_atom.Chain_get_sequence_key()
10147 def get_sequence_offset_key():
10148 r"""get_sequence_offset_key() -> SparseIntKey"""
10149 return _IMP_atom.Chain_get_sequence_offset_key()
10152 def get_uniprot_accession_key():
10153 r"""get_uniprot_accession_key() -> SparseStringKey"""
10154 return _IMP_atom.Chain_get_uniprot_accession_key()
10157 def get_chain_type_key():
10158 r"""get_chain_type_key() -> SparseIntKey"""
10159 return _IMP_atom.Chain_get_chain_type_key()
10161 def add_attribute(self, *args):
10163 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
10164 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
10165 add_attribute(Chain self, IntKey a0, IMP::Int a1)
10166 add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
10167 add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
10168 add_attribute(Chain self, StringKey a0, IMP::String a1)
10169 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
10170 add_attribute(Chain self, ObjectKey a0, Object a1)
10171 add_attribute(Chain self, SparseFloatKey a0, IMP::Float a1)
10172 add_attribute(Chain self, SparseIntKey a0, IMP::Int a1)
10173 add_attribute(Chain self, SparseStringKey a0, IMP::String a1)
10174 add_attribute(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
10176 return _IMP_atom.Chain_add_attribute(self, *args)
10178 def get_value(self, *args):
10180 get_value(Chain self, FloatKey a0) -> IMP::Float
10181 get_value(Chain self, IntKey a0) -> IMP::Int
10182 get_value(Chain self, FloatsKey a0) -> IMP::Floats
10183 get_value(Chain self, IntsKey a0) -> IMP::Ints
10184 get_value(Chain self, StringKey a0) -> IMP::String
10185 get_value(Chain self, ParticleIndexKey a0) -> Particle
10186 get_value(Chain self, ObjectKey a0) -> Object
10187 get_value(Chain self, SparseFloatKey a0) -> IMP::Float
10188 get_value(Chain self, SparseIntKey a0) -> IMP::Int
10189 get_value(Chain self, SparseStringKey a0) -> IMP::String
10190 get_value(Chain self, SparseParticleIndexKey a0) -> ParticleIndex
10192 return _IMP_atom.Chain_get_value(self, *args)
10194 def set_value(self, *args):
10196 set_value(Chain self, FloatKey a0, IMP::Float a1)
10197 set_value(Chain self, IntKey a0, IMP::Int a1)
10198 set_value(Chain self, FloatsKey a0, IMP::Floats a1)
10199 set_value(Chain self, IntsKey a0, IMP::Ints a1)
10200 set_value(Chain self, StringKey a0, IMP::String a1)
10201 set_value(Chain self, ParticleIndexKey a0, Particle a1)
10202 set_value(Chain self, ObjectKey a0, Object a1)
10203 set_value(Chain self, SparseFloatKey a0, IMP::Float a1)
10204 set_value(Chain self, SparseIntKey a0, IMP::Int a1)
10205 set_value(Chain self, SparseStringKey a0, IMP::String a1)
10206 set_value(Chain self, SparseParticleIndexKey a0, ParticleIndex a1)
10208 return _IMP_atom.Chain_set_value(self, *args)
10210 def remove_attribute(self, *args):
10212 remove_attribute(Chain self, FloatKey a0)
10213 remove_attribute(Chain self, IntKey a0)
10214 remove_attribute(Chain self, FloatsKey a0)
10215 remove_attribute(Chain self, IntsKey a0)
10216 remove_attribute(Chain self, StringKey a0)
10217 remove_attribute(Chain self, ParticleIndexKey a0)
10218 remove_attribute(Chain self, ObjectKey a0)
10219 remove_attribute(Chain self, SparseFloatKey a0)
10220 remove_attribute(Chain self, SparseIntKey a0)
10221 remove_attribute(Chain self, SparseStringKey a0)
10222 remove_attribute(Chain self, SparseParticleIndexKey a0)
10224 return _IMP_atom.Chain_remove_attribute(self, *args)
10226 def has_attribute(self, *args):
10228 has_attribute(Chain self, FloatKey a0) -> bool
10229 has_attribute(Chain self, IntKey a0) -> bool
10230 has_attribute(Chain self, FloatsKey a0) -> bool
10231 has_attribute(Chain self, IntsKey a0) -> bool
10232 has_attribute(Chain self, StringKey a0) -> bool
10233 has_attribute(Chain self, ParticleIndexKey a0) -> bool
10234 has_attribute(Chain self, ObjectKey a0) -> bool
10235 has_attribute(Chain self, SparseFloatKey a0) -> bool
10236 has_attribute(Chain self, SparseIntKey a0) -> bool
10237 has_attribute(Chain self, SparseStringKey a0) -> bool
10238 has_attribute(Chain self, SparseParticleIndexKey a0) -> bool
10240 return _IMP_atom.Chain_has_attribute(self, *args)
10242 def get_derivative(self, a0):
10243 r"""get_derivative(Chain self, FloatKey a0) -> double"""
10244 return _IMP_atom.Chain_get_derivative(self, a0)
10246 def get_name(self):
10247 r"""get_name(Chain self) -> std::string"""
10248 return _IMP_atom.Chain_get_name(self)
10250 def clear_caches(self):
10251 r"""clear_caches(Chain self)"""
10252 return _IMP_atom.Chain_clear_caches(self)
10254 def set_name(self, a0):
10255 r"""set_name(Chain self, std::string a0)"""
10256 return _IMP_atom.Chain_set_name(self, a0)
10259 r"""set_check_level(Chain self, IMP::CheckLevel a0)"""
10260 return _IMP_atom.Chain_set_check_level(self, a0)
10262 def add_to_derivative(self, a0, a1, a2):
10263 r"""add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10264 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
10266 def set_is_optimized(self, a0, a1):
10267 r"""set_is_optimized(Chain self, FloatKey a0, bool a1)"""
10268 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
10270 def get_is_optimized(self, a0):
10271 r"""get_is_optimized(Chain self, FloatKey a0) -> bool"""
10272 return _IMP_atom.Chain_get_is_optimized(self, a0)
10275 r"""get_check_level(Chain self) -> IMP::CheckLevel"""
10276 return _IMP_atom.Chain_get_check_level(self)
10278 def __eq__(self, *args):
10280 __eq__(Chain self, Chain o) -> bool
10281 __eq__(Chain self, Particle d) -> bool
10283 return _IMP_atom.Chain___eq__(self, *args)
10285 def __ne__(self, *args):
10287 __ne__(Chain self, Chain o) -> bool
10288 __ne__(Chain self, Particle d) -> bool
10290 return _IMP_atom.Chain___ne__(self, *args)
10292 def __le__(self, *args):
10294 __le__(Chain self, Chain o) -> bool
10295 __le__(Chain self, Particle d) -> bool
10297 return _IMP_atom.Chain___le__(self, *args)
10299 def __lt__(self, *args):
10301 __lt__(Chain self, Chain o) -> bool
10302 __lt__(Chain self, Particle d) -> bool
10304 return _IMP_atom.Chain___lt__(self, *args)
10306 def __ge__(self, *args):
10308 __ge__(Chain self, Chain o) -> bool
10309 __ge__(Chain self, Particle d) -> bool
10311 return _IMP_atom.Chain___ge__(self, *args)
10313 def __gt__(self, *args):
10315 __gt__(Chain self, Chain o) -> bool
10316 __gt__(Chain self, Particle d) -> bool
10318 return _IMP_atom.Chain___gt__(self, *args)
10320 def __hash__(self):
10321 r"""__hash__(Chain self) -> std::size_t"""
10322 return _IMP_atom.Chain___hash__(self)
10325 r"""__str__(Chain self) -> std::string"""
10326 return _IMP_atom.Chain___str__(self)
10328 def __repr__(self):
10329 r"""__repr__(Chain self) -> std::string"""
10330 return _IMP_atom.Chain___repr__(self)
10332 def _get_as_binary(self):
10333 r"""_get_as_binary(Chain self) -> PyObject *"""
10334 return _IMP_atom.Chain__get_as_binary(self)
10336 def _set_from_binary(self, p):
10337 r"""_set_from_binary(Chain self, PyObject * p)"""
10338 return _IMP_atom.Chain__set_from_binary(self, p)
10340 def __getstate__(self):
10341 p = self._get_as_binary()
10342 if len(self.__dict__) > 1:
10343 d = self.__dict__.copy()
10348 def __setstate__(self, p):
10349 if not hasattr(self,
'this'):
10351 if isinstance(p, tuple):
10353 self.__dict__.update(d)
10354 return self._set_from_binary(p)
10356 __swig_destroy__ = _IMP_atom.delete_Chain
10359 _IMP_atom.Chain_swigregister(Chain)
10360 UnknownChainType = cvar.UnknownChainType
10361 DPolypeptide = cvar.DPolypeptide
10362 LPolypeptide = cvar.LPolypeptide
10363 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
10364 Polyribonucleotide = cvar.Polyribonucleotide
10365 DPolysaccharide = cvar.DPolysaccharide
10366 LPolysaccharide = cvar.LPolysaccharide
10367 Protein = cvar.Protein
10373 r"""get_chain(Hierarchy h) -> Chain"""
10374 return _IMP_atom.get_chain(h)
10377 r"""get_chain_id(Hierarchy h) -> std::string"""
10378 return _IMP_atom.get_chain_id(h)
10379 class Selection(IMP._ParticleIndexesAdaptor):
10380 r"""Proxy of C++ IMP::atom::Selection class."""
10382 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10383 NONE = _IMP_atom.Selection_NONE
10385 C = _IMP_atom.Selection_C
10387 N = _IMP_atom.Selection_N
10390 def __init__(self, *args):
10392 __init__(Selection self) -> Selection
10393 __init__(Selection self, Hierarchy h) -> Selection
10394 __init__(Selection self, Particle h) -> Selection
10395 __init__(Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10396 __init__(Selection self, IMP::ParticlesTemp const & h) -> Selection
10398 _IMP_atom.Selection_swiginit(self, _IMP_atom.new_Selection(*args))
10401 r"""create_clone(Selection self) -> Selection"""
10402 return _IMP_atom.Selection_create_clone(self)
10404 def get_hierarchies(self):
10405 r"""get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10406 return _IMP_atom.Selection_get_hierarchies(self)
10408 def set_molecules(self, mols):
10409 r"""set_molecules(Selection self, IMP::Strings mols)"""
10410 return _IMP_atom.Selection_set_molecules(self, mols)
10412 def set_resolution(self, r):
10413 r"""set_resolution(Selection self, double r)"""
10414 return _IMP_atom.Selection_set_resolution(self, r)
10416 def set_representation_type(self, t):
10417 r"""set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10418 return _IMP_atom.Selection_set_representation_type(self, t)
10420 def set_state_index(self, state):
10421 r"""set_state_index(Selection self, int state)"""
10422 return _IMP_atom.Selection_set_state_index(self, state)
10424 def set_state_indexes(self, states):
10425 r"""set_state_indexes(Selection self, IMP::Ints states)"""
10426 return _IMP_atom.Selection_set_state_indexes(self, states)
10428 def set_terminus(self, t):
10429 r"""set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10430 return _IMP_atom.Selection_set_terminus(self, t)
10432 def set_element(self, e):
10433 r"""set_element(Selection self, IMP::atom::Element e)"""
10434 return _IMP_atom.Selection_set_element(self, e)
10436 def set_chain_ids(self, chains):
10437 r"""set_chain_ids(Selection self, IMP::Strings chains)"""
10438 return _IMP_atom.Selection_set_chain_ids(self, chains)
10440 def set_chains(self, chains):
10441 r"""set_chains(Selection self, IMP::Strings chains)"""
10442 return _IMP_atom.Selection_set_chains(self, chains)
10444 def set_residue_indexes(self, indexes):
10445 r"""set_residue_indexes(Selection self, IMP::Ints indexes)"""
10446 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10448 def set_atom_types(self, types):
10449 r"""set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10450 return _IMP_atom.Selection_set_atom_types(self, types)
10452 def set_residue_types(self, types):
10453 r"""set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10454 return _IMP_atom.Selection_set_residue_types(self, types)
10456 def set_domains(self, names):
10457 r"""set_domains(Selection self, IMP::Strings names)"""
10458 return _IMP_atom.Selection_set_domains(self, names)
10460 def set_molecule(self, mol):
10461 r"""set_molecule(Selection self, std::string mol)"""
10462 return _IMP_atom.Selection_set_molecule(self, mol)
10464 def set_chain_id(self, c):
10465 r"""set_chain_id(Selection self, std::string c)"""
10466 return _IMP_atom.Selection_set_chain_id(self, c)
10468 def set_chain(self, c):
10469 r"""set_chain(Selection self, std::string c)"""
10470 return _IMP_atom.Selection_set_chain(self, c)
10472 def set_residue_index(self, i):
10473 r"""set_residue_index(Selection self, int i)"""
10474 return _IMP_atom.Selection_set_residue_index(self, i)
10476 def set_atom_type(self, types):
10477 r"""set_atom_type(Selection self, AtomType types)"""
10478 return _IMP_atom.Selection_set_atom_type(self, types)
10480 def set_residue_type(self, type):
10481 r"""set_residue_type(Selection self, ResidueType type)"""
10482 return _IMP_atom.Selection_set_residue_type(self, type)
10484 def set_domain(self, name):
10485 r"""set_domain(Selection self, std::string name)"""
10486 return _IMP_atom.Selection_set_domain(self, name)
10488 def set_copy_index(self, copy):
10489 r"""set_copy_index(Selection self, unsigned int copy)"""
10490 return _IMP_atom.Selection_set_copy_index(self, copy)
10492 def set_copy_indexes(self, copies):
10493 r"""set_copy_indexes(Selection self, IMP::Ints copies)"""
10494 return _IMP_atom.Selection_set_copy_indexes(self, copies)
10496 def set_particle_type(self, t):
10497 r"""set_particle_type(Selection self, ParticleType t)"""
10498 return _IMP_atom.Selection_set_particle_type(self, t)
10500 def set_particle_types(self, t):
10501 r"""set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10502 return _IMP_atom.Selection_set_particle_types(self, t)
10504 def set_hierarchy_types(self, types):
10505 r"""set_hierarchy_types(Selection self, IMP::Ints types)"""
10506 return _IMP_atom.Selection_set_hierarchy_types(self, types)
10508 def set_intersection(self, s):
10509 r"""set_intersection(Selection self, Selection s)"""
10510 return _IMP_atom.Selection_set_intersection(self, s)
10512 def set_union(self, s):
10513 r"""set_union(Selection self, Selection s)"""
10514 return _IMP_atom.Selection_set_union(self, s)
10516 def set_symmetric_difference(self, s):
10517 r"""set_symmetric_difference(Selection self, Selection s)"""
10518 return _IMP_atom.Selection_set_symmetric_difference(self, s)
10520 def set_difference(self, s):
10521 r"""set_difference(Selection self, Selection s)"""
10522 return _IMP_atom.Selection_set_difference(self, s)
10524 def get_selected_particles(self, with_representation=True):
10525 r"""get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp"""
10526 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10528 def get_selected_particle_indexes(self, with_representation=True):
10529 r"""get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes"""
10530 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10532 def show(self, *args):
10533 r"""show(Selection self, _ostream out=std::cout)"""
10534 return _IMP_atom.Selection_show(self, *args)
10537 r"""__str__(Selection self) -> std::string"""
10538 return _IMP_atom.Selection___str__(self)
10540 def __repr__(self):
10541 r"""__repr__(Selection self) -> std::string"""
10542 return _IMP_atom.Selection___repr__(self)
10544 def __init__(self, hierarchy=None,
10545 hierarchies=
None, **params):
10546 if hierarchy
and hierarchies:
10547 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
10549 this = _IMP_atom.new_Selection(hierarchy)
10550 try: self.this.append(this)
10551 except: self.this = this
10553 this = _IMP_atom.new_Selection(hierarchies)
10554 try: self.this.append(this)
10555 except: self.this = this
10557 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
10558 for k
in params.keys():
10559 eval(
"self.set_%s(params[k])"%k)
10561 def union(self, s):
10562 news = self.create_clone()
10563 news.union_update(s)
10565 def intersection(self, s):
10566 news = self.create_clone()
10567 news.intersection_update(s)
10569 def symmetric_difference(self, s):
10570 news = self.create_clone()
10571 news.symmetric_difference_update(s)
10573 def difference(self, s):
10574 news = self.create_clone()
10575 news.difference_update(s)
10577 def union_update(self, s):
10580 def intersection_update(self, s):
10581 self.set_intersection(s)
10583 def symmetric_difference_update(self, s):
10584 self.set_symmetric_difference(s)
10586 def difference_update(self, s):
10587 self.set_difference(s)
10590 __and__ = intersection
10591 __xor__ = symmetric_difference
10592 __sub__ = difference
10593 __ior__ = union_update
10594 __iand__ = intersection_update
10595 __ixor__ = symmetric_difference_update
10596 __isub__ = difference_update
10598 __swig_destroy__ = _IMP_atom.delete_Selection
10601 _IMP_atom.Selection_swigregister(Selection)
10604 r"""create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint"""
10605 return _IMP_atom.create_distance_restraint(*args)
10609 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
10610 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10612 return _IMP_atom.create_connectivity_restraint(*args)
10616 create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
10617 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
10619 return _IMP_atom.create_internal_connectivity_restraint(*args)
10622 r"""create_cover(Selection s, std::string name=std::string()) -> XYZR"""
10623 return _IMP_atom.create_cover(*args)
10627 get_mass(ResidueType c) -> double
10628 get_mass(Selection s) -> double
10630 return _IMP_atom.get_mass(*args)
10633 r"""get_volume(Selection s) -> double"""
10634 return _IMP_atom.get_volume(s)
10637 r"""get_surface_area(Selection s) -> double"""
10638 return _IMP_atom.get_surface_area(s)
10642 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10643 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10644 get_leaves(Selection h) -> IMP::atom::Hierarchies
10646 return _IMP_atom.get_leaves(*args)
10648 r"""Proxy of C++ IMP::atom::SelectionGeometry class."""
10650 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10652 def __init__(self, *args):
10653 r"""__init__(SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry"""
10654 _IMP_atom.SelectionGeometry_swiginit(self, _IMP_atom.new_SelectionGeometry(*args))
10656 def get_version_info(self):
10657 r"""get_version_info(SelectionGeometry self) -> VersionInfo"""
10658 return _IMP_atom.SelectionGeometry_get_version_info(self)
10659 __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
10662 r"""__str__(SelectionGeometry self) -> std::string"""
10663 return _IMP_atom.SelectionGeometry___str__(self)
10665 def __repr__(self):
10666 r"""__repr__(SelectionGeometry self) -> std::string"""
10667 return _IMP_atom.SelectionGeometry___repr__(self)
10671 return _object_cast_to_SelectionGeometry(o)
10675 _IMP_atom.SelectionGeometry_swigregister(SelectionGeometry)
10679 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10680 get_rmsd(Selection s0, Selection s1) -> double
10682 return _IMP_atom.get_rmsd(*args)
10686 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10687 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10689 return _IMP_atom.get_rmsd_transforming_first(*args)
10692 r"""get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10693 return _IMP_atom.get_placement_score(source, target)
10696 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"""
10697 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10700 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"""
10701 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10705 get_radius_of_gyration(Selection s) -> double
10706 get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10708 return _IMP_atom.get_radius_of_gyration(*args)
10710 r"""Proxy of C++ IMP::atom::ForceFieldParameters class."""
10712 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10714 def __init__(self):
10715 r"""__init__(ForceFieldParameters self) -> ForceFieldParameters"""
10716 _IMP_atom.ForceFieldParameters_swiginit(self, _IMP_atom.new_ForceFieldParameters())
10718 def get_radius(self, atom):
10719 r"""get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10720 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10722 def get_epsilon(self, atom):
10723 r"""get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10724 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10727 r"""add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=IMP::FloatKey("radius"))"""
10728 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10730 def add_well_depths(self, mhd):
10731 r"""add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10732 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10734 def add_lennard_jones_types(self, mhd):
10735 r"""add_lennard_jones_types(ForceFieldParameters self, Hierarchy mhd)"""
10736 return _IMP_atom.ForceFieldParameters_add_lennard_jones_types(self, mhd)
10739 r"""add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10740 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10741 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10744 r"""__str__(ForceFieldParameters self) -> std::string"""
10745 return _IMP_atom.ForceFieldParameters___str__(self)
10747 def __repr__(self):
10748 r"""__repr__(ForceFieldParameters self) -> std::string"""
10749 return _IMP_atom.ForceFieldParameters___repr__(self)
10753 return _object_cast_to_ForceFieldParameters(o)
10757 _IMP_atom.ForceFieldParameters_swigregister(ForceFieldParameters)
10758 class CHARMMAtomTopology(object):
10759 r"""Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10761 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10763 def __init__(self, *args):
10765 __init__(CHARMMAtomTopology self) -> CHARMMAtomTopology
10766 __init__(CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10767 __init__(CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10769 _IMP_atom.CHARMMAtomTopology_swiginit(self, _IMP_atom.new_CHARMMAtomTopology(*args))
10771 def get_name(self):
10772 r"""get_name(CHARMMAtomTopology self) -> std::string"""
10773 return _IMP_atom.CHARMMAtomTopology_get_name(self)
10775 def get_charmm_type(self):
10776 r"""get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10777 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10779 def get_charge(self):
10780 r"""get_charge(CHARMMAtomTopology self) -> double"""
10781 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10783 def set_charmm_type(self, charmm_type):
10784 r"""set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10785 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10787 def set_charge(self, charge):
10788 r"""set_charge(CHARMMAtomTopology self, double charge)"""
10789 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10791 def show(self, *args):
10792 r"""show(CHARMMAtomTopology self, _ostream out=std::cout)"""
10793 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10796 r"""__str__(CHARMMAtomTopology self) -> std::string"""
10797 return _IMP_atom.CHARMMAtomTopology___str__(self)
10799 def __repr__(self):
10800 r"""__repr__(CHARMMAtomTopology self) -> std::string"""
10801 return _IMP_atom.CHARMMAtomTopology___repr__(self)
10803 def _get_as_binary(self):
10804 r"""_get_as_binary(CHARMMAtomTopology self) -> PyObject *"""
10805 return _IMP_atom.CHARMMAtomTopology__get_as_binary(self)
10807 def _set_from_binary(self, p):
10808 r"""_set_from_binary(CHARMMAtomTopology self, PyObject * p)"""
10809 return _IMP_atom.CHARMMAtomTopology__set_from_binary(self, p)
10811 def __getstate__(self):
10812 p = self._get_as_binary()
10813 if len(self.__dict__) > 1:
10814 d = self.__dict__.copy()
10819 def __setstate__(self, p):
10820 if not hasattr(self,
'this'):
10822 if isinstance(p, tuple):
10824 self.__dict__.update(d)
10825 return self._set_from_binary(p)
10827 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10830 _IMP_atom.CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10831 class CHARMMBondEndpoint(object):
10832 r"""Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10834 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10836 def __init__(self, atom_name, residue=None):
10837 r"""__init__(CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint"""
10838 _IMP_atom.CHARMMBondEndpoint_swiginit(self, _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue))
10840 def get_atom_name(self):
10841 r"""get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10842 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10844 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10845 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"""
10846 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10848 def show(self, *args):
10849 r"""show(CHARMMBondEndpoint self, _ostream out=std::cout)"""
10850 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10853 r"""__str__(CHARMMBondEndpoint self) -> std::string"""
10854 return _IMP_atom.CHARMMBondEndpoint___str__(self)
10856 def __repr__(self):
10857 r"""__repr__(CHARMMBondEndpoint self) -> std::string"""
10858 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10859 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10862 _IMP_atom.CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10863 class CHARMMDihedral(object):
10864 r"""Proxy of C++ IMP::atom::CHARMMConnection< 4 > class."""
10866 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10867 __repr__ = _swig_repr
10869 def __init__(self, atoms):
10870 r"""__init__(CHARMMDihedral self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10871 _IMP_atom.CHARMMDihedral_swiginit(self, _IMP_atom.new_CHARMMDihedral(atoms))
10873 def get_endpoint(self, i):
10874 r"""get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10875 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10877 def get_contains_atom(self, name):
10878 r"""get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10879 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10881 def show(self, *args):
10882 r"""show(CHARMMDihedral self, _ostream out=std::cout)"""
10883 return _IMP_atom.CHARMMDihedral_show(self, *args)
10884 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10887 _IMP_atom.CHARMMDihedral_swigregister(CHARMMDihedral)
10888 class CHARMMInternalCoordinate(CHARMMDihedral):
10889 r"""Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10891 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10893 def __init__(self, *args):
10895 __init__(CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10896 __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
10898 _IMP_atom.CHARMMInternalCoordinate_swiginit(self, _IMP_atom.new_CHARMMInternalCoordinate(*args))
10900 def get_first_distance(self):
10901 r"""get_first_distance(CHARMMInternalCoordinate self) -> float"""
10902 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10904 def get_second_distance(self):
10905 r"""get_second_distance(CHARMMInternalCoordinate self) -> float"""
10906 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10908 def get_first_angle(self):
10909 r"""get_first_angle(CHARMMInternalCoordinate self) -> float"""
10910 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10912 def get_second_angle(self):
10913 r"""get_second_angle(CHARMMInternalCoordinate self) -> float"""
10914 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10917 r"""get_dihedral(CHARMMInternalCoordinate self) -> float"""
10918 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10920 def get_improper(self):
10921 r"""get_improper(CHARMMInternalCoordinate self) -> bool"""
10922 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10924 def show(self, *args):
10925 r"""show(CHARMMInternalCoordinate self, _ostream out=std::cout)"""
10926 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10929 r"""__str__(CHARMMInternalCoordinate self) -> std::string"""
10930 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10932 def __repr__(self):
10933 r"""__repr__(CHARMMInternalCoordinate self) -> std::string"""
10934 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10935 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10938 _IMP_atom.CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10939 class CHARMMResidueTopologyBase(
IMP.Object):
10940 r"""Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10942 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10944 def __init__(self, *args, **kwargs):
10945 raise AttributeError(
"No constructor defined")
10947 def get_type(self):
10948 r"""get_type(CHARMMResidueTopologyBase self) -> std::string"""
10949 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10951 def get_number_of_atoms(self):
10952 r"""get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10953 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10955 def add_atom(self, atom):
10956 r"""add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10957 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10961 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10962 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10963 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10965 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10967 def get_number_of_bonds(self):
10968 r"""get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10969 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10971 def add_bond(self, bond):
10972 r"""add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
10973 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10975 def get_number_of_angles(self):
10976 r"""get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10977 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10979 def add_angle(self, bond):
10980 r"""add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
10981 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10983 def get_number_of_dihedrals(self):
10984 r"""get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10985 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10987 def add_dihedral(self, bond):
10988 r"""add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10989 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10991 def get_number_of_impropers(self):
10992 r"""get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10993 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10995 def add_improper(self, bond):
10996 r"""add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10997 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10999 def get_number_of_internal_coordinates(self):
11000 r"""get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11001 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11003 def add_internal_coordinate(self, ic):
11004 r"""add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11005 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11007 def get_internal_coordinate(self, index):
11008 r"""get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11009 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11012 r"""get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
11013 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11016 r"""get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
11017 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11020 r"""get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11021 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11023 def get_improper(self, index):
11024 r"""get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11025 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11027 def get_version_info(self):
11028 r"""get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11029 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11030 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
11033 r"""__str__(CHARMMResidueTopologyBase self) -> std::string"""
11034 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11036 def __repr__(self):
11037 r"""__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11038 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11042 return _object_cast_to_CHARMMResidueTopologyBase(o)
11046 _IMP_atom.CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11047 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11048 r"""Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
11050 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11052 def __init__(self, *args):
11054 __init__(CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11055 __init__(CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11057 _IMP_atom.CHARMMIdealResidueTopology_swiginit(self, _IMP_atom.new_CHARMMIdealResidueTopology(*args))
11059 def remove_atom(self, name):
11060 r"""remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11061 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11063 def set_default_first_patch(self, patch):
11064 r"""set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11065 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11067 def set_default_last_patch(self, patch):
11068 r"""set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11069 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11071 def get_default_first_patch(self):
11072 r"""get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11073 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11075 def get_default_last_patch(self):
11076 r"""get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11077 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11078 __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
11081 r"""__str__(CHARMMIdealResidueTopology self) -> std::string"""
11082 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11084 def __repr__(self):
11085 r"""__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11086 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11090 return _object_cast_to_CHARMMIdealResidueTopology(o)
11094 _IMP_atom.CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11095 class CHARMMPatch(CHARMMResidueTopologyBase):
11096 r"""Proxy of C++ IMP::atom::CHARMMPatch class."""
11098 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11100 def __init__(self, type):
11101 r"""__init__(CHARMMPatch self, std::string type) -> CHARMMPatch"""
11102 _IMP_atom.CHARMMPatch_swiginit(self, _IMP_atom.new_CHARMMPatch(type))
11104 def add_removed_atom(self, name):
11105 r"""add_removed_atom(CHARMMPatch self, std::string name)"""
11106 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11108 def get_number_of_removed_atoms(self):
11109 r"""get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11110 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11112 def get_removed_atom(self, i):
11113 r"""get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11114 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11116 def apply(self, *args):
11118 apply(CHARMMPatch self, CHARMMResidueTopology res)
11119 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11121 return _IMP_atom.CHARMMPatch_apply(self, *args)
11122 __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
11125 r"""__str__(CHARMMPatch self) -> std::string"""
11126 return _IMP_atom.CHARMMPatch___str__(self)
11128 def __repr__(self):
11129 r"""__repr__(CHARMMPatch self) -> std::string"""
11130 return _IMP_atom.CHARMMPatch___repr__(self)
11134 return _object_cast_to_CHARMMPatch(o)
11138 _IMP_atom.CHARMMPatch_swigregister(CHARMMPatch)
11139 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11140 r"""Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
11142 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11144 def __init__(self, *args):
11146 __init__(CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11147 __init__(CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11149 _IMP_atom.CHARMMResidueTopology_swiginit(self, _IMP_atom.new_CHARMMResidueTopology(*args))
11151 def get_patched(self):
11152 r"""get_patched(CHARMMResidueTopology self) -> bool"""
11153 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11155 def set_patched(self, patched):
11156 r"""set_patched(CHARMMResidueTopology self, bool patched)"""
11157 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11158 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
11161 r"""__str__(CHARMMResidueTopology self) -> std::string"""
11162 return _IMP_atom.CHARMMResidueTopology___str__(self)
11164 def __repr__(self):
11165 r"""__repr__(CHARMMResidueTopology self) -> std::string"""
11166 return _IMP_atom.CHARMMResidueTopology___repr__(self)
11170 return _object_cast_to_CHARMMResidueTopology(o)
11174 _IMP_atom.CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11175 class CHARMMAtom(Atom):
11176 r"""Proxy of C++ IMP::atom::CHARMMAtom class."""
11178 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11180 def __init__(self, *args):
11182 __init__(CHARMMAtom self) -> CHARMMAtom
11183 __init__(CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11184 __init__(CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11186 _IMP_atom.CHARMMAtom_swiginit(self, _IMP_atom.new_CHARMMAtom(*args))
11188 def show(self, *args):
11189 r"""show(CHARMMAtom self, _ostream out=std::cout)"""
11190 return _IMP_atom.CHARMMAtom_show(self, *args)
11193 def setup_particle(*args):
11195 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11196 setup_particle(_ParticleAdaptor pa, IMP::String charmm_type) -> CHARMMAtom
11198 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11200 def get_charmm_type(self):
11201 r"""get_charmm_type(CHARMMAtom self) -> IMP::String"""
11202 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11204 def set_charmm_type(self, t):
11205 r"""set_charmm_type(CHARMMAtom self, IMP::String t)"""
11206 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11209 def get_is_setup(*args):
11211 get_is_setup(_ParticleAdaptor p) -> bool
11212 get_is_setup(Model m, ParticleIndex pi) -> bool
11214 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11217 def get_charmm_type_key():
11218 r"""get_charmm_type_key() -> StringKey"""
11219 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11221 def add_attribute(self, *args):
11223 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11224 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11225 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11226 add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11227 add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11228 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11229 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11230 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11231 add_attribute(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
11232 add_attribute(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
11233 add_attribute(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
11234 add_attribute(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
11236 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11238 def get_value(self, *args):
11240 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11241 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11242 get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
11243 get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
11244 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11245 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11246 get_value(CHARMMAtom self, ObjectKey a0) -> Object
11247 get_value(CHARMMAtom self, SparseFloatKey a0) -> IMP::Float
11248 get_value(CHARMMAtom self, SparseIntKey a0) -> IMP::Int
11249 get_value(CHARMMAtom self, SparseStringKey a0) -> IMP::String
11250 get_value(CHARMMAtom self, SparseParticleIndexKey a0) -> ParticleIndex
11252 return _IMP_atom.CHARMMAtom_get_value(self, *args)
11254 def set_value(self, *args):
11256 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11257 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11258 set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11259 set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11260 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11261 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11262 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11263 set_value(CHARMMAtom self, SparseFloatKey a0, IMP::Float a1)
11264 set_value(CHARMMAtom self, SparseIntKey a0, IMP::Int a1)
11265 set_value(CHARMMAtom self, SparseStringKey a0, IMP::String a1)
11266 set_value(CHARMMAtom self, SparseParticleIndexKey a0, ParticleIndex a1)
11268 return _IMP_atom.CHARMMAtom_set_value(self, *args)
11270 def remove_attribute(self, *args):
11272 remove_attribute(CHARMMAtom self, FloatKey a0)
11273 remove_attribute(CHARMMAtom self, IntKey a0)
11274 remove_attribute(CHARMMAtom self, FloatsKey a0)
11275 remove_attribute(CHARMMAtom self, IntsKey a0)
11276 remove_attribute(CHARMMAtom self, StringKey a0)
11277 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11278 remove_attribute(CHARMMAtom self, ObjectKey a0)
11279 remove_attribute(CHARMMAtom self, SparseFloatKey a0)
11280 remove_attribute(CHARMMAtom self, SparseIntKey a0)
11281 remove_attribute(CHARMMAtom self, SparseStringKey a0)
11282 remove_attribute(CHARMMAtom self, SparseParticleIndexKey a0)
11284 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11286 def has_attribute(self, *args):
11288 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11289 has_attribute(CHARMMAtom self, IntKey a0) -> bool
11290 has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
11291 has_attribute(CHARMMAtom self, IntsKey a0) -> bool
11292 has_attribute(CHARMMAtom self, StringKey a0) -> bool
11293 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11294 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11295 has_attribute(CHARMMAtom self, SparseFloatKey a0) -> bool
11296 has_attribute(CHARMMAtom self, SparseIntKey a0) -> bool
11297 has_attribute(CHARMMAtom self, SparseStringKey a0) -> bool
11298 has_attribute(CHARMMAtom self, SparseParticleIndexKey a0) -> bool
11300 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11302 def get_derivative(self, a0):
11303 r"""get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11304 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11306 def get_name(self):
11307 r"""get_name(CHARMMAtom self) -> std::string"""
11308 return _IMP_atom.CHARMMAtom_get_name(self)
11310 def clear_caches(self):
11311 r"""clear_caches(CHARMMAtom self)"""
11312 return _IMP_atom.CHARMMAtom_clear_caches(self)
11314 def set_name(self, a0):
11315 r"""set_name(CHARMMAtom self, std::string a0)"""
11316 return _IMP_atom.CHARMMAtom_set_name(self, a0)
11319 r"""set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11320 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11322 def add_to_derivative(self, a0, a1, a2):
11323 r"""add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11324 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11326 def set_is_optimized(self, a0, a1):
11327 r"""set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11328 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11330 def get_is_optimized(self, a0):
11331 r"""get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11332 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11335 r"""get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11336 return _IMP_atom.CHARMMAtom_get_check_level(self)
11338 def __eq__(self, *args):
11340 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11341 __eq__(CHARMMAtom self, Particle d) -> bool
11343 return _IMP_atom.CHARMMAtom___eq__(self, *args)
11345 def __ne__(self, *args):
11347 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11348 __ne__(CHARMMAtom self, Particle d) -> bool
11350 return _IMP_atom.CHARMMAtom___ne__(self, *args)
11352 def __le__(self, *args):
11354 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11355 __le__(CHARMMAtom self, Particle d) -> bool
11357 return _IMP_atom.CHARMMAtom___le__(self, *args)
11359 def __lt__(self, *args):
11361 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11362 __lt__(CHARMMAtom self, Particle d) -> bool
11364 return _IMP_atom.CHARMMAtom___lt__(self, *args)
11366 def __ge__(self, *args):
11368 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11369 __ge__(CHARMMAtom self, Particle d) -> bool
11371 return _IMP_atom.CHARMMAtom___ge__(self, *args)
11373 def __gt__(self, *args):
11375 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11376 __gt__(CHARMMAtom self, Particle d) -> bool
11378 return _IMP_atom.CHARMMAtom___gt__(self, *args)
11380 def __hash__(self):
11381 r"""__hash__(CHARMMAtom self) -> std::size_t"""
11382 return _IMP_atom.CHARMMAtom___hash__(self)
11385 r"""__str__(CHARMMAtom self) -> std::string"""
11386 return _IMP_atom.CHARMMAtom___str__(self)
11388 def __repr__(self):
11389 r"""__repr__(CHARMMAtom self) -> std::string"""
11390 return _IMP_atom.CHARMMAtom___repr__(self)
11392 def _get_as_binary(self):
11393 r"""_get_as_binary(CHARMMAtom self) -> PyObject *"""
11394 return _IMP_atom.CHARMMAtom__get_as_binary(self)
11396 def _set_from_binary(self, p):
11397 r"""_set_from_binary(CHARMMAtom self, PyObject * p)"""
11398 return _IMP_atom.CHARMMAtom__set_from_binary(self, p)
11400 def __getstate__(self):
11401 p = self._get_as_binary()
11402 if len(self.__dict__) > 1:
11403 d = self.__dict__.copy()
11408 def __setstate__(self, p):
11409 if not hasattr(self,
'this'):
11411 if isinstance(p, tuple):
11413 self.__dict__.update(d)
11414 return self._set_from_binary(p)
11416 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11419 _IMP_atom.CHARMMAtom_swigregister(CHARMMAtom)
11422 r"""get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11423 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11426 r"""remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11427 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11428 class CHARMMBondParameters(object):
11429 r"""Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11431 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11432 force_constant = property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set, doc=
r"""force_constant : double""")
11433 ideal = property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set, doc=
r"""ideal : double""")
11435 def __init__(self):
11436 r"""__init__(CHARMMBondParameters self) -> CHARMMBondParameters"""
11437 _IMP_atom.CHARMMBondParameters_swiginit(self, _IMP_atom.new_CHARMMBondParameters())
11439 def show(self, *args):
11440 r"""show(CHARMMBondParameters self, _ostream out=std::cout)"""
11441 return _IMP_atom.CHARMMBondParameters_show(self, *args)
11444 r"""__str__(CHARMMBondParameters self) -> std::string"""
11445 return _IMP_atom.CHARMMBondParameters___str__(self)
11447 def __repr__(self):
11448 r"""__repr__(CHARMMBondParameters self) -> std::string"""
11449 return _IMP_atom.CHARMMBondParameters___repr__(self)
11451 def _get_as_binary(self):
11452 r"""_get_as_binary(CHARMMBondParameters self) -> PyObject *"""
11453 return _IMP_atom.CHARMMBondParameters__get_as_binary(self)
11455 def _set_from_binary(self, p):
11456 r"""_set_from_binary(CHARMMBondParameters self, PyObject * p)"""
11457 return _IMP_atom.CHARMMBondParameters__set_from_binary(self, p)
11459 def __getstate__(self):
11460 p = self._get_as_binary()
11461 if len(self.__dict__) > 1:
11462 d = self.__dict__.copy()
11467 def __setstate__(self, p):
11468 if not hasattr(self,
'this'):
11470 if isinstance(p, tuple):
11472 self.__dict__.update(d)
11473 return self._set_from_binary(p)
11475 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11478 _IMP_atom.CHARMMBondParameters_swigregister(CHARMMBondParameters)
11479 class CHARMMDihedralParameters(object):
11480 r"""Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11482 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11483 force_constant = property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set, doc=
r"""force_constant : double""")
11484 multiplicity = property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set, doc=
r"""multiplicity : int""")
11485 ideal = property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set, doc=
r"""ideal : double""")
11487 def __init__(self):
11488 r"""__init__(CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11489 _IMP_atom.CHARMMDihedralParameters_swiginit(self, _IMP_atom.new_CHARMMDihedralParameters())
11491 def show(self, *args):
11492 r"""show(CHARMMDihedralParameters self, _ostream out=std::cout)"""
11493 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11496 r"""__str__(CHARMMDihedralParameters self) -> std::string"""
11497 return _IMP_atom.CHARMMDihedralParameters___str__(self)
11499 def __repr__(self):
11500 r"""__repr__(CHARMMDihedralParameters self) -> std::string"""
11501 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11503 def _get_as_binary(self):
11504 r"""_get_as_binary(CHARMMDihedralParameters self) -> PyObject *"""
11505 return _IMP_atom.CHARMMDihedralParameters__get_as_binary(self)
11507 def _set_from_binary(self, p):
11508 r"""_set_from_binary(CHARMMDihedralParameters self, PyObject * p)"""
11509 return _IMP_atom.CHARMMDihedralParameters__set_from_binary(self, p)
11511 def __getstate__(self):
11512 p = self._get_as_binary()
11513 if len(self.__dict__) > 1:
11514 d = self.__dict__.copy()
11519 def __setstate__(self, p):
11520 if not hasattr(self,
'this'):
11522 if isinstance(p, tuple):
11524 self.__dict__.update(d)
11525 return self._set_from_binary(p)
11527 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11530 _IMP_atom.CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11531 class CHARMMParameters(ForceFieldParameters):
11532 r"""Proxy of C++ IMP::atom::CHARMMParameters class."""
11534 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11536 def __init__(self, *args):
11537 r"""__init__(CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters"""
11538 _IMP_atom.CHARMMParameters_swiginit(self, _IMP_atom.new_CHARMMParameters(*args))
11540 def add_residue_topology(self, res):
11541 r"""add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11542 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11544 def get_residue_topology(self, type):
11545 r"""get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11546 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11548 def add_patch(self, patch):
11549 r"""add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11550 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11552 def get_patch(self, name):
11553 r"""get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11554 return _IMP_atom.CHARMMParameters_get_patch(self, name)
11556 def create_topology(self, hierarchy):
11557 r"""create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11558 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11560 def get_bond_parameters(self, type1, type2):
11561 r"""get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11562 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11564 def get_angle_parameters(self, type1, type2, type3):
11565 r"""get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11566 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11568 def get_dihedral_parameters(self, type1, type2, type3, type4):
11569 r"""get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11570 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11572 def get_improper_parameters(self, type1, type2, type3, type4):
11573 r"""get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11574 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11576 def create_angles(self, bonds):
11577 r"""create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11578 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11580 def create_dihedrals(self, bonds):
11581 r"""create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11582 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11584 def get_version_info(self):
11585 r"""get_version_info(CHARMMParameters self) -> VersionInfo"""
11586 return _IMP_atom.CHARMMParameters_get_version_info(self)
11587 __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
11590 r"""__str__(CHARMMParameters self) -> std::string"""
11591 return _IMP_atom.CHARMMParameters___str__(self)
11593 def __repr__(self):
11594 r"""__repr__(CHARMMParameters self) -> std::string"""
11595 return _IMP_atom.CHARMMParameters___repr__(self)
11599 return _object_cast_to_CHARMMParameters(o)
11603 _IMP_atom.CHARMMParameters_swigregister(CHARMMParameters)
11606 r"""get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11607 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11610 r"""get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11611 return _IMP_atom.get_all_atom_CHARMM_parameters()
11613 r"""Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11615 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11616 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)
11617 def __set_residues(self, obj): IMP._list_util.set_varlist(self.residues, obj)
11618 def __del_residues(self): IMP._list_util.del_varlist(self.residues)
11619 residues = property(__get_residues, __set_residues, __del_residues, doc=
"List of ##ucnames")
11621 def remove_residue(self, d):
11622 r"""remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11623 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11625 def _python_index_residue(self, d, start, stop):
11626 r"""_python_index_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11627 return _IMP_atom.CHARMMSegmentTopology__python_index_residue(self, d, start, stop)
11629 def remove_residues(self, d):
11630 r"""remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11631 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11633 def set_residues(self, ps):
11634 r"""set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11635 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11637 def set_residues_order(self, objs):
11638 r"""set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11639 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11641 def add_residue(self, obj):
11642 r"""add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11643 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11645 def add_residues(self, objs):
11646 r"""add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11647 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11649 def clear_residues(self):
11650 r"""clear_residues(CHARMMSegmentTopology self)"""
11651 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11653 def get_number_of_residues(self):
11654 r"""get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11655 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11657 def get_has_residues(self):
11658 r"""get_has_residues(CHARMMSegmentTopology self) -> bool"""
11659 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11662 r"""get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11663 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11665 def get_residues(self):
11666 r"""get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11667 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11669 def erase_residue(self, i):
11670 r"""erase_residue(CHARMMSegmentTopology self, unsigned int i)"""
11671 return _IMP_atom.CHARMMSegmentTopology_erase_residue(self, i)
11673 def reserve_residues(self, sz):
11674 r"""reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11675 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11677 def get_version_info(self):
11678 r"""get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11679 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11680 __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
11682 def __init__(self, *args):
11683 r"""__init__(CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology"""
11684 _IMP_atom.CHARMMSegmentTopology_swiginit(self, _IMP_atom.new_CHARMMSegmentTopology(*args))
11686 def apply_default_patches(self, ff):
11687 r"""apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11688 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11691 r"""__str__(CHARMMSegmentTopology self) -> std::string"""
11692 return _IMP_atom.CHARMMSegmentTopology___str__(self)
11694 def __repr__(self):
11695 r"""__repr__(CHARMMSegmentTopology self) -> std::string"""
11696 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11700 return _object_cast_to_CHARMMSegmentTopology(o)
11704 _IMP_atom.CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11706 r"""Proxy of C++ IMP::atom::CHARMMTopology class."""
11708 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11710 def __init__(self, *args):
11711 r"""__init__(CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology"""
11712 _IMP_atom.CHARMMTopology_swiginit(self, _IMP_atom.new_CHARMMTopology(*args))
11714 def get_parameters(self):
11715 r"""get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11716 return _IMP_atom.CHARMMTopology_get_parameters(self)
11718 def add_sequence(self, sequence):
11719 r"""add_sequence(CHARMMTopology self, std::string sequence)"""
11720 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11722 def apply_default_patches(self):
11723 r"""apply_default_patches(CHARMMTopology self)"""
11724 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11726 def create_hierarchy(self, model):
11727 r"""create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11728 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11730 def add_atom_types(self, hierarchy):
11731 r"""add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11732 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11734 def add_coordinates(self, hierarchy):
11735 r"""add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11736 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11738 def add_missing_atoms(self, hierarchy):
11739 r"""add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11740 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11742 def setup_hierarchy(self, hierarchy):
11743 r"""setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11744 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11746 def add_charges(self, hierarchy):
11747 r"""add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11748 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11751 r"""add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11752 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11754 def add_dihedrals(self, hierarchy):
11755 r"""add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11756 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11758 def add_impropers(self, hierarchy):
11759 r"""add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11760 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11761 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)
11762 def __set_segments(self, obj): IMP._list_util.set_varlist(self.segments, obj)
11763 def __del_segments(self): IMP._list_util.del_varlist(self.segments)
11764 segments = property(__get_segments, __set_segments, __del_segments, doc=
"List of ##ucnames")
11766 def remove_segment(self, d):
11767 r"""remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11768 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11770 def _python_index_segment(self, d, start, stop):
11771 r"""_python_index_segment(CHARMMTopology self, CHARMMSegmentTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
11772 return _IMP_atom.CHARMMTopology__python_index_segment(self, d, start, stop)
11774 def remove_segments(self, d):
11775 r"""remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11776 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11778 def set_segments(self, ps):
11779 r"""set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11780 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11782 def set_segments_order(self, objs):
11783 r"""set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11784 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11786 def add_segment(self, obj):
11787 r"""add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11788 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11790 def add_segments(self, objs):
11791 r"""add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11792 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11794 def clear_segments(self):
11795 r"""clear_segments(CHARMMTopology self)"""
11796 return _IMP_atom.CHARMMTopology_clear_segments(self)
11798 def get_number_of_segments(self):
11799 r"""get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11800 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11802 def get_has_segments(self):
11803 r"""get_has_segments(CHARMMTopology self) -> bool"""
11804 return _IMP_atom.CHARMMTopology_get_has_segments(self)
11807 r"""get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11808 return _IMP_atom.CHARMMTopology_get_segment(self, i)
11810 def get_segments(self):
11811 r"""get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11812 return _IMP_atom.CHARMMTopology_get_segments(self)
11814 def erase_segment(self, i):
11815 r"""erase_segment(CHARMMTopology self, unsigned int i)"""
11816 return _IMP_atom.CHARMMTopology_erase_segment(self, i)
11818 def reserve_segments(self, sz):
11819 r"""reserve_segments(CHARMMTopology self, unsigned int sz)"""
11820 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11822 def get_version_info(self):
11823 r"""get_version_info(CHARMMTopology self) -> VersionInfo"""
11824 return _IMP_atom.CHARMMTopology_get_version_info(self)
11825 __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
11828 r"""__str__(CHARMMTopology self) -> std::string"""
11829 return _IMP_atom.CHARMMTopology___str__(self)
11831 def __repr__(self):
11832 r"""__repr__(CHARMMTopology self) -> std::string"""
11833 return _IMP_atom.CHARMMTopology___repr__(self)
11837 return _object_cast_to_CHARMMTopology(o)
11841 _IMP_atom.CHARMMTopology_swigregister(CHARMMTopology)
11843 r"""Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11845 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11847 def __init__(self, *args):
11849 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11850 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11852 _IMP_atom.CHARMMStereochemistryRestraint_swiginit(self, _IMP_atom.new_CHARMMStereochemistryRestraint(*args))
11854 def get_pair_filter(self):
11855 r"""get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11856 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11858 def get_full_pair_filter(self):
11859 r"""get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11860 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11862 def do_get_inputs(self):
11863 r"""do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11864 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11866 def get_version_info(self):
11867 r"""get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11868 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11869 __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
11872 r"""__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11873 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11875 def __repr__(self):
11876 r"""__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11877 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11881 return _object_cast_to_CHARMMStereochemistryRestraint(o)
11885 _IMP_atom.CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11888 r"""add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())"""
11889 return _IMP_atom.add_bonds(*args)
11892 r"""add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(), FloatKey radius_key=IMP::FloatKey("radius"))"""
11893 return _IMP_atom.add_radii(*args)
11894 ALBER = _IMP_atom.ALBER
11896 HARPAZ = _IMP_atom.HARPAZ
11898 ANDERSSON = _IMP_atom.ANDERSSON
11900 TSAI = _IMP_atom.TSAI
11902 QUILLIN = _IMP_atom.QUILLIN
11904 SQUIRE = _IMP_atom.SQUIRE
11908 r"""get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11909 return _IMP_atom.get_protein_density_from_reference(densityReference)
11912 r"""get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11913 return _IMP_atom.get_volume_from_mass(*args)
11916 r"""get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
11917 return _IMP_atom.get_mass_from_volume(*args)
11920 r"""get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11921 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11924 r"""get_volume_from_residue_type(ResidueType rt) -> double"""
11925 return _IMP_atom.get_volume_from_residue_type(rt)
11928 r"""get_molarity(double n, double volume) -> double"""
11929 return _IMP_atom.get_molarity(n, volume)
11931 def get_kd(na, nb, nab, volume):
11932 r"""get_kd(double na, double nb, double nab, double volume) -> double"""
11933 return _IMP_atom.get_kd(na, nb, nab, volume)
11936 r"""get_einstein_diffusion_coefficient(double r, double temp=-1) -> double"""
11937 return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
11940 r"""get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double"""
11941 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
11945 get_diffusion_length(double D, double t) -> double
11946 get_diffusion_length(double D, double force, double t, double temp=-1) -> double
11948 return _IMP_atom.get_diffusion_length(*args)
11951 r"""get_diffusion_angle(double D, double dtfs) -> double"""
11952 return _IMP_atom.get_diffusion_angle(D, dtfs)
11956 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
11957 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
11959 return _IMP_atom.get_diffusion_coefficient(*args)
11962 r"""get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
11963 return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
11965 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11966 r"""get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11967 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11970 r"""get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11971 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11974 r"""get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11975 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11977 r"""Proxy of C++ IMP::atom::EzRestraint class."""
11979 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11981 def __init__(self, m, ps):
11982 r"""__init__(EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11983 _IMP_atom.EzRestraint_swiginit(self, _IMP_atom.new_EzRestraint(m, ps))
11985 def get_version_info(self):
11986 r"""get_version_info(EzRestraint self) -> VersionInfo"""
11987 return _IMP_atom.EzRestraint_get_version_info(self)
11988 __swig_destroy__ = _IMP_atom.delete_EzRestraint
11991 r"""__str__(EzRestraint self) -> std::string"""
11992 return _IMP_atom.EzRestraint___str__(self)
11994 def __repr__(self):
11995 r"""__repr__(EzRestraint self) -> std::string"""
11996 return _IMP_atom.EzRestraint___repr__(self)
12000 return _object_cast_to_EzRestraint(o)
12004 _IMP_atom.EzRestraint_swigregister(EzRestraint)
12008 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
12009 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12011 return _IMP_atom.create_protein(*args)
12015 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12016 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12018 return _IMP_atom.create_simplified_along_backbone(*args)
12021 r"""create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12022 return _IMP_atom.create_simplified_from_volume(h, resolution)
12025 r"""create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12026 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12028 def get_residue_indexes(h):
12029 r"""get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12030 return _IMP_atom.get_residue_indexes(h)
12032 def get_residue_type(*args):
12034 get_residue_type(char c) -> ResidueType
12035 get_residue_type(Hierarchy h) -> ResidueType
12037 return _IMP_atom.get_residue_type(*args)
12039 def get_atom_type(h):
12040 r"""get_atom_type(Hierarchy h) -> AtomType"""
12041 return _IMP_atom.get_atom_type(h)
12043 def get_domain_name(h):
12044 r"""get_domain_name(Hierarchy h) -> std::string"""
12045 return _IMP_atom.get_domain_name(h)
12049 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12050 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12052 return _IMP_atom.create_excluded_volume_restraint(*args)
12056 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12057 setup_as_approximation(Hierarchy h, double resolution=-1)
12059 return _IMP_atom.setup_as_approximation(*args)
12060 class _HierarchyTreeVertexIndex(object):
12061 r"""Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
12063 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12064 __repr__ = _swig_repr
12066 def __init__(self):
12067 r"""__init__(_HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12068 _IMP_atom._HierarchyTreeVertexIndex_swiginit(self, _IMP_atom.new__HierarchyTreeVertexIndex())
12069 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12072 _IMP_atom._HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12074 def show_as_graphviz(name, out):
12075 r"""show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12076 return _IMP_atom.show_as_graphviz(name, out)
12078 def get_vertex_index(g):
12079 r"""get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12080 return _IMP_atom.get_vertex_index(g)
12083 r"""get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12084 return _IMP_atom.get_hierarchy_tree(h)
12086 r"""Proxy of C++ IMP::atom::HierarchyGeometry class."""
12088 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12090 def __init__(self, d, resolution=0):
12091 r"""__init__(HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry"""
12092 _IMP_atom.HierarchyGeometry_swiginit(self, _IMP_atom.new_HierarchyGeometry(d, resolution))
12094 def get_version_info(self):
12095 r"""get_version_info(HierarchyGeometry self) -> VersionInfo"""
12096 return _IMP_atom.HierarchyGeometry_get_version_info(self)
12097 __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
12100 r"""__str__(HierarchyGeometry self) -> std::string"""
12101 return _IMP_atom.HierarchyGeometry___str__(self)
12103 def __repr__(self):
12104 r"""__repr__(HierarchyGeometry self) -> std::string"""
12105 return _IMP_atom.HierarchyGeometry___repr__(self)
12109 return _object_cast_to_HierarchyGeometry(o)
12113 _IMP_atom.HierarchyGeometry_swigregister(HierarchyGeometry)
12115 r"""Proxy of C++ IMP::atom::HierarchiesGeometry class."""
12117 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12119 def __init__(self, sc, resolution=-1):
12120 r"""__init__(HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry"""
12121 _IMP_atom.HierarchiesGeometry_swiginit(self, _IMP_atom.new_HierarchiesGeometry(sc, resolution))
12123 def get_version_info(self):
12124 r"""get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12125 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12126 __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
12129 r"""__str__(HierarchiesGeometry self) -> std::string"""
12130 return _IMP_atom.HierarchiesGeometry___str__(self)
12132 def __repr__(self):
12133 r"""__repr__(HierarchiesGeometry self) -> std::string"""
12134 return _IMP_atom.HierarchiesGeometry___repr__(self)
12138 return _object_cast_to_HierarchiesGeometry(o)
12142 _IMP_atom.HierarchiesGeometry_swigregister(HierarchiesGeometry)
12146 transform(Hierarchy h, Transformation3D tr)
12147 transform(Hierarchy h, Transformation3D tr)
12149 return _IMP_atom.transform(*args)
12150 class DopePairScore(_ADopeBase):
12151 r"""Proxy of C++ IMP::atom::DopePairScore class."""
12153 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12155 def __init__(self, *args):
12157 __init__(DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
12158 __init__(DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12160 _IMP_atom.DopePairScore_swiginit(self, _IMP_atom.new_DopePairScore(*args))
12163 r"""__str__(DopePairScore self) -> std::string"""
12164 return _IMP_atom.DopePairScore___str__(self)
12166 def __repr__(self):
12167 r"""__repr__(DopePairScore self) -> std::string"""
12168 return _IMP_atom.DopePairScore___repr__(self)
12172 return _object_cast_to_DopePairScore(o)
12174 __swig_destroy__ = _IMP_atom.delete_DopePairScore
12177 _IMP_atom.DopePairScore_swigregister(DopePairScore)
12180 r"""add_dope_score_data(Hierarchy h)"""
12181 return _IMP_atom.add_dope_score_data(h)
12182 class LoopStatisticalPairScore(_ALoopStatisticalBase):
12183 r"""Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
12185 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12187 def __init__(self, *args):
12189 __init__(LoopStatisticalPairScore self, double threshold=std::numeric_limits< double >::max()) -> LoopStatisticalPairScore
12190 __init__(LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
12192 _IMP_atom.LoopStatisticalPairScore_swiginit(self, _IMP_atom.new_LoopStatisticalPairScore(*args))
12195 r"""__str__(LoopStatisticalPairScore self) -> std::string"""
12196 return _IMP_atom.LoopStatisticalPairScore___str__(self)
12198 def __repr__(self):
12199 r"""__repr__(LoopStatisticalPairScore self) -> std::string"""
12200 return _IMP_atom.LoopStatisticalPairScore___repr__(self)
12204 return _object_cast_to_LoopStatisticalPairScore(o)
12206 __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
12209 _IMP_atom.LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
12212 r"""add_loop_statistical_score_data(Hierarchy h)"""
12213 return _IMP_atom.add_loop_statistical_score_data(h)
12214 class OrientedSoapPairScore(_OrientedSoapBase):
12215 r"""Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
12217 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12219 def __init__(self, library):
12220 r"""__init__(OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12221 _IMP_atom.OrientedSoapPairScore_swiginit(self, _IMP_atom.new_OrientedSoapPairScore(library))
12223 def get_pair_filter(self):
12224 r"""get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12225 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12228 r"""__str__(OrientedSoapPairScore self) -> std::string"""
12229 return _IMP_atom.OrientedSoapPairScore___str__(self)
12231 def __repr__(self):
12232 r"""__repr__(OrientedSoapPairScore self) -> std::string"""
12233 return _IMP_atom.OrientedSoapPairScore___repr__(self)
12237 return _object_cast_to_OrientedSoapPairScore(o)
12239 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12242 _IMP_atom.OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12244 r"""Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12246 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12248 def __init__(self):
12249 r"""__init__(SameResiduePairFilter self) -> SameResiduePairFilter"""
12250 _IMP_atom.SameResiduePairFilter_swiginit(self, _IMP_atom.new_SameResiduePairFilter())
12252 def do_get_inputs(self, m, pis):
12253 r"""do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12254 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12256 def get_value(self, *args):
12258 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12259 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12261 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12263 def get_value_index(self, *args):
12265 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12266 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12268 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12270 def get_version_info(self):
12271 r"""get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12272 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12273 __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
12276 r"""__str__(SameResiduePairFilter self) -> std::string"""
12277 return _IMP_atom.SameResiduePairFilter___str__(self)
12279 def __repr__(self):
12280 r"""__repr__(SameResiduePairFilter self) -> std::string"""
12281 return _IMP_atom.SameResiduePairFilter___repr__(self)
12285 return _object_cast_to_SameResiduePairFilter(o)
12289 _IMP_atom.SameResiduePairFilter_swigregister(SameResiduePairFilter)
12291 r"""Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12293 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12295 def __init__(self, m, pis):
12296 r"""__init__(RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12297 _IMP_atom.RemoveRigidMotionOptimizerState_swiginit(self, _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis))
12299 def set_particles(self, pis):
12300 r"""set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12301 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12303 def remove_rigid_motion(self):
12304 r"""remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12305 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12307 def get_version_info(self):
12308 r"""get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12309 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12310 __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
12313 r"""__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12314 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12316 def __repr__(self):
12317 r"""__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12318 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12322 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12326 _IMP_atom.RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12328 r"""Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12330 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12332 def __init__(self, pis, temperature, tau):
12333 r"""__init__(BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12334 _IMP_atom.BerendsenThermostatOptimizerState_swiginit(self, _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau))
12336 def set_particles(self, pis):
12337 r"""set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12338 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12340 def get_temperature(self):
12341 r"""get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12342 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12345 r"""get_tau(BerendsenThermostatOptimizerState self) -> double"""
12346 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12348 def set_temperature(self, temperature):
12349 r"""set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12350 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12352 def set_tau(self, tau):
12353 r"""set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12354 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12356 def rescale_velocities(self):
12357 r"""rescale_velocities(BerendsenThermostatOptimizerState self)"""
12358 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12360 def get_version_info(self):
12361 r"""get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12362 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12363 __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
12366 r"""__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12367 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12369 def __repr__(self):
12370 r"""__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12371 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12375 return _object_cast_to_BerendsenThermostatOptimizerState(o)
12379 _IMP_atom.BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12381 r"""Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12383 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12385 def __init__(self, m, pis, temperature, gamma):
12386 r"""__init__(LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12387 _IMP_atom.LangevinThermostatOptimizerState_swiginit(self, _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma))
12389 def set_particles(self, pis):
12390 r"""set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12391 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12393 def get_temperature(self):
12394 r"""get_temperature(LangevinThermostatOptimizerState self) -> double"""
12395 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12397 def get_gamma(self):
12398 r"""get_gamma(LangevinThermostatOptimizerState self) -> double"""
12399 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12401 def set_temperature(self, temperature):
12402 r"""set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12403 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12405 def set_gamma(self, gamma):
12406 r"""set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12407 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12409 def rescale_velocities(self):
12410 r"""rescale_velocities(LangevinThermostatOptimizerState self)"""
12411 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12413 def get_version_info(self):
12414 r"""get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12415 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12416 __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
12419 r"""__str__(LangevinThermostatOptimizerState self) -> std::string"""
12420 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12422 def __repr__(self):
12423 r"""__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12424 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12428 return _object_cast_to_LangevinThermostatOptimizerState(o)
12432 _IMP_atom.LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12433 class PDBRecord(IMP._Value):
12434 r"""Proxy of C++ IMP::atom::PDBRecord class."""
12436 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12438 def __init__(self):
12439 r"""__init__(PDBRecord self) -> PDBRecord"""
12440 _IMP_atom.PDBRecord_swiginit(self, _IMP_atom.new_PDBRecord())
12442 def get_alt_loc_indicator(self):
12443 r"""get_alt_loc_indicator(PDBRecord self) -> std::string"""
12444 return _IMP_atom.PDBRecord_get_alt_loc_indicator(self)
12446 def get_is_atom(self):
12447 r"""get_is_atom(PDBRecord self) -> bool"""
12448 return _IMP_atom.PDBRecord_get_is_atom(self)
12450 def get_trimmed_atom_name(self):
12451 r"""get_trimmed_atom_name(PDBRecord self) -> std::string"""
12452 return _IMP_atom.PDBRecord_get_trimmed_atom_name(self)
12454 def get_padded_atom_name(self):
12455 r"""get_padded_atom_name(PDBRecord self) -> std::string"""
12456 return _IMP_atom.PDBRecord_get_padded_atom_name(self)
12458 def get_residue_name(self):
12459 r"""get_residue_name(PDBRecord self) -> std::string"""
12460 return _IMP_atom.PDBRecord_get_residue_name(self)
12463 r"""get_chain_id(PDBRecord self) -> std::string"""
12464 return _IMP_atom.PDBRecord_get_chain_id(self)
12466 def get_element(self):
12467 r"""get_element(PDBRecord self) -> std::string"""
12468 return _IMP_atom.PDBRecord_get_element(self)
12470 def show(self, *args):
12471 r"""show(PDBRecord self, _ostream out=std::cout)"""
12472 return _IMP_atom.PDBRecord_show(self, *args)
12475 r"""__str__(PDBRecord self) -> std::string"""
12476 return _IMP_atom.PDBRecord___str__(self)
12478 def __repr__(self):
12479 r"""__repr__(PDBRecord self) -> std::string"""
12480 return _IMP_atom.PDBRecord___repr__(self)
12481 __swig_destroy__ = _IMP_atom.delete_PDBRecord
12484 _IMP_atom.PDBRecord_swigregister(PDBRecord)
12486 r"""Proxy of C++ IMP::atom::PDBSelector class."""
12488 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12490 def __init__(self, name):
12491 r"""__init__(PDBSelector self, std::string name) -> PDBSelector"""
12492 if self.__class__ == PDBSelector:
12496 _IMP_atom.PDBSelector_swiginit(self, _IMP_atom.new_PDBSelector(_self, name))
12498 if self.__class__ != PDBSelector:
12499 _director_objects.register(self)
12504 def get_is_selected(self, record):
12505 r"""get_is_selected(PDBSelector self, PDBRecord record) -> bool"""
12506 return _IMP_atom.PDBSelector_get_is_selected(self, record)
12507 __swig_destroy__ = _IMP_atom.delete_PDBSelector
12510 r"""__str__(PDBSelector self) -> std::string"""
12511 return _IMP_atom.PDBSelector___str__(self)
12513 def __repr__(self):
12514 r"""__repr__(PDBSelector self) -> std::string"""
12515 return _IMP_atom.PDBSelector___repr__(self)
12519 return _object_cast_to_PDBSelector(o)
12522 def get_type_name(self):
12523 return self.__class__.__name__
12524 def do_show(self, out):
12526 def get_version_info(self):
12527 if"IMP::atom" ==
"IMP":
12528 return VersionInfo(self.__module__,
12535 return _object_cast_to_PDBSelector(o)
12538 def __and__(self, s):
12539 return AndPDBSelector(self, s)
12540 def __or__(self, s):
12541 return OrPDBSelector(self, s)
12542 def __xor__(self, s):
12543 return XorPDBSelector(self, s)
12544 def __invert__(self):
12545 return NotPDBSelector(self)
12546 def __sub__(self, s):
12547 return AndPDBSelector(self, NotPDBSelector(s))
12549 def __disown__(self):
12551 _IMP_atom.disown_PDBSelector(self)
12552 return weakref.proxy(self)
12554 def do_destroy(self):
12555 r"""do_destroy(PDBSelector self)"""
12556 return _IMP_atom.PDBSelector_do_destroy(self)
12559 _IMP_atom.PDBSelector_swigregister(PDBSelector)
12560 class NonAlternativePDBSelector(PDBSelector):
12561 r"""Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12563 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12565 def __init__(self, *args):
12566 r"""__init__(NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector"""
12567 _IMP_atom.NonAlternativePDBSelector_swiginit(self, _IMP_atom.new_NonAlternativePDBSelector(*args))
12569 def get_version_info(self):
12570 r"""get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12571 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12572 __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
12575 r"""__str__(NonAlternativePDBSelector self) -> std::string"""
12576 return _IMP_atom.NonAlternativePDBSelector___str__(self)
12578 def __repr__(self):
12579 r"""__repr__(NonAlternativePDBSelector self) -> std::string"""
12580 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12584 return _object_cast_to_NonAlternativePDBSelector(o)
12588 _IMP_atom.NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12589 class ATOMPDBSelector(NonAlternativePDBSelector):
12590 r"""Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12592 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12594 def __init__(self, *args):
12595 r"""__init__(ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector"""
12596 _IMP_atom.ATOMPDBSelector_swiginit(self, _IMP_atom.new_ATOMPDBSelector(*args))
12597 __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
12600 r"""__str__(ATOMPDBSelector self) -> std::string"""
12601 return _IMP_atom.ATOMPDBSelector___str__(self)
12603 def __repr__(self):
12604 r"""__repr__(ATOMPDBSelector self) -> std::string"""
12605 return _IMP_atom.ATOMPDBSelector___repr__(self)
12609 return _object_cast_to_ATOMPDBSelector(o)
12613 _IMP_atom.ATOMPDBSelector_swigregister(ATOMPDBSelector)
12614 class CAlphaPDBSelector(NonAlternativePDBSelector):
12615 r"""Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12617 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12619 def __init__(self, *args):
12620 r"""__init__(CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector"""
12621 _IMP_atom.CAlphaPDBSelector_swiginit(self, _IMP_atom.new_CAlphaPDBSelector(*args))
12622 __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
12625 r"""__str__(CAlphaPDBSelector self) -> std::string"""
12626 return _IMP_atom.CAlphaPDBSelector___str__(self)
12628 def __repr__(self):
12629 r"""__repr__(CAlphaPDBSelector self) -> std::string"""
12630 return _IMP_atom.CAlphaPDBSelector___repr__(self)
12634 return _object_cast_to_CAlphaPDBSelector(o)
12638 _IMP_atom.CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12639 class CBetaPDBSelector(NonAlternativePDBSelector):
12640 r"""Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12642 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12644 def __init__(self, *args):
12645 r"""__init__(CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector"""
12646 _IMP_atom.CBetaPDBSelector_swiginit(self, _IMP_atom.new_CBetaPDBSelector(*args))
12647 __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
12650 r"""__str__(CBetaPDBSelector self) -> std::string"""
12651 return _IMP_atom.CBetaPDBSelector___str__(self)
12653 def __repr__(self):
12654 r"""__repr__(CBetaPDBSelector self) -> std::string"""
12655 return _IMP_atom.CBetaPDBSelector___repr__(self)
12659 return _object_cast_to_CBetaPDBSelector(o)
12663 _IMP_atom.CBetaPDBSelector_swigregister(CBetaPDBSelector)
12664 class AtomTypePDBSelector(PDBSelector):
12665 r"""Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12667 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12669 def __init__(self, *args):
12670 r"""__init__(AtomTypePDBSelector self, IMP::Strings atom_types, std::string name="AtomTypePDBSelector%1%") -> AtomTypePDBSelector"""
12671 _IMP_atom.AtomTypePDBSelector_swiginit(self, _IMP_atom.new_AtomTypePDBSelector(*args))
12673 def get_version_info(self):
12674 r"""get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12675 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12676 __swig_destroy__ = _IMP_atom.delete_AtomTypePDBSelector
12679 r"""__str__(AtomTypePDBSelector self) -> std::string"""
12680 return _IMP_atom.AtomTypePDBSelector___str__(self)
12682 def __repr__(self):
12683 r"""__repr__(AtomTypePDBSelector self) -> std::string"""
12684 return _IMP_atom.AtomTypePDBSelector___repr__(self)
12688 return _object_cast_to_AtomTypePDBSelector(o)
12692 _IMP_atom.AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12693 class ResidueTypePDBSelector(PDBSelector):
12694 r"""Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12696 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12698 def __init__(self, *args):
12699 r"""__init__(ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name="ResidueTypePDBSelector%1%") -> ResidueTypePDBSelector"""
12700 _IMP_atom.ResidueTypePDBSelector_swiginit(self, _IMP_atom.new_ResidueTypePDBSelector(*args))
12702 def get_version_info(self):
12703 r"""get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12704 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12705 __swig_destroy__ = _IMP_atom.delete_ResidueTypePDBSelector
12708 r"""__str__(ResidueTypePDBSelector self) -> std::string"""
12709 return _IMP_atom.ResidueTypePDBSelector___str__(self)
12711 def __repr__(self):
12712 r"""__repr__(ResidueTypePDBSelector self) -> std::string"""
12713 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12717 return _object_cast_to_ResidueTypePDBSelector(o)
12721 _IMP_atom.ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12722 class CPDBSelector(NonAlternativePDBSelector):
12723 r"""Proxy of C++ IMP::atom::CPDBSelector class."""
12725 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12727 def __init__(self, *args):
12728 r"""__init__(CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector"""
12729 _IMP_atom.CPDBSelector_swiginit(self, _IMP_atom.new_CPDBSelector(*args))
12730 __swig_destroy__ = _IMP_atom.delete_CPDBSelector
12733 r"""__str__(CPDBSelector self) -> std::string"""
12734 return _IMP_atom.CPDBSelector___str__(self)
12736 def __repr__(self):
12737 r"""__repr__(CPDBSelector self) -> std::string"""
12738 return _IMP_atom.CPDBSelector___repr__(self)
12742 return _object_cast_to_CPDBSelector(o)
12746 _IMP_atom.CPDBSelector_swigregister(CPDBSelector)
12747 class NPDBSelector(NonAlternativePDBSelector):
12748 r"""Proxy of C++ IMP::atom::NPDBSelector class."""
12750 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12752 def __init__(self, *args):
12753 r"""__init__(NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector"""
12754 _IMP_atom.NPDBSelector_swiginit(self, _IMP_atom.new_NPDBSelector(*args))
12755 __swig_destroy__ = _IMP_atom.delete_NPDBSelector
12758 r"""__str__(NPDBSelector self) -> std::string"""
12759 return _IMP_atom.NPDBSelector___str__(self)
12761 def __repr__(self):
12762 r"""__repr__(NPDBSelector self) -> std::string"""
12763 return _IMP_atom.NPDBSelector___repr__(self)
12767 return _object_cast_to_NPDBSelector(o)
12771 _IMP_atom.NPDBSelector_swigregister(NPDBSelector)
12772 class AllPDBSelector(PDBSelector):
12773 r"""Proxy of C++ IMP::atom::AllPDBSelector class."""
12775 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12777 def __init__(self, *args):
12778 r"""__init__(AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector"""
12779 _IMP_atom.AllPDBSelector_swiginit(self, _IMP_atom.new_AllPDBSelector(*args))
12781 def get_version_info(self):
12782 r"""get_version_info(AllPDBSelector self) -> VersionInfo"""
12783 return _IMP_atom.AllPDBSelector_get_version_info(self)
12784 __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
12787 r"""__str__(AllPDBSelector self) -> std::string"""
12788 return _IMP_atom.AllPDBSelector___str__(self)
12790 def __repr__(self):
12791 r"""__repr__(AllPDBSelector self) -> std::string"""
12792 return _IMP_atom.AllPDBSelector___repr__(self)
12796 return _object_cast_to_AllPDBSelector(o)
12800 _IMP_atom.AllPDBSelector_swigregister(AllPDBSelector)
12801 class ChainPDBSelector(NonAlternativePDBSelector):
12802 r"""Proxy of C++ IMP::atom::ChainPDBSelector class."""
12804 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12805 __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
12807 def __init__(self, *args):
12808 r"""__init__(ChainPDBSelector self, IMP::Strings chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector"""
12809 _IMP_atom.ChainPDBSelector_swiginit(self, _IMP_atom.new_ChainPDBSelector(*args))
12812 r"""__str__(ChainPDBSelector self) -> std::string"""
12813 return _IMP_atom.ChainPDBSelector___str__(self)
12815 def __repr__(self):
12816 r"""__repr__(ChainPDBSelector self) -> std::string"""
12817 return _IMP_atom.ChainPDBSelector___repr__(self)
12821 return _object_cast_to_ChainPDBSelector(o)
12825 _IMP_atom.ChainPDBSelector_swigregister(ChainPDBSelector)
12826 class WaterPDBSelector(NonAlternativePDBSelector):
12827 r"""Proxy of C++ IMP::atom::WaterPDBSelector class."""
12829 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12831 def __init__(self, *args):
12832 r"""__init__(WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector"""
12833 _IMP_atom.WaterPDBSelector_swiginit(self, _IMP_atom.new_WaterPDBSelector(*args))
12834 __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
12837 r"""__str__(WaterPDBSelector self) -> std::string"""
12838 return _IMP_atom.WaterPDBSelector___str__(self)
12840 def __repr__(self):
12841 r"""__repr__(WaterPDBSelector self) -> std::string"""
12842 return _IMP_atom.WaterPDBSelector___repr__(self)
12846 return _object_cast_to_WaterPDBSelector(o)
12850 _IMP_atom.WaterPDBSelector_swigregister(WaterPDBSelector)
12851 class HydrogenPDBSelector(NonAlternativePDBSelector):
12852 r"""Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12854 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12856 def __init__(self, *args):
12857 r"""__init__(HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector"""
12858 _IMP_atom.HydrogenPDBSelector_swiginit(self, _IMP_atom.new_HydrogenPDBSelector(*args))
12859 __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
12862 r"""__str__(HydrogenPDBSelector self) -> std::string"""
12863 return _IMP_atom.HydrogenPDBSelector___str__(self)
12865 def __repr__(self):
12866 r"""__repr__(HydrogenPDBSelector self) -> std::string"""
12867 return _IMP_atom.HydrogenPDBSelector___repr__(self)
12871 return _object_cast_to_HydrogenPDBSelector(o)
12875 _IMP_atom.HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12876 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12877 r"""Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12879 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12880 __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
12882 def __init__(self, *args):
12884 __init__(NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12885 __init__(NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12887 _IMP_atom.NonWaterNonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args))
12890 r"""__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12891 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12893 def __repr__(self):
12894 r"""__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12895 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12899 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12903 _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12904 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12905 r"""Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12907 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12908 __swig_destroy__ = _IMP_atom.delete_NonHydrogenPDBSelector
12910 def __init__(self, *args):
12912 __init__(NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12913 __init__(NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12915 _IMP_atom.NonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonHydrogenPDBSelector(*args))
12918 r"""__str__(NonHydrogenPDBSelector self) -> std::string"""
12919 return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12921 def __repr__(self):
12922 r"""__repr__(NonHydrogenPDBSelector self) -> std::string"""
12923 return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12927 return _object_cast_to_NonHydrogenPDBSelector(o)
12931 _IMP_atom.NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12932 class NonWaterPDBSelector(NonAlternativePDBSelector):
12933 r"""Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12935 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12936 __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
12938 def __init__(self, *args):
12940 __init__(NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12941 __init__(NonWaterPDBSelector self) -> NonWaterPDBSelector
12943 _IMP_atom.NonWaterPDBSelector_swiginit(self, _IMP_atom.new_NonWaterPDBSelector(*args))
12946 r"""__str__(NonWaterPDBSelector self) -> std::string"""
12947 return _IMP_atom.NonWaterPDBSelector___str__(self)
12949 def __repr__(self):
12950 r"""__repr__(NonWaterPDBSelector self) -> std::string"""
12951 return _IMP_atom.NonWaterPDBSelector___repr__(self)
12955 return _object_cast_to_NonWaterPDBSelector(o)
12959 _IMP_atom.NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12960 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12961 r"""Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12963 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12965 def __init__(self, *args):
12966 r"""__init__(BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector"""
12967 _IMP_atom.BackbonePDBSelector_swiginit(self, _IMP_atom.new_BackbonePDBSelector(*args))
12968 __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
12971 r"""__str__(BackbonePDBSelector self) -> std::string"""
12972 return _IMP_atom.BackbonePDBSelector___str__(self)
12974 def __repr__(self):
12975 r"""__repr__(BackbonePDBSelector self) -> std::string"""
12976 return _IMP_atom.BackbonePDBSelector___repr__(self)
12980 return _object_cast_to_BackbonePDBSelector(o)
12984 _IMP_atom.BackbonePDBSelector_swigregister(BackbonePDBSelector)
12985 class PPDBSelector(NonAlternativePDBSelector):
12986 r"""Proxy of C++ IMP::atom::PPDBSelector class."""
12988 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12990 def __init__(self, *args):
12991 r"""__init__(PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector"""
12992 _IMP_atom.PPDBSelector_swiginit(self, _IMP_atom.new_PPDBSelector(*args))
12993 __swig_destroy__ = _IMP_atom.delete_PPDBSelector
12996 r"""__str__(PPDBSelector self) -> std::string"""
12997 return _IMP_atom.PPDBSelector___str__(self)
12999 def __repr__(self):
13000 r"""__repr__(PPDBSelector self) -> std::string"""
13001 return _IMP_atom.PPDBSelector___repr__(self)
13005 return _object_cast_to_PPDBSelector(o)
13009 _IMP_atom.PPDBSelector_swigregister(PPDBSelector)
13010 class AndPDBSelector(PDBSelector):
13011 r"""Proxy of C++ IMP::atom::AndPDBSelector class."""
13013 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13015 def get_version_info(self):
13016 r"""get_version_info(AndPDBSelector self) -> VersionInfo"""
13017 return _IMP_atom.AndPDBSelector_get_version_info(self)
13018 __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
13020 def __init__(self, a, b):
13021 r"""__init__(AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13022 _IMP_atom.AndPDBSelector_swiginit(self, _IMP_atom.new_AndPDBSelector(a, b))
13025 r"""__str__(AndPDBSelector self) -> std::string"""
13026 return _IMP_atom.AndPDBSelector___str__(self)
13028 def __repr__(self):
13029 r"""__repr__(AndPDBSelector self) -> std::string"""
13030 return _IMP_atom.AndPDBSelector___repr__(self)
13034 return _object_cast_to_AndPDBSelector(o)
13038 _IMP_atom.AndPDBSelector_swigregister(AndPDBSelector)
13039 class OrPDBSelector(PDBSelector):
13040 r"""Proxy of C++ IMP::atom::OrPDBSelector class."""
13042 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13044 def get_version_info(self):
13045 r"""get_version_info(OrPDBSelector self) -> VersionInfo"""
13046 return _IMP_atom.OrPDBSelector_get_version_info(self)
13047 __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
13049 def __init__(self, a, b):
13050 r"""__init__(OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13051 _IMP_atom.OrPDBSelector_swiginit(self, _IMP_atom.new_OrPDBSelector(a, b))
13054 r"""__str__(OrPDBSelector self) -> std::string"""
13055 return _IMP_atom.OrPDBSelector___str__(self)
13057 def __repr__(self):
13058 r"""__repr__(OrPDBSelector self) -> std::string"""
13059 return _IMP_atom.OrPDBSelector___repr__(self)
13063 return _object_cast_to_OrPDBSelector(o)
13067 _IMP_atom.OrPDBSelector_swigregister(OrPDBSelector)
13068 class XorPDBSelector(PDBSelector):
13069 r"""Proxy of C++ IMP::atom::XorPDBSelector class."""
13071 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13073 def get_version_info(self):
13074 r"""get_version_info(XorPDBSelector self) -> VersionInfo"""
13075 return _IMP_atom.XorPDBSelector_get_version_info(self)
13076 __swig_destroy__ = _IMP_atom.delete_XorPDBSelector
13078 def __init__(self, a, b):
13079 r"""__init__(XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13080 _IMP_atom.XorPDBSelector_swiginit(self, _IMP_atom.new_XorPDBSelector(a, b))
13083 r"""__str__(XorPDBSelector self) -> std::string"""
13084 return _IMP_atom.XorPDBSelector___str__(self)
13086 def __repr__(self):
13087 r"""__repr__(XorPDBSelector self) -> std::string"""
13088 return _IMP_atom.XorPDBSelector___repr__(self)
13092 return _object_cast_to_XorPDBSelector(o)
13096 _IMP_atom.XorPDBSelector_swigregister(XorPDBSelector)
13097 class NotPDBSelector(PDBSelector):
13098 r"""Proxy of C++ IMP::atom::NotPDBSelector class."""
13100 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13102 def get_version_info(self):
13103 r"""get_version_info(NotPDBSelector self) -> VersionInfo"""
13104 return _IMP_atom.NotPDBSelector_get_version_info(self)
13105 __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
13107 def __init__(self, a):
13108 r"""__init__(NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13109 _IMP_atom.NotPDBSelector_swiginit(self, _IMP_atom.new_NotPDBSelector(a))
13112 r"""__str__(NotPDBSelector self) -> std::string"""
13113 return _IMP_atom.NotPDBSelector___str__(self)
13115 def __repr__(self):
13116 r"""__repr__(NotPDBSelector self) -> std::string"""
13117 return _IMP_atom.NotPDBSelector___repr__(self)
13121 return _object_cast_to_NotPDBSelector(o)
13125 _IMP_atom.NotPDBSelector_swigregister(NotPDBSelector)
13127 def get_default_pdb_selector():
13128 r"""get_default_pdb_selector() -> PDBSelector"""
13129 return _IMP_atom.get_default_pdb_selector()
13133 read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool no_radii=False) -> Hierarchy
13134 read_pdb(TextInput input, int model, Hierarchy h)
13136 return _IMP_atom.read_pdb(*args)
13139 r"""read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13140 return _IMP_atom.read_multimodel_pdb(*args)
13143 r"""write_pdb(Selection mhd, TextOutput out, unsigned int model=1)"""
13144 return _IMP_atom.write_pdb(mhd, out, model)
13147 r"""write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)"""
13148 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13151 r"""write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13152 return _IMP_atom.write_multimodel_pdb(mhd, out)
13154 def get_pdb_string(*args):
13155 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"""
13156 return _IMP_atom.get_pdb_string(*args)
13158 def get_pdb_conect_record_string(arg1, arg2):
13159 r"""get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13160 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13162 r"""Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13164 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13166 def __init__(self, *args):
13168 __init__(WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13169 __init__(WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13170 __init__(WritePDBOptimizerState self) -> WritePDBOptimizerState
13172 _IMP_atom.WritePDBOptimizerState_swiginit(self, _IMP_atom.new_WritePDBOptimizerState(*args))
13174 def get_version_info(self):
13175 r"""get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13176 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13177 __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
13180 r"""__str__(WritePDBOptimizerState self) -> std::string"""
13181 return _IMP_atom.WritePDBOptimizerState___str__(self)
13183 def __repr__(self):
13184 r"""__repr__(WritePDBOptimizerState self) -> std::string"""
13185 return _IMP_atom.WritePDBOptimizerState___repr__(self)
13189 return _object_cast_to_WritePDBOptimizerState(o)
13192 def _get_as_binary(self):
13193 r"""_get_as_binary(WritePDBOptimizerState self) -> PyObject *"""
13194 return _IMP_atom.WritePDBOptimizerState__get_as_binary(self)
13196 def _set_from_binary(self, p):
13197 r"""_set_from_binary(WritePDBOptimizerState self, PyObject * p)"""
13198 return _IMP_atom.WritePDBOptimizerState__set_from_binary(self, p)
13200 def __getstate__(self):
13201 p = self._get_as_binary()
13202 if len(self.__dict__) > 1:
13203 d = self.__dict__.copy()
13208 def __setstate__(self, p):
13209 if not hasattr(self,
'this'):
13211 if isinstance(p, tuple):
13213 self.__dict__.update(d)
13214 return self._set_from_binary(p)
13218 _IMP_atom.WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13221 r"""read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13222 return _IMP_atom.read_multimodel_mmcif(*args)
13225 r"""read_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13226 return _IMP_atom.read_mmcif(*args)
13229 r"""read_multimodel_bcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13230 return _IMP_atom.read_multimodel_bcif(*args)
13233 r"""read_bcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13234 return _IMP_atom.read_bcif(*args)
13237 r"""read_pdb_any(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
13238 return _IMP_atom.read_pdb_any(*args)
13241 r"""read_multimodel_pdb_any(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13242 return _IMP_atom.read_multimodel_pdb_any(*args)
13244 def read_pdb_or_mmcif(*args):
13245 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"""
13246 return _IMP_atom.read_pdb_or_mmcif(*args)
13248 def read_multimodel_pdb_or_mmcif(*args):
13249 r"""read_multimodel_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
13250 return _IMP_atom.read_multimodel_pdb_or_mmcif(*args)
13253 r"""get_kt(double T) -> double"""
13254 return _IMP_atom.get_kt(T)
13256 r"""Proxy of C++ IMP::atom::CAAngleRestraint class."""
13258 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13260 def __init__(self, m, p1, p2, p3, phi0, score):
13261 r"""__init__(CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13262 _IMP_atom.CAAngleRestraint_swiginit(self, _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score))
13264 def do_get_inputs(self):
13265 r"""do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13266 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13268 def get_version_info(self):
13269 r"""get_version_info(CAAngleRestraint self) -> VersionInfo"""
13270 return _IMP_atom.CAAngleRestraint_get_version_info(self)
13271 __swig_destroy__ = _IMP_atom.delete_CAAngleRestraint
13274 r"""__str__(CAAngleRestraint self) -> std::string"""
13275 return _IMP_atom.CAAngleRestraint___str__(self)
13277 def __repr__(self):
13278 r"""__repr__(CAAngleRestraint self) -> std::string"""
13279 return _IMP_atom.CAAngleRestraint___repr__(self)
13283 return _object_cast_to_CAAngleRestraint(o)
13287 _IMP_atom.CAAngleRestraint_swigregister(CAAngleRestraint)
13289 r"""Proxy of C++ IMP::atom::CADihedralRestraint class."""
13291 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13293 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13294 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"""
13295 _IMP_atom.CADihedralRestraint_swiginit(self, _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score))
13297 def do_get_inputs(self):
13298 r"""do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13299 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13301 def get_version_info(self):
13302 r"""get_version_info(CADihedralRestraint self) -> VersionInfo"""
13303 return _IMP_atom.CADihedralRestraint_get_version_info(self)
13304 __swig_destroy__ = _IMP_atom.delete_CADihedralRestraint
13307 r"""__str__(CADihedralRestraint self) -> std::string"""
13308 return _IMP_atom.CADihedralRestraint___str__(self)
13310 def __repr__(self):
13311 r"""__repr__(CADihedralRestraint self) -> std::string"""
13312 return _IMP_atom.CADihedralRestraint___repr__(self)
13316 return _object_cast_to_CADihedralRestraint(o)
13320 _IMP_atom.CADihedralRestraint_swigregister(CADihedralRestraint)
13322 r"""Proxy of C++ IMP::atom::StructureSource class."""
13324 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13326 def get_source_id(self):
13327 r"""get_source_id(StructureSource self) -> std::string"""
13328 return _IMP_atom.StructureSource_get_source_id(self)
13330 def get_source_chain_id(self):
13331 r"""get_source_chain_id(StructureSource self) -> std::string"""
13332 return _IMP_atom.StructureSource_get_source_chain_id(self)
13334 def set_source_id(self, source_id):
13335 r"""set_source_id(StructureSource self, std::string source_id)"""
13336 return _IMP_atom.StructureSource_set_source_id(self, source_id)
13338 def set_source_chain_id(self, source_chain_id):
13339 r"""set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13340 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13342 def __init__(self, *args):
13344 __init__(StructureSource self) -> StructureSource
13345 __init__(StructureSource self, Model m, ParticleIndex id) -> StructureSource
13346 __init__(StructureSource self, _ParticleAdaptor d) -> StructureSource
13348 _IMP_atom.StructureSource_swiginit(self, _IMP_atom.new_StructureSource(*args))
13351 def get_is_setup(*args):
13353 get_is_setup(Model m, ParticleIndex pi) -> bool
13354 get_is_setup(_ParticleAdaptor p) -> bool
13356 return _IMP_atom.StructureSource_get_is_setup(*args)
13358 def show(self, *args):
13359 r"""show(StructureSource self, _ostream out=std::cout)"""
13360 return _IMP_atom.StructureSource_show(self, *args)
13363 def setup_particle(*args):
13365 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13366 setup_particle(_ParticleAdaptor pa, std::string source_id, std::string source_chain_id) -> StructureSource
13368 return _IMP_atom.StructureSource_setup_particle(*args)
13370 def add_attribute(self, *args):
13372 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13373 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13374 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13375 add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
13376 add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
13377 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13378 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13379 add_attribute(StructureSource self, ObjectKey a0, Object a1)
13380 add_attribute(StructureSource self, SparseFloatKey a0, IMP::Float a1)
13381 add_attribute(StructureSource self, SparseIntKey a0, IMP::Int a1)
13382 add_attribute(StructureSource self, SparseStringKey a0, IMP::String a1)
13383 add_attribute(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
13385 return _IMP_atom.StructureSource_add_attribute(self, *args)
13387 def get_value(self, *args):
13389 get_value(StructureSource self, FloatKey a0) -> IMP::Float
13390 get_value(StructureSource self, IntKey a0) -> IMP::Int
13391 get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
13392 get_value(StructureSource self, IntsKey a0) -> IMP::Ints
13393 get_value(StructureSource self, StringKey a0) -> IMP::String
13394 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13395 get_value(StructureSource self, ObjectKey a0) -> Object
13396 get_value(StructureSource self, SparseFloatKey a0) -> IMP::Float
13397 get_value(StructureSource self, SparseIntKey a0) -> IMP::Int
13398 get_value(StructureSource self, SparseStringKey a0) -> IMP::String
13399 get_value(StructureSource self, SparseParticleIndexKey a0) -> ParticleIndex
13401 return _IMP_atom.StructureSource_get_value(self, *args)
13403 def set_value(self, *args):
13405 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13406 set_value(StructureSource self, IntKey a0, IMP::Int a1)
13407 set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
13408 set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
13409 set_value(StructureSource self, StringKey a0, IMP::String a1)
13410 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13411 set_value(StructureSource self, ObjectKey a0, Object a1)
13412 set_value(StructureSource self, SparseFloatKey a0, IMP::Float a1)
13413 set_value(StructureSource self, SparseIntKey a0, IMP::Int a1)
13414 set_value(StructureSource self, SparseStringKey a0, IMP::String a1)
13415 set_value(StructureSource self, SparseParticleIndexKey a0, ParticleIndex a1)
13417 return _IMP_atom.StructureSource_set_value(self, *args)
13419 def remove_attribute(self, *args):
13421 remove_attribute(StructureSource self, FloatKey a0)
13422 remove_attribute(StructureSource self, IntKey a0)
13423 remove_attribute(StructureSource self, FloatsKey a0)
13424 remove_attribute(StructureSource self, IntsKey a0)
13425 remove_attribute(StructureSource self, StringKey a0)
13426 remove_attribute(StructureSource self, ParticleIndexKey a0)
13427 remove_attribute(StructureSource self, ObjectKey a0)
13428 remove_attribute(StructureSource self, SparseFloatKey a0)
13429 remove_attribute(StructureSource self, SparseIntKey a0)
13430 remove_attribute(StructureSource self, SparseStringKey a0)
13431 remove_attribute(StructureSource self, SparseParticleIndexKey a0)
13433 return _IMP_atom.StructureSource_remove_attribute(self, *args)
13435 def has_attribute(self, *args):
13437 has_attribute(StructureSource self, FloatKey a0) -> bool
13438 has_attribute(StructureSource self, IntKey a0) -> bool
13439 has_attribute(StructureSource self, FloatsKey a0) -> bool
13440 has_attribute(StructureSource self, IntsKey a0) -> bool
13441 has_attribute(StructureSource self, StringKey a0) -> bool
13442 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13443 has_attribute(StructureSource self, ObjectKey a0) -> bool
13444 has_attribute(StructureSource self, SparseFloatKey a0) -> bool
13445 has_attribute(StructureSource self, SparseIntKey a0) -> bool
13446 has_attribute(StructureSource self, SparseStringKey a0) -> bool
13447 has_attribute(StructureSource self, SparseParticleIndexKey a0) -> bool
13449 return _IMP_atom.StructureSource_has_attribute(self, *args)
13451 def get_derivative(self, a0):
13452 r"""get_derivative(StructureSource self, FloatKey a0) -> double"""
13453 return _IMP_atom.StructureSource_get_derivative(self, a0)
13455 def get_name(self):
13456 r"""get_name(StructureSource self) -> std::string"""
13457 return _IMP_atom.StructureSource_get_name(self)
13459 def clear_caches(self):
13460 r"""clear_caches(StructureSource self)"""
13461 return _IMP_atom.StructureSource_clear_caches(self)
13463 def set_name(self, a0):
13464 r"""set_name(StructureSource self, std::string a0)"""
13465 return _IMP_atom.StructureSource_set_name(self, a0)
13468 r"""set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13469 return _IMP_atom.StructureSource_set_check_level(self, a0)
13471 def add_to_derivative(self, a0, a1, a2):
13472 r"""add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13473 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13475 def set_is_optimized(self, a0, a1):
13476 r"""set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13477 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13479 def get_is_optimized(self, a0):
13480 r"""get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13481 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13484 r"""get_check_level(StructureSource self) -> IMP::CheckLevel"""
13485 return _IMP_atom.StructureSource_get_check_level(self)
13487 def __eq__(self, *args):
13489 __eq__(StructureSource self, StructureSource o) -> bool
13490 __eq__(StructureSource self, Particle d) -> bool
13492 return _IMP_atom.StructureSource___eq__(self, *args)
13494 def __ne__(self, *args):
13496 __ne__(StructureSource self, StructureSource o) -> bool
13497 __ne__(StructureSource self, Particle d) -> bool
13499 return _IMP_atom.StructureSource___ne__(self, *args)
13501 def __le__(self, *args):
13503 __le__(StructureSource self, StructureSource o) -> bool
13504 __le__(StructureSource self, Particle d) -> bool
13506 return _IMP_atom.StructureSource___le__(self, *args)
13508 def __lt__(self, *args):
13510 __lt__(StructureSource self, StructureSource o) -> bool
13511 __lt__(StructureSource self, Particle d) -> bool
13513 return _IMP_atom.StructureSource___lt__(self, *args)
13515 def __ge__(self, *args):
13517 __ge__(StructureSource self, StructureSource o) -> bool
13518 __ge__(StructureSource self, Particle d) -> bool
13520 return _IMP_atom.StructureSource___ge__(self, *args)
13522 def __gt__(self, *args):
13524 __gt__(StructureSource self, StructureSource o) -> bool
13525 __gt__(StructureSource self, Particle d) -> bool
13527 return _IMP_atom.StructureSource___gt__(self, *args)
13529 def __hash__(self):
13530 r"""__hash__(StructureSource self) -> std::size_t"""
13531 return _IMP_atom.StructureSource___hash__(self)
13534 r"""__str__(StructureSource self) -> std::string"""
13535 return _IMP_atom.StructureSource___str__(self)
13537 def __repr__(self):
13538 r"""__repr__(StructureSource self) -> std::string"""
13539 return _IMP_atom.StructureSource___repr__(self)
13541 def _get_as_binary(self):
13542 r"""_get_as_binary(StructureSource self) -> PyObject *"""
13543 return _IMP_atom.StructureSource__get_as_binary(self)
13545 def _set_from_binary(self, p):
13546 r"""_set_from_binary(StructureSource self, PyObject * p)"""
13547 return _IMP_atom.StructureSource__set_from_binary(self, p)
13549 def __getstate__(self):
13550 p = self._get_as_binary()
13551 if len(self.__dict__) > 1:
13552 d = self.__dict__.copy()
13557 def __setstate__(self, p):
13558 if not hasattr(self,
'this'):
13560 if isinstance(p, tuple):
13562 self.__dict__.update(d)
13563 return self._set_from_binary(p)
13565 __swig_destroy__ = _IMP_atom.delete_StructureSource
13568 _IMP_atom.StructureSource_swigregister(StructureSource)
13570 def __lshift__(*args):
13572 __lshift__(_ostream out, Bonded n) -> _ostream
13573 __lshift__(_ostream out, Bond n) -> _ostream
13574 __lshift__(_ostream out, Hierarchy n) -> _ostream
13575 __lshift__(_ostream out, Angle n) -> _ostream
13576 __lshift__(_ostream out, Dihedral n) -> _ostream
13577 __lshift__(_ostream out, CenterOfMass n) -> _ostream
13578 __lshift__(_ostream out, Diffusion n) -> _ostream
13579 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13580 __lshift__(_ostream out, TAMDParticle n) -> _ostream
13581 __lshift__(_ostream out, Charged n) -> _ostream
13582 __lshift__(_ostream out, Domain n) -> _ostream
13583 __lshift__(_ostream out, LennardJones n) -> _ostream
13584 __lshift__(_ostream out, LennardJonesTyped n) -> _ostream
13585 __lshift__(_ostream out, Fragment n) -> _ostream
13586 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13587 __lshift__(_ostream out, Atom n) -> _ostream
13588 __lshift__(_ostream out, Residue n) -> _ostream
13589 __lshift__(_ostream out, Representation n) -> _ostream
13590 __lshift__(_ostream out, State n) -> _ostream
13591 __lshift__(_ostream out, Molecule n) -> _ostream
13592 __lshift__(_ostream out, Copy n) -> _ostream
13593 __lshift__(_ostream out, Chain n) -> _ostream
13594 __lshift__(_ostream out, StructureSource n) -> _ostream
13596 return _IMP_atom.__lshift__(*args)
13598 r"""Proxy of C++ IMP::atom::HelixRestraint class."""
13600 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13602 def __init__(self, rs, ideal=True):
13603 r"""__init__(HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint"""
13604 _IMP_atom.HelixRestraint_swiginit(self, _IMP_atom.new_HelixRestraint(rs, ideal))
13606 def get_number_of_bonds(self):
13607 r"""get_number_of_bonds(HelixRestraint self) -> int"""
13608 return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13610 def get_number_of_dihedrals(self):
13611 r"""get_number_of_dihedrals(HelixRestraint self) -> int"""
13612 return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13614 def do_get_inputs(self):
13615 r"""do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13616 return _IMP_atom.HelixRestraint_do_get_inputs(self)
13618 def get_version_info(self):
13619 r"""get_version_info(HelixRestraint self) -> VersionInfo"""
13620 return _IMP_atom.HelixRestraint_get_version_info(self)
13621 __swig_destroy__ = _IMP_atom.delete_HelixRestraint
13624 r"""__str__(HelixRestraint self) -> std::string"""
13625 return _IMP_atom.HelixRestraint___str__(self)
13627 def __repr__(self):
13628 r"""__repr__(HelixRestraint self) -> std::string"""
13629 return _IMP_atom.HelixRestraint___repr__(self)
13633 return _object_cast_to_HelixRestraint(o)
13637 _IMP_atom.HelixRestraint_swigregister(HelixRestraint)
13640 r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
13641 return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
13644 r"""show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream"""
13645 return _IMP_atom.show_molecular_hierarchy(*args)
13646 class CHARMMBond(object):
13647 r"""Proxy of C++ IMP::atom::CHARMMConnection< 2 > class."""
13649 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13650 __repr__ = _swig_repr
13652 def __init__(self, atoms):
13653 r"""__init__(CHARMMBond self, IMP::Strings const & atoms) -> CHARMMBond"""
13654 _IMP_atom.CHARMMBond_swiginit(self, _IMP_atom.new_CHARMMBond(atoms))
13656 def get_endpoint(self, i):
13657 r"""get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13658 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13660 def get_contains_atom(self, name):
13661 r"""get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13662 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13664 def show(self, *args):
13665 r"""show(CHARMMBond self, _ostream out=std::cout)"""
13666 return _IMP_atom.CHARMMBond_show(self, *args)
13667 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13670 _IMP_atom.CHARMMBond_swigregister(CHARMMBond)
13671 class CHARMMAngle(object):
13672 r"""Proxy of C++ IMP::atom::CHARMMConnection< 3 > class."""
13674 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13675 __repr__ = _swig_repr
13677 def __init__(self, atoms):
13678 r"""__init__(CHARMMAngle self, IMP::Strings const & atoms) -> CHARMMAngle"""
13679 _IMP_atom.CHARMMAngle_swiginit(self, _IMP_atom.new_CHARMMAngle(atoms))
13681 def get_endpoint(self, i):
13682 r"""get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13683 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13685 def get_contains_atom(self, name):
13686 r"""get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13687 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13689 def show(self, *args):
13690 r"""show(CHARMMAngle self, _ostream out=std::cout)"""
13691 return _IMP_atom.CHARMMAngle_show(self, *args)
13692 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13695 _IMP_atom.CHARMMAngle_swigregister(CHARMMAngle)
13697 def _get_native_overlap_cpp(m1, m2, threshold):
13698 r"""_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2, double threshold) -> double"""
13699 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13701 def _get_drmsd_cpp(m0, m1):
13702 r"""_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1) -> double"""
13703 return _IMP_atom._get_drmsd_cpp(m0, m1)
13705 def _get_drmsd_Q_cpp(m0, m1, threshold):
13706 r"""_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, double threshold) -> double"""
13707 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13709 def _get_drms_cpp(m1, m2):
13710 r"""_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2) -> double"""
13711 return _IMP_atom._get_drms_cpp(m1, m2)
13713 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13714 r"""_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 >,std::allocator< IMP::algebra::VectorD< 3 > > > const & m2, IMP::IntRanges const & ranges) -> double"""
13715 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13718 va= [IMP.algebra.get_vector(x)
for x
in a]
13719 vb= [IMP.algebra.get_vector(x)
for x
in b]
13720 return _get_native_overlap_cpp(va, vb, d)
13723 va= [IMP.algebra.get_vector(x)
for x
in a]
13724 vb= [IMP.algebra.get_vector(x)
for x
in b]
13725 return _get_drmsd_cpp(va, vb)
13728 va= [IMP.algebra.get_vector(x)
for x
in a]
13729 vb= [IMP.algebra.get_vector(x)
for x
in b]
13730 return _get_drms_cpp(va, vb)
13733 va= [IMP.algebra.get_vector(x)
for x
in a]
13734 vb= [IMP.algebra.get_vector(x)
for x
in b]
13735 return _get_drmsd_Q_cpp(va, vb, t)
13738 va= [IMP.algebra.get_vector(x)
for x
in a]
13739 vb= [IMP.algebra.get_vector(x)
for x
in b]
13741 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13745 r"""Proxy of C++ IMP::atom::LennardJonesTypedPairScore< IMP::atom::SmoothingFunction > class."""
13747 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13748 __repr__ = _swig_repr
13750 def __init__(self, f):
13751 r"""__init__(_LennardJonesTypedPairScore self, SmoothingFunction f) -> _LennardJonesTypedPairScore"""
13752 _IMP_atom._LennardJonesTypedPairScore_swiginit(self, _IMP_atom.new__LennardJonesTypedPairScore(f))
13754 def set_repulsive_weight(self, repulsive_weight):
13755 r"""set_repulsive_weight(_LennardJonesTypedPairScore self, double repulsive_weight)"""
13756 return _IMP_atom._LennardJonesTypedPairScore_set_repulsive_weight(self, repulsive_weight)
13758 def get_repulsive_weight(self):
13759 r"""get_repulsive_weight(_LennardJonesTypedPairScore self) -> double"""
13760 return _IMP_atom._LennardJonesTypedPairScore_get_repulsive_weight(self)
13762 def set_attractive_weight(self, attractive_weight):
13763 r"""set_attractive_weight(_LennardJonesTypedPairScore self, double attractive_weight)"""
13764 return _IMP_atom._LennardJonesTypedPairScore_set_attractive_weight(self, attractive_weight)
13766 def get_attractive_weight(self):
13767 r"""get_attractive_weight(_LennardJonesTypedPairScore self) -> double"""
13768 return _IMP_atom._LennardJonesTypedPairScore_get_attractive_weight(self)
13770 def do_get_inputs(self, m, pis):
13771 r"""do_get_inputs(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
13772 return _IMP_atom._LennardJonesTypedPairScore_do_get_inputs(self, m, pis)
13774 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
13775 r"""evaluate_indexes(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13776 return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
13778 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
13779 r"""evaluate_indexes_scores(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13780 return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
13782 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
13783 r"""evaluate_indexes_delta(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13784 return _IMP_atom._LennardJonesTypedPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
13786 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
13787 r"""evaluate_if_good_indexes(_LennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13788 return _IMP_atom._LennardJonesTypedPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
13790 def get_version_info(self):
13791 r"""get_version_info(_LennardJonesTypedPairScore self) -> VersionInfo"""
13792 return _IMP_atom._LennardJonesTypedPairScore_get_version_info(self)
13793 __swig_destroy__ = _IMP_atom.delete__LennardJonesTypedPairScore
13797 return _object_cast_to__LennardJonesTypedPairScore(o)
13801 _IMP_atom._LennardJonesTypedPairScore_swigregister(_LennardJonesTypedPairScore)
13803 r"""Proxy of C++ IMP::atom::LennardJonesTypedPairScore< IMP::atom::ForceSwitch > class."""
13805 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
13806 __repr__ = _swig_repr
13808 def __init__(self, f):
13809 r"""__init__(_SwitchedLennardJonesTypedPairScore self, ForceSwitch f) -> _SwitchedLennardJonesTypedPairScore"""
13810 _IMP_atom._SwitchedLennardJonesTypedPairScore_swiginit(self, _IMP_atom.new__SwitchedLennardJonesTypedPairScore(f))
13812 def set_repulsive_weight(self, repulsive_weight):
13813 r"""set_repulsive_weight(_SwitchedLennardJonesTypedPairScore self, double repulsive_weight)"""
13814 return _IMP_atom._SwitchedLennardJonesTypedPairScore_set_repulsive_weight(self, repulsive_weight)
13816 def get_repulsive_weight(self):
13817 r"""get_repulsive_weight(_SwitchedLennardJonesTypedPairScore self) -> double"""
13818 return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_repulsive_weight(self)
13820 def set_attractive_weight(self, attractive_weight):
13821 r"""set_attractive_weight(_SwitchedLennardJonesTypedPairScore self, double attractive_weight)"""
13822 return _IMP_atom._SwitchedLennardJonesTypedPairScore_set_attractive_weight(self, attractive_weight)
13824 def get_attractive_weight(self):
13825 r"""get_attractive_weight(_SwitchedLennardJonesTypedPairScore self) -> double"""
13826 return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_attractive_weight(self)
13828 def do_get_inputs(self, m, pis):
13829 r"""do_get_inputs(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
13830 return _IMP_atom._SwitchedLennardJonesTypedPairScore_do_get_inputs(self, m, pis)
13832 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
13833 r"""evaluate_indexes(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13834 return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
13836 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
13837 r"""evaluate_indexes_scores(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13838 return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
13840 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
13841 r"""evaluate_indexes_delta(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
13842 return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
13844 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
13845 r"""evaluate_if_good_indexes(_SwitchedLennardJonesTypedPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
13846 return _IMP_atom._SwitchedLennardJonesTypedPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
13848 def get_version_info(self):
13849 r"""get_version_info(_SwitchedLennardJonesTypedPairScore self) -> VersionInfo"""
13850 return _IMP_atom._SwitchedLennardJonesTypedPairScore_get_version_info(self)
13851 __swig_destroy__ = _IMP_atom.delete__SwitchedLennardJonesTypedPairScore
13855 return _object_cast_to__SwitchedLennardJonesTypedPairScore(o)
13859 _IMP_atom._SwitchedLennardJonesTypedPairScore_swigregister(_SwitchedLennardJonesTypedPairScore)
13861 class LennardJonesTypedPairScore(_SwitchedLennardJonesTypedPairScore.__bases__[0]):
13862 def __init__(self, f):
13863 if isinstance(f, ForceSwitch):
13864 p = _SwitchedLennardJonesTypedPairScore(f)
13866 p = _LennardJonesTypedPairScore(f)
13867 self.__dict__[
'_proxied'] = p
13868 def __getattr__(self, key):
13869 return getattr(self._proxied, key)
13870 def __setattr__(self, key, val):
13871 return setattr(self._proxied, key, val)
13876 p = _SwitchedLennardJonesTypedPairScore.get_from(o)
13878 p = _LennardJonesTypedPairScore.get_from(o)
13879 obj = object.__new__(LennardJonesTypedPairScore)
13880 obj.__dict__[
'_proxied'] = p
13885 r"""get_module_version() -> std::string const"""
13886 return _IMP_atom.get_module_version()
13889 r"""get_example_path(std::string fname) -> std::string"""
13890 return _IMP_atom.get_example_path(fname)
13893 r"""get_data_path(std::string fname) -> std::string"""
13894 return _IMP_atom.get_data_path(fname)
13896 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.
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)
Hierarchies read_multimodel_pdb_any(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB-like file.
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
Hierarchies read_multimodel_bcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the BinaryCIF file.
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.
Hierarchy read_bcif(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 BinaryCIF file.
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.
Hierarchy read_pdb_any(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-like file.
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)
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.