11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_ATOM_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
72 def __init__(self, *args, **kwargs):
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
78 r"""value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
79 return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
82 r"""incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
83 return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator"""
87 return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
95 return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
99 return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
102 r"""next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
103 return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
106 r"""__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
107 return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
110 r"""previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
111 return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
115 return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
119 return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
123 return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
127 return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
131 return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
135 return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
140 __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
147 _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
154 IMP_DEBUG = _IMP_atom.IMP_DEBUG
156 IMP_RELEASE = _IMP_atom.IMP_RELEASE
158 IMP_SILENT = _IMP_atom.IMP_SILENT
160 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
162 IMP_TERSE = _IMP_atom.IMP_TERSE
164 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
166 IMP_MEMORY = _IMP_atom.IMP_MEMORY
168 IMP_NONE = _IMP_atom.IMP_NONE
170 IMP_USAGE = _IMP_atom.IMP_USAGE
172 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_atom.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_atom.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_atom.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_atom._ostream_write(self, osa_buf)
237 _IMP_atom._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
321 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
323 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
325 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
327 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
350 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
352 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
363 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
367 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
369 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
371 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
373 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
375 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
377 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
381 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
385 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
387 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
389 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
391 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
393 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
396 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex > class."""
398 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
399 __repr__ = _swig_repr
402 r"""__init__(HierarchyTree self) -> HierarchyTree"""
403 _IMP_atom.HierarchyTree_swiginit(self, _IMP_atom.new_HierarchyTree())
406 r"""get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
407 return _IMP_atom.HierarchyTree_get_graph(self)
410 r"""get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
411 return _IMP_atom.HierarchyTree_get_vertices(self)
413 def get_vertex_name(self, i):
414 r"""get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
415 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
417 def get_in_neighbors(self, v):
418 r"""get_in_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
419 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
421 def get_out_neighbors(self, v):
422 r"""get_out_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
423 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
426 r"""show_graphviz(HierarchyTree self, _ostream out=std::cout)"""
427 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
429 def get_graphviz_string(self):
430 r"""get_graphviz_string(HierarchyTree self) -> std::string"""
431 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
433 def add_edge(self, v0, v1):
434 r"""add_edge(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)"""
435 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
437 def add_vertex(self, l):
438 r"""add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
439 return _IMP_atom.HierarchyTree_add_vertex(self, l)
441 def remove_vertex(self, l):
442 r"""remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
443 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
444 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
447 _IMP_atom.HierarchyTree_swigregister(HierarchyTree)
449 _value_types.append(
"HierarchyTree")
452 _object_types.append(
"PDBSelector")
455 def _object_cast_to_PDBSelector(o):
456 r"""_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
457 return _IMP_atom._object_cast_to_PDBSelector(o)
460 return [Angle(x)
for x
in l]
461 _plural_types.append(
"Angles")
464 _value_types.append(
"Angle")
468 return [Atom(x)
for x
in l]
469 _plural_types.append(
"Atoms")
472 _value_types.append(
"Atom")
476 return [Bond(x)
for x
in l]
477 _plural_types.append(
"Bonds")
480 _value_types.append(
"Bond")
484 return [Bonded(x)
for x
in l]
485 _plural_types.append(
"Bondeds")
488 _value_types.append(
"Bonded")
491 def CHARMMAtomList(l=[]):
492 return [CHARMMAtom(x)
for x
in l]
493 _plural_types.append(
"CHARMMAtomList")
496 _value_types.append(
"CHARMMAtom")
500 return [Chain(x)
for x
in l]
501 _plural_types.append(
"Chains")
504 _value_types.append(
"Chain")
507 def CenterOfMasses(l=[]):
508 return [CenterOfMass(x)
for x
in l]
509 _plural_types.append(
"CenterOfMasses")
512 _value_types.append(
"CenterOfMass")
516 return [Charged(x)
for x
in l]
517 _plural_types.append(
"Chargeds")
520 _value_types.append(
"Charged")
523 def Diffusions(l=[]):
524 return [Diffusion(x)
for x
in l]
525 _plural_types.append(
"Diffusions")
528 _value_types.append(
"Diffusion")
531 def RigidBodyDiffusions(l=[]):
532 return [RigidBodyDiffusion(x)
for x
in l]
533 _plural_types.append(
"RigidBodyDiffusions")
536 _value_types.append(
"RigidBodyDiffusion")
539 def TAMDParticles(l=[]):
540 return [TAMDParticle(x)
for x
in l]
541 _plural_types.append(
"TAMDParticles")
544 _value_types.append(
"TAMDParticle")
547 def TAMDCentroids(l=[]):
548 return [TAMDCentroid(x)
for x
in l]
549 _plural_types.append(
"TAMDCentroids")
552 _value_types.append(
"TAMDCentroid")
556 return [Dihedral(x)
for x
in l]
557 _plural_types.append(
"Dihedrals")
560 _value_types.append(
"Dihedral")
564 return [Domain(x)
for x
in l]
565 _plural_types.append(
"Domains")
568 _value_types.append(
"Domain")
572 return [Fragment(x)
for x
in l]
573 _plural_types.append(
"Fragments")
576 _value_types.append(
"Fragment")
579 def Hierarchies(l=[]):
580 return [Hierarchy(x)
for x
in l]
581 _plural_types.append(
"Hierarchies")
584 _value_types.append(
"Hierarchy")
587 def LennardJonesList(l=[]):
588 return [LennardJones(x)
for x
in l]
589 _plural_types.append(
"LennardJonesList")
592 _value_types.append(
"LennardJones")
596 return [Mass(x)
for x
in l]
597 _plural_types.append(
"Masses")
600 _value_types.append(
"Mass")
603 def LinearVelocities(l=[]):
604 return [LinearVelocity(x)
for x
in l]
605 _plural_types.append(
"LinearVelocities")
608 _value_types.append(
"LinearVelocity")
611 def AngularVelocities(l=[]):
612 return [AngularVelocity(x)
for x
in l]
613 _plural_types.append(
"AngularVelocities")
616 _value_types.append(
"AngularVelocity")
620 return [Molecule(x)
for x
in l]
621 _plural_types.append(
"Molecules")
624 _value_types.append(
"Molecule")
628 return [Residue(x)
for x
in l]
629 _plural_types.append(
"Residues")
632 _value_types.append(
"Residue")
635 def Representations(l=[]):
636 return [Representation(x)
for x
in l]
637 _plural_types.append(
"Representations")
640 _value_types.append(
"Representation")
644 return [State(x)
for x
in l]
645 _plural_types.append(
"States")
648 _value_types.append(
"State")
652 return [Copy(x)
for x
in l]
653 _plural_types.append(
"Copies")
656 _value_types.append(
"Copy")
659 def SecondaryStructureResidues(l=[]):
660 return [SecondaryStructureResidue(x)
for x
in l]
661 _plural_types.append(
"SecondaryStructureResidues")
664 _value_types.append(
"SecondaryStructureResidue")
667 def StructureSources(l=[]):
668 return [StructureSource(x)
for x
in l]
669 _plural_types.append(
"StructureSources")
672 _value_types.append(
"StructureSource")
675 _object_types.append(
"Simulator")
678 def _object_cast_to_Simulator(o):
679 r"""_object_cast_to_Simulator(Object o) -> Simulator"""
680 return _IMP_atom._object_cast_to_Simulator(o)
682 _object_types.append(
"ATOMPDBSelector")
685 def _object_cast_to_ATOMPDBSelector(o):
686 r"""_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
687 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
689 _object_types.append(
"AllMol2Selector")
692 def _object_cast_to_AllMol2Selector(o):
693 r"""_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
694 return _IMP_atom._object_cast_to_AllMol2Selector(o)
696 _object_types.append(
"AllPDBSelector")
699 def _object_cast_to_AllPDBSelector(o):
700 r"""_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
701 return _IMP_atom._object_cast_to_AllPDBSelector(o)
703 _object_types.append(
"AndPDBSelector")
706 def _object_cast_to_AndPDBSelector(o):
707 r"""_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
708 return _IMP_atom._object_cast_to_AndPDBSelector(o)
710 _object_types.append(
"XorPDBSelector")
713 def _object_cast_to_XorPDBSelector(o):
714 r"""_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
715 return _IMP_atom._object_cast_to_XorPDBSelector(o)
717 _object_types.append(
"ResidueTypePDBSelector")
720 def _object_cast_to_ResidueTypePDBSelector(o):
721 r"""_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
722 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
724 _object_types.append(
"AtomTypePDBSelector")
727 def _object_cast_to_AtomTypePDBSelector(o):
728 r"""_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
729 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
731 _object_types.append(
"AngleSingletonScore")
734 def _object_cast_to_AngleSingletonScore(o):
735 r"""_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
736 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
738 _object_types.append(
"BondEndpointsRefiner")
741 def _object_cast_to_BondEndpointsRefiner(o):
742 r"""_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
743 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
745 _object_types.append(
"BondPairContainer")
748 def _object_cast_to_BondPairContainer(o):
749 r"""_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
750 return _IMP_atom._object_cast_to_BondPairContainer(o)
752 _object_types.append(
"BondSingletonScore")
755 def _object_cast_to_BondSingletonScore(o):
756 r"""_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
757 return _IMP_atom._object_cast_to_BondSingletonScore(o)
759 _object_types.append(
"BondedPairFilter")
762 def _object_cast_to_BondedPairFilter(o):
763 r"""_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
764 return _IMP_atom._object_cast_to_BondedPairFilter(o)
766 _object_types.append(
"BrownianDynamics")
769 def _object_cast_to_BrownianDynamics(o):
770 r"""_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
771 return _IMP_atom._object_cast_to_BrownianDynamics(o)
773 _object_types.append(
"BrownianDynamicsTAMD")
776 def _object_cast_to_BrownianDynamicsTAMD(o):
777 r"""_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
778 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
780 _object_types.append(
"CAlphaPDBSelector")
783 def _object_cast_to_CAlphaPDBSelector(o):
784 r"""_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
785 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
787 _object_types.append(
"CBetaPDBSelector")
790 def _object_cast_to_CBetaPDBSelector(o):
791 r"""_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
792 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
794 _object_types.append(
"BackbonePDBSelector")
797 def _object_cast_to_BackbonePDBSelector(o):
798 r"""_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
799 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
801 _object_types.append(
"CHARMMParameters")
804 def _object_cast_to_CHARMMParameters(o):
805 r"""_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
806 return _IMP_atom._object_cast_to_CHARMMParameters(o)
808 _object_types.append(
"CHARMMResidueTopology")
811 def _object_cast_to_CHARMMResidueTopology(o):
812 r"""_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
813 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
815 _object_types.append(
"CHARMMSegmentTopology")
818 def _object_cast_to_CHARMMSegmentTopology(o):
819 r"""_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
820 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
822 _object_types.append(
"CHARMMStereochemistryRestraint")
825 def _object_cast_to_CHARMMStereochemistryRestraint(o):
826 r"""_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
827 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
829 _object_types.append(
"CHARMMTopology")
832 def _object_cast_to_CHARMMTopology(o):
833 r"""_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
834 return _IMP_atom._object_cast_to_CHARMMTopology(o)
836 _object_types.append(
"CPDBSelector")
839 def _object_cast_to_CPDBSelector(o):
840 r"""_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
841 return _IMP_atom._object_cast_to_CPDBSelector(o)
843 _object_types.append(
"ChainPDBSelector")
846 def _object_cast_to_ChainPDBSelector(o):
847 r"""_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
848 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
850 _object_types.append(
"CoulombPairScore")
853 def _object_cast_to_CoulombPairScore(o):
854 r"""_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
855 return _IMP_atom._object_cast_to_CoulombPairScore(o)
857 _object_types.append(
"CoverBond")
860 def _object_cast_to_CoverBond(o):
861 r"""_object_cast_to_CoverBond(Object o) -> CoverBond"""
862 return _IMP_atom._object_cast_to_CoverBond(o)
864 _object_types.append(
"DihedralSingletonScore")
867 def _object_cast_to_DihedralSingletonScore(o):
868 r"""_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
869 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
871 _object_types.append(
"DopePairScore")
874 def _object_cast_to_DopePairScore(o):
875 r"""_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
876 return _IMP_atom._object_cast_to_DopePairScore(o)
878 _object_types.append(
"LoopStatisticalPairScore")
881 def _object_cast_to_LoopStatisticalPairScore(o):
882 r"""_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
883 return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
885 _object_types.append(
"OrientedSoapPairScore")
888 def _object_cast_to_OrientedSoapPairScore(o):
889 r"""_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
890 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
892 _object_types.append(
"EzRestraint")
895 def _object_cast_to_EzRestraint(o):
896 r"""_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
897 return _IMP_atom._object_cast_to_EzRestraint(o)
899 _object_types.append(
"ForceFieldParameters")
902 def _object_cast_to_ForceFieldParameters(o):
903 r"""_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
904 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
906 _object_types.append(
"ForceSwitch")
909 def _object_cast_to_ForceSwitch(o):
910 r"""_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
911 return _IMP_atom._object_cast_to_ForceSwitch(o)
913 _object_types.append(
"HydrogenPDBSelector")
916 def _object_cast_to_HydrogenPDBSelector(o):
917 r"""_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
918 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
920 _object_types.append(
"ImproperSingletonScore")
923 def _object_cast_to_ImproperSingletonScore(o):
924 r"""_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
925 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
927 _object_types.append(
"LennardJonesPairScore")
930 def _object_cast_to_LennardJonesPairScore(o):
931 r"""_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
932 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
934 _object_types.append(
"Mol2Selector")
937 def _object_cast_to_Mol2Selector(o):
938 r"""_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
939 return _IMP_atom._object_cast_to_Mol2Selector(o)
941 _object_types.append(
"MolecularDynamics")
944 def _object_cast_to_MolecularDynamics(o):
945 r"""_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
946 return _IMP_atom._object_cast_to_MolecularDynamics(o)
948 _object_types.append(
"NPDBSelector")
951 def _object_cast_to_NPDBSelector(o):
952 r"""_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
953 return _IMP_atom._object_cast_to_NPDBSelector(o)
955 _object_types.append(
"NonAlternativePDBSelector")
958 def _object_cast_to_NonAlternativePDBSelector(o):
959 r"""_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
960 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
962 _object_types.append(
"NonHydrogenMol2Selector")
965 def _object_cast_to_NonHydrogenMol2Selector(o):
966 r"""_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
967 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
969 _object_types.append(
"NonHydrogenPDBSelector")
972 def _object_cast_to_NonHydrogenPDBSelector(o):
973 r"""_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
974 return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
976 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
979 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
980 r"""_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
981 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
983 _object_types.append(
"NonWaterPDBSelector")
986 def _object_cast_to_NonWaterPDBSelector(o):
987 r"""_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
988 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
990 _object_types.append(
"NotPDBSelector")
993 def _object_cast_to_NotPDBSelector(o):
994 r"""_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
995 return _IMP_atom._object_cast_to_NotPDBSelector(o)
997 _object_types.append(
"OrPDBSelector")
1000 def _object_cast_to_OrPDBSelector(o):
1001 r"""_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1002 return _IMP_atom._object_cast_to_OrPDBSelector(o)
1004 _object_types.append(
"PPDBSelector")
1007 def _object_cast_to_PPDBSelector(o):
1008 r"""_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1009 return _IMP_atom._object_cast_to_PPDBSelector(o)
1011 _object_types.append(
"ProteinLigandAtomPairScore")
1014 def _object_cast_to_ProteinLigandAtomPairScore(o):
1015 r"""_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1016 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1018 _object_types.append(
"ProteinLigandRestraint")
1021 def _object_cast_to_ProteinLigandRestraint(o):
1022 r"""_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1023 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1025 _object_types.append(
"SameResiduePairFilter")
1028 def _object_cast_to_SameResiduePairFilter(o):
1029 r"""_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1030 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1032 _object_types.append(
"SoapPairFilter")
1035 def _object_cast_to_SoapPairFilter(o):
1036 r"""_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1037 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1039 _object_types.append(
"SmoothingFunction")
1042 def _object_cast_to_SmoothingFunction(o):
1043 r"""_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1044 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1046 _object_types.append(
"StereochemistryPairFilter")
1049 def _object_cast_to_StereochemistryPairFilter(o):
1050 r"""_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1051 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1053 _object_types.append(
"VelocityScalingOptimizerState")
1056 def _object_cast_to_VelocityScalingOptimizerState(o):
1057 r"""_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1058 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1060 _object_types.append(
"WaterPDBSelector")
1063 def _object_cast_to_WaterPDBSelector(o):
1064 r"""_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1065 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1067 _object_types.append(
"WritePDBOptimizerState")
1070 def _object_cast_to_WritePDBOptimizerState(o):
1071 r"""_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1072 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1075 _plural_types.append(
"AtomTypes")
1076 _value_types.append(
"AtomType")
1079 CHARMMAtomTopologies=list
1080 _plural_types.append(
"CHARMMAtomTopologies")
1081 _value_types.append(
"CHARMMAtomTopology")
1084 CHARMMBondEndpoints=list
1085 _plural_types.append(
"CHARMMBondEndpoints")
1086 _value_types.append(
"CHARMMBondEndpoint")
1089 CHARMMBondParametersList=list
1090 _plural_types.append(
"CHARMMBondParametersList")
1091 _value_types.append(
"CHARMMBondParameters")
1094 CHARMMDihedralParametersList=list
1095 _plural_types.append(
"CHARMMDihedralParametersList")
1096 _value_types.append(
"CHARMMDihedralParameters")
1099 _object_types.append(
"CHARMMIdealResidueTopology")
1102 def _object_cast_to_CHARMMIdealResidueTopology(o):
1103 r"""_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1104 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1106 CHARMMInternalCoordinates=list
1107 _plural_types.append(
"CHARMMInternalCoordinates")
1108 _value_types.append(
"CHARMMInternalCoordinate")
1111 _object_types.append(
"CHARMMPatch")
1114 def _object_cast_to_CHARMMPatch(o):
1115 r"""_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1116 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1118 _object_types.append(
"CHARMMResidueTopologyBase")
1121 def _object_cast_to_CHARMMResidueTopologyBase(o):
1122 r"""_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1123 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1126 _plural_types.append(
"ResidueTypes")
1127 _value_types.append(
"ResidueType")
1131 _plural_types.append(
"ChainTypes")
1132 _value_types.append(
"ChainType")
1136 _plural_types.append(
"Selections")
1137 _value_types.append(
"Selection")
1140 _object_types.append(
"RemoveRigidMotionOptimizerState")
1143 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1144 r"""_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1145 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1147 _object_types.append(
"BerendsenThermostatOptimizerState")
1150 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1151 r"""_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1152 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1154 _object_types.append(
"LangevinThermostatOptimizerState")
1157 def _object_cast_to_LangevinThermostatOptimizerState(o):
1158 r"""_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1159 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1161 _object_types.append(
"SelectionGeometry")
1164 def _object_cast_to_SelectionGeometry(o):
1165 r"""_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1166 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1168 _object_types.append(
"HierarchyGeometry")
1171 def _object_cast_to_HierarchyGeometry(o):
1172 r"""_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1173 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1175 _object_types.append(
"HierarchiesGeometry")
1178 def _object_cast_to_HierarchiesGeometry(o):
1179 r"""_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1180 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1182 _object_types.append(
"BondGeometry")
1185 def _object_cast_to_BondGeometry(o):
1186 r"""_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1187 return _IMP_atom._object_cast_to_BondGeometry(o)
1189 _object_types.append(
"BondsGeometry")
1192 def _object_cast_to_BondsGeometry(o):
1193 r"""_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1194 return _IMP_atom._object_cast_to_BondsGeometry(o)
1196 _object_types.append(
"CAAngleRestraint")
1199 def _object_cast_to_CAAngleRestraint(o):
1200 r"""_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1201 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1203 _object_types.append(
"CADihedralRestraint")
1206 def _object_cast_to_CADihedralRestraint(o):
1207 r"""_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1208 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1210 _object_types.append(
"HelixRestraint")
1213 def _object_cast_to_HelixRestraint(o):
1214 r"""_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1215 return _IMP_atom._object_cast_to_HelixRestraint(o)
1217 CHARMMDihedrals=list
1218 _plural_types.append(
"CHARMMDihedrals")
1219 _value_types.append(
"CHARMMDihedral")
1223 _plural_types.append(
"CHARMMBonds")
1224 _value_types.append(
"CHARMMBond")
1228 _plural_types.append(
"CHARMMAngles")
1229 _value_types.append(
"CHARMMAngle")
1232 r"""Proxy of C++ IMP::atom::Bond class."""
1234 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1236 def __init__(self, *args):
1238 __init__(Bond self) -> Bond
1239 __init__(Bond self, Model m, ParticleIndex id) -> Bond
1240 __init__(Bond self, _ParticleAdaptor d) -> Bond
1242 _IMP_atom.Bond_swiginit(self, _IMP_atom.new_Bond(*args))
1244 def show(self, *args):
1245 r"""show(Bond self, _ostream out=std::cout)"""
1246 return _IMP_atom.Bond_show(self, *args)
1249 def get_is_setup(*args):
1251 get_is_setup(_ParticleAdaptor p) -> bool
1252 get_is_setup(Model m, ParticleIndex pi) -> bool
1254 return _IMP_atom.Bond_get_is_setup(*args)
1255 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1257 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1259 SINGLE = _IMP_atom.Bond_SINGLE
1261 DOUBLE = _IMP_atom.Bond_DOUBLE
1263 TRIPLE = _IMP_atom.Bond_TRIPLE
1265 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1267 SALT = _IMP_atom.Bond_SALT
1269 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1271 AMIDE = _IMP_atom.Bond_AMIDE
1273 AROMATIC = _IMP_atom.Bond_AROMATIC
1276 def get_bonded(self, i):
1277 r"""get_bonded(Bond self, unsigned int i) -> Bonded"""
1278 return _IMP_atom.Bond_get_bonded(self, i)
1281 r"""get_type(Bond self) -> IMP::Int"""
1282 return _IMP_atom.Bond_get_type(self)
1284 def set_type(self, t):
1285 r"""set_type(Bond self, IMP::Int t)"""
1286 return _IMP_atom.Bond_set_type(self, t)
1289 r"""get_order(Bond self) -> IMP::Int"""
1290 return _IMP_atom.Bond_get_order(self)
1292 def set_order(self, t):
1293 r"""set_order(Bond self, IMP::Int t)"""
1294 return _IMP_atom.Bond_set_order(self, t)
1296 def get_length(self):
1297 r"""get_length(Bond self) -> IMP::Float"""
1298 return _IMP_atom.Bond_get_length(self)
1300 def set_length(self, t):
1301 r"""set_length(Bond self, IMP::Float t)"""
1302 return _IMP_atom.Bond_set_length(self, t)
1304 def get_stiffness(self):
1305 r"""get_stiffness(Bond self) -> IMP::Float"""
1306 return _IMP_atom.Bond_get_stiffness(self)
1308 def set_stiffness(self, t):
1309 r"""set_stiffness(Bond self, IMP::Float t)"""
1310 return _IMP_atom.Bond_set_stiffness(self, t)
1313 def get_length_key():
1314 r"""get_length_key() -> FloatKey"""
1315 return _IMP_atom.Bond_get_length_key()
1317 def add_attribute(self, *args):
1319 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1320 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1321 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1322 add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1323 add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1324 add_attribute(Bond self, StringKey a0, IMP::String a1)
1325 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1326 add_attribute(Bond self, ObjectKey a0, Object a1)
1328 return _IMP_atom.Bond_add_attribute(self, *args)
1330 def get_value(self, *args):
1332 get_value(Bond self, FloatKey a0) -> IMP::Float
1333 get_value(Bond self, IntKey a0) -> IMP::Int
1334 get_value(Bond self, FloatsKey a0) -> IMP::Floats
1335 get_value(Bond self, IntsKey a0) -> IMP::Ints
1336 get_value(Bond self, StringKey a0) -> IMP::String
1337 get_value(Bond self, ParticleIndexKey a0) -> Particle
1338 get_value(Bond self, ObjectKey a0) -> Object
1340 return _IMP_atom.Bond_get_value(self, *args)
1342 def set_value(self, *args):
1344 set_value(Bond self, FloatKey a0, IMP::Float a1)
1345 set_value(Bond self, IntKey a0, IMP::Int a1)
1346 set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1347 set_value(Bond self, IntsKey a0, IMP::Ints a1)
1348 set_value(Bond self, StringKey a0, IMP::String a1)
1349 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1350 set_value(Bond self, ObjectKey a0, Object a1)
1352 return _IMP_atom.Bond_set_value(self, *args)
1354 def remove_attribute(self, *args):
1356 remove_attribute(Bond self, FloatKey a0)
1357 remove_attribute(Bond self, IntKey a0)
1358 remove_attribute(Bond self, FloatsKey a0)
1359 remove_attribute(Bond self, IntsKey a0)
1360 remove_attribute(Bond self, StringKey a0)
1361 remove_attribute(Bond self, ParticleIndexKey a0)
1362 remove_attribute(Bond self, ObjectKey a0)
1364 return _IMP_atom.Bond_remove_attribute(self, *args)
1366 def has_attribute(self, *args):
1368 has_attribute(Bond self, FloatKey a0) -> bool
1369 has_attribute(Bond self, IntKey a0) -> bool
1370 has_attribute(Bond self, FloatsKey a0) -> bool
1371 has_attribute(Bond self, IntsKey a0) -> bool
1372 has_attribute(Bond self, StringKey a0) -> bool
1373 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1374 has_attribute(Bond self, ObjectKey a0) -> bool
1376 return _IMP_atom.Bond_has_attribute(self, *args)
1378 def get_derivative(self, a0):
1379 r"""get_derivative(Bond self, FloatKey a0) -> double"""
1380 return _IMP_atom.Bond_get_derivative(self, a0)
1383 r"""get_name(Bond self) -> std::string"""
1384 return _IMP_atom.Bond_get_name(self)
1386 def clear_caches(self):
1387 r"""clear_caches(Bond self)"""
1388 return _IMP_atom.Bond_clear_caches(self)
1390 def set_name(self, a0):
1391 r"""set_name(Bond self, std::string a0)"""
1392 return _IMP_atom.Bond_set_name(self, a0)
1395 r"""set_check_level(Bond self, IMP::CheckLevel a0)"""
1396 return _IMP_atom.Bond_set_check_level(self, a0)
1398 def add_to_derivative(self, a0, a1, a2):
1399 r"""add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1400 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1402 def set_is_optimized(self, a0, a1):
1403 r"""set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1404 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1406 def get_is_optimized(self, a0):
1407 r"""get_is_optimized(Bond self, FloatKey a0) -> bool"""
1408 return _IMP_atom.Bond_get_is_optimized(self, a0)
1411 r"""get_check_level(Bond self) -> IMP::CheckLevel"""
1412 return _IMP_atom.Bond_get_check_level(self)
1414 def __eq__(self, *args):
1416 __eq__(Bond self, Bond o) -> bool
1417 __eq__(Bond self, Particle d) -> bool
1419 return _IMP_atom.Bond___eq__(self, *args)
1421 def __ne__(self, *args):
1423 __ne__(Bond self, Bond o) -> bool
1424 __ne__(Bond self, Particle d) -> bool
1426 return _IMP_atom.Bond___ne__(self, *args)
1428 def __le__(self, *args):
1430 __le__(Bond self, Bond o) -> bool
1431 __le__(Bond self, Particle d) -> bool
1433 return _IMP_atom.Bond___le__(self, *args)
1435 def __lt__(self, *args):
1437 __lt__(Bond self, Bond o) -> bool
1438 __lt__(Bond self, Particle d) -> bool
1440 return _IMP_atom.Bond___lt__(self, *args)
1442 def __ge__(self, *args):
1444 __ge__(Bond self, Bond o) -> bool
1445 __ge__(Bond self, Particle d) -> bool
1447 return _IMP_atom.Bond___ge__(self, *args)
1449 def __gt__(self, *args):
1451 __gt__(Bond self, Bond o) -> bool
1452 __gt__(Bond self, Particle d) -> bool
1454 return _IMP_atom.Bond___gt__(self, *args)
1457 r"""__hash__(Bond self) -> std::size_t"""
1458 return _IMP_atom.Bond___hash__(self)
1461 r"""__str__(Bond self) -> std::string"""
1462 return _IMP_atom.Bond___str__(self)
1465 r"""__repr__(Bond self) -> std::string"""
1466 return _IMP_atom.Bond___repr__(self)
1468 def _get_as_binary(self):
1469 r"""_get_as_binary(Bond self) -> PyObject *"""
1470 return _IMP_atom.Bond__get_as_binary(self)
1472 def _set_from_binary(self, p):
1473 r"""_set_from_binary(Bond self, PyObject * p)"""
1474 return _IMP_atom.Bond__set_from_binary(self, p)
1476 def __getstate__(self):
1477 p = self._get_as_binary()
1478 if len(self.__dict__) > 1:
1479 d = self.__dict__.copy()
1484 def __setstate__(self, p):
1485 if not hasattr(self,
'this'):
1487 if isinstance(p, tuple):
1489 self.__dict__.update(d)
1490 return self._set_from_binary(p)
1492 __swig_destroy__ = _IMP_atom.delete_Bond
1495 _IMP_atom.Bond_swigregister(Bond)
1497 r"""Proxy of C++ IMP::atom::Bonded class."""
1499 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1501 def __init__(self, *args):
1503 __init__(Bonded self) -> Bonded
1504 __init__(Bonded self, Model m, ParticleIndex id) -> Bonded
1505 __init__(Bonded self, _ParticleAdaptor d) -> Bonded
1507 _IMP_atom.Bonded_swiginit(self, _IMP_atom.new_Bonded(*args))
1509 def show(self, *args):
1510 r"""show(Bonded self, _ostream out=std::cout)"""
1511 return _IMP_atom.Bonded_show(self, *args)
1514 def setup_particle(*args):
1516 setup_particle(Model m, ParticleIndex pi) -> Bonded
1517 setup_particle(_ParticleAdaptor pa) -> Bonded
1519 return _IMP_atom.Bonded_setup_particle(*args)
1522 def get_is_setup(*args):
1524 get_is_setup(_ParticleAdaptor p) -> bool
1525 get_is_setup(Model m, ParticleIndex pi) -> bool
1527 return _IMP_atom.Bonded_get_is_setup(*args)
1529 def get_number_of_bonds(self):
1530 r"""get_number_of_bonds(Bonded self) -> unsigned int"""
1531 return _IMP_atom.Bonded_get_number_of_bonds(self)
1533 def get_bond_indexes(self):
1534 r"""get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1535 return _IMP_atom.Bonded_get_bond_indexes(self)
1538 r"""get_bond(Bonded self, unsigned int i) -> Bond"""
1539 return _IMP_atom.Bonded_get_bond(self, i)
1541 def get_bonded(self, i):
1542 r"""get_bonded(Bonded self, unsigned int i) -> Bonded"""
1543 return _IMP_atom.Bonded_get_bonded(self, i)
1545 def add_attribute(self, *args):
1547 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1548 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1549 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1550 add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1551 add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1552 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1553 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1554 add_attribute(Bonded self, ObjectKey a0, Object a1)
1556 return _IMP_atom.Bonded_add_attribute(self, *args)
1558 def get_value(self, *args):
1560 get_value(Bonded self, FloatKey a0) -> IMP::Float
1561 get_value(Bonded self, IntKey a0) -> IMP::Int
1562 get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1563 get_value(Bonded self, IntsKey a0) -> IMP::Ints
1564 get_value(Bonded self, StringKey a0) -> IMP::String
1565 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1566 get_value(Bonded self, ObjectKey a0) -> Object
1568 return _IMP_atom.Bonded_get_value(self, *args)
1570 def set_value(self, *args):
1572 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1573 set_value(Bonded self, IntKey a0, IMP::Int a1)
1574 set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1575 set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1576 set_value(Bonded self, StringKey a0, IMP::String a1)
1577 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1578 set_value(Bonded self, ObjectKey a0, Object a1)
1580 return _IMP_atom.Bonded_set_value(self, *args)
1582 def remove_attribute(self, *args):
1584 remove_attribute(Bonded self, FloatKey a0)
1585 remove_attribute(Bonded self, IntKey a0)
1586 remove_attribute(Bonded self, FloatsKey a0)
1587 remove_attribute(Bonded self, IntsKey a0)
1588 remove_attribute(Bonded self, StringKey a0)
1589 remove_attribute(Bonded self, ParticleIndexKey a0)
1590 remove_attribute(Bonded self, ObjectKey a0)
1592 return _IMP_atom.Bonded_remove_attribute(self, *args)
1594 def has_attribute(self, *args):
1596 has_attribute(Bonded self, FloatKey a0) -> bool
1597 has_attribute(Bonded self, IntKey a0) -> bool
1598 has_attribute(Bonded self, FloatsKey a0) -> bool
1599 has_attribute(Bonded self, IntsKey a0) -> bool
1600 has_attribute(Bonded self, StringKey a0) -> bool
1601 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1602 has_attribute(Bonded self, ObjectKey a0) -> bool
1604 return _IMP_atom.Bonded_has_attribute(self, *args)
1606 def get_derivative(self, a0):
1607 r"""get_derivative(Bonded self, FloatKey a0) -> double"""
1608 return _IMP_atom.Bonded_get_derivative(self, a0)
1611 r"""get_name(Bonded self) -> std::string"""
1612 return _IMP_atom.Bonded_get_name(self)
1614 def clear_caches(self):
1615 r"""clear_caches(Bonded self)"""
1616 return _IMP_atom.Bonded_clear_caches(self)
1618 def set_name(self, a0):
1619 r"""set_name(Bonded self, std::string a0)"""
1620 return _IMP_atom.Bonded_set_name(self, a0)
1623 r"""set_check_level(Bonded self, IMP::CheckLevel a0)"""
1624 return _IMP_atom.Bonded_set_check_level(self, a0)
1626 def add_to_derivative(self, a0, a1, a2):
1627 r"""add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1628 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1630 def set_is_optimized(self, a0, a1):
1631 r"""set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1632 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1634 def get_is_optimized(self, a0):
1635 r"""get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1636 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1639 r"""get_check_level(Bonded self) -> IMP::CheckLevel"""
1640 return _IMP_atom.Bonded_get_check_level(self)
1642 def __eq__(self, *args):
1644 __eq__(Bonded self, Bonded o) -> bool
1645 __eq__(Bonded self, Particle d) -> bool
1647 return _IMP_atom.Bonded___eq__(self, *args)
1649 def __ne__(self, *args):
1651 __ne__(Bonded self, Bonded o) -> bool
1652 __ne__(Bonded self, Particle d) -> bool
1654 return _IMP_atom.Bonded___ne__(self, *args)
1656 def __le__(self, *args):
1658 __le__(Bonded self, Bonded o) -> bool
1659 __le__(Bonded self, Particle d) -> bool
1661 return _IMP_atom.Bonded___le__(self, *args)
1663 def __lt__(self, *args):
1665 __lt__(Bonded self, Bonded o) -> bool
1666 __lt__(Bonded self, Particle d) -> bool
1668 return _IMP_atom.Bonded___lt__(self, *args)
1670 def __ge__(self, *args):
1672 __ge__(Bonded self, Bonded o) -> bool
1673 __ge__(Bonded self, Particle d) -> bool
1675 return _IMP_atom.Bonded___ge__(self, *args)
1677 def __gt__(self, *args):
1679 __gt__(Bonded self, Bonded o) -> bool
1680 __gt__(Bonded self, Particle d) -> bool
1682 return _IMP_atom.Bonded___gt__(self, *args)
1685 r"""__hash__(Bonded self) -> std::size_t"""
1686 return _IMP_atom.Bonded___hash__(self)
1689 r"""__str__(Bonded self) -> std::string"""
1690 return _IMP_atom.Bonded___str__(self)
1693 r"""__repr__(Bonded self) -> std::string"""
1694 return _IMP_atom.Bonded___repr__(self)
1696 def _get_as_binary(self):
1697 r"""_get_as_binary(Bonded self) -> PyObject *"""
1698 return _IMP_atom.Bonded__get_as_binary(self)
1700 def _set_from_binary(self, p):
1701 r"""_set_from_binary(Bonded self, PyObject * p)"""
1702 return _IMP_atom.Bonded__set_from_binary(self, p)
1704 def __getstate__(self):
1705 p = self._get_as_binary()
1706 if len(self.__dict__) > 1:
1707 d = self.__dict__.copy()
1712 def __setstate__(self, p):
1713 if not hasattr(self,
'this'):
1715 if isinstance(p, tuple):
1717 self.__dict__.update(d)
1718 return self._set_from_binary(p)
1720 __swig_destroy__ = _IMP_atom.delete_Bonded
1723 _IMP_atom.Bonded_swigregister(Bonded)
1726 r"""create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond"""
1727 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1731 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1732 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1734 return _IMP_atom.create_bond(*args)
1737 r"""destroy_bond(Bond b)"""
1738 return _IMP_atom.destroy_bond(b)
1741 r"""get_bond(Bonded a, Bonded b) -> Bond"""
1742 return _IMP_atom.get_bond(a, b)
1744 r"""Proxy of C++ IMP::atom::BondGeometry class."""
1746 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1748 def __init__(self, *args):
1750 __init__(BondGeometry self, Particle p) -> BondGeometry
1751 __init__(BondGeometry self, Bond d) -> BondGeometry
1753 _IMP_atom.BondGeometry_swiginit(self, _IMP_atom.new_BondGeometry(*args))
1755 def get_version_info(self):
1756 r"""get_version_info(BondGeometry self) -> VersionInfo"""
1757 return _IMP_atom.BondGeometry_get_version_info(self)
1758 __swig_destroy__ = _IMP_atom.delete_BondGeometry
1761 r"""__str__(BondGeometry self) -> std::string"""
1762 return _IMP_atom.BondGeometry___str__(self)
1765 r"""__repr__(BondGeometry self) -> std::string"""
1766 return _IMP_atom.BondGeometry___repr__(self)
1770 return _object_cast_to_BondGeometry(o)
1774 _IMP_atom.BondGeometry_swigregister(BondGeometry)
1776 r"""Proxy of C++ IMP::atom::BondsGeometry class."""
1778 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1780 def __init__(self, sc):
1781 r"""__init__(BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1782 _IMP_atom.BondsGeometry_swiginit(self, _IMP_atom.new_BondsGeometry(sc))
1784 def get_version_info(self):
1785 r"""get_version_info(BondsGeometry self) -> VersionInfo"""
1786 return _IMP_atom.BondsGeometry_get_version_info(self)
1787 __swig_destroy__ = _IMP_atom.delete_BondsGeometry
1790 r"""__str__(BondsGeometry self) -> std::string"""
1791 return _IMP_atom.BondsGeometry___str__(self)
1794 r"""__repr__(BondsGeometry self) -> std::string"""
1795 return _IMP_atom.BondsGeometry___repr__(self)
1799 return _object_cast_to_BondsGeometry(o)
1803 _IMP_atom.BondsGeometry_swigregister(BondsGeometry)
1805 r"""Proxy of C++ IMP::atom::Hierarchy class."""
1807 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1809 def __init__(self, *args):
1811 __init__(Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1812 __init__(Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1813 __init__(Hierarchy self) -> Hierarchy
1814 __init__(Hierarchy self, Hierarchy h) -> Hierarchy
1816 _IMP_atom.Hierarchy_swiginit(self, _IMP_atom.new_Hierarchy(*args))
1819 def setup_particle(*args):
1821 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1822 setup_particle(Particle p) -> Hierarchy
1823 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children=IMP::ParticleIndexesAdaptor()) -> Hierarchy
1825 return _IMP_atom.Hierarchy_setup_particle(*args)
1828 def get_is_setup(*args):
1830 get_is_setup(Particle p) -> bool
1831 get_is_setup(Model m, ParticleIndex p) -> bool
1833 return _IMP_atom.Hierarchy_get_is_setup(*args)
1835 def get_is_valid(self, print_info=False):
1836 r"""get_is_valid(Hierarchy self, bool print_info=False) -> bool"""
1837 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1839 def add_child(self, o):
1840 r"""add_child(Hierarchy self, Hierarchy o)"""
1841 return _IMP_atom.Hierarchy_add_child(self, o)
1843 def get_child(self, i):
1844 r"""get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1845 return _IMP_atom.Hierarchy_get_child(self, i)
1847 def get_children(self):
1848 r"""get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1849 return _IMP_atom.Hierarchy_get_children(self)
1851 def get_parent(self):
1852 r"""get_parent(Hierarchy self) -> Hierarchy"""
1853 return _IMP_atom.Hierarchy_get_parent(self)
1857 r"""get_traits() -> HierarchyTraits"""
1858 return _IMP_atom.Hierarchy_get_traits()
1860 def show(self, *args):
1862 show(Hierarchy self, _ostream out, std::string delimiter)
1863 show(Hierarchy self, _ostream out=std::cout)
1865 return _IMP_atom.Hierarchy_show(self, *args)
1867 def add_attribute(self, *args):
1869 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1870 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1871 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1872 add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1873 add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1874 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1875 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1876 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1878 return _IMP_atom.Hierarchy_add_attribute(self, *args)
1880 def get_value(self, *args):
1882 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1883 get_value(Hierarchy self, IntKey a0) -> IMP::Int
1884 get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1885 get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1886 get_value(Hierarchy self, StringKey a0) -> IMP::String
1887 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1888 get_value(Hierarchy self, ObjectKey a0) -> Object
1890 return _IMP_atom.Hierarchy_get_value(self, *args)
1892 def set_value(self, *args):
1894 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1895 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1896 set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1897 set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1898 set_value(Hierarchy self, StringKey a0, IMP::String a1)
1899 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1900 set_value(Hierarchy self, ObjectKey a0, Object a1)
1902 return _IMP_atom.Hierarchy_set_value(self, *args)
1904 def remove_attribute(self, *args):
1906 remove_attribute(Hierarchy self, FloatKey a0)
1907 remove_attribute(Hierarchy self, IntKey a0)
1908 remove_attribute(Hierarchy self, FloatsKey a0)
1909 remove_attribute(Hierarchy self, IntsKey a0)
1910 remove_attribute(Hierarchy self, StringKey a0)
1911 remove_attribute(Hierarchy self, ParticleIndexKey a0)
1912 remove_attribute(Hierarchy self, ObjectKey a0)
1914 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1916 def has_attribute(self, *args):
1918 has_attribute(Hierarchy self, FloatKey a0) -> bool
1919 has_attribute(Hierarchy self, IntKey a0) -> bool
1920 has_attribute(Hierarchy self, FloatsKey a0) -> bool
1921 has_attribute(Hierarchy self, IntsKey a0) -> bool
1922 has_attribute(Hierarchy self, StringKey a0) -> bool
1923 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1924 has_attribute(Hierarchy self, ObjectKey a0) -> bool
1926 return _IMP_atom.Hierarchy_has_attribute(self, *args)
1928 def get_derivative(self, a0):
1929 r"""get_derivative(Hierarchy self, FloatKey a0) -> double"""
1930 return _IMP_atom.Hierarchy_get_derivative(self, a0)
1933 r"""get_name(Hierarchy self) -> std::string"""
1934 return _IMP_atom.Hierarchy_get_name(self)
1936 def clear_caches(self):
1937 r"""clear_caches(Hierarchy self)"""
1938 return _IMP_atom.Hierarchy_clear_caches(self)
1940 def set_name(self, a0):
1941 r"""set_name(Hierarchy self, std::string a0)"""
1942 return _IMP_atom.Hierarchy_set_name(self, a0)
1945 r"""set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
1946 return _IMP_atom.Hierarchy_set_check_level(self, a0)
1948 def add_to_derivative(self, a0, a1, a2):
1949 r"""add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1950 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
1952 def set_is_optimized(self, a0, a1):
1953 r"""set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1954 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
1956 def get_is_optimized(self, a0):
1957 r"""get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1958 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
1961 r"""get_check_level(Hierarchy self) -> IMP::CheckLevel"""
1962 return _IMP_atom.Hierarchy_get_check_level(self)
1964 def __eq__(self, *args):
1966 __eq__(Hierarchy self, Hierarchy o) -> bool
1967 __eq__(Hierarchy self, Particle d) -> bool
1969 return _IMP_atom.Hierarchy___eq__(self, *args)
1971 def __ne__(self, *args):
1973 __ne__(Hierarchy self, Hierarchy o) -> bool
1974 __ne__(Hierarchy self, Particle d) -> bool
1976 return _IMP_atom.Hierarchy___ne__(self, *args)
1978 def __le__(self, *args):
1980 __le__(Hierarchy self, Hierarchy o) -> bool
1981 __le__(Hierarchy self, Particle d) -> bool
1983 return _IMP_atom.Hierarchy___le__(self, *args)
1985 def __lt__(self, *args):
1987 __lt__(Hierarchy self, Hierarchy o) -> bool
1988 __lt__(Hierarchy self, Particle d) -> bool
1990 return _IMP_atom.Hierarchy___lt__(self, *args)
1992 def __ge__(self, *args):
1994 __ge__(Hierarchy self, Hierarchy o) -> bool
1995 __ge__(Hierarchy self, Particle d) -> bool
1997 return _IMP_atom.Hierarchy___ge__(self, *args)
1999 def __gt__(self, *args):
2001 __gt__(Hierarchy self, Hierarchy o) -> bool
2002 __gt__(Hierarchy self, Particle d) -> bool
2004 return _IMP_atom.Hierarchy___gt__(self, *args)
2007 r"""__hash__(Hierarchy self) -> std::size_t"""
2008 return _IMP_atom.Hierarchy___hash__(self)
2011 r"""__str__(Hierarchy self) -> std::string"""
2012 return _IMP_atom.Hierarchy___str__(self)
2015 r"""__repr__(Hierarchy self) -> std::string"""
2016 return _IMP_atom.Hierarchy___repr__(self)
2018 def _get_as_binary(self):
2019 r"""_get_as_binary(Hierarchy self) -> PyObject *"""
2020 return _IMP_atom.Hierarchy__get_as_binary(self)
2022 def _set_from_binary(self, p):
2023 r"""_set_from_binary(Hierarchy self, PyObject * p)"""
2024 return _IMP_atom.Hierarchy__set_from_binary(self, p)
2026 def __getstate__(self):
2027 p = self._get_as_binary()
2028 if len(self.__dict__) > 1:
2029 d = self.__dict__.copy()
2034 def __setstate__(self, p):
2035 if not hasattr(self,
'this'):
2037 if isinstance(p, tuple):
2039 self.__dict__.update(d)
2040 return self._set_from_binary(p)
2042 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2045 _IMP_atom.Hierarchy_swigregister(Hierarchy)
2046 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2048 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2050 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2052 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2054 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2056 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2058 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2060 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2062 MASS_TYPE = _IMP_atom.MASS_TYPE
2064 STATE_TYPE = _IMP_atom.STATE_TYPE
2067 def get_by_type(mhd, t):
2068 r"""get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2069 return _IMP_atom.get_by_type(mhd, t)
2071 def create_fragment(ps):
2072 r"""create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2073 return _IMP_atom.create_fragment(ps)
2075 def get_internal_bonds(mhd):
2076 r"""get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2077 return _IMP_atom.get_internal_bonds(mhd)
2080 r"""get_root(Hierarchy h) -> Hierarchy"""
2081 return _IMP_atom.get_root(h)
2084 r"""show(Hierarchy h, _ostream out=std::cout)"""
2085 return _IMP_atom.show(*args)
2089 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name=std::string("created rigid body")) -> RigidBody
2090 create_rigid_body(Hierarchy h) -> RigidBody
2092 return _IMP_atom.create_rigid_body(*args)
2095 r"""create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2096 return _IMP_atom.create_compatible_rigid_body(h, reference)
2098 def get_is_heterogen(h):
2099 r"""get_is_heterogen(Hierarchy h) -> bool"""
2100 return _IMP_atom.get_is_heterogen(h)
2103 r"""create_clone(Hierarchy d) -> Hierarchy"""
2104 return _IMP_atom.create_clone(d)
2106 def create_clone_one(d):
2107 r"""create_clone_one(Hierarchy d) -> Hierarchy"""
2108 return _IMP_atom.create_clone_one(d)
2111 r"""destroy(Hierarchy d)"""
2112 return _IMP_atom.destroy(d)
2114 def get_bounding_box(h):
2115 r"""get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2116 return _IMP_atom.get_bounding_box(h)
2118 def get_bounding_sphere(h):
2119 r"""get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2120 return _IMP_atom.get_bounding_sphere(h)
2122 r"""Proxy of C++ IMP::atom::Angle class."""
2124 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2126 def __init__(self, *args):
2128 __init__(Angle self) -> Angle
2129 __init__(Angle self, Model m, ParticleIndex id) -> Angle
2130 __init__(Angle self, _ParticleAdaptor d) -> Angle
2132 _IMP_atom.Angle_swiginit(self, _IMP_atom.new_Angle(*args))
2134 def show(self, *args):
2135 r"""show(Angle self, _ostream out=std::cout)"""
2136 return _IMP_atom.Angle_show(self, *args)
2139 def setup_particle(*args):
2141 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2142 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c) -> Angle
2144 return _IMP_atom.Angle_setup_particle(*args)
2147 def get_is_setup(*args):
2149 get_is_setup(_ParticleAdaptor p) -> bool
2150 get_is_setup(Model m, ParticleIndex pi) -> bool
2152 return _IMP_atom.Angle_get_is_setup(*args)
2154 def get_particle(self, *args):
2156 get_particle(Angle self) -> Particle
2157 get_particle(Angle self, unsigned int i) -> Particle
2159 return _IMP_atom.Angle_get_particle(self, *args)
2161 def get_ideal(self):
2162 r"""get_ideal(Angle self) -> IMP::Float"""
2163 return _IMP_atom.Angle_get_ideal(self)
2165 def set_ideal(self, t):
2166 r"""set_ideal(Angle self, IMP::Float t)"""
2167 return _IMP_atom.Angle_set_ideal(self, t)
2169 def get_stiffness(self):
2170 r"""get_stiffness(Angle self) -> IMP::Float"""
2171 return _IMP_atom.Angle_get_stiffness(self)
2173 def set_stiffness(self, t):
2174 r"""set_stiffness(Angle self, IMP::Float t)"""
2175 return _IMP_atom.Angle_set_stiffness(self, t)
2178 def get_particle_key(i):
2179 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2180 return _IMP_atom.Angle_get_particle_key(i)
2183 def get_ideal_key():
2184 r"""get_ideal_key() -> FloatKey"""
2185 return _IMP_atom.Angle_get_ideal_key()
2188 def get_stiffness_key():
2189 r"""get_stiffness_key() -> FloatKey"""
2190 return _IMP_atom.Angle_get_stiffness_key()
2192 def add_attribute(self, *args):
2194 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2195 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2196 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2197 add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2198 add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2199 add_attribute(Angle self, StringKey a0, IMP::String a1)
2200 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2201 add_attribute(Angle self, ObjectKey a0, Object a1)
2203 return _IMP_atom.Angle_add_attribute(self, *args)
2205 def get_value(self, *args):
2207 get_value(Angle self, FloatKey a0) -> IMP::Float
2208 get_value(Angle self, IntKey a0) -> IMP::Int
2209 get_value(Angle self, FloatsKey a0) -> IMP::Floats
2210 get_value(Angle self, IntsKey a0) -> IMP::Ints
2211 get_value(Angle self, StringKey a0) -> IMP::String
2212 get_value(Angle self, ParticleIndexKey a0) -> Particle
2213 get_value(Angle self, ObjectKey a0) -> Object
2215 return _IMP_atom.Angle_get_value(self, *args)
2217 def set_value(self, *args):
2219 set_value(Angle self, FloatKey a0, IMP::Float a1)
2220 set_value(Angle self, IntKey a0, IMP::Int a1)
2221 set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2222 set_value(Angle self, IntsKey a0, IMP::Ints a1)
2223 set_value(Angle self, StringKey a0, IMP::String a1)
2224 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2225 set_value(Angle self, ObjectKey a0, Object a1)
2227 return _IMP_atom.Angle_set_value(self, *args)
2229 def remove_attribute(self, *args):
2231 remove_attribute(Angle self, FloatKey a0)
2232 remove_attribute(Angle self, IntKey a0)
2233 remove_attribute(Angle self, FloatsKey a0)
2234 remove_attribute(Angle self, IntsKey a0)
2235 remove_attribute(Angle self, StringKey a0)
2236 remove_attribute(Angle self, ParticleIndexKey a0)
2237 remove_attribute(Angle self, ObjectKey a0)
2239 return _IMP_atom.Angle_remove_attribute(self, *args)
2241 def has_attribute(self, *args):
2243 has_attribute(Angle self, FloatKey a0) -> bool
2244 has_attribute(Angle self, IntKey a0) -> bool
2245 has_attribute(Angle self, FloatsKey a0) -> bool
2246 has_attribute(Angle self, IntsKey a0) -> bool
2247 has_attribute(Angle self, StringKey a0) -> bool
2248 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2249 has_attribute(Angle self, ObjectKey a0) -> bool
2251 return _IMP_atom.Angle_has_attribute(self, *args)
2253 def get_derivative(self, a0):
2254 r"""get_derivative(Angle self, FloatKey a0) -> double"""
2255 return _IMP_atom.Angle_get_derivative(self, a0)
2258 r"""get_name(Angle self) -> std::string"""
2259 return _IMP_atom.Angle_get_name(self)
2261 def clear_caches(self):
2262 r"""clear_caches(Angle self)"""
2263 return _IMP_atom.Angle_clear_caches(self)
2265 def set_name(self, a0):
2266 r"""set_name(Angle self, std::string a0)"""
2267 return _IMP_atom.Angle_set_name(self, a0)
2270 r"""set_check_level(Angle self, IMP::CheckLevel a0)"""
2271 return _IMP_atom.Angle_set_check_level(self, a0)
2273 def add_to_derivative(self, a0, a1, a2):
2274 r"""add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2275 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2277 def set_is_optimized(self, a0, a1):
2278 r"""set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2279 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2281 def get_is_optimized(self, a0):
2282 r"""get_is_optimized(Angle self, FloatKey a0) -> bool"""
2283 return _IMP_atom.Angle_get_is_optimized(self, a0)
2286 r"""get_check_level(Angle self) -> IMP::CheckLevel"""
2287 return _IMP_atom.Angle_get_check_level(self)
2289 def __eq__(self, *args):
2291 __eq__(Angle self, Angle o) -> bool
2292 __eq__(Angle self, Particle d) -> bool
2294 return _IMP_atom.Angle___eq__(self, *args)
2296 def __ne__(self, *args):
2298 __ne__(Angle self, Angle o) -> bool
2299 __ne__(Angle self, Particle d) -> bool
2301 return _IMP_atom.Angle___ne__(self, *args)
2303 def __le__(self, *args):
2305 __le__(Angle self, Angle o) -> bool
2306 __le__(Angle self, Particle d) -> bool
2308 return _IMP_atom.Angle___le__(self, *args)
2310 def __lt__(self, *args):
2312 __lt__(Angle self, Angle o) -> bool
2313 __lt__(Angle self, Particle d) -> bool
2315 return _IMP_atom.Angle___lt__(self, *args)
2317 def __ge__(self, *args):
2319 __ge__(Angle self, Angle o) -> bool
2320 __ge__(Angle self, Particle d) -> bool
2322 return _IMP_atom.Angle___ge__(self, *args)
2324 def __gt__(self, *args):
2326 __gt__(Angle self, Angle o) -> bool
2327 __gt__(Angle self, Particle d) -> bool
2329 return _IMP_atom.Angle___gt__(self, *args)
2332 r"""__hash__(Angle self) -> std::size_t"""
2333 return _IMP_atom.Angle___hash__(self)
2336 r"""__str__(Angle self) -> std::string"""
2337 return _IMP_atom.Angle___str__(self)
2340 r"""__repr__(Angle self) -> std::string"""
2341 return _IMP_atom.Angle___repr__(self)
2343 def _get_as_binary(self):
2344 r"""_get_as_binary(Angle self) -> PyObject *"""
2345 return _IMP_atom.Angle__get_as_binary(self)
2347 def _set_from_binary(self, p):
2348 r"""_set_from_binary(Angle self, PyObject * p)"""
2349 return _IMP_atom.Angle__set_from_binary(self, p)
2351 def __getstate__(self):
2352 p = self._get_as_binary()
2353 if len(self.__dict__) > 1:
2354 d = self.__dict__.copy()
2359 def __setstate__(self, p):
2360 if not hasattr(self,
'this'):
2362 if isinstance(p, tuple):
2364 self.__dict__.update(d)
2365 return self._set_from_binary(p)
2367 __swig_destroy__ = _IMP_atom.delete_Angle
2370 _IMP_atom.Angle_swigregister(Angle)
2372 r"""Proxy of C++ IMP::atom::Dihedral class."""
2374 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2376 def __init__(self, *args):
2378 __init__(Dihedral self) -> Dihedral
2379 __init__(Dihedral self, Model m, ParticleIndex id) -> Dihedral
2380 __init__(Dihedral self, _ParticleAdaptor d) -> Dihedral
2382 _IMP_atom.Dihedral_swiginit(self, _IMP_atom.new_Dihedral(*args))
2384 def show(self, *args):
2385 r"""show(Dihedral self, _ostream out=std::cout)"""
2386 return _IMP_atom.Dihedral_show(self, *args)
2389 def setup_particle(*args):
2391 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2392 setup_particle(_ParticleAdaptor pa, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2394 return _IMP_atom.Dihedral_setup_particle(*args)
2397 def get_is_setup(*args):
2399 get_is_setup(_ParticleAdaptor p) -> bool
2400 get_is_setup(Model m, ParticleIndex pi) -> bool
2402 return _IMP_atom.Dihedral_get_is_setup(*args)
2404 def get_particle(self, *args):
2406 get_particle(Dihedral self) -> Particle
2407 get_particle(Dihedral self, unsigned int i) -> Particle
2409 return _IMP_atom.Dihedral_get_particle(self, *args)
2411 def get_ideal(self):
2412 r"""get_ideal(Dihedral self) -> IMP::Float"""
2413 return _IMP_atom.Dihedral_get_ideal(self)
2415 def set_ideal(self, t):
2416 r"""set_ideal(Dihedral self, IMP::Float t)"""
2417 return _IMP_atom.Dihedral_set_ideal(self, t)
2419 def get_multiplicity(self):
2420 r"""get_multiplicity(Dihedral self) -> IMP::Int"""
2421 return _IMP_atom.Dihedral_get_multiplicity(self)
2423 def set_multiplicity(self, t):
2424 r"""set_multiplicity(Dihedral self, IMP::Int t)"""
2425 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2427 def get_stiffness(self):
2428 r"""get_stiffness(Dihedral self) -> IMP::Float"""
2429 return _IMP_atom.Dihedral_get_stiffness(self)
2431 def set_stiffness(self, t):
2432 r"""set_stiffness(Dihedral self, IMP::Float t)"""
2433 return _IMP_atom.Dihedral_set_stiffness(self, t)
2436 def get_particle_key(i):
2437 r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2438 return _IMP_atom.Dihedral_get_particle_key(i)
2441 def get_ideal_key():
2442 r"""get_ideal_key() -> FloatKey"""
2443 return _IMP_atom.Dihedral_get_ideal_key()
2446 def get_multiplicity_key():
2447 r"""get_multiplicity_key() -> IntKey"""
2448 return _IMP_atom.Dihedral_get_multiplicity_key()
2451 def get_stiffness_key():
2452 r"""get_stiffness_key() -> FloatKey"""
2453 return _IMP_atom.Dihedral_get_stiffness_key()
2455 def add_attribute(self, *args):
2457 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2458 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2459 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2460 add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2461 add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2462 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2463 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2464 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2466 return _IMP_atom.Dihedral_add_attribute(self, *args)
2468 def get_value(self, *args):
2470 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2471 get_value(Dihedral self, IntKey a0) -> IMP::Int
2472 get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2473 get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2474 get_value(Dihedral self, StringKey a0) -> IMP::String
2475 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2476 get_value(Dihedral self, ObjectKey a0) -> Object
2478 return _IMP_atom.Dihedral_get_value(self, *args)
2480 def set_value(self, *args):
2482 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2483 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2484 set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2485 set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2486 set_value(Dihedral self, StringKey a0, IMP::String a1)
2487 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2488 set_value(Dihedral self, ObjectKey a0, Object a1)
2490 return _IMP_atom.Dihedral_set_value(self, *args)
2492 def remove_attribute(self, *args):
2494 remove_attribute(Dihedral self, FloatKey a0)
2495 remove_attribute(Dihedral self, IntKey a0)
2496 remove_attribute(Dihedral self, FloatsKey a0)
2497 remove_attribute(Dihedral self, IntsKey a0)
2498 remove_attribute(Dihedral self, StringKey a0)
2499 remove_attribute(Dihedral self, ParticleIndexKey a0)
2500 remove_attribute(Dihedral self, ObjectKey a0)
2502 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2504 def has_attribute(self, *args):
2506 has_attribute(Dihedral self, FloatKey a0) -> bool
2507 has_attribute(Dihedral self, IntKey a0) -> bool
2508 has_attribute(Dihedral self, FloatsKey a0) -> bool
2509 has_attribute(Dihedral self, IntsKey a0) -> bool
2510 has_attribute(Dihedral self, StringKey a0) -> bool
2511 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2512 has_attribute(Dihedral self, ObjectKey a0) -> bool
2514 return _IMP_atom.Dihedral_has_attribute(self, *args)
2516 def get_derivative(self, a0):
2517 r"""get_derivative(Dihedral self, FloatKey a0) -> double"""
2518 return _IMP_atom.Dihedral_get_derivative(self, a0)
2521 r"""get_name(Dihedral self) -> std::string"""
2522 return _IMP_atom.Dihedral_get_name(self)
2524 def clear_caches(self):
2525 r"""clear_caches(Dihedral self)"""
2526 return _IMP_atom.Dihedral_clear_caches(self)
2528 def set_name(self, a0):
2529 r"""set_name(Dihedral self, std::string a0)"""
2530 return _IMP_atom.Dihedral_set_name(self, a0)
2533 r"""set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2534 return _IMP_atom.Dihedral_set_check_level(self, a0)
2536 def add_to_derivative(self, a0, a1, a2):
2537 r"""add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2538 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2540 def set_is_optimized(self, a0, a1):
2541 r"""set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2542 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2544 def get_is_optimized(self, a0):
2545 r"""get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2546 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2549 r"""get_check_level(Dihedral self) -> IMP::CheckLevel"""
2550 return _IMP_atom.Dihedral_get_check_level(self)
2552 def __eq__(self, *args):
2554 __eq__(Dihedral self, Dihedral o) -> bool
2555 __eq__(Dihedral self, Particle d) -> bool
2557 return _IMP_atom.Dihedral___eq__(self, *args)
2559 def __ne__(self, *args):
2561 __ne__(Dihedral self, Dihedral o) -> bool
2562 __ne__(Dihedral self, Particle d) -> bool
2564 return _IMP_atom.Dihedral___ne__(self, *args)
2566 def __le__(self, *args):
2568 __le__(Dihedral self, Dihedral o) -> bool
2569 __le__(Dihedral self, Particle d) -> bool
2571 return _IMP_atom.Dihedral___le__(self, *args)
2573 def __lt__(self, *args):
2575 __lt__(Dihedral self, Dihedral o) -> bool
2576 __lt__(Dihedral self, Particle d) -> bool
2578 return _IMP_atom.Dihedral___lt__(self, *args)
2580 def __ge__(self, *args):
2582 __ge__(Dihedral self, Dihedral o) -> bool
2583 __ge__(Dihedral self, Particle d) -> bool
2585 return _IMP_atom.Dihedral___ge__(self, *args)
2587 def __gt__(self, *args):
2589 __gt__(Dihedral self, Dihedral o) -> bool
2590 __gt__(Dihedral self, Particle d) -> bool
2592 return _IMP_atom.Dihedral___gt__(self, *args)
2595 r"""__hash__(Dihedral self) -> std::size_t"""
2596 return _IMP_atom.Dihedral___hash__(self)
2599 r"""__str__(Dihedral self) -> std::string"""
2600 return _IMP_atom.Dihedral___str__(self)
2603 r"""__repr__(Dihedral self) -> std::string"""
2604 return _IMP_atom.Dihedral___repr__(self)
2606 def _get_as_binary(self):
2607 r"""_get_as_binary(Dihedral self) -> PyObject *"""
2608 return _IMP_atom.Dihedral__get_as_binary(self)
2610 def _set_from_binary(self, p):
2611 r"""_set_from_binary(Dihedral self, PyObject * p)"""
2612 return _IMP_atom.Dihedral__set_from_binary(self, p)
2614 def __getstate__(self):
2615 p = self._get_as_binary()
2616 if len(self.__dict__) > 1:
2617 d = self.__dict__.copy()
2622 def __setstate__(self, p):
2623 if not hasattr(self,
'this'):
2625 if isinstance(p, tuple):
2627 self.__dict__.update(d)
2628 return self._set_from_binary(p)
2630 __swig_destroy__ = _IMP_atom.delete_Dihedral
2633 _IMP_atom.Dihedral_swigregister(Dihedral)
2635 r"""Proxy of C++ IMP::atom::SmoothingFunction class."""
2637 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2639 def __init__(self, *args, **kwargs):
2640 raise AttributeError(
"No constructor defined - class is abstract")
2642 def __call__(self, *args):
2644 __call__(SmoothingFunction self, double score, double distance) -> double
2645 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2647 return _IMP_atom.SmoothingFunction___call__(self, *args)
2648 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2651 r"""__str__(SmoothingFunction self) -> std::string"""
2652 return _IMP_atom.SmoothingFunction___str__(self)
2655 r"""__repr__(SmoothingFunction self) -> std::string"""
2656 return _IMP_atom.SmoothingFunction___repr__(self)
2660 return _object_cast_to_SmoothingFunction(o)
2664 _IMP_atom.SmoothingFunction_swigregister(SmoothingFunction)
2665 class ForceSwitch(SmoothingFunction):
2666 r"""Proxy of C++ IMP::atom::ForceSwitch class."""
2668 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2670 def __init__(self, min_distance, max_distance):
2671 r"""__init__(ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2672 _IMP_atom.ForceSwitch_swiginit(self, _IMP_atom.new_ForceSwitch(min_distance, max_distance))
2674 def __call__(self, *args):
2676 __call__(ForceSwitch self, double score, double distance) -> double
2677 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2679 return _IMP_atom.ForceSwitch___call__(self, *args)
2681 def get_version_info(self):
2682 r"""get_version_info(ForceSwitch self) -> VersionInfo"""
2683 return _IMP_atom.ForceSwitch_get_version_info(self)
2684 __swig_destroy__ = _IMP_atom.delete_ForceSwitch
2687 r"""__str__(ForceSwitch self) -> std::string"""
2688 return _IMP_atom.ForceSwitch___str__(self)
2691 r"""__repr__(ForceSwitch self) -> std::string"""
2692 return _IMP_atom.ForceSwitch___repr__(self)
2696 return _object_cast_to_ForceSwitch(o)
2700 _IMP_atom.ForceSwitch_swigregister(ForceSwitch)
2702 r"""Proxy of C++ IMP::atom::AngleSingletonScore class."""
2704 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2706 def __init__(self, f):
2707 r"""__init__(AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2708 _IMP_atom.AngleSingletonScore_swiginit(self, _IMP_atom.new_AngleSingletonScore(f))
2710 def do_get_inputs(self, m, pis):
2711 r"""do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2712 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2714 def get_version_info(self):
2715 r"""get_version_info(AngleSingletonScore self) -> VersionInfo"""
2716 return _IMP_atom.AngleSingletonScore_get_version_info(self)
2717 __swig_destroy__ = _IMP_atom.delete_AngleSingletonScore
2720 r"""__str__(AngleSingletonScore self) -> std::string"""
2721 return _IMP_atom.AngleSingletonScore___str__(self)
2724 r"""__repr__(AngleSingletonScore self) -> std::string"""
2725 return _IMP_atom.AngleSingletonScore___repr__(self)
2729 return _object_cast_to_AngleSingletonScore(o)
2733 _IMP_atom.AngleSingletonScore_swigregister(AngleSingletonScore)
2735 r"""Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2737 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2740 r"""__init__(BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2741 _IMP_atom.BondEndpointsRefiner_swiginit(self, _IMP_atom.new_BondEndpointsRefiner())
2743 def do_get_inputs(self, m, pis):
2744 r"""do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2745 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2747 def get_version_info(self):
2748 r"""get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2749 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2750 __swig_destroy__ = _IMP_atom.delete_BondEndpointsRefiner
2753 r"""__str__(BondEndpointsRefiner self) -> std::string"""
2754 return _IMP_atom.BondEndpointsRefiner___str__(self)
2757 r"""__repr__(BondEndpointsRefiner self) -> std::string"""
2758 return _IMP_atom.BondEndpointsRefiner___repr__(self)
2762 return _object_cast_to_BondEndpointsRefiner(o)
2766 _IMP_atom.BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2768 r"""Proxy of C++ IMP::atom::BondPairContainer class."""
2770 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2772 def __init__(self, sc):
2773 r"""__init__(BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2774 _IMP_atom.BondPairContainer_swiginit(self, _IMP_atom.new_BondPairContainer(sc))
2776 def do_get_inputs(self):
2777 r"""do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2778 return _IMP_atom.BondPairContainer_do_get_inputs(self)
2780 def do_apply(self, sm):
2781 r"""do_apply(BondPairContainer self, PairModifier sm)"""
2782 return _IMP_atom.BondPairContainer_do_apply(self, sm)
2784 def do_apply_moved(self, sm, moved_pis, reset_pis):
2785 r"""do_apply_moved(BondPairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
2786 return _IMP_atom.BondPairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
2788 def get_version_info(self):
2789 r"""get_version_info(BondPairContainer self) -> VersionInfo"""
2790 return _IMP_atom.BondPairContainer_get_version_info(self)
2791 __swig_destroy__ = _IMP_atom.delete_BondPairContainer
2794 r"""__str__(BondPairContainer self) -> std::string"""
2795 return _IMP_atom.BondPairContainer___str__(self)
2798 r"""__repr__(BondPairContainer self) -> std::string"""
2799 return _IMP_atom.BondPairContainer___repr__(self)
2803 return _object_cast_to_BondPairContainer(o)
2807 _IMP_atom.BondPairContainer_swigregister(BondPairContainer)
2809 r"""Proxy of C++ IMP::atom::BondSingletonScore class."""
2811 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2813 def __init__(self, f):
2814 r"""__init__(BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2815 _IMP_atom.BondSingletonScore_swiginit(self, _IMP_atom.new_BondSingletonScore(f))
2817 def get_unary_function(self):
2818 r"""get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2819 return _IMP_atom.BondSingletonScore_get_unary_function(self)
2821 def do_get_inputs(self, m, pis):
2822 r"""do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2823 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2825 def get_version_info(self):
2826 r"""get_version_info(BondSingletonScore self) -> VersionInfo"""
2827 return _IMP_atom.BondSingletonScore_get_version_info(self)
2828 __swig_destroy__ = _IMP_atom.delete_BondSingletonScore
2831 r"""__str__(BondSingletonScore self) -> std::string"""
2832 return _IMP_atom.BondSingletonScore___str__(self)
2835 r"""__repr__(BondSingletonScore self) -> std::string"""
2836 return _IMP_atom.BondSingletonScore___repr__(self)
2840 return _object_cast_to_BondSingletonScore(o)
2844 _IMP_atom.BondSingletonScore_swigregister(BondSingletonScore)
2846 r"""Proxy of C++ IMP::atom::DihedralSingletonScore class."""
2848 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2851 r"""__init__(DihedralSingletonScore self) -> DihedralSingletonScore"""
2852 _IMP_atom.DihedralSingletonScore_swiginit(self, _IMP_atom.new_DihedralSingletonScore())
2854 def do_get_inputs(self, m, pis):
2855 r"""do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2856 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
2858 def get_version_info(self):
2859 r"""get_version_info(DihedralSingletonScore self) -> VersionInfo"""
2860 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
2861 __swig_destroy__ = _IMP_atom.delete_DihedralSingletonScore
2864 r"""__str__(DihedralSingletonScore self) -> std::string"""
2865 return _IMP_atom.DihedralSingletonScore___str__(self)
2868 r"""__repr__(DihedralSingletonScore self) -> std::string"""
2869 return _IMP_atom.DihedralSingletonScore___repr__(self)
2873 return _object_cast_to_DihedralSingletonScore(o)
2876 def _get_as_binary(self):
2877 r"""_get_as_binary(DihedralSingletonScore self) -> PyObject *"""
2878 return _IMP_atom.DihedralSingletonScore__get_as_binary(self)
2880 def _set_from_binary(self, p):
2881 r"""_set_from_binary(DihedralSingletonScore self, PyObject * p)"""
2882 return _IMP_atom.DihedralSingletonScore__set_from_binary(self, p)
2884 def __getstate__(self):
2885 p = self._get_as_binary()
2886 if len(self.__dict__) > 1:
2887 d = self.__dict__.copy()
2892 def __setstate__(self, p):
2893 if not hasattr(self,
'this'):
2895 if isinstance(p, tuple):
2897 self.__dict__.update(d)
2898 return self._set_from_binary(p)
2902 _IMP_atom.DihedralSingletonScore_swigregister(DihedralSingletonScore)
2904 r"""Proxy of C++ IMP::atom::ImproperSingletonScore class."""
2906 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2908 def __init__(self, f):
2909 r"""__init__(ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
2910 _IMP_atom.ImproperSingletonScore_swiginit(self, _IMP_atom.new_ImproperSingletonScore(f))
2912 def do_get_inputs(self, m, pis):
2913 r"""do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2914 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
2916 def get_version_info(self):
2917 r"""get_version_info(ImproperSingletonScore self) -> VersionInfo"""
2918 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
2919 __swig_destroy__ = _IMP_atom.delete_ImproperSingletonScore
2922 r"""__str__(ImproperSingletonScore self) -> std::string"""
2923 return _IMP_atom.ImproperSingletonScore___str__(self)
2926 r"""__repr__(ImproperSingletonScore self) -> std::string"""
2927 return _IMP_atom.ImproperSingletonScore___repr__(self)
2931 return _object_cast_to_ImproperSingletonScore(o)
2935 _IMP_atom.ImproperSingletonScore_swigregister(ImproperSingletonScore)
2937 r"""Proxy of C++ IMP::atom::CenterOfMass class."""
2939 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2941 def get_constraint(self):
2942 r"""get_constraint(CenterOfMass self) -> Constraint"""
2943 return _IMP_atom.CenterOfMass_get_constraint(self)
2946 r"""get_mass(CenterOfMass self) -> IMP::Float"""
2947 return _IMP_atom.CenterOfMass_get_mass(self)
2949 def get_coordinate(self, i):
2950 r"""get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
2951 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
2953 def get_coordinates(self):
2954 r"""get_coordinates(CenterOfMass self) -> Vector3D"""
2955 return _IMP_atom.CenterOfMass_get_coordinates(self)
2957 def __init__(self, *args):
2959 __init__(CenterOfMass self) -> CenterOfMass
2960 __init__(CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
2961 __init__(CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
2963 _IMP_atom.CenterOfMass_swiginit(self, _IMP_atom.new_CenterOfMass(*args))
2965 def show(self, *args):
2966 r"""show(CenterOfMass self, _ostream out=std::cout)"""
2967 return _IMP_atom.CenterOfMass_show(self, *args)
2970 def setup_particle(*args):
2972 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
2973 setup_particle(_ParticleAdaptor pa, _ParticleIndexesAdaptor members) -> CenterOfMass
2974 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
2975 setup_particle(_ParticleAdaptor pa, Refiner refiner) -> CenterOfMass
2977 return _IMP_atom.CenterOfMass_setup_particle(*args)
2980 def teardown_particle(com):
2981 r"""teardown_particle(CenterOfMass com)"""
2982 return _IMP_atom.CenterOfMass_teardown_particle(com)
2985 def get_is_setup(*args):
2987 get_is_setup(_ParticleAdaptor p) -> bool
2988 get_is_setup(Model m, ParticleIndex pi) -> bool
2990 return _IMP_atom.CenterOfMass_get_is_setup(*args)
2992 def add_attribute(self, *args):
2994 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
2995 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
2996 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
2997 add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
2998 add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
2999 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3000 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3001 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3003 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3005 def get_value(self, *args):
3007 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3008 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3009 get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3010 get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3011 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3012 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3013 get_value(CenterOfMass self, ObjectKey a0) -> Object
3015 return _IMP_atom.CenterOfMass_get_value(self, *args)
3017 def set_value(self, *args):
3019 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3020 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3021 set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3022 set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3023 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3024 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3025 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3027 return _IMP_atom.CenterOfMass_set_value(self, *args)
3029 def remove_attribute(self, *args):
3031 remove_attribute(CenterOfMass self, FloatKey a0)
3032 remove_attribute(CenterOfMass self, IntKey a0)
3033 remove_attribute(CenterOfMass self, FloatsKey a0)
3034 remove_attribute(CenterOfMass self, IntsKey a0)
3035 remove_attribute(CenterOfMass self, StringKey a0)
3036 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3037 remove_attribute(CenterOfMass self, ObjectKey a0)
3039 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3041 def has_attribute(self, *args):
3043 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3044 has_attribute(CenterOfMass self, IntKey a0) -> bool
3045 has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3046 has_attribute(CenterOfMass self, IntsKey a0) -> bool
3047 has_attribute(CenterOfMass self, StringKey a0) -> bool
3048 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3049 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3051 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3053 def get_derivative(self, a0):
3054 r"""get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3055 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3058 r"""get_name(CenterOfMass self) -> std::string"""
3059 return _IMP_atom.CenterOfMass_get_name(self)
3061 def clear_caches(self):
3062 r"""clear_caches(CenterOfMass self)"""
3063 return _IMP_atom.CenterOfMass_clear_caches(self)
3065 def set_name(self, a0):
3066 r"""set_name(CenterOfMass self, std::string a0)"""
3067 return _IMP_atom.CenterOfMass_set_name(self, a0)
3070 r"""set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3071 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3073 def add_to_derivative(self, a0, a1, a2):
3074 r"""add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3075 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3077 def set_is_optimized(self, a0, a1):
3078 r"""set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3079 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3081 def get_is_optimized(self, a0):
3082 r"""get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3083 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3086 r"""get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3087 return _IMP_atom.CenterOfMass_get_check_level(self)
3089 def __eq__(self, *args):
3091 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3092 __eq__(CenterOfMass self, Particle d) -> bool
3094 return _IMP_atom.CenterOfMass___eq__(self, *args)
3096 def __ne__(self, *args):
3098 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3099 __ne__(CenterOfMass self, Particle d) -> bool
3101 return _IMP_atom.CenterOfMass___ne__(self, *args)
3103 def __le__(self, *args):
3105 __le__(CenterOfMass self, CenterOfMass o) -> bool
3106 __le__(CenterOfMass self, Particle d) -> bool
3108 return _IMP_atom.CenterOfMass___le__(self, *args)
3110 def __lt__(self, *args):
3112 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3113 __lt__(CenterOfMass self, Particle d) -> bool
3115 return _IMP_atom.CenterOfMass___lt__(self, *args)
3117 def __ge__(self, *args):
3119 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3120 __ge__(CenterOfMass self, Particle d) -> bool
3122 return _IMP_atom.CenterOfMass___ge__(self, *args)
3124 def __gt__(self, *args):
3126 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3127 __gt__(CenterOfMass self, Particle d) -> bool
3129 return _IMP_atom.CenterOfMass___gt__(self, *args)
3132 r"""__hash__(CenterOfMass self) -> std::size_t"""
3133 return _IMP_atom.CenterOfMass___hash__(self)
3136 r"""__str__(CenterOfMass self) -> std::string"""
3137 return _IMP_atom.CenterOfMass___str__(self)
3140 r"""__repr__(CenterOfMass self) -> std::string"""
3141 return _IMP_atom.CenterOfMass___repr__(self)
3143 def _get_as_binary(self):
3144 r"""_get_as_binary(CenterOfMass self) -> PyObject *"""
3145 return _IMP_atom.CenterOfMass__get_as_binary(self)
3147 def _set_from_binary(self, p):
3148 r"""_set_from_binary(CenterOfMass self, PyObject * p)"""
3149 return _IMP_atom.CenterOfMass__set_from_binary(self, p)
3151 def __getstate__(self):
3152 p = self._get_as_binary()
3153 if len(self.__dict__) > 1:
3154 d = self.__dict__.copy()
3159 def __setstate__(self, p):
3160 if not hasattr(self,
'this'):
3162 if isinstance(p, tuple):
3164 self.__dict__.update(d)
3165 return self._set_from_binary(p)
3167 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3170 _IMP_atom.CenterOfMass_swigregister(CenterOfMass)
3172 r"""Proxy of C++ IMP::atom::CoverBond class."""
3174 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3177 r"""__init__(CoverBond self) -> CoverBond"""
3178 _IMP_atom.CoverBond_swiginit(self, _IMP_atom.new_CoverBond())
3180 def do_get_inputs(self, m, pis):
3181 r"""do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3182 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3184 def do_get_outputs(self, m, pis):
3185 r"""do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3186 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3188 def get_version_info(self):
3189 r"""get_version_info(CoverBond self) -> VersionInfo"""
3190 return _IMP_atom.CoverBond_get_version_info(self)
3191 __swig_destroy__ = _IMP_atom.delete_CoverBond
3194 r"""__str__(CoverBond self) -> std::string"""
3195 return _IMP_atom.CoverBond___str__(self)
3198 r"""__repr__(CoverBond self) -> std::string"""
3199 return _IMP_atom.CoverBond___repr__(self)
3203 return _object_cast_to_CoverBond(o)
3207 _IMP_atom.CoverBond_swigregister(CoverBond)
3209 r"""Proxy of C++ IMP::atom::Simulator class."""
3211 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3213 def __init__(self, *args):
3214 r"""__init__(Simulator self, Model m, std::string name="Simulator %1%", double wave_factor=1.0) -> Simulator"""
3215 if self.__class__ == Simulator:
3219 _IMP_atom.Simulator_swiginit(self, _IMP_atom.new_Simulator(_self, *args))
3221 if self.__class__ != Simulator:
3222 _director_objects.register(self)
3227 def simulate(self, time_in_fs):
3228 r"""simulate(Simulator self, double time_in_fs) -> double"""
3229 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3231 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3232 r"""simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3233 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3235 def get_temperature(self):
3236 r"""get_temperature(Simulator self) -> double"""
3237 return _IMP_atom.Simulator_get_temperature(self)
3239 def set_temperature(self, d):
3240 r"""set_temperature(Simulator self, double d)"""
3241 return _IMP_atom.Simulator_set_temperature(self, d)
3243 def set_maximum_time_step(self, ts):
3244 r"""set_maximum_time_step(Simulator self, double ts)"""
3245 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3247 def get_maximum_time_step(self):
3248 r"""get_maximum_time_step(Simulator self) -> double"""
3249 return _IMP_atom.Simulator_get_maximum_time_step(self)
3251 def get_last_time_step(self):
3252 r"""get_last_time_step(Simulator self) -> double"""
3253 return _IMP_atom.Simulator_get_last_time_step(self)
3255 def set_time_step(self, ts):
3256 r"""set_time_step(Simulator self, double ts)"""
3257 return _IMP_atom.Simulator_set_time_step(self, ts)
3260 r"""get_kt(Simulator self) -> double"""
3261 return _IMP_atom.Simulator_get_kt(self)
3263 def get_current_time(self):
3264 r"""get_current_time(Simulator self) -> double"""
3265 return _IMP_atom.Simulator_get_current_time(self)
3267 def set_current_time(self, ct):
3268 r"""set_current_time(Simulator self, double ct)"""
3269 return _IMP_atom.Simulator_set_current_time(self, ct)
3271 def get_simulation_particles(self):
3272 r"""get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3273 return _IMP_atom.Simulator_get_simulation_particles(self)
3275 def get_simulation_particle_indexes(self):
3276 r"""get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3277 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3278 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)
3279 def __set_particles(self, obj): IMP._list_util.set_varlist(self.particles, obj)
3280 def __del_particles(self): IMP._list_util.del_varlist(self.particles)
3281 particles = property(__get_particles, __set_particles, __del_particles, doc=
"List of ##ucnames")
3283 def remove_particle(self, d):
3284 r"""remove_particle(Simulator self, Particle d)"""
3285 return _IMP_atom.Simulator_remove_particle(self, d)
3287 def _python_index_particle(self, d, start, stop):
3288 r"""_python_index_particle(Simulator self, Particle d, unsigned int start, unsigned int stop) -> unsigned int"""
3289 return _IMP_atom.Simulator__python_index_particle(self, d, start, stop)
3291 def remove_particles(self, d):
3292 r"""remove_particles(Simulator self, IMP::Particles const & d)"""
3293 return _IMP_atom.Simulator_remove_particles(self, d)
3295 def set_particles(self, ps):
3296 r"""set_particles(Simulator self, IMP::Particles const & ps)"""
3297 return _IMP_atom.Simulator_set_particles(self, ps)
3299 def set_particles_order(self, objs):
3300 r"""set_particles_order(Simulator self, IMP::Particles const & objs)"""
3301 return _IMP_atom.Simulator_set_particles_order(self, objs)
3304 r"""add_particle(Simulator self, Particle obj) -> unsigned int"""
3305 return _IMP_atom.Simulator_add_particle(self, obj)
3308 r"""add_particles(Simulator self, IMP::Particles const & objs)"""
3309 return _IMP_atom.Simulator_add_particles(self, objs)
3311 def clear_particles(self):
3312 r"""clear_particles(Simulator self)"""
3313 return _IMP_atom.Simulator_clear_particles(self)
3315 def get_number_of_particles(self):
3316 r"""get_number_of_particles(Simulator self) -> unsigned int"""
3317 return _IMP_atom.Simulator_get_number_of_particles(self)
3319 def get_has_particles(self):
3320 r"""get_has_particles(Simulator self) -> bool"""
3321 return _IMP_atom.Simulator_get_has_particles(self)
3323 def get_particle(self, i):
3324 r"""get_particle(Simulator self, unsigned int i) -> Particle"""
3325 return _IMP_atom.Simulator_get_particle(self, i)
3328 r"""get_particles(Simulator self) -> IMP::Particles"""
3329 return _IMP_atom.Simulator_get_particles(self)
3331 def erase_particle(self, i):
3332 r"""erase_particle(Simulator self, unsigned int i)"""
3333 return _IMP_atom.Simulator_erase_particle(self, i)
3335 def reserve_particles(self, sz):
3336 r"""reserve_particles(Simulator self, unsigned int sz)"""
3337 return _IMP_atom.Simulator_reserve_particles(self, sz)
3339 def do_optimize(self, max_steps):
3340 r"""do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3341 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3343 def setup(self, arg0):
3344 r"""setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3345 return _IMP_atom.Simulator_setup(self, arg0)
3347 def do_step(self, sc, dt):
3348 r"""do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3349 return _IMP_atom.Simulator_do_step(self, sc, dt)
3351 def get_is_simulation_particle(self, p):
3352 r"""get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3353 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3355 def do_simulate(self, time):
3356 r"""do_simulate(Simulator self, double time) -> double"""
3357 return _IMP_atom.Simulator_do_simulate(self, time)
3359 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3360 r"""do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double"""
3361 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3364 r"""__str__(Simulator self) -> std::string"""
3365 return _IMP_atom.Simulator___str__(self)
3368 r"""__repr__(Simulator self) -> std::string"""
3369 return _IMP_atom.Simulator___repr__(self)
3373 return _object_cast_to_Simulator(o)
3376 def get_type_name(self):
3377 return self.__class__.__name__
3378 def do_show(self, out):
3380 def get_version_info(self):
3381 if"IMP::atom" ==
"IMP":
3382 return VersionInfo(self.__module__,
3389 return _object_cast_to_Simulator(o)
3391 __swig_destroy__ = _IMP_atom.delete_Simulator
3392 def __disown__(self):
3394 _IMP_atom.disown_Simulator(self)
3395 return weakref.proxy(self)
3397 def do_destroy(self):
3398 r"""do_destroy(Simulator self)"""
3399 return _IMP_atom.Simulator_do_destroy(self)
3401 def handle_set_has_required_score_states(self, arg0):
3402 r"""handle_set_has_required_score_states(Simulator self, bool arg0)"""
3403 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3405 def do_get_inputs(self):
3406 r"""do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3407 return _IMP_atom.Simulator_do_get_inputs(self)
3409 def do_get_outputs(self):
3410 r"""do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3411 return _IMP_atom.Simulator_do_get_outputs(self)
3413 def do_get_interactions(self):
3414 r"""do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3415 return _IMP_atom.Simulator_do_get_interactions(self)
3418 _IMP_atom.Simulator_swigregister(Simulator)
3419 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3421 class BrownianDynamics(Simulator):
3422 r"""Proxy of C++ IMP::atom::BrownianDynamics class."""
3424 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3426 def __init__(self, *args):
3427 r"""__init__(BrownianDynamics self, Model m, std::string name="BrownianDynamics%1%", double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics"""
3428 _IMP_atom.BrownianDynamics_swiginit(self, _IMP_atom.new_BrownianDynamics(*args))
3430 def set_maximum_move(self, ms_in_A):
3431 r"""set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3432 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3434 def set_use_stochastic_runge_kutta(self, tf):
3435 r"""set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3436 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3438 def get_version_info(self):
3439 r"""get_version_info(BrownianDynamics self) -> VersionInfo"""
3440 return _IMP_atom.BrownianDynamics_get_version_info(self)
3441 __swig_destroy__ = _IMP_atom.delete_BrownianDynamics
3444 r"""__str__(BrownianDynamics self) -> std::string"""
3445 return _IMP_atom.BrownianDynamics___str__(self)
3448 r"""__repr__(BrownianDynamics self) -> std::string"""
3449 return _IMP_atom.BrownianDynamics___repr__(self)
3453 return _object_cast_to_BrownianDynamics(o)
3457 _IMP_atom.BrownianDynamics_swigregister(BrownianDynamics)
3460 r"""get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3461 return _IMP_atom.get_maximum_time_step_estimate(bd)
3463 def get_harmonic_sigma(D, f):
3464 r"""get_harmonic_sigma(double D, double f) -> double"""
3465 return _IMP_atom.get_harmonic_sigma(D, f)
3466 class BrownianDynamicsTAMD(BrownianDynamics):
3467 r"""Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3469 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3471 def __init__(self, *args):
3472 r"""__init__(BrownianDynamicsTAMD self, Model m, std::string name="BrownianDynamicsTAMD%1%", double wave_factor=1.0) -> BrownianDynamicsTAMD"""
3473 _IMP_atom.BrownianDynamicsTAMD_swiginit(self, _IMP_atom.new_BrownianDynamicsTAMD(*args))
3476 r"""__str__(BrownianDynamicsTAMD self) -> std::string"""
3477 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3480 r"""__repr__(BrownianDynamicsTAMD self) -> std::string"""
3481 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3485 return _object_cast_to_BrownianDynamicsTAMD(o)
3487 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3490 _IMP_atom.BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3492 r"""Proxy of C++ IMP::atom::Diffusion class."""
3494 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3496 def __init__(self, *args):
3498 __init__(Diffusion self) -> Diffusion
3499 __init__(Diffusion self, Model m, ParticleIndex id) -> Diffusion
3500 __init__(Diffusion self, _ParticleAdaptor d) -> Diffusion
3502 _IMP_atom.Diffusion_swiginit(self, _IMP_atom.new_Diffusion(*args))
3504 def show(self, *args):
3505 r"""show(Diffusion self, _ostream out=std::cout)"""
3506 return _IMP_atom.Diffusion_show(self, *args)
3509 def setup_particle(*args):
3511 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3512 setup_particle(_ParticleAdaptor pa, IMP::Float D) -> Diffusion
3513 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3514 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float D) -> Diffusion
3515 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3516 setup_particle(_ParticleAdaptor pa) -> Diffusion
3518 return _IMP_atom.Diffusion_setup_particle(*args)
3521 def get_is_setup(*args):
3523 get_is_setup(_ParticleAdaptor p) -> bool
3524 get_is_setup(Model m, ParticleIndex p) -> bool
3526 return _IMP_atom.Diffusion_get_is_setup(*args)
3528 def set_diffusion_coefficient(self, d):
3529 r"""set_diffusion_coefficient(Diffusion self, double d)"""
3530 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3533 r"""get_diffusion_coefficient(Diffusion self) -> double"""
3534 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3537 def get_diffusion_coefficient_key():
3538 r"""get_diffusion_coefficient_key() -> FloatKey"""
3539 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3541 def add_attribute(self, *args):
3543 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3544 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3545 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3546 add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3547 add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3548 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3549 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3550 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3552 return _IMP_atom.Diffusion_add_attribute(self, *args)
3554 def get_value(self, *args):
3556 get_value(Diffusion self, FloatKey a0) -> IMP::Float
3557 get_value(Diffusion self, IntKey a0) -> IMP::Int
3558 get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3559 get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3560 get_value(Diffusion self, StringKey a0) -> IMP::String
3561 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3562 get_value(Diffusion self, ObjectKey a0) -> Object
3564 return _IMP_atom.Diffusion_get_value(self, *args)
3566 def set_value(self, *args):
3568 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3569 set_value(Diffusion self, IntKey a0, IMP::Int a1)
3570 set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3571 set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3572 set_value(Diffusion self, StringKey a0, IMP::String a1)
3573 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3574 set_value(Diffusion self, ObjectKey a0, Object a1)
3576 return _IMP_atom.Diffusion_set_value(self, *args)
3578 def remove_attribute(self, *args):
3580 remove_attribute(Diffusion self, FloatKey a0)
3581 remove_attribute(Diffusion self, IntKey a0)
3582 remove_attribute(Diffusion self, FloatsKey a0)
3583 remove_attribute(Diffusion self, IntsKey a0)
3584 remove_attribute(Diffusion self, StringKey a0)
3585 remove_attribute(Diffusion self, ParticleIndexKey a0)
3586 remove_attribute(Diffusion self, ObjectKey a0)
3588 return _IMP_atom.Diffusion_remove_attribute(self, *args)
3590 def has_attribute(self, *args):
3592 has_attribute(Diffusion self, FloatKey a0) -> bool
3593 has_attribute(Diffusion self, IntKey a0) -> bool
3594 has_attribute(Diffusion self, FloatsKey a0) -> bool
3595 has_attribute(Diffusion self, IntsKey a0) -> bool
3596 has_attribute(Diffusion self, StringKey a0) -> bool
3597 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3598 has_attribute(Diffusion self, ObjectKey a0) -> bool
3600 return _IMP_atom.Diffusion_has_attribute(self, *args)
3602 def get_derivative(self, a0):
3603 r"""get_derivative(Diffusion self, FloatKey a0) -> double"""
3604 return _IMP_atom.Diffusion_get_derivative(self, a0)
3607 r"""get_name(Diffusion self) -> std::string"""
3608 return _IMP_atom.Diffusion_get_name(self)
3610 def clear_caches(self):
3611 r"""clear_caches(Diffusion self)"""
3612 return _IMP_atom.Diffusion_clear_caches(self)
3614 def set_name(self, a0):
3615 r"""set_name(Diffusion self, std::string a0)"""
3616 return _IMP_atom.Diffusion_set_name(self, a0)
3619 r"""set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3620 return _IMP_atom.Diffusion_set_check_level(self, a0)
3622 def add_to_derivative(self, a0, a1, a2):
3623 r"""add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3624 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3626 def set_is_optimized(self, a0, a1):
3627 r"""set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3628 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3630 def get_is_optimized(self, a0):
3631 r"""get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3632 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3635 r"""get_check_level(Diffusion self) -> IMP::CheckLevel"""
3636 return _IMP_atom.Diffusion_get_check_level(self)
3638 def __eq__(self, *args):
3640 __eq__(Diffusion self, Diffusion o) -> bool
3641 __eq__(Diffusion self, Particle d) -> bool
3643 return _IMP_atom.Diffusion___eq__(self, *args)
3645 def __ne__(self, *args):
3647 __ne__(Diffusion self, Diffusion o) -> bool
3648 __ne__(Diffusion self, Particle d) -> bool
3650 return _IMP_atom.Diffusion___ne__(self, *args)
3652 def __le__(self, *args):
3654 __le__(Diffusion self, Diffusion o) -> bool
3655 __le__(Diffusion self, Particle d) -> bool
3657 return _IMP_atom.Diffusion___le__(self, *args)
3659 def __lt__(self, *args):
3661 __lt__(Diffusion self, Diffusion o) -> bool
3662 __lt__(Diffusion self, Particle d) -> bool
3664 return _IMP_atom.Diffusion___lt__(self, *args)
3666 def __ge__(self, *args):
3668 __ge__(Diffusion self, Diffusion o) -> bool
3669 __ge__(Diffusion self, Particle d) -> bool
3671 return _IMP_atom.Diffusion___ge__(self, *args)
3673 def __gt__(self, *args):
3675 __gt__(Diffusion self, Diffusion o) -> bool
3676 __gt__(Diffusion self, Particle d) -> bool
3678 return _IMP_atom.Diffusion___gt__(self, *args)
3681 r"""__hash__(Diffusion self) -> std::size_t"""
3682 return _IMP_atom.Diffusion___hash__(self)
3685 r"""__str__(Diffusion self) -> std::string"""
3686 return _IMP_atom.Diffusion___str__(self)
3689 r"""__repr__(Diffusion self) -> std::string"""
3690 return _IMP_atom.Diffusion___repr__(self)
3692 def _get_as_binary(self):
3693 r"""_get_as_binary(Diffusion self) -> PyObject *"""
3694 return _IMP_atom.Diffusion__get_as_binary(self)
3696 def _set_from_binary(self, p):
3697 r"""_set_from_binary(Diffusion self, PyObject * p)"""
3698 return _IMP_atom.Diffusion__set_from_binary(self, p)
3700 def __getstate__(self):
3701 p = self._get_as_binary()
3702 if len(self.__dict__) > 1:
3703 d = self.__dict__.copy()
3708 def __setstate__(self, p):
3709 if not hasattr(self,
'this'):
3711 if isinstance(p, tuple):
3713 self.__dict__.update(d)
3714 return self._set_from_binary(p)
3716 __swig_destroy__ = _IMP_atom.delete_Diffusion
3719 _IMP_atom.Diffusion_swigregister(Diffusion)
3721 def get_diffusion_coefficient_from_cm2_per_second(din):
3722 r"""get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3723 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3724 class RigidBodyDiffusion(Diffusion):
3725 r"""Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3727 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3729 def __init__(self, *args):
3731 __init__(RigidBodyDiffusion self) -> RigidBodyDiffusion
3732 __init__(RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3733 __init__(RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3735 _IMP_atom.RigidBodyDiffusion_swiginit(self, _IMP_atom.new_RigidBodyDiffusion(*args))
3737 def show(self, *args):
3738 r"""show(RigidBodyDiffusion self, _ostream out=std::cout)"""
3739 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3742 def setup_particle(*args):
3744 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3745 setup_particle(_ParticleAdaptor pa) -> RigidBodyDiffusion
3747 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
3750 r"""get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
3751 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
3753 def set_rotational_diffusion_coefficient(self, d):
3754 r"""set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
3755 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
3758 def get_is_setup(*args):
3760 get_is_setup(_ParticleAdaptor p) -> bool
3761 get_is_setup(Model m, ParticleIndex p) -> bool
3763 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
3766 def get_rotational_diffusion_coefficient_key():
3767 r"""get_rotational_diffusion_coefficient_key() -> FloatKey"""
3768 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
3770 def add_attribute(self, *args):
3772 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
3773 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3774 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3775 add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3776 add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3777 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3778 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3779 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3781 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
3783 def get_value(self, *args):
3785 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
3786 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
3787 get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
3788 get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
3789 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
3790 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
3791 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
3793 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
3795 def set_value(self, *args):
3797 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
3798 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
3799 set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
3800 set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
3801 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
3802 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
3803 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
3805 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
3807 def remove_attribute(self, *args):
3809 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
3810 remove_attribute(RigidBodyDiffusion self, IntKey a0)
3811 remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
3812 remove_attribute(RigidBodyDiffusion self, IntsKey a0)
3813 remove_attribute(RigidBodyDiffusion self, StringKey a0)
3814 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
3815 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
3817 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
3819 def has_attribute(self, *args):
3821 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
3822 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
3823 has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
3824 has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
3825 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
3826 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
3827 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
3829 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
3831 def get_derivative(self, a0):
3832 r"""get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
3833 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
3836 r"""get_name(RigidBodyDiffusion self) -> std::string"""
3837 return _IMP_atom.RigidBodyDiffusion_get_name(self)
3839 def clear_caches(self):
3840 r"""clear_caches(RigidBodyDiffusion self)"""
3841 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
3843 def set_name(self, a0):
3844 r"""set_name(RigidBodyDiffusion self, std::string a0)"""
3845 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
3848 r"""set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
3849 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
3851 def add_to_derivative(self, a0, a1, a2):
3852 r"""add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3853 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
3855 def set_is_optimized(self, a0, a1):
3856 r"""set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
3857 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
3859 def get_is_optimized(self, a0):
3860 r"""get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
3861 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
3864 r"""get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
3865 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
3867 def __eq__(self, *args):
3869 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3870 __eq__(RigidBodyDiffusion self, Particle d) -> bool
3872 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
3874 def __ne__(self, *args):
3876 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3877 __ne__(RigidBodyDiffusion self, Particle d) -> bool
3879 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
3881 def __le__(self, *args):
3883 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3884 __le__(RigidBodyDiffusion self, Particle d) -> bool
3886 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
3888 def __lt__(self, *args):
3890 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3891 __lt__(RigidBodyDiffusion self, Particle d) -> bool
3893 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
3895 def __ge__(self, *args):
3897 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3898 __ge__(RigidBodyDiffusion self, Particle d) -> bool
3900 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
3902 def __gt__(self, *args):
3904 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
3905 __gt__(RigidBodyDiffusion self, Particle d) -> bool
3907 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
3910 r"""__hash__(RigidBodyDiffusion self) -> std::size_t"""
3911 return _IMP_atom.RigidBodyDiffusion___hash__(self)
3914 r"""__str__(RigidBodyDiffusion self) -> std::string"""
3915 return _IMP_atom.RigidBodyDiffusion___str__(self)
3918 r"""__repr__(RigidBodyDiffusion self) -> std::string"""
3919 return _IMP_atom.RigidBodyDiffusion___repr__(self)
3921 def _get_as_binary(self):
3922 r"""_get_as_binary(RigidBodyDiffusion self) -> PyObject *"""
3923 return _IMP_atom.RigidBodyDiffusion__get_as_binary(self)
3925 def _set_from_binary(self, p):
3926 r"""_set_from_binary(RigidBodyDiffusion self, PyObject * p)"""
3927 return _IMP_atom.RigidBodyDiffusion__set_from_binary(self, p)
3929 def __getstate__(self):
3930 p = self._get_as_binary()
3931 if len(self.__dict__) > 1:
3932 d = self.__dict__.copy()
3937 def __setstate__(self, p):
3938 if not hasattr(self,
'this'):
3940 if isinstance(p, tuple):
3942 self.__dict__.update(d)
3943 return self._set_from_binary(p)
3945 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
3948 _IMP_atom.RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
3950 r"""Proxy of C++ IMP::atom::TAMDParticle class."""
3952 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3954 def __init__(self, *args):
3956 __init__(TAMDParticle self) -> TAMDParticle
3957 __init__(TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
3958 __init__(TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
3960 _IMP_atom.TAMDParticle_swiginit(self, _IMP_atom.new_TAMDParticle(*args))
3962 def show(self, *args):
3963 r"""show(TAMDParticle self, _ostream out=std::cout)"""
3964 return _IMP_atom.TAMDParticle_show(self, *args)
3967 def setup_particle(*args):
3969 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
3970 setup_particle(_ParticleAdaptor pa, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
3971 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
3972 setup_particle(_ParticleAdaptor pa, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
3974 return _IMP_atom.TAMDParticle_setup_particle(*args)
3977 def get_is_setup(*args):
3979 get_is_setup(_ParticleAdaptor p) -> bool
3980 get_is_setup(Model m, ParticleIndex p) -> bool
3982 return _IMP_atom.TAMDParticle_get_is_setup(*args)
3984 def get_reference_particle_index(self):
3985 r"""get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
3986 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
3988 def set_temperature_scale_factor(self, tsf):
3989 r"""set_temperature_scale_factor(TAMDParticle self, float tsf)"""
3990 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
3992 def get_temperature_scale_factor(self):
3993 r"""get_temperature_scale_factor(TAMDParticle self) -> double"""
3994 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
3996 def set_friction_scale_factor(self, tsf):
3997 r"""set_friction_scale_factor(TAMDParticle self, float tsf)"""
3998 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4000 def get_friction_scale_factor(self):
4001 r"""get_friction_scale_factor(TAMDParticle self) -> double"""
4002 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4004 def update_coordinates_from_ref(self):
4005 r"""update_coordinates_from_ref(TAMDParticle self)"""
4006 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4009 def get_temperature_scale_factor_key():
4010 r"""get_temperature_scale_factor_key() -> FloatKey"""
4011 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4014 def get_friction_scale_factor_key():
4015 r"""get_friction_scale_factor_key() -> FloatKey"""
4016 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4019 def get_reference_particle_index_key():
4020 r"""get_reference_particle_index_key() -> ParticleIndexKey"""
4021 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4023 def add_attribute(self, *args):
4025 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4026 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4027 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4028 add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4029 add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4030 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4031 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4032 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4034 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4036 def get_value(self, *args):
4038 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4039 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4040 get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4041 get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4042 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4043 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4044 get_value(TAMDParticle self, ObjectKey a0) -> Object
4046 return _IMP_atom.TAMDParticle_get_value(self, *args)
4048 def set_value(self, *args):
4050 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4051 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4052 set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4053 set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4054 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4055 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4056 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4058 return _IMP_atom.TAMDParticle_set_value(self, *args)
4060 def remove_attribute(self, *args):
4062 remove_attribute(TAMDParticle self, FloatKey a0)
4063 remove_attribute(TAMDParticle self, IntKey a0)
4064 remove_attribute(TAMDParticle self, FloatsKey a0)
4065 remove_attribute(TAMDParticle self, IntsKey a0)
4066 remove_attribute(TAMDParticle self, StringKey a0)
4067 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4068 remove_attribute(TAMDParticle self, ObjectKey a0)
4070 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4072 def has_attribute(self, *args):
4074 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4075 has_attribute(TAMDParticle self, IntKey a0) -> bool
4076 has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4077 has_attribute(TAMDParticle self, IntsKey a0) -> bool
4078 has_attribute(TAMDParticle self, StringKey a0) -> bool
4079 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4080 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4082 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4084 def get_derivative(self, a0):
4085 r"""get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4086 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4089 r"""get_name(TAMDParticle self) -> std::string"""
4090 return _IMP_atom.TAMDParticle_get_name(self)
4092 def clear_caches(self):
4093 r"""clear_caches(TAMDParticle self)"""
4094 return _IMP_atom.TAMDParticle_clear_caches(self)
4096 def set_name(self, a0):
4097 r"""set_name(TAMDParticle self, std::string a0)"""
4098 return _IMP_atom.TAMDParticle_set_name(self, a0)
4101 r"""set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4102 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4104 def add_to_derivative(self, a0, a1, a2):
4105 r"""add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4106 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4108 def set_is_optimized(self, a0, a1):
4109 r"""set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4110 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4112 def get_is_optimized(self, a0):
4113 r"""get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4114 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4117 r"""get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4118 return _IMP_atom.TAMDParticle_get_check_level(self)
4120 def __eq__(self, *args):
4122 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4123 __eq__(TAMDParticle self, Particle d) -> bool
4125 return _IMP_atom.TAMDParticle___eq__(self, *args)
4127 def __ne__(self, *args):
4129 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4130 __ne__(TAMDParticle self, Particle d) -> bool
4132 return _IMP_atom.TAMDParticle___ne__(self, *args)
4134 def __le__(self, *args):
4136 __le__(TAMDParticle self, TAMDParticle o) -> bool
4137 __le__(TAMDParticle self, Particle d) -> bool
4139 return _IMP_atom.TAMDParticle___le__(self, *args)
4141 def __lt__(self, *args):
4143 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4144 __lt__(TAMDParticle self, Particle d) -> bool
4146 return _IMP_atom.TAMDParticle___lt__(self, *args)
4148 def __ge__(self, *args):
4150 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4151 __ge__(TAMDParticle self, Particle d) -> bool
4153 return _IMP_atom.TAMDParticle___ge__(self, *args)
4155 def __gt__(self, *args):
4157 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4158 __gt__(TAMDParticle self, Particle d) -> bool
4160 return _IMP_atom.TAMDParticle___gt__(self, *args)
4163 r"""__hash__(TAMDParticle self) -> std::size_t"""
4164 return _IMP_atom.TAMDParticle___hash__(self)
4167 r"""__str__(TAMDParticle self) -> std::string"""
4168 return _IMP_atom.TAMDParticle___str__(self)
4171 r"""__repr__(TAMDParticle self) -> std::string"""
4172 return _IMP_atom.TAMDParticle___repr__(self)
4174 def _get_as_binary(self):
4175 r"""_get_as_binary(TAMDParticle self) -> PyObject *"""
4176 return _IMP_atom.TAMDParticle__get_as_binary(self)
4178 def _set_from_binary(self, p):
4179 r"""_set_from_binary(TAMDParticle self, PyObject * p)"""
4180 return _IMP_atom.TAMDParticle__set_from_binary(self, p)
4182 def __getstate__(self):
4183 p = self._get_as_binary()
4184 if len(self.__dict__) > 1:
4185 d = self.__dict__.copy()
4190 def __setstate__(self, p):
4191 if not hasattr(self,
'this'):
4193 if isinstance(p, tuple):
4195 self.__dict__.update(d)
4196 return self._set_from_binary(p)
4198 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4201 _IMP_atom.TAMDParticle_swigregister(TAMDParticle)
4202 class Chain(Hierarchy):
4203 r"""Proxy of C++ IMP::atom::Chain class."""
4205 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4207 def __init__(self, *args):
4209 __init__(Chain self) -> Chain
4210 __init__(Chain self, Model m, ParticleIndex id) -> Chain
4211 __init__(Chain self, _ParticleAdaptor d) -> Chain
4213 _IMP_atom.Chain_swiginit(self, _IMP_atom.new_Chain(*args))
4215 def show(self, *args):
4216 r"""show(Chain self, _ostream out=std::cout)"""
4217 return _IMP_atom.Chain_show(self, *args)
4220 def setup_particle(*args):
4222 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4223 setup_particle(_ParticleAdaptor pa, std::string id) -> Chain
4224 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4225 setup_particle(_ParticleAdaptor pa, char id) -> Chain
4226 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4227 setup_particle(_ParticleAdaptor pa, Chain other) -> Chain
4229 return _IMP_atom.Chain_setup_particle(*args)
4232 def get_is_setup(*args):
4234 get_is_setup(_ParticleAdaptor p) -> bool
4235 get_is_setup(Model m, ParticleIndex pi) -> bool
4237 return _IMP_atom.Chain_get_is_setup(*args)
4240 r"""get_id(Chain self) -> std::string"""
4241 return _IMP_atom.Chain_get_id(self)
4243 def set_id(self, c):
4244 r"""set_id(Chain self, std::string c)"""
4245 return _IMP_atom.Chain_set_id(self, c)
4247 def get_sequence(self):
4248 r"""get_sequence(Chain self) -> std::string"""
4249 return _IMP_atom.Chain_get_sequence(self)
4251 def set_sequence(self, sequence):
4252 r"""set_sequence(Chain self, std::string sequence)"""
4253 return _IMP_atom.Chain_set_sequence(self, sequence)
4255 def get_chain_type(self):
4256 r"""get_chain_type(Chain self) -> ChainType"""
4257 return _IMP_atom.Chain_get_chain_type(self)
4259 def set_chain_type(self, t):
4260 r"""set_chain_type(Chain self, ChainType t)"""
4261 return _IMP_atom.Chain_set_chain_type(self, t)
4265 r"""get_id_key() -> StringKey"""
4266 return _IMP_atom.Chain_get_id_key()
4269 def get_sequence_key():
4270 r"""get_sequence_key() -> StringKey"""
4271 return _IMP_atom.Chain_get_sequence_key()
4274 def get_chain_type_key():
4275 r"""get_chain_type_key() -> IntKey"""
4276 return _IMP_atom.Chain_get_chain_type_key()
4278 def add_attribute(self, *args):
4280 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4281 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4282 add_attribute(Chain self, IntKey a0, IMP::Int a1)
4283 add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
4284 add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
4285 add_attribute(Chain self, StringKey a0, IMP::String a1)
4286 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4287 add_attribute(Chain self, ObjectKey a0, Object a1)
4289 return _IMP_atom.Chain_add_attribute(self, *args)
4291 def get_value(self, *args):
4293 get_value(Chain self, FloatKey a0) -> IMP::Float
4294 get_value(Chain self, IntKey a0) -> IMP::Int
4295 get_value(Chain self, FloatsKey a0) -> IMP::Floats
4296 get_value(Chain self, IntsKey a0) -> IMP::Ints
4297 get_value(Chain self, StringKey a0) -> IMP::String
4298 get_value(Chain self, ParticleIndexKey a0) -> Particle
4299 get_value(Chain self, ObjectKey a0) -> Object
4301 return _IMP_atom.Chain_get_value(self, *args)
4303 def set_value(self, *args):
4305 set_value(Chain self, FloatKey a0, IMP::Float a1)
4306 set_value(Chain self, IntKey a0, IMP::Int a1)
4307 set_value(Chain self, FloatsKey a0, IMP::Floats a1)
4308 set_value(Chain self, IntsKey a0, IMP::Ints a1)
4309 set_value(Chain self, StringKey a0, IMP::String a1)
4310 set_value(Chain self, ParticleIndexKey a0, Particle a1)
4311 set_value(Chain self, ObjectKey a0, Object a1)
4313 return _IMP_atom.Chain_set_value(self, *args)
4315 def remove_attribute(self, *args):
4317 remove_attribute(Chain self, FloatKey a0)
4318 remove_attribute(Chain self, IntKey a0)
4319 remove_attribute(Chain self, FloatsKey a0)
4320 remove_attribute(Chain self, IntsKey a0)
4321 remove_attribute(Chain self, StringKey a0)
4322 remove_attribute(Chain self, ParticleIndexKey a0)
4323 remove_attribute(Chain self, ObjectKey a0)
4325 return _IMP_atom.Chain_remove_attribute(self, *args)
4327 def has_attribute(self, *args):
4329 has_attribute(Chain self, FloatKey a0) -> bool
4330 has_attribute(Chain self, IntKey a0) -> bool
4331 has_attribute(Chain self, FloatsKey a0) -> bool
4332 has_attribute(Chain self, IntsKey a0) -> bool
4333 has_attribute(Chain self, StringKey a0) -> bool
4334 has_attribute(Chain self, ParticleIndexKey a0) -> bool
4335 has_attribute(Chain self, ObjectKey a0) -> bool
4337 return _IMP_atom.Chain_has_attribute(self, *args)
4339 def get_derivative(self, a0):
4340 r"""get_derivative(Chain self, FloatKey a0) -> double"""
4341 return _IMP_atom.Chain_get_derivative(self, a0)
4344 r"""get_name(Chain self) -> std::string"""
4345 return _IMP_atom.Chain_get_name(self)
4347 def clear_caches(self):
4348 r"""clear_caches(Chain self)"""
4349 return _IMP_atom.Chain_clear_caches(self)
4351 def set_name(self, a0):
4352 r"""set_name(Chain self, std::string a0)"""
4353 return _IMP_atom.Chain_set_name(self, a0)
4356 r"""set_check_level(Chain self, IMP::CheckLevel a0)"""
4357 return _IMP_atom.Chain_set_check_level(self, a0)
4359 def add_to_derivative(self, a0, a1, a2):
4360 r"""add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4361 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4363 def set_is_optimized(self, a0, a1):
4364 r"""set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4365 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4367 def get_is_optimized(self, a0):
4368 r"""get_is_optimized(Chain self, FloatKey a0) -> bool"""
4369 return _IMP_atom.Chain_get_is_optimized(self, a0)
4372 r"""get_check_level(Chain self) -> IMP::CheckLevel"""
4373 return _IMP_atom.Chain_get_check_level(self)
4375 def __eq__(self, *args):
4377 __eq__(Chain self, Chain o) -> bool
4378 __eq__(Chain self, Particle d) -> bool
4380 return _IMP_atom.Chain___eq__(self, *args)
4382 def __ne__(self, *args):
4384 __ne__(Chain self, Chain o) -> bool
4385 __ne__(Chain self, Particle d) -> bool
4387 return _IMP_atom.Chain___ne__(self, *args)
4389 def __le__(self, *args):
4391 __le__(Chain self, Chain o) -> bool
4392 __le__(Chain self, Particle d) -> bool
4394 return _IMP_atom.Chain___le__(self, *args)
4396 def __lt__(self, *args):
4398 __lt__(Chain self, Chain o) -> bool
4399 __lt__(Chain self, Particle d) -> bool
4401 return _IMP_atom.Chain___lt__(self, *args)
4403 def __ge__(self, *args):
4405 __ge__(Chain self, Chain o) -> bool
4406 __ge__(Chain self, Particle d) -> bool
4408 return _IMP_atom.Chain___ge__(self, *args)
4410 def __gt__(self, *args):
4412 __gt__(Chain self, Chain o) -> bool
4413 __gt__(Chain self, Particle d) -> bool
4415 return _IMP_atom.Chain___gt__(self, *args)
4418 r"""__hash__(Chain self) -> std::size_t"""
4419 return _IMP_atom.Chain___hash__(self)
4422 r"""__str__(Chain self) -> std::string"""
4423 return _IMP_atom.Chain___str__(self)
4426 r"""__repr__(Chain self) -> std::string"""
4427 return _IMP_atom.Chain___repr__(self)
4429 def _get_as_binary(self):
4430 r"""_get_as_binary(Chain self) -> PyObject *"""
4431 return _IMP_atom.Chain__get_as_binary(self)
4433 def _set_from_binary(self, p):
4434 r"""_set_from_binary(Chain self, PyObject * p)"""
4435 return _IMP_atom.Chain__set_from_binary(self, p)
4437 def __getstate__(self):
4438 p = self._get_as_binary()
4439 if len(self.__dict__) > 1:
4440 d = self.__dict__.copy()
4445 def __setstate__(self, p):
4446 if not hasattr(self,
'this'):
4448 if isinstance(p, tuple):
4450 self.__dict__.update(d)
4451 return self._set_from_binary(p)
4453 __swig_destroy__ = _IMP_atom.delete_Chain
4456 _IMP_atom.Chain_swigregister(Chain)
4457 cvar = _IMP_atom.cvar
4458 UnknownChainType = cvar.UnknownChainType
4459 DPolypeptide = cvar.DPolypeptide
4460 LPolypeptide = cvar.LPolypeptide
4461 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
4462 Polyribonucleotide = cvar.Polyribonucleotide
4463 DPolysaccharide = cvar.DPolysaccharide
4464 LPolysaccharide = cvar.LPolysaccharide
4465 Protein = cvar.Protein
4471 r"""get_chain(Hierarchy h) -> Chain"""
4472 return _IMP_atom.get_chain(h)
4475 r"""get_chain_id(Hierarchy h) -> std::string"""
4476 return _IMP_atom.get_chain_id(h)
4478 r"""Proxy of C++ IMP::atom::Charged class."""
4480 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4482 def __init__(self, *args):
4484 __init__(Charged self) -> Charged
4485 __init__(Charged self, Model m, ParticleIndex id) -> Charged
4486 __init__(Charged self, _ParticleAdaptor d) -> Charged
4488 _IMP_atom.Charged_swiginit(self, _IMP_atom.new_Charged(*args))
4490 def show(self, *args):
4491 r"""show(Charged self, _ostream out=std::cout)"""
4492 return _IMP_atom.Charged_show(self, *args)
4495 def setup_particle(*args):
4497 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4498 setup_particle(_ParticleAdaptor pa, IMP::Float charge) -> Charged
4499 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4500 setup_particle(_ParticleAdaptor pa, Vector3D v, IMP::Float charge) -> Charged
4502 return _IMP_atom.Charged_setup_particle(*args)
4504 def get_charge(self):
4505 r"""get_charge(Charged self) -> IMP::Float"""
4506 return _IMP_atom.Charged_get_charge(self)
4508 def set_charge(self, t):
4509 r"""set_charge(Charged self, IMP::Float t)"""
4510 return _IMP_atom.Charged_set_charge(self, t)
4513 def get_is_setup(*args):
4515 get_is_setup(_ParticleAdaptor p) -> bool
4516 get_is_setup(Model m, ParticleIndex pi) -> bool
4518 return _IMP_atom.Charged_get_is_setup(*args)
4521 def get_charge_key():
4522 r"""get_charge_key() -> FloatKey"""
4523 return _IMP_atom.Charged_get_charge_key()
4525 def add_attribute(self, *args):
4527 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4528 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4529 add_attribute(Charged self, IntKey a0, IMP::Int a1)
4530 add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
4531 add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
4532 add_attribute(Charged self, StringKey a0, IMP::String a1)
4533 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4534 add_attribute(Charged self, ObjectKey a0, Object a1)
4536 return _IMP_atom.Charged_add_attribute(self, *args)
4538 def get_value(self, *args):
4540 get_value(Charged self, FloatKey a0) -> IMP::Float
4541 get_value(Charged self, IntKey a0) -> IMP::Int
4542 get_value(Charged self, FloatsKey a0) -> IMP::Floats
4543 get_value(Charged self, IntsKey a0) -> IMP::Ints
4544 get_value(Charged self, StringKey a0) -> IMP::String
4545 get_value(Charged self, ParticleIndexKey a0) -> Particle
4546 get_value(Charged self, ObjectKey a0) -> Object
4548 return _IMP_atom.Charged_get_value(self, *args)
4550 def set_value(self, *args):
4552 set_value(Charged self, FloatKey a0, IMP::Float a1)
4553 set_value(Charged self, IntKey a0, IMP::Int a1)
4554 set_value(Charged self, FloatsKey a0, IMP::Floats a1)
4555 set_value(Charged self, IntsKey a0, IMP::Ints a1)
4556 set_value(Charged self, StringKey a0, IMP::String a1)
4557 set_value(Charged self, ParticleIndexKey a0, Particle a1)
4558 set_value(Charged self, ObjectKey a0, Object a1)
4560 return _IMP_atom.Charged_set_value(self, *args)
4562 def remove_attribute(self, *args):
4564 remove_attribute(Charged self, FloatKey a0)
4565 remove_attribute(Charged self, IntKey a0)
4566 remove_attribute(Charged self, FloatsKey a0)
4567 remove_attribute(Charged self, IntsKey a0)
4568 remove_attribute(Charged self, StringKey a0)
4569 remove_attribute(Charged self, ParticleIndexKey a0)
4570 remove_attribute(Charged self, ObjectKey a0)
4572 return _IMP_atom.Charged_remove_attribute(self, *args)
4574 def has_attribute(self, *args):
4576 has_attribute(Charged self, FloatKey a0) -> bool
4577 has_attribute(Charged self, IntKey a0) -> bool
4578 has_attribute(Charged self, FloatsKey a0) -> bool
4579 has_attribute(Charged self, IntsKey a0) -> bool
4580 has_attribute(Charged self, StringKey a0) -> bool
4581 has_attribute(Charged self, ParticleIndexKey a0) -> bool
4582 has_attribute(Charged self, ObjectKey a0) -> bool
4584 return _IMP_atom.Charged_has_attribute(self, *args)
4586 def get_derivative(self, a0):
4587 r"""get_derivative(Charged self, FloatKey a0) -> double"""
4588 return _IMP_atom.Charged_get_derivative(self, a0)
4591 r"""get_name(Charged self) -> std::string"""
4592 return _IMP_atom.Charged_get_name(self)
4594 def clear_caches(self):
4595 r"""clear_caches(Charged self)"""
4596 return _IMP_atom.Charged_clear_caches(self)
4598 def set_name(self, a0):
4599 r"""set_name(Charged self, std::string a0)"""
4600 return _IMP_atom.Charged_set_name(self, a0)
4603 r"""set_check_level(Charged self, IMP::CheckLevel a0)"""
4604 return _IMP_atom.Charged_set_check_level(self, a0)
4606 def add_to_derivative(self, a0, a1, a2):
4607 r"""add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4608 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4610 def set_is_optimized(self, a0, a1):
4611 r"""set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4612 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4614 def get_is_optimized(self, a0):
4615 r"""get_is_optimized(Charged self, FloatKey a0) -> bool"""
4616 return _IMP_atom.Charged_get_is_optimized(self, a0)
4619 r"""get_check_level(Charged self) -> IMP::CheckLevel"""
4620 return _IMP_atom.Charged_get_check_level(self)
4622 def __eq__(self, *args):
4624 __eq__(Charged self, Charged o) -> bool
4625 __eq__(Charged self, Particle d) -> bool
4627 return _IMP_atom.Charged___eq__(self, *args)
4629 def __ne__(self, *args):
4631 __ne__(Charged self, Charged o) -> bool
4632 __ne__(Charged self, Particle d) -> bool
4634 return _IMP_atom.Charged___ne__(self, *args)
4636 def __le__(self, *args):
4638 __le__(Charged self, Charged o) -> bool
4639 __le__(Charged self, Particle d) -> bool
4641 return _IMP_atom.Charged___le__(self, *args)
4643 def __lt__(self, *args):
4645 __lt__(Charged self, Charged o) -> bool
4646 __lt__(Charged self, Particle d) -> bool
4648 return _IMP_atom.Charged___lt__(self, *args)
4650 def __ge__(self, *args):
4652 __ge__(Charged self, Charged o) -> bool
4653 __ge__(Charged self, Particle d) -> bool
4655 return _IMP_atom.Charged___ge__(self, *args)
4657 def __gt__(self, *args):
4659 __gt__(Charged self, Charged o) -> bool
4660 __gt__(Charged self, Particle d) -> bool
4662 return _IMP_atom.Charged___gt__(self, *args)
4665 r"""__hash__(Charged self) -> std::size_t"""
4666 return _IMP_atom.Charged___hash__(self)
4669 r"""__str__(Charged self) -> std::string"""
4670 return _IMP_atom.Charged___str__(self)
4673 r"""__repr__(Charged self) -> std::string"""
4674 return _IMP_atom.Charged___repr__(self)
4676 def _get_as_binary(self):
4677 r"""_get_as_binary(Charged self) -> PyObject *"""
4678 return _IMP_atom.Charged__get_as_binary(self)
4680 def _set_from_binary(self, p):
4681 r"""_set_from_binary(Charged self, PyObject * p)"""
4682 return _IMP_atom.Charged__set_from_binary(self, p)
4684 def __getstate__(self):
4685 p = self._get_as_binary()
4686 if len(self.__dict__) > 1:
4687 d = self.__dict__.copy()
4692 def __setstate__(self, p):
4693 if not hasattr(self,
'this'):
4695 if isinstance(p, tuple):
4697 self.__dict__.update(d)
4698 return self._set_from_binary(p)
4700 __swig_destroy__ = _IMP_atom.delete_Charged
4703 _IMP_atom.Charged_swigregister(Charged)
4705 r"""Proxy of C++ IMP::atom::CoulombPairScore class."""
4707 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4709 def __init__(self, f):
4710 r"""__init__(CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
4711 _IMP_atom.CoulombPairScore_swiginit(self, _IMP_atom.new_CoulombPairScore(f))
4713 def set_relative_dielectric(self, relative_dielectric):
4714 r"""set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
4715 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
4717 def get_relative_dielectric(self):
4718 r"""get_relative_dielectric(CoulombPairScore self) -> double"""
4719 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
4721 def do_get_inputs(self, m, pis):
4722 r"""do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4723 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
4725 def get_version_info(self):
4726 r"""get_version_info(CoulombPairScore self) -> VersionInfo"""
4727 return _IMP_atom.CoulombPairScore_get_version_info(self)
4728 __swig_destroy__ = _IMP_atom.delete_CoulombPairScore
4731 r"""__str__(CoulombPairScore self) -> std::string"""
4732 return _IMP_atom.CoulombPairScore___str__(self)
4735 r"""__repr__(CoulombPairScore self) -> std::string"""
4736 return _IMP_atom.CoulombPairScore___repr__(self)
4740 return _object_cast_to_CoulombPairScore(o)
4744 _IMP_atom.CoulombPairScore_swigregister(CoulombPairScore)
4745 class Domain(Hierarchy):
4746 r"""Proxy of C++ IMP::atom::Domain class."""
4748 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4750 def set_index_range(self, ir):
4751 r"""set_index_range(Domain self, IMP::IntRange ir)"""
4752 return _IMP_atom.Domain_set_index_range(self, ir)
4754 def get_index_range(self):
4755 r"""get_index_range(Domain self) -> IMP::IntRange"""
4756 return _IMP_atom.Domain_get_index_range(self)
4758 def __init__(self, *args):
4760 __init__(Domain self) -> Domain
4761 __init__(Domain self, Model m, ParticleIndex id) -> Domain
4762 __init__(Domain self, _ParticleAdaptor d) -> Domain
4764 _IMP_atom.Domain_swiginit(self, _IMP_atom.new_Domain(*args))
4767 def get_is_setup(*args):
4769 get_is_setup(Model m, ParticleIndex pi) -> bool
4770 get_is_setup(_ParticleAdaptor p) -> bool
4772 return _IMP_atom.Domain_get_is_setup(*args)
4774 def show(self, *args):
4775 r"""show(Domain self, _ostream out=std::cout)"""
4776 return _IMP_atom.Domain_show(self, *args)
4779 def setup_particle(*args):
4781 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
4782 setup_particle(_ParticleAdaptor pa, Domain other) -> Domain
4783 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
4784 setup_particle(_ParticleAdaptor pa, IMP::IntRange residues) -> Domain
4786 return _IMP_atom.Domain_setup_particle(*args)
4788 def add_attribute(self, *args):
4790 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
4791 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
4792 add_attribute(Domain self, IntKey a0, IMP::Int a1)
4793 add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
4794 add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
4795 add_attribute(Domain self, StringKey a0, IMP::String a1)
4796 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
4797 add_attribute(Domain self, ObjectKey a0, Object a1)
4799 return _IMP_atom.Domain_add_attribute(self, *args)
4801 def get_value(self, *args):
4803 get_value(Domain self, FloatKey a0) -> IMP::Float
4804 get_value(Domain self, IntKey a0) -> IMP::Int
4805 get_value(Domain self, FloatsKey a0) -> IMP::Floats
4806 get_value(Domain self, IntsKey a0) -> IMP::Ints
4807 get_value(Domain self, StringKey a0) -> IMP::String
4808 get_value(Domain self, ParticleIndexKey a0) -> Particle
4809 get_value(Domain self, ObjectKey a0) -> Object
4811 return _IMP_atom.Domain_get_value(self, *args)
4813 def set_value(self, *args):
4815 set_value(Domain self, FloatKey a0, IMP::Float a1)
4816 set_value(Domain self, IntKey a0, IMP::Int a1)
4817 set_value(Domain self, FloatsKey a0, IMP::Floats a1)
4818 set_value(Domain self, IntsKey a0, IMP::Ints a1)
4819 set_value(Domain self, StringKey a0, IMP::String a1)
4820 set_value(Domain self, ParticleIndexKey a0, Particle a1)
4821 set_value(Domain self, ObjectKey a0, Object a1)
4823 return _IMP_atom.Domain_set_value(self, *args)
4825 def remove_attribute(self, *args):
4827 remove_attribute(Domain self, FloatKey a0)
4828 remove_attribute(Domain self, IntKey a0)
4829 remove_attribute(Domain self, FloatsKey a0)
4830 remove_attribute(Domain self, IntsKey a0)
4831 remove_attribute(Domain self, StringKey a0)
4832 remove_attribute(Domain self, ParticleIndexKey a0)
4833 remove_attribute(Domain self, ObjectKey a0)
4835 return _IMP_atom.Domain_remove_attribute(self, *args)
4837 def has_attribute(self, *args):
4839 has_attribute(Domain self, FloatKey a0) -> bool
4840 has_attribute(Domain self, IntKey a0) -> bool
4841 has_attribute(Domain self, FloatsKey a0) -> bool
4842 has_attribute(Domain self, IntsKey a0) -> bool
4843 has_attribute(Domain self, StringKey a0) -> bool
4844 has_attribute(Domain self, ParticleIndexKey a0) -> bool
4845 has_attribute(Domain self, ObjectKey a0) -> bool
4847 return _IMP_atom.Domain_has_attribute(self, *args)
4849 def get_derivative(self, a0):
4850 r"""get_derivative(Domain self, FloatKey a0) -> double"""
4851 return _IMP_atom.Domain_get_derivative(self, a0)
4854 r"""get_name(Domain self) -> std::string"""
4855 return _IMP_atom.Domain_get_name(self)
4857 def clear_caches(self):
4858 r"""clear_caches(Domain self)"""
4859 return _IMP_atom.Domain_clear_caches(self)
4861 def set_name(self, a0):
4862 r"""set_name(Domain self, std::string a0)"""
4863 return _IMP_atom.Domain_set_name(self, a0)
4866 r"""set_check_level(Domain self, IMP::CheckLevel a0)"""
4867 return _IMP_atom.Domain_set_check_level(self, a0)
4869 def add_to_derivative(self, a0, a1, a2):
4870 r"""add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4871 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
4873 def set_is_optimized(self, a0, a1):
4874 r"""set_is_optimized(Domain self, FloatKey a0, bool a1)"""
4875 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
4877 def get_is_optimized(self, a0):
4878 r"""get_is_optimized(Domain self, FloatKey a0) -> bool"""
4879 return _IMP_atom.Domain_get_is_optimized(self, a0)
4882 r"""get_check_level(Domain self) -> IMP::CheckLevel"""
4883 return _IMP_atom.Domain_get_check_level(self)
4885 def __eq__(self, *args):
4887 __eq__(Domain self, Domain o) -> bool
4888 __eq__(Domain self, Particle d) -> bool
4890 return _IMP_atom.Domain___eq__(self, *args)
4892 def __ne__(self, *args):
4894 __ne__(Domain self, Domain o) -> bool
4895 __ne__(Domain self, Particle d) -> bool
4897 return _IMP_atom.Domain___ne__(self, *args)
4899 def __le__(self, *args):
4901 __le__(Domain self, Domain o) -> bool
4902 __le__(Domain self, Particle d) -> bool
4904 return _IMP_atom.Domain___le__(self, *args)
4906 def __lt__(self, *args):
4908 __lt__(Domain self, Domain o) -> bool
4909 __lt__(Domain self, Particle d) -> bool
4911 return _IMP_atom.Domain___lt__(self, *args)
4913 def __ge__(self, *args):
4915 __ge__(Domain self, Domain o) -> bool
4916 __ge__(Domain self, Particle d) -> bool
4918 return _IMP_atom.Domain___ge__(self, *args)
4920 def __gt__(self, *args):
4922 __gt__(Domain self, Domain o) -> bool
4923 __gt__(Domain self, Particle d) -> bool
4925 return _IMP_atom.Domain___gt__(self, *args)
4928 r"""__hash__(Domain self) -> std::size_t"""
4929 return _IMP_atom.Domain___hash__(self)
4932 r"""__str__(Domain self) -> std::string"""
4933 return _IMP_atom.Domain___str__(self)
4936 r"""__repr__(Domain self) -> std::string"""
4937 return _IMP_atom.Domain___repr__(self)
4939 def _get_as_binary(self):
4940 r"""_get_as_binary(Domain self) -> PyObject *"""
4941 return _IMP_atom.Domain__get_as_binary(self)
4943 def _set_from_binary(self, p):
4944 r"""_set_from_binary(Domain self, PyObject * p)"""
4945 return _IMP_atom.Domain__set_from_binary(self, p)
4947 def __getstate__(self):
4948 p = self._get_as_binary()
4949 if len(self.__dict__) > 1:
4950 d = self.__dict__.copy()
4955 def __setstate__(self, p):
4956 if not hasattr(self,
'this'):
4958 if isinstance(p, tuple):
4960 self.__dict__.update(d)
4961 return self._set_from_binary(p)
4963 __swig_destroy__ = _IMP_atom.delete_Domain
4966 _IMP_atom.Domain_swigregister(Domain)
4968 r"""Proxy of C++ IMP::atom::LennardJones class."""
4970 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4972 def __init__(self, *args):
4974 __init__(LennardJones self) -> LennardJones
4975 __init__(LennardJones self, Model m, ParticleIndex id) -> LennardJones
4976 __init__(LennardJones self, _ParticleAdaptor d) -> LennardJones
4978 _IMP_atom.LennardJones_swiginit(self, _IMP_atom.new_LennardJones(*args))
4980 def show(self, *args):
4981 r"""show(LennardJones self, _ostream out=std::cout)"""
4982 return _IMP_atom.LennardJones_show(self, *args)
4985 def setup_particle(*args):
4987 setup_particle(Model m, ParticleIndex pi) -> LennardJones
4988 setup_particle(_ParticleAdaptor pa) -> LennardJones
4989 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
4990 setup_particle(_ParticleAdaptor pa, IMP::Float well_depth) -> LennardJones
4992 return _IMP_atom.LennardJones_setup_particle(*args)
4994 def get_well_depth(self):
4995 r"""get_well_depth(LennardJones self) -> IMP::Float"""
4996 return _IMP_atom.LennardJones_get_well_depth(self)
4998 def set_well_depth(self, well_depth):
4999 r"""set_well_depth(LennardJones self, IMP::Float well_depth)"""
5000 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5003 def get_is_setup(*args):
5005 get_is_setup(_ParticleAdaptor p) -> bool
5006 get_is_setup(Model m, ParticleIndex pi) -> bool
5008 return _IMP_atom.LennardJones_get_is_setup(*args)
5011 def get_well_depth_key():
5012 r"""get_well_depth_key() -> FloatKey"""
5013 return _IMP_atom.LennardJones_get_well_depth_key()
5015 def add_attribute(self, *args):
5017 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5018 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5019 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5020 add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
5021 add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
5022 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5023 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5024 add_attribute(LennardJones self, ObjectKey a0, Object a1)
5026 return _IMP_atom.LennardJones_add_attribute(self, *args)
5028 def get_value(self, *args):
5030 get_value(LennardJones self, FloatKey a0) -> IMP::Float
5031 get_value(LennardJones self, IntKey a0) -> IMP::Int
5032 get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
5033 get_value(LennardJones self, IntsKey a0) -> IMP::Ints
5034 get_value(LennardJones self, StringKey a0) -> IMP::String
5035 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5036 get_value(LennardJones self, ObjectKey a0) -> Object
5038 return _IMP_atom.LennardJones_get_value(self, *args)
5040 def set_value(self, *args):
5042 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5043 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5044 set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5045 set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5046 set_value(LennardJones self, StringKey a0, IMP::String a1)
5047 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5048 set_value(LennardJones self, ObjectKey a0, Object a1)
5050 return _IMP_atom.LennardJones_set_value(self, *args)
5052 def remove_attribute(self, *args):
5054 remove_attribute(LennardJones self, FloatKey a0)
5055 remove_attribute(LennardJones self, IntKey a0)
5056 remove_attribute(LennardJones self, FloatsKey a0)
5057 remove_attribute(LennardJones self, IntsKey a0)
5058 remove_attribute(LennardJones self, StringKey a0)
5059 remove_attribute(LennardJones self, ParticleIndexKey a0)
5060 remove_attribute(LennardJones self, ObjectKey a0)
5062 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5064 def has_attribute(self, *args):
5066 has_attribute(LennardJones self, FloatKey a0) -> bool
5067 has_attribute(LennardJones self, IntKey a0) -> bool
5068 has_attribute(LennardJones self, FloatsKey a0) -> bool
5069 has_attribute(LennardJones self, IntsKey a0) -> bool
5070 has_attribute(LennardJones self, StringKey a0) -> bool
5071 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5072 has_attribute(LennardJones self, ObjectKey a0) -> bool
5074 return _IMP_atom.LennardJones_has_attribute(self, *args)
5076 def get_derivative(self, a0):
5077 r"""get_derivative(LennardJones self, FloatKey a0) -> double"""
5078 return _IMP_atom.LennardJones_get_derivative(self, a0)
5081 r"""get_name(LennardJones self) -> std::string"""
5082 return _IMP_atom.LennardJones_get_name(self)
5084 def clear_caches(self):
5085 r"""clear_caches(LennardJones self)"""
5086 return _IMP_atom.LennardJones_clear_caches(self)
5088 def set_name(self, a0):
5089 r"""set_name(LennardJones self, std::string a0)"""
5090 return _IMP_atom.LennardJones_set_name(self, a0)
5093 r"""set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5094 return _IMP_atom.LennardJones_set_check_level(self, a0)
5096 def add_to_derivative(self, a0, a1, a2):
5097 r"""add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5098 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5100 def set_is_optimized(self, a0, a1):
5101 r"""set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5102 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5104 def get_is_optimized(self, a0):
5105 r"""get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5106 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5109 r"""get_check_level(LennardJones self) -> IMP::CheckLevel"""
5110 return _IMP_atom.LennardJones_get_check_level(self)
5112 def __eq__(self, *args):
5114 __eq__(LennardJones self, LennardJones o) -> bool
5115 __eq__(LennardJones self, Particle d) -> bool
5117 return _IMP_atom.LennardJones___eq__(self, *args)
5119 def __ne__(self, *args):
5121 __ne__(LennardJones self, LennardJones o) -> bool
5122 __ne__(LennardJones self, Particle d) -> bool
5124 return _IMP_atom.LennardJones___ne__(self, *args)
5126 def __le__(self, *args):
5128 __le__(LennardJones self, LennardJones o) -> bool
5129 __le__(LennardJones self, Particle d) -> bool
5131 return _IMP_atom.LennardJones___le__(self, *args)
5133 def __lt__(self, *args):
5135 __lt__(LennardJones self, LennardJones o) -> bool
5136 __lt__(LennardJones self, Particle d) -> bool
5138 return _IMP_atom.LennardJones___lt__(self, *args)
5140 def __ge__(self, *args):
5142 __ge__(LennardJones self, LennardJones o) -> bool
5143 __ge__(LennardJones self, Particle d) -> bool
5145 return _IMP_atom.LennardJones___ge__(self, *args)
5147 def __gt__(self, *args):
5149 __gt__(LennardJones self, LennardJones o) -> bool
5150 __gt__(LennardJones self, Particle d) -> bool
5152 return _IMP_atom.LennardJones___gt__(self, *args)
5155 r"""__hash__(LennardJones self) -> std::size_t"""
5156 return _IMP_atom.LennardJones___hash__(self)
5159 r"""__str__(LennardJones self) -> std::string"""
5160 return _IMP_atom.LennardJones___str__(self)
5163 r"""__repr__(LennardJones self) -> std::string"""
5164 return _IMP_atom.LennardJones___repr__(self)
5166 def _get_as_binary(self):
5167 r"""_get_as_binary(LennardJones self) -> PyObject *"""
5168 return _IMP_atom.LennardJones__get_as_binary(self)
5170 def _set_from_binary(self, p):
5171 r"""_set_from_binary(LennardJones self, PyObject * p)"""
5172 return _IMP_atom.LennardJones__set_from_binary(self, p)
5174 def __getstate__(self):
5175 p = self._get_as_binary()
5176 if len(self.__dict__) > 1:
5177 d = self.__dict__.copy()
5182 def __setstate__(self, p):
5183 if not hasattr(self,
'this'):
5185 if isinstance(p, tuple):
5187 self.__dict__.update(d)
5188 return self._set_from_binary(p)
5190 __swig_destroy__ = _IMP_atom.delete_LennardJones
5193 _IMP_atom.LennardJones_swigregister(LennardJones)
5195 r"""Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5197 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5199 def __init__(self, f):
5200 r"""__init__(LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5201 _IMP_atom.LennardJonesPairScore_swiginit(self, _IMP_atom.new_LennardJonesPairScore(f))
5203 def set_repulsive_weight(self, repulsive_weight):
5204 r"""set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5205 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5207 def get_repulsive_weight(self):
5208 r"""get_repulsive_weight(LennardJonesPairScore self) -> double"""
5209 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5211 def set_attractive_weight(self, attractive_weight):
5212 r"""set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5213 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5215 def get_attractive_weight(self):
5216 r"""get_attractive_weight(LennardJonesPairScore self) -> double"""
5217 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5219 def do_get_inputs(self, m, pis):
5220 r"""do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5221 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5223 def get_version_info(self):
5224 r"""get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5225 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5226 __swig_destroy__ = _IMP_atom.delete_LennardJonesPairScore
5229 r"""__str__(LennardJonesPairScore self) -> std::string"""
5230 return _IMP_atom.LennardJonesPairScore___str__(self)
5233 r"""__repr__(LennardJonesPairScore self) -> std::string"""
5234 return _IMP_atom.LennardJonesPairScore___repr__(self)
5238 return _object_cast_to_LennardJonesPairScore(o)
5242 _IMP_atom.LennardJonesPairScore_swigregister(LennardJonesPairScore)
5244 r"""Proxy of C++ IMP::atom::LinearVelocity class."""
5246 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5248 def __init__(self, *args):
5250 __init__(LinearVelocity self) -> LinearVelocity
5251 __init__(LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5252 __init__(LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5254 _IMP_atom.LinearVelocity_swiginit(self, _IMP_atom.new_LinearVelocity(*args))
5257 def get_is_setup(*args):
5259 get_is_setup(Model m, ParticleIndex pi) -> bool
5260 get_is_setup(_ParticleAdaptor p) -> bool
5262 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5264 def show(self, *args):
5265 r"""show(LinearVelocity self, _ostream out=std::cout)"""
5266 return _IMP_atom.LinearVelocity_show(self, *args)
5269 def setup_particle(*args):
5271 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5272 setup_particle(_ParticleAdaptor pa) -> LinearVelocity
5273 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5274 setup_particle(_ParticleAdaptor pa, Vector3D v) -> LinearVelocity
5276 return _IMP_atom.LinearVelocity_setup_particle(*args)
5278 def set_velocity(self, v):
5279 r"""set_velocity(LinearVelocity self, Vector3D v)"""
5280 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5282 def get_velocity(self):
5283 r"""get_velocity(LinearVelocity self) -> Vector3D"""
5284 return _IMP_atom.LinearVelocity_get_velocity(self)
5286 def add_attribute(self, *args):
5288 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5289 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5290 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5291 add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5292 add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5293 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5294 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5295 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5297 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5299 def get_value(self, *args):
5301 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5302 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5303 get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5304 get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5305 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5306 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5307 get_value(LinearVelocity self, ObjectKey a0) -> Object
5309 return _IMP_atom.LinearVelocity_get_value(self, *args)
5311 def set_value(self, *args):
5313 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5314 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5315 set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5316 set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5317 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5318 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5319 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5321 return _IMP_atom.LinearVelocity_set_value(self, *args)
5323 def remove_attribute(self, *args):
5325 remove_attribute(LinearVelocity self, FloatKey a0)
5326 remove_attribute(LinearVelocity self, IntKey a0)
5327 remove_attribute(LinearVelocity self, FloatsKey a0)
5328 remove_attribute(LinearVelocity self, IntsKey a0)
5329 remove_attribute(LinearVelocity self, StringKey a0)
5330 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5331 remove_attribute(LinearVelocity self, ObjectKey a0)
5333 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5335 def has_attribute(self, *args):
5337 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5338 has_attribute(LinearVelocity self, IntKey a0) -> bool
5339 has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5340 has_attribute(LinearVelocity self, IntsKey a0) -> bool
5341 has_attribute(LinearVelocity self, StringKey a0) -> bool
5342 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5343 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5345 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5347 def get_derivative(self, a0):
5348 r"""get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5349 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5352 r"""get_name(LinearVelocity self) -> std::string"""
5353 return _IMP_atom.LinearVelocity_get_name(self)
5355 def clear_caches(self):
5356 r"""clear_caches(LinearVelocity self)"""
5357 return _IMP_atom.LinearVelocity_clear_caches(self)
5359 def set_name(self, a0):
5360 r"""set_name(LinearVelocity self, std::string a0)"""
5361 return _IMP_atom.LinearVelocity_set_name(self, a0)
5364 r"""set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5365 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5367 def add_to_derivative(self, a0, a1, a2):
5368 r"""add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5369 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5371 def set_is_optimized(self, a0, a1):
5372 r"""set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5373 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5375 def get_is_optimized(self, a0):
5376 r"""get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5377 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5380 r"""get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5381 return _IMP_atom.LinearVelocity_get_check_level(self)
5383 def __eq__(self, *args):
5385 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5386 __eq__(LinearVelocity self, Particle d) -> bool
5388 return _IMP_atom.LinearVelocity___eq__(self, *args)
5390 def __ne__(self, *args):
5392 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5393 __ne__(LinearVelocity self, Particle d) -> bool
5395 return _IMP_atom.LinearVelocity___ne__(self, *args)
5397 def __le__(self, *args):
5399 __le__(LinearVelocity self, LinearVelocity o) -> bool
5400 __le__(LinearVelocity self, Particle d) -> bool
5402 return _IMP_atom.LinearVelocity___le__(self, *args)
5404 def __lt__(self, *args):
5406 __lt__(LinearVelocity self, LinearVelocity o) -> bool
5407 __lt__(LinearVelocity self, Particle d) -> bool
5409 return _IMP_atom.LinearVelocity___lt__(self, *args)
5411 def __ge__(self, *args):
5413 __ge__(LinearVelocity self, LinearVelocity o) -> bool
5414 __ge__(LinearVelocity self, Particle d) -> bool
5416 return _IMP_atom.LinearVelocity___ge__(self, *args)
5418 def __gt__(self, *args):
5420 __gt__(LinearVelocity self, LinearVelocity o) -> bool
5421 __gt__(LinearVelocity self, Particle d) -> bool
5423 return _IMP_atom.LinearVelocity___gt__(self, *args)
5426 r"""__hash__(LinearVelocity self) -> std::size_t"""
5427 return _IMP_atom.LinearVelocity___hash__(self)
5430 r"""__str__(LinearVelocity self) -> std::string"""
5431 return _IMP_atom.LinearVelocity___str__(self)
5434 r"""__repr__(LinearVelocity self) -> std::string"""
5435 return _IMP_atom.LinearVelocity___repr__(self)
5437 def _get_as_binary(self):
5438 r"""_get_as_binary(LinearVelocity self) -> PyObject *"""
5439 return _IMP_atom.LinearVelocity__get_as_binary(self)
5441 def _set_from_binary(self, p):
5442 r"""_set_from_binary(LinearVelocity self, PyObject * p)"""
5443 return _IMP_atom.LinearVelocity__set_from_binary(self, p)
5445 def __getstate__(self):
5446 p = self._get_as_binary()
5447 if len(self.__dict__) > 1:
5448 d = self.__dict__.copy()
5453 def __setstate__(self, p):
5454 if not hasattr(self,
'this'):
5456 if isinstance(p, tuple):
5458 self.__dict__.update(d)
5459 return self._set_from_binary(p)
5461 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5464 _IMP_atom.LinearVelocity_swigregister(LinearVelocity)
5466 r"""Proxy of C++ IMP::atom::AngularVelocity class."""
5468 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5470 def __init__(self, *args):
5472 __init__(AngularVelocity self) -> AngularVelocity
5473 __init__(AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5474 __init__(AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5476 _IMP_atom.AngularVelocity_swiginit(self, _IMP_atom.new_AngularVelocity(*args))
5479 def get_is_setup(*args):
5481 get_is_setup(Model m, ParticleIndex pi) -> bool
5482 get_is_setup(_ParticleAdaptor p) -> bool
5484 return _IMP_atom.AngularVelocity_get_is_setup(*args)
5486 def show(self, *args):
5487 r"""show(AngularVelocity self, _ostream out=std::cout)"""
5488 return _IMP_atom.AngularVelocity_show(self, *args)
5491 def setup_particle(*args):
5493 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5494 setup_particle(_ParticleAdaptor pa) -> AngularVelocity
5495 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5496 setup_particle(_ParticleAdaptor pa, Vector4D v) -> AngularVelocity
5498 return _IMP_atom.AngularVelocity_setup_particle(*args)
5500 def set_velocity(self, v):
5501 r"""set_velocity(AngularVelocity self, Vector4D v)"""
5502 return _IMP_atom.AngularVelocity_set_velocity(self, v)
5504 def get_velocity(self):
5505 r"""get_velocity(AngularVelocity self) -> Vector4D"""
5506 return _IMP_atom.AngularVelocity_get_velocity(self)
5508 def add_attribute(self, *args):
5510 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5511 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5512 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5513 add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5514 add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5515 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5516 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5517 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5519 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5521 def get_value(self, *args):
5523 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5524 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5525 get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
5526 get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
5527 get_value(AngularVelocity self, StringKey a0) -> IMP::String
5528 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5529 get_value(AngularVelocity self, ObjectKey a0) -> Object
5531 return _IMP_atom.AngularVelocity_get_value(self, *args)
5533 def set_value(self, *args):
5535 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5536 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5537 set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
5538 set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
5539 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5540 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5541 set_value(AngularVelocity self, ObjectKey a0, Object a1)
5543 return _IMP_atom.AngularVelocity_set_value(self, *args)
5545 def remove_attribute(self, *args):
5547 remove_attribute(AngularVelocity self, FloatKey a0)
5548 remove_attribute(AngularVelocity self, IntKey a0)
5549 remove_attribute(AngularVelocity self, FloatsKey a0)
5550 remove_attribute(AngularVelocity self, IntsKey a0)
5551 remove_attribute(AngularVelocity self, StringKey a0)
5552 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5553 remove_attribute(AngularVelocity self, ObjectKey a0)
5555 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5557 def has_attribute(self, *args):
5559 has_attribute(AngularVelocity self, FloatKey a0) -> bool
5560 has_attribute(AngularVelocity self, IntKey a0) -> bool
5561 has_attribute(AngularVelocity self, FloatsKey a0) -> bool
5562 has_attribute(AngularVelocity self, IntsKey a0) -> bool
5563 has_attribute(AngularVelocity self, StringKey a0) -> bool
5564 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
5565 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
5567 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
5569 def get_derivative(self, a0):
5570 r"""get_derivative(AngularVelocity self, FloatKey a0) -> double"""
5571 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
5574 r"""get_name(AngularVelocity self) -> std::string"""
5575 return _IMP_atom.AngularVelocity_get_name(self)
5577 def clear_caches(self):
5578 r"""clear_caches(AngularVelocity self)"""
5579 return _IMP_atom.AngularVelocity_clear_caches(self)
5581 def set_name(self, a0):
5582 r"""set_name(AngularVelocity self, std::string a0)"""
5583 return _IMP_atom.AngularVelocity_set_name(self, a0)
5586 r"""set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
5587 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
5589 def add_to_derivative(self, a0, a1, a2):
5590 r"""add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5591 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
5593 def set_is_optimized(self, a0, a1):
5594 r"""set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
5595 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
5597 def get_is_optimized(self, a0):
5598 r"""get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
5599 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
5602 r"""get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
5603 return _IMP_atom.AngularVelocity_get_check_level(self)
5605 def __eq__(self, *args):
5607 __eq__(AngularVelocity self, AngularVelocity o) -> bool
5608 __eq__(AngularVelocity self, Particle d) -> bool
5610 return _IMP_atom.AngularVelocity___eq__(self, *args)
5612 def __ne__(self, *args):
5614 __ne__(AngularVelocity self, AngularVelocity o) -> bool
5615 __ne__(AngularVelocity self, Particle d) -> bool
5617 return _IMP_atom.AngularVelocity___ne__(self, *args)
5619 def __le__(self, *args):
5621 __le__(AngularVelocity self, AngularVelocity o) -> bool
5622 __le__(AngularVelocity self, Particle d) -> bool
5624 return _IMP_atom.AngularVelocity___le__(self, *args)
5626 def __lt__(self, *args):
5628 __lt__(AngularVelocity self, AngularVelocity o) -> bool
5629 __lt__(AngularVelocity self, Particle d) -> bool
5631 return _IMP_atom.AngularVelocity___lt__(self, *args)
5633 def __ge__(self, *args):
5635 __ge__(AngularVelocity self, AngularVelocity o) -> bool
5636 __ge__(AngularVelocity self, Particle d) -> bool
5638 return _IMP_atom.AngularVelocity___ge__(self, *args)
5640 def __gt__(self, *args):
5642 __gt__(AngularVelocity self, AngularVelocity o) -> bool
5643 __gt__(AngularVelocity self, Particle d) -> bool
5645 return _IMP_atom.AngularVelocity___gt__(self, *args)
5648 r"""__hash__(AngularVelocity self) -> std::size_t"""
5649 return _IMP_atom.AngularVelocity___hash__(self)
5652 r"""__str__(AngularVelocity self) -> std::string"""
5653 return _IMP_atom.AngularVelocity___str__(self)
5656 r"""__repr__(AngularVelocity self) -> std::string"""
5657 return _IMP_atom.AngularVelocity___repr__(self)
5659 def _get_as_binary(self):
5660 r"""_get_as_binary(AngularVelocity self) -> PyObject *"""
5661 return _IMP_atom.AngularVelocity__get_as_binary(self)
5663 def _set_from_binary(self, p):
5664 r"""_set_from_binary(AngularVelocity self, PyObject * p)"""
5665 return _IMP_atom.AngularVelocity__set_from_binary(self, p)
5667 def __getstate__(self):
5668 p = self._get_as_binary()
5669 if len(self.__dict__) > 1:
5670 d = self.__dict__.copy()
5675 def __setstate__(self, p):
5676 if not hasattr(self,
'this'):
5678 if isinstance(p, tuple):
5680 self.__dict__.update(d)
5681 return self._set_from_binary(p)
5683 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
5686 _IMP_atom.AngularVelocity_swigregister(AngularVelocity)
5687 class MolecularDynamics(Simulator):
5688 r"""Proxy of C++ IMP::atom::MolecularDynamics class."""
5690 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5692 def __init__(self, m):
5693 r"""__init__(MolecularDynamics self, Model m) -> MolecularDynamics"""
5694 _IMP_atom.MolecularDynamics_swiginit(self, _IMP_atom.new_MolecularDynamics(m))
5696 def get_kinetic_energy(self):
5697 r"""get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
5698 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
5700 def get_kinetic_temperature(self, ekinetic):
5701 r"""get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
5702 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
5704 def set_velocity_cap(self, velocity_cap):
5705 r"""set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
5706 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
5708 def assign_velocities(self, temperature):
5709 r"""assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
5710 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
5712 def setup(self, ps):
5713 r"""setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
5714 return _IMP_atom.MolecularDynamics_setup(self, ps)
5716 def do_step(self, sc, dt):
5717 r"""do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
5718 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
5720 def get_is_simulation_particle(self, p):
5721 r"""get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
5722 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
5724 def get_version_info(self):
5725 r"""get_version_info(MolecularDynamics self) -> VersionInfo"""
5726 return _IMP_atom.MolecularDynamics_get_version_info(self)
5727 __swig_destroy__ = _IMP_atom.delete_MolecularDynamics
5730 r"""__str__(MolecularDynamics self) -> std::string"""
5731 return _IMP_atom.MolecularDynamics___str__(self)
5734 r"""__repr__(MolecularDynamics self) -> std::string"""
5735 return _IMP_atom.MolecularDynamics___repr__(self)
5739 return _object_cast_to_MolecularDynamics(o)
5743 _IMP_atom.MolecularDynamics_swigregister(MolecularDynamics)
5745 r"""Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
5747 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5749 def __init__(self, m, pis, temperature):
5750 r"""__init__(VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
5751 _IMP_atom.VelocityScalingOptimizerState_swiginit(self, _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature))
5753 def set_particles(self, pis):
5754 r"""set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
5755 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
5757 def set_temperature(self, temperature):
5758 r"""set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
5759 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
5761 def rescale_velocities(self):
5762 r"""rescale_velocities(VelocityScalingOptimizerState self)"""
5763 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
5765 def get_version_info(self):
5766 r"""get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
5767 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
5768 __swig_destroy__ = _IMP_atom.delete_VelocityScalingOptimizerState
5771 r"""__str__(VelocityScalingOptimizerState self) -> std::string"""
5772 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
5775 r"""__repr__(VelocityScalingOptimizerState self) -> std::string"""
5776 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
5780 return _object_cast_to_VelocityScalingOptimizerState(o)
5784 _IMP_atom.VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
5785 class Fragment(Hierarchy):
5786 r"""Proxy of C++ IMP::atom::Fragment class."""
5788 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5790 def set_residue_indexes(self, o):
5791 r"""set_residue_indexes(Fragment self, IMP::Ints o)"""
5792 return _IMP_atom.Fragment_set_residue_indexes(self, o)
5794 def get_residue_indexes(self):
5795 r"""get_residue_indexes(Fragment self) -> IMP::Ints"""
5796 return _IMP_atom.Fragment_get_residue_indexes(self)
5798 def get_contains_residue(self, rindex):
5799 r"""get_contains_residue(Fragment self, int rindex) -> bool"""
5800 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
5802 def get_contains_any_sorted_residue(self, rinds):
5803 r"""get_contains_any_sorted_residue(Fragment self, IMP::Ints const & rinds) -> bool"""
5804 return _IMP_atom.Fragment_get_contains_any_sorted_residue(self, rinds)
5806 def __init__(self, *args):
5808 __init__(Fragment self) -> Fragment
5809 __init__(Fragment self, Model m, ParticleIndex id) -> Fragment
5810 __init__(Fragment self, _ParticleAdaptor d) -> Fragment
5812 _IMP_atom.Fragment_swiginit(self, _IMP_atom.new_Fragment(*args))
5815 def get_is_setup(*args):
5817 get_is_setup(Model m, ParticleIndex pi) -> bool
5818 get_is_setup(_ParticleAdaptor p) -> bool
5820 return _IMP_atom.Fragment_get_is_setup(*args)
5822 def show(self, *args):
5823 r"""show(Fragment self, _ostream out=std::cout)"""
5824 return _IMP_atom.Fragment_show(self, *args)
5827 def setup_particle(*args):
5829 setup_particle(Model m, ParticleIndex pi) -> Fragment
5830 setup_particle(_ParticleAdaptor pa) -> Fragment
5831 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
5832 setup_particle(_ParticleAdaptor pa, Fragment other) -> Fragment
5833 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
5834 setup_particle(_ParticleAdaptor pa, IMP::Ints residue_indexes) -> Fragment
5836 return _IMP_atom.Fragment_setup_particle(*args)
5838 def add_attribute(self, *args):
5840 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
5841 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
5842 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
5843 add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
5844 add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
5845 add_attribute(Fragment self, StringKey a0, IMP::String a1)
5846 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
5847 add_attribute(Fragment self, ObjectKey a0, Object a1)
5849 return _IMP_atom.Fragment_add_attribute(self, *args)
5851 def get_value(self, *args):
5853 get_value(Fragment self, FloatKey a0) -> IMP::Float
5854 get_value(Fragment self, IntKey a0) -> IMP::Int
5855 get_value(Fragment self, FloatsKey a0) -> IMP::Floats
5856 get_value(Fragment self, IntsKey a0) -> IMP::Ints
5857 get_value(Fragment self, StringKey a0) -> IMP::String
5858 get_value(Fragment self, ParticleIndexKey a0) -> Particle
5859 get_value(Fragment self, ObjectKey a0) -> Object
5861 return _IMP_atom.Fragment_get_value(self, *args)
5863 def set_value(self, *args):
5865 set_value(Fragment self, FloatKey a0, IMP::Float a1)
5866 set_value(Fragment self, IntKey a0, IMP::Int a1)
5867 set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
5868 set_value(Fragment self, IntsKey a0, IMP::Ints a1)
5869 set_value(Fragment self, StringKey a0, IMP::String a1)
5870 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
5871 set_value(Fragment self, ObjectKey a0, Object a1)
5873 return _IMP_atom.Fragment_set_value(self, *args)
5875 def remove_attribute(self, *args):
5877 remove_attribute(Fragment self, FloatKey a0)
5878 remove_attribute(Fragment self, IntKey a0)
5879 remove_attribute(Fragment self, FloatsKey a0)
5880 remove_attribute(Fragment self, IntsKey a0)
5881 remove_attribute(Fragment self, StringKey a0)
5882 remove_attribute(Fragment self, ParticleIndexKey a0)
5883 remove_attribute(Fragment self, ObjectKey a0)
5885 return _IMP_atom.Fragment_remove_attribute(self, *args)
5887 def has_attribute(self, *args):
5889 has_attribute(Fragment self, FloatKey a0) -> bool
5890 has_attribute(Fragment self, IntKey a0) -> bool
5891 has_attribute(Fragment self, FloatsKey a0) -> bool
5892 has_attribute(Fragment self, IntsKey a0) -> bool
5893 has_attribute(Fragment self, StringKey a0) -> bool
5894 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
5895 has_attribute(Fragment self, ObjectKey a0) -> bool
5897 return _IMP_atom.Fragment_has_attribute(self, *args)
5899 def get_derivative(self, a0):
5900 r"""get_derivative(Fragment self, FloatKey a0) -> double"""
5901 return _IMP_atom.Fragment_get_derivative(self, a0)
5904 r"""get_name(Fragment self) -> std::string"""
5905 return _IMP_atom.Fragment_get_name(self)
5907 def clear_caches(self):
5908 r"""clear_caches(Fragment self)"""
5909 return _IMP_atom.Fragment_clear_caches(self)
5911 def set_name(self, a0):
5912 r"""set_name(Fragment self, std::string a0)"""
5913 return _IMP_atom.Fragment_set_name(self, a0)
5916 r"""set_check_level(Fragment self, IMP::CheckLevel a0)"""
5917 return _IMP_atom.Fragment_set_check_level(self, a0)
5919 def add_to_derivative(self, a0, a1, a2):
5920 r"""add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5921 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
5923 def set_is_optimized(self, a0, a1):
5924 r"""set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
5925 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
5927 def get_is_optimized(self, a0):
5928 r"""get_is_optimized(Fragment self, FloatKey a0) -> bool"""
5929 return _IMP_atom.Fragment_get_is_optimized(self, a0)
5932 r"""get_check_level(Fragment self) -> IMP::CheckLevel"""
5933 return _IMP_atom.Fragment_get_check_level(self)
5935 def __eq__(self, *args):
5937 __eq__(Fragment self, Fragment o) -> bool
5938 __eq__(Fragment self, Particle d) -> bool
5940 return _IMP_atom.Fragment___eq__(self, *args)
5942 def __ne__(self, *args):
5944 __ne__(Fragment self, Fragment o) -> bool
5945 __ne__(Fragment self, Particle d) -> bool
5947 return _IMP_atom.Fragment___ne__(self, *args)
5949 def __le__(self, *args):
5951 __le__(Fragment self, Fragment o) -> bool
5952 __le__(Fragment self, Particle d) -> bool
5954 return _IMP_atom.Fragment___le__(self, *args)
5956 def __lt__(self, *args):
5958 __lt__(Fragment self, Fragment o) -> bool
5959 __lt__(Fragment self, Particle d) -> bool
5961 return _IMP_atom.Fragment___lt__(self, *args)
5963 def __ge__(self, *args):
5965 __ge__(Fragment self, Fragment o) -> bool
5966 __ge__(Fragment self, Particle d) -> bool
5968 return _IMP_atom.Fragment___ge__(self, *args)
5970 def __gt__(self, *args):
5972 __gt__(Fragment self, Fragment o) -> bool
5973 __gt__(Fragment self, Particle d) -> bool
5975 return _IMP_atom.Fragment___gt__(self, *args)
5978 r"""__hash__(Fragment self) -> std::size_t"""
5979 return _IMP_atom.Fragment___hash__(self)
5982 r"""__str__(Fragment self) -> std::string"""
5983 return _IMP_atom.Fragment___str__(self)
5986 r"""__repr__(Fragment self) -> std::string"""
5987 return _IMP_atom.Fragment___repr__(self)
5989 def _get_as_binary(self):
5990 r"""_get_as_binary(Fragment self) -> PyObject *"""
5991 return _IMP_atom.Fragment__get_as_binary(self)
5993 def _set_from_binary(self, p):
5994 r"""_set_from_binary(Fragment self, PyObject * p)"""
5995 return _IMP_atom.Fragment__set_from_binary(self, p)
5997 def __getstate__(self):
5998 p = self._get_as_binary()
5999 if len(self.__dict__) > 1:
6000 d = self.__dict__.copy()
6005 def __setstate__(self, p):
6006 if not hasattr(self,
'this'):
6008 if isinstance(p, tuple):
6010 self.__dict__.update(d)
6011 return self._set_from_binary(p)
6013 __swig_destroy__ = _IMP_atom.delete_Fragment
6016 _IMP_atom.Fragment_swigregister(Fragment)
6018 r"""Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6020 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6023 r"""__init__(StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6024 _IMP_atom.StereochemistryPairFilter_swiginit(self, _IMP_atom.new_StereochemistryPairFilter())
6026 def set_bonds(self, bonds):
6027 r"""set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6028 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6030 def set_angles(self, angles):
6031 r"""set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6032 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6034 def set_dihedrals(self, dihedrals):
6035 r"""set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6036 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6038 def do_get_inputs(self, m, pis):
6039 r"""do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6040 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6042 def get_value(self, *args):
6044 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6045 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6047 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6049 def get_value_index(self, *args):
6051 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6052 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6054 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6056 def get_version_info(self):
6057 r"""get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6058 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6059 __swig_destroy__ = _IMP_atom.delete_StereochemistryPairFilter
6062 r"""__str__(StereochemistryPairFilter self) -> std::string"""
6063 return _IMP_atom.StereochemistryPairFilter___str__(self)
6066 r"""__repr__(StereochemistryPairFilter self) -> std::string"""
6067 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6071 return _object_cast_to_StereochemistryPairFilter(o)
6075 _IMP_atom.StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6077 r"""Proxy of C++ IMP::atom::SoapPairFilter class."""
6079 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6081 def __init__(self, library):
6082 r"""__init__(SoapPairFilter self, std::string library) -> SoapPairFilter"""
6083 _IMP_atom.SoapPairFilter_swiginit(self, _IMP_atom.new_SoapPairFilter(library))
6085 def do_get_inputs(self, m, pis):
6086 r"""do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6087 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6089 def get_value(self, *args):
6091 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6092 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6094 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6096 def get_value_index(self, *args):
6098 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6099 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6101 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6103 def get_version_info(self):
6104 r"""get_version_info(SoapPairFilter self) -> VersionInfo"""
6105 return _IMP_atom.SoapPairFilter_get_version_info(self)
6106 __swig_destroy__ = _IMP_atom.delete_SoapPairFilter
6109 r"""__str__(SoapPairFilter self) -> std::string"""
6110 return _IMP_atom.SoapPairFilter___str__(self)
6113 r"""__repr__(SoapPairFilter self) -> std::string"""
6114 return _IMP_atom.SoapPairFilter___repr__(self)
6118 return _object_cast_to_SoapPairFilter(o)
6122 _IMP_atom.SoapPairFilter_swigregister(SoapPairFilter)
6124 r"""Proxy of C++ IMP::atom::Mass class."""
6126 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6129 r"""get_mass(Mass self) -> IMP::Float"""
6130 return _IMP_atom.Mass_get_mass(self)
6132 def set_mass(self, d):
6133 r"""set_mass(Mass self, IMP::Float d)"""
6134 return _IMP_atom.Mass_set_mass(self, d)
6136 def __init__(self, *args):
6138 __init__(Mass self) -> Mass
6139 __init__(Mass self, Model m, ParticleIndex id) -> Mass
6140 __init__(Mass self, _ParticleAdaptor d) -> Mass
6142 _IMP_atom.Mass_swiginit(self, _IMP_atom.new_Mass(*args))
6145 def get_is_setup(*args):
6147 get_is_setup(Model m, ParticleIndex pi) -> bool
6148 get_is_setup(_ParticleAdaptor p) -> bool
6150 return _IMP_atom.Mass_get_is_setup(*args)
6152 def show(self, *args):
6153 r"""show(Mass self, _ostream out=std::cout)"""
6154 return _IMP_atom.Mass_show(self, *args)
6157 def setup_particle(*args):
6159 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6160 setup_particle(_ParticleAdaptor pa, IMP::Float mass) -> Mass
6161 setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6162 setup_particle(_ParticleAdaptor pa, Mass other) -> Mass
6164 return _IMP_atom.Mass_setup_particle(*args)
6168 r"""get_mass_key() -> FloatKey"""
6169 return _IMP_atom.Mass_get_mass_key()
6171 def add_attribute(self, *args):
6173 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6174 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6175 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6176 add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6177 add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6178 add_attribute(Mass self, StringKey a0, IMP::String a1)
6179 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6180 add_attribute(Mass self, ObjectKey a0, Object a1)
6182 return _IMP_atom.Mass_add_attribute(self, *args)
6184 def get_value(self, *args):
6186 get_value(Mass self, FloatKey a0) -> IMP::Float
6187 get_value(Mass self, IntKey a0) -> IMP::Int
6188 get_value(Mass self, FloatsKey a0) -> IMP::Floats
6189 get_value(Mass self, IntsKey a0) -> IMP::Ints
6190 get_value(Mass self, StringKey a0) -> IMP::String
6191 get_value(Mass self, ParticleIndexKey a0) -> Particle
6192 get_value(Mass self, ObjectKey a0) -> Object
6194 return _IMP_atom.Mass_get_value(self, *args)
6196 def set_value(self, *args):
6198 set_value(Mass self, FloatKey a0, IMP::Float a1)
6199 set_value(Mass self, IntKey a0, IMP::Int a1)
6200 set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6201 set_value(Mass self, IntsKey a0, IMP::Ints a1)
6202 set_value(Mass self, StringKey a0, IMP::String a1)
6203 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6204 set_value(Mass self, ObjectKey a0, Object a1)
6206 return _IMP_atom.Mass_set_value(self, *args)
6208 def remove_attribute(self, *args):
6210 remove_attribute(Mass self, FloatKey a0)
6211 remove_attribute(Mass self, IntKey a0)
6212 remove_attribute(Mass self, FloatsKey a0)
6213 remove_attribute(Mass self, IntsKey a0)
6214 remove_attribute(Mass self, StringKey a0)
6215 remove_attribute(Mass self, ParticleIndexKey a0)
6216 remove_attribute(Mass self, ObjectKey a0)
6218 return _IMP_atom.Mass_remove_attribute(self, *args)
6220 def has_attribute(self, *args):
6222 has_attribute(Mass self, FloatKey a0) -> bool
6223 has_attribute(Mass self, IntKey a0) -> bool
6224 has_attribute(Mass self, FloatsKey a0) -> bool
6225 has_attribute(Mass self, IntsKey a0) -> bool
6226 has_attribute(Mass self, StringKey a0) -> bool
6227 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6228 has_attribute(Mass self, ObjectKey a0) -> bool
6230 return _IMP_atom.Mass_has_attribute(self, *args)
6232 def get_derivative(self, a0):
6233 r"""get_derivative(Mass self, FloatKey a0) -> double"""
6234 return _IMP_atom.Mass_get_derivative(self, a0)
6237 r"""get_name(Mass self) -> std::string"""
6238 return _IMP_atom.Mass_get_name(self)
6240 def clear_caches(self):
6241 r"""clear_caches(Mass self)"""
6242 return _IMP_atom.Mass_clear_caches(self)
6244 def set_name(self, a0):
6245 r"""set_name(Mass self, std::string a0)"""
6246 return _IMP_atom.Mass_set_name(self, a0)
6249 r"""set_check_level(Mass self, IMP::CheckLevel a0)"""
6250 return _IMP_atom.Mass_set_check_level(self, a0)
6252 def add_to_derivative(self, a0, a1, a2):
6253 r"""add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6254 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6256 def set_is_optimized(self, a0, a1):
6257 r"""set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6258 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6260 def get_is_optimized(self, a0):
6261 r"""get_is_optimized(Mass self, FloatKey a0) -> bool"""
6262 return _IMP_atom.Mass_get_is_optimized(self, a0)
6265 r"""get_check_level(Mass self) -> IMP::CheckLevel"""
6266 return _IMP_atom.Mass_get_check_level(self)
6268 def __eq__(self, *args):
6270 __eq__(Mass self, Mass o) -> bool
6271 __eq__(Mass self, Particle d) -> bool
6273 return _IMP_atom.Mass___eq__(self, *args)
6275 def __ne__(self, *args):
6277 __ne__(Mass self, Mass o) -> bool
6278 __ne__(Mass self, Particle d) -> bool
6280 return _IMP_atom.Mass___ne__(self, *args)
6282 def __le__(self, *args):
6284 __le__(Mass self, Mass o) -> bool
6285 __le__(Mass self, Particle d) -> bool
6287 return _IMP_atom.Mass___le__(self, *args)
6289 def __lt__(self, *args):
6291 __lt__(Mass self, Mass o) -> bool
6292 __lt__(Mass self, Particle d) -> bool
6294 return _IMP_atom.Mass___lt__(self, *args)
6296 def __ge__(self, *args):
6298 __ge__(Mass self, Mass o) -> bool
6299 __ge__(Mass self, Particle d) -> bool
6301 return _IMP_atom.Mass___ge__(self, *args)
6303 def __gt__(self, *args):
6305 __gt__(Mass self, Mass o) -> bool
6306 __gt__(Mass self, Particle d) -> bool
6308 return _IMP_atom.Mass___gt__(self, *args)
6311 r"""__hash__(Mass self) -> std::size_t"""
6312 return _IMP_atom.Mass___hash__(self)
6315 r"""__str__(Mass self) -> std::string"""
6316 return _IMP_atom.Mass___str__(self)
6319 r"""__repr__(Mass self) -> std::string"""
6320 return _IMP_atom.Mass___repr__(self)
6322 def _get_as_binary(self):
6323 r"""_get_as_binary(Mass self) -> PyObject *"""
6324 return _IMP_atom.Mass__get_as_binary(self)
6326 def _set_from_binary(self, p):
6327 r"""_set_from_binary(Mass self, PyObject * p)"""
6328 return _IMP_atom.Mass__set_from_binary(self, p)
6330 def __getstate__(self):
6331 p = self._get_as_binary()
6332 if len(self.__dict__) > 1:
6333 d = self.__dict__.copy()
6338 def __setstate__(self, p):
6339 if not hasattr(self,
'this'):
6341 if isinstance(p, tuple):
6343 self.__dict__.update(d)
6344 return self._set_from_binary(p)
6346 __swig_destroy__ = _IMP_atom.delete_Mass
6349 _IMP_atom.Mass_swigregister(Mass)
6351 r"""Proxy of C++ IMP::atom::BondedPairFilter class."""
6353 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6356 r"""__init__(BondedPairFilter self) -> BondedPairFilter"""
6357 _IMP_atom.BondedPairFilter_swiginit(self, _IMP_atom.new_BondedPairFilter())
6359 def do_get_inputs(self, m, pis):
6360 r"""do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6361 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6363 def get_value(self, *args):
6365 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6366 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6368 return _IMP_atom.BondedPairFilter_get_value(self, *args)
6370 def get_value_index(self, *args):
6372 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6373 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6375 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6377 def get_version_info(self):
6378 r"""get_version_info(BondedPairFilter self) -> VersionInfo"""
6379 return _IMP_atom.BondedPairFilter_get_version_info(self)
6380 __swig_destroy__ = _IMP_atom.delete_BondedPairFilter
6383 r"""__str__(BondedPairFilter self) -> std::string"""
6384 return _IMP_atom.BondedPairFilter___str__(self)
6387 r"""__repr__(BondedPairFilter self) -> std::string"""
6388 return _IMP_atom.BondedPairFilter___repr__(self)
6392 return _object_cast_to_BondedPairFilter(o)
6396 _IMP_atom.BondedPairFilter_swigregister(BondedPairFilter)
6398 r"""Proxy of C++ IMP::atom::Mol2Selector class."""
6400 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6402 def __init__(self, *args, **kwargs):
6403 raise AttributeError(
"No constructor defined - class is abstract")
6405 def get_is_selected(self, atom_line):
6406 r"""get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6407 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6408 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6411 r"""__str__(Mol2Selector self) -> std::string"""
6412 return _IMP_atom.Mol2Selector___str__(self)
6415 r"""__repr__(Mol2Selector self) -> std::string"""
6416 return _IMP_atom.Mol2Selector___repr__(self)
6420 return _object_cast_to_Mol2Selector(o)
6424 _IMP_atom.Mol2Selector_swigregister(Mol2Selector)
6425 class AllMol2Selector(Mol2Selector):
6426 r"""Proxy of C++ IMP::atom::AllMol2Selector class."""
6428 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6431 r"""__str__(AllMol2Selector self) -> std::string"""
6432 return _IMP_atom.AllMol2Selector___str__(self)
6435 r"""__repr__(AllMol2Selector self) -> std::string"""
6436 return _IMP_atom.AllMol2Selector___repr__(self)
6440 return _object_cast_to_AllMol2Selector(o)
6444 r"""__init__(AllMol2Selector self) -> AllMol2Selector"""
6445 _IMP_atom.AllMol2Selector_swiginit(self, _IMP_atom.new_AllMol2Selector())
6446 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6449 _IMP_atom.AllMol2Selector_swigregister(AllMol2Selector)
6450 class NonHydrogenMol2Selector(Mol2Selector):
6451 r"""Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6453 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6456 r"""__str__(NonHydrogenMol2Selector self) -> std::string"""
6457 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6460 r"""__repr__(NonHydrogenMol2Selector self) -> std::string"""
6461 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6465 return _object_cast_to_NonHydrogenMol2Selector(o)
6469 r"""__init__(NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6470 _IMP_atom.NonHydrogenMol2Selector_swiginit(self, _IMP_atom.new_NonHydrogenMol2Selector())
6471 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6474 _IMP_atom.NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
6476 def read_mol2(mol2_file, model, mol2sel=None):
6477 r"""read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy"""
6478 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
6481 r"""write_mol2(Hierarchy rhd, TextOutput file_name)"""
6482 return _IMP_atom.write_mol2(rhd, file_name)
6484 r"""Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
6486 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6488 def __init__(self, *args):
6490 __init__(SecondaryStructureResidue self) -> SecondaryStructureResidue
6491 __init__(SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
6492 __init__(SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
6494 _IMP_atom.SecondaryStructureResidue_swiginit(self, _IMP_atom.new_SecondaryStructureResidue(*args))
6496 def show(self, *args):
6497 r"""show(SecondaryStructureResidue self, _ostream out=std::cout)"""
6498 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
6501 def setup_particle(*args):
6503 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6504 setup_particle(_ParticleAdaptor pa, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
6505 setup_particle(Particle res_p) -> SecondaryStructureResidue
6507 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
6510 def get_is_setup(*args):
6512 get_is_setup(_ParticleAdaptor p) -> bool
6513 get_is_setup(Model m, ParticleIndex pi) -> bool
6515 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
6517 def get_particle(self):
6518 r"""get_particle(SecondaryStructureResidue self) -> Particle"""
6519 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
6521 def get_all_probabilities(self):
6522 r"""get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
6523 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
6525 def get_prob_helix(self):
6526 r"""get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
6527 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
6529 def set_prob_helix(self, t):
6530 r"""set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
6531 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
6533 def get_prob_strand(self):
6534 r"""get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
6535 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
6537 def set_prob_strand(self, t):
6538 r"""set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
6539 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
6541 def get_prob_coil(self):
6542 r"""get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
6543 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
6545 def set_prob_coil(self, t):
6546 r"""set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
6547 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
6550 def get_prob_helix_key():
6551 r"""get_prob_helix_key() -> FloatKey"""
6552 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
6555 def get_prob_strand_key():
6556 r"""get_prob_strand_key() -> FloatKey"""
6557 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
6560 def get_prob_coil_key():
6561 r"""get_prob_coil_key() -> FloatKey"""
6562 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
6564 def add_attribute(self, *args):
6566 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
6567 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6568 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6569 add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6570 add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6571 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6572 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6573 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6575 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
6577 def get_value(self, *args):
6579 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
6580 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
6581 get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
6582 get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
6583 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
6584 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
6585 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
6587 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
6589 def set_value(self, *args):
6591 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
6592 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
6593 set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
6594 set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
6595 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
6596 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
6597 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
6599 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
6601 def remove_attribute(self, *args):
6603 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
6604 remove_attribute(SecondaryStructureResidue self, IntKey a0)
6605 remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
6606 remove_attribute(SecondaryStructureResidue self, IntsKey a0)
6607 remove_attribute(SecondaryStructureResidue self, StringKey a0)
6608 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
6609 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
6611 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
6613 def has_attribute(self, *args):
6615 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
6616 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
6617 has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
6618 has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
6619 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
6620 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
6621 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
6623 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
6625 def get_derivative(self, a0):
6626 r"""get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
6627 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
6630 r"""get_name(SecondaryStructureResidue self) -> std::string"""
6631 return _IMP_atom.SecondaryStructureResidue_get_name(self)
6633 def clear_caches(self):
6634 r"""clear_caches(SecondaryStructureResidue self)"""
6635 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
6637 def set_name(self, a0):
6638 r"""set_name(SecondaryStructureResidue self, std::string a0)"""
6639 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
6642 r"""set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
6643 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
6645 def add_to_derivative(self, a0, a1, a2):
6646 r"""add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6647 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
6649 def set_is_optimized(self, a0, a1):
6650 r"""set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
6651 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
6653 def get_is_optimized(self, a0):
6654 r"""get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
6655 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
6658 r"""get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
6659 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
6661 def __eq__(self, *args):
6663 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6664 __eq__(SecondaryStructureResidue self, Particle d) -> bool
6666 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
6668 def __ne__(self, *args):
6670 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6671 __ne__(SecondaryStructureResidue self, Particle d) -> bool
6673 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
6675 def __le__(self, *args):
6677 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6678 __le__(SecondaryStructureResidue self, Particle d) -> bool
6680 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
6682 def __lt__(self, *args):
6684 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6685 __lt__(SecondaryStructureResidue self, Particle d) -> bool
6687 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
6689 def __ge__(self, *args):
6691 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6692 __ge__(SecondaryStructureResidue self, Particle d) -> bool
6694 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
6696 def __gt__(self, *args):
6698 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
6699 __gt__(SecondaryStructureResidue self, Particle d) -> bool
6701 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
6704 r"""__hash__(SecondaryStructureResidue self) -> std::size_t"""
6705 return _IMP_atom.SecondaryStructureResidue___hash__(self)
6708 r"""__str__(SecondaryStructureResidue self) -> std::string"""
6709 return _IMP_atom.SecondaryStructureResidue___str__(self)
6712 r"""__repr__(SecondaryStructureResidue self) -> std::string"""
6713 return _IMP_atom.SecondaryStructureResidue___repr__(self)
6715 def _get_as_binary(self):
6716 r"""_get_as_binary(SecondaryStructureResidue self) -> PyObject *"""
6717 return _IMP_atom.SecondaryStructureResidue__get_as_binary(self)
6719 def _set_from_binary(self, p):
6720 r"""_set_from_binary(SecondaryStructureResidue self, PyObject * p)"""
6721 return _IMP_atom.SecondaryStructureResidue__set_from_binary(self, p)
6723 def __getstate__(self):
6724 p = self._get_as_binary()
6725 if len(self.__dict__) > 1:
6726 d = self.__dict__.copy()
6731 def __setstate__(self, p):
6732 if not hasattr(self,
'this'):
6734 if isinstance(p, tuple):
6736 self.__dict__.update(d)
6737 return self._set_from_binary(p)
6739 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
6742 _IMP_atom.SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
6745 r"""setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue"""
6746 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
6749 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"""
6750 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
6753 r"""get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
6754 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
6756 def read_psipred(*args):
6758 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
6759 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
6761 return _IMP_atom.read_psipred(*args)
6763 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Dope > class."""
6765 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6766 __repr__ = _swig_repr
6768 def __init__(self, *args):
6770 __init__(_ADopeBase self, Dope t0, std::string name="FunctorDistancePairScore %1%") -> _ADopeBase
6771 __init__(_ADopeBase self) -> _ADopeBase
6773 _IMP_atom._ADopeBase_swiginit(self, _IMP_atom.new__ADopeBase(*args))
6775 def do_get_inputs(self, m, pis):
6776 r"""do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6777 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
6779 def get_score_functor(self):
6780 r"""get_score_functor(_ADopeBase self) -> Dope"""
6781 return _IMP_atom._ADopeBase_get_score_functor(self)
6783 def get_version_info(self):
6784 r"""get_version_info(_ADopeBase self) -> VersionInfo"""
6785 return _IMP_atom._ADopeBase_get_version_info(self)
6786 __swig_destroy__ = _IMP_atom.delete__ADopeBase
6789 _IMP_atom._ADopeBase_swigregister(_ADopeBase)
6791 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > > class."""
6793 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6794 __repr__ = _swig_repr
6796 def __init__(self, *args):
6798 __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
6799 __init__(_BDopeBase self) -> _BDopeBase
6801 _IMP_atom._BDopeBase_swiginit(self, _IMP_atom.new__BDopeBase(*args))
6803 def do_get_inputs(self, m, pis):
6804 r"""do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6805 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
6807 def get_score_functor(self):
6808 r"""get_score_functor(_BDopeBase self) -> _DopeBase"""
6809 return _IMP_atom._BDopeBase_get_score_functor(self)
6811 def get_version_info(self):
6812 r"""get_version_info(_BDopeBase self) -> VersionInfo"""
6813 return _IMP_atom._BDopeBase_get_version_info(self)
6814 __swig_destroy__ = _IMP_atom.delete__BDopeBase
6817 _IMP_atom._BDopeBase_swigregister(_BDopeBase)
6819 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::LoopStatistical > class."""
6821 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6822 __repr__ = _swig_repr
6824 def __init__(self, *args):
6826 __init__(_ALoopStatisticalBase self, LoopStatistical t0, std::string name="FunctorDistancePairScore %1%") -> _ALoopStatisticalBase
6827 __init__(_ALoopStatisticalBase self) -> _ALoopStatisticalBase
6829 _IMP_atom._ALoopStatisticalBase_swiginit(self, _IMP_atom.new__ALoopStatisticalBase(*args))
6831 def do_get_inputs(self, m, pis):
6832 r"""do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6833 return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
6835 def get_score_functor(self):
6836 r"""get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
6837 return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
6839 def get_version_info(self):
6840 r"""get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
6841 return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
6842 __swig_destroy__ = _IMP_atom.delete__ALoopStatisticalBase
6845 _IMP_atom._ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
6847 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > > class."""
6849 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6850 __repr__ = _swig_repr
6852 def __init__(self, *args):
6854 __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
6855 __init__(_BLoopStatisticalBase self) -> _BLoopStatisticalBase
6857 _IMP_atom._BLoopStatisticalBase_swiginit(self, _IMP_atom.new__BLoopStatisticalBase(*args))
6859 def do_get_inputs(self, m, pis):
6860 r"""do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6861 return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
6863 def get_score_functor(self):
6864 r"""get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
6865 return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
6867 def get_version_info(self):
6868 r"""get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
6869 return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
6870 __swig_destroy__ = _IMP_atom.delete__BLoopStatisticalBase
6873 _IMP_atom._BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
6875 r"""Proxy of C++ IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap > class."""
6877 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6878 __repr__ = _swig_repr
6880 def __init__(self, *args):
6881 r"""__init__(_OrientedSoapBase self, IMP::score_functor::DistancePairScoreWithCache< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name="FunctorDistancePairScoreWithCache %1%") -> _OrientedSoapBase"""
6882 _IMP_atom._OrientedSoapBase_swiginit(self, _IMP_atom.new__OrientedSoapBase(*args))
6884 def do_get_inputs(self, m, pis):
6885 r"""do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6886 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
6888 def get_score_functor(self):
6889 r"""get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
6890 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
6892 def get_version_info(self):
6893 r"""get_version_info(_OrientedSoapBase self) -> VersionInfo"""
6894 return _IMP_atom._OrientedSoapBase_get_version_info(self)
6895 __swig_destroy__ = _IMP_atom.delete__OrientedSoapBase
6898 _IMP_atom._OrientedSoapBase_swigregister(_OrientedSoapBase)
6900 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > > class."""
6902 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6903 __repr__ = _swig_repr
6905 def __init__(self, *args):
6907 __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
6908 __init__(_SPSFTB self) -> _SPSFTB
6910 _IMP_atom._SPSFTB_swiginit(self, _IMP_atom.new__SPSFTB(*args))
6912 def do_get_inputs(self, m, pis):
6913 r"""do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6914 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
6916 def get_score_functor(self):
6917 r"""get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
6918 return _IMP_atom._SPSFTB_get_score_functor(self)
6920 def get_version_info(self):
6921 r"""get_version_info(_SPSFTB self) -> VersionInfo"""
6922 return _IMP_atom._SPSFTB_get_version_info(self)
6923 __swig_destroy__ = _IMP_atom.delete__SPSFTB
6926 _IMP_atom._SPSFTB_swigregister(_SPSFTB)
6927 class _SPSTF(_SPSFTB):
6928 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType,true,false > class."""
6930 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6931 __repr__ = _swig_repr
6933 def __init__(self, *args):
6935 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
6936 __init__(_SPSTF self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
6938 _IMP_atom._SPSTF_swiginit(self, _IMP_atom.new__SPSTF(*args))
6939 __swig_destroy__ = _IMP_atom.delete__SPSTF
6942 _IMP_atom._SPSTF_swigregister(_SPSTF)
6943 class _SPSFT(_BDopeBase):
6944 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::DopeType,false,true > class."""
6946 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6947 __repr__ = _swig_repr
6949 def __init__(self, *args):
6951 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
6952 __init__(_SPSFT self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
6954 _IMP_atom._SPSFT_swiginit(self, _IMP_atom.new__SPSFT(*args))
6955 __swig_destroy__ = _IMP_atom.delete__SPSFT
6958 _IMP_atom._SPSFT_swigregister(_SPSFT)
6959 class _SPSFTL(_BLoopStatisticalBase):
6960 r"""Proxy of C++ IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType,false,true > class."""
6962 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6963 __repr__ = _swig_repr
6965 def __init__(self, *args):
6967 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
6968 __init__(_SPSFTL self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
6970 _IMP_atom._SPSFTL_swiginit(self, _IMP_atom.new__SPSFTL(*args))
6971 __swig_destroy__ = _IMP_atom.delete__SPSFTL
6974 _IMP_atom._SPSFTL_swigregister(_SPSFTL)
6975 class ProteinLigandAtomPairScore(_SPSTF):
6976 r"""Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
6978 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6980 def __init__(self, *args):
6982 __init__(ProteinLigandAtomPairScore self, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandAtomPairScore
6983 __init__(ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
6985 _IMP_atom.ProteinLigandAtomPairScore_swiginit(self, _IMP_atom.new_ProteinLigandAtomPairScore(*args))
6987 def get_maximum_distance(self):
6988 r"""get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
6989 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
6992 r"""__str__(ProteinLigandAtomPairScore self) -> std::string"""
6993 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
6996 r"""__repr__(ProteinLigandAtomPairScore self) -> std::string"""
6997 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7001 return _object_cast_to_ProteinLigandAtomPairScore(o)
7003 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7006 _IMP_atom.ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7008 r"""Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7010 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7012 def __init__(self, *args):
7014 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold=std::numeric_limits< double >::max()) -> ProteinLigandRestraint
7015 __init__(ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7017 _IMP_atom.ProteinLigandRestraint_swiginit(self, _IMP_atom.new_ProteinLigandRestraint(*args))
7020 r"""__str__(ProteinLigandRestraint self) -> std::string"""
7021 return _IMP_atom.ProteinLigandRestraint___str__(self)
7024 r"""__repr__(ProteinLigandRestraint self) -> std::string"""
7025 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7029 return _object_cast_to_ProteinLigandRestraint(o)
7031 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7034 _IMP_atom.ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7037 r"""add_protein_ligand_score_data(Hierarchy h)"""
7038 return _IMP_atom.add_protein_ligand_score_data(h)
7039 class AtomType(IMP._Value):
7040 r"""Proxy of C++ IMP::Key< 8974343 > class."""
7042 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7044 def __init__(self, *args):
7046 __init__(AtomType self) -> AtomType
7047 __init__(AtomType self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7048 __init__(AtomType self, unsigned int i) -> AtomType
7050 _IMP_atom.AtomType_swiginit(self, _IMP_atom.new_AtomType(*args))
7054 r"""add_key(std::string sc) -> unsigned int"""
7055 return _IMP_atom.AtomType_add_key(sc)
7058 def get_key_exists(sc):
7059 r"""get_key_exists(std::string sc) -> bool"""
7060 return _IMP_atom.AtomType_get_key_exists(sc)
7062 def get_string(self):
7063 r"""get_string(AtomType self) -> std::string const"""
7064 return _IMP_atom.AtomType_get_string(self)
7066 def __cmp__(self, o):
7067 r"""__cmp__(AtomType self, AtomType o) -> int"""
7068 return _IMP_atom.AtomType___cmp__(self, o)
7070 def __eq__(self, o):
7071 r"""__eq__(AtomType self, AtomType o) -> bool"""
7072 return _IMP_atom.AtomType___eq__(self, o)
7074 def __ne__(self, o):
7075 r"""__ne__(AtomType self, AtomType o) -> bool"""
7076 return _IMP_atom.AtomType___ne__(self, o)
7078 def __lt__(self, o):
7079 r"""__lt__(AtomType self, AtomType o) -> bool"""
7080 return _IMP_atom.AtomType___lt__(self, o)
7082 def __gt__(self, o):
7083 r"""__gt__(AtomType self, AtomType o) -> bool"""
7084 return _IMP_atom.AtomType___gt__(self, o)
7086 def __ge__(self, o):
7087 r"""__ge__(AtomType self, AtomType o) -> bool"""
7088 return _IMP_atom.AtomType___ge__(self, o)
7090 def __le__(self, o):
7091 r"""__le__(AtomType self, AtomType o) -> bool"""
7092 return _IMP_atom.AtomType___le__(self, o)
7095 r"""__hash__(AtomType self) -> std::size_t"""
7096 return _IMP_atom.AtomType___hash__(self)
7098 def show(self, *args):
7099 r"""show(AtomType self, _ostream out=std::cout)"""
7100 return _IMP_atom.AtomType_show(self, *args)
7103 def add_alias(old_key, new_name):
7104 r"""add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7105 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7108 def get_number_of_keys():
7109 r"""get_number_of_keys() -> unsigned int"""
7110 return _IMP_atom.AtomType_get_number_of_keys()
7113 r"""get_index(AtomType self) -> unsigned int"""
7114 return _IMP_atom.AtomType_get_index(self)
7118 r"""show_all(_ostream out)"""
7119 return _IMP_atom.AtomType_show_all(out)
7122 def get_all_strings():
7123 r"""get_all_strings() -> IMP::Vector< std::string >"""
7124 return _IMP_atom.AtomType_get_all_strings()
7127 def get_number_unique():
7128 r"""get_number_unique() -> unsigned int"""
7129 return _IMP_atom.AtomType_get_number_unique()
7132 r"""__str__(AtomType self) -> std::string"""
7133 return _IMP_atom.AtomType___str__(self)
7136 r"""__repr__(AtomType self) -> std::string"""
7137 return _IMP_atom.AtomType___repr__(self)
7138 __swig_destroy__ = _IMP_atom.delete_AtomType
7141 _IMP_atom.AtomType_swigregister(AtomType)
7142 class ResidueType(IMP._Value):
7143 r"""Proxy of C++ IMP::Key< 90784334 > class."""
7145 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7147 def __init__(self, *args):
7149 __init__(ResidueType self) -> ResidueType
7150 __init__(ResidueType self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7151 __init__(ResidueType self, unsigned int i) -> ResidueType
7153 _IMP_atom.ResidueType_swiginit(self, _IMP_atom.new_ResidueType(*args))
7157 r"""add_key(std::string sc) -> unsigned int"""
7158 return _IMP_atom.ResidueType_add_key(sc)
7161 def get_key_exists(sc):
7162 r"""get_key_exists(std::string sc) -> bool"""
7163 return _IMP_atom.ResidueType_get_key_exists(sc)
7165 def get_string(self):
7166 r"""get_string(ResidueType self) -> std::string const"""
7167 return _IMP_atom.ResidueType_get_string(self)
7169 def __cmp__(self, o):
7170 r"""__cmp__(ResidueType self, ResidueType o) -> int"""
7171 return _IMP_atom.ResidueType___cmp__(self, o)
7173 def __eq__(self, o):
7174 r"""__eq__(ResidueType self, ResidueType o) -> bool"""
7175 return _IMP_atom.ResidueType___eq__(self, o)
7177 def __ne__(self, o):
7178 r"""__ne__(ResidueType self, ResidueType o) -> bool"""
7179 return _IMP_atom.ResidueType___ne__(self, o)
7181 def __lt__(self, o):
7182 r"""__lt__(ResidueType self, ResidueType o) -> bool"""
7183 return _IMP_atom.ResidueType___lt__(self, o)
7185 def __gt__(self, o):
7186 r"""__gt__(ResidueType self, ResidueType o) -> bool"""
7187 return _IMP_atom.ResidueType___gt__(self, o)
7189 def __ge__(self, o):
7190 r"""__ge__(ResidueType self, ResidueType o) -> bool"""
7191 return _IMP_atom.ResidueType___ge__(self, o)
7193 def __le__(self, o):
7194 r"""__le__(ResidueType self, ResidueType o) -> bool"""
7195 return _IMP_atom.ResidueType___le__(self, o)
7198 r"""__hash__(ResidueType self) -> std::size_t"""
7199 return _IMP_atom.ResidueType___hash__(self)
7201 def show(self, *args):
7202 r"""show(ResidueType self, _ostream out=std::cout)"""
7203 return _IMP_atom.ResidueType_show(self, *args)
7206 def add_alias(old_key, new_name):
7207 r"""add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7208 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7211 def get_number_of_keys():
7212 r"""get_number_of_keys() -> unsigned int"""
7213 return _IMP_atom.ResidueType_get_number_of_keys()
7216 r"""get_index(ResidueType self) -> unsigned int"""
7217 return _IMP_atom.ResidueType_get_index(self)
7221 r"""show_all(_ostream out)"""
7222 return _IMP_atom.ResidueType_show_all(out)
7225 def get_all_strings():
7226 r"""get_all_strings() -> IMP::Vector< std::string >"""
7227 return _IMP_atom.ResidueType_get_all_strings()
7230 def get_number_unique():
7231 r"""get_number_unique() -> unsigned int"""
7232 return _IMP_atom.ResidueType_get_number_unique()
7235 r"""__str__(ResidueType self) -> std::string"""
7236 return _IMP_atom.ResidueType___str__(self)
7239 r"""__repr__(ResidueType self) -> std::string"""
7240 return _IMP_atom.ResidueType___repr__(self)
7241 __swig_destroy__ = _IMP_atom.delete_ResidueType
7244 _IMP_atom.ResidueType_swigregister(ResidueType)
7245 class ChainType(IMP._Value):
7246 r"""Proxy of C++ IMP::Key< 90784336 > class."""
7248 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7250 def __init__(self, *args):
7252 __init__(ChainType self) -> ChainType
7253 __init__(ChainType self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
7254 __init__(ChainType self, unsigned int i) -> ChainType
7256 _IMP_atom.ChainType_swiginit(self, _IMP_atom.new_ChainType(*args))
7260 r"""add_key(std::string sc) -> unsigned int"""
7261 return _IMP_atom.ChainType_add_key(sc)
7264 def get_key_exists(sc):
7265 r"""get_key_exists(std::string sc) -> bool"""
7266 return _IMP_atom.ChainType_get_key_exists(sc)
7268 def get_string(self):
7269 r"""get_string(ChainType self) -> std::string const"""
7270 return _IMP_atom.ChainType_get_string(self)
7272 def __cmp__(self, o):
7273 r"""__cmp__(ChainType self, ChainType o) -> int"""
7274 return _IMP_atom.ChainType___cmp__(self, o)
7276 def __eq__(self, o):
7277 r"""__eq__(ChainType self, ChainType o) -> bool"""
7278 return _IMP_atom.ChainType___eq__(self, o)
7280 def __ne__(self, o):
7281 r"""__ne__(ChainType self, ChainType o) -> bool"""
7282 return _IMP_atom.ChainType___ne__(self, o)
7284 def __lt__(self, o):
7285 r"""__lt__(ChainType self, ChainType o) -> bool"""
7286 return _IMP_atom.ChainType___lt__(self, o)
7288 def __gt__(self, o):
7289 r"""__gt__(ChainType self, ChainType o) -> bool"""
7290 return _IMP_atom.ChainType___gt__(self, o)
7292 def __ge__(self, o):
7293 r"""__ge__(ChainType self, ChainType o) -> bool"""
7294 return _IMP_atom.ChainType___ge__(self, o)
7296 def __le__(self, o):
7297 r"""__le__(ChainType self, ChainType o) -> bool"""
7298 return _IMP_atom.ChainType___le__(self, o)
7301 r"""__hash__(ChainType self) -> std::size_t"""
7302 return _IMP_atom.ChainType___hash__(self)
7304 def show(self, *args):
7305 r"""show(ChainType self, _ostream out=std::cout)"""
7306 return _IMP_atom.ChainType_show(self, *args)
7309 def add_alias(old_key, new_name):
7310 r"""add_alias(ChainType old_key, std::string new_name) -> ChainType"""
7311 return _IMP_atom.ChainType_add_alias(old_key, new_name)
7314 def get_number_of_keys():
7315 r"""get_number_of_keys() -> unsigned int"""
7316 return _IMP_atom.ChainType_get_number_of_keys()
7319 r"""get_index(ChainType self) -> unsigned int"""
7320 return _IMP_atom.ChainType_get_index(self)
7324 r"""show_all(_ostream out)"""
7325 return _IMP_atom.ChainType_show_all(out)
7328 def get_all_strings():
7329 r"""get_all_strings() -> IMP::Vector< std::string >"""
7330 return _IMP_atom.ChainType_get_all_strings()
7333 def get_number_unique():
7334 r"""get_number_unique() -> unsigned int"""
7335 return _IMP_atom.ChainType_get_number_unique()
7338 r"""__str__(ChainType self) -> std::string"""
7339 return _IMP_atom.ChainType___str__(self)
7342 r"""__repr__(ChainType self) -> std::string"""
7343 return _IMP_atom.ChainType___repr__(self)
7344 __swig_destroy__ = _IMP_atom.delete_ChainType
7347 _IMP_atom.ChainType_swigregister(ChainType)
7348 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
7566 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
7570 r"""hash_value(IMP::atom::Element e) -> size_t"""
7571 return _IMP_atom.hash_value(e)
7572 class ElementTable(object):
7573 r"""Proxy of C++ IMP::atom::ElementTable class."""
7575 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7576 __repr__ = _swig_repr
7579 r"""__init__(ElementTable self) -> ElementTable"""
7580 _IMP_atom.ElementTable_swiginit(self, _IMP_atom.new_ElementTable())
7582 def get_element(self, s):
7583 r"""get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
7584 return _IMP_atom.ElementTable_get_element(self, s)
7586 def get_name(self, e):
7587 r"""get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
7588 return _IMP_atom.ElementTable_get_name(self, e)
7591 r"""get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
7592 return _IMP_atom.ElementTable_get_mass(self, e)
7593 __swig_destroy__ = _IMP_atom.delete_ElementTable
7596 _IMP_atom.ElementTable_swigregister(ElementTable)
7598 def get_element_table():
7599 r"""get_element_table() -> ElementTable"""
7600 return _IMP_atom.get_element_table()
7601 class Atom(Hierarchy):
7602 r"""Proxy of C++ IMP::atom::Atom class."""
7604 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7606 def __init__(self, *args):
7608 __init__(Atom self) -> Atom
7609 __init__(Atom self, Model m, ParticleIndex id) -> Atom
7610 __init__(Atom self, _ParticleAdaptor d) -> Atom
7612 _IMP_atom.Atom_swiginit(self, _IMP_atom.new_Atom(*args))
7614 def show(self, *args):
7615 r"""show(Atom self, _ostream out=std::cout)"""
7616 return _IMP_atom.Atom_show(self, *args)
7619 def setup_particle(*args):
7621 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
7622 setup_particle(_ParticleAdaptor pa, Atom other) -> Atom
7623 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
7624 setup_particle(_ParticleAdaptor pa, AtomType atom_type) -> Atom
7626 return _IMP_atom.Atom_setup_particle(*args)
7629 def get_is_setup(*args):
7631 get_is_setup(_ParticleAdaptor p) -> bool
7632 get_is_setup(Model m, ParticleIndex pi) -> bool
7634 return _IMP_atom.Atom_get_is_setup(*args)
7636 def get_atom_type(self):
7637 r"""get_atom_type(Atom self) -> AtomType"""
7638 return _IMP_atom.Atom_get_atom_type(self)
7640 def set_atom_type(self, t):
7641 r"""set_atom_type(Atom self, AtomType t)"""
7642 return _IMP_atom.Atom_set_atom_type(self, t)
7644 def get_element(self):
7645 r"""get_element(Atom self) -> IMP::atom::Element"""
7646 return _IMP_atom.Atom_get_element(self)
7648 def set_element(self, e):
7649 r"""set_element(Atom self, IMP::atom::Element e)"""
7650 return _IMP_atom.Atom_set_element(self, e)
7652 def get_occupancy(self):
7653 r"""get_occupancy(Atom self) -> double"""
7654 return _IMP_atom.Atom_get_occupancy(self)
7656 def set_occupancy(self, occupancy):
7657 r"""set_occupancy(Atom self, double occupancy)"""
7658 return _IMP_atom.Atom_set_occupancy(self, occupancy)
7660 def get_temperature_factor(self):
7661 r"""get_temperature_factor(Atom self) -> double"""
7662 return _IMP_atom.Atom_get_temperature_factor(self)
7664 def set_temperature_factor(self, tempFactor):
7665 r"""set_temperature_factor(Atom self, double tempFactor)"""
7666 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
7668 def get_input_index(self):
7669 r"""get_input_index(Atom self) -> IMP::Int"""
7670 return _IMP_atom.Atom_get_input_index(self)
7672 def set_input_index(self, t):
7673 r"""set_input_index(Atom self, IMP::Int t)"""
7674 return _IMP_atom.Atom_set_input_index(self, t)
7677 def get_atom_type_key():
7678 r"""get_atom_type_key() -> IntKey"""
7679 return _IMP_atom.Atom_get_atom_type_key()
7682 def get_element_key():
7683 r"""get_element_key() -> IntKey"""
7684 return _IMP_atom.Atom_get_element_key()
7687 def get_input_index_key():
7688 r"""get_input_index_key() -> IntKey"""
7689 return _IMP_atom.Atom_get_input_index_key()
7692 def get_occupancy_key():
7693 r"""get_occupancy_key() -> FloatKey"""
7694 return _IMP_atom.Atom_get_occupancy_key()
7697 def get_temperature_factor_key():
7698 r"""get_temperature_factor_key() -> FloatKey"""
7699 return _IMP_atom.Atom_get_temperature_factor_key()
7701 def add_attribute(self, *args):
7703 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
7704 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
7705 add_attribute(Atom self, IntKey a0, IMP::Int a1)
7706 add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
7707 add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
7708 add_attribute(Atom self, StringKey a0, IMP::String a1)
7709 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
7710 add_attribute(Atom self, ObjectKey a0, Object a1)
7712 return _IMP_atom.Atom_add_attribute(self, *args)
7714 def get_value(self, *args):
7716 get_value(Atom self, FloatKey a0) -> IMP::Float
7717 get_value(Atom self, IntKey a0) -> IMP::Int
7718 get_value(Atom self, FloatsKey a0) -> IMP::Floats
7719 get_value(Atom self, IntsKey a0) -> IMP::Ints
7720 get_value(Atom self, StringKey a0) -> IMP::String
7721 get_value(Atom self, ParticleIndexKey a0) -> Particle
7722 get_value(Atom self, ObjectKey a0) -> Object
7724 return _IMP_atom.Atom_get_value(self, *args)
7726 def set_value(self, *args):
7728 set_value(Atom self, FloatKey a0, IMP::Float a1)
7729 set_value(Atom self, IntKey a0, IMP::Int a1)
7730 set_value(Atom self, FloatsKey a0, IMP::Floats a1)
7731 set_value(Atom self, IntsKey a0, IMP::Ints a1)
7732 set_value(Atom self, StringKey a0, IMP::String a1)
7733 set_value(Atom self, ParticleIndexKey a0, Particle a1)
7734 set_value(Atom self, ObjectKey a0, Object a1)
7736 return _IMP_atom.Atom_set_value(self, *args)
7738 def remove_attribute(self, *args):
7740 remove_attribute(Atom self, FloatKey a0)
7741 remove_attribute(Atom self, IntKey a0)
7742 remove_attribute(Atom self, FloatsKey a0)
7743 remove_attribute(Atom self, IntsKey a0)
7744 remove_attribute(Atom self, StringKey a0)
7745 remove_attribute(Atom self, ParticleIndexKey a0)
7746 remove_attribute(Atom self, ObjectKey a0)
7748 return _IMP_atom.Atom_remove_attribute(self, *args)
7750 def has_attribute(self, *args):
7752 has_attribute(Atom self, FloatKey a0) -> bool
7753 has_attribute(Atom self, IntKey a0) -> bool
7754 has_attribute(Atom self, FloatsKey a0) -> bool
7755 has_attribute(Atom self, IntsKey a0) -> bool
7756 has_attribute(Atom self, StringKey a0) -> bool
7757 has_attribute(Atom self, ParticleIndexKey a0) -> bool
7758 has_attribute(Atom self, ObjectKey a0) -> bool
7760 return _IMP_atom.Atom_has_attribute(self, *args)
7762 def get_derivative(self, a0):
7763 r"""get_derivative(Atom self, FloatKey a0) -> double"""
7764 return _IMP_atom.Atom_get_derivative(self, a0)
7767 r"""get_name(Atom self) -> std::string"""
7768 return _IMP_atom.Atom_get_name(self)
7770 def clear_caches(self):
7771 r"""clear_caches(Atom self)"""
7772 return _IMP_atom.Atom_clear_caches(self)
7774 def set_name(self, a0):
7775 r"""set_name(Atom self, std::string a0)"""
7776 return _IMP_atom.Atom_set_name(self, a0)
7779 r"""set_check_level(Atom self, IMP::CheckLevel a0)"""
7780 return _IMP_atom.Atom_set_check_level(self, a0)
7782 def add_to_derivative(self, a0, a1, a2):
7783 r"""add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7784 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
7786 def set_is_optimized(self, a0, a1):
7787 r"""set_is_optimized(Atom self, FloatKey a0, bool a1)"""
7788 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
7790 def get_is_optimized(self, a0):
7791 r"""get_is_optimized(Atom self, FloatKey a0) -> bool"""
7792 return _IMP_atom.Atom_get_is_optimized(self, a0)
7795 r"""get_check_level(Atom self) -> IMP::CheckLevel"""
7796 return _IMP_atom.Atom_get_check_level(self)
7798 def __eq__(self, *args):
7800 __eq__(Atom self, Atom o) -> bool
7801 __eq__(Atom self, Particle d) -> bool
7803 return _IMP_atom.Atom___eq__(self, *args)
7805 def __ne__(self, *args):
7807 __ne__(Atom self, Atom o) -> bool
7808 __ne__(Atom self, Particle d) -> bool
7810 return _IMP_atom.Atom___ne__(self, *args)
7812 def __le__(self, *args):
7814 __le__(Atom self, Atom o) -> bool
7815 __le__(Atom self, Particle d) -> bool
7817 return _IMP_atom.Atom___le__(self, *args)
7819 def __lt__(self, *args):
7821 __lt__(Atom self, Atom o) -> bool
7822 __lt__(Atom self, Particle d) -> bool
7824 return _IMP_atom.Atom___lt__(self, *args)
7826 def __ge__(self, *args):
7828 __ge__(Atom self, Atom o) -> bool
7829 __ge__(Atom self, Particle d) -> bool
7831 return _IMP_atom.Atom___ge__(self, *args)
7833 def __gt__(self, *args):
7835 __gt__(Atom self, Atom o) -> bool
7836 __gt__(Atom self, Particle d) -> bool
7838 return _IMP_atom.Atom___gt__(self, *args)
7841 r"""__hash__(Atom self) -> std::size_t"""
7842 return _IMP_atom.Atom___hash__(self)
7845 r"""__str__(Atom self) -> std::string"""
7846 return _IMP_atom.Atom___str__(self)
7849 r"""__repr__(Atom self) -> std::string"""
7850 return _IMP_atom.Atom___repr__(self)
7852 def _get_as_binary(self):
7853 r"""_get_as_binary(Atom self) -> PyObject *"""
7854 return _IMP_atom.Atom__get_as_binary(self)
7856 def _set_from_binary(self, p):
7857 r"""_set_from_binary(Atom self, PyObject * p)"""
7858 return _IMP_atom.Atom__set_from_binary(self, p)
7860 def __getstate__(self):
7861 p = self._get_as_binary()
7862 if len(self.__dict__) > 1:
7863 d = self.__dict__.copy()
7868 def __setstate__(self, p):
7869 if not hasattr(self,
'this'):
7871 if isinstance(p, tuple):
7873 self.__dict__.update(d)
7874 return self._set_from_binary(p)
7876 __swig_destroy__ = _IMP_atom.delete_Atom
7879 _IMP_atom.Atom_swigregister(Atom)
7880 AT_UNKNOWN = cvar.AT_UNKNOWN
7890 AT_HA1 = cvar.AT_HA1
7891 AT_HA2 = cvar.AT_HA2
7892 AT_HA3 = cvar.AT_HA3
7895 AT_HB1 = cvar.AT_HB1
7896 AT_HB2 = cvar.AT_HB2
7897 AT_HB3 = cvar.AT_HB3
7898 AT_OXT = cvar.AT_OXT
7899 AT_CH3 = cvar.AT_CH3
7902 AT_CG1 = cvar.AT_CG1
7903 AT_CG2 = cvar.AT_CG2
7905 AT_HG1 = cvar.AT_HG1
7906 AT_HG2 = cvar.AT_HG2
7907 AT_HG3 = cvar.AT_HG3
7908 AT_HG11 = cvar.AT_HG11
7909 AT_HG21 = cvar.AT_HG21
7910 AT_HG31 = cvar.AT_HG31
7911 AT_HG12 = cvar.AT_HG12
7912 AT_HG13 = cvar.AT_HG13
7913 AT_HG22 = cvar.AT_HG22
7914 AT_HG23 = cvar.AT_HG23
7915 AT_HG32 = cvar.AT_HG32
7917 AT_OG1 = cvar.AT_OG1
7920 AT_CD1 = cvar.AT_CD1
7921 AT_CD2 = cvar.AT_CD2
7923 AT_HD1 = cvar.AT_HD1
7924 AT_HD2 = cvar.AT_HD2
7925 AT_HD3 = cvar.AT_HD3
7926 AT_HD11 = cvar.AT_HD11
7927 AT_HD21 = cvar.AT_HD21
7928 AT_HD31 = cvar.AT_HD31
7929 AT_HD12 = cvar.AT_HD12
7930 AT_HD13 = cvar.AT_HD13
7931 AT_HD22 = cvar.AT_HD22
7932 AT_HD23 = cvar.AT_HD23
7933 AT_HD32 = cvar.AT_HD32
7935 AT_OD1 = cvar.AT_OD1
7936 AT_OD2 = cvar.AT_OD2
7937 AT_ND1 = cvar.AT_ND1
7938 AT_ND2 = cvar.AT_ND2
7940 AT_CE1 = cvar.AT_CE1
7941 AT_CE2 = cvar.AT_CE2
7942 AT_CE3 = cvar.AT_CE3
7944 AT_HE1 = cvar.AT_HE1
7945 AT_HE2 = cvar.AT_HE2
7946 AT_HE3 = cvar.AT_HE3
7947 AT_HE21 = cvar.AT_HE21
7948 AT_HE22 = cvar.AT_HE22
7949 AT_OE1 = cvar.AT_OE1
7950 AT_OE2 = cvar.AT_OE2
7952 AT_NE1 = cvar.AT_NE1
7953 AT_NE2 = cvar.AT_NE2
7955 AT_CZ2 = cvar.AT_CZ2
7956 AT_CZ3 = cvar.AT_CZ3
7959 AT_HZ1 = cvar.AT_HZ1
7960 AT_HZ2 = cvar.AT_HZ2
7961 AT_HZ3 = cvar.AT_HZ3
7962 AT_CH2 = cvar.AT_CH2
7963 AT_NH1 = cvar.AT_NH1
7964 AT_NH2 = cvar.AT_NH2
7967 AT_HH11 = cvar.AT_HH11
7968 AT_HH21 = cvar.AT_HH21
7969 AT_HH2 = cvar.AT_HH2
7970 AT_HH12 = cvar.AT_HH12
7971 AT_HH22 = cvar.AT_HH22
7972 AT_HH13 = cvar.AT_HH13
7973 AT_HH23 = cvar.AT_HH23
7974 AT_HH33 = cvar.AT_HH33
7976 AT_OP1 = cvar.AT_OP1
7977 AT_OP2 = cvar.AT_OP2
7978 AT_OP3 = cvar.AT_OP3
7979 AT_O5p = cvar.AT_O5p
7980 AT_C5p = cvar.AT_C5p
7981 AT_H5p = cvar.AT_H5p
7982 AT_H5pp = cvar.AT_H5pp
7983 AT_C4p = cvar.AT_C4p
7984 AT_H4p = cvar.AT_H4p
7985 AT_O4p = cvar.AT_O4p
7986 AT_C1p = cvar.AT_C1p
7987 AT_H1p = cvar.AT_H1p
7988 AT_C3p = cvar.AT_C3p
7989 AT_H3p = cvar.AT_H3p
7990 AT_O3p = cvar.AT_O3p
7991 AT_C2p = cvar.AT_C2p
7992 AT_H2p = cvar.AT_H2p
7993 AT_H2pp = cvar.AT_H2pp
7994 AT_O2p = cvar.AT_O2p
7995 AT_HO2p = cvar.AT_HO2p
8007 AT_H61 = cvar.AT_H61
8008 AT_H62 = cvar.AT_H62
8012 AT_H21 = cvar.AT_H21
8013 AT_H22 = cvar.AT_H22
8018 AT_H41 = cvar.AT_H41
8019 AT_H42 = cvar.AT_H42
8022 AT_H71 = cvar.AT_H71
8023 AT_H72 = cvar.AT_H72
8024 AT_H73 = cvar.AT_H73
8025 AT_O1A = cvar.AT_O1A
8026 AT_O2A = cvar.AT_O2A
8027 AT_O3A = cvar.AT_O3A
8028 AT_O1B = cvar.AT_O1B
8029 AT_O2B = cvar.AT_O2B
8030 AT_O3B = cvar.AT_O3B
8031 AT_CAY = cvar.AT_CAY
8034 AT_CAT = cvar.AT_CAT
8039 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8040 get_residue(Atom d, bool nothrow=False) -> Residue
8042 return _IMP_atom.get_residue(*args)
8045 r"""get_atom(Residue rd, AtomType at) -> Atom"""
8046 return _IMP_atom.get_atom(rd, at)
8049 r"""add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8050 return _IMP_atom.add_atom_type(name, e)
8052 def get_element_for_atom_type(at):
8053 r"""get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8054 return _IMP_atom.get_element_for_atom_type(at)
8057 r"""get_atom_type_exists(std::string name) -> bool"""
8058 return _IMP_atom.get_atom_type_exists(name)
8059 class Residue(Hierarchy):
8060 r"""Proxy of C++ IMP::atom::Residue class."""
8062 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8064 def __init__(self, *args):
8066 __init__(Residue self) -> Residue
8067 __init__(Residue self, Model m, ParticleIndex id) -> Residue
8068 __init__(Residue self, _ParticleAdaptor d) -> Residue
8070 _IMP_atom.Residue_swiginit(self, _IMP_atom.new_Residue(*args))
8072 def show(self, *args):
8073 r"""show(Residue self, _ostream out=std::cout)"""
8074 return _IMP_atom.Residue_show(self, *args)
8077 def setup_particle(*args):
8079 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8080 setup_particle(_ParticleAdaptor pa, ResidueType t, int index, int insertion_code) -> Residue
8081 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8082 setup_particle(_ParticleAdaptor pa, ResidueType t, int index) -> Residue
8083 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8084 setup_particle(_ParticleAdaptor pa, ResidueType t) -> Residue
8085 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8086 setup_particle(_ParticleAdaptor pa, Residue other) -> Residue
8088 return _IMP_atom.Residue_setup_particle(*args)
8091 def get_is_setup(*args):
8093 get_is_setup(_ParticleAdaptor p) -> bool
8094 get_is_setup(Model m, ParticleIndex pi) -> bool
8096 return _IMP_atom.Residue_get_is_setup(*args)
8098 def get_residue_type(self):
8099 r"""get_residue_type(Residue self) -> ResidueType"""
8100 return _IMP_atom.Residue_get_residue_type(self)
8102 def set_residue_type(self, t):
8103 r"""set_residue_type(Residue self, ResidueType t)"""
8104 return _IMP_atom.Residue_set_residue_type(self, t)
8106 def get_is_protein(self):
8107 r"""get_is_protein(Residue self) -> bool"""
8108 return _IMP_atom.Residue_get_is_protein(self)
8110 def get_is_dna(self):
8111 r"""get_is_dna(Residue self) -> bool"""
8112 return _IMP_atom.Residue_get_is_dna(self)
8114 def get_is_rna(self):
8115 r"""get_is_rna(Residue self) -> bool"""
8116 return _IMP_atom.Residue_get_is_rna(self)
8119 r"""get_index(Residue self) -> IMP::Int"""
8120 return _IMP_atom.Residue_get_index(self)
8122 def set_index(self, t):
8123 r"""set_index(Residue self, IMP::Int t)"""
8124 return _IMP_atom.Residue_set_index(self, t)
8126 def get_insertion_code(self):
8127 r"""get_insertion_code(Residue self) -> char"""
8128 return _IMP_atom.Residue_get_insertion_code(self)
8130 def set_insertion_code(self, insertion_code):
8131 r"""set_insertion_code(Residue self, char insertion_code)"""
8132 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8135 def get_index_key():
8136 r"""get_index_key() -> IntKey"""
8137 return _IMP_atom.Residue_get_index_key()
8140 def get_residue_type_key():
8141 r"""get_residue_type_key() -> IntKey"""
8142 return _IMP_atom.Residue_get_residue_type_key()
8145 def get_insertion_code_key():
8146 r"""get_insertion_code_key() -> IntKey"""
8147 return _IMP_atom.Residue_get_insertion_code_key()
8150 def get_type_changed_key():
8151 r"""get_type_changed_key() -> TriggerKey"""
8152 return _IMP_atom.Residue_get_type_changed_key()
8154 def add_attribute(self, *args):
8156 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8157 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8158 add_attribute(Residue self, IntKey a0, IMP::Int a1)
8159 add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
8160 add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
8161 add_attribute(Residue self, StringKey a0, IMP::String a1)
8162 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8163 add_attribute(Residue self, ObjectKey a0, Object a1)
8165 return _IMP_atom.Residue_add_attribute(self, *args)
8167 def get_value(self, *args):
8169 get_value(Residue self, FloatKey a0) -> IMP::Float
8170 get_value(Residue self, IntKey a0) -> IMP::Int
8171 get_value(Residue self, FloatsKey a0) -> IMP::Floats
8172 get_value(Residue self, IntsKey a0) -> IMP::Ints
8173 get_value(Residue self, StringKey a0) -> IMP::String
8174 get_value(Residue self, ParticleIndexKey a0) -> Particle
8175 get_value(Residue self, ObjectKey a0) -> Object
8177 return _IMP_atom.Residue_get_value(self, *args)
8179 def set_value(self, *args):
8181 set_value(Residue self, FloatKey a0, IMP::Float a1)
8182 set_value(Residue self, IntKey a0, IMP::Int a1)
8183 set_value(Residue self, FloatsKey a0, IMP::Floats a1)
8184 set_value(Residue self, IntsKey a0, IMP::Ints a1)
8185 set_value(Residue self, StringKey a0, IMP::String a1)
8186 set_value(Residue self, ParticleIndexKey a0, Particle a1)
8187 set_value(Residue self, ObjectKey a0, Object a1)
8189 return _IMP_atom.Residue_set_value(self, *args)
8191 def remove_attribute(self, *args):
8193 remove_attribute(Residue self, FloatKey a0)
8194 remove_attribute(Residue self, IntKey a0)
8195 remove_attribute(Residue self, FloatsKey a0)
8196 remove_attribute(Residue self, IntsKey a0)
8197 remove_attribute(Residue self, StringKey a0)
8198 remove_attribute(Residue self, ParticleIndexKey a0)
8199 remove_attribute(Residue self, ObjectKey a0)
8201 return _IMP_atom.Residue_remove_attribute(self, *args)
8203 def has_attribute(self, *args):
8205 has_attribute(Residue self, FloatKey a0) -> bool
8206 has_attribute(Residue self, IntKey a0) -> bool
8207 has_attribute(Residue self, FloatsKey a0) -> bool
8208 has_attribute(Residue self, IntsKey a0) -> bool
8209 has_attribute(Residue self, StringKey a0) -> bool
8210 has_attribute(Residue self, ParticleIndexKey a0) -> bool
8211 has_attribute(Residue self, ObjectKey a0) -> bool
8213 return _IMP_atom.Residue_has_attribute(self, *args)
8215 def get_derivative(self, a0):
8216 r"""get_derivative(Residue self, FloatKey a0) -> double"""
8217 return _IMP_atom.Residue_get_derivative(self, a0)
8220 r"""get_name(Residue self) -> std::string"""
8221 return _IMP_atom.Residue_get_name(self)
8223 def clear_caches(self):
8224 r"""clear_caches(Residue self)"""
8225 return _IMP_atom.Residue_clear_caches(self)
8227 def set_name(self, a0):
8228 r"""set_name(Residue self, std::string a0)"""
8229 return _IMP_atom.Residue_set_name(self, a0)
8232 r"""set_check_level(Residue self, IMP::CheckLevel a0)"""
8233 return _IMP_atom.Residue_set_check_level(self, a0)
8235 def add_to_derivative(self, a0, a1, a2):
8236 r"""add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8237 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8239 def set_is_optimized(self, a0, a1):
8240 r"""set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8241 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8243 def get_is_optimized(self, a0):
8244 r"""get_is_optimized(Residue self, FloatKey a0) -> bool"""
8245 return _IMP_atom.Residue_get_is_optimized(self, a0)
8248 r"""get_check_level(Residue self) -> IMP::CheckLevel"""
8249 return _IMP_atom.Residue_get_check_level(self)
8251 def __eq__(self, *args):
8253 __eq__(Residue self, Residue o) -> bool
8254 __eq__(Residue self, Particle d) -> bool
8256 return _IMP_atom.Residue___eq__(self, *args)
8258 def __ne__(self, *args):
8260 __ne__(Residue self, Residue o) -> bool
8261 __ne__(Residue self, Particle d) -> bool
8263 return _IMP_atom.Residue___ne__(self, *args)
8265 def __le__(self, *args):
8267 __le__(Residue self, Residue o) -> bool
8268 __le__(Residue self, Particle d) -> bool
8270 return _IMP_atom.Residue___le__(self, *args)
8272 def __lt__(self, *args):
8274 __lt__(Residue self, Residue o) -> bool
8275 __lt__(Residue self, Particle d) -> bool
8277 return _IMP_atom.Residue___lt__(self, *args)
8279 def __ge__(self, *args):
8281 __ge__(Residue self, Residue o) -> bool
8282 __ge__(Residue self, Particle d) -> bool
8284 return _IMP_atom.Residue___ge__(self, *args)
8286 def __gt__(self, *args):
8288 __gt__(Residue self, Residue o) -> bool
8289 __gt__(Residue self, Particle d) -> bool
8291 return _IMP_atom.Residue___gt__(self, *args)
8294 r"""__hash__(Residue self) -> std::size_t"""
8295 return _IMP_atom.Residue___hash__(self)
8298 r"""__str__(Residue self) -> std::string"""
8299 return _IMP_atom.Residue___str__(self)
8302 r"""__repr__(Residue self) -> std::string"""
8303 return _IMP_atom.Residue___repr__(self)
8305 def _get_as_binary(self):
8306 r"""_get_as_binary(Residue self) -> PyObject *"""
8307 return _IMP_atom.Residue__get_as_binary(self)
8309 def _set_from_binary(self, p):
8310 r"""_set_from_binary(Residue self, PyObject * p)"""
8311 return _IMP_atom.Residue__set_from_binary(self, p)
8313 def __getstate__(self):
8314 p = self._get_as_binary()
8315 if len(self.__dict__) > 1:
8316 d = self.__dict__.copy()
8321 def __setstate__(self, p):
8322 if not hasattr(self,
'this'):
8324 if isinstance(p, tuple):
8326 self.__dict__.update(d)
8327 return self._set_from_binary(p)
8329 __swig_destroy__ = _IMP_atom.delete_Residue
8332 _IMP_atom.Residue_swigregister(Residue)
8373 r"""get_next_residue(Residue rd) -> Hierarchy"""
8374 return _IMP_atom.get_next_residue(rd)
8377 r"""get_previous_residue(Residue rd) -> Hierarchy"""
8378 return _IMP_atom.get_previous_residue(rd)
8381 r"""get_one_letter_code(ResidueType c) -> char"""
8382 return _IMP_atom.get_one_letter_code(c)
8383 BALLS = _IMP_atom.BALLS
8385 DENSITIES = _IMP_atom.DENSITIES
8387 class Representation(Hierarchy):
8388 r"""Proxy of C++ IMP::atom::Representation class."""
8390 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8393 def setup_particle(*args):
8395 setup_particle(Model m, ParticleIndex pi) -> Representation
8396 setup_particle(_ParticleAdaptor pa) -> Representation
8397 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
8398 setup_particle(_ParticleAdaptor pa, double resolution) -> Representation
8399 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
8400 setup_particle(_ParticleAdaptor pa, Representation other) -> Representation
8402 return _IMP_atom.Representation_setup_particle(*args)
8404 def __init__(self, *args):
8406 __init__(Representation self) -> Representation
8407 __init__(Representation self, Model m, ParticleIndex id) -> Representation
8408 __init__(Representation self, _ParticleAdaptor d) -> Representation
8410 _IMP_atom.Representation_swiginit(self, _IMP_atom.new_Representation(*args))
8412 def show(self, *args):
8413 r"""show(Representation self, _ostream out=std::cout)"""
8414 return _IMP_atom.Representation_show(self, *args)
8417 def get_is_setup(*args):
8419 get_is_setup(_ParticleAdaptor p) -> bool
8420 get_is_setup(Model m, ParticleIndex pi) -> bool
8422 return _IMP_atom.Representation_get_is_setup(*args)
8425 r"""get_representation(Representation self, double resolution, IMP::atom::RepresentationType type=BALLS) -> Hierarchy"""
8426 return _IMP_atom.Representation_get_representation(self, *args)
8428 def get_representations(self, *args):
8429 r"""get_representations(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::atom::Hierarchies"""
8430 return _IMP_atom.Representation_get_representations(self, *args)
8432 def add_representation(self, *args):
8433 r"""add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type=BALLS, double resolution=-1)"""
8434 return _IMP_atom.Representation_add_representation(self, *args)
8436 def get_resolutions(self, *args):
8437 r"""get_resolutions(Representation self, IMP::atom::RepresentationType type=BALLS) -> IMP::Floats"""
8438 return _IMP_atom.Representation_get_resolutions(self, *args)
8440 def remove_representation(self, rep):
8441 r"""remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
8442 return _IMP_atom.Representation_remove_representation(self, rep)
8444 def update_parents(self):
8445 r"""update_parents(Representation self)"""
8446 return _IMP_atom.Representation_update_parents(self)
8448 def add_attribute(self, *args):
8450 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
8451 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
8452 add_attribute(Representation self, IntKey a0, IMP::Int a1)
8453 add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
8454 add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
8455 add_attribute(Representation self, StringKey a0, IMP::String a1)
8456 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
8457 add_attribute(Representation self, ObjectKey a0, Object a1)
8459 return _IMP_atom.Representation_add_attribute(self, *args)
8461 def get_value(self, *args):
8463 get_value(Representation self, FloatKey a0) -> IMP::Float
8464 get_value(Representation self, IntKey a0) -> IMP::Int
8465 get_value(Representation self, FloatsKey a0) -> IMP::Floats
8466 get_value(Representation self, IntsKey a0) -> IMP::Ints
8467 get_value(Representation self, StringKey a0) -> IMP::String
8468 get_value(Representation self, ParticleIndexKey a0) -> Particle
8469 get_value(Representation self, ObjectKey a0) -> Object
8471 return _IMP_atom.Representation_get_value(self, *args)
8473 def set_value(self, *args):
8475 set_value(Representation self, FloatKey a0, IMP::Float a1)
8476 set_value(Representation self, IntKey a0, IMP::Int a1)
8477 set_value(Representation self, FloatsKey a0, IMP::Floats a1)
8478 set_value(Representation self, IntsKey a0, IMP::Ints a1)
8479 set_value(Representation self, StringKey a0, IMP::String a1)
8480 set_value(Representation self, ParticleIndexKey a0, Particle a1)
8481 set_value(Representation self, ObjectKey a0, Object a1)
8483 return _IMP_atom.Representation_set_value(self, *args)
8485 def remove_attribute(self, *args):
8487 remove_attribute(Representation self, FloatKey a0)
8488 remove_attribute(Representation self, IntKey a0)
8489 remove_attribute(Representation self, FloatsKey a0)
8490 remove_attribute(Representation self, IntsKey a0)
8491 remove_attribute(Representation self, StringKey a0)
8492 remove_attribute(Representation self, ParticleIndexKey a0)
8493 remove_attribute(Representation self, ObjectKey a0)
8495 return _IMP_atom.Representation_remove_attribute(self, *args)
8497 def has_attribute(self, *args):
8499 has_attribute(Representation self, FloatKey a0) -> bool
8500 has_attribute(Representation self, IntKey a0) -> bool
8501 has_attribute(Representation self, FloatsKey a0) -> bool
8502 has_attribute(Representation self, IntsKey a0) -> bool
8503 has_attribute(Representation self, StringKey a0) -> bool
8504 has_attribute(Representation self, ParticleIndexKey a0) -> bool
8505 has_attribute(Representation self, ObjectKey a0) -> bool
8507 return _IMP_atom.Representation_has_attribute(self, *args)
8509 def get_derivative(self, a0):
8510 r"""get_derivative(Representation self, FloatKey a0) -> double"""
8511 return _IMP_atom.Representation_get_derivative(self, a0)
8514 r"""get_name(Representation self) -> std::string"""
8515 return _IMP_atom.Representation_get_name(self)
8517 def clear_caches(self):
8518 r"""clear_caches(Representation self)"""
8519 return _IMP_atom.Representation_clear_caches(self)
8521 def set_name(self, a0):
8522 r"""set_name(Representation self, std::string a0)"""
8523 return _IMP_atom.Representation_set_name(self, a0)
8526 r"""set_check_level(Representation self, IMP::CheckLevel a0)"""
8527 return _IMP_atom.Representation_set_check_level(self, a0)
8529 def add_to_derivative(self, a0, a1, a2):
8530 r"""add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8531 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
8533 def set_is_optimized(self, a0, a1):
8534 r"""set_is_optimized(Representation self, FloatKey a0, bool a1)"""
8535 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
8537 def get_is_optimized(self, a0):
8538 r"""get_is_optimized(Representation self, FloatKey a0) -> bool"""
8539 return _IMP_atom.Representation_get_is_optimized(self, a0)
8542 r"""get_check_level(Representation self) -> IMP::CheckLevel"""
8543 return _IMP_atom.Representation_get_check_level(self)
8545 def __eq__(self, *args):
8547 __eq__(Representation self, Representation o) -> bool
8548 __eq__(Representation self, Particle d) -> bool
8550 return _IMP_atom.Representation___eq__(self, *args)
8552 def __ne__(self, *args):
8554 __ne__(Representation self, Representation o) -> bool
8555 __ne__(Representation self, Particle d) -> bool
8557 return _IMP_atom.Representation___ne__(self, *args)
8559 def __le__(self, *args):
8561 __le__(Representation self, Representation o) -> bool
8562 __le__(Representation self, Particle d) -> bool
8564 return _IMP_atom.Representation___le__(self, *args)
8566 def __lt__(self, *args):
8568 __lt__(Representation self, Representation o) -> bool
8569 __lt__(Representation self, Particle d) -> bool
8571 return _IMP_atom.Representation___lt__(self, *args)
8573 def __ge__(self, *args):
8575 __ge__(Representation self, Representation o) -> bool
8576 __ge__(Representation self, Particle d) -> bool
8578 return _IMP_atom.Representation___ge__(self, *args)
8580 def __gt__(self, *args):
8582 __gt__(Representation self, Representation o) -> bool
8583 __gt__(Representation self, Particle d) -> bool
8585 return _IMP_atom.Representation___gt__(self, *args)
8588 r"""__hash__(Representation self) -> std::size_t"""
8589 return _IMP_atom.Representation___hash__(self)
8592 r"""__str__(Representation self) -> std::string"""
8593 return _IMP_atom.Representation___str__(self)
8596 r"""__repr__(Representation self) -> std::string"""
8597 return _IMP_atom.Representation___repr__(self)
8599 def _get_as_binary(self):
8600 r"""_get_as_binary(Representation self) -> PyObject *"""
8601 return _IMP_atom.Representation__get_as_binary(self)
8603 def _set_from_binary(self, p):
8604 r"""_set_from_binary(Representation self, PyObject * p)"""
8605 return _IMP_atom.Representation__set_from_binary(self, p)
8607 def __getstate__(self):
8608 p = self._get_as_binary()
8609 if len(self.__dict__) > 1:
8610 d = self.__dict__.copy()
8615 def __setstate__(self, p):
8616 if not hasattr(self,
'this'):
8618 if isinstance(p, tuple):
8620 self.__dict__.update(d)
8621 return self._set_from_binary(p)
8623 __swig_destroy__ = _IMP_atom.delete_Representation
8626 _IMP_atom.Representation_swigregister(Representation)
8627 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
8632 get_resolution(Model m, ParticleIndex pi) -> double
8633 get_resolution(Hierarchy h) -> double
8635 return _IMP_atom.get_resolution(*args)
8638 r"""get_representation(Hierarchy h, bool nothrow=False) -> Representation"""
8639 return _IMP_atom.get_representation(h, nothrow)
8642 r"""show_with_representations(Hierarchy h, _ostream out=std::cout)"""
8643 return _IMP_atom.show_with_representations(*args)
8644 class State(Hierarchy):
8645 r"""Proxy of C++ IMP::atom::State class."""
8647 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8650 def setup_particle(*args):
8652 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
8653 setup_particle(_ParticleAdaptor pa, unsigned int index) -> State
8654 setup_particle(Model m, ParticleIndex pi, State other) -> State
8655 setup_particle(_ParticleAdaptor pa, State other) -> State
8657 return _IMP_atom.State_setup_particle(*args)
8659 def __init__(self, *args):
8661 __init__(State self) -> State
8662 __init__(State self, Model m, ParticleIndex id) -> State
8663 __init__(State self, _ParticleAdaptor d) -> State
8665 _IMP_atom.State_swiginit(self, _IMP_atom.new_State(*args))
8667 def show(self, *args):
8668 r"""show(State self, _ostream out=std::cout)"""
8669 return _IMP_atom.State_show(self, *args)
8672 def get_is_setup(*args):
8674 get_is_setup(_ParticleAdaptor p) -> bool
8675 get_is_setup(Model m, ParticleIndex pi) -> bool
8677 return _IMP_atom.State_get_is_setup(*args)
8680 r"""get_state_index(State self) -> unsigned int"""
8681 return _IMP_atom.State_get_state_index(self)
8683 def add_attribute(self, *args):
8685 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
8686 add_attribute(State self, FloatKey a0, IMP::Float a1)
8687 add_attribute(State self, IntKey a0, IMP::Int a1)
8688 add_attribute(State self, FloatsKey a0, IMP::Floats a1)
8689 add_attribute(State self, IntsKey a0, IMP::Ints a1)
8690 add_attribute(State self, StringKey a0, IMP::String a1)
8691 add_attribute(State self, ParticleIndexKey a0, Particle a1)
8692 add_attribute(State self, ObjectKey a0, Object a1)
8694 return _IMP_atom.State_add_attribute(self, *args)
8696 def get_value(self, *args):
8698 get_value(State self, FloatKey a0) -> IMP::Float
8699 get_value(State self, IntKey a0) -> IMP::Int
8700 get_value(State self, FloatsKey a0) -> IMP::Floats
8701 get_value(State self, IntsKey a0) -> IMP::Ints
8702 get_value(State self, StringKey a0) -> IMP::String
8703 get_value(State self, ParticleIndexKey a0) -> Particle
8704 get_value(State self, ObjectKey a0) -> Object
8706 return _IMP_atom.State_get_value(self, *args)
8708 def set_value(self, *args):
8710 set_value(State self, FloatKey a0, IMP::Float a1)
8711 set_value(State self, IntKey a0, IMP::Int a1)
8712 set_value(State self, FloatsKey a0, IMP::Floats a1)
8713 set_value(State self, IntsKey a0, IMP::Ints a1)
8714 set_value(State self, StringKey a0, IMP::String a1)
8715 set_value(State self, ParticleIndexKey a0, Particle a1)
8716 set_value(State self, ObjectKey a0, Object a1)
8718 return _IMP_atom.State_set_value(self, *args)
8720 def remove_attribute(self, *args):
8722 remove_attribute(State self, FloatKey a0)
8723 remove_attribute(State self, IntKey a0)
8724 remove_attribute(State self, FloatsKey a0)
8725 remove_attribute(State self, IntsKey a0)
8726 remove_attribute(State self, StringKey a0)
8727 remove_attribute(State self, ParticleIndexKey a0)
8728 remove_attribute(State self, ObjectKey a0)
8730 return _IMP_atom.State_remove_attribute(self, *args)
8732 def has_attribute(self, *args):
8734 has_attribute(State self, FloatKey a0) -> bool
8735 has_attribute(State self, IntKey a0) -> bool
8736 has_attribute(State self, FloatsKey a0) -> bool
8737 has_attribute(State self, IntsKey a0) -> bool
8738 has_attribute(State self, StringKey a0) -> bool
8739 has_attribute(State self, ParticleIndexKey a0) -> bool
8740 has_attribute(State self, ObjectKey a0) -> bool
8742 return _IMP_atom.State_has_attribute(self, *args)
8744 def get_derivative(self, a0):
8745 r"""get_derivative(State self, FloatKey a0) -> double"""
8746 return _IMP_atom.State_get_derivative(self, a0)
8749 r"""get_name(State self) -> std::string"""
8750 return _IMP_atom.State_get_name(self)
8752 def clear_caches(self):
8753 r"""clear_caches(State self)"""
8754 return _IMP_atom.State_clear_caches(self)
8756 def set_name(self, a0):
8757 r"""set_name(State self, std::string a0)"""
8758 return _IMP_atom.State_set_name(self, a0)
8761 r"""set_check_level(State self, IMP::CheckLevel a0)"""
8762 return _IMP_atom.State_set_check_level(self, a0)
8764 def add_to_derivative(self, a0, a1, a2):
8765 r"""add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8766 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
8768 def set_is_optimized(self, a0, a1):
8769 r"""set_is_optimized(State self, FloatKey a0, bool a1)"""
8770 return _IMP_atom.State_set_is_optimized(self, a0, a1)
8772 def get_is_optimized(self, a0):
8773 r"""get_is_optimized(State self, FloatKey a0) -> bool"""
8774 return _IMP_atom.State_get_is_optimized(self, a0)
8777 r"""get_check_level(State self) -> IMP::CheckLevel"""
8778 return _IMP_atom.State_get_check_level(self)
8780 def __eq__(self, *args):
8782 __eq__(State self, State o) -> bool
8783 __eq__(State self, Particle d) -> bool
8785 return _IMP_atom.State___eq__(self, *args)
8787 def __ne__(self, *args):
8789 __ne__(State self, State o) -> bool
8790 __ne__(State self, Particle d) -> bool
8792 return _IMP_atom.State___ne__(self, *args)
8794 def __le__(self, *args):
8796 __le__(State self, State o) -> bool
8797 __le__(State self, Particle d) -> bool
8799 return _IMP_atom.State___le__(self, *args)
8801 def __lt__(self, *args):
8803 __lt__(State self, State o) -> bool
8804 __lt__(State self, Particle d) -> bool
8806 return _IMP_atom.State___lt__(self, *args)
8808 def __ge__(self, *args):
8810 __ge__(State self, State o) -> bool
8811 __ge__(State self, Particle d) -> bool
8813 return _IMP_atom.State___ge__(self, *args)
8815 def __gt__(self, *args):
8817 __gt__(State self, State o) -> bool
8818 __gt__(State self, Particle d) -> bool
8820 return _IMP_atom.State___gt__(self, *args)
8823 r"""__hash__(State self) -> std::size_t"""
8824 return _IMP_atom.State___hash__(self)
8827 r"""__str__(State self) -> std::string"""
8828 return _IMP_atom.State___str__(self)
8831 r"""__repr__(State self) -> std::string"""
8832 return _IMP_atom.State___repr__(self)
8834 def _get_as_binary(self):
8835 r"""_get_as_binary(State self) -> PyObject *"""
8836 return _IMP_atom.State__get_as_binary(self)
8838 def _set_from_binary(self, p):
8839 r"""_set_from_binary(State self, PyObject * p)"""
8840 return _IMP_atom.State__set_from_binary(self, p)
8842 def __getstate__(self):
8843 p = self._get_as_binary()
8844 if len(self.__dict__) > 1:
8845 d = self.__dict__.copy()
8850 def __setstate__(self, p):
8851 if not hasattr(self,
'this'):
8853 if isinstance(p, tuple):
8855 self.__dict__.update(d)
8856 return self._set_from_binary(p)
8858 __swig_destroy__ = _IMP_atom.delete_State
8861 _IMP_atom.State_swigregister(State)
8864 r"""get_state_index(Hierarchy h) -> int"""
8865 return _IMP_atom.get_state_index(h)
8868 r"""get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
8869 return _IMP_atom.get_phi_dihedral_atoms(rd)
8872 r"""get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
8873 return _IMP_atom.get_psi_dihedral_atoms(rd)
8876 r"""get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
8877 return _IMP_atom.get_omega_dihedral_atoms(rd)
8880 r"""get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
8881 return _IMP_atom.get_chi_dihedral_atom_types(rt)
8884 r"""get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
8885 return _IMP_atom.get_chi_dihedral_atoms(rd)
8888 r"""get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
8889 return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
8890 class Molecule(Hierarchy):
8891 r"""Proxy of C++ IMP::atom::Molecule class."""
8893 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8895 def __init__(self, *args):
8897 __init__(Molecule self) -> Molecule
8898 __init__(Molecule self, Model m, ParticleIndex id) -> Molecule
8899 __init__(Molecule self, _ParticleAdaptor d) -> Molecule
8901 _IMP_atom.Molecule_swiginit(self, _IMP_atom.new_Molecule(*args))
8903 def show(self, *args):
8904 r"""show(Molecule self, _ostream out=std::cout)"""
8905 return _IMP_atom.Molecule_show(self, *args)
8908 def setup_particle(*args):
8910 setup_particle(Model m, ParticleIndex pi) -> Molecule
8911 setup_particle(_ParticleAdaptor pa) -> Molecule
8912 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
8913 setup_particle(_ParticleAdaptor pa, Molecule other) -> Molecule
8915 return _IMP_atom.Molecule_setup_particle(*args)
8918 def get_is_setup(*args):
8920 get_is_setup(_ParticleAdaptor p) -> bool
8921 get_is_setup(Model m, ParticleIndex pi) -> bool
8923 return _IMP_atom.Molecule_get_is_setup(*args)
8925 def add_attribute(self, *args):
8927 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
8928 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
8929 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
8930 add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
8931 add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
8932 add_attribute(Molecule self, StringKey a0, IMP::String a1)
8933 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
8934 add_attribute(Molecule self, ObjectKey a0, Object a1)
8936 return _IMP_atom.Molecule_add_attribute(self, *args)
8938 def get_value(self, *args):
8940 get_value(Molecule self, FloatKey a0) -> IMP::Float
8941 get_value(Molecule self, IntKey a0) -> IMP::Int
8942 get_value(Molecule self, FloatsKey a0) -> IMP::Floats
8943 get_value(Molecule self, IntsKey a0) -> IMP::Ints
8944 get_value(Molecule self, StringKey a0) -> IMP::String
8945 get_value(Molecule self, ParticleIndexKey a0) -> Particle
8946 get_value(Molecule self, ObjectKey a0) -> Object
8948 return _IMP_atom.Molecule_get_value(self, *args)
8950 def set_value(self, *args):
8952 set_value(Molecule self, FloatKey a0, IMP::Float a1)
8953 set_value(Molecule self, IntKey a0, IMP::Int a1)
8954 set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
8955 set_value(Molecule self, IntsKey a0, IMP::Ints a1)
8956 set_value(Molecule self, StringKey a0, IMP::String a1)
8957 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
8958 set_value(Molecule self, ObjectKey a0, Object a1)
8960 return _IMP_atom.Molecule_set_value(self, *args)
8962 def remove_attribute(self, *args):
8964 remove_attribute(Molecule self, FloatKey a0)
8965 remove_attribute(Molecule self, IntKey a0)
8966 remove_attribute(Molecule self, FloatsKey a0)
8967 remove_attribute(Molecule self, IntsKey a0)
8968 remove_attribute(Molecule self, StringKey a0)
8969 remove_attribute(Molecule self, ParticleIndexKey a0)
8970 remove_attribute(Molecule self, ObjectKey a0)
8972 return _IMP_atom.Molecule_remove_attribute(self, *args)
8974 def has_attribute(self, *args):
8976 has_attribute(Molecule self, FloatKey a0) -> bool
8977 has_attribute(Molecule self, IntKey a0) -> bool
8978 has_attribute(Molecule self, FloatsKey a0) -> bool
8979 has_attribute(Molecule self, IntsKey a0) -> bool
8980 has_attribute(Molecule self, StringKey a0) -> bool
8981 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
8982 has_attribute(Molecule self, ObjectKey a0) -> bool
8984 return _IMP_atom.Molecule_has_attribute(self, *args)
8986 def get_derivative(self, a0):
8987 r"""get_derivative(Molecule self, FloatKey a0) -> double"""
8988 return _IMP_atom.Molecule_get_derivative(self, a0)
8991 r"""get_name(Molecule self) -> std::string"""
8992 return _IMP_atom.Molecule_get_name(self)
8994 def clear_caches(self):
8995 r"""clear_caches(Molecule self)"""
8996 return _IMP_atom.Molecule_clear_caches(self)
8998 def set_name(self, a0):
8999 r"""set_name(Molecule self, std::string a0)"""
9000 return _IMP_atom.Molecule_set_name(self, a0)
9003 r"""set_check_level(Molecule self, IMP::CheckLevel a0)"""
9004 return _IMP_atom.Molecule_set_check_level(self, a0)
9006 def add_to_derivative(self, a0, a1, a2):
9007 r"""add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9008 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9010 def set_is_optimized(self, a0, a1):
9011 r"""set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9012 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9014 def get_is_optimized(self, a0):
9015 r"""get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9016 return _IMP_atom.Molecule_get_is_optimized(self, a0)
9019 r"""get_check_level(Molecule self) -> IMP::CheckLevel"""
9020 return _IMP_atom.Molecule_get_check_level(self)
9022 def __eq__(self, *args):
9024 __eq__(Molecule self, Molecule o) -> bool
9025 __eq__(Molecule self, Particle d) -> bool
9027 return _IMP_atom.Molecule___eq__(self, *args)
9029 def __ne__(self, *args):
9031 __ne__(Molecule self, Molecule o) -> bool
9032 __ne__(Molecule self, Particle d) -> bool
9034 return _IMP_atom.Molecule___ne__(self, *args)
9036 def __le__(self, *args):
9038 __le__(Molecule self, Molecule o) -> bool
9039 __le__(Molecule self, Particle d) -> bool
9041 return _IMP_atom.Molecule___le__(self, *args)
9043 def __lt__(self, *args):
9045 __lt__(Molecule self, Molecule o) -> bool
9046 __lt__(Molecule self, Particle d) -> bool
9048 return _IMP_atom.Molecule___lt__(self, *args)
9050 def __ge__(self, *args):
9052 __ge__(Molecule self, Molecule o) -> bool
9053 __ge__(Molecule self, Particle d) -> bool
9055 return _IMP_atom.Molecule___ge__(self, *args)
9057 def __gt__(self, *args):
9059 __gt__(Molecule self, Molecule o) -> bool
9060 __gt__(Molecule self, Particle d) -> bool
9062 return _IMP_atom.Molecule___gt__(self, *args)
9065 r"""__hash__(Molecule self) -> std::size_t"""
9066 return _IMP_atom.Molecule___hash__(self)
9069 r"""__str__(Molecule self) -> std::string"""
9070 return _IMP_atom.Molecule___str__(self)
9073 r"""__repr__(Molecule self) -> std::string"""
9074 return _IMP_atom.Molecule___repr__(self)
9076 def _get_as_binary(self):
9077 r"""_get_as_binary(Molecule self) -> PyObject *"""
9078 return _IMP_atom.Molecule__get_as_binary(self)
9080 def _set_from_binary(self, p):
9081 r"""_set_from_binary(Molecule self, PyObject * p)"""
9082 return _IMP_atom.Molecule__set_from_binary(self, p)
9084 def __getstate__(self):
9085 p = self._get_as_binary()
9086 if len(self.__dict__) > 1:
9087 d = self.__dict__.copy()
9092 def __setstate__(self, p):
9093 if not hasattr(self,
'this'):
9095 if isinstance(p, tuple):
9097 self.__dict__.update(d)
9098 return self._set_from_binary(p)
9100 __swig_destroy__ = _IMP_atom.delete_Molecule
9103 _IMP_atom.Molecule_swigregister(Molecule)
9106 r"""get_molecule_name(Hierarchy h) -> std::string"""
9107 return _IMP_atom.get_molecule_name(h)
9108 class Copy(Molecule):
9109 r"""Proxy of C++ IMP::atom::Copy class."""
9111 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9114 def get_copy_index_key():
9115 r"""get_copy_index_key() -> IntKey"""
9116 return _IMP_atom.Copy_get_copy_index_key()
9118 def __init__(self, *args):
9120 __init__(Copy self) -> Copy
9121 __init__(Copy self, Model m, ParticleIndex id) -> Copy
9122 __init__(Copy self, _ParticleAdaptor d) -> Copy
9124 _IMP_atom.Copy_swiginit(self, _IMP_atom.new_Copy(*args))
9126 def show(self, *args):
9127 r"""show(Copy self, _ostream out=std::cout)"""
9128 return _IMP_atom.Copy_show(self, *args)
9131 def setup_particle(*args):
9133 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9134 setup_particle(_ParticleAdaptor pa, IMP::Int number) -> Copy
9136 return _IMP_atom.Copy_setup_particle(*args)
9139 def get_is_setup(*args):
9141 get_is_setup(_ParticleAdaptor p) -> bool
9142 get_is_setup(Model m, ParticleIndex pi) -> bool
9144 return _IMP_atom.Copy_get_is_setup(*args)
9147 r"""get_copy_index(Copy self) -> int"""
9148 return _IMP_atom.Copy_get_copy_index(self)
9150 def add_attribute(self, *args):
9152 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9153 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9154 add_attribute(Copy self, IntKey a0, IMP::Int a1)
9155 add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
9156 add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
9157 add_attribute(Copy self, StringKey a0, IMP::String a1)
9158 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9159 add_attribute(Copy self, ObjectKey a0, Object a1)
9161 return _IMP_atom.Copy_add_attribute(self, *args)
9163 def get_value(self, *args):
9165 get_value(Copy self, FloatKey a0) -> IMP::Float
9166 get_value(Copy self, IntKey a0) -> IMP::Int
9167 get_value(Copy self, FloatsKey a0) -> IMP::Floats
9168 get_value(Copy self, IntsKey a0) -> IMP::Ints
9169 get_value(Copy self, StringKey a0) -> IMP::String
9170 get_value(Copy self, ParticleIndexKey a0) -> Particle
9171 get_value(Copy self, ObjectKey a0) -> Object
9173 return _IMP_atom.Copy_get_value(self, *args)
9175 def set_value(self, *args):
9177 set_value(Copy self, FloatKey a0, IMP::Float a1)
9178 set_value(Copy self, IntKey a0, IMP::Int a1)
9179 set_value(Copy self, FloatsKey a0, IMP::Floats a1)
9180 set_value(Copy self, IntsKey a0, IMP::Ints a1)
9181 set_value(Copy self, StringKey a0, IMP::String a1)
9182 set_value(Copy self, ParticleIndexKey a0, Particle a1)
9183 set_value(Copy self, ObjectKey a0, Object a1)
9185 return _IMP_atom.Copy_set_value(self, *args)
9187 def remove_attribute(self, *args):
9189 remove_attribute(Copy self, FloatKey a0)
9190 remove_attribute(Copy self, IntKey a0)
9191 remove_attribute(Copy self, FloatsKey a0)
9192 remove_attribute(Copy self, IntsKey a0)
9193 remove_attribute(Copy self, StringKey a0)
9194 remove_attribute(Copy self, ParticleIndexKey a0)
9195 remove_attribute(Copy self, ObjectKey a0)
9197 return _IMP_atom.Copy_remove_attribute(self, *args)
9199 def has_attribute(self, *args):
9201 has_attribute(Copy self, FloatKey a0) -> bool
9202 has_attribute(Copy self, IntKey a0) -> bool
9203 has_attribute(Copy self, FloatsKey a0) -> bool
9204 has_attribute(Copy self, IntsKey a0) -> bool
9205 has_attribute(Copy self, StringKey a0) -> bool
9206 has_attribute(Copy self, ParticleIndexKey a0) -> bool
9207 has_attribute(Copy self, ObjectKey a0) -> bool
9209 return _IMP_atom.Copy_has_attribute(self, *args)
9211 def get_derivative(self, a0):
9212 r"""get_derivative(Copy self, FloatKey a0) -> double"""
9213 return _IMP_atom.Copy_get_derivative(self, a0)
9216 r"""get_name(Copy self) -> std::string"""
9217 return _IMP_atom.Copy_get_name(self)
9219 def clear_caches(self):
9220 r"""clear_caches(Copy self)"""
9221 return _IMP_atom.Copy_clear_caches(self)
9223 def set_name(self, a0):
9224 r"""set_name(Copy self, std::string a0)"""
9225 return _IMP_atom.Copy_set_name(self, a0)
9228 r"""set_check_level(Copy self, IMP::CheckLevel a0)"""
9229 return _IMP_atom.Copy_set_check_level(self, a0)
9231 def add_to_derivative(self, a0, a1, a2):
9232 r"""add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9233 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9235 def set_is_optimized(self, a0, a1):
9236 r"""set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9237 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9239 def get_is_optimized(self, a0):
9240 r"""get_is_optimized(Copy self, FloatKey a0) -> bool"""
9241 return _IMP_atom.Copy_get_is_optimized(self, a0)
9244 r"""get_check_level(Copy self) -> IMP::CheckLevel"""
9245 return _IMP_atom.Copy_get_check_level(self)
9247 def __eq__(self, *args):
9249 __eq__(Copy self, Copy o) -> bool
9250 __eq__(Copy self, Particle d) -> bool
9252 return _IMP_atom.Copy___eq__(self, *args)
9254 def __ne__(self, *args):
9256 __ne__(Copy self, Copy o) -> bool
9257 __ne__(Copy self, Particle d) -> bool
9259 return _IMP_atom.Copy___ne__(self, *args)
9261 def __le__(self, *args):
9263 __le__(Copy self, Copy o) -> bool
9264 __le__(Copy self, Particle d) -> bool
9266 return _IMP_atom.Copy___le__(self, *args)
9268 def __lt__(self, *args):
9270 __lt__(Copy self, Copy o) -> bool
9271 __lt__(Copy self, Particle d) -> bool
9273 return _IMP_atom.Copy___lt__(self, *args)
9275 def __ge__(self, *args):
9277 __ge__(Copy self, Copy o) -> bool
9278 __ge__(Copy self, Particle d) -> bool
9280 return _IMP_atom.Copy___ge__(self, *args)
9282 def __gt__(self, *args):
9284 __gt__(Copy self, Copy o) -> bool
9285 __gt__(Copy self, Particle d) -> bool
9287 return _IMP_atom.Copy___gt__(self, *args)
9290 r"""__hash__(Copy self) -> std::size_t"""
9291 return _IMP_atom.Copy___hash__(self)
9294 r"""__str__(Copy self) -> std::string"""
9295 return _IMP_atom.Copy___str__(self)
9298 r"""__repr__(Copy self) -> std::string"""
9299 return _IMP_atom.Copy___repr__(self)
9301 def _get_as_binary(self):
9302 r"""_get_as_binary(Copy self) -> PyObject *"""
9303 return _IMP_atom.Copy__get_as_binary(self)
9305 def _set_from_binary(self, p):
9306 r"""_set_from_binary(Copy self, PyObject * p)"""
9307 return _IMP_atom.Copy__set_from_binary(self, p)
9309 def __getstate__(self):
9310 p = self._get_as_binary()
9311 if len(self.__dict__) > 1:
9312 d = self.__dict__.copy()
9317 def __setstate__(self, p):
9318 if not hasattr(self,
'this'):
9320 if isinstance(p, tuple):
9322 self.__dict__.update(d)
9323 return self._set_from_binary(p)
9325 __swig_destroy__ = _IMP_atom.delete_Copy
9328 _IMP_atom.Copy_swigregister(Copy)
9331 r"""get_copy_index(Hierarchy h) -> int"""
9332 return _IMP_atom.get_copy_index(h)
9333 class Selection(IMP._ParticleIndexesAdaptor):
9334 r"""Proxy of C++ IMP::atom::Selection class."""
9336 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9337 NONE = _IMP_atom.Selection_NONE
9339 C = _IMP_atom.Selection_C
9341 N = _IMP_atom.Selection_N
9344 def __init__(self, *args):
9346 __init__(Selection self) -> Selection
9347 __init__(Selection self, Hierarchy h) -> Selection
9348 __init__(Selection self, Particle h) -> Selection
9349 __init__(Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
9350 __init__(Selection self, IMP::ParticlesTemp const & h) -> Selection
9352 _IMP_atom.Selection_swiginit(self, _IMP_atom.new_Selection(*args))
9355 r"""create_clone(Selection self) -> Selection"""
9356 return _IMP_atom.Selection_create_clone(self)
9358 def get_hierarchies(self):
9359 r"""get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
9360 return _IMP_atom.Selection_get_hierarchies(self)
9362 def set_molecules(self, mols):
9363 r"""set_molecules(Selection self, IMP::Strings mols)"""
9364 return _IMP_atom.Selection_set_molecules(self, mols)
9366 def set_resolution(self, r):
9367 r"""set_resolution(Selection self, double r)"""
9368 return _IMP_atom.Selection_set_resolution(self, r)
9370 def set_representation_type(self, t):
9371 r"""set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
9372 return _IMP_atom.Selection_set_representation_type(self, t)
9374 def set_state_index(self, state):
9375 r"""set_state_index(Selection self, int state)"""
9376 return _IMP_atom.Selection_set_state_index(self, state)
9378 def set_state_indexes(self, states):
9379 r"""set_state_indexes(Selection self, IMP::Ints states)"""
9380 return _IMP_atom.Selection_set_state_indexes(self, states)
9382 def set_terminus(self, t):
9383 r"""set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
9384 return _IMP_atom.Selection_set_terminus(self, t)
9386 def set_element(self, e):
9387 r"""set_element(Selection self, IMP::atom::Element e)"""
9388 return _IMP_atom.Selection_set_element(self, e)
9390 def set_chain_ids(self, chains):
9391 r"""set_chain_ids(Selection self, IMP::Strings chains)"""
9392 return _IMP_atom.Selection_set_chain_ids(self, chains)
9394 def set_chains(self, chains):
9395 r"""set_chains(Selection self, IMP::Strings chains)"""
9396 return _IMP_atom.Selection_set_chains(self, chains)
9398 def set_residue_indexes(self, indexes):
9399 r"""set_residue_indexes(Selection self, IMP::Ints indexes)"""
9400 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
9402 def set_atom_types(self, types):
9403 r"""set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
9404 return _IMP_atom.Selection_set_atom_types(self, types)
9406 def set_residue_types(self, types):
9407 r"""set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
9408 return _IMP_atom.Selection_set_residue_types(self, types)
9410 def set_domains(self, names):
9411 r"""set_domains(Selection self, IMP::Strings names)"""
9412 return _IMP_atom.Selection_set_domains(self, names)
9414 def set_molecule(self, mol):
9415 r"""set_molecule(Selection self, std::string mol)"""
9416 return _IMP_atom.Selection_set_molecule(self, mol)
9418 def set_chain_id(self, c):
9419 r"""set_chain_id(Selection self, std::string c)"""
9420 return _IMP_atom.Selection_set_chain_id(self, c)
9422 def set_chain(self, c):
9423 r"""set_chain(Selection self, std::string c)"""
9424 return _IMP_atom.Selection_set_chain(self, c)
9426 def set_residue_index(self, i):
9427 r"""set_residue_index(Selection self, int i)"""
9428 return _IMP_atom.Selection_set_residue_index(self, i)
9430 def set_atom_type(self, types):
9431 r"""set_atom_type(Selection self, AtomType types)"""
9432 return _IMP_atom.Selection_set_atom_type(self, types)
9434 def set_residue_type(self, type):
9435 r"""set_residue_type(Selection self, ResidueType type)"""
9436 return _IMP_atom.Selection_set_residue_type(self, type)
9438 def set_domain(self, name):
9439 r"""set_domain(Selection self, std::string name)"""
9440 return _IMP_atom.Selection_set_domain(self, name)
9442 def set_copy_index(self, copy):
9443 r"""set_copy_index(Selection self, unsigned int copy)"""
9444 return _IMP_atom.Selection_set_copy_index(self, copy)
9446 def set_copy_indexes(self, copies):
9447 r"""set_copy_indexes(Selection self, IMP::Ints copies)"""
9448 return _IMP_atom.Selection_set_copy_indexes(self, copies)
9450 def set_particle_type(self, t):
9451 r"""set_particle_type(Selection self, ParticleType t)"""
9452 return _IMP_atom.Selection_set_particle_type(self, t)
9454 def set_particle_types(self, t):
9455 r"""set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
9456 return _IMP_atom.Selection_set_particle_types(self, t)
9458 def set_hierarchy_types(self, types):
9459 r"""set_hierarchy_types(Selection self, IMP::Ints types)"""
9460 return _IMP_atom.Selection_set_hierarchy_types(self, types)
9462 def set_intersection(self, s):
9463 r"""set_intersection(Selection self, Selection s)"""
9464 return _IMP_atom.Selection_set_intersection(self, s)
9466 def set_union(self, s):
9467 r"""set_union(Selection self, Selection s)"""
9468 return _IMP_atom.Selection_set_union(self, s)
9470 def set_symmetric_difference(self, s):
9471 r"""set_symmetric_difference(Selection self, Selection s)"""
9472 return _IMP_atom.Selection_set_symmetric_difference(self, s)
9474 def set_difference(self, s):
9475 r"""set_difference(Selection self, Selection s)"""
9476 return _IMP_atom.Selection_set_difference(self, s)
9478 def get_selected_particles(self, with_representation=True):
9479 r"""get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp"""
9480 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
9482 def get_selected_particle_indexes(self, with_representation=True):
9483 r"""get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes"""
9484 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
9486 def show(self, *args):
9487 r"""show(Selection self, _ostream out=std::cout)"""
9488 return _IMP_atom.Selection_show(self, *args)
9491 r"""__str__(Selection self) -> std::string"""
9492 return _IMP_atom.Selection___str__(self)
9495 r"""__repr__(Selection self) -> std::string"""
9496 return _IMP_atom.Selection___repr__(self)
9498 def __init__(self, hierarchy=None,
9499 hierarchies=
None, **params):
9500 if hierarchy
and hierarchies:
9501 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
9503 this = _IMP_atom.new_Selection(hierarchy)
9504 try: self.this.append(this)
9505 except: self.this = this
9507 this = _IMP_atom.new_Selection(hierarchies)
9508 try: self.this.append(this)
9509 except: self.this = this
9511 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
9512 for k
in params.keys():
9513 eval(
"self.set_%s(params[k])"%k)
9516 news = self.create_clone()
9517 news.union_update(s)
9519 def intersection(self, s):
9520 news = self.create_clone()
9521 news.intersection_update(s)
9523 def symmetric_difference(self, s):
9524 news = self.create_clone()
9525 news.symmetric_difference_update(s)
9527 def difference(self, s):
9528 news = self.create_clone()
9529 news.difference_update(s)
9531 def union_update(self, s):
9534 def intersection_update(self, s):
9535 self.set_intersection(s)
9537 def symmetric_difference_update(self, s):
9538 self.set_symmetric_difference(s)
9540 def difference_update(self, s):
9541 self.set_difference(s)
9544 __and__ = intersection
9545 __xor__ = symmetric_difference
9546 __sub__ = difference
9547 __ior__ = union_update
9548 __iand__ = intersection_update
9549 __ixor__ = symmetric_difference_update
9550 __isub__ = difference_update
9552 __swig_destroy__ = _IMP_atom.delete_Selection
9555 _IMP_atom.Selection_swigregister(Selection)
9558 r"""create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name="Distance%1%") -> Restraint"""
9559 return _IMP_atom.create_distance_restraint(*args)
9563 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name="Connectivity%1%") -> Restraint
9564 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
9566 return _IMP_atom.create_connectivity_restraint(*args)
9570 create_internal_connectivity_restraint(Selection s, double k, std::string name="Connectivity%1%") -> Restraint
9571 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name="Connectivity%1%") -> Restraint
9573 return _IMP_atom.create_internal_connectivity_restraint(*args)
9576 r"""create_cover(Selection s, std::string name=std::string()) -> XYZR"""
9577 return _IMP_atom.create_cover(*args)
9581 get_mass(ResidueType c) -> double
9582 get_mass(Selection s) -> double
9584 return _IMP_atom.get_mass(*args)
9587 r"""get_volume(Selection s) -> double"""
9588 return _IMP_atom.get_volume(s)
9591 r"""get_surface_area(Selection s) -> double"""
9592 return _IMP_atom.get_surface_area(s)
9596 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
9597 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
9598 get_leaves(Selection h) -> IMP::atom::Hierarchies
9600 return _IMP_atom.get_leaves(*args)
9602 r"""Proxy of C++ IMP::atom::SelectionGeometry class."""
9604 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9606 def __init__(self, *args):
9607 r"""__init__(SelectionGeometry self, Selection d, std::string name="Selection") -> SelectionGeometry"""
9608 _IMP_atom.SelectionGeometry_swiginit(self, _IMP_atom.new_SelectionGeometry(*args))
9610 def get_version_info(self):
9611 r"""get_version_info(SelectionGeometry self) -> VersionInfo"""
9612 return _IMP_atom.SelectionGeometry_get_version_info(self)
9613 __swig_destroy__ = _IMP_atom.delete_SelectionGeometry
9616 r"""__str__(SelectionGeometry self) -> std::string"""
9617 return _IMP_atom.SelectionGeometry___str__(self)
9620 r"""__repr__(SelectionGeometry self) -> std::string"""
9621 return _IMP_atom.SelectionGeometry___repr__(self)
9625 return _object_cast_to_SelectionGeometry(o)
9629 _IMP_atom.SelectionGeometry_swigregister(SelectionGeometry)
9633 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
9634 get_rmsd(Selection s0, Selection s1) -> double
9636 return _IMP_atom.get_rmsd(*args)
9640 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
9641 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
9643 return _IMP_atom.get_rmsd_transforming_first(*args)
9646 r"""get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
9647 return _IMP_atom.get_placement_score(source, target)
9650 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"""
9651 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
9654 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"""
9655 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
9659 get_radius_of_gyration(Selection s) -> double
9660 get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
9662 return _IMP_atom.get_radius_of_gyration(*args)
9664 r"""Proxy of C++ IMP::atom::ForceFieldParameters class."""
9666 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9669 r"""__init__(ForceFieldParameters self) -> ForceFieldParameters"""
9670 _IMP_atom.ForceFieldParameters_swiginit(self, _IMP_atom.new_ForceFieldParameters())
9672 def get_radius(self, atom):
9673 r"""get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
9674 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
9676 def get_epsilon(self, atom):
9677 r"""get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
9678 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
9681 r"""add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius"))"""
9682 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
9684 def add_well_depths(self, mhd):
9685 r"""add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
9686 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
9689 r"""add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
9690 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
9691 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
9694 r"""__str__(ForceFieldParameters self) -> std::string"""
9695 return _IMP_atom.ForceFieldParameters___str__(self)
9698 r"""__repr__(ForceFieldParameters self) -> std::string"""
9699 return _IMP_atom.ForceFieldParameters___repr__(self)
9703 return _object_cast_to_ForceFieldParameters(o)
9707 _IMP_atom.ForceFieldParameters_swigregister(ForceFieldParameters)
9708 class CHARMMAtomTopology(object):
9709 r"""Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
9711 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9713 def __init__(self, *args):
9715 __init__(CHARMMAtomTopology self) -> CHARMMAtomTopology
9716 __init__(CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
9717 __init__(CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
9719 _IMP_atom.CHARMMAtomTopology_swiginit(self, _IMP_atom.new_CHARMMAtomTopology(*args))
9722 r"""get_name(CHARMMAtomTopology self) -> std::string"""
9723 return _IMP_atom.CHARMMAtomTopology_get_name(self)
9725 def get_charmm_type(self):
9726 r"""get_charmm_type(CHARMMAtomTopology self) -> std::string"""
9727 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
9729 def get_charge(self):
9730 r"""get_charge(CHARMMAtomTopology self) -> double"""
9731 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
9733 def set_charmm_type(self, charmm_type):
9734 r"""set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
9735 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
9737 def set_charge(self, charge):
9738 r"""set_charge(CHARMMAtomTopology self, double charge)"""
9739 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
9741 def show(self, *args):
9742 r"""show(CHARMMAtomTopology self, _ostream out=std::cout)"""
9743 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
9746 r"""__str__(CHARMMAtomTopology self) -> std::string"""
9747 return _IMP_atom.CHARMMAtomTopology___str__(self)
9750 r"""__repr__(CHARMMAtomTopology self) -> std::string"""
9751 return _IMP_atom.CHARMMAtomTopology___repr__(self)
9753 def _get_as_binary(self):
9754 r"""_get_as_binary(CHARMMAtomTopology self) -> PyObject *"""
9755 return _IMP_atom.CHARMMAtomTopology__get_as_binary(self)
9757 def _set_from_binary(self, p):
9758 r"""_set_from_binary(CHARMMAtomTopology self, PyObject * p)"""
9759 return _IMP_atom.CHARMMAtomTopology__set_from_binary(self, p)
9761 def __getstate__(self):
9762 p = self._get_as_binary()
9763 if len(self.__dict__) > 1:
9764 d = self.__dict__.copy()
9769 def __setstate__(self, p):
9770 if not hasattr(self,
'this'):
9772 if isinstance(p, tuple):
9774 self.__dict__.update(d)
9775 return self._set_from_binary(p)
9777 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
9780 _IMP_atom.CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
9781 class CHARMMBondEndpoint(object):
9782 r"""Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
9784 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9786 def __init__(self, atom_name, residue=None):
9787 r"""__init__(CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint"""
9788 _IMP_atom.CHARMMBondEndpoint_swiginit(self, _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue))
9790 def get_atom_name(self):
9791 r"""get_atom_name(CHARMMBondEndpoint self) -> std::string"""
9792 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
9794 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
9795 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"""
9796 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
9798 def show(self, *args):
9799 r"""show(CHARMMBondEndpoint self, _ostream out=std::cout)"""
9800 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
9803 r"""__str__(CHARMMBondEndpoint self) -> std::string"""
9804 return _IMP_atom.CHARMMBondEndpoint___str__(self)
9807 r"""__repr__(CHARMMBondEndpoint self) -> std::string"""
9808 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
9809 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
9812 _IMP_atom.CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
9813 class CHARMMDihedral(object):
9814 r"""Proxy of C++ IMP::atom::CHARMMConnection< 4 > class."""
9816 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9817 __repr__ = _swig_repr
9819 def __init__(self, atoms):
9820 r"""__init__(CHARMMDihedral self, IMP::Strings const & atoms) -> CHARMMDihedral"""
9821 _IMP_atom.CHARMMDihedral_swiginit(self, _IMP_atom.new_CHARMMDihedral(atoms))
9823 def get_endpoint(self, i):
9824 r"""get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
9825 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
9827 def get_contains_atom(self, name):
9828 r"""get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
9829 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
9831 def show(self, *args):
9832 r"""show(CHARMMDihedral self, _ostream out=std::cout)"""
9833 return _IMP_atom.CHARMMDihedral_show(self, *args)
9834 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
9837 _IMP_atom.CHARMMDihedral_swigregister(CHARMMDihedral)
9838 class CHARMMInternalCoordinate(CHARMMDihedral):
9839 r"""Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
9841 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9843 def __init__(self, *args):
9845 __init__(CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
9846 __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
9848 _IMP_atom.CHARMMInternalCoordinate_swiginit(self, _IMP_atom.new_CHARMMInternalCoordinate(*args))
9850 def get_first_distance(self):
9851 r"""get_first_distance(CHARMMInternalCoordinate self) -> float"""
9852 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
9854 def get_second_distance(self):
9855 r"""get_second_distance(CHARMMInternalCoordinate self) -> float"""
9856 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
9858 def get_first_angle(self):
9859 r"""get_first_angle(CHARMMInternalCoordinate self) -> float"""
9860 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
9862 def get_second_angle(self):
9863 r"""get_second_angle(CHARMMInternalCoordinate self) -> float"""
9864 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
9867 r"""get_dihedral(CHARMMInternalCoordinate self) -> float"""
9868 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
9870 def get_improper(self):
9871 r"""get_improper(CHARMMInternalCoordinate self) -> bool"""
9872 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
9874 def show(self, *args):
9875 r"""show(CHARMMInternalCoordinate self, _ostream out=std::cout)"""
9876 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
9879 r"""__str__(CHARMMInternalCoordinate self) -> std::string"""
9880 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
9883 r"""__repr__(CHARMMInternalCoordinate self) -> std::string"""
9884 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
9885 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
9888 _IMP_atom.CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
9890 r"""Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
9892 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9894 def __init__(self, *args, **kwargs):
9895 raise AttributeError(
"No constructor defined")
9898 r"""get_type(CHARMMResidueTopologyBase self) -> std::string"""
9899 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
9901 def get_number_of_atoms(self):
9902 r"""get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
9903 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
9905 def add_atom(self, atom):
9906 r"""add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
9907 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
9911 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
9912 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
9913 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
9915 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
9917 def get_number_of_bonds(self):
9918 r"""get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
9919 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
9921 def add_bond(self, bond):
9922 r"""add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
9923 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
9925 def get_number_of_angles(self):
9926 r"""get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
9927 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
9929 def add_angle(self, bond):
9930 r"""add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
9931 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
9933 def get_number_of_dihedrals(self):
9934 r"""get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
9935 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
9937 def add_dihedral(self, bond):
9938 r"""add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
9939 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
9941 def get_number_of_impropers(self):
9942 r"""get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
9943 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
9945 def add_improper(self, bond):
9946 r"""add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
9947 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
9949 def get_number_of_internal_coordinates(self):
9950 r"""get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
9951 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
9953 def add_internal_coordinate(self, ic):
9954 r"""add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
9955 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
9957 def get_internal_coordinate(self, index):
9958 r"""get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
9959 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
9962 r"""get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
9963 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
9966 r"""get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
9967 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
9970 r"""get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
9971 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
9973 def get_improper(self, index):
9974 r"""get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
9975 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
9977 def get_version_info(self):
9978 r"""get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
9979 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
9980 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopologyBase
9983 r"""__str__(CHARMMResidueTopologyBase self) -> std::string"""
9984 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
9987 r"""__repr__(CHARMMResidueTopologyBase self) -> std::string"""
9988 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
9992 return _object_cast_to_CHARMMResidueTopologyBase(o)
9996 _IMP_atom.CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
9997 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
9998 r"""Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
10000 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10002 def __init__(self, *args):
10004 __init__(CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
10005 __init__(CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
10007 _IMP_atom.CHARMMIdealResidueTopology_swiginit(self, _IMP_atom.new_CHARMMIdealResidueTopology(*args))
10009 def remove_atom(self, name):
10010 r"""remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
10011 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
10013 def set_default_first_patch(self, patch):
10014 r"""set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10015 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
10017 def set_default_last_patch(self, patch):
10018 r"""set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10019 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
10021 def get_default_first_patch(self):
10022 r"""get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
10023 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
10025 def get_default_last_patch(self):
10026 r"""get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
10027 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
10028 __swig_destroy__ = _IMP_atom.delete_CHARMMIdealResidueTopology
10031 r"""__str__(CHARMMIdealResidueTopology self) -> std::string"""
10032 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
10034 def __repr__(self):
10035 r"""__repr__(CHARMMIdealResidueTopology self) -> std::string"""
10036 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
10040 return _object_cast_to_CHARMMIdealResidueTopology(o)
10044 _IMP_atom.CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
10045 class CHARMMPatch(CHARMMResidueTopologyBase):
10046 r"""Proxy of C++ IMP::atom::CHARMMPatch class."""
10048 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10050 def __init__(self, type):
10051 r"""__init__(CHARMMPatch self, std::string type) -> CHARMMPatch"""
10052 _IMP_atom.CHARMMPatch_swiginit(self, _IMP_atom.new_CHARMMPatch(type))
10054 def add_removed_atom(self, name):
10055 r"""add_removed_atom(CHARMMPatch self, std::string name)"""
10056 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
10058 def get_number_of_removed_atoms(self):
10059 r"""get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
10060 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
10062 def get_removed_atom(self, i):
10063 r"""get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
10064 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
10066 def apply(self, *args):
10068 apply(CHARMMPatch self, CHARMMResidueTopology res)
10069 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
10071 return _IMP_atom.CHARMMPatch_apply(self, *args)
10072 __swig_destroy__ = _IMP_atom.delete_CHARMMPatch
10075 r"""__str__(CHARMMPatch self) -> std::string"""
10076 return _IMP_atom.CHARMMPatch___str__(self)
10078 def __repr__(self):
10079 r"""__repr__(CHARMMPatch self) -> std::string"""
10080 return _IMP_atom.CHARMMPatch___repr__(self)
10084 return _object_cast_to_CHARMMPatch(o)
10088 _IMP_atom.CHARMMPatch_swigregister(CHARMMPatch)
10089 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
10090 r"""Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
10092 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10094 def __init__(self, *args):
10096 __init__(CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
10097 __init__(CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
10099 _IMP_atom.CHARMMResidueTopology_swiginit(self, _IMP_atom.new_CHARMMResidueTopology(*args))
10101 def get_patched(self):
10102 r"""get_patched(CHARMMResidueTopology self) -> bool"""
10103 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
10105 def set_patched(self, patched):
10106 r"""set_patched(CHARMMResidueTopology self, bool patched)"""
10107 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
10108 __swig_destroy__ = _IMP_atom.delete_CHARMMResidueTopology
10111 r"""__str__(CHARMMResidueTopology self) -> std::string"""
10112 return _IMP_atom.CHARMMResidueTopology___str__(self)
10114 def __repr__(self):
10115 r"""__repr__(CHARMMResidueTopology self) -> std::string"""
10116 return _IMP_atom.CHARMMResidueTopology___repr__(self)
10120 return _object_cast_to_CHARMMResidueTopology(o)
10124 _IMP_atom.CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
10125 class CHARMMAtom(Atom):
10126 r"""Proxy of C++ IMP::atom::CHARMMAtom class."""
10128 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10130 def __init__(self, *args):
10132 __init__(CHARMMAtom self) -> CHARMMAtom
10133 __init__(CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
10134 __init__(CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
10136 _IMP_atom.CHARMMAtom_swiginit(self, _IMP_atom.new_CHARMMAtom(*args))
10138 def show(self, *args):
10139 r"""show(CHARMMAtom self, _ostream out=std::cout)"""
10140 return _IMP_atom.CHARMMAtom_show(self, *args)
10143 def setup_particle(*args):
10145 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
10146 setup_particle(_ParticleAdaptor pa, IMP::String charmm_type) -> CHARMMAtom
10148 return _IMP_atom.CHARMMAtom_setup_particle(*args)
10150 def get_charmm_type(self):
10151 r"""get_charmm_type(CHARMMAtom self) -> IMP::String"""
10152 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
10154 def set_charmm_type(self, t):
10155 r"""set_charmm_type(CHARMMAtom self, IMP::String t)"""
10156 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
10159 def get_is_setup(*args):
10161 get_is_setup(_ParticleAdaptor p) -> bool
10162 get_is_setup(Model m, ParticleIndex pi) -> bool
10164 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
10167 def get_charmm_type_key():
10168 r"""get_charmm_type_key() -> StringKey"""
10169 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
10171 def add_attribute(self, *args):
10173 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
10174 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10175 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
10176 add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10177 add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10178 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
10179 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10180 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
10182 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
10184 def get_value(self, *args):
10186 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
10187 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
10188 get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
10189 get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
10190 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
10191 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
10192 get_value(CHARMMAtom self, ObjectKey a0) -> Object
10194 return _IMP_atom.CHARMMAtom_get_value(self, *args)
10196 def set_value(self, *args):
10198 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10199 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
10200 set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
10201 set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
10202 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
10203 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10204 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
10206 return _IMP_atom.CHARMMAtom_set_value(self, *args)
10208 def remove_attribute(self, *args):
10210 remove_attribute(CHARMMAtom self, FloatKey a0)
10211 remove_attribute(CHARMMAtom self, IntKey a0)
10212 remove_attribute(CHARMMAtom self, FloatsKey a0)
10213 remove_attribute(CHARMMAtom self, IntsKey a0)
10214 remove_attribute(CHARMMAtom self, StringKey a0)
10215 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
10216 remove_attribute(CHARMMAtom self, ObjectKey a0)
10218 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
10220 def has_attribute(self, *args):
10222 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
10223 has_attribute(CHARMMAtom self, IntKey a0) -> bool
10224 has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
10225 has_attribute(CHARMMAtom self, IntsKey a0) -> bool
10226 has_attribute(CHARMMAtom self, StringKey a0) -> bool
10227 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
10228 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
10230 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
10232 def get_derivative(self, a0):
10233 r"""get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
10234 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
10236 def get_name(self):
10237 r"""get_name(CHARMMAtom self) -> std::string"""
10238 return _IMP_atom.CHARMMAtom_get_name(self)
10240 def clear_caches(self):
10241 r"""clear_caches(CHARMMAtom self)"""
10242 return _IMP_atom.CHARMMAtom_clear_caches(self)
10244 def set_name(self, a0):
10245 r"""set_name(CHARMMAtom self, std::string a0)"""
10246 return _IMP_atom.CHARMMAtom_set_name(self, a0)
10249 r"""set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
10250 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
10252 def add_to_derivative(self, a0, a1, a2):
10253 r"""add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10254 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
10256 def set_is_optimized(self, a0, a1):
10257 r"""set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
10258 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
10260 def get_is_optimized(self, a0):
10261 r"""get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
10262 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
10265 r"""get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
10266 return _IMP_atom.CHARMMAtom_get_check_level(self)
10268 def __eq__(self, *args):
10270 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
10271 __eq__(CHARMMAtom self, Particle d) -> bool
10273 return _IMP_atom.CHARMMAtom___eq__(self, *args)
10275 def __ne__(self, *args):
10277 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
10278 __ne__(CHARMMAtom self, Particle d) -> bool
10280 return _IMP_atom.CHARMMAtom___ne__(self, *args)
10282 def __le__(self, *args):
10284 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
10285 __le__(CHARMMAtom self, Particle d) -> bool
10287 return _IMP_atom.CHARMMAtom___le__(self, *args)
10289 def __lt__(self, *args):
10291 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
10292 __lt__(CHARMMAtom self, Particle d) -> bool
10294 return _IMP_atom.CHARMMAtom___lt__(self, *args)
10296 def __ge__(self, *args):
10298 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
10299 __ge__(CHARMMAtom self, Particle d) -> bool
10301 return _IMP_atom.CHARMMAtom___ge__(self, *args)
10303 def __gt__(self, *args):
10305 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
10306 __gt__(CHARMMAtom self, Particle d) -> bool
10308 return _IMP_atom.CHARMMAtom___gt__(self, *args)
10310 def __hash__(self):
10311 r"""__hash__(CHARMMAtom self) -> std::size_t"""
10312 return _IMP_atom.CHARMMAtom___hash__(self)
10315 r"""__str__(CHARMMAtom self) -> std::string"""
10316 return _IMP_atom.CHARMMAtom___str__(self)
10318 def __repr__(self):
10319 r"""__repr__(CHARMMAtom self) -> std::string"""
10320 return _IMP_atom.CHARMMAtom___repr__(self)
10322 def _get_as_binary(self):
10323 r"""_get_as_binary(CHARMMAtom self) -> PyObject *"""
10324 return _IMP_atom.CHARMMAtom__get_as_binary(self)
10326 def _set_from_binary(self, p):
10327 r"""_set_from_binary(CHARMMAtom self, PyObject * p)"""
10328 return _IMP_atom.CHARMMAtom__set_from_binary(self, p)
10330 def __getstate__(self):
10331 p = self._get_as_binary()
10332 if len(self.__dict__) > 1:
10333 d = self.__dict__.copy()
10338 def __setstate__(self, p):
10339 if not hasattr(self,
'this'):
10341 if isinstance(p, tuple):
10343 self.__dict__.update(d)
10344 return self._set_from_binary(p)
10346 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
10349 _IMP_atom.CHARMMAtom_swigregister(CHARMMAtom)
10352 r"""get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
10353 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
10356 r"""remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
10357 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
10358 class CHARMMBondParameters(object):
10359 r"""Proxy of C++ IMP::atom::CHARMMBondParameters class."""
10361 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10362 force_constant = property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set, doc=
r"""force_constant : double""")
10363 ideal = property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set, doc=
r"""ideal : double""")
10365 def __init__(self):
10366 r"""__init__(CHARMMBondParameters self) -> CHARMMBondParameters"""
10367 _IMP_atom.CHARMMBondParameters_swiginit(self, _IMP_atom.new_CHARMMBondParameters())
10369 def show(self, *args):
10370 r"""show(CHARMMBondParameters self, _ostream out=std::cout)"""
10371 return _IMP_atom.CHARMMBondParameters_show(self, *args)
10374 r"""__str__(CHARMMBondParameters self) -> std::string"""
10375 return _IMP_atom.CHARMMBondParameters___str__(self)
10377 def __repr__(self):
10378 r"""__repr__(CHARMMBondParameters self) -> std::string"""
10379 return _IMP_atom.CHARMMBondParameters___repr__(self)
10381 def _get_as_binary(self):
10382 r"""_get_as_binary(CHARMMBondParameters self) -> PyObject *"""
10383 return _IMP_atom.CHARMMBondParameters__get_as_binary(self)
10385 def _set_from_binary(self, p):
10386 r"""_set_from_binary(CHARMMBondParameters self, PyObject * p)"""
10387 return _IMP_atom.CHARMMBondParameters__set_from_binary(self, p)
10389 def __getstate__(self):
10390 p = self._get_as_binary()
10391 if len(self.__dict__) > 1:
10392 d = self.__dict__.copy()
10397 def __setstate__(self, p):
10398 if not hasattr(self,
'this'):
10400 if isinstance(p, tuple):
10402 self.__dict__.update(d)
10403 return self._set_from_binary(p)
10405 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
10408 _IMP_atom.CHARMMBondParameters_swigregister(CHARMMBondParameters)
10409 class CHARMMDihedralParameters(object):
10410 r"""Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
10412 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10413 force_constant = property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set, doc=
r"""force_constant : double""")
10414 multiplicity = property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set, doc=
r"""multiplicity : int""")
10415 ideal = property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set, doc=
r"""ideal : double""")
10417 def __init__(self):
10418 r"""__init__(CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
10419 _IMP_atom.CHARMMDihedralParameters_swiginit(self, _IMP_atom.new_CHARMMDihedralParameters())
10421 def show(self, *args):
10422 r"""show(CHARMMDihedralParameters self, _ostream out=std::cout)"""
10423 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
10426 r"""__str__(CHARMMDihedralParameters self) -> std::string"""
10427 return _IMP_atom.CHARMMDihedralParameters___str__(self)
10429 def __repr__(self):
10430 r"""__repr__(CHARMMDihedralParameters self) -> std::string"""
10431 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
10433 def _get_as_binary(self):
10434 r"""_get_as_binary(CHARMMDihedralParameters self) -> PyObject *"""
10435 return _IMP_atom.CHARMMDihedralParameters__get_as_binary(self)
10437 def _set_from_binary(self, p):
10438 r"""_set_from_binary(CHARMMDihedralParameters self, PyObject * p)"""
10439 return _IMP_atom.CHARMMDihedralParameters__set_from_binary(self, p)
10441 def __getstate__(self):
10442 p = self._get_as_binary()
10443 if len(self.__dict__) > 1:
10444 d = self.__dict__.copy()
10449 def __setstate__(self, p):
10450 if not hasattr(self,
'this'):
10452 if isinstance(p, tuple):
10454 self.__dict__.update(d)
10455 return self._set_from_binary(p)
10457 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
10460 _IMP_atom.CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
10461 class CHARMMParameters(ForceFieldParameters):
10462 r"""Proxy of C++ IMP::atom::CHARMMParameters class."""
10464 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10466 def __init__(self, *args):
10467 r"""__init__(CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name=IMP::TextInput(), bool translate_names_to_pdb=False) -> CHARMMParameters"""
10468 _IMP_atom.CHARMMParameters_swiginit(self, _IMP_atom.new_CHARMMParameters(*args))
10470 def add_residue_topology(self, res):
10471 r"""add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
10472 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
10474 def get_residue_topology(self, type):
10475 r"""get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
10476 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
10478 def add_patch(self, patch):
10479 r"""add_patch(CHARMMParameters self, CHARMMPatch patch)"""
10480 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
10482 def get_patch(self, name):
10483 r"""get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
10484 return _IMP_atom.CHARMMParameters_get_patch(self, name)
10486 def create_topology(self, hierarchy):
10487 r"""create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
10488 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
10490 def get_bond_parameters(self, type1, type2):
10491 r"""get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
10492 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
10494 def get_angle_parameters(self, type1, type2, type3):
10495 r"""get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
10496 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
10498 def get_dihedral_parameters(self, type1, type2, type3, type4):
10499 r"""get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
10500 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
10502 def get_improper_parameters(self, type1, type2, type3, type4):
10503 r"""get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
10504 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
10506 def create_angles(self, bonds):
10507 r"""create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
10508 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
10510 def create_dihedrals(self, bonds):
10511 r"""create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
10512 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
10514 def get_version_info(self):
10515 r"""get_version_info(CHARMMParameters self) -> VersionInfo"""
10516 return _IMP_atom.CHARMMParameters_get_version_info(self)
10517 __swig_destroy__ = _IMP_atom.delete_CHARMMParameters
10520 r"""__str__(CHARMMParameters self) -> std::string"""
10521 return _IMP_atom.CHARMMParameters___str__(self)
10523 def __repr__(self):
10524 r"""__repr__(CHARMMParameters self) -> std::string"""
10525 return _IMP_atom.CHARMMParameters___repr__(self)
10529 return _object_cast_to_CHARMMParameters(o)
10533 _IMP_atom.CHARMMParameters_swigregister(CHARMMParameters)
10536 r"""get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
10537 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
10540 r"""get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
10541 return _IMP_atom.get_all_atom_CHARMM_parameters()
10543 r"""Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
10545 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10546 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)
10547 def __set_residues(self, obj): IMP._list_util.set_varlist(self.residues, obj)
10548 def __del_residues(self): IMP._list_util.del_varlist(self.residues)
10549 residues = property(__get_residues, __set_residues, __del_residues, doc=
"List of ##ucnames")
10551 def remove_residue(self, d):
10552 r"""remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
10553 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
10555 def _python_index_residue(self, d, start, stop):
10556 r"""_python_index_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
10557 return _IMP_atom.CHARMMSegmentTopology__python_index_residue(self, d, start, stop)
10559 def remove_residues(self, d):
10560 r"""remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
10561 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
10563 def set_residues(self, ps):
10564 r"""set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
10565 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
10567 def set_residues_order(self, objs):
10568 r"""set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
10569 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
10571 def add_residue(self, obj):
10572 r"""add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
10573 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
10575 def add_residues(self, objs):
10576 r"""add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
10577 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
10579 def clear_residues(self):
10580 r"""clear_residues(CHARMMSegmentTopology self)"""
10581 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
10583 def get_number_of_residues(self):
10584 r"""get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
10585 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
10587 def get_has_residues(self):
10588 r"""get_has_residues(CHARMMSegmentTopology self) -> bool"""
10589 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
10592 r"""get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
10593 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
10595 def get_residues(self):
10596 r"""get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
10597 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
10599 def erase_residue(self, i):
10600 r"""erase_residue(CHARMMSegmentTopology self, unsigned int i)"""
10601 return _IMP_atom.CHARMMSegmentTopology_erase_residue(self, i)
10603 def reserve_residues(self, sz):
10604 r"""reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
10605 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
10607 def get_version_info(self):
10608 r"""get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
10609 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
10610 __swig_destroy__ = _IMP_atom.delete_CHARMMSegmentTopology
10612 def __init__(self, *args):
10613 r"""__init__(CHARMMSegmentTopology self, std::string name="CHARMM segment topology %1%") -> CHARMMSegmentTopology"""
10614 _IMP_atom.CHARMMSegmentTopology_swiginit(self, _IMP_atom.new_CHARMMSegmentTopology(*args))
10616 def apply_default_patches(self, ff):
10617 r"""apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
10618 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
10621 r"""__str__(CHARMMSegmentTopology self) -> std::string"""
10622 return _IMP_atom.CHARMMSegmentTopology___str__(self)
10624 def __repr__(self):
10625 r"""__repr__(CHARMMSegmentTopology self) -> std::string"""
10626 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
10630 return _object_cast_to_CHARMMSegmentTopology(o)
10634 _IMP_atom.CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
10636 r"""Proxy of C++ IMP::atom::CHARMMTopology class."""
10638 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10640 def __init__(self, *args):
10641 r"""__init__(CHARMMTopology self, CHARMMParameters force_field, std::string name="CHARMM topology %1%") -> CHARMMTopology"""
10642 _IMP_atom.CHARMMTopology_swiginit(self, _IMP_atom.new_CHARMMTopology(*args))
10644 def get_parameters(self):
10645 r"""get_parameters(CHARMMTopology self) -> CHARMMParameters"""
10646 return _IMP_atom.CHARMMTopology_get_parameters(self)
10648 def add_sequence(self, sequence):
10649 r"""add_sequence(CHARMMTopology self, std::string sequence)"""
10650 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
10652 def apply_default_patches(self):
10653 r"""apply_default_patches(CHARMMTopology self)"""
10654 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
10656 def create_hierarchy(self, model):
10657 r"""create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
10658 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
10660 def add_atom_types(self, hierarchy):
10661 r"""add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
10662 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
10664 def add_coordinates(self, hierarchy):
10665 r"""add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
10666 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
10668 def add_missing_atoms(self, hierarchy):
10669 r"""add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
10670 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
10672 def setup_hierarchy(self, hierarchy):
10673 r"""setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
10674 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
10676 def add_charges(self, hierarchy):
10677 r"""add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
10678 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
10681 r"""add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
10682 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
10684 def add_dihedrals(self, hierarchy):
10685 r"""add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
10686 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
10688 def add_impropers(self, hierarchy):
10689 r"""add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
10690 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
10691 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)
10692 def __set_segments(self, obj): IMP._list_util.set_varlist(self.segments, obj)
10693 def __del_segments(self): IMP._list_util.del_varlist(self.segments)
10694 segments = property(__get_segments, __set_segments, __del_segments, doc=
"List of ##ucnames")
10696 def remove_segment(self, d):
10697 r"""remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
10698 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
10700 def _python_index_segment(self, d, start, stop):
10701 r"""_python_index_segment(CHARMMTopology self, CHARMMSegmentTopology d, unsigned int start, unsigned int stop) -> unsigned int"""
10702 return _IMP_atom.CHARMMTopology__python_index_segment(self, d, start, stop)
10704 def remove_segments(self, d):
10705 r"""remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
10706 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
10708 def set_segments(self, ps):
10709 r"""set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
10710 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
10712 def set_segments_order(self, objs):
10713 r"""set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
10714 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
10716 def add_segment(self, obj):
10717 r"""add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
10718 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
10720 def add_segments(self, objs):
10721 r"""add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
10722 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
10724 def clear_segments(self):
10725 r"""clear_segments(CHARMMTopology self)"""
10726 return _IMP_atom.CHARMMTopology_clear_segments(self)
10728 def get_number_of_segments(self):
10729 r"""get_number_of_segments(CHARMMTopology self) -> unsigned int"""
10730 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
10732 def get_has_segments(self):
10733 r"""get_has_segments(CHARMMTopology self) -> bool"""
10734 return _IMP_atom.CHARMMTopology_get_has_segments(self)
10737 r"""get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
10738 return _IMP_atom.CHARMMTopology_get_segment(self, i)
10740 def get_segments(self):
10741 r"""get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
10742 return _IMP_atom.CHARMMTopology_get_segments(self)
10744 def erase_segment(self, i):
10745 r"""erase_segment(CHARMMTopology self, unsigned int i)"""
10746 return _IMP_atom.CHARMMTopology_erase_segment(self, i)
10748 def reserve_segments(self, sz):
10749 r"""reserve_segments(CHARMMTopology self, unsigned int sz)"""
10750 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
10752 def get_version_info(self):
10753 r"""get_version_info(CHARMMTopology self) -> VersionInfo"""
10754 return _IMP_atom.CHARMMTopology_get_version_info(self)
10755 __swig_destroy__ = _IMP_atom.delete_CHARMMTopology
10758 r"""__str__(CHARMMTopology self) -> std::string"""
10759 return _IMP_atom.CHARMMTopology___str__(self)
10761 def __repr__(self):
10762 r"""__repr__(CHARMMTopology self) -> std::string"""
10763 return _IMP_atom.CHARMMTopology___repr__(self)
10767 return _object_cast_to_CHARMMTopology(o)
10771 _IMP_atom.CHARMMTopology_swigregister(CHARMMTopology)
10773 r"""Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
10775 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10777 def __init__(self, *args):
10779 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
10780 __init__(CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
10782 _IMP_atom.CHARMMStereochemistryRestraint_swiginit(self, _IMP_atom.new_CHARMMStereochemistryRestraint(*args))
10784 def get_pair_filter(self):
10785 r"""get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
10786 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
10788 def get_full_pair_filter(self):
10789 r"""get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
10790 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
10792 def do_get_inputs(self):
10793 r"""do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
10794 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
10796 def get_version_info(self):
10797 r"""get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
10798 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
10799 __swig_destroy__ = _IMP_atom.delete_CHARMMStereochemistryRestraint
10802 r"""__str__(CHARMMStereochemistryRestraint self) -> std::string"""
10803 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
10805 def __repr__(self):
10806 r"""__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
10807 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
10811 return _object_cast_to_CHARMMStereochemistryRestraint(o)
10815 _IMP_atom.CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
10818 r"""add_bonds(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters())"""
10819 return _IMP_atom.add_bonds(*args)
10822 r"""add_radii(Hierarchy d, ForceFieldParameters ffp=IMP::atom::get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))"""
10823 return _IMP_atom.add_radii(*args)
10824 ALBER = _IMP_atom.ALBER
10826 HARPAZ = _IMP_atom.HARPAZ
10828 ANDERSSON = _IMP_atom.ANDERSSON
10830 TSAI = _IMP_atom.TSAI
10832 QUILLIN = _IMP_atom.QUILLIN
10834 SQUIRE = _IMP_atom.SQUIRE
10838 r"""get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
10839 return _IMP_atom.get_protein_density_from_reference(densityReference)
10842 r"""get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
10843 return _IMP_atom.get_volume_from_mass(*args)
10846 r"""get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref=ALBER) -> double"""
10847 return _IMP_atom.get_mass_from_volume(*args)
10850 r"""get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
10851 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
10854 r"""get_volume_from_residue_type(ResidueType rt) -> double"""
10855 return _IMP_atom.get_volume_from_residue_type(rt)
10858 r"""get_molarity(double n, double volume) -> double"""
10859 return _IMP_atom.get_molarity(n, volume)
10861 def get_kd(na, nb, nab, volume):
10862 r"""get_kd(double na, double nb, double nab, double volume) -> double"""
10863 return _IMP_atom.get_kd(na, nb, nab, volume)
10866 r"""get_einstein_diffusion_coefficient(double r, double temp=-1) -> double"""
10867 return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
10870 r"""get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double"""
10871 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
10875 get_diffusion_length(double D, double t) -> double
10876 get_diffusion_length(double D, double force, double t, double temp=-1) -> double
10878 return _IMP_atom.get_diffusion_length(*args)
10881 r"""get_diffusion_angle(double D, double dtfs) -> double"""
10882 return _IMP_atom.get_diffusion_angle(D, dtfs)
10886 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
10887 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
10889 return _IMP_atom.get_diffusion_coefficient(*args)
10892 r"""get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
10893 return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
10895 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
10896 r"""get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
10897 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
10900 r"""get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
10901 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
10904 r"""get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
10905 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
10907 r"""Proxy of C++ IMP::atom::EzRestraint class."""
10909 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10911 def __init__(self, m, ps):
10912 r"""__init__(EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
10913 _IMP_atom.EzRestraint_swiginit(self, _IMP_atom.new_EzRestraint(m, ps))
10915 def get_version_info(self):
10916 r"""get_version_info(EzRestraint self) -> VersionInfo"""
10917 return _IMP_atom.EzRestraint_get_version_info(self)
10918 __swig_destroy__ = _IMP_atom.delete_EzRestraint
10921 r"""__str__(EzRestraint self) -> std::string"""
10922 return _IMP_atom.EzRestraint___str__(self)
10924 def __repr__(self):
10925 r"""__repr__(EzRestraint self) -> std::string"""
10926 return _IMP_atom.EzRestraint___repr__(self)
10930 return _object_cast_to_EzRestraint(o)
10934 _IMP_atom.EzRestraint_swigregister(EzRestraint)
10938 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
10939 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
10941 return _IMP_atom.create_protein(*args)
10945 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
10946 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
10948 return _IMP_atom.create_simplified_along_backbone(*args)
10951 r"""create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
10952 return _IMP_atom.create_simplified_from_volume(h, resolution)
10955 r"""create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
10956 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
10958 def get_residue_indexes(h):
10959 r"""get_residue_indexes(Hierarchy h) -> IMP::Ints"""
10960 return _IMP_atom.get_residue_indexes(h)
10962 def get_residue_type(*args):
10964 get_residue_type(char c) -> ResidueType
10965 get_residue_type(Hierarchy h) -> ResidueType
10967 return _IMP_atom.get_residue_type(*args)
10969 def get_atom_type(h):
10970 r"""get_atom_type(Hierarchy h) -> AtomType"""
10971 return _IMP_atom.get_atom_type(h)
10973 def get_domain_name(h):
10974 r"""get_domain_name(Hierarchy h) -> std::string"""
10975 return _IMP_atom.get_domain_name(h)
10979 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
10980 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
10982 return _IMP_atom.create_excluded_volume_restraint(*args)
10986 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
10987 setup_as_approximation(Hierarchy h, double resolution=-1)
10989 return _IMP_atom.setup_as_approximation(*args)
10990 class _HierarchyTreeVertexIndex(object):
10991 r"""Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
10993 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10994 __repr__ = _swig_repr
10996 def __init__(self):
10997 r"""__init__(_HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
10998 _IMP_atom._HierarchyTreeVertexIndex_swiginit(self, _IMP_atom.new__HierarchyTreeVertexIndex())
10999 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
11002 _IMP_atom._HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
11004 def show_as_graphviz(name, out):
11005 r"""show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
11006 return _IMP_atom.show_as_graphviz(name, out)
11008 def get_vertex_index(g):
11009 r"""get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
11010 return _IMP_atom.get_vertex_index(g)
11013 r"""get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
11014 return _IMP_atom.get_hierarchy_tree(h)
11016 r"""Proxy of C++ IMP::atom::HierarchyGeometry class."""
11018 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11020 def __init__(self, d, resolution=0):
11021 r"""__init__(HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry"""
11022 _IMP_atom.HierarchyGeometry_swiginit(self, _IMP_atom.new_HierarchyGeometry(d, resolution))
11024 def get_version_info(self):
11025 r"""get_version_info(HierarchyGeometry self) -> VersionInfo"""
11026 return _IMP_atom.HierarchyGeometry_get_version_info(self)
11027 __swig_destroy__ = _IMP_atom.delete_HierarchyGeometry
11030 r"""__str__(HierarchyGeometry self) -> std::string"""
11031 return _IMP_atom.HierarchyGeometry___str__(self)
11033 def __repr__(self):
11034 r"""__repr__(HierarchyGeometry self) -> std::string"""
11035 return _IMP_atom.HierarchyGeometry___repr__(self)
11039 return _object_cast_to_HierarchyGeometry(o)
11043 _IMP_atom.HierarchyGeometry_swigregister(HierarchyGeometry)
11045 r"""Proxy of C++ IMP::atom::HierarchiesGeometry class."""
11047 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11049 def __init__(self, sc, resolution=-1):
11050 r"""__init__(HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry"""
11051 _IMP_atom.HierarchiesGeometry_swiginit(self, _IMP_atom.new_HierarchiesGeometry(sc, resolution))
11053 def get_version_info(self):
11054 r"""get_version_info(HierarchiesGeometry self) -> VersionInfo"""
11055 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
11056 __swig_destroy__ = _IMP_atom.delete_HierarchiesGeometry
11059 r"""__str__(HierarchiesGeometry self) -> std::string"""
11060 return _IMP_atom.HierarchiesGeometry___str__(self)
11062 def __repr__(self):
11063 r"""__repr__(HierarchiesGeometry self) -> std::string"""
11064 return _IMP_atom.HierarchiesGeometry___repr__(self)
11068 return _object_cast_to_HierarchiesGeometry(o)
11072 _IMP_atom.HierarchiesGeometry_swigregister(HierarchiesGeometry)
11076 transform(Hierarchy h, Transformation3D tr)
11077 transform(Hierarchy h, Transformation3D tr)
11079 return _IMP_atom.transform(*args)
11080 class DopePairScore(_ADopeBase):
11081 r"""Proxy of C++ IMP::atom::DopePairScore class."""
11083 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11085 def __init__(self, *args):
11087 __init__(DopePairScore self, double threshold=std::numeric_limits< double >::max()) -> DopePairScore
11088 __init__(DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
11090 _IMP_atom.DopePairScore_swiginit(self, _IMP_atom.new_DopePairScore(*args))
11093 r"""__str__(DopePairScore self) -> std::string"""
11094 return _IMP_atom.DopePairScore___str__(self)
11096 def __repr__(self):
11097 r"""__repr__(DopePairScore self) -> std::string"""
11098 return _IMP_atom.DopePairScore___repr__(self)
11102 return _object_cast_to_DopePairScore(o)
11104 __swig_destroy__ = _IMP_atom.delete_DopePairScore
11107 _IMP_atom.DopePairScore_swigregister(DopePairScore)
11110 r"""add_dope_score_data(Hierarchy h)"""
11111 return _IMP_atom.add_dope_score_data(h)
11112 class LoopStatisticalPairScore(_ALoopStatisticalBase):
11113 r"""Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
11115 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11117 def __init__(self, *args):
11119 __init__(LoopStatisticalPairScore self, double threshold=std::numeric_limits< double >::max()) -> LoopStatisticalPairScore
11120 __init__(LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
11122 _IMP_atom.LoopStatisticalPairScore_swiginit(self, _IMP_atom.new_LoopStatisticalPairScore(*args))
11125 r"""__str__(LoopStatisticalPairScore self) -> std::string"""
11126 return _IMP_atom.LoopStatisticalPairScore___str__(self)
11128 def __repr__(self):
11129 r"""__repr__(LoopStatisticalPairScore self) -> std::string"""
11130 return _IMP_atom.LoopStatisticalPairScore___repr__(self)
11134 return _object_cast_to_LoopStatisticalPairScore(o)
11136 __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
11139 _IMP_atom.LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
11142 r"""add_loop_statistical_score_data(Hierarchy h)"""
11143 return _IMP_atom.add_loop_statistical_score_data(h)
11144 class OrientedSoapPairScore(_OrientedSoapBase):
11145 r"""Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
11147 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11149 def __init__(self, library):
11150 r"""__init__(OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
11151 _IMP_atom.OrientedSoapPairScore_swiginit(self, _IMP_atom.new_OrientedSoapPairScore(library))
11153 def get_pair_filter(self):
11154 r"""get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
11155 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
11158 r"""__str__(OrientedSoapPairScore self) -> std::string"""
11159 return _IMP_atom.OrientedSoapPairScore___str__(self)
11161 def __repr__(self):
11162 r"""__repr__(OrientedSoapPairScore self) -> std::string"""
11163 return _IMP_atom.OrientedSoapPairScore___repr__(self)
11167 return _object_cast_to_OrientedSoapPairScore(o)
11169 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
11172 _IMP_atom.OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
11174 r"""Proxy of C++ IMP::atom::SameResiduePairFilter class."""
11176 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11178 def __init__(self):
11179 r"""__init__(SameResiduePairFilter self) -> SameResiduePairFilter"""
11180 _IMP_atom.SameResiduePairFilter_swiginit(self, _IMP_atom.new_SameResiduePairFilter())
11182 def do_get_inputs(self, m, pis):
11183 r"""do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
11184 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
11186 def get_value(self, *args):
11188 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
11189 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
11191 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
11193 def get_value_index(self, *args):
11195 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
11196 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
11198 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
11200 def get_version_info(self):
11201 r"""get_version_info(SameResiduePairFilter self) -> VersionInfo"""
11202 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
11203 __swig_destroy__ = _IMP_atom.delete_SameResiduePairFilter
11206 r"""__str__(SameResiduePairFilter self) -> std::string"""
11207 return _IMP_atom.SameResiduePairFilter___str__(self)
11209 def __repr__(self):
11210 r"""__repr__(SameResiduePairFilter self) -> std::string"""
11211 return _IMP_atom.SameResiduePairFilter___repr__(self)
11215 return _object_cast_to_SameResiduePairFilter(o)
11219 _IMP_atom.SameResiduePairFilter_swigregister(SameResiduePairFilter)
11221 r"""Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
11223 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11225 def __init__(self, m, pis):
11226 r"""__init__(RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
11227 _IMP_atom.RemoveRigidMotionOptimizerState_swiginit(self, _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis))
11229 def set_particles(self, pis):
11230 r"""set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
11231 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
11233 def remove_rigid_motion(self):
11234 r"""remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
11235 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
11237 def get_version_info(self):
11238 r"""get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
11239 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
11240 __swig_destroy__ = _IMP_atom.delete_RemoveRigidMotionOptimizerState
11243 r"""__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
11244 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
11246 def __repr__(self):
11247 r"""__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
11248 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
11252 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
11256 _IMP_atom.RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
11258 r"""Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
11260 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11262 def __init__(self, pis, temperature, tau):
11263 r"""__init__(BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
11264 _IMP_atom.BerendsenThermostatOptimizerState_swiginit(self, _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau))
11266 def set_particles(self, pis):
11267 r"""set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
11268 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
11270 def get_temperature(self):
11271 r"""get_temperature(BerendsenThermostatOptimizerState self) -> double"""
11272 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
11275 r"""get_tau(BerendsenThermostatOptimizerState self) -> double"""
11276 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
11278 def set_temperature(self, temperature):
11279 r"""set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
11280 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
11282 def set_tau(self, tau):
11283 r"""set_tau(BerendsenThermostatOptimizerState self, double tau)"""
11284 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
11286 def rescale_velocities(self):
11287 r"""rescale_velocities(BerendsenThermostatOptimizerState self)"""
11288 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
11290 def get_version_info(self):
11291 r"""get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
11292 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
11293 __swig_destroy__ = _IMP_atom.delete_BerendsenThermostatOptimizerState
11296 r"""__str__(BerendsenThermostatOptimizerState self) -> std::string"""
11297 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
11299 def __repr__(self):
11300 r"""__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
11301 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
11305 return _object_cast_to_BerendsenThermostatOptimizerState(o)
11309 _IMP_atom.BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
11311 r"""Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
11313 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11315 def __init__(self, m, pis, temperature, gamma):
11316 r"""__init__(LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
11317 _IMP_atom.LangevinThermostatOptimizerState_swiginit(self, _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma))
11319 def set_particles(self, pis):
11320 r"""set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
11321 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
11323 def get_temperature(self):
11324 r"""get_temperature(LangevinThermostatOptimizerState self) -> double"""
11325 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
11327 def get_gamma(self):
11328 r"""get_gamma(LangevinThermostatOptimizerState self) -> double"""
11329 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
11331 def set_temperature(self, temperature):
11332 r"""set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
11333 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
11335 def set_gamma(self, gamma):
11336 r"""set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
11337 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
11339 def rescale_velocities(self):
11340 r"""rescale_velocities(LangevinThermostatOptimizerState self)"""
11341 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
11343 def get_version_info(self):
11344 r"""get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
11345 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
11346 __swig_destroy__ = _IMP_atom.delete_LangevinThermostatOptimizerState
11349 r"""__str__(LangevinThermostatOptimizerState self) -> std::string"""
11350 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
11352 def __repr__(self):
11353 r"""__repr__(LangevinThermostatOptimizerState self) -> std::string"""
11354 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
11358 return _object_cast_to_LangevinThermostatOptimizerState(o)
11362 _IMP_atom.LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
11364 r"""Proxy of C++ IMP::atom::PDBSelector class."""
11366 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11368 def __init__(self, name):
11369 r"""__init__(PDBSelector self, std::string name) -> PDBSelector"""
11370 if self.__class__ == PDBSelector:
11374 _IMP_atom.PDBSelector_swiginit(self, _IMP_atom.new_PDBSelector(_self, name))
11376 if self.__class__ != PDBSelector:
11377 _director_objects.register(self)
11382 def get_is_selected(self, pdb_line):
11383 r"""get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
11384 return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
11385 __swig_destroy__ = _IMP_atom.delete_PDBSelector
11388 r"""__str__(PDBSelector self) -> std::string"""
11389 return _IMP_atom.PDBSelector___str__(self)
11391 def __repr__(self):
11392 r"""__repr__(PDBSelector self) -> std::string"""
11393 return _IMP_atom.PDBSelector___repr__(self)
11397 return _object_cast_to_PDBSelector(o)
11400 def get_type_name(self):
11401 return self.__class__.__name__
11402 def do_show(self, out):
11404 def get_version_info(self):
11405 if"IMP::atom" ==
"IMP":
11406 return VersionInfo(self.__module__,
11413 return _object_cast_to_PDBSelector(o)
11416 def __and__(self, s):
11417 return AndPDBSelector(self, s)
11418 def __or__(self, s):
11419 return OrPDBSelector(self, s)
11420 def __xor__(self, s):
11421 return XorPDBSelector(self, s)
11422 def __invert__(self):
11423 return NotPDBSelector(self)
11424 def __sub__(self, s):
11425 return AndPDBSelector(self, NotPDBSelector(s))
11427 def __disown__(self):
11429 _IMP_atom.disown_PDBSelector(self)
11430 return weakref.proxy(self)
11432 def do_destroy(self):
11433 r"""do_destroy(PDBSelector self)"""
11434 return _IMP_atom.PDBSelector_do_destroy(self)
11437 _IMP_atom.PDBSelector_swigregister(PDBSelector)
11438 class NonAlternativePDBSelector(PDBSelector):
11439 r"""Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
11441 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11443 def __init__(self, *args):
11444 r"""__init__(NonAlternativePDBSelector self, std::string name="NonAlternativePDBSelector%1%") -> NonAlternativePDBSelector"""
11445 _IMP_atom.NonAlternativePDBSelector_swiginit(self, _IMP_atom.new_NonAlternativePDBSelector(*args))
11447 def get_version_info(self):
11448 r"""get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
11449 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
11450 __swig_destroy__ = _IMP_atom.delete_NonAlternativePDBSelector
11453 r"""__str__(NonAlternativePDBSelector self) -> std::string"""
11454 return _IMP_atom.NonAlternativePDBSelector___str__(self)
11456 def __repr__(self):
11457 r"""__repr__(NonAlternativePDBSelector self) -> std::string"""
11458 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
11462 return _object_cast_to_NonAlternativePDBSelector(o)
11466 _IMP_atom.NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
11467 class ATOMPDBSelector(NonAlternativePDBSelector):
11468 r"""Proxy of C++ IMP::atom::ATOMPDBSelector class."""
11470 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11472 def __init__(self, *args):
11473 r"""__init__(ATOMPDBSelector self, std::string name="ATOMPDBSelector%1%") -> ATOMPDBSelector"""
11474 _IMP_atom.ATOMPDBSelector_swiginit(self, _IMP_atom.new_ATOMPDBSelector(*args))
11475 __swig_destroy__ = _IMP_atom.delete_ATOMPDBSelector
11478 r"""__str__(ATOMPDBSelector self) -> std::string"""
11479 return _IMP_atom.ATOMPDBSelector___str__(self)
11481 def __repr__(self):
11482 r"""__repr__(ATOMPDBSelector self) -> std::string"""
11483 return _IMP_atom.ATOMPDBSelector___repr__(self)
11487 return _object_cast_to_ATOMPDBSelector(o)
11491 _IMP_atom.ATOMPDBSelector_swigregister(ATOMPDBSelector)
11492 class CAlphaPDBSelector(NonAlternativePDBSelector):
11493 r"""Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
11495 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11497 def __init__(self, *args):
11498 r"""__init__(CAlphaPDBSelector self, std::string name="CAlphaPDBSelector%1%") -> CAlphaPDBSelector"""
11499 _IMP_atom.CAlphaPDBSelector_swiginit(self, _IMP_atom.new_CAlphaPDBSelector(*args))
11500 __swig_destroy__ = _IMP_atom.delete_CAlphaPDBSelector
11503 r"""__str__(CAlphaPDBSelector self) -> std::string"""
11504 return _IMP_atom.CAlphaPDBSelector___str__(self)
11506 def __repr__(self):
11507 r"""__repr__(CAlphaPDBSelector self) -> std::string"""
11508 return _IMP_atom.CAlphaPDBSelector___repr__(self)
11512 return _object_cast_to_CAlphaPDBSelector(o)
11516 _IMP_atom.CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
11517 class CBetaPDBSelector(NonAlternativePDBSelector):
11518 r"""Proxy of C++ IMP::atom::CBetaPDBSelector class."""
11520 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11522 def __init__(self, *args):
11523 r"""__init__(CBetaPDBSelector self, std::string name="CBetaPDBSelector%1%") -> CBetaPDBSelector"""
11524 _IMP_atom.CBetaPDBSelector_swiginit(self, _IMP_atom.new_CBetaPDBSelector(*args))
11525 __swig_destroy__ = _IMP_atom.delete_CBetaPDBSelector
11528 r"""__str__(CBetaPDBSelector self) -> std::string"""
11529 return _IMP_atom.CBetaPDBSelector___str__(self)
11531 def __repr__(self):
11532 r"""__repr__(CBetaPDBSelector self) -> std::string"""
11533 return _IMP_atom.CBetaPDBSelector___repr__(self)
11537 return _object_cast_to_CBetaPDBSelector(o)
11541 _IMP_atom.CBetaPDBSelector_swigregister(CBetaPDBSelector)
11542 class AtomTypePDBSelector(PDBSelector):
11543 r"""Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
11545 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11547 def __init__(self, *args):
11548 r"""__init__(AtomTypePDBSelector self, IMP::Strings atom_types, std::string name="AtomTypePDBSelector%1%") -> AtomTypePDBSelector"""
11549 _IMP_atom.AtomTypePDBSelector_swiginit(self, _IMP_atom.new_AtomTypePDBSelector(*args))
11551 def get_version_info(self):
11552 r"""get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
11553 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
11554 __swig_destroy__ = _IMP_atom.delete_AtomTypePDBSelector
11557 r"""__str__(AtomTypePDBSelector self) -> std::string"""
11558 return _IMP_atom.AtomTypePDBSelector___str__(self)
11560 def __repr__(self):
11561 r"""__repr__(AtomTypePDBSelector self) -> std::string"""
11562 return _IMP_atom.AtomTypePDBSelector___repr__(self)
11566 return _object_cast_to_AtomTypePDBSelector(o)
11570 _IMP_atom.AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
11571 class ResidueTypePDBSelector(PDBSelector):
11572 r"""Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
11574 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11576 def __init__(self, *args):
11577 r"""__init__(ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name="ResidueTypePDBSelector%1%") -> ResidueTypePDBSelector"""
11578 _IMP_atom.ResidueTypePDBSelector_swiginit(self, _IMP_atom.new_ResidueTypePDBSelector(*args))
11580 def get_version_info(self):
11581 r"""get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
11582 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
11583 __swig_destroy__ = _IMP_atom.delete_ResidueTypePDBSelector
11586 r"""__str__(ResidueTypePDBSelector self) -> std::string"""
11587 return _IMP_atom.ResidueTypePDBSelector___str__(self)
11589 def __repr__(self):
11590 r"""__repr__(ResidueTypePDBSelector self) -> std::string"""
11591 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
11595 return _object_cast_to_ResidueTypePDBSelector(o)
11599 _IMP_atom.ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
11600 class CPDBSelector(NonAlternativePDBSelector):
11601 r"""Proxy of C++ IMP::atom::CPDBSelector class."""
11603 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11605 def __init__(self, *args):
11606 r"""__init__(CPDBSelector self, std::string name="CPDBSelector%1%") -> CPDBSelector"""
11607 _IMP_atom.CPDBSelector_swiginit(self, _IMP_atom.new_CPDBSelector(*args))
11608 __swig_destroy__ = _IMP_atom.delete_CPDBSelector
11611 r"""__str__(CPDBSelector self) -> std::string"""
11612 return _IMP_atom.CPDBSelector___str__(self)
11614 def __repr__(self):
11615 r"""__repr__(CPDBSelector self) -> std::string"""
11616 return _IMP_atom.CPDBSelector___repr__(self)
11620 return _object_cast_to_CPDBSelector(o)
11624 _IMP_atom.CPDBSelector_swigregister(CPDBSelector)
11625 class NPDBSelector(NonAlternativePDBSelector):
11626 r"""Proxy of C++ IMP::atom::NPDBSelector class."""
11628 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11630 def __init__(self, *args):
11631 r"""__init__(NPDBSelector self, std::string name="NPDBSelector%1%") -> NPDBSelector"""
11632 _IMP_atom.NPDBSelector_swiginit(self, _IMP_atom.new_NPDBSelector(*args))
11633 __swig_destroy__ = _IMP_atom.delete_NPDBSelector
11636 r"""__str__(NPDBSelector self) -> std::string"""
11637 return _IMP_atom.NPDBSelector___str__(self)
11639 def __repr__(self):
11640 r"""__repr__(NPDBSelector self) -> std::string"""
11641 return _IMP_atom.NPDBSelector___repr__(self)
11645 return _object_cast_to_NPDBSelector(o)
11649 _IMP_atom.NPDBSelector_swigregister(NPDBSelector)
11650 class AllPDBSelector(PDBSelector):
11651 r"""Proxy of C++ IMP::atom::AllPDBSelector class."""
11653 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11655 def __init__(self, *args):
11656 r"""__init__(AllPDBSelector self, std::string name="AllPDBSelector%1%") -> AllPDBSelector"""
11657 _IMP_atom.AllPDBSelector_swiginit(self, _IMP_atom.new_AllPDBSelector(*args))
11659 def get_version_info(self):
11660 r"""get_version_info(AllPDBSelector self) -> VersionInfo"""
11661 return _IMP_atom.AllPDBSelector_get_version_info(self)
11662 __swig_destroy__ = _IMP_atom.delete_AllPDBSelector
11665 r"""__str__(AllPDBSelector self) -> std::string"""
11666 return _IMP_atom.AllPDBSelector___str__(self)
11668 def __repr__(self):
11669 r"""__repr__(AllPDBSelector self) -> std::string"""
11670 return _IMP_atom.AllPDBSelector___repr__(self)
11674 return _object_cast_to_AllPDBSelector(o)
11678 _IMP_atom.AllPDBSelector_swigregister(AllPDBSelector)
11679 class ChainPDBSelector(NonAlternativePDBSelector):
11680 r"""Proxy of C++ IMP::atom::ChainPDBSelector class."""
11682 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11683 __swig_destroy__ = _IMP_atom.delete_ChainPDBSelector
11685 def __init__(self, *args):
11686 r"""__init__(ChainPDBSelector self, std::string const & chains, std::string name="ChainPDBSelector%1%") -> ChainPDBSelector"""
11687 _IMP_atom.ChainPDBSelector_swiginit(self, _IMP_atom.new_ChainPDBSelector(*args))
11690 r"""__str__(ChainPDBSelector self) -> std::string"""
11691 return _IMP_atom.ChainPDBSelector___str__(self)
11693 def __repr__(self):
11694 r"""__repr__(ChainPDBSelector self) -> std::string"""
11695 return _IMP_atom.ChainPDBSelector___repr__(self)
11699 return _object_cast_to_ChainPDBSelector(o)
11703 _IMP_atom.ChainPDBSelector_swigregister(ChainPDBSelector)
11704 class WaterPDBSelector(NonAlternativePDBSelector):
11705 r"""Proxy of C++ IMP::atom::WaterPDBSelector class."""
11707 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11709 def __init__(self, *args):
11710 r"""__init__(WaterPDBSelector self, std::string name="WaterPDBSelector%1%") -> WaterPDBSelector"""
11711 _IMP_atom.WaterPDBSelector_swiginit(self, _IMP_atom.new_WaterPDBSelector(*args))
11712 __swig_destroy__ = _IMP_atom.delete_WaterPDBSelector
11715 r"""__str__(WaterPDBSelector self) -> std::string"""
11716 return _IMP_atom.WaterPDBSelector___str__(self)
11718 def __repr__(self):
11719 r"""__repr__(WaterPDBSelector self) -> std::string"""
11720 return _IMP_atom.WaterPDBSelector___repr__(self)
11724 return _object_cast_to_WaterPDBSelector(o)
11728 _IMP_atom.WaterPDBSelector_swigregister(WaterPDBSelector)
11729 class HydrogenPDBSelector(NonAlternativePDBSelector):
11730 r"""Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
11732 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11734 def __init__(self, *args):
11735 r"""__init__(HydrogenPDBSelector self, std::string name="HydrogenPDBSelector%1%") -> HydrogenPDBSelector"""
11736 _IMP_atom.HydrogenPDBSelector_swiginit(self, _IMP_atom.new_HydrogenPDBSelector(*args))
11737 __swig_destroy__ = _IMP_atom.delete_HydrogenPDBSelector
11740 r"""__str__(HydrogenPDBSelector self) -> std::string"""
11741 return _IMP_atom.HydrogenPDBSelector___str__(self)
11743 def __repr__(self):
11744 r"""__repr__(HydrogenPDBSelector self) -> std::string"""
11745 return _IMP_atom.HydrogenPDBSelector___repr__(self)
11749 return _object_cast_to_HydrogenPDBSelector(o)
11753 _IMP_atom.HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
11754 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
11755 r"""Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
11757 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11758 __swig_destroy__ = _IMP_atom.delete_NonWaterNonHydrogenPDBSelector
11760 def __init__(self, *args):
11762 __init__(NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
11763 __init__(NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
11765 _IMP_atom.NonWaterNonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args))
11768 r"""__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
11769 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
11771 def __repr__(self):
11772 r"""__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
11773 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
11777 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
11781 _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
11782 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
11783 r"""Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
11785 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11786 __swig_destroy__ = _IMP_atom.delete_NonHydrogenPDBSelector
11788 def __init__(self, *args):
11790 __init__(NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
11791 __init__(NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
11793 _IMP_atom.NonHydrogenPDBSelector_swiginit(self, _IMP_atom.new_NonHydrogenPDBSelector(*args))
11796 r"""__str__(NonHydrogenPDBSelector self) -> std::string"""
11797 return _IMP_atom.NonHydrogenPDBSelector___str__(self)
11799 def __repr__(self):
11800 r"""__repr__(NonHydrogenPDBSelector self) -> std::string"""
11801 return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
11805 return _object_cast_to_NonHydrogenPDBSelector(o)
11809 _IMP_atom.NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
11810 class NonWaterPDBSelector(NonAlternativePDBSelector):
11811 r"""Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
11813 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11814 __swig_destroy__ = _IMP_atom.delete_NonWaterPDBSelector
11816 def __init__(self, *args):
11818 __init__(NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
11819 __init__(NonWaterPDBSelector self) -> NonWaterPDBSelector
11821 _IMP_atom.NonWaterPDBSelector_swiginit(self, _IMP_atom.new_NonWaterPDBSelector(*args))
11824 r"""__str__(NonWaterPDBSelector self) -> std::string"""
11825 return _IMP_atom.NonWaterPDBSelector___str__(self)
11827 def __repr__(self):
11828 r"""__repr__(NonWaterPDBSelector self) -> std::string"""
11829 return _IMP_atom.NonWaterPDBSelector___repr__(self)
11833 return _object_cast_to_NonWaterPDBSelector(o)
11837 _IMP_atom.NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
11838 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
11839 r"""Proxy of C++ IMP::atom::BackbonePDBSelector class."""
11841 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11843 def __init__(self, *args):
11844 r"""__init__(BackbonePDBSelector self, std::string name="BackbonePDBSelector%1%") -> BackbonePDBSelector"""
11845 _IMP_atom.BackbonePDBSelector_swiginit(self, _IMP_atom.new_BackbonePDBSelector(*args))
11846 __swig_destroy__ = _IMP_atom.delete_BackbonePDBSelector
11849 r"""__str__(BackbonePDBSelector self) -> std::string"""
11850 return _IMP_atom.BackbonePDBSelector___str__(self)
11852 def __repr__(self):
11853 r"""__repr__(BackbonePDBSelector self) -> std::string"""
11854 return _IMP_atom.BackbonePDBSelector___repr__(self)
11858 return _object_cast_to_BackbonePDBSelector(o)
11862 _IMP_atom.BackbonePDBSelector_swigregister(BackbonePDBSelector)
11863 class PPDBSelector(NonAlternativePDBSelector):
11864 r"""Proxy of C++ IMP::atom::PPDBSelector class."""
11866 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11868 def __init__(self, *args):
11869 r"""__init__(PPDBSelector self, std::string name="PPDBSelector%1%") -> PPDBSelector"""
11870 _IMP_atom.PPDBSelector_swiginit(self, _IMP_atom.new_PPDBSelector(*args))
11871 __swig_destroy__ = _IMP_atom.delete_PPDBSelector
11874 r"""__str__(PPDBSelector self) -> std::string"""
11875 return _IMP_atom.PPDBSelector___str__(self)
11877 def __repr__(self):
11878 r"""__repr__(PPDBSelector self) -> std::string"""
11879 return _IMP_atom.PPDBSelector___repr__(self)
11883 return _object_cast_to_PPDBSelector(o)
11887 _IMP_atom.PPDBSelector_swigregister(PPDBSelector)
11888 class AndPDBSelector(PDBSelector):
11889 r"""Proxy of C++ IMP::atom::AndPDBSelector class."""
11891 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11893 def get_version_info(self):
11894 r"""get_version_info(AndPDBSelector self) -> VersionInfo"""
11895 return _IMP_atom.AndPDBSelector_get_version_info(self)
11896 __swig_destroy__ = _IMP_atom.delete_AndPDBSelector
11898 def __init__(self, a, b):
11899 r"""__init__(AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
11900 _IMP_atom.AndPDBSelector_swiginit(self, _IMP_atom.new_AndPDBSelector(a, b))
11903 r"""__str__(AndPDBSelector self) -> std::string"""
11904 return _IMP_atom.AndPDBSelector___str__(self)
11906 def __repr__(self):
11907 r"""__repr__(AndPDBSelector self) -> std::string"""
11908 return _IMP_atom.AndPDBSelector___repr__(self)
11912 return _object_cast_to_AndPDBSelector(o)
11916 _IMP_atom.AndPDBSelector_swigregister(AndPDBSelector)
11917 class OrPDBSelector(PDBSelector):
11918 r"""Proxy of C++ IMP::atom::OrPDBSelector class."""
11920 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11922 def get_version_info(self):
11923 r"""get_version_info(OrPDBSelector self) -> VersionInfo"""
11924 return _IMP_atom.OrPDBSelector_get_version_info(self)
11925 __swig_destroy__ = _IMP_atom.delete_OrPDBSelector
11927 def __init__(self, a, b):
11928 r"""__init__(OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
11929 _IMP_atom.OrPDBSelector_swiginit(self, _IMP_atom.new_OrPDBSelector(a, b))
11932 r"""__str__(OrPDBSelector self) -> std::string"""
11933 return _IMP_atom.OrPDBSelector___str__(self)
11935 def __repr__(self):
11936 r"""__repr__(OrPDBSelector self) -> std::string"""
11937 return _IMP_atom.OrPDBSelector___repr__(self)
11941 return _object_cast_to_OrPDBSelector(o)
11945 _IMP_atom.OrPDBSelector_swigregister(OrPDBSelector)
11946 class XorPDBSelector(PDBSelector):
11947 r"""Proxy of C++ IMP::atom::XorPDBSelector class."""
11949 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11951 def get_version_info(self):
11952 r"""get_version_info(XorPDBSelector self) -> VersionInfo"""
11953 return _IMP_atom.XorPDBSelector_get_version_info(self)
11954 __swig_destroy__ = _IMP_atom.delete_XorPDBSelector
11956 def __init__(self, a, b):
11957 r"""__init__(XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
11958 _IMP_atom.XorPDBSelector_swiginit(self, _IMP_atom.new_XorPDBSelector(a, b))
11961 r"""__str__(XorPDBSelector self) -> std::string"""
11962 return _IMP_atom.XorPDBSelector___str__(self)
11964 def __repr__(self):
11965 r"""__repr__(XorPDBSelector self) -> std::string"""
11966 return _IMP_atom.XorPDBSelector___repr__(self)
11970 return _object_cast_to_XorPDBSelector(o)
11974 _IMP_atom.XorPDBSelector_swigregister(XorPDBSelector)
11975 class NotPDBSelector(PDBSelector):
11976 r"""Proxy of C++ IMP::atom::NotPDBSelector class."""
11978 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11980 def get_version_info(self):
11981 r"""get_version_info(NotPDBSelector self) -> VersionInfo"""
11982 return _IMP_atom.NotPDBSelector_get_version_info(self)
11983 __swig_destroy__ = _IMP_atom.delete_NotPDBSelector
11985 def __init__(self, a):
11986 r"""__init__(NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
11987 _IMP_atom.NotPDBSelector_swiginit(self, _IMP_atom.new_NotPDBSelector(a))
11990 r"""__str__(NotPDBSelector self) -> std::string"""
11991 return _IMP_atom.NotPDBSelector___str__(self)
11993 def __repr__(self):
11994 r"""__repr__(NotPDBSelector self) -> std::string"""
11995 return _IMP_atom.NotPDBSelector___repr__(self)
11999 return _object_cast_to_NotPDBSelector(o)
12003 _IMP_atom.NotPDBSelector_swigregister(NotPDBSelector)
12005 def get_default_pdb_selector():
12006 r"""get_default_pdb_selector() -> PDBSelector"""
12007 return _IMP_atom.get_default_pdb_selector()
12011 read_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool no_radii=False) -> Hierarchy
12012 read_pdb(TextInput input, int model, Hierarchy h)
12014 return _IMP_atom.read_pdb(*args)
12017 r"""read_multimodel_pdb(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12018 return _IMP_atom.read_multimodel_pdb(*args)
12021 r"""write_pdb(Selection mhd, TextOutput out, unsigned int model=1)"""
12022 return _IMP_atom.write_pdb(mhd, out, model)
12025 r"""write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)"""
12026 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
12029 r"""write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
12030 return _IMP_atom.write_multimodel_pdb(mhd, out)
12032 def get_pdb_string(*args):
12033 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"""
12034 return _IMP_atom.get_pdb_string(*args)
12036 def get_pdb_conect_record_string(arg1, arg2):
12037 r"""get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
12038 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
12040 r"""Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
12042 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12044 def __init__(self, *args):
12046 __init__(WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
12047 __init__(WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
12048 __init__(WritePDBOptimizerState self) -> WritePDBOptimizerState
12050 _IMP_atom.WritePDBOptimizerState_swiginit(self, _IMP_atom.new_WritePDBOptimizerState(*args))
12052 def get_version_info(self):
12053 r"""get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
12054 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
12055 __swig_destroy__ = _IMP_atom.delete_WritePDBOptimizerState
12058 r"""__str__(WritePDBOptimizerState self) -> std::string"""
12059 return _IMP_atom.WritePDBOptimizerState___str__(self)
12061 def __repr__(self):
12062 r"""__repr__(WritePDBOptimizerState self) -> std::string"""
12063 return _IMP_atom.WritePDBOptimizerState___repr__(self)
12067 return _object_cast_to_WritePDBOptimizerState(o)
12070 def _get_as_binary(self):
12071 r"""_get_as_binary(WritePDBOptimizerState self) -> PyObject *"""
12072 return _IMP_atom.WritePDBOptimizerState__get_as_binary(self)
12074 def _set_from_binary(self, p):
12075 r"""_set_from_binary(WritePDBOptimizerState self, PyObject * p)"""
12076 return _IMP_atom.WritePDBOptimizerState__set_from_binary(self, p)
12078 def __getstate__(self):
12079 p = self._get_as_binary()
12080 if len(self.__dict__) > 1:
12081 d = self.__dict__.copy()
12086 def __setstate__(self, p):
12087 if not hasattr(self,
'this'):
12089 if isinstance(p, tuple):
12091 self.__dict__.update(d)
12092 return self._set_from_binary(p)
12096 _IMP_atom.WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
12099 r"""read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12100 return _IMP_atom.read_multimodel_mmcif(*args)
12103 r"""read_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool select_first_model=True, bool noradii=False) -> Hierarchy"""
12104 return _IMP_atom.read_mmcif(*args)
12107 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"""
12108 return _IMP_atom.read_pdb_or_mmcif(*args)
12111 r"""read_multimodel_pdb_or_mmcif(TextInput input, Model model, PDBSelector selector=IMP::atom::get_default_pdb_selector(), bool noradii=False) -> IMP::atom::Hierarchies"""
12112 return _IMP_atom.read_multimodel_pdb_or_mmcif(*args)
12115 r"""get_kt(double T) -> double"""
12116 return _IMP_atom.get_kt(T)
12118 r"""Proxy of C++ IMP::atom::CAAngleRestraint class."""
12120 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12122 def __init__(self, m, p1, p2, p3, phi0, score):
12123 r"""__init__(CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
12124 _IMP_atom.CAAngleRestraint_swiginit(self, _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score))
12126 def do_get_inputs(self):
12127 r"""do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
12128 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
12130 def get_version_info(self):
12131 r"""get_version_info(CAAngleRestraint self) -> VersionInfo"""
12132 return _IMP_atom.CAAngleRestraint_get_version_info(self)
12133 __swig_destroy__ = _IMP_atom.delete_CAAngleRestraint
12136 r"""__str__(CAAngleRestraint self) -> std::string"""
12137 return _IMP_atom.CAAngleRestraint___str__(self)
12139 def __repr__(self):
12140 r"""__repr__(CAAngleRestraint self) -> std::string"""
12141 return _IMP_atom.CAAngleRestraint___repr__(self)
12145 return _object_cast_to_CAAngleRestraint(o)
12149 _IMP_atom.CAAngleRestraint_swigregister(CAAngleRestraint)
12151 r"""Proxy of C++ IMP::atom::CADihedralRestraint class."""
12153 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12155 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
12156 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"""
12157 _IMP_atom.CADihedralRestraint_swiginit(self, _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score))
12159 def do_get_inputs(self):
12160 r"""do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
12161 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
12163 def get_version_info(self):
12164 r"""get_version_info(CADihedralRestraint self) -> VersionInfo"""
12165 return _IMP_atom.CADihedralRestraint_get_version_info(self)
12166 __swig_destroy__ = _IMP_atom.delete_CADihedralRestraint
12169 r"""__str__(CADihedralRestraint self) -> std::string"""
12170 return _IMP_atom.CADihedralRestraint___str__(self)
12172 def __repr__(self):
12173 r"""__repr__(CADihedralRestraint self) -> std::string"""
12174 return _IMP_atom.CADihedralRestraint___repr__(self)
12178 return _object_cast_to_CADihedralRestraint(o)
12182 _IMP_atom.CADihedralRestraint_swigregister(CADihedralRestraint)
12184 r"""Proxy of C++ IMP::atom::StructureSource class."""
12186 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12188 def get_source_id(self):
12189 r"""get_source_id(StructureSource self) -> std::string"""
12190 return _IMP_atom.StructureSource_get_source_id(self)
12192 def get_source_chain_id(self):
12193 r"""get_source_chain_id(StructureSource self) -> std::string"""
12194 return _IMP_atom.StructureSource_get_source_chain_id(self)
12196 def set_source_id(self, source_id):
12197 r"""set_source_id(StructureSource self, std::string source_id)"""
12198 return _IMP_atom.StructureSource_set_source_id(self, source_id)
12200 def set_source_chain_id(self, source_chain_id):
12201 r"""set_source_chain_id(StructureSource self, std::string source_chain_id)"""
12202 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
12204 def __init__(self, *args):
12206 __init__(StructureSource self) -> StructureSource
12207 __init__(StructureSource self, Model m, ParticleIndex id) -> StructureSource
12208 __init__(StructureSource self, _ParticleAdaptor d) -> StructureSource
12210 _IMP_atom.StructureSource_swiginit(self, _IMP_atom.new_StructureSource(*args))
12213 def get_is_setup(*args):
12215 get_is_setup(Model m, ParticleIndex pi) -> bool
12216 get_is_setup(_ParticleAdaptor p) -> bool
12218 return _IMP_atom.StructureSource_get_is_setup(*args)
12220 def show(self, *args):
12221 r"""show(StructureSource self, _ostream out=std::cout)"""
12222 return _IMP_atom.StructureSource_show(self, *args)
12225 def setup_particle(*args):
12227 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
12228 setup_particle(_ParticleAdaptor pa, std::string source_id, std::string source_chain_id) -> StructureSource
12230 return _IMP_atom.StructureSource_setup_particle(*args)
12232 def add_attribute(self, *args):
12234 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
12235 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
12236 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
12237 add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
12238 add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
12239 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
12240 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
12241 add_attribute(StructureSource self, ObjectKey a0, Object a1)
12243 return _IMP_atom.StructureSource_add_attribute(self, *args)
12245 def get_value(self, *args):
12247 get_value(StructureSource self, FloatKey a0) -> IMP::Float
12248 get_value(StructureSource self, IntKey a0) -> IMP::Int
12249 get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
12250 get_value(StructureSource self, IntsKey a0) -> IMP::Ints
12251 get_value(StructureSource self, StringKey a0) -> IMP::String
12252 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
12253 get_value(StructureSource self, ObjectKey a0) -> Object
12255 return _IMP_atom.StructureSource_get_value(self, *args)
12257 def set_value(self, *args):
12259 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
12260 set_value(StructureSource self, IntKey a0, IMP::Int a1)
12261 set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
12262 set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
12263 set_value(StructureSource self, StringKey a0, IMP::String a1)
12264 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
12265 set_value(StructureSource self, ObjectKey a0, Object a1)
12267 return _IMP_atom.StructureSource_set_value(self, *args)
12269 def remove_attribute(self, *args):
12271 remove_attribute(StructureSource self, FloatKey a0)
12272 remove_attribute(StructureSource self, IntKey a0)
12273 remove_attribute(StructureSource self, FloatsKey a0)
12274 remove_attribute(StructureSource self, IntsKey a0)
12275 remove_attribute(StructureSource self, StringKey a0)
12276 remove_attribute(StructureSource self, ParticleIndexKey a0)
12277 remove_attribute(StructureSource self, ObjectKey a0)
12279 return _IMP_atom.StructureSource_remove_attribute(self, *args)
12281 def has_attribute(self, *args):
12283 has_attribute(StructureSource self, FloatKey a0) -> bool
12284 has_attribute(StructureSource self, IntKey a0) -> bool
12285 has_attribute(StructureSource self, FloatsKey a0) -> bool
12286 has_attribute(StructureSource self, IntsKey a0) -> bool
12287 has_attribute(StructureSource self, StringKey a0) -> bool
12288 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
12289 has_attribute(StructureSource self, ObjectKey a0) -> bool
12291 return _IMP_atom.StructureSource_has_attribute(self, *args)
12293 def get_derivative(self, a0):
12294 r"""get_derivative(StructureSource self, FloatKey a0) -> double"""
12295 return _IMP_atom.StructureSource_get_derivative(self, a0)
12297 def get_name(self):
12298 r"""get_name(StructureSource self) -> std::string"""
12299 return _IMP_atom.StructureSource_get_name(self)
12301 def clear_caches(self):
12302 r"""clear_caches(StructureSource self)"""
12303 return _IMP_atom.StructureSource_clear_caches(self)
12305 def set_name(self, a0):
12306 r"""set_name(StructureSource self, std::string a0)"""
12307 return _IMP_atom.StructureSource_set_name(self, a0)
12310 r"""set_check_level(StructureSource self, IMP::CheckLevel a0)"""
12311 return _IMP_atom.StructureSource_set_check_level(self, a0)
12313 def add_to_derivative(self, a0, a1, a2):
12314 r"""add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
12315 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
12317 def set_is_optimized(self, a0, a1):
12318 r"""set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
12319 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
12321 def get_is_optimized(self, a0):
12322 r"""get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
12323 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
12326 r"""get_check_level(StructureSource self) -> IMP::CheckLevel"""
12327 return _IMP_atom.StructureSource_get_check_level(self)
12329 def __eq__(self, *args):
12331 __eq__(StructureSource self, StructureSource o) -> bool
12332 __eq__(StructureSource self, Particle d) -> bool
12334 return _IMP_atom.StructureSource___eq__(self, *args)
12336 def __ne__(self, *args):
12338 __ne__(StructureSource self, StructureSource o) -> bool
12339 __ne__(StructureSource self, Particle d) -> bool
12341 return _IMP_atom.StructureSource___ne__(self, *args)
12343 def __le__(self, *args):
12345 __le__(StructureSource self, StructureSource o) -> bool
12346 __le__(StructureSource self, Particle d) -> bool
12348 return _IMP_atom.StructureSource___le__(self, *args)
12350 def __lt__(self, *args):
12352 __lt__(StructureSource self, StructureSource o) -> bool
12353 __lt__(StructureSource self, Particle d) -> bool
12355 return _IMP_atom.StructureSource___lt__(self, *args)
12357 def __ge__(self, *args):
12359 __ge__(StructureSource self, StructureSource o) -> bool
12360 __ge__(StructureSource self, Particle d) -> bool
12362 return _IMP_atom.StructureSource___ge__(self, *args)
12364 def __gt__(self, *args):
12366 __gt__(StructureSource self, StructureSource o) -> bool
12367 __gt__(StructureSource self, Particle d) -> bool
12369 return _IMP_atom.StructureSource___gt__(self, *args)
12371 def __hash__(self):
12372 r"""__hash__(StructureSource self) -> std::size_t"""
12373 return _IMP_atom.StructureSource___hash__(self)
12376 r"""__str__(StructureSource self) -> std::string"""
12377 return _IMP_atom.StructureSource___str__(self)
12379 def __repr__(self):
12380 r"""__repr__(StructureSource self) -> std::string"""
12381 return _IMP_atom.StructureSource___repr__(self)
12383 def _get_as_binary(self):
12384 r"""_get_as_binary(StructureSource self) -> PyObject *"""
12385 return _IMP_atom.StructureSource__get_as_binary(self)
12387 def _set_from_binary(self, p):
12388 r"""_set_from_binary(StructureSource self, PyObject * p)"""
12389 return _IMP_atom.StructureSource__set_from_binary(self, p)
12391 def __getstate__(self):
12392 p = self._get_as_binary()
12393 if len(self.__dict__) > 1:
12394 d = self.__dict__.copy()
12399 def __setstate__(self, p):
12400 if not hasattr(self,
'this'):
12402 if isinstance(p, tuple):
12404 self.__dict__.update(d)
12405 return self._set_from_binary(p)
12407 __swig_destroy__ = _IMP_atom.delete_StructureSource
12410 _IMP_atom.StructureSource_swigregister(StructureSource)
12412 def __lshift__(*args):
12414 __lshift__(_ostream out, Bonded n) -> _ostream
12415 __lshift__(_ostream out, Bond n) -> _ostream
12416 __lshift__(_ostream out, Hierarchy n) -> _ostream
12417 __lshift__(_ostream out, Angle n) -> _ostream
12418 __lshift__(_ostream out, Dihedral n) -> _ostream
12419 __lshift__(_ostream out, CenterOfMass n) -> _ostream
12420 __lshift__(_ostream out, Diffusion n) -> _ostream
12421 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
12422 __lshift__(_ostream out, TAMDParticle n) -> _ostream
12423 __lshift__(_ostream out, Chain n) -> _ostream
12424 __lshift__(_ostream out, Charged n) -> _ostream
12425 __lshift__(_ostream out, Domain n) -> _ostream
12426 __lshift__(_ostream out, LennardJones n) -> _ostream
12427 __lshift__(_ostream out, Fragment n) -> _ostream
12428 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
12429 __lshift__(_ostream out, Atom n) -> _ostream
12430 __lshift__(_ostream out, Residue n) -> _ostream
12431 __lshift__(_ostream out, Representation n) -> _ostream
12432 __lshift__(_ostream out, State n) -> _ostream
12433 __lshift__(_ostream out, Molecule n) -> _ostream
12434 __lshift__(_ostream out, Copy n) -> _ostream
12435 __lshift__(_ostream out, StructureSource n) -> _ostream
12437 return _IMP_atom.__lshift__(*args)
12439 r"""Proxy of C++ IMP::atom::HelixRestraint class."""
12441 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12443 def __init__(self, rs, ideal=True):
12444 r"""__init__(HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint"""
12445 _IMP_atom.HelixRestraint_swiginit(self, _IMP_atom.new_HelixRestraint(rs, ideal))
12447 def get_number_of_bonds(self):
12448 r"""get_number_of_bonds(HelixRestraint self) -> int"""
12449 return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
12451 def get_number_of_dihedrals(self):
12452 r"""get_number_of_dihedrals(HelixRestraint self) -> int"""
12453 return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
12455 def do_get_inputs(self):
12456 r"""do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
12457 return _IMP_atom.HelixRestraint_do_get_inputs(self)
12459 def get_version_info(self):
12460 r"""get_version_info(HelixRestraint self) -> VersionInfo"""
12461 return _IMP_atom.HelixRestraint_get_version_info(self)
12462 __swig_destroy__ = _IMP_atom.delete_HelixRestraint
12465 r"""__str__(HelixRestraint self) -> std::string"""
12466 return _IMP_atom.HelixRestraint___str__(self)
12468 def __repr__(self):
12469 r"""__repr__(HelixRestraint self) -> std::string"""
12470 return _IMP_atom.HelixRestraint___repr__(self)
12474 return _object_cast_to_HelixRestraint(o)
12478 _IMP_atom.HelixRestraint_swigregister(HelixRestraint)
12481 r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
12482 return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
12485 r"""show_molecular_hierarchy(Hierarchy h, _ostream out=std::cout) -> _ostream"""
12486 return _IMP_atom.show_molecular_hierarchy(*args)
12487 class CHARMMBond(object):
12488 r"""Proxy of C++ IMP::atom::CHARMMConnection< 2 > class."""
12490 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12491 __repr__ = _swig_repr
12493 def __init__(self, atoms):
12494 r"""__init__(CHARMMBond self, IMP::Strings const & atoms) -> CHARMMBond"""
12495 _IMP_atom.CHARMMBond_swiginit(self, _IMP_atom.new_CHARMMBond(atoms))
12497 def get_endpoint(self, i):
12498 r"""get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
12499 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
12501 def get_contains_atom(self, name):
12502 r"""get_contains_atom(CHARMMBond self, std::string name) -> bool"""
12503 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
12505 def show(self, *args):
12506 r"""show(CHARMMBond self, _ostream out=std::cout)"""
12507 return _IMP_atom.CHARMMBond_show(self, *args)
12508 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
12511 _IMP_atom.CHARMMBond_swigregister(CHARMMBond)
12512 class CHARMMAngle(object):
12513 r"""Proxy of C++ IMP::atom::CHARMMConnection< 3 > class."""
12515 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12516 __repr__ = _swig_repr
12518 def __init__(self, atoms):
12519 r"""__init__(CHARMMAngle self, IMP::Strings const & atoms) -> CHARMMAngle"""
12520 _IMP_atom.CHARMMAngle_swiginit(self, _IMP_atom.new_CHARMMAngle(atoms))
12522 def get_endpoint(self, i):
12523 r"""get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
12524 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
12526 def get_contains_atom(self, name):
12527 r"""get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
12528 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
12530 def show(self, *args):
12531 r"""show(CHARMMAngle self, _ostream out=std::cout)"""
12532 return _IMP_atom.CHARMMAngle_show(self, *args)
12533 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
12536 _IMP_atom.CHARMMAngle_swigregister(CHARMMAngle)
12538 def _get_native_overlap_cpp(m1, m2, threshold):
12539 r"""_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
12540 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
12542 def _get_drmsd_cpp(m0, m1):
12543 r"""_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
12544 return _IMP_atom._get_drmsd_cpp(m0, m1)
12546 def _get_drmsd_Q_cpp(m0, m1, threshold):
12547 r"""_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
12548 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
12550 def _get_drms_cpp(m1, m2):
12551 r"""_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
12552 return _IMP_atom._get_drms_cpp(m1, m2)
12554 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
12555 r"""_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, IMP::IntRanges const & ranges) -> double"""
12556 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
12559 va= [IMP.algebra.get_vector(x)
for x
in a]
12560 vb= [IMP.algebra.get_vector(x)
for x
in b]
12561 return _get_native_overlap_cpp(va, vb, d)
12564 va= [IMP.algebra.get_vector(x)
for x
in a]
12565 vb= [IMP.algebra.get_vector(x)
for x
in b]
12566 return _get_drmsd_cpp(va, vb)
12569 va= [IMP.algebra.get_vector(x)
for x
in a]
12570 vb= [IMP.algebra.get_vector(x)
for x
in b]
12571 return _get_drms_cpp(va, vb)
12574 va= [IMP.algebra.get_vector(x)
for x
in a]
12575 vb= [IMP.algebra.get_vector(x)
for x
in b]
12576 return _get_drmsd_Q_cpp(va, vb, t)
12579 va= [IMP.algebra.get_vector(x)
for x
in a]
12580 vb= [IMP.algebra.get_vector(x)
for x
in b]
12582 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
12587 r"""get_module_version() -> std::string const"""
12588 return _IMP_atom.get_module_version()
12591 r"""get_example_path(std::string fname) -> std::string"""
12592 return _IMP_atom.get_example_path(fname)
12595 r"""get_data_path(std::string fname) -> std::string"""
12596 return _IMP_atom.get_data_path(fname)
12598 from .
import _version_check
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Hierarchy read_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB or mmCIF file.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
double get_einstein_rotational_diffusion_coefficient(double r, double temp=-1)
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the mmCIF file.
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
CheckLevel get_check_level()
Get the current audit mode.
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square)
Convert spring constant from kcal/mol/A^2 to femtonewton/A.
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
Add vdW radius from given force field.
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
ParticleIndexQuads get_chi_dihedral_particle_indexes(Residue rd)
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Composable functors to implement scores via compile-time composition.
double get_angle(const Line3D &a, const Line3D &b)
Get angle in radians between two lines around their closest points.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
double get_kd(double na, double nb, double nab, double volume)
double get_diffusion_angle(double D, double dtfs)
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &orientations, double dt)
Base class for all optimizers.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
A decorator for a particle with x,y,z coordinates.
void add_loop_statistical_score_data(atom::Hierarchy h)
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
Hierarchies read_multimodel_pdb_or_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the PDB or mmCIF file.
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom)
Convert force from kcal/mol/A to femtonewtons.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
Add bonds using definitions from given force field parameters.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
double get_diffusion_length(double D, double t)
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
A decorator for a particle with x,y,z coordinates and a radius.