10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_atom')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_atom')
25 _IMP_atom = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_atom', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_atom', fp, pathname, description)
43 _IMP_atom = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_ATOM_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
126 return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
131 incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
132 incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
134 return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
139 decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
140 decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
142 return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
151 """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
152 return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
156 """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
157 return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
161 """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
162 return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
166 """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
167 return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
171 """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
172 return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
177 return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
182 return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
187 return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
192 return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
197 return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
202 return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
208 __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
214 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
215 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
223 IMP_DEBUG = _IMP_atom.IMP_DEBUG
224 IMP_RELEASE = _IMP_atom.IMP_RELEASE
225 IMP_SILENT = _IMP_atom.IMP_SILENT
226 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
227 IMP_TERSE = _IMP_atom.IMP_TERSE
228 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
229 IMP_MEMORY = _IMP_atom.IMP_MEMORY
230 IMP_NONE = _IMP_atom.IMP_NONE
231 IMP_USAGE = _IMP_atom.IMP_USAGE
232 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_atom._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_atom._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
331 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
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
334 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
335 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
336 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
337 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
339 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
340 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
341 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
342 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
344 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
345 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
346 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
347 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
348 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
349 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
350 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
351 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
352 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
353 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
354 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
355 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
356 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
358 """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class."""
360 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
361 __repr__ = _swig_repr
364 """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
365 this = _IMP_atom.new_HierarchyTree()
367 self.this.append(this)
368 except __builtin__.Exception:
372 """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
373 return _IMP_atom.HierarchyTree_get_graph(self)
377 """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
378 return _IMP_atom.HierarchyTree_get_vertices(self)
381 def get_vertex_name(self, i):
382 """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
383 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
386 def get_in_neighbors(self, v):
387 """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"""
388 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
391 def get_out_neighbors(self, v):
392 """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"""
393 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
398 show_graphviz(HierarchyTree self, _ostream out)
399 show_graphviz(HierarchyTree self)
401 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
404 def get_graphviz_string(self):
405 """get_graphviz_string(HierarchyTree self) -> std::string"""
406 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
409 def add_edge(self, v0, v1):
410 """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)"""
411 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
414 def add_vertex(self, l):
415 """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
416 return _IMP_atom.HierarchyTree_add_vertex(self, l)
419 def remove_vertex(self, l):
420 """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
421 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
423 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
424 __del__ =
lambda self:
None
425 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
426 HierarchyTree_swigregister(HierarchyTree)
429 _value_types.append(
"HierarchyTree")
432 _object_types.append(
"PDBSelector")
435 def _object_cast_to_PDBSelector(o):
436 """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
437 return _IMP_atom._object_cast_to_PDBSelector(o)
440 return [Angle(x)
for x
in l]
441 _plural_types.append(
"Angles")
444 _value_types.append(
"Angle")
448 return [Atom(x)
for x
in l]
449 _plural_types.append(
"Atoms")
452 _value_types.append(
"Atom")
456 return [Bond(x)
for x
in l]
457 _plural_types.append(
"Bonds")
460 _value_types.append(
"Bond")
464 return [Bonded(x)
for x
in l]
465 _plural_types.append(
"Bondeds")
468 _value_types.append(
"Bonded")
471 def CHARMMAtomList(l=[]):
472 return [CHARMMAtom(x)
for x
in l]
473 _plural_types.append(
"CHARMMAtomList")
476 _value_types.append(
"CHARMMAtom")
480 return [Chain(x)
for x
in l]
481 _plural_types.append(
"Chains")
484 _value_types.append(
"Chain")
487 def CenterOfMasses(l=[]):
488 return [CenterOfMass(x)
for x
in l]
489 _plural_types.append(
"CenterOfMasses")
492 _value_types.append(
"CenterOfMass")
496 return [Charged(x)
for x
in l]
497 _plural_types.append(
"Chargeds")
500 _value_types.append(
"Charged")
503 def Diffusions(l=[]):
504 return [Diffusion(x)
for x
in l]
505 _plural_types.append(
"Diffusions")
508 _value_types.append(
"Diffusion")
511 def RigidBodyDiffusions(l=[]):
512 return [RigidBodyDiffusion(x)
for x
in l]
513 _plural_types.append(
"RigidBodyDiffusions")
516 _value_types.append(
"RigidBodyDiffusion")
519 def TAMDParticles(l=[]):
520 return [TAMDParticle(x)
for x
in l]
521 _plural_types.append(
"TAMDParticles")
524 _value_types.append(
"TAMDParticle")
527 def TAMDCentroids(l=[]):
528 return [TAMDCentroid(x)
for x
in l]
529 _plural_types.append(
"TAMDCentroids")
532 _value_types.append(
"TAMDCentroid")
536 return [Dihedral(x)
for x
in l]
537 _plural_types.append(
"Dihedrals")
540 _value_types.append(
"Dihedral")
544 return [Domain(x)
for x
in l]
545 _plural_types.append(
"Domains")
548 _value_types.append(
"Domain")
552 return [Fragment(x)
for x
in l]
553 _plural_types.append(
"Fragments")
556 _value_types.append(
"Fragment")
559 def Hierarchies(l=[]):
560 return [Hierarchy(x)
for x
in l]
561 _plural_types.append(
"Hierarchies")
564 _value_types.append(
"Hierarchy")
567 def LennardJonesList(l=[]):
568 return [LennardJones(x)
for x
in l]
569 _plural_types.append(
"LennardJonesList")
572 _value_types.append(
"LennardJones")
576 return [Mass(x)
for x
in l]
577 _plural_types.append(
"Masses")
580 _value_types.append(
"Mass")
583 def LinearVelocities(l=[]):
584 return [LinearVelocity(x)
for x
in l]
585 _plural_types.append(
"LinearVelocities")
588 _value_types.append(
"LinearVelocity")
591 def AngularVelocities(l=[]):
592 return [AngularVelocity(x)
for x
in l]
593 _plural_types.append(
"AngularVelocities")
596 _value_types.append(
"AngularVelocity")
600 return [Molecule(x)
for x
in l]
601 _plural_types.append(
"Molecules")
604 _value_types.append(
"Molecule")
608 return [Residue(x)
for x
in l]
609 _plural_types.append(
"Residues")
612 _value_types.append(
"Residue")
615 def Representations(l=[]):
616 return [Representation(x)
for x
in l]
617 _plural_types.append(
"Representations")
620 _value_types.append(
"Representation")
624 return [State(x)
for x
in l]
625 _plural_types.append(
"States")
628 _value_types.append(
"State")
632 return [Copy(x)
for x
in l]
633 _plural_types.append(
"Copies")
636 _value_types.append(
"Copy")
639 def SecondaryStructureResidues(l=[]):
640 return [SecondaryStructureResidue(x)
for x
in l]
641 _plural_types.append(
"SecondaryStructureResidues")
644 _value_types.append(
"SecondaryStructureResidue")
647 def StructureSources(l=[]):
648 return [StructureSource(x)
for x
in l]
649 _plural_types.append(
"StructureSources")
652 _value_types.append(
"StructureSource")
655 _object_types.append(
"Simulator")
658 def _object_cast_to_Simulator(o):
659 """_object_cast_to_Simulator(Object o) -> Simulator"""
660 return _IMP_atom._object_cast_to_Simulator(o)
662 _object_types.append(
"ATOMPDBSelector")
665 def _object_cast_to_ATOMPDBSelector(o):
666 """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
667 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
669 _object_types.append(
"AllMol2Selector")
672 def _object_cast_to_AllMol2Selector(o):
673 """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
674 return _IMP_atom._object_cast_to_AllMol2Selector(o)
676 _object_types.append(
"AllPDBSelector")
679 def _object_cast_to_AllPDBSelector(o):
680 """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
681 return _IMP_atom._object_cast_to_AllPDBSelector(o)
683 _object_types.append(
"AndPDBSelector")
686 def _object_cast_to_AndPDBSelector(o):
687 """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
688 return _IMP_atom._object_cast_to_AndPDBSelector(o)
690 _object_types.append(
"XorPDBSelector")
693 def _object_cast_to_XorPDBSelector(o):
694 """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
695 return _IMP_atom._object_cast_to_XorPDBSelector(o)
697 _object_types.append(
"ResidueTypePDBSelector")
700 def _object_cast_to_ResidueTypePDBSelector(o):
701 """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
702 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
704 _object_types.append(
"AtomTypePDBSelector")
707 def _object_cast_to_AtomTypePDBSelector(o):
708 """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
709 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
711 _object_types.append(
"AngleSingletonScore")
714 def _object_cast_to_AngleSingletonScore(o):
715 """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
716 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
718 _object_types.append(
"BondEndpointsRefiner")
721 def _object_cast_to_BondEndpointsRefiner(o):
722 """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
723 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
725 _object_types.append(
"BondPairContainer")
728 def _object_cast_to_BondPairContainer(o):
729 """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
730 return _IMP_atom._object_cast_to_BondPairContainer(o)
732 _object_types.append(
"BondSingletonScore")
735 def _object_cast_to_BondSingletonScore(o):
736 """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
737 return _IMP_atom._object_cast_to_BondSingletonScore(o)
739 _object_types.append(
"BondedPairFilter")
742 def _object_cast_to_BondedPairFilter(o):
743 """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
744 return _IMP_atom._object_cast_to_BondedPairFilter(o)
746 _object_types.append(
"BrownianDynamics")
749 def _object_cast_to_BrownianDynamics(o):
750 """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
751 return _IMP_atom._object_cast_to_BrownianDynamics(o)
753 _object_types.append(
"BrownianDynamicsTAMD")
756 def _object_cast_to_BrownianDynamicsTAMD(o):
757 """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
758 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
760 _object_types.append(
"CAlphaPDBSelector")
763 def _object_cast_to_CAlphaPDBSelector(o):
764 """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
765 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
767 _object_types.append(
"CBetaPDBSelector")
770 def _object_cast_to_CBetaPDBSelector(o):
771 """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
772 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
774 _object_types.append(
"BackbonePDBSelector")
777 def _object_cast_to_BackbonePDBSelector(o):
778 """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
779 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
781 _object_types.append(
"CHARMMParameters")
784 def _object_cast_to_CHARMMParameters(o):
785 """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
786 return _IMP_atom._object_cast_to_CHARMMParameters(o)
788 _object_types.append(
"CHARMMResidueTopology")
791 def _object_cast_to_CHARMMResidueTopology(o):
792 """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
793 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
795 _object_types.append(
"CHARMMSegmentTopology")
798 def _object_cast_to_CHARMMSegmentTopology(o):
799 """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
800 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
802 _object_types.append(
"CHARMMStereochemistryRestraint")
805 def _object_cast_to_CHARMMStereochemistryRestraint(o):
806 """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
807 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
809 _object_types.append(
"CHARMMTopology")
812 def _object_cast_to_CHARMMTopology(o):
813 """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
814 return _IMP_atom._object_cast_to_CHARMMTopology(o)
816 _object_types.append(
"CPDBSelector")
819 def _object_cast_to_CPDBSelector(o):
820 """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
821 return _IMP_atom._object_cast_to_CPDBSelector(o)
823 _object_types.append(
"ChainPDBSelector")
826 def _object_cast_to_ChainPDBSelector(o):
827 """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
828 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
830 _object_types.append(
"CoulombPairScore")
833 def _object_cast_to_CoulombPairScore(o):
834 """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
835 return _IMP_atom._object_cast_to_CoulombPairScore(o)
837 _object_types.append(
"CoverBond")
840 def _object_cast_to_CoverBond(o):
841 """_object_cast_to_CoverBond(Object o) -> CoverBond"""
842 return _IMP_atom._object_cast_to_CoverBond(o)
844 _object_types.append(
"DihedralSingletonScore")
847 def _object_cast_to_DihedralSingletonScore(o):
848 """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
849 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
851 _object_types.append(
"DopePairScore")
854 def _object_cast_to_DopePairScore(o):
855 """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
856 return _IMP_atom._object_cast_to_DopePairScore(o)
858 _object_types.append(
"OrientedSoapPairScore")
861 def _object_cast_to_OrientedSoapPairScore(o):
862 """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
863 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
865 _object_types.append(
"EzRestraint")
868 def _object_cast_to_EzRestraint(o):
869 """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
870 return _IMP_atom._object_cast_to_EzRestraint(o)
872 _object_types.append(
"ForceFieldParameters")
875 def _object_cast_to_ForceFieldParameters(o):
876 """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
877 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
879 _object_types.append(
"ForceSwitch")
882 def _object_cast_to_ForceSwitch(o):
883 """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
884 return _IMP_atom._object_cast_to_ForceSwitch(o)
886 _object_types.append(
"HydrogenPDBSelector")
889 def _object_cast_to_HydrogenPDBSelector(o):
890 """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
891 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
893 _object_types.append(
"ImproperSingletonScore")
896 def _object_cast_to_ImproperSingletonScore(o):
897 """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
898 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
900 _object_types.append(
"LennardJonesPairScore")
903 def _object_cast_to_LennardJonesPairScore(o):
904 """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
905 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
907 _object_types.append(
"Mol2Selector")
910 def _object_cast_to_Mol2Selector(o):
911 """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
912 return _IMP_atom._object_cast_to_Mol2Selector(o)
914 _object_types.append(
"MolecularDynamics")
917 def _object_cast_to_MolecularDynamics(o):
918 """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
919 return _IMP_atom._object_cast_to_MolecularDynamics(o)
921 _object_types.append(
"NPDBSelector")
924 def _object_cast_to_NPDBSelector(o):
925 """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
926 return _IMP_atom._object_cast_to_NPDBSelector(o)
928 _object_types.append(
"NonAlternativePDBSelector")
931 def _object_cast_to_NonAlternativePDBSelector(o):
932 """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
933 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
935 _object_types.append(
"NonHydrogenMol2Selector")
938 def _object_cast_to_NonHydrogenMol2Selector(o):
939 """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
940 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
942 _object_types.append(
"NonHydrogenPDBSelector")
945 def _object_cast_to_NonHydrogenPDBSelector(o):
946 """_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
947 return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
949 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
952 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
953 """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
954 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
956 _object_types.append(
"NonWaterPDBSelector")
959 def _object_cast_to_NonWaterPDBSelector(o):
960 """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
961 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
963 _object_types.append(
"NotPDBSelector")
966 def _object_cast_to_NotPDBSelector(o):
967 """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
968 return _IMP_atom._object_cast_to_NotPDBSelector(o)
970 _object_types.append(
"OrPDBSelector")
973 def _object_cast_to_OrPDBSelector(o):
974 """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
975 return _IMP_atom._object_cast_to_OrPDBSelector(o)
977 _object_types.append(
"PPDBSelector")
980 def _object_cast_to_PPDBSelector(o):
981 """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
982 return _IMP_atom._object_cast_to_PPDBSelector(o)
984 _object_types.append(
"ProteinLigandAtomPairScore")
987 def _object_cast_to_ProteinLigandAtomPairScore(o):
988 """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
989 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
991 _object_types.append(
"ProteinLigandRestraint")
994 def _object_cast_to_ProteinLigandRestraint(o):
995 """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
996 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
998 _object_types.append(
"SameResiduePairFilter")
1001 def _object_cast_to_SameResiduePairFilter(o):
1002 """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1003 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1005 _object_types.append(
"SoapPairFilter")
1008 def _object_cast_to_SoapPairFilter(o):
1009 """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1010 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1012 _object_types.append(
"SmoothingFunction")
1015 def _object_cast_to_SmoothingFunction(o):
1016 """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1017 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1019 _object_types.append(
"StereochemistryPairFilter")
1022 def _object_cast_to_StereochemistryPairFilter(o):
1023 """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1024 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1026 _object_types.append(
"VelocityScalingOptimizerState")
1029 def _object_cast_to_VelocityScalingOptimizerState(o):
1030 """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1031 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1033 _object_types.append(
"WaterPDBSelector")
1036 def _object_cast_to_WaterPDBSelector(o):
1037 """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1038 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1040 _object_types.append(
"WritePDBOptimizerState")
1043 def _object_cast_to_WritePDBOptimizerState(o):
1044 """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1045 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1048 _plural_types.append(
"AtomTypes")
1049 _value_types.append(
"AtomType")
1052 CHARMMAtomTopologies=list
1053 _plural_types.append(
"CHARMMAtomTopologies")
1054 _value_types.append(
"CHARMMAtomTopology")
1057 CHARMMBondEndpoints=list
1058 _plural_types.append(
"CHARMMBondEndpoints")
1059 _value_types.append(
"CHARMMBondEndpoint")
1062 CHARMMBondParametersList=list
1063 _plural_types.append(
"CHARMMBondParametersList")
1064 _value_types.append(
"CHARMMBondParameters")
1067 CHARMMDihedralParametersList=list
1068 _plural_types.append(
"CHARMMDihedralParametersList")
1069 _value_types.append(
"CHARMMDihedralParameters")
1072 _object_types.append(
"CHARMMIdealResidueTopology")
1075 def _object_cast_to_CHARMMIdealResidueTopology(o):
1076 """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1077 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1079 CHARMMInternalCoordinates=list
1080 _plural_types.append(
"CHARMMInternalCoordinates")
1081 _value_types.append(
"CHARMMInternalCoordinate")
1084 _object_types.append(
"CHARMMPatch")
1087 def _object_cast_to_CHARMMPatch(o):
1088 """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1089 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1091 _object_types.append(
"CHARMMResidueTopologyBase")
1094 def _object_cast_to_CHARMMResidueTopologyBase(o):
1095 """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1096 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1099 _plural_types.append(
"ResidueTypes")
1100 _value_types.append(
"ResidueType")
1104 _plural_types.append(
"Selections")
1105 _value_types.append(
"Selection")
1108 _object_types.append(
"RemoveRigidMotionOptimizerState")
1111 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1112 """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1113 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1115 _object_types.append(
"BerendsenThermostatOptimizerState")
1118 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1119 """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1120 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1122 _object_types.append(
"LangevinThermostatOptimizerState")
1125 def _object_cast_to_LangevinThermostatOptimizerState(o):
1126 """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1127 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1129 _object_types.append(
"SelectionGeometry")
1132 def _object_cast_to_SelectionGeometry(o):
1133 """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1134 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1136 _object_types.append(
"HierarchyGeometry")
1139 def _object_cast_to_HierarchyGeometry(o):
1140 """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1141 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1143 _object_types.append(
"HierarchiesGeometry")
1146 def _object_cast_to_HierarchiesGeometry(o):
1147 """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1148 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1150 _object_types.append(
"BondGeometry")
1153 def _object_cast_to_BondGeometry(o):
1154 """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1155 return _IMP_atom._object_cast_to_BondGeometry(o)
1157 _object_types.append(
"BondsGeometry")
1160 def _object_cast_to_BondsGeometry(o):
1161 """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1162 return _IMP_atom._object_cast_to_BondsGeometry(o)
1164 _object_types.append(
"CAAngleRestraint")
1167 def _object_cast_to_CAAngleRestraint(o):
1168 """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1169 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1171 _object_types.append(
"CADihedralRestraint")
1174 def _object_cast_to_CADihedralRestraint(o):
1175 """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1176 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1178 _object_types.append(
"HelixRestraint")
1181 def _object_cast_to_HelixRestraint(o):
1182 """_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1183 return _IMP_atom._object_cast_to_HelixRestraint(o)
1185 CHARMMDihedrals=list
1186 _plural_types.append(
"CHARMMDihedrals")
1187 _value_types.append(
"CHARMMDihedral")
1191 _plural_types.append(
"CHARMMBonds")
1192 _value_types.append(
"CHARMMBond")
1196 _plural_types.append(
"CHARMMAngles")
1197 _value_types.append(
"CHARMMAngle")
1200 """Proxy of C++ IMP::atom::Bond class."""
1202 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1204 def __init__(self, *args):
1206 __init__(IMP::atom::Bond self) -> Bond
1207 __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1208 __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1210 this = _IMP_atom.new_Bond(*args)
1212 self.this.append(this)
1213 except __builtin__.Exception:
1216 def show(self, *args):
1218 show(Bond self, _ostream out)
1221 return _IMP_atom.Bond_show(self, *args)
1224 def get_is_setup(*args):
1226 get_is_setup(_ParticleAdaptor p) -> bool
1227 get_is_setup(Model m, ParticleIndex pi) -> bool
1229 return _IMP_atom.Bond_get_is_setup(*args)
1231 get_is_setup = staticmethod(get_is_setup)
1232 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1233 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1234 SINGLE = _IMP_atom.Bond_SINGLE
1235 DOUBLE = _IMP_atom.Bond_DOUBLE
1236 TRIPLE = _IMP_atom.Bond_TRIPLE
1237 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1238 SALT = _IMP_atom.Bond_SALT
1239 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1240 AMIDE = _IMP_atom.Bond_AMIDE
1241 AROMATIC = _IMP_atom.Bond_AROMATIC
1243 def get_bonded(self, i):
1244 """get_bonded(Bond self, unsigned int i) -> Bonded"""
1245 return _IMP_atom.Bond_get_bonded(self, i)
1249 """get_type(Bond self) -> IMP::Int"""
1250 return _IMP_atom.Bond_get_type(self)
1253 def set_type(self, t):
1254 """set_type(Bond self, IMP::Int t)"""
1255 return _IMP_atom.Bond_set_type(self, t)
1259 """get_order(Bond self) -> IMP::Int"""
1260 return _IMP_atom.Bond_get_order(self)
1263 def set_order(self, t):
1264 """set_order(Bond self, IMP::Int t)"""
1265 return _IMP_atom.Bond_set_order(self, t)
1268 def get_length(self):
1269 """get_length(Bond self) -> IMP::Float"""
1270 return _IMP_atom.Bond_get_length(self)
1273 def set_length(self, t):
1274 """set_length(Bond self, IMP::Float t)"""
1275 return _IMP_atom.Bond_set_length(self, t)
1278 def get_stiffness(self):
1279 """get_stiffness(Bond self) -> IMP::Float"""
1280 return _IMP_atom.Bond_get_stiffness(self)
1283 def set_stiffness(self, t):
1284 """set_stiffness(Bond self, IMP::Float t)"""
1285 return _IMP_atom.Bond_set_stiffness(self, t)
1288 def get_length_key():
1289 """get_length_key() -> FloatKey"""
1290 return _IMP_atom.Bond_get_length_key()
1292 get_length_key = staticmethod(get_length_key)
1294 def add_attribute(self, *args):
1296 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1297 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1298 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1299 add_attribute(Bond self, StringKey a0, IMP::String a1)
1300 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1301 add_attribute(Bond self, ObjectKey a0, Object a1)
1303 return _IMP_atom.Bond_add_attribute(self, *args)
1306 def get_value(self, *args):
1308 get_value(Bond self, FloatKey a0) -> IMP::Float
1309 get_value(Bond self, IntKey a0) -> IMP::Int
1310 get_value(Bond self, StringKey a0) -> IMP::String
1311 get_value(Bond self, ParticleIndexKey a0) -> Particle
1312 get_value(Bond self, ObjectKey a0) -> Object
1314 return _IMP_atom.Bond_get_value(self, *args)
1317 def set_value(self, *args):
1319 set_value(Bond self, FloatKey a0, IMP::Float a1)
1320 set_value(Bond self, IntKey a0, IMP::Int a1)
1321 set_value(Bond self, StringKey a0, IMP::String a1)
1322 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1323 set_value(Bond self, ObjectKey a0, Object a1)
1325 return _IMP_atom.Bond_set_value(self, *args)
1328 def remove_attribute(self, *args):
1330 remove_attribute(Bond self, FloatKey a0)
1331 remove_attribute(Bond self, IntKey a0)
1332 remove_attribute(Bond self, StringKey a0)
1333 remove_attribute(Bond self, ParticleIndexKey a0)
1334 remove_attribute(Bond self, ObjectKey a0)
1336 return _IMP_atom.Bond_remove_attribute(self, *args)
1339 def has_attribute(self, *args):
1341 has_attribute(Bond self, FloatKey a0) -> bool
1342 has_attribute(Bond self, IntKey a0) -> bool
1343 has_attribute(Bond self, StringKey a0) -> bool
1344 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1345 has_attribute(Bond self, ObjectKey a0) -> bool
1347 return _IMP_atom.Bond_has_attribute(self, *args)
1350 def get_derivative(self, a0):
1351 """get_derivative(Bond self, FloatKey a0) -> double"""
1352 return _IMP_atom.Bond_get_derivative(self, a0)
1356 """get_name(Bond self) -> std::string"""
1357 return _IMP_atom.Bond_get_name(self)
1360 def clear_caches(self):
1361 """clear_caches(Bond self)"""
1362 return _IMP_atom.Bond_clear_caches(self)
1365 def set_name(self, a0):
1366 """set_name(Bond self, std::string a0)"""
1367 return _IMP_atom.Bond_set_name(self, a0)
1371 """set_check_level(Bond self, IMP::CheckLevel a0)"""
1372 return _IMP_atom.Bond_set_check_level(self, a0)
1375 def add_to_derivative(self, a0, a1, a2):
1376 """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1377 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1380 def set_is_optimized(self, a0, a1):
1381 """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1382 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1385 def get_is_optimized(self, a0):
1386 """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1387 return _IMP_atom.Bond_get_is_optimized(self, a0)
1391 """get_check_level(Bond self) -> IMP::CheckLevel"""
1392 return _IMP_atom.Bond_get_check_level(self)
1395 def __eq__(self, *args):
1397 __eq__(Bond self, Bond o) -> bool
1398 __eq__(Bond self, Particle d) -> bool
1400 return _IMP_atom.Bond___eq__(self, *args)
1403 def __ne__(self, *args):
1405 __ne__(Bond self, Bond o) -> bool
1406 __ne__(Bond self, Particle d) -> bool
1408 return _IMP_atom.Bond___ne__(self, *args)
1411 def __le__(self, *args):
1413 __le__(Bond self, Bond o) -> bool
1414 __le__(Bond self, Particle d) -> bool
1416 return _IMP_atom.Bond___le__(self, *args)
1419 def __lt__(self, *args):
1421 __lt__(Bond self, Bond o) -> bool
1422 __lt__(Bond self, Particle d) -> bool
1424 return _IMP_atom.Bond___lt__(self, *args)
1427 def __ge__(self, *args):
1429 __ge__(Bond self, Bond o) -> bool
1430 __ge__(Bond self, Particle d) -> bool
1432 return _IMP_atom.Bond___ge__(self, *args)
1435 def __gt__(self, *args):
1437 __gt__(Bond self, Bond o) -> bool
1438 __gt__(Bond self, Particle d) -> bool
1440 return _IMP_atom.Bond___gt__(self, *args)
1444 """__hash__(Bond self) -> std::size_t"""
1445 return _IMP_atom.Bond___hash__(self)
1449 """__str__(Bond self) -> std::string"""
1450 return _IMP_atom.Bond___str__(self)
1454 """__repr__(Bond self) -> std::string"""
1455 return _IMP_atom.Bond___repr__(self)
1457 __swig_destroy__ = _IMP_atom.delete_Bond
1458 __del__ =
lambda self:
None
1459 Bond_swigregister = _IMP_atom.Bond_swigregister
1460 Bond_swigregister(Bond)
1462 def Bond_get_is_setup(*args):
1464 get_is_setup(_ParticleAdaptor p) -> bool
1465 Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1467 return _IMP_atom.Bond_get_is_setup(*args)
1469 def Bond_get_length_key():
1470 """Bond_get_length_key() -> FloatKey"""
1471 return _IMP_atom.Bond_get_length_key()
1474 """Proxy of C++ IMP::atom::Bonded class."""
1476 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1478 def __init__(self, *args):
1480 __init__(IMP::atom::Bonded self) -> Bonded
1481 __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1482 __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1484 this = _IMP_atom.new_Bonded(*args)
1486 self.this.append(this)
1487 except __builtin__.Exception:
1490 def show(self, *args):
1492 show(Bonded self, _ostream out)
1495 return _IMP_atom.Bonded_show(self, *args)
1498 def setup_particle(*args):
1500 setup_particle(Model m, ParticleIndex pi) -> Bonded
1501 setup_particle(_ParticleAdaptor decorator) -> Bonded
1503 return _IMP_atom.Bonded_setup_particle(*args)
1505 setup_particle = staticmethod(setup_particle)
1507 def get_is_setup(*args):
1509 get_is_setup(_ParticleAdaptor p) -> bool
1510 get_is_setup(Model m, ParticleIndex pi) -> bool
1512 return _IMP_atom.Bonded_get_is_setup(*args)
1514 get_is_setup = staticmethod(get_is_setup)
1516 def get_number_of_bonds(self):
1517 """get_number_of_bonds(Bonded self) -> unsigned int"""
1518 return _IMP_atom.Bonded_get_number_of_bonds(self)
1521 def get_bond_indexes(self):
1522 """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1523 return _IMP_atom.Bonded_get_bond_indexes(self)
1527 """get_bond(Bonded self, unsigned int i) -> Bond"""
1528 return _IMP_atom.Bonded_get_bond(self, i)
1531 def get_bonded(self, i):
1532 """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1533 return _IMP_atom.Bonded_get_bonded(self, i)
1536 def add_attribute(self, *args):
1538 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1539 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1540 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1541 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1542 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1543 add_attribute(Bonded self, ObjectKey a0, Object a1)
1545 return _IMP_atom.Bonded_add_attribute(self, *args)
1548 def get_value(self, *args):
1550 get_value(Bonded self, FloatKey a0) -> IMP::Float
1551 get_value(Bonded self, IntKey a0) -> IMP::Int
1552 get_value(Bonded self, StringKey a0) -> IMP::String
1553 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1554 get_value(Bonded self, ObjectKey a0) -> Object
1556 return _IMP_atom.Bonded_get_value(self, *args)
1559 def set_value(self, *args):
1561 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1562 set_value(Bonded self, IntKey a0, IMP::Int a1)
1563 set_value(Bonded self, StringKey a0, IMP::String a1)
1564 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1565 set_value(Bonded self, ObjectKey a0, Object a1)
1567 return _IMP_atom.Bonded_set_value(self, *args)
1570 def remove_attribute(self, *args):
1572 remove_attribute(Bonded self, FloatKey a0)
1573 remove_attribute(Bonded self, IntKey a0)
1574 remove_attribute(Bonded self, StringKey a0)
1575 remove_attribute(Bonded self, ParticleIndexKey a0)
1576 remove_attribute(Bonded self, ObjectKey a0)
1578 return _IMP_atom.Bonded_remove_attribute(self, *args)
1581 def has_attribute(self, *args):
1583 has_attribute(Bonded self, FloatKey a0) -> bool
1584 has_attribute(Bonded self, IntKey a0) -> bool
1585 has_attribute(Bonded self, StringKey a0) -> bool
1586 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1587 has_attribute(Bonded self, ObjectKey a0) -> bool
1589 return _IMP_atom.Bonded_has_attribute(self, *args)
1592 def get_derivative(self, a0):
1593 """get_derivative(Bonded self, FloatKey a0) -> double"""
1594 return _IMP_atom.Bonded_get_derivative(self, a0)
1598 """get_name(Bonded self) -> std::string"""
1599 return _IMP_atom.Bonded_get_name(self)
1602 def clear_caches(self):
1603 """clear_caches(Bonded self)"""
1604 return _IMP_atom.Bonded_clear_caches(self)
1607 def set_name(self, a0):
1608 """set_name(Bonded self, std::string a0)"""
1609 return _IMP_atom.Bonded_set_name(self, a0)
1613 """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1614 return _IMP_atom.Bonded_set_check_level(self, a0)
1617 def add_to_derivative(self, a0, a1, a2):
1618 """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1619 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1622 def set_is_optimized(self, a0, a1):
1623 """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1624 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1627 def get_is_optimized(self, a0):
1628 """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1629 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1633 """get_check_level(Bonded self) -> IMP::CheckLevel"""
1634 return _IMP_atom.Bonded_get_check_level(self)
1637 def __eq__(self, *args):
1639 __eq__(Bonded self, Bonded o) -> bool
1640 __eq__(Bonded self, Particle d) -> bool
1642 return _IMP_atom.Bonded___eq__(self, *args)
1645 def __ne__(self, *args):
1647 __ne__(Bonded self, Bonded o) -> bool
1648 __ne__(Bonded self, Particle d) -> bool
1650 return _IMP_atom.Bonded___ne__(self, *args)
1653 def __le__(self, *args):
1655 __le__(Bonded self, Bonded o) -> bool
1656 __le__(Bonded self, Particle d) -> bool
1658 return _IMP_atom.Bonded___le__(self, *args)
1661 def __lt__(self, *args):
1663 __lt__(Bonded self, Bonded o) -> bool
1664 __lt__(Bonded self, Particle d) -> bool
1666 return _IMP_atom.Bonded___lt__(self, *args)
1669 def __ge__(self, *args):
1671 __ge__(Bonded self, Bonded o) -> bool
1672 __ge__(Bonded self, Particle d) -> bool
1674 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)
1686 """__hash__(Bonded self) -> std::size_t"""
1687 return _IMP_atom.Bonded___hash__(self)
1691 """__str__(Bonded self) -> std::string"""
1692 return _IMP_atom.Bonded___str__(self)
1696 """__repr__(Bonded self) -> std::string"""
1697 return _IMP_atom.Bonded___repr__(self)
1699 __swig_destroy__ = _IMP_atom.delete_Bonded
1700 __del__ =
lambda self:
None
1701 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1702 Bonded_swigregister(Bonded)
1704 def Bonded_setup_particle(*args):
1706 setup_particle(Model m, ParticleIndex pi) -> Bonded
1707 Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1709 return _IMP_atom.Bonded_setup_particle(*args)
1711 def Bonded_get_is_setup(*args):
1713 get_is_setup(_ParticleAdaptor p) -> bool
1714 Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1716 return _IMP_atom.Bonded_get_is_setup(*args)
1721 create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1722 create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1724 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1728 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1729 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1731 return _IMP_atom.create_bond(*args)
1734 """destroy_bond(Bond b)"""
1735 return _IMP_atom.destroy_bond(b)
1738 """get_bond(Bonded a, Bonded b) -> Bond"""
1739 return _IMP_atom.get_bond(a, b)
1741 """Proxy of C++ IMP::atom::BondGeometry class."""
1743 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1745 def __init__(self, *args):
1747 __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1748 __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1750 this = _IMP_atom.new_BondGeometry(*args)
1752 self.this.append(this)
1753 except __builtin__.Exception:
1756 def get_version_info(self):
1757 """get_version_info(BondGeometry self) -> VersionInfo"""
1758 return _IMP_atom.BondGeometry_get_version_info(self)
1762 """__str__(BondGeometry self) -> std::string"""
1763 return _IMP_atom.BondGeometry___str__(self)
1767 """__repr__(BondGeometry self) -> std::string"""
1768 return _IMP_atom.BondGeometry___repr__(self)
1773 return _object_cast_to_BondGeometry(o)
1775 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1776 BondGeometry_swigregister(BondGeometry)
1779 """Proxy of C++ IMP::atom::BondsGeometry class."""
1781 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1783 def __init__(self, sc):
1784 """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1785 this = _IMP_atom.new_BondsGeometry(sc)
1787 self.this.append(this)
1788 except __builtin__.Exception:
1791 def get_version_info(self):
1792 """get_version_info(BondsGeometry self) -> VersionInfo"""
1793 return _IMP_atom.BondsGeometry_get_version_info(self)
1797 """__str__(BondsGeometry self) -> std::string"""
1798 return _IMP_atom.BondsGeometry___str__(self)
1802 """__repr__(BondsGeometry self) -> std::string"""
1803 return _IMP_atom.BondsGeometry___repr__(self)
1808 return _object_cast_to_BondsGeometry(o)
1810 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1811 BondsGeometry_swigregister(BondsGeometry)
1814 """Proxy of C++ IMP::atom::Hierarchy class."""
1816 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1818 def __init__(self, *args):
1820 __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1821 __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1822 __init__(IMP::atom::Hierarchy self) -> Hierarchy
1823 __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1825 this = _IMP_atom.new_Hierarchy(*args)
1827 self.this.append(this)
1828 except __builtin__.Exception:
1831 def setup_particle(*args):
1833 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1834 setup_particle(Particle p) -> Hierarchy
1835 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1836 setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1838 return _IMP_atom.Hierarchy_setup_particle(*args)
1840 setup_particle = staticmethod(setup_particle)
1842 def get_is_setup(*args):
1844 get_is_setup(Particle p) -> bool
1845 get_is_setup(Model m, ParticleIndex p) -> bool
1847 return _IMP_atom.Hierarchy_get_is_setup(*args)
1849 get_is_setup = staticmethod(get_is_setup)
1851 def get_is_valid(self, print_info=False):
1853 get_is_valid(Hierarchy self, bool print_info=False) -> bool
1854 get_is_valid(Hierarchy self) -> bool
1856 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1859 def add_child(self, o):
1860 """add_child(Hierarchy self, Hierarchy o)"""
1861 return _IMP_atom.Hierarchy_add_child(self, o)
1864 def get_child(self, i):
1865 """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1866 return _IMP_atom.Hierarchy_get_child(self, i)
1869 def get_children(self):
1870 """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1871 return _IMP_atom.Hierarchy_get_children(self)
1874 def get_parent(self):
1875 """get_parent(Hierarchy self) -> Hierarchy"""
1876 return _IMP_atom.Hierarchy_get_parent(self)
1880 """get_traits() -> HierarchyTraits"""
1881 return _IMP_atom.Hierarchy_get_traits()
1883 get_traits = staticmethod(get_traits)
1885 def show(self, *args):
1887 show(Hierarchy self, _ostream out, std::string delimiter)
1888 show(Hierarchy self, _ostream out)
1889 show(Hierarchy self)
1891 return _IMP_atom.Hierarchy_show(self, *args)
1894 def add_attribute(self, *args):
1896 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1897 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1898 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1899 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1900 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1901 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1903 return _IMP_atom.Hierarchy_add_attribute(self, *args)
1906 def get_value(self, *args):
1908 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1909 get_value(Hierarchy self, IntKey a0) -> IMP::Int
1910 get_value(Hierarchy self, StringKey a0) -> IMP::String
1911 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1912 get_value(Hierarchy self, ObjectKey a0) -> Object
1914 return _IMP_atom.Hierarchy_get_value(self, *args)
1917 def set_value(self, *args):
1919 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1920 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1921 set_value(Hierarchy self, StringKey a0, IMP::String a1)
1922 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1923 set_value(Hierarchy self, ObjectKey a0, Object a1)
1925 return _IMP_atom.Hierarchy_set_value(self, *args)
1928 def remove_attribute(self, *args):
1930 remove_attribute(Hierarchy self, FloatKey a0)
1931 remove_attribute(Hierarchy self, IntKey a0)
1932 remove_attribute(Hierarchy self, StringKey a0)
1933 remove_attribute(Hierarchy self, ParticleIndexKey a0)
1934 remove_attribute(Hierarchy self, ObjectKey a0)
1936 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1939 def has_attribute(self, *args):
1941 has_attribute(Hierarchy self, FloatKey a0) -> bool
1942 has_attribute(Hierarchy self, IntKey a0) -> bool
1943 has_attribute(Hierarchy self, StringKey a0) -> bool
1944 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
1945 has_attribute(Hierarchy self, ObjectKey a0) -> bool
1947 return _IMP_atom.Hierarchy_has_attribute(self, *args)
1950 def get_derivative(self, a0):
1951 """get_derivative(Hierarchy self, FloatKey a0) -> double"""
1952 return _IMP_atom.Hierarchy_get_derivative(self, a0)
1956 """get_name(Hierarchy self) -> std::string"""
1957 return _IMP_atom.Hierarchy_get_name(self)
1960 def clear_caches(self):
1961 """clear_caches(Hierarchy self)"""
1962 return _IMP_atom.Hierarchy_clear_caches(self)
1965 def set_name(self, a0):
1966 """set_name(Hierarchy self, std::string a0)"""
1967 return _IMP_atom.Hierarchy_set_name(self, a0)
1971 """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
1972 return _IMP_atom.Hierarchy_set_check_level(self, a0)
1975 def add_to_derivative(self, a0, a1, a2):
1976 """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1977 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
1980 def set_is_optimized(self, a0, a1):
1981 """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
1982 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
1985 def get_is_optimized(self, a0):
1986 """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
1987 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
1991 """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
1992 return _IMP_atom.Hierarchy_get_check_level(self)
1995 def __eq__(self, *args):
1997 __eq__(Hierarchy self, Hierarchy o) -> bool
1998 __eq__(Hierarchy self, Particle d) -> bool
2000 return _IMP_atom.Hierarchy___eq__(self, *args)
2003 def __ne__(self, *args):
2005 __ne__(Hierarchy self, Hierarchy o) -> bool
2006 __ne__(Hierarchy self, Particle d) -> bool
2008 return _IMP_atom.Hierarchy___ne__(self, *args)
2011 def __le__(self, *args):
2013 __le__(Hierarchy self, Hierarchy o) -> bool
2014 __le__(Hierarchy self, Particle d) -> bool
2016 return _IMP_atom.Hierarchy___le__(self, *args)
2019 def __lt__(self, *args):
2021 __lt__(Hierarchy self, Hierarchy o) -> bool
2022 __lt__(Hierarchy self, Particle d) -> bool
2024 return _IMP_atom.Hierarchy___lt__(self, *args)
2027 def __ge__(self, *args):
2029 __ge__(Hierarchy self, Hierarchy o) -> bool
2030 __ge__(Hierarchy self, Particle d) -> bool
2032 return _IMP_atom.Hierarchy___ge__(self, *args)
2035 def __gt__(self, *args):
2037 __gt__(Hierarchy self, Hierarchy o) -> bool
2038 __gt__(Hierarchy self, Particle d) -> bool
2040 return _IMP_atom.Hierarchy___gt__(self, *args)
2044 """__hash__(Hierarchy self) -> std::size_t"""
2045 return _IMP_atom.Hierarchy___hash__(self)
2049 """__str__(Hierarchy self) -> std::string"""
2050 return _IMP_atom.Hierarchy___str__(self)
2054 """__repr__(Hierarchy self) -> std::string"""
2055 return _IMP_atom.Hierarchy___repr__(self)
2057 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2058 __del__ =
lambda self:
None
2059 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2060 Hierarchy_swigregister(Hierarchy)
2062 def Hierarchy_setup_particle(*args):
2064 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2065 setup_particle(Particle p) -> Hierarchy
2066 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2067 Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2069 return _IMP_atom.Hierarchy_setup_particle(*args)
2071 def Hierarchy_get_is_setup(*args):
2073 get_is_setup(Particle p) -> bool
2074 Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2076 return _IMP_atom.Hierarchy_get_is_setup(*args)
2078 def Hierarchy_get_traits():
2079 """Hierarchy_get_traits() -> HierarchyTraits"""
2080 return _IMP_atom.Hierarchy_get_traits()
2082 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2083 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2084 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2085 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2086 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2087 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2088 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2089 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2090 MASS_TYPE = _IMP_atom.MASS_TYPE
2091 STATE_TYPE = _IMP_atom.STATE_TYPE
2093 def get_by_type(mhd, t):
2094 """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2095 return _IMP_atom.get_by_type(mhd, t)
2097 def create_fragment(ps):
2098 """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2099 return _IMP_atom.create_fragment(ps)
2101 def get_internal_bonds(mhd):
2102 """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2103 return _IMP_atom.get_internal_bonds(mhd)
2106 """get_root(Hierarchy h) -> Hierarchy"""
2107 return _IMP_atom.get_root(h)
2111 show(Hierarchy h, _ostream out)
2114 return _IMP_atom.show(*args)
2118 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2119 create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2120 create_rigid_body(Hierarchy h) -> RigidBody
2122 return _IMP_atom.create_rigid_body(*args)
2125 """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2126 return _IMP_atom.create_compatible_rigid_body(h, reference)
2128 def setup_as_rigid_body(h):
2129 """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
2130 return _IMP_atom.setup_as_rigid_body(h)
2132 def get_is_heterogen(h):
2133 """get_is_heterogen(Hierarchy h) -> bool"""
2134 return _IMP_atom.get_is_heterogen(h)
2136 def create_clone(d):
2137 """create_clone(Hierarchy d) -> Hierarchy"""
2138 return _IMP_atom.create_clone(d)
2140 def create_clone_one(d):
2141 """create_clone_one(Hierarchy d) -> Hierarchy"""
2142 return _IMP_atom.create_clone_one(d)
2145 """destroy(Hierarchy d)"""
2146 return _IMP_atom.destroy(d)
2148 def get_bounding_box(h):
2149 """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2150 return _IMP_atom.get_bounding_box(h)
2152 def get_bounding_sphere(h):
2153 """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2154 return _IMP_atom.get_bounding_sphere(h)
2156 """Proxy of C++ IMP::atom::Angle class."""
2158 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2160 def __init__(self, *args):
2162 __init__(IMP::atom::Angle self) -> Angle
2163 __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2164 __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2166 this = _IMP_atom.new_Angle(*args)
2168 self.this.append(this)
2169 except __builtin__.Exception:
2172 def show(self, *args):
2174 show(Angle self, _ostream out)
2177 return _IMP_atom.Angle_show(self, *args)
2180 def setup_particle(*args):
2182 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2183 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2185 return _IMP_atom.Angle_setup_particle(*args)
2187 setup_particle = staticmethod(setup_particle)
2189 def get_is_setup(*args):
2191 get_is_setup(_ParticleAdaptor p) -> bool
2192 get_is_setup(Model m, ParticleIndex pi) -> bool
2194 return _IMP_atom.Angle_get_is_setup(*args)
2196 get_is_setup = staticmethod(get_is_setup)
2198 def get_particle(self, *args):
2200 get_particle(Angle self) -> Particle
2201 get_particle(Angle self, unsigned int i) -> Particle
2203 return _IMP_atom.Angle_get_particle(self, *args)
2206 def get_ideal(self):
2207 """get_ideal(Angle self) -> IMP::Float"""
2208 return _IMP_atom.Angle_get_ideal(self)
2211 def set_ideal(self, t):
2212 """set_ideal(Angle self, IMP::Float t)"""
2213 return _IMP_atom.Angle_set_ideal(self, t)
2216 def get_stiffness(self):
2217 """get_stiffness(Angle self) -> IMP::Float"""
2218 return _IMP_atom.Angle_get_stiffness(self)
2221 def set_stiffness(self, t):
2222 """set_stiffness(Angle self, IMP::Float t)"""
2223 return _IMP_atom.Angle_set_stiffness(self, t)
2226 def get_particle_key(i):
2227 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2228 return _IMP_atom.Angle_get_particle_key(i)
2230 get_particle_key = staticmethod(get_particle_key)
2232 def get_ideal_key():
2233 """get_ideal_key() -> FloatKey"""
2234 return _IMP_atom.Angle_get_ideal_key()
2236 get_ideal_key = staticmethod(get_ideal_key)
2238 def get_stiffness_key():
2239 """get_stiffness_key() -> FloatKey"""
2240 return _IMP_atom.Angle_get_stiffness_key()
2242 get_stiffness_key = staticmethod(get_stiffness_key)
2244 def add_attribute(self, *args):
2246 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2247 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2248 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2249 add_attribute(Angle self, StringKey a0, IMP::String a1)
2250 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2251 add_attribute(Angle self, ObjectKey a0, Object a1)
2253 return _IMP_atom.Angle_add_attribute(self, *args)
2256 def get_value(self, *args):
2258 get_value(Angle self, FloatKey a0) -> IMP::Float
2259 get_value(Angle self, IntKey a0) -> IMP::Int
2260 get_value(Angle self, StringKey a0) -> IMP::String
2261 get_value(Angle self, ParticleIndexKey a0) -> Particle
2262 get_value(Angle self, ObjectKey a0) -> Object
2264 return _IMP_atom.Angle_get_value(self, *args)
2267 def set_value(self, *args):
2269 set_value(Angle self, FloatKey a0, IMP::Float a1)
2270 set_value(Angle self, IntKey a0, IMP::Int a1)
2271 set_value(Angle self, StringKey a0, IMP::String a1)
2272 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2273 set_value(Angle self, ObjectKey a0, Object a1)
2275 return _IMP_atom.Angle_set_value(self, *args)
2278 def remove_attribute(self, *args):
2280 remove_attribute(Angle self, FloatKey a0)
2281 remove_attribute(Angle self, IntKey a0)
2282 remove_attribute(Angle self, StringKey a0)
2283 remove_attribute(Angle self, ParticleIndexKey a0)
2284 remove_attribute(Angle self, ObjectKey a0)
2286 return _IMP_atom.Angle_remove_attribute(self, *args)
2289 def has_attribute(self, *args):
2291 has_attribute(Angle self, FloatKey a0) -> bool
2292 has_attribute(Angle self, IntKey a0) -> bool
2293 has_attribute(Angle self, StringKey a0) -> bool
2294 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2295 has_attribute(Angle self, ObjectKey a0) -> bool
2297 return _IMP_atom.Angle_has_attribute(self, *args)
2300 def get_derivative(self, a0):
2301 """get_derivative(Angle self, FloatKey a0) -> double"""
2302 return _IMP_atom.Angle_get_derivative(self, a0)
2306 """get_name(Angle self) -> std::string"""
2307 return _IMP_atom.Angle_get_name(self)
2310 def clear_caches(self):
2311 """clear_caches(Angle self)"""
2312 return _IMP_atom.Angle_clear_caches(self)
2315 def set_name(self, a0):
2316 """set_name(Angle self, std::string a0)"""
2317 return _IMP_atom.Angle_set_name(self, a0)
2321 """set_check_level(Angle self, IMP::CheckLevel a0)"""
2322 return _IMP_atom.Angle_set_check_level(self, a0)
2325 def add_to_derivative(self, a0, a1, a2):
2326 """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2327 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2330 def set_is_optimized(self, a0, a1):
2331 """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2332 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2335 def get_is_optimized(self, a0):
2336 """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2337 return _IMP_atom.Angle_get_is_optimized(self, a0)
2341 """get_check_level(Angle self) -> IMP::CheckLevel"""
2342 return _IMP_atom.Angle_get_check_level(self)
2345 def __eq__(self, *args):
2347 __eq__(Angle self, Angle o) -> bool
2348 __eq__(Angle self, Particle d) -> bool
2350 return _IMP_atom.Angle___eq__(self, *args)
2353 def __ne__(self, *args):
2355 __ne__(Angle self, Angle o) -> bool
2356 __ne__(Angle self, Particle d) -> bool
2358 return _IMP_atom.Angle___ne__(self, *args)
2361 def __le__(self, *args):
2363 __le__(Angle self, Angle o) -> bool
2364 __le__(Angle self, Particle d) -> bool
2366 return _IMP_atom.Angle___le__(self, *args)
2369 def __lt__(self, *args):
2371 __lt__(Angle self, Angle o) -> bool
2372 __lt__(Angle self, Particle d) -> bool
2374 return _IMP_atom.Angle___lt__(self, *args)
2377 def __ge__(self, *args):
2379 __ge__(Angle self, Angle o) -> bool
2380 __ge__(Angle self, Particle d) -> bool
2382 return _IMP_atom.Angle___ge__(self, *args)
2385 def __gt__(self, *args):
2387 __gt__(Angle self, Angle o) -> bool
2388 __gt__(Angle self, Particle d) -> bool
2390 return _IMP_atom.Angle___gt__(self, *args)
2394 """__hash__(Angle self) -> std::size_t"""
2395 return _IMP_atom.Angle___hash__(self)
2399 """__str__(Angle self) -> std::string"""
2400 return _IMP_atom.Angle___str__(self)
2404 """__repr__(Angle self) -> std::string"""
2405 return _IMP_atom.Angle___repr__(self)
2407 __swig_destroy__ = _IMP_atom.delete_Angle
2408 __del__ =
lambda self:
None
2409 Angle_swigregister = _IMP_atom.Angle_swigregister
2410 Angle_swigregister(Angle)
2412 def Angle_setup_particle(*args):
2414 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2415 Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2417 return _IMP_atom.Angle_setup_particle(*args)
2419 def Angle_get_is_setup(*args):
2421 get_is_setup(_ParticleAdaptor p) -> bool
2422 Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2424 return _IMP_atom.Angle_get_is_setup(*args)
2426 def Angle_get_particle_key(i):
2427 """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2428 return _IMP_atom.Angle_get_particle_key(i)
2430 def Angle_get_ideal_key():
2431 """Angle_get_ideal_key() -> FloatKey"""
2432 return _IMP_atom.Angle_get_ideal_key()
2434 def Angle_get_stiffness_key():
2435 """Angle_get_stiffness_key() -> FloatKey"""
2436 return _IMP_atom.Angle_get_stiffness_key()
2439 """Proxy of C++ IMP::atom::Dihedral class."""
2441 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2443 def __init__(self, *args):
2445 __init__(IMP::atom::Dihedral self) -> Dihedral
2446 __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2447 __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2449 this = _IMP_atom.new_Dihedral(*args)
2451 self.this.append(this)
2452 except __builtin__.Exception:
2455 def show(self, *args):
2457 show(Dihedral self, _ostream out)
2460 return _IMP_atom.Dihedral_show(self, *args)
2463 def setup_particle(*args):
2465 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2466 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2468 return _IMP_atom.Dihedral_setup_particle(*args)
2470 setup_particle = staticmethod(setup_particle)
2472 def get_is_setup(*args):
2474 get_is_setup(_ParticleAdaptor p) -> bool
2475 get_is_setup(Model m, ParticleIndex pi) -> bool
2477 return _IMP_atom.Dihedral_get_is_setup(*args)
2479 get_is_setup = staticmethod(get_is_setup)
2481 def get_particle(self, *args):
2483 get_particle(Dihedral self) -> Particle
2484 get_particle(Dihedral self, unsigned int i) -> Particle
2486 return _IMP_atom.Dihedral_get_particle(self, *args)
2489 def get_ideal(self):
2490 """get_ideal(Dihedral self) -> IMP::Float"""
2491 return _IMP_atom.Dihedral_get_ideal(self)
2494 def set_ideal(self, t):
2495 """set_ideal(Dihedral self, IMP::Float t)"""
2496 return _IMP_atom.Dihedral_set_ideal(self, t)
2499 def get_multiplicity(self):
2500 """get_multiplicity(Dihedral self) -> IMP::Int"""
2501 return _IMP_atom.Dihedral_get_multiplicity(self)
2504 def set_multiplicity(self, t):
2505 """set_multiplicity(Dihedral self, IMP::Int t)"""
2506 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2509 def get_stiffness(self):
2510 """get_stiffness(Dihedral self) -> IMP::Float"""
2511 return _IMP_atom.Dihedral_get_stiffness(self)
2514 def set_stiffness(self, t):
2515 """set_stiffness(Dihedral self, IMP::Float t)"""
2516 return _IMP_atom.Dihedral_set_stiffness(self, t)
2519 def get_particle_key(i):
2520 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2521 return _IMP_atom.Dihedral_get_particle_key(i)
2523 get_particle_key = staticmethod(get_particle_key)
2525 def get_ideal_key():
2526 """get_ideal_key() -> FloatKey"""
2527 return _IMP_atom.Dihedral_get_ideal_key()
2529 get_ideal_key = staticmethod(get_ideal_key)
2531 def get_multiplicity_key():
2532 """get_multiplicity_key() -> IntKey"""
2533 return _IMP_atom.Dihedral_get_multiplicity_key()
2535 get_multiplicity_key = staticmethod(get_multiplicity_key)
2537 def get_stiffness_key():
2538 """get_stiffness_key() -> FloatKey"""
2539 return _IMP_atom.Dihedral_get_stiffness_key()
2541 get_stiffness_key = staticmethod(get_stiffness_key)
2543 def add_attribute(self, *args):
2545 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2546 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2547 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2548 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2549 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2550 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2552 return _IMP_atom.Dihedral_add_attribute(self, *args)
2555 def get_value(self, *args):
2557 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2558 get_value(Dihedral self, IntKey a0) -> IMP::Int
2559 get_value(Dihedral self, StringKey a0) -> IMP::String
2560 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2561 get_value(Dihedral self, ObjectKey a0) -> Object
2563 return _IMP_atom.Dihedral_get_value(self, *args)
2566 def set_value(self, *args):
2568 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2569 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2570 set_value(Dihedral self, StringKey a0, IMP::String a1)
2571 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2572 set_value(Dihedral self, ObjectKey a0, Object a1)
2574 return _IMP_atom.Dihedral_set_value(self, *args)
2577 def remove_attribute(self, *args):
2579 remove_attribute(Dihedral self, FloatKey a0)
2580 remove_attribute(Dihedral self, IntKey a0)
2581 remove_attribute(Dihedral self, StringKey a0)
2582 remove_attribute(Dihedral self, ParticleIndexKey a0)
2583 remove_attribute(Dihedral self, ObjectKey a0)
2585 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2588 def has_attribute(self, *args):
2590 has_attribute(Dihedral self, FloatKey a0) -> bool
2591 has_attribute(Dihedral self, IntKey a0) -> bool
2592 has_attribute(Dihedral self, StringKey a0) -> bool
2593 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2594 has_attribute(Dihedral self, ObjectKey a0) -> bool
2596 return _IMP_atom.Dihedral_has_attribute(self, *args)
2599 def get_derivative(self, a0):
2600 """get_derivative(Dihedral self, FloatKey a0) -> double"""
2601 return _IMP_atom.Dihedral_get_derivative(self, a0)
2605 """get_name(Dihedral self) -> std::string"""
2606 return _IMP_atom.Dihedral_get_name(self)
2609 def clear_caches(self):
2610 """clear_caches(Dihedral self)"""
2611 return _IMP_atom.Dihedral_clear_caches(self)
2614 def set_name(self, a0):
2615 """set_name(Dihedral self, std::string a0)"""
2616 return _IMP_atom.Dihedral_set_name(self, a0)
2620 """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2621 return _IMP_atom.Dihedral_set_check_level(self, a0)
2624 def add_to_derivative(self, a0, a1, a2):
2625 """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2626 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2629 def set_is_optimized(self, a0, a1):
2630 """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2631 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2634 def get_is_optimized(self, a0):
2635 """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2636 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2640 """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2641 return _IMP_atom.Dihedral_get_check_level(self)
2644 def __eq__(self, *args):
2646 __eq__(Dihedral self, Dihedral o) -> bool
2647 __eq__(Dihedral self, Particle d) -> bool
2649 return _IMP_atom.Dihedral___eq__(self, *args)
2652 def __ne__(self, *args):
2654 __ne__(Dihedral self, Dihedral o) -> bool
2655 __ne__(Dihedral self, Particle d) -> bool
2657 return _IMP_atom.Dihedral___ne__(self, *args)
2660 def __le__(self, *args):
2662 __le__(Dihedral self, Dihedral o) -> bool
2663 __le__(Dihedral self, Particle d) -> bool
2665 return _IMP_atom.Dihedral___le__(self, *args)
2668 def __lt__(self, *args):
2670 __lt__(Dihedral self, Dihedral o) -> bool
2671 __lt__(Dihedral self, Particle d) -> bool
2673 return _IMP_atom.Dihedral___lt__(self, *args)
2676 def __ge__(self, *args):
2678 __ge__(Dihedral self, Dihedral o) -> bool
2679 __ge__(Dihedral self, Particle d) -> bool
2681 return _IMP_atom.Dihedral___ge__(self, *args)
2684 def __gt__(self, *args):
2686 __gt__(Dihedral self, Dihedral o) -> bool
2687 __gt__(Dihedral self, Particle d) -> bool
2689 return _IMP_atom.Dihedral___gt__(self, *args)
2693 """__hash__(Dihedral self) -> std::size_t"""
2694 return _IMP_atom.Dihedral___hash__(self)
2698 """__str__(Dihedral self) -> std::string"""
2699 return _IMP_atom.Dihedral___str__(self)
2703 """__repr__(Dihedral self) -> std::string"""
2704 return _IMP_atom.Dihedral___repr__(self)
2706 __swig_destroy__ = _IMP_atom.delete_Dihedral
2707 __del__ =
lambda self:
None
2708 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2709 Dihedral_swigregister(Dihedral)
2711 def Dihedral_setup_particle(*args):
2713 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2714 Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2716 return _IMP_atom.Dihedral_setup_particle(*args)
2718 def Dihedral_get_is_setup(*args):
2720 get_is_setup(_ParticleAdaptor p) -> bool
2721 Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2723 return _IMP_atom.Dihedral_get_is_setup(*args)
2725 def Dihedral_get_particle_key(i):
2726 """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2727 return _IMP_atom.Dihedral_get_particle_key(i)
2729 def Dihedral_get_ideal_key():
2730 """Dihedral_get_ideal_key() -> FloatKey"""
2731 return _IMP_atom.Dihedral_get_ideal_key()
2733 def Dihedral_get_multiplicity_key():
2734 """Dihedral_get_multiplicity_key() -> IntKey"""
2735 return _IMP_atom.Dihedral_get_multiplicity_key()
2737 def Dihedral_get_stiffness_key():
2738 """Dihedral_get_stiffness_key() -> FloatKey"""
2739 return _IMP_atom.Dihedral_get_stiffness_key()
2742 """Proxy of C++ IMP::atom::SmoothingFunction class."""
2744 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2746 def __init__(self, *args, **kwargs):
2747 raise AttributeError(
"No constructor defined - class is abstract")
2749 def __call__(self, *args):
2751 __call__(SmoothingFunction self, double score, double distance) -> double
2752 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2754 return _IMP_atom.SmoothingFunction___call__(self, *args)
2756 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2757 __del__ =
lambda self:
None
2760 """__str__(SmoothingFunction self) -> std::string"""
2761 return _IMP_atom.SmoothingFunction___str__(self)
2765 """__repr__(SmoothingFunction self) -> std::string"""
2766 return _IMP_atom.SmoothingFunction___repr__(self)
2771 return _object_cast_to_SmoothingFunction(o)
2773 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2774 SmoothingFunction_swigregister(SmoothingFunction)
2776 class ForceSwitch(SmoothingFunction):
2777 """Proxy of C++ IMP::atom::ForceSwitch class."""
2779 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2781 def __init__(self, min_distance, max_distance):
2782 """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2783 this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2785 self.this.append(this)
2786 except __builtin__.Exception:
2789 def __call__(self, *args):
2791 __call__(ForceSwitch self, double score, double distance) -> double
2792 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2794 return _IMP_atom.ForceSwitch___call__(self, *args)
2797 def get_version_info(self):
2798 """get_version_info(ForceSwitch self) -> VersionInfo"""
2799 return _IMP_atom.ForceSwitch_get_version_info(self)
2803 """__str__(ForceSwitch self) -> std::string"""
2804 return _IMP_atom.ForceSwitch___str__(self)
2808 """__repr__(ForceSwitch self) -> std::string"""
2809 return _IMP_atom.ForceSwitch___repr__(self)
2814 return _object_cast_to_ForceSwitch(o)
2816 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2817 ForceSwitch_swigregister(ForceSwitch)
2820 """Proxy of C++ IMP::atom::AngleSingletonScore class."""
2822 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2824 def __init__(self, f):
2825 """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2826 this = _IMP_atom.new_AngleSingletonScore(f)
2828 self.this.append(this)
2829 except __builtin__.Exception:
2832 def do_get_inputs(self, m, pis):
2833 """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2834 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2837 def get_version_info(self):
2838 """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2839 return _IMP_atom.AngleSingletonScore_get_version_info(self)
2843 """__str__(AngleSingletonScore self) -> std::string"""
2844 return _IMP_atom.AngleSingletonScore___str__(self)
2848 """__repr__(AngleSingletonScore self) -> std::string"""
2849 return _IMP_atom.AngleSingletonScore___repr__(self)
2854 return _object_cast_to_AngleSingletonScore(o)
2856 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2857 AngleSingletonScore_swigregister(AngleSingletonScore)
2860 """Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2862 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2865 """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2866 this = _IMP_atom.new_BondEndpointsRefiner()
2868 self.this.append(this)
2869 except __builtin__.Exception:
2872 def do_get_inputs(self, m, pis):
2873 """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2874 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2877 def get_version_info(self):
2878 """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2879 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2883 """__str__(BondEndpointsRefiner self) -> std::string"""
2884 return _IMP_atom.BondEndpointsRefiner___str__(self)
2888 """__repr__(BondEndpointsRefiner self) -> std::string"""
2889 return _IMP_atom.BondEndpointsRefiner___repr__(self)
2894 return _object_cast_to_BondEndpointsRefiner(o)
2896 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2897 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2900 """Proxy of C++ IMP::atom::BondPairContainer class."""
2902 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2904 def __init__(self, sc):
2905 """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2906 this = _IMP_atom.new_BondPairContainer(sc)
2908 self.this.append(this)
2909 except __builtin__.Exception:
2912 def do_get_inputs(self):
2913 """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2914 return _IMP_atom.BondPairContainer_do_get_inputs(self)
2917 def do_apply(self, sm):
2918 """do_apply(BondPairContainer self, PairModifier sm)"""
2919 return _IMP_atom.BondPairContainer_do_apply(self, sm)
2922 def get_version_info(self):
2923 """get_version_info(BondPairContainer self) -> VersionInfo"""
2924 return _IMP_atom.BondPairContainer_get_version_info(self)
2928 """__str__(BondPairContainer self) -> std::string"""
2929 return _IMP_atom.BondPairContainer___str__(self)
2933 """__repr__(BondPairContainer self) -> std::string"""
2934 return _IMP_atom.BondPairContainer___repr__(self)
2939 return _object_cast_to_BondPairContainer(o)
2941 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
2942 BondPairContainer_swigregister(BondPairContainer)
2945 """Proxy of C++ IMP::atom::BondSingletonScore class."""
2947 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2949 def __init__(self, f):
2950 """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
2951 this = _IMP_atom.new_BondSingletonScore(f)
2953 self.this.append(this)
2954 except __builtin__.Exception:
2957 def get_unary_function(self):
2958 """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
2959 return _IMP_atom.BondSingletonScore_get_unary_function(self)
2962 def do_get_inputs(self, m, pis):
2963 """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2964 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
2967 def get_version_info(self):
2968 """get_version_info(BondSingletonScore self) -> VersionInfo"""
2969 return _IMP_atom.BondSingletonScore_get_version_info(self)
2973 """__str__(BondSingletonScore self) -> std::string"""
2974 return _IMP_atom.BondSingletonScore___str__(self)
2978 """__repr__(BondSingletonScore self) -> std::string"""
2979 return _IMP_atom.BondSingletonScore___repr__(self)
2984 return _object_cast_to_BondSingletonScore(o)
2986 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
2987 BondSingletonScore_swigregister(BondSingletonScore)
2990 """Proxy of C++ IMP::atom::DihedralSingletonScore class."""
2992 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2995 """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
2996 this = _IMP_atom.new_DihedralSingletonScore()
2998 self.this.append(this)
2999 except __builtin__.Exception:
3002 def do_get_inputs(self, m, pis):
3003 """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3004 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3007 def get_version_info(self):
3008 """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3009 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3013 """__str__(DihedralSingletonScore self) -> std::string"""
3014 return _IMP_atom.DihedralSingletonScore___str__(self)
3018 """__repr__(DihedralSingletonScore self) -> std::string"""
3019 return _IMP_atom.DihedralSingletonScore___repr__(self)
3024 return _object_cast_to_DihedralSingletonScore(o)
3026 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3027 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3030 """Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3032 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3034 def __init__(self, f):
3035 """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3036 this = _IMP_atom.new_ImproperSingletonScore(f)
3038 self.this.append(this)
3039 except __builtin__.Exception:
3042 def do_get_inputs(self, m, pis):
3043 """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3044 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3047 def get_version_info(self):
3048 """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3049 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3053 """__str__(ImproperSingletonScore self) -> std::string"""
3054 return _IMP_atom.ImproperSingletonScore___str__(self)
3058 """__repr__(ImproperSingletonScore self) -> std::string"""
3059 return _IMP_atom.ImproperSingletonScore___repr__(self)
3064 return _object_cast_to_ImproperSingletonScore(o)
3066 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3067 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3070 """Proxy of C++ IMP::atom::CenterOfMass class."""
3072 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3074 def get_constraint(self):
3075 """get_constraint(CenterOfMass self) -> Constraint"""
3076 return _IMP_atom.CenterOfMass_get_constraint(self)
3080 """get_mass(CenterOfMass self) -> IMP::Float"""
3081 return _IMP_atom.CenterOfMass_get_mass(self)
3084 def get_coordinate(self, i):
3085 """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3086 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3089 def get_coordinates(self):
3090 """get_coordinates(CenterOfMass self) -> Vector3D"""
3091 return _IMP_atom.CenterOfMass_get_coordinates(self)
3094 def __init__(self, *args):
3096 __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3097 __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3098 __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3100 this = _IMP_atom.new_CenterOfMass(*args)
3102 self.this.append(this)
3103 except __builtin__.Exception:
3106 def show(self, *args):
3108 show(CenterOfMass self, _ostream out)
3109 show(CenterOfMass self)
3111 return _IMP_atom.CenterOfMass_show(self, *args)
3114 def setup_particle(*args):
3116 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3117 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3118 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3119 setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3121 return _IMP_atom.CenterOfMass_setup_particle(*args)
3123 setup_particle = staticmethod(setup_particle)
3125 def get_is_setup(*args):
3127 get_is_setup(_ParticleAdaptor p) -> bool
3128 get_is_setup(Model m, ParticleIndex pi) -> bool
3130 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3132 get_is_setup = staticmethod(get_is_setup)
3134 def add_attribute(self, *args):
3136 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3137 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3138 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3139 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3140 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3141 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3143 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3146 def get_value(self, *args):
3148 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3149 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3150 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3151 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3152 get_value(CenterOfMass self, ObjectKey a0) -> Object
3154 return _IMP_atom.CenterOfMass_get_value(self, *args)
3157 def set_value(self, *args):
3159 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3160 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3161 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3162 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3163 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3165 return _IMP_atom.CenterOfMass_set_value(self, *args)
3168 def remove_attribute(self, *args):
3170 remove_attribute(CenterOfMass self, FloatKey a0)
3171 remove_attribute(CenterOfMass self, IntKey a0)
3172 remove_attribute(CenterOfMass self, StringKey a0)
3173 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3174 remove_attribute(CenterOfMass self, ObjectKey a0)
3176 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3179 def has_attribute(self, *args):
3181 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3182 has_attribute(CenterOfMass self, IntKey a0) -> bool
3183 has_attribute(CenterOfMass self, StringKey a0) -> bool
3184 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3185 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3187 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3190 def get_derivative(self, a0):
3191 """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3192 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3196 """get_name(CenterOfMass self) -> std::string"""
3197 return _IMP_atom.CenterOfMass_get_name(self)
3200 def clear_caches(self):
3201 """clear_caches(CenterOfMass self)"""
3202 return _IMP_atom.CenterOfMass_clear_caches(self)
3205 def set_name(self, a0):
3206 """set_name(CenterOfMass self, std::string a0)"""
3207 return _IMP_atom.CenterOfMass_set_name(self, a0)
3211 """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3212 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3215 def add_to_derivative(self, a0, a1, a2):
3216 """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3217 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3220 def set_is_optimized(self, a0, a1):
3221 """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3222 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3225 def get_is_optimized(self, a0):
3226 """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3227 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3231 """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3232 return _IMP_atom.CenterOfMass_get_check_level(self)
3235 def __eq__(self, *args):
3237 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3238 __eq__(CenterOfMass self, Particle d) -> bool
3240 return _IMP_atom.CenterOfMass___eq__(self, *args)
3243 def __ne__(self, *args):
3245 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3246 __ne__(CenterOfMass self, Particle d) -> bool
3248 return _IMP_atom.CenterOfMass___ne__(self, *args)
3251 def __le__(self, *args):
3253 __le__(CenterOfMass self, CenterOfMass o) -> bool
3254 __le__(CenterOfMass self, Particle d) -> bool
3256 return _IMP_atom.CenterOfMass___le__(self, *args)
3259 def __lt__(self, *args):
3261 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3262 __lt__(CenterOfMass self, Particle d) -> bool
3264 return _IMP_atom.CenterOfMass___lt__(self, *args)
3267 def __ge__(self, *args):
3269 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3270 __ge__(CenterOfMass self, Particle d) -> bool
3272 return _IMP_atom.CenterOfMass___ge__(self, *args)
3275 def __gt__(self, *args):
3277 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3278 __gt__(CenterOfMass self, Particle d) -> bool
3280 return _IMP_atom.CenterOfMass___gt__(self, *args)
3284 """__hash__(CenterOfMass self) -> std::size_t"""
3285 return _IMP_atom.CenterOfMass___hash__(self)
3289 """__str__(CenterOfMass self) -> std::string"""
3290 return _IMP_atom.CenterOfMass___str__(self)
3294 """__repr__(CenterOfMass self) -> std::string"""
3295 return _IMP_atom.CenterOfMass___repr__(self)
3297 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3298 __del__ =
lambda self:
None
3299 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3300 CenterOfMass_swigregister(CenterOfMass)
3302 def CenterOfMass_setup_particle(*args):
3304 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3305 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3306 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3307 CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3309 return _IMP_atom.CenterOfMass_setup_particle(*args)
3311 def CenterOfMass_get_is_setup(*args):
3313 get_is_setup(_ParticleAdaptor p) -> bool
3314 CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3316 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3319 """Proxy of C++ IMP::atom::CoverBond class."""
3321 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3324 """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3325 this = _IMP_atom.new_CoverBond()
3327 self.this.append(this)
3328 except __builtin__.Exception:
3331 def do_get_inputs(self, m, pis):
3332 """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3333 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3336 def do_get_outputs(self, m, pis):
3337 """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3338 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3341 def get_version_info(self):
3342 """get_version_info(CoverBond self) -> VersionInfo"""
3343 return _IMP_atom.CoverBond_get_version_info(self)
3347 """__str__(CoverBond self) -> std::string"""
3348 return _IMP_atom.CoverBond___str__(self)
3352 """__repr__(CoverBond self) -> std::string"""
3353 return _IMP_atom.CoverBond___repr__(self)
3358 return _object_cast_to_CoverBond(o)
3360 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3361 CoverBond_swigregister(CoverBond)
3364 """Proxy of C++ IMP::atom::Simulator class."""
3366 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3368 def __init__(self, *args):
3370 __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3371 __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3372 __init__(IMP::atom::Simulator self, Model m) -> Simulator
3374 if self.__class__ == Simulator:
3378 this = _IMP_atom.new_Simulator(_self, *args)
3380 self.this.append(this)
3381 except __builtin__.Exception:
3384 if self.__class__ != Simulator:
3385 _director_objects.register(self)
3390 def simulate(self, time_in_fs):
3391 """simulate(Simulator self, double time_in_fs) -> double"""
3392 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3395 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3397 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3398 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3399 simulate_wave(Simulator self, double time_in_fs) -> double
3401 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3404 def get_temperature(self):
3405 """get_temperature(Simulator self) -> double"""
3406 return _IMP_atom.Simulator_get_temperature(self)
3409 def set_temperature(self, d):
3410 """set_temperature(Simulator self, double d)"""
3411 return _IMP_atom.Simulator_set_temperature(self, d)
3414 def set_maximum_time_step(self, ts):
3415 """set_maximum_time_step(Simulator self, double ts)"""
3416 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3419 def get_maximum_time_step(self):
3420 """get_maximum_time_step(Simulator self) -> double"""
3421 return _IMP_atom.Simulator_get_maximum_time_step(self)
3424 def get_last_time_step(self):
3425 """get_last_time_step(Simulator self) -> double"""
3426 return _IMP_atom.Simulator_get_last_time_step(self)
3429 def set_time_step(self, ts):
3430 """set_time_step(Simulator self, double ts)"""
3431 return _IMP_atom.Simulator_set_time_step(self, ts)
3435 """get_kt(Simulator self) -> double"""
3436 return _IMP_atom.Simulator_get_kt(self)
3439 def get_current_time(self):
3440 """get_current_time(Simulator self) -> double"""
3441 return _IMP_atom.Simulator_get_current_time(self)
3444 def set_current_time(self, ct):
3445 """set_current_time(Simulator self, double ct)"""
3446 return _IMP_atom.Simulator_set_current_time(self, ct)
3449 def get_simulation_particles(self):
3450 """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3451 return _IMP_atom.Simulator_get_simulation_particles(self)
3454 def get_simulation_particle_indexes(self):
3455 """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3456 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3459 def remove_particle(self, d):
3460 """remove_particle(Simulator self, Particle d)"""
3461 return _IMP_atom.Simulator_remove_particle(self, d)
3464 def remove_particles(self, d):
3465 """remove_particles(Simulator self, IMP::Particles const & d)"""
3466 return _IMP_atom.Simulator_remove_particles(self, d)
3469 def set_particles(self, ps):
3470 """set_particles(Simulator self, IMP::Particles const & ps)"""
3471 return _IMP_atom.Simulator_set_particles(self, ps)
3474 def set_particles_order(self, objs):
3475 """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3476 return _IMP_atom.Simulator_set_particles_order(self, objs)
3480 """add_particle(Simulator self, Particle obj) -> unsigned int"""
3481 return _IMP_atom.Simulator_add_particle(self, obj)
3485 """add_particles(Simulator self, IMP::Particles const & objs)"""
3486 return _IMP_atom.Simulator_add_particles(self, objs)
3489 def clear_particles(self):
3490 """clear_particles(Simulator self)"""
3491 return _IMP_atom.Simulator_clear_particles(self)
3494 def get_number_of_particles(self):
3495 """get_number_of_particles(Simulator self) -> unsigned int"""
3496 return _IMP_atom.Simulator_get_number_of_particles(self)
3499 def get_has_particles(self):
3500 """get_has_particles(Simulator self) -> bool"""
3501 return _IMP_atom.Simulator_get_has_particles(self)
3504 def get_particle(self, i):
3505 """get_particle(Simulator self, unsigned int i) -> Particle"""
3506 return _IMP_atom.Simulator_get_particle(self, i)
3510 """get_particles(Simulator self) -> IMP::Particles"""
3511 return _IMP_atom.Simulator_get_particles(self)
3514 def reserve_particles(self, sz):
3515 """reserve_particles(Simulator self, unsigned int sz)"""
3516 return _IMP_atom.Simulator_reserve_particles(self, sz)
3519 def do_optimize(self, max_steps):
3520 """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3521 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3524 def setup(self, arg0):
3525 """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3526 return _IMP_atom.Simulator_setup(self, arg0)
3529 def do_step(self, sc, dt):
3530 """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3531 return _IMP_atom.Simulator_do_step(self, sc, dt)
3534 def get_is_simulation_particle(self, p):
3535 """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3536 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3539 def do_simulate(self, time):
3540 """do_simulate(Simulator self, double time) -> double"""
3541 return _IMP_atom.Simulator_do_simulate(self, time)
3544 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3546 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3547 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3548 do_simulate_wave(Simulator self, double time_in_fs) -> double
3550 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3554 """__str__(Simulator self) -> std::string"""
3555 return _IMP_atom.Simulator___str__(self)
3559 """__repr__(Simulator self) -> std::string"""
3560 return _IMP_atom.Simulator___repr__(self)
3565 return _object_cast_to_Simulator(o)
3568 def get_type_name(self):
3569 return self.__class__.__name__
3570 def do_show(self, out):
3572 def get_version_info(self):
3573 if"IMP::atom" ==
"IMP":
3574 return VersionInfo(self.__module__,
3575 __import__(self.__module__).get_module_version())
3578 __import__(self.__module__).get_module_version())
3581 return _object_cast_to_Simulator(o)
3583 __swig_destroy__ = _IMP_atom.delete_Simulator
3584 __del__ =
lambda self:
None
3585 def __disown__(self):
3587 _IMP_atom.disown_Simulator(self)
3588 return weakref_proxy(self)
3590 def do_destroy(self):
3591 """do_destroy(Simulator self)"""
3592 return _IMP_atom.Simulator_do_destroy(self)
3595 def handle_set_has_required_score_states(self, arg0):
3596 """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3597 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3600 def do_get_inputs(self):
3601 """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3602 return _IMP_atom.Simulator_do_get_inputs(self)
3605 def do_get_outputs(self):
3606 """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3607 return _IMP_atom.Simulator_do_get_outputs(self)
3610 def do_get_interactions(self):
3611 """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3612 return _IMP_atom.Simulator_do_get_interactions(self)
3614 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3615 Simulator_swigregister(Simulator)
3617 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3618 class BrownianDynamics(Simulator):
3619 """Proxy of C++ IMP::atom::BrownianDynamics class."""
3621 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3623 def __init__(self, *args):
3625 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics
3626 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3627 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3628 __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3630 this = _IMP_atom.new_BrownianDynamics(*args)
3632 self.this.append(this)
3633 except __builtin__.Exception:
3636 def set_maximum_move(self, ms):
3637 """set_maximum_move(BrownianDynamics self, double ms)"""
3638 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms)
3641 def set_use_stochastic_runge_kutta(self, tf):
3642 """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3643 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3646 def get_version_info(self):
3647 """get_version_info(BrownianDynamics self) -> VersionInfo"""
3648 return _IMP_atom.BrownianDynamics_get_version_info(self)
3652 """__str__(BrownianDynamics self) -> std::string"""
3653 return _IMP_atom.BrownianDynamics___str__(self)
3657 """__repr__(BrownianDynamics self) -> std::string"""
3658 return _IMP_atom.BrownianDynamics___repr__(self)
3663 return _object_cast_to_BrownianDynamics(o)
3665 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3666 BrownianDynamics_swigregister(BrownianDynamics)
3670 """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3671 return _IMP_atom.get_maximum_time_step_estimate(bd)
3673 def get_harmonic_sigma(D, f):
3674 """get_harmonic_sigma(double D, double f) -> double"""
3675 return _IMP_atom.get_harmonic_sigma(D, f)
3676 class BrownianDynamicsTAMD(BrownianDynamics):
3677 """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3679 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3681 def __init__(self, *args):
3683 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3684 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3685 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3687 this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3689 self.this.append(this)
3690 except __builtin__.Exception:
3694 """__str__(BrownianDynamicsTAMD self) -> std::string"""
3695 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3699 """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3700 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3705 return _object_cast_to_BrownianDynamicsTAMD(o)
3707 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3708 __del__ =
lambda self:
None
3709 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3710 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3713 """Proxy of C++ IMP::atom::Diffusion class."""
3715 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3717 def __init__(self, *args):
3719 __init__(IMP::atom::Diffusion self) -> Diffusion
3720 __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3721 __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3723 this = _IMP_atom.new_Diffusion(*args)
3725 self.this.append(this)
3726 except __builtin__.Exception:
3729 def show(self, *args):
3731 show(Diffusion self, _ostream out)
3732 show(Diffusion self)
3734 return _IMP_atom.Diffusion_show(self, *args)
3737 def setup_particle(*args):
3739 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3740 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3741 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3742 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3743 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3744 setup_particle(_ParticleAdaptor decorator) -> Diffusion
3746 return _IMP_atom.Diffusion_setup_particle(*args)
3748 setup_particle = staticmethod(setup_particle)
3750 def get_is_setup(*args):
3752 get_is_setup(_ParticleAdaptor p) -> bool
3753 get_is_setup(Model m, ParticleIndex p) -> bool
3755 return _IMP_atom.Diffusion_get_is_setup(*args)
3757 get_is_setup = staticmethod(get_is_setup)
3759 def set_diffusion_coefficient(self, d):
3760 """set_diffusion_coefficient(Diffusion self, double d)"""
3761 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3765 """get_diffusion_coefficient(Diffusion self) -> double"""
3766 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3769 def get_diffusion_coefficient_key():
3770 """get_diffusion_coefficient_key() -> FloatKey"""
3771 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3773 get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3775 def add_attribute(self, *args):
3777 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3778 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3779 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3780 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3781 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3782 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3784 return _IMP_atom.Diffusion_add_attribute(self, *args)
3787 def get_value(self, *args):
3789 get_value(Diffusion self, FloatKey a0) -> IMP::Float
3790 get_value(Diffusion self, IntKey a0) -> IMP::Int
3791 get_value(Diffusion self, StringKey a0) -> IMP::String
3792 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3793 get_value(Diffusion self, ObjectKey a0) -> Object
3795 return _IMP_atom.Diffusion_get_value(self, *args)
3798 def set_value(self, *args):
3800 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3801 set_value(Diffusion self, IntKey a0, IMP::Int a1)
3802 set_value(Diffusion self, StringKey a0, IMP::String a1)
3803 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3804 set_value(Diffusion self, ObjectKey a0, Object a1)
3806 return _IMP_atom.Diffusion_set_value(self, *args)
3809 def remove_attribute(self, *args):
3811 remove_attribute(Diffusion self, FloatKey a0)
3812 remove_attribute(Diffusion self, IntKey a0)
3813 remove_attribute(Diffusion self, StringKey a0)
3814 remove_attribute(Diffusion self, ParticleIndexKey a0)
3815 remove_attribute(Diffusion self, ObjectKey a0)
3817 return _IMP_atom.Diffusion_remove_attribute(self, *args)
3820 def has_attribute(self, *args):
3822 has_attribute(Diffusion self, FloatKey a0) -> bool
3823 has_attribute(Diffusion self, IntKey a0) -> bool
3824 has_attribute(Diffusion self, StringKey a0) -> bool
3825 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3826 has_attribute(Diffusion self, ObjectKey a0) -> bool
3828 return _IMP_atom.Diffusion_has_attribute(self, *args)
3831 def get_derivative(self, a0):
3832 """get_derivative(Diffusion self, FloatKey a0) -> double"""
3833 return _IMP_atom.Diffusion_get_derivative(self, a0)
3837 """get_name(Diffusion self) -> std::string"""
3838 return _IMP_atom.Diffusion_get_name(self)
3841 def clear_caches(self):
3842 """clear_caches(Diffusion self)"""
3843 return _IMP_atom.Diffusion_clear_caches(self)
3846 def set_name(self, a0):
3847 """set_name(Diffusion self, std::string a0)"""
3848 return _IMP_atom.Diffusion_set_name(self, a0)
3852 """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3853 return _IMP_atom.Diffusion_set_check_level(self, a0)
3856 def add_to_derivative(self, a0, a1, a2):
3857 """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3858 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3861 def set_is_optimized(self, a0, a1):
3862 """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3863 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3866 def get_is_optimized(self, a0):
3867 """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3868 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3872 """get_check_level(Diffusion self) -> IMP::CheckLevel"""
3873 return _IMP_atom.Diffusion_get_check_level(self)
3876 def __eq__(self, *args):
3878 __eq__(Diffusion self, Diffusion o) -> bool
3879 __eq__(Diffusion self, Particle d) -> bool
3881 return _IMP_atom.Diffusion___eq__(self, *args)
3884 def __ne__(self, *args):
3886 __ne__(Diffusion self, Diffusion o) -> bool
3887 __ne__(Diffusion self, Particle d) -> bool
3889 return _IMP_atom.Diffusion___ne__(self, *args)
3892 def __le__(self, *args):
3894 __le__(Diffusion self, Diffusion o) -> bool
3895 __le__(Diffusion self, Particle d) -> bool
3897 return _IMP_atom.Diffusion___le__(self, *args)
3900 def __lt__(self, *args):
3902 __lt__(Diffusion self, Diffusion o) -> bool
3903 __lt__(Diffusion self, Particle d) -> bool
3905 return _IMP_atom.Diffusion___lt__(self, *args)
3908 def __ge__(self, *args):
3910 __ge__(Diffusion self, Diffusion o) -> bool
3911 __ge__(Diffusion self, Particle d) -> bool
3913 return _IMP_atom.Diffusion___ge__(self, *args)
3916 def __gt__(self, *args):
3918 __gt__(Diffusion self, Diffusion o) -> bool
3919 __gt__(Diffusion self, Particle d) -> bool
3921 return _IMP_atom.Diffusion___gt__(self, *args)
3925 """__hash__(Diffusion self) -> std::size_t"""
3926 return _IMP_atom.Diffusion___hash__(self)
3930 """__str__(Diffusion self) -> std::string"""
3931 return _IMP_atom.Diffusion___str__(self)
3935 """__repr__(Diffusion self) -> std::string"""
3936 return _IMP_atom.Diffusion___repr__(self)
3938 __swig_destroy__ = _IMP_atom.delete_Diffusion
3939 __del__ =
lambda self:
None
3940 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
3941 Diffusion_swigregister(Diffusion)
3943 def Diffusion_setup_particle(*args):
3945 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3946 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3947 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3948 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3949 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3950 Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
3952 return _IMP_atom.Diffusion_setup_particle(*args)
3954 def Diffusion_get_is_setup(*args):
3956 get_is_setup(_ParticleAdaptor p) -> bool
3957 Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
3959 return _IMP_atom.Diffusion_get_is_setup(*args)
3961 def Diffusion_get_diffusion_coefficient_key():
3962 """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
3963 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3966 def get_diffusion_coefficient_from_cm2_per_second(din):
3967 """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
3968 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
3969 class RigidBodyDiffusion(Diffusion):
3970 """Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
3972 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3974 def __init__(self, *args):
3976 __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
3977 __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
3978 __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
3980 this = _IMP_atom.new_RigidBodyDiffusion(*args)
3982 self.this.append(this)
3983 except __builtin__.Exception:
3986 def show(self, *args):
3988 show(RigidBodyDiffusion self, _ostream out)
3989 show(RigidBodyDiffusion self)
3991 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
3994 def setup_particle(*args):
3996 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
3997 setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
3999 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4001 setup_particle = staticmethod(setup_particle)
4004 """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4005 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4008 def set_rotational_diffusion_coefficient(self, d):
4009 """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4010 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4013 def get_is_setup(*args):
4015 get_is_setup(_ParticleAdaptor p) -> bool
4016 get_is_setup(Model m, ParticleIndex p) -> bool
4018 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4020 get_is_setup = staticmethod(get_is_setup)
4022 def get_rotational_diffusion_coefficient_key():
4023 """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4024 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4026 get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4028 def add_attribute(self, *args):
4030 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4031 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4032 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4033 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4034 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4035 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4037 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4040 def get_value(self, *args):
4042 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4043 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4044 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4045 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4046 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4048 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4051 def set_value(self, *args):
4053 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4054 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4055 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4056 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4057 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4059 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4062 def remove_attribute(self, *args):
4064 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4065 remove_attribute(RigidBodyDiffusion self, IntKey a0)
4066 remove_attribute(RigidBodyDiffusion self, StringKey a0)
4067 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4068 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4070 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4073 def has_attribute(self, *args):
4075 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4076 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4077 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4078 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4079 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4081 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4084 def get_derivative(self, a0):
4085 """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4086 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4090 """get_name(RigidBodyDiffusion self) -> std::string"""
4091 return _IMP_atom.RigidBodyDiffusion_get_name(self)
4094 def clear_caches(self):
4095 """clear_caches(RigidBodyDiffusion self)"""
4096 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4099 def set_name(self, a0):
4100 """set_name(RigidBodyDiffusion self, std::string a0)"""
4101 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4105 """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4106 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4109 def add_to_derivative(self, a0, a1, a2):
4110 """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4111 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4114 def set_is_optimized(self, a0, a1):
4115 """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4116 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4119 def get_is_optimized(self, a0):
4120 """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4121 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4125 """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4126 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4129 def __eq__(self, *args):
4131 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4132 __eq__(RigidBodyDiffusion self, Particle d) -> bool
4134 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4137 def __ne__(self, *args):
4139 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4140 __ne__(RigidBodyDiffusion self, Particle d) -> bool
4142 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4145 def __le__(self, *args):
4147 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4148 __le__(RigidBodyDiffusion self, Particle d) -> bool
4150 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4153 def __lt__(self, *args):
4155 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4156 __lt__(RigidBodyDiffusion self, Particle d) -> bool
4158 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4161 def __ge__(self, *args):
4163 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4164 __ge__(RigidBodyDiffusion self, Particle d) -> bool
4166 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4169 def __gt__(self, *args):
4171 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4172 __gt__(RigidBodyDiffusion self, Particle d) -> bool
4174 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4178 """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4179 return _IMP_atom.RigidBodyDiffusion___hash__(self)
4183 """__str__(RigidBodyDiffusion self) -> std::string"""
4184 return _IMP_atom.RigidBodyDiffusion___str__(self)
4188 """__repr__(RigidBodyDiffusion self) -> std::string"""
4189 return _IMP_atom.RigidBodyDiffusion___repr__(self)
4191 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4192 __del__ =
lambda self:
None
4193 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4194 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4196 def RigidBodyDiffusion_setup_particle(*args):
4198 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4199 RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4201 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4203 def RigidBodyDiffusion_get_is_setup(*args):
4205 get_is_setup(_ParticleAdaptor p) -> bool
4206 RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4208 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4210 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4211 """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4212 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4215 """Proxy of C++ IMP::atom::TAMDParticle class."""
4217 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4219 def __init__(self, *args):
4221 __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4222 __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4223 __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4225 this = _IMP_atom.new_TAMDParticle(*args)
4227 self.this.append(this)
4228 except __builtin__.Exception:
4231 def show(self, *args):
4233 show(TAMDParticle self, _ostream out)
4234 show(TAMDParticle self)
4236 return _IMP_atom.TAMDParticle_show(self, *args)
4239 def setup_particle(*args):
4241 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4242 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4243 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4244 setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4246 return _IMP_atom.TAMDParticle_setup_particle(*args)
4248 setup_particle = staticmethod(setup_particle)
4250 def get_is_setup(*args):
4252 get_is_setup(_ParticleAdaptor p) -> bool
4253 get_is_setup(Model m, ParticleIndex p) -> bool
4255 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4257 get_is_setup = staticmethod(get_is_setup)
4259 def get_reference_particle_index(self):
4260 """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4261 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4264 def set_temperature_scale_factor(self, tsf):
4265 """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4266 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4269 def get_temperature_scale_factor(self):
4270 """get_temperature_scale_factor(TAMDParticle self) -> double"""
4271 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4274 def set_friction_scale_factor(self, tsf):
4275 """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4276 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4279 def get_friction_scale_factor(self):
4280 """get_friction_scale_factor(TAMDParticle self) -> double"""
4281 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4284 def update_coordinates_from_ref(self):
4285 """update_coordinates_from_ref(TAMDParticle self)"""
4286 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4289 def get_temperature_scale_factor_key():
4290 """get_temperature_scale_factor_key() -> FloatKey"""
4291 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4293 get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4295 def get_friction_scale_factor_key():
4296 """get_friction_scale_factor_key() -> FloatKey"""
4297 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4299 get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4301 def get_reference_particle_index_key():
4302 """get_reference_particle_index_key() -> ParticleIndexKey"""
4303 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4305 get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4307 def add_attribute(self, *args):
4309 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4310 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4311 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4312 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4313 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4314 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4316 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4319 def get_value(self, *args):
4321 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4322 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4323 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4324 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4325 get_value(TAMDParticle self, ObjectKey a0) -> Object
4327 return _IMP_atom.TAMDParticle_get_value(self, *args)
4330 def set_value(self, *args):
4332 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4333 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4334 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4335 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4336 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4338 return _IMP_atom.TAMDParticle_set_value(self, *args)
4341 def remove_attribute(self, *args):
4343 remove_attribute(TAMDParticle self, FloatKey a0)
4344 remove_attribute(TAMDParticle self, IntKey a0)
4345 remove_attribute(TAMDParticle self, StringKey a0)
4346 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4347 remove_attribute(TAMDParticle self, ObjectKey a0)
4349 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4352 def has_attribute(self, *args):
4354 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4355 has_attribute(TAMDParticle self, IntKey a0) -> bool
4356 has_attribute(TAMDParticle self, StringKey a0) -> bool
4357 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4358 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4360 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4363 def get_derivative(self, a0):
4364 """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4365 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4369 """get_name(TAMDParticle self) -> std::string"""
4370 return _IMP_atom.TAMDParticle_get_name(self)
4373 def clear_caches(self):
4374 """clear_caches(TAMDParticle self)"""
4375 return _IMP_atom.TAMDParticle_clear_caches(self)
4378 def set_name(self, a0):
4379 """set_name(TAMDParticle self, std::string a0)"""
4380 return _IMP_atom.TAMDParticle_set_name(self, a0)
4384 """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4385 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4388 def add_to_derivative(self, a0, a1, a2):
4389 """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4390 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4393 def set_is_optimized(self, a0, a1):
4394 """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4395 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4398 def get_is_optimized(self, a0):
4399 """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4400 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4404 """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4405 return _IMP_atom.TAMDParticle_get_check_level(self)
4408 def __eq__(self, *args):
4410 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4411 __eq__(TAMDParticle self, Particle d) -> bool
4413 return _IMP_atom.TAMDParticle___eq__(self, *args)
4416 def __ne__(self, *args):
4418 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4419 __ne__(TAMDParticle self, Particle d) -> bool
4421 return _IMP_atom.TAMDParticle___ne__(self, *args)
4424 def __le__(self, *args):
4426 __le__(TAMDParticle self, TAMDParticle o) -> bool
4427 __le__(TAMDParticle self, Particle d) -> bool
4429 return _IMP_atom.TAMDParticle___le__(self, *args)
4432 def __lt__(self, *args):
4434 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4435 __lt__(TAMDParticle self, Particle d) -> bool
4437 return _IMP_atom.TAMDParticle___lt__(self, *args)
4440 def __ge__(self, *args):
4442 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4443 __ge__(TAMDParticle self, Particle d) -> bool
4445 return _IMP_atom.TAMDParticle___ge__(self, *args)
4448 def __gt__(self, *args):
4450 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4451 __gt__(TAMDParticle self, Particle d) -> bool
4453 return _IMP_atom.TAMDParticle___gt__(self, *args)
4457 """__hash__(TAMDParticle self) -> std::size_t"""
4458 return _IMP_atom.TAMDParticle___hash__(self)
4462 """__str__(TAMDParticle self) -> std::string"""
4463 return _IMP_atom.TAMDParticle___str__(self)
4467 """__repr__(TAMDParticle self) -> std::string"""
4468 return _IMP_atom.TAMDParticle___repr__(self)
4470 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4471 __del__ =
lambda self:
None
4472 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4473 TAMDParticle_swigregister(TAMDParticle)
4475 def TAMDParticle_setup_particle(*args):
4477 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4478 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4479 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4480 TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4482 return _IMP_atom.TAMDParticle_setup_particle(*args)
4484 def TAMDParticle_get_is_setup(*args):
4486 get_is_setup(_ParticleAdaptor p) -> bool
4487 TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4489 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4491 def TAMDParticle_get_temperature_scale_factor_key():
4492 """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4493 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4495 def TAMDParticle_get_friction_scale_factor_key():
4496 """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4497 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4499 def TAMDParticle_get_reference_particle_index_key():
4500 """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4501 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4503 class Chain(Hierarchy):
4504 """Proxy of C++ IMP::atom::Chain class."""
4506 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4508 def __init__(self, *args):
4510 __init__(IMP::atom::Chain self) -> Chain
4511 __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4512 __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4514 this = _IMP_atom.new_Chain(*args)
4516 self.this.append(this)
4517 except __builtin__.Exception:
4520 def show(self, *args):
4522 show(Chain self, _ostream out)
4525 return _IMP_atom.Chain_show(self, *args)
4528 def setup_particle(*args):
4530 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4531 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4532 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4533 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4534 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4535 setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4537 return _IMP_atom.Chain_setup_particle(*args)
4539 setup_particle = staticmethod(setup_particle)
4541 def get_is_setup(*args):
4543 get_is_setup(_ParticleAdaptor p) -> bool
4544 get_is_setup(Model m, ParticleIndex pi) -> bool
4546 return _IMP_atom.Chain_get_is_setup(*args)
4548 get_is_setup = staticmethod(get_is_setup)
4551 """get_id(Chain self) -> std::string"""
4552 return _IMP_atom.Chain_get_id(self)
4555 def set_id(self, c):
4556 """set_id(Chain self, std::string c)"""
4557 return _IMP_atom.Chain_set_id(self, c)
4561 """get_id_key() -> StringKey"""
4562 return _IMP_atom.Chain_get_id_key()
4564 get_id_key = staticmethod(get_id_key)
4566 def add_attribute(self, *args):
4568 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4569 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4570 add_attribute(Chain self, IntKey a0, IMP::Int a1)
4571 add_attribute(Chain self, StringKey a0, IMP::String a1)
4572 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4573 add_attribute(Chain self, ObjectKey a0, Object a1)
4575 return _IMP_atom.Chain_add_attribute(self, *args)
4578 def get_value(self, *args):
4580 get_value(Chain self, FloatKey a0) -> IMP::Float
4581 get_value(Chain self, IntKey a0) -> IMP::Int
4582 get_value(Chain self, StringKey a0) -> IMP::String
4583 get_value(Chain self, ParticleIndexKey a0) -> Particle
4584 get_value(Chain self, ObjectKey a0) -> Object
4586 return _IMP_atom.Chain_get_value(self, *args)
4589 def set_value(self, *args):
4591 set_value(Chain self, FloatKey a0, IMP::Float a1)
4592 set_value(Chain self, IntKey a0, IMP::Int a1)
4593 set_value(Chain self, StringKey a0, IMP::String a1)
4594 set_value(Chain self, ParticleIndexKey a0, Particle a1)
4595 set_value(Chain self, ObjectKey a0, Object a1)
4597 return _IMP_atom.Chain_set_value(self, *args)
4600 def remove_attribute(self, *args):
4602 remove_attribute(Chain self, FloatKey a0)
4603 remove_attribute(Chain self, IntKey a0)
4604 remove_attribute(Chain self, StringKey a0)
4605 remove_attribute(Chain self, ParticleIndexKey a0)
4606 remove_attribute(Chain self, ObjectKey a0)
4608 return _IMP_atom.Chain_remove_attribute(self, *args)
4611 def has_attribute(self, *args):
4613 has_attribute(Chain self, FloatKey a0) -> bool
4614 has_attribute(Chain self, IntKey a0) -> bool
4615 has_attribute(Chain self, StringKey a0) -> bool
4616 has_attribute(Chain self, ParticleIndexKey a0) -> bool
4617 has_attribute(Chain self, ObjectKey a0) -> bool
4619 return _IMP_atom.Chain_has_attribute(self, *args)
4622 def get_derivative(self, a0):
4623 """get_derivative(Chain self, FloatKey a0) -> double"""
4624 return _IMP_atom.Chain_get_derivative(self, a0)
4628 """get_name(Chain self) -> std::string"""
4629 return _IMP_atom.Chain_get_name(self)
4632 def clear_caches(self):
4633 """clear_caches(Chain self)"""
4634 return _IMP_atom.Chain_clear_caches(self)
4637 def set_name(self, a0):
4638 """set_name(Chain self, std::string a0)"""
4639 return _IMP_atom.Chain_set_name(self, a0)
4643 """set_check_level(Chain self, IMP::CheckLevel a0)"""
4644 return _IMP_atom.Chain_set_check_level(self, a0)
4647 def add_to_derivative(self, a0, a1, a2):
4648 """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4649 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4652 def set_is_optimized(self, a0, a1):
4653 """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4654 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4657 def get_is_optimized(self, a0):
4658 """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4659 return _IMP_atom.Chain_get_is_optimized(self, a0)
4663 """get_check_level(Chain self) -> IMP::CheckLevel"""
4664 return _IMP_atom.Chain_get_check_level(self)
4667 def __eq__(self, *args):
4669 __eq__(Chain self, Chain o) -> bool
4670 __eq__(Chain self, Particle d) -> bool
4672 return _IMP_atom.Chain___eq__(self, *args)
4675 def __ne__(self, *args):
4677 __ne__(Chain self, Chain o) -> bool
4678 __ne__(Chain self, Particle d) -> bool
4680 return _IMP_atom.Chain___ne__(self, *args)
4683 def __le__(self, *args):
4685 __le__(Chain self, Chain o) -> bool
4686 __le__(Chain self, Particle d) -> bool
4688 return _IMP_atom.Chain___le__(self, *args)
4691 def __lt__(self, *args):
4693 __lt__(Chain self, Chain o) -> bool
4694 __lt__(Chain self, Particle d) -> bool
4696 return _IMP_atom.Chain___lt__(self, *args)
4699 def __ge__(self, *args):
4701 __ge__(Chain self, Chain o) -> bool
4702 __ge__(Chain self, Particle d) -> bool
4704 return _IMP_atom.Chain___ge__(self, *args)
4707 def __gt__(self, *args):
4709 __gt__(Chain self, Chain o) -> bool
4710 __gt__(Chain self, Particle d) -> bool
4712 return _IMP_atom.Chain___gt__(self, *args)
4716 """__hash__(Chain self) -> std::size_t"""
4717 return _IMP_atom.Chain___hash__(self)
4721 """__str__(Chain self) -> std::string"""
4722 return _IMP_atom.Chain___str__(self)
4726 """__repr__(Chain self) -> std::string"""
4727 return _IMP_atom.Chain___repr__(self)
4729 __swig_destroy__ = _IMP_atom.delete_Chain
4730 __del__ =
lambda self:
None
4731 Chain_swigregister = _IMP_atom.Chain_swigregister
4732 Chain_swigregister(Chain)
4734 def Chain_setup_particle(*args):
4736 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4737 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4738 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4739 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4740 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4741 Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4743 return _IMP_atom.Chain_setup_particle(*args)
4745 def Chain_get_is_setup(*args):
4747 get_is_setup(_ParticleAdaptor p) -> bool
4748 Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4750 return _IMP_atom.Chain_get_is_setup(*args)
4752 def Chain_get_id_key():
4753 """Chain_get_id_key() -> StringKey"""
4754 return _IMP_atom.Chain_get_id_key()
4758 """get_chain(Hierarchy h) -> Chain"""
4759 return _IMP_atom.get_chain(h)
4762 """get_chain_id(Hierarchy h) -> std::string"""
4763 return _IMP_atom.get_chain_id(h)
4765 """Proxy of C++ IMP::atom::Charged class."""
4767 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4769 def __init__(self, *args):
4771 __init__(IMP::atom::Charged self) -> Charged
4772 __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4773 __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4775 this = _IMP_atom.new_Charged(*args)
4777 self.this.append(this)
4778 except __builtin__.Exception:
4781 def show(self, *args):
4783 show(Charged self, _ostream out)
4786 return _IMP_atom.Charged_show(self, *args)
4789 def setup_particle(*args):
4791 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4792 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4793 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4794 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4796 return _IMP_atom.Charged_setup_particle(*args)
4798 setup_particle = staticmethod(setup_particle)
4800 def get_charge(self):
4801 """get_charge(Charged self) -> IMP::Float"""
4802 return _IMP_atom.Charged_get_charge(self)
4805 def set_charge(self, t):
4806 """set_charge(Charged self, IMP::Float t)"""
4807 return _IMP_atom.Charged_set_charge(self, t)
4810 def get_is_setup(*args):
4812 get_is_setup(_ParticleAdaptor p) -> bool
4813 get_is_setup(Model m, ParticleIndex pi) -> bool
4815 return _IMP_atom.Charged_get_is_setup(*args)
4817 get_is_setup = staticmethod(get_is_setup)
4819 def get_charge_key():
4820 """get_charge_key() -> FloatKey"""
4821 return _IMP_atom.Charged_get_charge_key()
4823 get_charge_key = staticmethod(get_charge_key)
4825 def add_attribute(self, *args):
4827 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
4828 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
4829 add_attribute(Charged self, IntKey a0, IMP::Int a1)
4830 add_attribute(Charged self, StringKey a0, IMP::String a1)
4831 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
4832 add_attribute(Charged self, ObjectKey a0, Object a1)
4834 return _IMP_atom.Charged_add_attribute(self, *args)
4837 def get_value(self, *args):
4839 get_value(Charged self, FloatKey a0) -> IMP::Float
4840 get_value(Charged self, IntKey a0) -> IMP::Int
4841 get_value(Charged self, StringKey a0) -> IMP::String
4842 get_value(Charged self, ParticleIndexKey a0) -> Particle
4843 get_value(Charged self, ObjectKey a0) -> Object
4845 return _IMP_atom.Charged_get_value(self, *args)
4848 def set_value(self, *args):
4850 set_value(Charged self, FloatKey a0, IMP::Float a1)
4851 set_value(Charged self, IntKey a0, IMP::Int a1)
4852 set_value(Charged self, StringKey a0, IMP::String a1)
4853 set_value(Charged self, ParticleIndexKey a0, Particle a1)
4854 set_value(Charged self, ObjectKey a0, Object a1)
4856 return _IMP_atom.Charged_set_value(self, *args)
4859 def remove_attribute(self, *args):
4861 remove_attribute(Charged self, FloatKey a0)
4862 remove_attribute(Charged self, IntKey a0)
4863 remove_attribute(Charged self, StringKey a0)
4864 remove_attribute(Charged self, ParticleIndexKey a0)
4865 remove_attribute(Charged self, ObjectKey a0)
4867 return _IMP_atom.Charged_remove_attribute(self, *args)
4870 def has_attribute(self, *args):
4872 has_attribute(Charged self, FloatKey a0) -> bool
4873 has_attribute(Charged self, IntKey a0) -> bool
4874 has_attribute(Charged self, StringKey a0) -> bool
4875 has_attribute(Charged self, ParticleIndexKey a0) -> bool
4876 has_attribute(Charged self, ObjectKey a0) -> bool
4878 return _IMP_atom.Charged_has_attribute(self, *args)
4881 def get_derivative(self, a0):
4882 """get_derivative(Charged self, FloatKey a0) -> double"""
4883 return _IMP_atom.Charged_get_derivative(self, a0)
4887 """get_name(Charged self) -> std::string"""
4888 return _IMP_atom.Charged_get_name(self)
4891 def clear_caches(self):
4892 """clear_caches(Charged self)"""
4893 return _IMP_atom.Charged_clear_caches(self)
4896 def set_name(self, a0):
4897 """set_name(Charged self, std::string a0)"""
4898 return _IMP_atom.Charged_set_name(self, a0)
4902 """set_check_level(Charged self, IMP::CheckLevel a0)"""
4903 return _IMP_atom.Charged_set_check_level(self, a0)
4906 def add_to_derivative(self, a0, a1, a2):
4907 """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4908 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
4911 def set_is_optimized(self, a0, a1):
4912 """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
4913 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
4916 def get_is_optimized(self, a0):
4917 """get_is_optimized(Charged self, FloatKey a0) -> bool"""
4918 return _IMP_atom.Charged_get_is_optimized(self, a0)
4922 """get_check_level(Charged self) -> IMP::CheckLevel"""
4923 return _IMP_atom.Charged_get_check_level(self)
4926 def __eq__(self, *args):
4928 __eq__(Charged self, Charged o) -> bool
4929 __eq__(Charged self, Particle d) -> bool
4931 return _IMP_atom.Charged___eq__(self, *args)
4934 def __ne__(self, *args):
4936 __ne__(Charged self, Charged o) -> bool
4937 __ne__(Charged self, Particle d) -> bool
4939 return _IMP_atom.Charged___ne__(self, *args)
4942 def __le__(self, *args):
4944 __le__(Charged self, Charged o) -> bool
4945 __le__(Charged self, Particle d) -> bool
4947 return _IMP_atom.Charged___le__(self, *args)
4950 def __lt__(self, *args):
4952 __lt__(Charged self, Charged o) -> bool
4953 __lt__(Charged self, Particle d) -> bool
4955 return _IMP_atom.Charged___lt__(self, *args)
4958 def __ge__(self, *args):
4960 __ge__(Charged self, Charged o) -> bool
4961 __ge__(Charged self, Particle d) -> bool
4963 return _IMP_atom.Charged___ge__(self, *args)
4966 def __gt__(self, *args):
4968 __gt__(Charged self, Charged o) -> bool
4969 __gt__(Charged self, Particle d) -> bool
4971 return _IMP_atom.Charged___gt__(self, *args)
4975 """__hash__(Charged self) -> std::size_t"""
4976 return _IMP_atom.Charged___hash__(self)
4980 """__str__(Charged self) -> std::string"""
4981 return _IMP_atom.Charged___str__(self)
4985 """__repr__(Charged self) -> std::string"""
4986 return _IMP_atom.Charged___repr__(self)
4988 __swig_destroy__ = _IMP_atom.delete_Charged
4989 __del__ =
lambda self:
None
4990 Charged_swigregister = _IMP_atom.Charged_swigregister
4991 Charged_swigregister(Charged)
4993 def Charged_setup_particle(*args):
4995 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4996 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4997 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4998 Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5000 return _IMP_atom.Charged_setup_particle(*args)
5002 def Charged_get_is_setup(*args):
5004 get_is_setup(_ParticleAdaptor p) -> bool
5005 Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5007 return _IMP_atom.Charged_get_is_setup(*args)
5009 def Charged_get_charge_key():
5010 """Charged_get_charge_key() -> FloatKey"""
5011 return _IMP_atom.Charged_get_charge_key()
5014 """Proxy of C++ IMP::atom::CoulombPairScore class."""
5016 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5018 def __init__(self, f):
5019 """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5020 this = _IMP_atom.new_CoulombPairScore(f)
5022 self.this.append(this)
5023 except __builtin__.Exception:
5026 def set_relative_dielectric(self, relative_dielectric):
5027 """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5028 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5031 def get_relative_dielectric(self):
5032 """get_relative_dielectric(CoulombPairScore self) -> double"""
5033 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5036 def do_get_inputs(self, m, pis):
5037 """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5038 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5041 def get_version_info(self):
5042 """get_version_info(CoulombPairScore self) -> VersionInfo"""
5043 return _IMP_atom.CoulombPairScore_get_version_info(self)
5047 """__str__(CoulombPairScore self) -> std::string"""
5048 return _IMP_atom.CoulombPairScore___str__(self)
5052 """__repr__(CoulombPairScore self) -> std::string"""
5053 return _IMP_atom.CoulombPairScore___repr__(self)
5058 return _object_cast_to_CoulombPairScore(o)
5060 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5061 CoulombPairScore_swigregister(CoulombPairScore)
5063 class Domain(Hierarchy):
5064 """Proxy of C++ IMP::atom::Domain class."""
5066 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5068 def set_index_range(self, ir):
5069 """set_index_range(Domain self, IMP::IntRange ir)"""
5070 return _IMP_atom.Domain_set_index_range(self, ir)
5073 def get_index_range(self):
5074 """get_index_range(Domain self) -> IMP::IntRange"""
5075 return _IMP_atom.Domain_get_index_range(self)
5078 def __init__(self, *args):
5080 __init__(IMP::atom::Domain self) -> Domain
5081 __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5082 __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5084 this = _IMP_atom.new_Domain(*args)
5086 self.this.append(this)
5087 except __builtin__.Exception:
5090 def get_is_setup(*args):
5092 get_is_setup(Model m, ParticleIndex pi) -> bool
5093 get_is_setup(_ParticleAdaptor p) -> bool
5095 return _IMP_atom.Domain_get_is_setup(*args)
5097 get_is_setup = staticmethod(get_is_setup)
5099 def show(self, *args):
5101 show(Domain self, _ostream out)
5104 return _IMP_atom.Domain_show(self, *args)
5107 def setup_particle(*args):
5109 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5110 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5111 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5112 setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5114 return _IMP_atom.Domain_setup_particle(*args)
5116 setup_particle = staticmethod(setup_particle)
5118 def add_attribute(self, *args):
5120 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5121 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5122 add_attribute(Domain self, IntKey a0, IMP::Int a1)
5123 add_attribute(Domain self, StringKey a0, IMP::String a1)
5124 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5125 add_attribute(Domain self, ObjectKey a0, Object a1)
5127 return _IMP_atom.Domain_add_attribute(self, *args)
5130 def get_value(self, *args):
5132 get_value(Domain self, FloatKey a0) -> IMP::Float
5133 get_value(Domain self, IntKey a0) -> IMP::Int
5134 get_value(Domain self, StringKey a0) -> IMP::String
5135 get_value(Domain self, ParticleIndexKey a0) -> Particle
5136 get_value(Domain self, ObjectKey a0) -> Object
5138 return _IMP_atom.Domain_get_value(self, *args)
5141 def set_value(self, *args):
5143 set_value(Domain self, FloatKey a0, IMP::Float a1)
5144 set_value(Domain self, IntKey a0, IMP::Int a1)
5145 set_value(Domain self, StringKey a0, IMP::String a1)
5146 set_value(Domain self, ParticleIndexKey a0, Particle a1)
5147 set_value(Domain self, ObjectKey a0, Object a1)
5149 return _IMP_atom.Domain_set_value(self, *args)
5152 def remove_attribute(self, *args):
5154 remove_attribute(Domain self, FloatKey a0)
5155 remove_attribute(Domain self, IntKey a0)
5156 remove_attribute(Domain self, StringKey a0)
5157 remove_attribute(Domain self, ParticleIndexKey a0)
5158 remove_attribute(Domain self, ObjectKey a0)
5160 return _IMP_atom.Domain_remove_attribute(self, *args)
5163 def has_attribute(self, *args):
5165 has_attribute(Domain self, FloatKey a0) -> bool
5166 has_attribute(Domain self, IntKey a0) -> bool
5167 has_attribute(Domain self, StringKey a0) -> bool
5168 has_attribute(Domain self, ParticleIndexKey a0) -> bool
5169 has_attribute(Domain self, ObjectKey a0) -> bool
5171 return _IMP_atom.Domain_has_attribute(self, *args)
5174 def get_derivative(self, a0):
5175 """get_derivative(Domain self, FloatKey a0) -> double"""
5176 return _IMP_atom.Domain_get_derivative(self, a0)
5180 """get_name(Domain self) -> std::string"""
5181 return _IMP_atom.Domain_get_name(self)
5184 def clear_caches(self):
5185 """clear_caches(Domain self)"""
5186 return _IMP_atom.Domain_clear_caches(self)
5189 def set_name(self, a0):
5190 """set_name(Domain self, std::string a0)"""
5191 return _IMP_atom.Domain_set_name(self, a0)
5195 """set_check_level(Domain self, IMP::CheckLevel a0)"""
5196 return _IMP_atom.Domain_set_check_level(self, a0)
5199 def add_to_derivative(self, a0, a1, a2):
5200 """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5201 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5204 def set_is_optimized(self, a0, a1):
5205 """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5206 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5209 def get_is_optimized(self, a0):
5210 """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5211 return _IMP_atom.Domain_get_is_optimized(self, a0)
5215 """get_check_level(Domain self) -> IMP::CheckLevel"""
5216 return _IMP_atom.Domain_get_check_level(self)
5219 def __eq__(self, *args):
5221 __eq__(Domain self, Domain o) -> bool
5222 __eq__(Domain self, Particle d) -> bool
5224 return _IMP_atom.Domain___eq__(self, *args)
5227 def __ne__(self, *args):
5229 __ne__(Domain self, Domain o) -> bool
5230 __ne__(Domain self, Particle d) -> bool
5232 return _IMP_atom.Domain___ne__(self, *args)
5235 def __le__(self, *args):
5237 __le__(Domain self, Domain o) -> bool
5238 __le__(Domain self, Particle d) -> bool
5240 return _IMP_atom.Domain___le__(self, *args)
5243 def __lt__(self, *args):
5245 __lt__(Domain self, Domain o) -> bool
5246 __lt__(Domain self, Particle d) -> bool
5248 return _IMP_atom.Domain___lt__(self, *args)
5251 def __ge__(self, *args):
5253 __ge__(Domain self, Domain o) -> bool
5254 __ge__(Domain self, Particle d) -> bool
5256 return _IMP_atom.Domain___ge__(self, *args)
5259 def __gt__(self, *args):
5261 __gt__(Domain self, Domain o) -> bool
5262 __gt__(Domain self, Particle d) -> bool
5264 return _IMP_atom.Domain___gt__(self, *args)
5268 """__hash__(Domain self) -> std::size_t"""
5269 return _IMP_atom.Domain___hash__(self)
5273 """__str__(Domain self) -> std::string"""
5274 return _IMP_atom.Domain___str__(self)
5278 """__repr__(Domain self) -> std::string"""
5279 return _IMP_atom.Domain___repr__(self)
5281 __swig_destroy__ = _IMP_atom.delete_Domain
5282 __del__ =
lambda self:
None
5283 Domain_swigregister = _IMP_atom.Domain_swigregister
5284 Domain_swigregister(Domain)
5286 def Domain_get_is_setup(*args):
5288 get_is_setup(Model m, ParticleIndex pi) -> bool
5289 Domain_get_is_setup(_ParticleAdaptor p) -> bool
5291 return _IMP_atom.Domain_get_is_setup(*args)
5293 def Domain_setup_particle(*args):
5295 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5296 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5297 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5298 Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5300 return _IMP_atom.Domain_setup_particle(*args)
5303 """Proxy of C++ IMP::atom::LennardJones class."""
5305 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5307 def __init__(self, *args):
5309 __init__(IMP::atom::LennardJones self) -> LennardJones
5310 __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5311 __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5313 this = _IMP_atom.new_LennardJones(*args)
5315 self.this.append(this)
5316 except __builtin__.Exception:
5319 def show(self, *args):
5321 show(LennardJones self, _ostream out)
5322 show(LennardJones self)
5324 return _IMP_atom.LennardJones_show(self, *args)
5327 def setup_particle(*args):
5329 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5330 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5331 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5332 setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5334 return _IMP_atom.LennardJones_setup_particle(*args)
5336 setup_particle = staticmethod(setup_particle)
5338 def get_well_depth(self):
5339 """get_well_depth(LennardJones self) -> IMP::Float"""
5340 return _IMP_atom.LennardJones_get_well_depth(self)
5343 def set_well_depth(self, well_depth):
5344 """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5345 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5348 def get_is_setup(*args):
5350 get_is_setup(_ParticleAdaptor p) -> bool
5351 get_is_setup(Model m, ParticleIndex pi) -> bool
5353 return _IMP_atom.LennardJones_get_is_setup(*args)
5355 get_is_setup = staticmethod(get_is_setup)
5357 def get_well_depth_key():
5358 """get_well_depth_key() -> FloatKey"""
5359 return _IMP_atom.LennardJones_get_well_depth_key()
5361 get_well_depth_key = staticmethod(get_well_depth_key)
5363 def add_attribute(self, *args):
5365 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5366 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5367 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5368 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5369 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5370 add_attribute(LennardJones self, ObjectKey a0, Object a1)
5372 return _IMP_atom.LennardJones_add_attribute(self, *args)
5375 def get_value(self, *args):
5377 get_value(LennardJones self, FloatKey a0) -> IMP::Float
5378 get_value(LennardJones self, IntKey a0) -> IMP::Int
5379 get_value(LennardJones self, StringKey a0) -> IMP::String
5380 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5381 get_value(LennardJones self, ObjectKey a0) -> Object
5383 return _IMP_atom.LennardJones_get_value(self, *args)
5386 def set_value(self, *args):
5388 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5389 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5390 set_value(LennardJones self, StringKey a0, IMP::String a1)
5391 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5392 set_value(LennardJones self, ObjectKey a0, Object a1)
5394 return _IMP_atom.LennardJones_set_value(self, *args)
5397 def remove_attribute(self, *args):
5399 remove_attribute(LennardJones self, FloatKey a0)
5400 remove_attribute(LennardJones self, IntKey a0)
5401 remove_attribute(LennardJones self, StringKey a0)
5402 remove_attribute(LennardJones self, ParticleIndexKey a0)
5403 remove_attribute(LennardJones self, ObjectKey a0)
5405 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5408 def has_attribute(self, *args):
5410 has_attribute(LennardJones self, FloatKey a0) -> bool
5411 has_attribute(LennardJones self, IntKey a0) -> bool
5412 has_attribute(LennardJones self, StringKey a0) -> bool
5413 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5414 has_attribute(LennardJones self, ObjectKey a0) -> bool
5416 return _IMP_atom.LennardJones_has_attribute(self, *args)
5419 def get_derivative(self, a0):
5420 """get_derivative(LennardJones self, FloatKey a0) -> double"""
5421 return _IMP_atom.LennardJones_get_derivative(self, a0)
5425 """get_name(LennardJones self) -> std::string"""
5426 return _IMP_atom.LennardJones_get_name(self)
5429 def clear_caches(self):
5430 """clear_caches(LennardJones self)"""
5431 return _IMP_atom.LennardJones_clear_caches(self)
5434 def set_name(self, a0):
5435 """set_name(LennardJones self, std::string a0)"""
5436 return _IMP_atom.LennardJones_set_name(self, a0)
5440 """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5441 return _IMP_atom.LennardJones_set_check_level(self, a0)
5444 def add_to_derivative(self, a0, a1, a2):
5445 """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5446 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5449 def set_is_optimized(self, a0, a1):
5450 """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5451 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5454 def get_is_optimized(self, a0):
5455 """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5456 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5460 """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5461 return _IMP_atom.LennardJones_get_check_level(self)
5464 def __eq__(self, *args):
5466 __eq__(LennardJones self, LennardJones o) -> bool
5467 __eq__(LennardJones self, Particle d) -> bool
5469 return _IMP_atom.LennardJones___eq__(self, *args)
5472 def __ne__(self, *args):
5474 __ne__(LennardJones self, LennardJones o) -> bool
5475 __ne__(LennardJones self, Particle d) -> bool
5477 return _IMP_atom.LennardJones___ne__(self, *args)
5480 def __le__(self, *args):
5482 __le__(LennardJones self, LennardJones o) -> bool
5483 __le__(LennardJones self, Particle d) -> bool
5485 return _IMP_atom.LennardJones___le__(self, *args)
5488 def __lt__(self, *args):
5490 __lt__(LennardJones self, LennardJones o) -> bool
5491 __lt__(LennardJones self, Particle d) -> bool
5493 return _IMP_atom.LennardJones___lt__(self, *args)
5496 def __ge__(self, *args):
5498 __ge__(LennardJones self, LennardJones o) -> bool
5499 __ge__(LennardJones self, Particle d) -> bool
5501 return _IMP_atom.LennardJones___ge__(self, *args)
5504 def __gt__(self, *args):
5506 __gt__(LennardJones self, LennardJones o) -> bool
5507 __gt__(LennardJones self, Particle d) -> bool
5509 return _IMP_atom.LennardJones___gt__(self, *args)
5513 """__hash__(LennardJones self) -> std::size_t"""
5514 return _IMP_atom.LennardJones___hash__(self)
5518 """__str__(LennardJones self) -> std::string"""
5519 return _IMP_atom.LennardJones___str__(self)
5523 """__repr__(LennardJones self) -> std::string"""
5524 return _IMP_atom.LennardJones___repr__(self)
5526 __swig_destroy__ = _IMP_atom.delete_LennardJones
5527 __del__ =
lambda self:
None
5528 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5529 LennardJones_swigregister(LennardJones)
5531 def LennardJones_setup_particle(*args):
5533 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5534 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5535 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5536 LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5538 return _IMP_atom.LennardJones_setup_particle(*args)
5540 def LennardJones_get_is_setup(*args):
5542 get_is_setup(_ParticleAdaptor p) -> bool
5543 LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5545 return _IMP_atom.LennardJones_get_is_setup(*args)
5547 def LennardJones_get_well_depth_key():
5548 """LennardJones_get_well_depth_key() -> FloatKey"""
5549 return _IMP_atom.LennardJones_get_well_depth_key()
5552 """Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5554 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5556 def __init__(self, f):
5557 """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5558 this = _IMP_atom.new_LennardJonesPairScore(f)
5560 self.this.append(this)
5561 except __builtin__.Exception:
5564 def set_repulsive_weight(self, repulsive_weight):
5565 """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5566 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5569 def get_repulsive_weight(self):
5570 """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5571 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5574 def set_attractive_weight(self, attractive_weight):
5575 """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5576 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5579 def get_attractive_weight(self):
5580 """get_attractive_weight(LennardJonesPairScore self) -> double"""
5581 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5584 def do_get_inputs(self, m, pis):
5585 """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5586 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5589 def get_version_info(self):
5590 """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5591 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5595 """__str__(LennardJonesPairScore self) -> std::string"""
5596 return _IMP_atom.LennardJonesPairScore___str__(self)
5600 """__repr__(LennardJonesPairScore self) -> std::string"""
5601 return _IMP_atom.LennardJonesPairScore___repr__(self)
5606 return _object_cast_to_LennardJonesPairScore(o)
5608 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5609 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5612 """Proxy of C++ IMP::atom::LinearVelocity class."""
5614 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5616 def get_velocity_key(i):
5617 """get_velocity_key(unsigned int i) -> FloatKey"""
5618 return _IMP_atom.LinearVelocity_get_velocity_key(i)
5620 get_velocity_key = staticmethod(get_velocity_key)
5622 def __init__(self, *args):
5624 __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5625 __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5626 __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5628 this = _IMP_atom.new_LinearVelocity(*args)
5630 self.this.append(this)
5631 except __builtin__.Exception:
5634 def get_is_setup(*args):
5636 get_is_setup(Model m, ParticleIndex pi) -> bool
5637 get_is_setup(_ParticleAdaptor p) -> bool
5639 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5641 get_is_setup = staticmethod(get_is_setup)
5643 def show(self, *args):
5645 show(LinearVelocity self, _ostream out)
5646 show(LinearVelocity self)
5648 return _IMP_atom.LinearVelocity_show(self, *args)
5651 def setup_particle(*args):
5653 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5654 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5655 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5656 setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5658 return _IMP_atom.LinearVelocity_setup_particle(*args)
5660 setup_particle = staticmethod(setup_particle)
5662 def set_velocity(self, v):
5663 """set_velocity(LinearVelocity self, Vector3D v)"""
5664 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5667 def get_velocity(self):
5668 """get_velocity(LinearVelocity self) -> Vector3D"""
5669 return _IMP_atom.LinearVelocity_get_velocity(self)
5672 def add_attribute(self, *args):
5674 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5675 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5676 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5677 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5678 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5679 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5681 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5684 def get_value(self, *args):
5686 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5687 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5688 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5689 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5690 get_value(LinearVelocity self, ObjectKey a0) -> Object
5692 return _IMP_atom.LinearVelocity_get_value(self, *args)
5695 def set_value(self, *args):
5697 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5698 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5699 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5700 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5701 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5703 return _IMP_atom.LinearVelocity_set_value(self, *args)
5706 def remove_attribute(self, *args):
5708 remove_attribute(LinearVelocity self, FloatKey a0)
5709 remove_attribute(LinearVelocity self, IntKey a0)
5710 remove_attribute(LinearVelocity self, StringKey a0)
5711 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5712 remove_attribute(LinearVelocity self, ObjectKey a0)
5714 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5717 def has_attribute(self, *args):
5719 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5720 has_attribute(LinearVelocity self, IntKey a0) -> bool
5721 has_attribute(LinearVelocity self, StringKey a0) -> bool
5722 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5723 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5725 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5728 def get_derivative(self, a0):
5729 """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5730 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5734 """get_name(LinearVelocity self) -> std::string"""
5735 return _IMP_atom.LinearVelocity_get_name(self)
5738 def clear_caches(self):
5739 """clear_caches(LinearVelocity self)"""
5740 return _IMP_atom.LinearVelocity_clear_caches(self)
5743 def set_name(self, a0):
5744 """set_name(LinearVelocity self, std::string a0)"""
5745 return _IMP_atom.LinearVelocity_set_name(self, a0)
5749 """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5750 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5753 def add_to_derivative(self, a0, a1, a2):
5754 """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5755 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5758 def set_is_optimized(self, a0, a1):
5759 """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5760 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5763 def get_is_optimized(self, a0):
5764 """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5765 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5769 """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5770 return _IMP_atom.LinearVelocity_get_check_level(self)
5773 def __eq__(self, *args):
5775 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5776 __eq__(LinearVelocity self, Particle d) -> bool
5778 return _IMP_atom.LinearVelocity___eq__(self, *args)
5781 def __ne__(self, *args):
5783 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5784 __ne__(LinearVelocity self, Particle d) -> bool
5786 return _IMP_atom.LinearVelocity___ne__(self, *args)
5789 def __le__(self, *args):
5791 __le__(LinearVelocity self, LinearVelocity o) -> bool
5792 __le__(LinearVelocity self, Particle d) -> bool
5794 return _IMP_atom.LinearVelocity___le__(self, *args)
5797 def __lt__(self, *args):
5799 __lt__(LinearVelocity self, LinearVelocity o) -> bool
5800 __lt__(LinearVelocity self, Particle d) -> bool
5802 return _IMP_atom.LinearVelocity___lt__(self, *args)
5805 def __ge__(self, *args):
5807 __ge__(LinearVelocity self, LinearVelocity o) -> bool
5808 __ge__(LinearVelocity self, Particle d) -> bool
5810 return _IMP_atom.LinearVelocity___ge__(self, *args)
5813 def __gt__(self, *args):
5815 __gt__(LinearVelocity self, LinearVelocity o) -> bool
5816 __gt__(LinearVelocity self, Particle d) -> bool
5818 return _IMP_atom.LinearVelocity___gt__(self, *args)
5822 """__hash__(LinearVelocity self) -> std::size_t"""
5823 return _IMP_atom.LinearVelocity___hash__(self)
5827 """__str__(LinearVelocity self) -> std::string"""
5828 return _IMP_atom.LinearVelocity___str__(self)
5832 """__repr__(LinearVelocity self) -> std::string"""
5833 return _IMP_atom.LinearVelocity___repr__(self)
5835 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
5836 __del__ =
lambda self:
None
5837 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
5838 LinearVelocity_swigregister(LinearVelocity)
5840 def LinearVelocity_get_velocity_key(i):
5841 """LinearVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
5842 return _IMP_atom.LinearVelocity_get_velocity_key(i)
5844 def LinearVelocity_get_is_setup(*args):
5846 get_is_setup(Model m, ParticleIndex pi) -> bool
5847 LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
5849 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5851 def LinearVelocity_setup_particle(*args):
5853 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5854 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5855 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5856 LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5858 return _IMP_atom.LinearVelocity_setup_particle(*args)
5861 """Proxy of C++ IMP::atom::AngularVelocity class."""
5863 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5865 def get_velocity_key(i):
5866 """get_velocity_key(unsigned int i) -> FloatKey"""
5867 return _IMP_atom.AngularVelocity_get_velocity_key(i)
5869 get_velocity_key = staticmethod(get_velocity_key)
5871 def __init__(self, *args):
5873 __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
5874 __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
5875 __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
5877 this = _IMP_atom.new_AngularVelocity(*args)
5879 self.this.append(this)
5880 except __builtin__.Exception:
5883 def get_is_setup(*args):
5885 get_is_setup(Model m, ParticleIndex pi) -> bool
5886 get_is_setup(_ParticleAdaptor p) -> bool
5888 return _IMP_atom.AngularVelocity_get_is_setup(*args)
5890 get_is_setup = staticmethod(get_is_setup)
5892 def show(self, *args):
5894 show(AngularVelocity self, _ostream out)
5895 show(AngularVelocity self)
5897 return _IMP_atom.AngularVelocity_show(self, *args)
5900 def setup_particle(*args):
5902 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
5903 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
5904 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
5905 setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
5907 return _IMP_atom.AngularVelocity_setup_particle(*args)
5909 setup_particle = staticmethod(setup_particle)
5911 def set_velocity(self, v):
5912 """set_velocity(AngularVelocity self, Vector4D v)"""
5913 return _IMP_atom.AngularVelocity_set_velocity(self, v)
5916 def get_velocity(self):
5917 """get_velocity(AngularVelocity self) -> Vector4D"""
5918 return _IMP_atom.AngularVelocity_get_velocity(self)
5921 def add_attribute(self, *args):
5923 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
5924 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
5925 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
5926 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
5927 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5928 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
5930 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
5933 def get_value(self, *args):
5935 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
5936 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
5937 get_value(AngularVelocity self, StringKey a0) -> IMP::String
5938 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
5939 get_value(AngularVelocity self, ObjectKey a0) -> Object
5941 return _IMP_atom.AngularVelocity_get_value(self, *args)
5944 def set_value(self, *args):
5946 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
5947 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
5948 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
5949 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
5950 set_value(AngularVelocity self, ObjectKey a0, Object a1)
5952 return _IMP_atom.AngularVelocity_set_value(self, *args)
5955 def remove_attribute(self, *args):
5957 remove_attribute(AngularVelocity self, FloatKey a0)
5958 remove_attribute(AngularVelocity self, IntKey a0)
5959 remove_attribute(AngularVelocity self, StringKey a0)
5960 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
5961 remove_attribute(AngularVelocity self, ObjectKey a0)
5963 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
5966 def has_attribute(self, *args):
5968 has_attribute(AngularVelocity self, FloatKey a0) -> bool
5969 has_attribute(AngularVelocity self, IntKey a0) -> bool
5970 has_attribute(AngularVelocity self, StringKey a0) -> bool
5971 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
5972 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
5974 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
5977 def get_derivative(self, a0):
5978 """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
5979 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
5983 """get_name(AngularVelocity self) -> std::string"""
5984 return _IMP_atom.AngularVelocity_get_name(self)
5987 def clear_caches(self):
5988 """clear_caches(AngularVelocity self)"""
5989 return _IMP_atom.AngularVelocity_clear_caches(self)
5992 def set_name(self, a0):
5993 """set_name(AngularVelocity self, std::string a0)"""
5994 return _IMP_atom.AngularVelocity_set_name(self, a0)
5998 """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
5999 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6002 def add_to_derivative(self, a0, a1, a2):
6003 """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6004 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6007 def set_is_optimized(self, a0, a1):
6008 """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6009 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6012 def get_is_optimized(self, a0):
6013 """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6014 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6018 """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6019 return _IMP_atom.AngularVelocity_get_check_level(self)
6022 def __eq__(self, *args):
6024 __eq__(AngularVelocity self, AngularVelocity o) -> bool
6025 __eq__(AngularVelocity self, Particle d) -> bool
6027 return _IMP_atom.AngularVelocity___eq__(self, *args)
6030 def __ne__(self, *args):
6032 __ne__(AngularVelocity self, AngularVelocity o) -> bool
6033 __ne__(AngularVelocity self, Particle d) -> bool
6035 return _IMP_atom.AngularVelocity___ne__(self, *args)
6038 def __le__(self, *args):
6040 __le__(AngularVelocity self, AngularVelocity o) -> bool
6041 __le__(AngularVelocity self, Particle d) -> bool
6043 return _IMP_atom.AngularVelocity___le__(self, *args)
6046 def __lt__(self, *args):
6048 __lt__(AngularVelocity self, AngularVelocity o) -> bool
6049 __lt__(AngularVelocity self, Particle d) -> bool
6051 return _IMP_atom.AngularVelocity___lt__(self, *args)
6054 def __ge__(self, *args):
6056 __ge__(AngularVelocity self, AngularVelocity o) -> bool
6057 __ge__(AngularVelocity self, Particle d) -> bool
6059 return _IMP_atom.AngularVelocity___ge__(self, *args)
6062 def __gt__(self, *args):
6064 __gt__(AngularVelocity self, AngularVelocity o) -> bool
6065 __gt__(AngularVelocity self, Particle d) -> bool
6067 return _IMP_atom.AngularVelocity___gt__(self, *args)
6071 """__hash__(AngularVelocity self) -> std::size_t"""
6072 return _IMP_atom.AngularVelocity___hash__(self)
6076 """__str__(AngularVelocity self) -> std::string"""
6077 return _IMP_atom.AngularVelocity___str__(self)
6081 """__repr__(AngularVelocity self) -> std::string"""
6082 return _IMP_atom.AngularVelocity___repr__(self)
6084 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6085 __del__ =
lambda self:
None
6086 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6087 AngularVelocity_swigregister(AngularVelocity)
6089 def AngularVelocity_get_velocity_key(i):
6090 """AngularVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6091 return _IMP_atom.AngularVelocity_get_velocity_key(i)
6093 def AngularVelocity_get_is_setup(*args):
6095 get_is_setup(Model m, ParticleIndex pi) -> bool
6096 AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6098 return _IMP_atom.AngularVelocity_get_is_setup(*args)
6100 def AngularVelocity_setup_particle(*args):
6102 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6103 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6104 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6105 AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6107 return _IMP_atom.AngularVelocity_setup_particle(*args)
6109 class MolecularDynamics(Simulator):
6110 """Proxy of C++ IMP::atom::MolecularDynamics class."""
6112 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6114 def __init__(self, m):
6115 """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6116 this = _IMP_atom.new_MolecularDynamics(m)
6118 self.this.append(this)
6119 except __builtin__.Exception:
6122 def get_kinetic_energy(self):
6123 """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6124 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6127 def get_kinetic_temperature(self, ekinetic):
6128 """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6129 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6132 def set_velocity_cap(self, velocity_cap):
6133 """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6134 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6137 def assign_velocities(self, temperature):
6138 """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6139 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6142 def setup(self, ps):
6143 """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6144 return _IMP_atom.MolecularDynamics_setup(self, ps)
6147 def do_step(self, sc, dt):
6148 """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6149 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6152 def get_is_simulation_particle(self, p):
6153 """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6154 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6157 def get_version_info(self):
6158 """get_version_info(MolecularDynamics self) -> VersionInfo"""
6159 return _IMP_atom.MolecularDynamics_get_version_info(self)
6163 """__str__(MolecularDynamics self) -> std::string"""
6164 return _IMP_atom.MolecularDynamics___str__(self)
6168 """__repr__(MolecularDynamics self) -> std::string"""
6169 return _IMP_atom.MolecularDynamics___repr__(self)
6174 return _object_cast_to_MolecularDynamics(o)
6176 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6177 MolecularDynamics_swigregister(MolecularDynamics)
6180 """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6182 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6184 def __init__(self, m, pis, temperature):
6185 """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6186 this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6188 self.this.append(this)
6189 except __builtin__.Exception:
6192 def set_particles(self, pis):
6193 """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6194 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6197 def set_temperature(self, temperature):
6198 """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6199 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6202 def rescale_velocities(self):
6203 """rescale_velocities(VelocityScalingOptimizerState self)"""
6204 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6207 def get_version_info(self):
6208 """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6209 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6213 """__str__(VelocityScalingOptimizerState self) -> std::string"""
6214 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6218 """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6219 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6224 return _object_cast_to_VelocityScalingOptimizerState(o)
6226 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6227 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6229 class Fragment(Hierarchy):
6230 """Proxy of C++ IMP::atom::Fragment class."""
6232 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6234 def set_residue_indexes(self, o):
6235 """set_residue_indexes(Fragment self, IMP::Ints o)"""
6236 return _IMP_atom.Fragment_set_residue_indexes(self, o)
6239 def get_residue_indexes(self):
6240 """get_residue_indexes(Fragment self) -> IMP::Ints"""
6241 return _IMP_atom.Fragment_get_residue_indexes(self)
6244 def get_contains_residue(self, rindex):
6245 """get_contains_residue(Fragment self, int rindex) -> bool"""
6246 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6249 def __init__(self, *args):
6251 __init__(IMP::atom::Fragment self) -> Fragment
6252 __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6253 __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6255 this = _IMP_atom.new_Fragment(*args)
6257 self.this.append(this)
6258 except __builtin__.Exception:
6261 def get_is_setup(*args):
6263 get_is_setup(Model m, ParticleIndex pi) -> bool
6264 get_is_setup(_ParticleAdaptor p) -> bool
6266 return _IMP_atom.Fragment_get_is_setup(*args)
6268 get_is_setup = staticmethod(get_is_setup)
6270 def show(self, *args):
6272 show(Fragment self, _ostream out)
6275 return _IMP_atom.Fragment_show(self, *args)
6278 def setup_particle(*args):
6280 setup_particle(Model m, ParticleIndex pi) -> Fragment
6281 setup_particle(_ParticleAdaptor decorator) -> Fragment
6282 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6283 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6284 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6285 setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6287 return _IMP_atom.Fragment_setup_particle(*args)
6289 setup_particle = staticmethod(setup_particle)
6291 def add_attribute(self, *args):
6293 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6294 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6295 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6296 add_attribute(Fragment self, StringKey a0, IMP::String a1)
6297 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6298 add_attribute(Fragment self, ObjectKey a0, Object a1)
6300 return _IMP_atom.Fragment_add_attribute(self, *args)
6303 def get_value(self, *args):
6305 get_value(Fragment self, FloatKey a0) -> IMP::Float
6306 get_value(Fragment self, IntKey a0) -> IMP::Int
6307 get_value(Fragment self, StringKey a0) -> IMP::String
6308 get_value(Fragment self, ParticleIndexKey a0) -> Particle
6309 get_value(Fragment self, ObjectKey a0) -> Object
6311 return _IMP_atom.Fragment_get_value(self, *args)
6314 def set_value(self, *args):
6316 set_value(Fragment self, FloatKey a0, IMP::Float a1)
6317 set_value(Fragment self, IntKey a0, IMP::Int a1)
6318 set_value(Fragment self, StringKey a0, IMP::String a1)
6319 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6320 set_value(Fragment self, ObjectKey a0, Object a1)
6322 return _IMP_atom.Fragment_set_value(self, *args)
6325 def remove_attribute(self, *args):
6327 remove_attribute(Fragment self, FloatKey a0)
6328 remove_attribute(Fragment self, IntKey a0)
6329 remove_attribute(Fragment self, StringKey a0)
6330 remove_attribute(Fragment self, ParticleIndexKey a0)
6331 remove_attribute(Fragment self, ObjectKey a0)
6333 return _IMP_atom.Fragment_remove_attribute(self, *args)
6336 def has_attribute(self, *args):
6338 has_attribute(Fragment self, FloatKey a0) -> bool
6339 has_attribute(Fragment self, IntKey a0) -> bool
6340 has_attribute(Fragment self, StringKey a0) -> bool
6341 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6342 has_attribute(Fragment self, ObjectKey a0) -> bool
6344 return _IMP_atom.Fragment_has_attribute(self, *args)
6347 def get_derivative(self, a0):
6348 """get_derivative(Fragment self, FloatKey a0) -> double"""
6349 return _IMP_atom.Fragment_get_derivative(self, a0)
6353 """get_name(Fragment self) -> std::string"""
6354 return _IMP_atom.Fragment_get_name(self)
6357 def clear_caches(self):
6358 """clear_caches(Fragment self)"""
6359 return _IMP_atom.Fragment_clear_caches(self)
6362 def set_name(self, a0):
6363 """set_name(Fragment self, std::string a0)"""
6364 return _IMP_atom.Fragment_set_name(self, a0)
6368 """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6369 return _IMP_atom.Fragment_set_check_level(self, a0)
6372 def add_to_derivative(self, a0, a1, a2):
6373 """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6374 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6377 def set_is_optimized(self, a0, a1):
6378 """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6379 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6382 def get_is_optimized(self, a0):
6383 """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6384 return _IMP_atom.Fragment_get_is_optimized(self, a0)
6388 """get_check_level(Fragment self) -> IMP::CheckLevel"""
6389 return _IMP_atom.Fragment_get_check_level(self)
6392 def __eq__(self, *args):
6394 __eq__(Fragment self, Fragment o) -> bool
6395 __eq__(Fragment self, Particle d) -> bool
6397 return _IMP_atom.Fragment___eq__(self, *args)
6400 def __ne__(self, *args):
6402 __ne__(Fragment self, Fragment o) -> bool
6403 __ne__(Fragment self, Particle d) -> bool
6405 return _IMP_atom.Fragment___ne__(self, *args)
6408 def __le__(self, *args):
6410 __le__(Fragment self, Fragment o) -> bool
6411 __le__(Fragment self, Particle d) -> bool
6413 return _IMP_atom.Fragment___le__(self, *args)
6416 def __lt__(self, *args):
6418 __lt__(Fragment self, Fragment o) -> bool
6419 __lt__(Fragment self, Particle d) -> bool
6421 return _IMP_atom.Fragment___lt__(self, *args)
6424 def __ge__(self, *args):
6426 __ge__(Fragment self, Fragment o) -> bool
6427 __ge__(Fragment self, Particle d) -> bool
6429 return _IMP_atom.Fragment___ge__(self, *args)
6432 def __gt__(self, *args):
6434 __gt__(Fragment self, Fragment o) -> bool
6435 __gt__(Fragment self, Particle d) -> bool
6437 return _IMP_atom.Fragment___gt__(self, *args)
6441 """__hash__(Fragment self) -> std::size_t"""
6442 return _IMP_atom.Fragment___hash__(self)
6446 """__str__(Fragment self) -> std::string"""
6447 return _IMP_atom.Fragment___str__(self)
6451 """__repr__(Fragment self) -> std::string"""
6452 return _IMP_atom.Fragment___repr__(self)
6454 __swig_destroy__ = _IMP_atom.delete_Fragment
6455 __del__ =
lambda self:
None
6456 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6457 Fragment_swigregister(Fragment)
6459 def Fragment_get_is_setup(*args):
6461 get_is_setup(Model m, ParticleIndex pi) -> bool
6462 Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6464 return _IMP_atom.Fragment_get_is_setup(*args)
6466 def Fragment_setup_particle(*args):
6468 setup_particle(Model m, ParticleIndex pi) -> Fragment
6469 setup_particle(_ParticleAdaptor decorator) -> Fragment
6470 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6471 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6472 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6473 Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6475 return _IMP_atom.Fragment_setup_particle(*args)
6478 """Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6480 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6483 """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6484 this = _IMP_atom.new_StereochemistryPairFilter()
6486 self.this.append(this)
6487 except __builtin__.Exception:
6490 def set_bonds(self, bonds):
6491 """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6492 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6495 def set_angles(self, angles):
6496 """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6497 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6500 def set_dihedrals(self, dihedrals):
6501 """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6502 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6505 def do_get_inputs(self, m, pis):
6506 """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6507 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6510 def get_value(self, *args):
6512 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6513 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6515 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6518 def get_value_index(self, *args):
6520 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6521 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6523 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6526 def get_version_info(self):
6527 """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6528 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6532 """__str__(StereochemistryPairFilter self) -> std::string"""
6533 return _IMP_atom.StereochemistryPairFilter___str__(self)
6537 """__repr__(StereochemistryPairFilter self) -> std::string"""
6538 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6543 return _object_cast_to_StereochemistryPairFilter(o)
6545 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6546 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6549 """Proxy of C++ IMP::atom::SoapPairFilter class."""
6551 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6553 def __init__(self, library):
6554 """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6555 this = _IMP_atom.new_SoapPairFilter(library)
6557 self.this.append(this)
6558 except __builtin__.Exception:
6561 def do_get_inputs(self, m, pis):
6562 """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6563 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6566 def get_value(self, *args):
6568 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6569 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6571 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6574 def get_value_index(self, *args):
6576 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6577 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6579 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6582 def get_version_info(self):
6583 """get_version_info(SoapPairFilter self) -> VersionInfo"""
6584 return _IMP_atom.SoapPairFilter_get_version_info(self)
6588 """__str__(SoapPairFilter self) -> std::string"""
6589 return _IMP_atom.SoapPairFilter___str__(self)
6593 """__repr__(SoapPairFilter self) -> std::string"""
6594 return _IMP_atom.SoapPairFilter___repr__(self)
6599 return _object_cast_to_SoapPairFilter(o)
6601 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6602 SoapPairFilter_swigregister(SoapPairFilter)
6605 """Proxy of C++ IMP::atom::Mass class."""
6607 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6610 """get_mass(Mass self) -> IMP::Float"""
6611 return _IMP_atom.Mass_get_mass(self)
6614 def set_mass(self, d):
6615 """set_mass(Mass self, IMP::Float d)"""
6616 return _IMP_atom.Mass_set_mass(self, d)
6619 def __init__(self, *args):
6621 __init__(IMP::atom::Mass self) -> Mass
6622 __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6623 __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6625 this = _IMP_atom.new_Mass(*args)
6627 self.this.append(this)
6628 except __builtin__.Exception:
6631 def get_is_setup(*args):
6633 get_is_setup(Model m, ParticleIndex pi) -> bool
6634 get_is_setup(_ParticleAdaptor p) -> bool
6636 return _IMP_atom.Mass_get_is_setup(*args)
6638 get_is_setup = staticmethod(get_is_setup)
6640 def show(self, *args):
6642 show(Mass self, _ostream out)
6645 return _IMP_atom.Mass_show(self, *args)
6648 def setup_particle(*args):
6650 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6651 setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6653 return _IMP_atom.Mass_setup_particle(*args)
6655 setup_particle = staticmethod(setup_particle)
6658 """get_mass_key() -> FloatKey"""
6659 return _IMP_atom.Mass_get_mass_key()
6661 get_mass_key = staticmethod(get_mass_key)
6663 def add_attribute(self, *args):
6665 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6666 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6667 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6668 add_attribute(Mass self, StringKey a0, IMP::String a1)
6669 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6670 add_attribute(Mass self, ObjectKey a0, Object a1)
6672 return _IMP_atom.Mass_add_attribute(self, *args)
6675 def get_value(self, *args):
6677 get_value(Mass self, FloatKey a0) -> IMP::Float
6678 get_value(Mass self, IntKey a0) -> IMP::Int
6679 get_value(Mass self, StringKey a0) -> IMP::String
6680 get_value(Mass self, ParticleIndexKey a0) -> Particle
6681 get_value(Mass self, ObjectKey a0) -> Object
6683 return _IMP_atom.Mass_get_value(self, *args)
6686 def set_value(self, *args):
6688 set_value(Mass self, FloatKey a0, IMP::Float a1)
6689 set_value(Mass self, IntKey a0, IMP::Int a1)
6690 set_value(Mass self, StringKey a0, IMP::String a1)
6691 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6692 set_value(Mass self, ObjectKey a0, Object a1)
6694 return _IMP_atom.Mass_set_value(self, *args)
6697 def remove_attribute(self, *args):
6699 remove_attribute(Mass self, FloatKey a0)
6700 remove_attribute(Mass self, IntKey a0)
6701 remove_attribute(Mass self, StringKey a0)
6702 remove_attribute(Mass self, ParticleIndexKey a0)
6703 remove_attribute(Mass self, ObjectKey a0)
6705 return _IMP_atom.Mass_remove_attribute(self, *args)
6708 def has_attribute(self, *args):
6710 has_attribute(Mass self, FloatKey a0) -> bool
6711 has_attribute(Mass self, IntKey a0) -> bool
6712 has_attribute(Mass self, StringKey a0) -> bool
6713 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6714 has_attribute(Mass self, ObjectKey a0) -> bool
6716 return _IMP_atom.Mass_has_attribute(self, *args)
6719 def get_derivative(self, a0):
6720 """get_derivative(Mass self, FloatKey a0) -> double"""
6721 return _IMP_atom.Mass_get_derivative(self, a0)
6725 """get_name(Mass self) -> std::string"""
6726 return _IMP_atom.Mass_get_name(self)
6729 def clear_caches(self):
6730 """clear_caches(Mass self)"""
6731 return _IMP_atom.Mass_clear_caches(self)
6734 def set_name(self, a0):
6735 """set_name(Mass self, std::string a0)"""
6736 return _IMP_atom.Mass_set_name(self, a0)
6740 """set_check_level(Mass self, IMP::CheckLevel a0)"""
6741 return _IMP_atom.Mass_set_check_level(self, a0)
6744 def add_to_derivative(self, a0, a1, a2):
6745 """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6746 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6749 def set_is_optimized(self, a0, a1):
6750 """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6751 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6754 def get_is_optimized(self, a0):
6755 """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6756 return _IMP_atom.Mass_get_is_optimized(self, a0)
6760 """get_check_level(Mass self) -> IMP::CheckLevel"""
6761 return _IMP_atom.Mass_get_check_level(self)
6764 def __eq__(self, *args):
6766 __eq__(Mass self, Mass o) -> bool
6767 __eq__(Mass self, Particle d) -> bool
6769 return _IMP_atom.Mass___eq__(self, *args)
6772 def __ne__(self, *args):
6774 __ne__(Mass self, Mass o) -> bool
6775 __ne__(Mass self, Particle d) -> bool
6777 return _IMP_atom.Mass___ne__(self, *args)
6780 def __le__(self, *args):
6782 __le__(Mass self, Mass o) -> bool
6783 __le__(Mass self, Particle d) -> bool
6785 return _IMP_atom.Mass___le__(self, *args)
6788 def __lt__(self, *args):
6790 __lt__(Mass self, Mass o) -> bool
6791 __lt__(Mass self, Particle d) -> bool
6793 return _IMP_atom.Mass___lt__(self, *args)
6796 def __ge__(self, *args):
6798 __ge__(Mass self, Mass o) -> bool
6799 __ge__(Mass self, Particle d) -> bool
6801 return _IMP_atom.Mass___ge__(self, *args)
6804 def __gt__(self, *args):
6806 __gt__(Mass self, Mass o) -> bool
6807 __gt__(Mass self, Particle d) -> bool
6809 return _IMP_atom.Mass___gt__(self, *args)
6813 """__hash__(Mass self) -> std::size_t"""
6814 return _IMP_atom.Mass___hash__(self)
6818 """__str__(Mass self) -> std::string"""
6819 return _IMP_atom.Mass___str__(self)
6823 """__repr__(Mass self) -> std::string"""
6824 return _IMP_atom.Mass___repr__(self)
6826 __swig_destroy__ = _IMP_atom.delete_Mass
6827 __del__ =
lambda self:
None
6828 Mass_swigregister = _IMP_atom.Mass_swigregister
6829 Mass_swigregister(Mass)
6831 def Mass_get_is_setup(*args):
6833 get_is_setup(Model m, ParticleIndex pi) -> bool
6834 Mass_get_is_setup(_ParticleAdaptor p) -> bool
6836 return _IMP_atom.Mass_get_is_setup(*args)
6838 def Mass_setup_particle(*args):
6840 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6841 Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6843 return _IMP_atom.Mass_setup_particle(*args)
6845 def Mass_get_mass_key():
6846 """Mass_get_mass_key() -> FloatKey"""
6847 return _IMP_atom.Mass_get_mass_key()
6850 """Proxy of C++ IMP::atom::BondedPairFilter class."""
6852 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6855 """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
6856 this = _IMP_atom.new_BondedPairFilter()
6858 self.this.append(this)
6859 except __builtin__.Exception:
6862 def do_get_inputs(self, m, pis):
6863 """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6864 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
6867 def get_value(self, *args):
6869 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
6870 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6872 return _IMP_atom.BondedPairFilter_get_value(self, *args)
6875 def get_value_index(self, *args):
6877 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6878 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6880 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
6883 def get_version_info(self):
6884 """get_version_info(BondedPairFilter self) -> VersionInfo"""
6885 return _IMP_atom.BondedPairFilter_get_version_info(self)
6889 """__str__(BondedPairFilter self) -> std::string"""
6890 return _IMP_atom.BondedPairFilter___str__(self)
6894 """__repr__(BondedPairFilter self) -> std::string"""
6895 return _IMP_atom.BondedPairFilter___repr__(self)
6900 return _object_cast_to_BondedPairFilter(o)
6902 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
6903 BondedPairFilter_swigregister(BondedPairFilter)
6906 """Proxy of C++ IMP::atom::Mol2Selector class."""
6908 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6910 def __init__(self, *args, **kwargs):
6911 raise AttributeError(
"No constructor defined - class is abstract")
6913 def get_is_selected(self, atom_line):
6914 """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
6915 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
6917 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
6918 __del__ =
lambda self:
None
6921 """__str__(Mol2Selector self) -> std::string"""
6922 return _IMP_atom.Mol2Selector___str__(self)
6926 """__repr__(Mol2Selector self) -> std::string"""
6927 return _IMP_atom.Mol2Selector___repr__(self)
6932 return _object_cast_to_Mol2Selector(o)
6934 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
6935 Mol2Selector_swigregister(Mol2Selector)
6937 class AllMol2Selector(Mol2Selector):
6938 """Proxy of C++ IMP::atom::AllMol2Selector class."""
6940 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6943 """__str__(AllMol2Selector self) -> std::string"""
6944 return _IMP_atom.AllMol2Selector___str__(self)
6948 """__repr__(AllMol2Selector self) -> std::string"""
6949 return _IMP_atom.AllMol2Selector___repr__(self)
6954 return _object_cast_to_AllMol2Selector(o)
6958 """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
6959 this = _IMP_atom.new_AllMol2Selector()
6961 self.this.append(this)
6962 except __builtin__.Exception:
6964 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
6965 __del__ =
lambda self:
None
6966 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
6967 AllMol2Selector_swigregister(AllMol2Selector)
6969 class NonHydrogenMol2Selector(Mol2Selector):
6970 """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
6972 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6975 """__str__(NonHydrogenMol2Selector self) -> std::string"""
6976 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
6980 """__repr__(NonHydrogenMol2Selector self) -> std::string"""
6981 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
6986 return _object_cast_to_NonHydrogenMol2Selector(o)
6990 """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
6991 this = _IMP_atom.new_NonHydrogenMol2Selector()
6993 self.this.append(this)
6994 except __builtin__.Exception:
6996 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
6997 __del__ =
lambda self:
None
6998 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
6999 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7002 def read_mol2(mol2_file, model, mol2sel=None):
7004 read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7005 read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7007 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7010 """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7011 return _IMP_atom.write_mol2(rhd, file_name)
7013 """Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
7015 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7017 def __init__(self, *args):
7019 __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7020 __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7021 __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7023 this = _IMP_atom.new_SecondaryStructureResidue(*args)
7025 self.this.append(this)
7026 except __builtin__.Exception:
7029 def show(self, *args):
7031 show(SecondaryStructureResidue self, _ostream out)
7032 show(SecondaryStructureResidue self)
7034 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7037 def setup_particle(*args):
7039 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7040 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7041 setup_particle(Particle res_p) -> SecondaryStructureResidue
7043 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7045 setup_particle = staticmethod(setup_particle)
7047 def get_is_setup(*args):
7049 get_is_setup(_ParticleAdaptor p) -> bool
7050 get_is_setup(Model m, ParticleIndex pi) -> bool
7052 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7054 get_is_setup = staticmethod(get_is_setup)
7056 def get_particle(self):
7057 """get_particle(SecondaryStructureResidue self) -> Particle"""
7058 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7061 def get_all_probabilities(self):
7062 """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7063 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7066 def get_prob_helix(self):
7067 """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7068 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7071 def set_prob_helix(self, t):
7072 """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7073 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7076 def get_prob_strand(self):
7077 """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7078 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7081 def set_prob_strand(self, t):
7082 """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7083 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7086 def get_prob_coil(self):
7087 """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7088 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7091 def set_prob_coil(self, t):
7092 """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7093 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7096 def get_prob_helix_key():
7097 """get_prob_helix_key() -> FloatKey"""
7098 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7100 get_prob_helix_key = staticmethod(get_prob_helix_key)
7102 def get_prob_strand_key():
7103 """get_prob_strand_key() -> FloatKey"""
7104 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7106 get_prob_strand_key = staticmethod(get_prob_strand_key)
7108 def get_prob_coil_key():
7109 """get_prob_coil_key() -> FloatKey"""
7110 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7112 get_prob_coil_key = staticmethod(get_prob_coil_key)
7114 def add_attribute(self, *args):
7116 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7117 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7118 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7119 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7120 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7121 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7123 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7126 def get_value(self, *args):
7128 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7129 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7130 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7131 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7132 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7134 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7137 def set_value(self, *args):
7139 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7140 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7141 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7142 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7143 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7145 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7148 def remove_attribute(self, *args):
7150 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7151 remove_attribute(SecondaryStructureResidue self, IntKey a0)
7152 remove_attribute(SecondaryStructureResidue self, StringKey a0)
7153 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7154 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7156 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7159 def has_attribute(self, *args):
7161 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7162 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7163 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7164 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7165 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7167 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7170 def get_derivative(self, a0):
7171 """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7172 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7176 """get_name(SecondaryStructureResidue self) -> std::string"""
7177 return _IMP_atom.SecondaryStructureResidue_get_name(self)
7180 def clear_caches(self):
7181 """clear_caches(SecondaryStructureResidue self)"""
7182 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7185 def set_name(self, a0):
7186 """set_name(SecondaryStructureResidue self, std::string a0)"""
7187 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7191 """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7192 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7195 def add_to_derivative(self, a0, a1, a2):
7196 """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7197 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7200 def set_is_optimized(self, a0, a1):
7201 """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7202 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7205 def get_is_optimized(self, a0):
7206 """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7207 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7211 """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7212 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7215 def __eq__(self, *args):
7217 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7218 __eq__(SecondaryStructureResidue self, Particle d) -> bool
7220 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7223 def __ne__(self, *args):
7225 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7226 __ne__(SecondaryStructureResidue self, Particle d) -> bool
7228 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7231 def __le__(self, *args):
7233 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7234 __le__(SecondaryStructureResidue self, Particle d) -> bool
7236 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7239 def __lt__(self, *args):
7241 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7242 __lt__(SecondaryStructureResidue self, Particle d) -> bool
7244 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7247 def __ge__(self, *args):
7249 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7250 __ge__(SecondaryStructureResidue self, Particle d) -> bool
7252 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7255 def __gt__(self, *args):
7257 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7258 __gt__(SecondaryStructureResidue self, Particle d) -> bool
7260 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7264 """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7265 return _IMP_atom.SecondaryStructureResidue___hash__(self)
7269 """__str__(SecondaryStructureResidue self) -> std::string"""
7270 return _IMP_atom.SecondaryStructureResidue___str__(self)
7274 """__repr__(SecondaryStructureResidue self) -> std::string"""
7275 return _IMP_atom.SecondaryStructureResidue___repr__(self)
7277 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7278 __del__ =
lambda self:
None
7279 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7280 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7282 def SecondaryStructureResidue_setup_particle(*args):
7284 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7285 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7286 SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7288 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7290 def SecondaryStructureResidue_get_is_setup(*args):
7292 get_is_setup(_ParticleAdaptor p) -> bool
7293 SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7295 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7297 def SecondaryStructureResidue_get_prob_helix_key():
7298 """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7299 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7301 def SecondaryStructureResidue_get_prob_strand_key():
7302 """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7303 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7305 def SecondaryStructureResidue_get_prob_coil_key():
7306 """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7307 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7312 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7313 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7315 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7319 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
7320 setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7322 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7325 """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7326 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7328 def read_psipred(*args):
7330 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7331 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7333 return _IMP_atom.read_psipred(*args)
7335 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class."""
7337 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7338 __repr__ = _swig_repr
7340 def __init__(self, *args):
7342 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7343 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7345 this = _IMP_atom.new__ADopeBase(*args)
7347 self.this.append(this)
7348 except __builtin__.Exception:
7351 def do_get_inputs(self, m, pis):
7352 """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7353 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7356 def get_score_functor(self):
7357 """get_score_functor(_ADopeBase self) -> Dope"""
7358 return _IMP_atom._ADopeBase_get_score_functor(self)
7361 def get_version_info(self):
7362 """get_version_info(_ADopeBase self) -> VersionInfo"""
7363 return _IMP_atom._ADopeBase_get_version_info(self)
7365 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7366 _ADopeBase_swigregister(_ADopeBase)
7369 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class."""
7371 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7372 __repr__ = _swig_repr
7374 def __init__(self, *args):
7376 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BDopeBase
7377 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0) -> _BDopeBase
7379 this = _IMP_atom.new__BDopeBase(*args)
7381 self.this.append(this)
7382 except __builtin__.Exception:
7385 def do_get_inputs(self, m, pis):
7386 """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7387 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7390 def get_score_functor(self):
7391 """get_score_functor(_BDopeBase self) -> _DopeBase"""
7392 return _IMP_atom._BDopeBase_get_score_functor(self)
7395 def get_version_info(self):
7396 """get_version_info(_BDopeBase self) -> VersionInfo"""
7397 return _IMP_atom._BDopeBase_get_version_info(self)
7399 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7400 _BDopeBase_swigregister(_BDopeBase)
7403 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class."""
7405 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7406 __repr__ = _swig_repr
7408 def __init__(self, *args):
7410 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name) -> _OrientedSoapBase
7411 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7413 this = _IMP_atom.new__OrientedSoapBase(*args)
7415 self.this.append(this)
7416 except __builtin__.Exception:
7419 def do_get_inputs(self, m, pis):
7420 """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7421 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7424 def get_score_functor(self):
7425 """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7426 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7429 def get_version_info(self):
7430 """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7431 return _IMP_atom._OrientedSoapBase_get_version_info(self)
7433 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7434 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7437 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class."""
7439 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7440 __repr__ = _swig_repr
7442 def __init__(self, *args):
7444 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name) -> _SPSFTB
7445 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0) -> _SPSFTB
7447 this = _IMP_atom.new__SPSFTB(*args)
7449 self.this.append(this)
7450 except __builtin__.Exception:
7453 def do_get_inputs(self, m, pis):
7454 """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7455 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7458 def get_score_functor(self):
7459 """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7460 return _IMP_atom._SPSFTB_get_score_functor(self)
7463 def get_version_info(self):
7464 """get_version_info(_SPSFTB self) -> VersionInfo"""
7465 return _IMP_atom._SPSFTB_get_version_info(self)
7467 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7468 _SPSFTB_swigregister(_SPSFTB)
7470 class _SPSTF(_SPSFTB):
7471 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class."""
7473 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7474 __repr__ = _swig_repr
7476 def __init__(self, *args):
7478 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7479 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7481 this = _IMP_atom.new__SPSTF(*args)
7483 self.this.append(this)
7484 except __builtin__.Exception:
7486 __swig_destroy__ = _IMP_atom.delete__SPSTF
7487 __del__ =
lambda self:
None
7488 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7489 _SPSTF_swigregister(_SPSTF)
7491 class _SPSFT(_BDopeBase):
7492 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class."""
7494 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7495 __repr__ = _swig_repr
7497 def __init__(self, *args):
7499 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7500 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7502 this = _IMP_atom.new__SPSFT(*args)
7504 self.this.append(this)
7505 except __builtin__.Exception:
7507 __swig_destroy__ = _IMP_atom.delete__SPSFT
7508 __del__ =
lambda self:
None
7509 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7510 _SPSFT_swigregister(_SPSFT)
7512 class ProteinLigandAtomPairScore(_SPSTF):
7513 """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7515 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7517 def __init__(self, *args):
7519 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7520 __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7521 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7523 this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7525 self.this.append(this)
7526 except __builtin__.Exception:
7529 def get_maximum_distance(self):
7530 """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7531 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7535 """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7536 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7540 """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7541 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7546 return _object_cast_to_ProteinLigandAtomPairScore(o)
7548 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7549 __del__ =
lambda self:
None
7550 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7551 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7554 """Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7556 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7558 def __init__(self, *args):
7560 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7561 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7562 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7564 this = _IMP_atom.new_ProteinLigandRestraint(*args)
7566 self.this.append(this)
7567 except __builtin__.Exception:
7571 """__str__(ProteinLigandRestraint self) -> std::string"""
7572 return _IMP_atom.ProteinLigandRestraint___str__(self)
7576 """__repr__(ProteinLigandRestraint self) -> std::string"""
7577 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7582 return _object_cast_to_ProteinLigandRestraint(o)
7584 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7585 __del__ =
lambda self:
None
7586 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7587 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7591 """add_protein_ligand_score_data(Hierarchy h)"""
7592 return _IMP_atom.add_protein_ligand_score_data(h)
7593 class AtomType(IMP._Value):
7594 """Proxy of C++ IMP::Key<(8974343)> class."""
7596 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7598 def __init__(self, *args):
7600 __init__(IMP::Key<(8974343)> self) -> AtomType
7601 __init__(IMP::Key<(8974343)> self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7602 __init__(IMP::Key<(8974343)> self, std::string const & c) -> AtomType
7603 __init__(IMP::Key<(8974343)> self, unsigned int i) -> AtomType
7605 this = _IMP_atom.new_AtomType(*args)
7607 self.this.append(this)
7608 except __builtin__.Exception:
7612 """add_key(std::string sc) -> unsigned int"""
7613 return _IMP_atom.AtomType_add_key(sc)
7615 add_key = staticmethod(add_key)
7617 def get_key_exists(sc):
7618 """get_key_exists(std::string sc) -> bool"""
7619 return _IMP_atom.AtomType_get_key_exists(sc)
7621 get_key_exists = staticmethod(get_key_exists)
7623 def get_string(self):
7624 """get_string(AtomType self) -> std::string const"""
7625 return _IMP_atom.AtomType_get_string(self)
7628 def __cmp__(self, o):
7629 """__cmp__(AtomType self, AtomType o) -> int"""
7630 return _IMP_atom.AtomType___cmp__(self, o)
7633 def __eq__(self, o):
7634 """__eq__(AtomType self, AtomType o) -> bool"""
7635 return _IMP_atom.AtomType___eq__(self, o)
7638 def __ne__(self, o):
7639 """__ne__(AtomType self, AtomType o) -> bool"""
7640 return _IMP_atom.AtomType___ne__(self, o)
7643 def __lt__(self, o):
7644 """__lt__(AtomType self, AtomType o) -> bool"""
7645 return _IMP_atom.AtomType___lt__(self, o)
7648 def __gt__(self, o):
7649 """__gt__(AtomType self, AtomType o) -> bool"""
7650 return _IMP_atom.AtomType___gt__(self, o)
7653 def __ge__(self, o):
7654 """__ge__(AtomType self, AtomType o) -> bool"""
7655 return _IMP_atom.AtomType___ge__(self, o)
7658 def __le__(self, o):
7659 """__le__(AtomType self, AtomType o) -> bool"""
7660 return _IMP_atom.AtomType___le__(self, o)
7664 """__hash__(AtomType self) -> std::size_t"""
7665 return _IMP_atom.AtomType___hash__(self)
7668 def show(self, *args):
7670 show(AtomType self, _ostream out)
7673 return _IMP_atom.AtomType_show(self, *args)
7676 def add_alias(old_key, new_name):
7677 """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7678 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7680 add_alias = staticmethod(add_alias)
7682 def get_number_of_keys():
7683 """get_number_of_keys() -> unsigned int"""
7684 return _IMP_atom.AtomType_get_number_of_keys()
7686 get_number_of_keys = staticmethod(get_number_of_keys)
7689 """get_index(AtomType self) -> unsigned int"""
7690 return _IMP_atom.AtomType_get_index(self)
7694 """show_all(_ostream out)"""
7695 return _IMP_atom.AtomType_show_all(out)
7697 show_all = staticmethod(show_all)
7699 def get_all_strings():
7700 """get_all_strings() -> IMP::Vector< std::string >"""
7701 return _IMP_atom.AtomType_get_all_strings()
7703 get_all_strings = staticmethod(get_all_strings)
7705 def get_number_unique():
7706 """get_number_unique() -> unsigned int"""
7707 return _IMP_atom.AtomType_get_number_unique()
7709 get_number_unique = staticmethod(get_number_unique)
7712 """__str__(AtomType self) -> std::string"""
7713 return _IMP_atom.AtomType___str__(self)
7717 """__repr__(AtomType self) -> std::string"""
7718 return _IMP_atom.AtomType___repr__(self)
7720 __swig_destroy__ = _IMP_atom.delete_AtomType
7721 __del__ =
lambda self:
None
7722 AtomType_swigregister = _IMP_atom.AtomType_swigregister
7723 AtomType_swigregister(AtomType)
7725 def AtomType_add_key(sc):
7726 """AtomType_add_key(std::string sc) -> unsigned int"""
7727 return _IMP_atom.AtomType_add_key(sc)
7729 def AtomType_get_key_exists(sc):
7730 """AtomType_get_key_exists(std::string sc) -> bool"""
7731 return _IMP_atom.AtomType_get_key_exists(sc)
7733 def AtomType_add_alias(old_key, new_name):
7734 """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7735 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7737 def AtomType_get_number_of_keys():
7738 """AtomType_get_number_of_keys() -> unsigned int"""
7739 return _IMP_atom.AtomType_get_number_of_keys()
7741 def AtomType_show_all(out):
7742 """AtomType_show_all(_ostream out)"""
7743 return _IMP_atom.AtomType_show_all(out)
7745 def AtomType_get_all_strings():
7746 """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
7747 return _IMP_atom.AtomType_get_all_strings()
7749 def AtomType_get_number_unique():
7750 """AtomType_get_number_unique() -> unsigned int"""
7751 return _IMP_atom.AtomType_get_number_unique()
7753 class ResidueType(IMP._Value):
7754 """Proxy of C++ IMP::Key<(90784334)> class."""
7756 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7758 def __init__(self, *args):
7760 __init__(IMP::Key<(90784334)> self) -> ResidueType
7761 __init__(IMP::Key<(90784334)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
7762 __init__(IMP::Key<(90784334)> self, std::string const & c) -> ResidueType
7763 __init__(IMP::Key<(90784334)> self, unsigned int i) -> ResidueType
7765 this = _IMP_atom.new_ResidueType(*args)
7767 self.this.append(this)
7768 except __builtin__.Exception:
7772 """add_key(std::string sc) -> unsigned int"""
7773 return _IMP_atom.ResidueType_add_key(sc)
7775 add_key = staticmethod(add_key)
7777 def get_key_exists(sc):
7778 """get_key_exists(std::string sc) -> bool"""
7779 return _IMP_atom.ResidueType_get_key_exists(sc)
7781 get_key_exists = staticmethod(get_key_exists)
7783 def get_string(self):
7784 """get_string(ResidueType self) -> std::string const"""
7785 return _IMP_atom.ResidueType_get_string(self)
7788 def __cmp__(self, o):
7789 """__cmp__(ResidueType self, ResidueType o) -> int"""
7790 return _IMP_atom.ResidueType___cmp__(self, o)
7793 def __eq__(self, o):
7794 """__eq__(ResidueType self, ResidueType o) -> bool"""
7795 return _IMP_atom.ResidueType___eq__(self, o)
7798 def __ne__(self, o):
7799 """__ne__(ResidueType self, ResidueType o) -> bool"""
7800 return _IMP_atom.ResidueType___ne__(self, o)
7803 def __lt__(self, o):
7804 """__lt__(ResidueType self, ResidueType o) -> bool"""
7805 return _IMP_atom.ResidueType___lt__(self, o)
7808 def __gt__(self, o):
7809 """__gt__(ResidueType self, ResidueType o) -> bool"""
7810 return _IMP_atom.ResidueType___gt__(self, o)
7813 def __ge__(self, o):
7814 """__ge__(ResidueType self, ResidueType o) -> bool"""
7815 return _IMP_atom.ResidueType___ge__(self, o)
7818 def __le__(self, o):
7819 """__le__(ResidueType self, ResidueType o) -> bool"""
7820 return _IMP_atom.ResidueType___le__(self, o)
7824 """__hash__(ResidueType self) -> std::size_t"""
7825 return _IMP_atom.ResidueType___hash__(self)
7828 def show(self, *args):
7830 show(ResidueType self, _ostream out)
7831 show(ResidueType self)
7833 return _IMP_atom.ResidueType_show(self, *args)
7836 def add_alias(old_key, new_name):
7837 """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7838 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7840 add_alias = staticmethod(add_alias)
7842 def get_number_of_keys():
7843 """get_number_of_keys() -> unsigned int"""
7844 return _IMP_atom.ResidueType_get_number_of_keys()
7846 get_number_of_keys = staticmethod(get_number_of_keys)
7849 """get_index(ResidueType self) -> unsigned int"""
7850 return _IMP_atom.ResidueType_get_index(self)
7854 """show_all(_ostream out)"""
7855 return _IMP_atom.ResidueType_show_all(out)
7857 show_all = staticmethod(show_all)
7859 def get_all_strings():
7860 """get_all_strings() -> IMP::Vector< std::string >"""
7861 return _IMP_atom.ResidueType_get_all_strings()
7863 get_all_strings = staticmethod(get_all_strings)
7865 def get_number_unique():
7866 """get_number_unique() -> unsigned int"""
7867 return _IMP_atom.ResidueType_get_number_unique()
7869 get_number_unique = staticmethod(get_number_unique)
7872 """__str__(ResidueType self) -> std::string"""
7873 return _IMP_atom.ResidueType___str__(self)
7877 """__repr__(ResidueType self) -> std::string"""
7878 return _IMP_atom.ResidueType___repr__(self)
7880 __swig_destroy__ = _IMP_atom.delete_ResidueType
7881 __del__ =
lambda self:
None
7882 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
7883 ResidueType_swigregister(ResidueType)
7885 def ResidueType_add_key(sc):
7886 """ResidueType_add_key(std::string sc) -> unsigned int"""
7887 return _IMP_atom.ResidueType_add_key(sc)
7889 def ResidueType_get_key_exists(sc):
7890 """ResidueType_get_key_exists(std::string sc) -> bool"""
7891 return _IMP_atom.ResidueType_get_key_exists(sc)
7893 def ResidueType_add_alias(old_key, new_name):
7894 """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
7895 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
7897 def ResidueType_get_number_of_keys():
7898 """ResidueType_get_number_of_keys() -> unsigned int"""
7899 return _IMP_atom.ResidueType_get_number_of_keys()
7901 def ResidueType_show_all(out):
7902 """ResidueType_show_all(_ostream out)"""
7903 return _IMP_atom.ResidueType_show_all(out)
7905 def ResidueType_get_all_strings():
7906 """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
7907 return _IMP_atom.ResidueType_get_all_strings()
7909 def ResidueType_get_number_unique():
7910 """ResidueType_get_number_unique() -> unsigned int"""
7911 return _IMP_atom.ResidueType_get_number_unique()
7913 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8022 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8025 """hash_value(IMP::atom::Element e) -> size_t"""
8026 return _IMP_atom.hash_value(e)
8027 class ElementTable(object):
8028 """Proxy of C++ IMP::atom::ElementTable class."""
8030 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8031 __repr__ = _swig_repr
8034 """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8035 this = _IMP_atom.new_ElementTable()
8037 self.this.append(this)
8038 except __builtin__.Exception:
8041 def get_element(self, s):
8042 """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8043 return _IMP_atom.ElementTable_get_element(self, s)
8046 def get_name(self, e):
8047 """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8048 return _IMP_atom.ElementTable_get_name(self, e)
8052 """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8053 return _IMP_atom.ElementTable_get_mass(self, e)
8055 __swig_destroy__ = _IMP_atom.delete_ElementTable
8056 __del__ =
lambda self:
None
8057 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8058 ElementTable_swigregister(ElementTable)
8061 def get_element_table():
8062 """get_element_table() -> ElementTable"""
8063 return _IMP_atom.get_element_table()
8064 class Atom(Hierarchy):
8065 """Proxy of C++ IMP::atom::Atom class."""
8067 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8069 def __init__(self, *args):
8071 __init__(IMP::atom::Atom self) -> Atom
8072 __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8073 __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8075 this = _IMP_atom.new_Atom(*args)
8077 self.this.append(this)
8078 except __builtin__.Exception:
8081 def show(self, *args):
8083 show(Atom self, _ostream out)
8086 return _IMP_atom.Atom_show(self, *args)
8089 def setup_particle(*args):
8091 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8092 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8093 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8094 setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8096 return _IMP_atom.Atom_setup_particle(*args)
8098 setup_particle = staticmethod(setup_particle)
8100 def get_is_setup(*args):
8102 get_is_setup(_ParticleAdaptor p) -> bool
8103 get_is_setup(Model m, ParticleIndex pi) -> bool
8105 return _IMP_atom.Atom_get_is_setup(*args)
8107 get_is_setup = staticmethod(get_is_setup)
8109 def get_atom_type(self):
8110 """get_atom_type(Atom self) -> AtomType"""
8111 return _IMP_atom.Atom_get_atom_type(self)
8114 def set_atom_type(self, t):
8115 """set_atom_type(Atom self, AtomType t)"""
8116 return _IMP_atom.Atom_set_atom_type(self, t)
8119 def get_element(self):
8120 """get_element(Atom self) -> IMP::atom::Element"""
8121 return _IMP_atom.Atom_get_element(self)
8124 def set_element(self, e):
8125 """set_element(Atom self, IMP::atom::Element e)"""
8126 return _IMP_atom.Atom_set_element(self, e)
8129 def get_occupancy(self):
8130 """get_occupancy(Atom self) -> double"""
8131 return _IMP_atom.Atom_get_occupancy(self)
8134 def set_occupancy(self, occupancy):
8135 """set_occupancy(Atom self, double occupancy)"""
8136 return _IMP_atom.Atom_set_occupancy(self, occupancy)
8139 def get_temperature_factor(self):
8140 """get_temperature_factor(Atom self) -> double"""
8141 return _IMP_atom.Atom_get_temperature_factor(self)
8144 def set_temperature_factor(self, tempFactor):
8145 """set_temperature_factor(Atom self, double tempFactor)"""
8146 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8149 def get_input_index(self):
8150 """get_input_index(Atom self) -> IMP::Int"""
8151 return _IMP_atom.Atom_get_input_index(self)
8154 def set_input_index(self, t):
8155 """set_input_index(Atom self, IMP::Int t)"""
8156 return _IMP_atom.Atom_set_input_index(self, t)
8159 def get_atom_type_key():
8160 """get_atom_type_key() -> IntKey"""
8161 return _IMP_atom.Atom_get_atom_type_key()
8163 get_atom_type_key = staticmethod(get_atom_type_key)
8165 def get_element_key():
8166 """get_element_key() -> IntKey"""
8167 return _IMP_atom.Atom_get_element_key()
8169 get_element_key = staticmethod(get_element_key)
8171 def get_input_index_key():
8172 """get_input_index_key() -> IntKey"""
8173 return _IMP_atom.Atom_get_input_index_key()
8175 get_input_index_key = staticmethod(get_input_index_key)
8177 def get_occupancy_key():
8178 """get_occupancy_key() -> FloatKey"""
8179 return _IMP_atom.Atom_get_occupancy_key()
8181 get_occupancy_key = staticmethod(get_occupancy_key)
8183 def get_temperature_factor_key():
8184 """get_temperature_factor_key() -> FloatKey"""
8185 return _IMP_atom.Atom_get_temperature_factor_key()
8187 get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8189 def add_attribute(self, *args):
8191 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8192 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8193 add_attribute(Atom self, IntKey a0, IMP::Int a1)
8194 add_attribute(Atom self, StringKey a0, IMP::String a1)
8195 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8196 add_attribute(Atom self, ObjectKey a0, Object a1)
8198 return _IMP_atom.Atom_add_attribute(self, *args)
8201 def get_value(self, *args):
8203 get_value(Atom self, FloatKey a0) -> IMP::Float
8204 get_value(Atom self, IntKey a0) -> IMP::Int
8205 get_value(Atom self, StringKey a0) -> IMP::String
8206 get_value(Atom self, ParticleIndexKey a0) -> Particle
8207 get_value(Atom self, ObjectKey a0) -> Object
8209 return _IMP_atom.Atom_get_value(self, *args)
8212 def set_value(self, *args):
8214 set_value(Atom self, FloatKey a0, IMP::Float a1)
8215 set_value(Atom self, IntKey a0, IMP::Int a1)
8216 set_value(Atom self, StringKey a0, IMP::String a1)
8217 set_value(Atom self, ParticleIndexKey a0, Particle a1)
8218 set_value(Atom self, ObjectKey a0, Object a1)
8220 return _IMP_atom.Atom_set_value(self, *args)
8223 def remove_attribute(self, *args):
8225 remove_attribute(Atom self, FloatKey a0)
8226 remove_attribute(Atom self, IntKey a0)
8227 remove_attribute(Atom self, StringKey a0)
8228 remove_attribute(Atom self, ParticleIndexKey a0)
8229 remove_attribute(Atom self, ObjectKey a0)
8231 return _IMP_atom.Atom_remove_attribute(self, *args)
8234 def has_attribute(self, *args):
8236 has_attribute(Atom self, FloatKey a0) -> bool
8237 has_attribute(Atom self, IntKey a0) -> bool
8238 has_attribute(Atom self, StringKey a0) -> bool
8239 has_attribute(Atom self, ParticleIndexKey a0) -> bool
8240 has_attribute(Atom self, ObjectKey a0) -> bool
8242 return _IMP_atom.Atom_has_attribute(self, *args)
8245 def get_derivative(self, a0):
8246 """get_derivative(Atom self, FloatKey a0) -> double"""
8247 return _IMP_atom.Atom_get_derivative(self, a0)
8251 """get_name(Atom self) -> std::string"""
8252 return _IMP_atom.Atom_get_name(self)
8255 def clear_caches(self):
8256 """clear_caches(Atom self)"""
8257 return _IMP_atom.Atom_clear_caches(self)
8260 def set_name(self, a0):
8261 """set_name(Atom self, std::string a0)"""
8262 return _IMP_atom.Atom_set_name(self, a0)
8266 """set_check_level(Atom self, IMP::CheckLevel a0)"""
8267 return _IMP_atom.Atom_set_check_level(self, a0)
8270 def add_to_derivative(self, a0, a1, a2):
8271 """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8272 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8275 def set_is_optimized(self, a0, a1):
8276 """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8277 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8280 def get_is_optimized(self, a0):
8281 """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8282 return _IMP_atom.Atom_get_is_optimized(self, a0)
8286 """get_check_level(Atom self) -> IMP::CheckLevel"""
8287 return _IMP_atom.Atom_get_check_level(self)
8290 def __eq__(self, *args):
8292 __eq__(Atom self, Atom o) -> bool
8293 __eq__(Atom self, Particle d) -> bool
8295 return _IMP_atom.Atom___eq__(self, *args)
8298 def __ne__(self, *args):
8300 __ne__(Atom self, Atom o) -> bool
8301 __ne__(Atom self, Particle d) -> bool
8303 return _IMP_atom.Atom___ne__(self, *args)
8306 def __le__(self, *args):
8308 __le__(Atom self, Atom o) -> bool
8309 __le__(Atom self, Particle d) -> bool
8311 return _IMP_atom.Atom___le__(self, *args)
8314 def __lt__(self, *args):
8316 __lt__(Atom self, Atom o) -> bool
8317 __lt__(Atom self, Particle d) -> bool
8319 return _IMP_atom.Atom___lt__(self, *args)
8322 def __ge__(self, *args):
8324 __ge__(Atom self, Atom o) -> bool
8325 __ge__(Atom self, Particle d) -> bool
8327 return _IMP_atom.Atom___ge__(self, *args)
8330 def __gt__(self, *args):
8332 __gt__(Atom self, Atom o) -> bool
8333 __gt__(Atom self, Particle d) -> bool
8335 return _IMP_atom.Atom___gt__(self, *args)
8339 """__hash__(Atom self) -> std::size_t"""
8340 return _IMP_atom.Atom___hash__(self)
8344 """__str__(Atom self) -> std::string"""
8345 return _IMP_atom.Atom___str__(self)
8349 """__repr__(Atom self) -> std::string"""
8350 return _IMP_atom.Atom___repr__(self)
8352 __swig_destroy__ = _IMP_atom.delete_Atom
8353 __del__ =
lambda self:
None
8354 Atom_swigregister = _IMP_atom.Atom_swigregister
8355 Atom_swigregister(Atom)
8356 cvar = _IMP_atom.cvar
8357 AT_UNKNOWN = cvar.AT_UNKNOWN
8367 AT_HA1 = cvar.AT_HA1
8368 AT_HA2 = cvar.AT_HA2
8369 AT_HA3 = cvar.AT_HA3
8372 AT_HB1 = cvar.AT_HB1
8373 AT_HB2 = cvar.AT_HB2
8374 AT_HB3 = cvar.AT_HB3
8375 AT_OXT = cvar.AT_OXT
8376 AT_CH3 = cvar.AT_CH3
8379 AT_CG1 = cvar.AT_CG1
8380 AT_CG2 = cvar.AT_CG2
8382 AT_HG1 = cvar.AT_HG1
8383 AT_HG2 = cvar.AT_HG2
8384 AT_HG3 = cvar.AT_HG3
8385 AT_HG11 = cvar.AT_HG11
8386 AT_HG21 = cvar.AT_HG21
8387 AT_HG31 = cvar.AT_HG31
8388 AT_HG12 = cvar.AT_HG12
8389 AT_HG13 = cvar.AT_HG13
8390 AT_HG22 = cvar.AT_HG22
8391 AT_HG23 = cvar.AT_HG23
8392 AT_HG32 = cvar.AT_HG32
8394 AT_OG1 = cvar.AT_OG1
8397 AT_CD1 = cvar.AT_CD1
8398 AT_CD2 = cvar.AT_CD2
8400 AT_HD1 = cvar.AT_HD1
8401 AT_HD2 = cvar.AT_HD2
8402 AT_HD3 = cvar.AT_HD3
8403 AT_HD11 = cvar.AT_HD11
8404 AT_HD21 = cvar.AT_HD21
8405 AT_HD31 = cvar.AT_HD31
8406 AT_HD12 = cvar.AT_HD12
8407 AT_HD13 = cvar.AT_HD13
8408 AT_HD22 = cvar.AT_HD22
8409 AT_HD23 = cvar.AT_HD23
8410 AT_HD32 = cvar.AT_HD32
8412 AT_OD1 = cvar.AT_OD1
8413 AT_OD2 = cvar.AT_OD2
8414 AT_ND1 = cvar.AT_ND1
8415 AT_ND2 = cvar.AT_ND2
8417 AT_CE1 = cvar.AT_CE1
8418 AT_CE2 = cvar.AT_CE2
8419 AT_CE3 = cvar.AT_CE3
8421 AT_HE1 = cvar.AT_HE1
8422 AT_HE2 = cvar.AT_HE2
8423 AT_HE3 = cvar.AT_HE3
8424 AT_HE21 = cvar.AT_HE21
8425 AT_HE22 = cvar.AT_HE22
8426 AT_OE1 = cvar.AT_OE1
8427 AT_OE2 = cvar.AT_OE2
8429 AT_NE1 = cvar.AT_NE1
8430 AT_NE2 = cvar.AT_NE2
8432 AT_CZ2 = cvar.AT_CZ2
8433 AT_CZ3 = cvar.AT_CZ3
8436 AT_HZ1 = cvar.AT_HZ1
8437 AT_HZ2 = cvar.AT_HZ2
8438 AT_HZ3 = cvar.AT_HZ3
8439 AT_CH2 = cvar.AT_CH2
8440 AT_NH1 = cvar.AT_NH1
8441 AT_NH2 = cvar.AT_NH2
8444 AT_HH11 = cvar.AT_HH11
8445 AT_HH21 = cvar.AT_HH21
8446 AT_HH2 = cvar.AT_HH2
8447 AT_HH12 = cvar.AT_HH12
8448 AT_HH22 = cvar.AT_HH22
8449 AT_HH13 = cvar.AT_HH13
8450 AT_HH23 = cvar.AT_HH23
8451 AT_HH33 = cvar.AT_HH33
8453 AT_OP1 = cvar.AT_OP1
8454 AT_OP2 = cvar.AT_OP2
8455 AT_OP3 = cvar.AT_OP3
8456 AT_O5p = cvar.AT_O5p
8457 AT_C5p = cvar.AT_C5p
8458 AT_H5p = cvar.AT_H5p
8459 AT_H5pp = cvar.AT_H5pp
8460 AT_C4p = cvar.AT_C4p
8461 AT_H4p = cvar.AT_H4p
8462 AT_O4p = cvar.AT_O4p
8463 AT_C1p = cvar.AT_C1p
8464 AT_H1p = cvar.AT_H1p
8465 AT_C3p = cvar.AT_C3p
8466 AT_H3p = cvar.AT_H3p
8467 AT_O3p = cvar.AT_O3p
8468 AT_C2p = cvar.AT_C2p
8469 AT_H2p = cvar.AT_H2p
8470 AT_H2pp = cvar.AT_H2pp
8471 AT_O2p = cvar.AT_O2p
8472 AT_HO2p = cvar.AT_HO2p
8484 AT_H61 = cvar.AT_H61
8485 AT_H62 = cvar.AT_H62
8489 AT_H21 = cvar.AT_H21
8490 AT_H22 = cvar.AT_H22
8495 AT_H41 = cvar.AT_H41
8496 AT_H42 = cvar.AT_H42
8499 AT_H71 = cvar.AT_H71
8500 AT_H72 = cvar.AT_H72
8501 AT_H73 = cvar.AT_H73
8502 AT_O1A = cvar.AT_O1A
8503 AT_O2A = cvar.AT_O2A
8504 AT_O3A = cvar.AT_O3A
8505 AT_O1B = cvar.AT_O1B
8506 AT_O2B = cvar.AT_O2B
8507 AT_O3B = cvar.AT_O3B
8509 def Atom_setup_particle(*args):
8511 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8512 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8513 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8514 Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8516 return _IMP_atom.Atom_setup_particle(*args)
8518 def Atom_get_is_setup(*args):
8520 get_is_setup(_ParticleAdaptor p) -> bool
8521 Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
8523 return _IMP_atom.Atom_get_is_setup(*args)
8525 def Atom_get_atom_type_key():
8526 """Atom_get_atom_type_key() -> IntKey"""
8527 return _IMP_atom.Atom_get_atom_type_key()
8529 def Atom_get_element_key():
8530 """Atom_get_element_key() -> IntKey"""
8531 return _IMP_atom.Atom_get_element_key()
8533 def Atom_get_input_index_key():
8534 """Atom_get_input_index_key() -> IntKey"""
8535 return _IMP_atom.Atom_get_input_index_key()
8537 def Atom_get_occupancy_key():
8538 """Atom_get_occupancy_key() -> FloatKey"""
8539 return _IMP_atom.Atom_get_occupancy_key()
8541 def Atom_get_temperature_factor_key():
8542 """Atom_get_temperature_factor_key() -> FloatKey"""
8543 return _IMP_atom.Atom_get_temperature_factor_key()
8548 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8549 get_residue(Atom d, bool nothrow=False) -> Residue
8550 get_residue(Atom d) -> Residue
8552 return _IMP_atom.get_residue(*args)
8555 """get_atom(Residue rd, AtomType at) -> Atom"""
8556 return _IMP_atom.get_atom(rd, at)
8559 """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8560 return _IMP_atom.add_atom_type(name, e)
8562 def get_element_for_atom_type(at):
8563 """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8564 return _IMP_atom.get_element_for_atom_type(at)
8567 """get_atom_type_exists(std::string name) -> bool"""
8568 return _IMP_atom.get_atom_type_exists(name)
8569 class Residue(Hierarchy):
8570 """Proxy of C++ IMP::atom::Residue class."""
8572 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8574 def __init__(self, *args):
8576 __init__(IMP::atom::Residue self) -> Residue
8577 __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
8578 __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
8580 this = _IMP_atom.new_Residue(*args)
8582 self.this.append(this)
8583 except __builtin__.Exception:
8586 def show(self, *args):
8588 show(Residue self, _ostream out)
8591 return _IMP_atom.Residue_show(self, *args)
8594 def setup_particle(*args):
8596 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8597 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8598 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8599 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8600 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8601 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8602 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8603 setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8605 return _IMP_atom.Residue_setup_particle(*args)
8607 setup_particle = staticmethod(setup_particle)
8609 def get_is_setup(*args):
8611 get_is_setup(_ParticleAdaptor p) -> bool
8612 get_is_setup(Model m, ParticleIndex pi) -> bool
8614 return _IMP_atom.Residue_get_is_setup(*args)
8616 get_is_setup = staticmethod(get_is_setup)
8618 def get_residue_type(self):
8619 """get_residue_type(Residue self) -> ResidueType"""
8620 return _IMP_atom.Residue_get_residue_type(self)
8623 def set_residue_type(self, t):
8624 """set_residue_type(Residue self, ResidueType t)"""
8625 return _IMP_atom.Residue_set_residue_type(self, t)
8628 def get_is_protein(self):
8629 """get_is_protein(Residue self) -> bool"""
8630 return _IMP_atom.Residue_get_is_protein(self)
8633 def get_is_dna(self):
8634 """get_is_dna(Residue self) -> bool"""
8635 return _IMP_atom.Residue_get_is_dna(self)
8638 def get_is_rna(self):
8639 """get_is_rna(Residue self) -> bool"""
8640 return _IMP_atom.Residue_get_is_rna(self)
8644 """get_index(Residue self) -> IMP::Int"""
8645 return _IMP_atom.Residue_get_index(self)
8648 def set_index(self, t):
8649 """set_index(Residue self, IMP::Int t)"""
8650 return _IMP_atom.Residue_set_index(self, t)
8653 def get_insertion_code(self):
8654 """get_insertion_code(Residue self) -> char"""
8655 return _IMP_atom.Residue_get_insertion_code(self)
8658 def set_insertion_code(self, insertion_code):
8659 """set_insertion_code(Residue self, char insertion_code)"""
8660 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
8663 def get_index_key():
8664 """get_index_key() -> IntKey"""
8665 return _IMP_atom.Residue_get_index_key()
8667 get_index_key = staticmethod(get_index_key)
8669 def get_residue_type_key():
8670 """get_residue_type_key() -> IntKey"""
8671 return _IMP_atom.Residue_get_residue_type_key()
8673 get_residue_type_key = staticmethod(get_residue_type_key)
8675 def get_insertion_code_key():
8676 """get_insertion_code_key() -> IntKey"""
8677 return _IMP_atom.Residue_get_insertion_code_key()
8679 get_insertion_code_key = staticmethod(get_insertion_code_key)
8681 def add_attribute(self, *args):
8683 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
8684 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
8685 add_attribute(Residue self, IntKey a0, IMP::Int a1)
8686 add_attribute(Residue self, StringKey a0, IMP::String a1)
8687 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
8688 add_attribute(Residue self, ObjectKey a0, Object a1)
8690 return _IMP_atom.Residue_add_attribute(self, *args)
8693 def get_value(self, *args):
8695 get_value(Residue self, FloatKey a0) -> IMP::Float
8696 get_value(Residue self, IntKey a0) -> IMP::Int
8697 get_value(Residue self, StringKey a0) -> IMP::String
8698 get_value(Residue self, ParticleIndexKey a0) -> Particle
8699 get_value(Residue self, ObjectKey a0) -> Object
8701 return _IMP_atom.Residue_get_value(self, *args)
8704 def set_value(self, *args):
8706 set_value(Residue self, FloatKey a0, IMP::Float a1)
8707 set_value(Residue self, IntKey a0, IMP::Int a1)
8708 set_value(Residue self, StringKey a0, IMP::String a1)
8709 set_value(Residue self, ParticleIndexKey a0, Particle a1)
8710 set_value(Residue self, ObjectKey a0, Object a1)
8712 return _IMP_atom.Residue_set_value(self, *args)
8715 def remove_attribute(self, *args):
8717 remove_attribute(Residue self, FloatKey a0)
8718 remove_attribute(Residue self, IntKey a0)
8719 remove_attribute(Residue self, StringKey a0)
8720 remove_attribute(Residue self, ParticleIndexKey a0)
8721 remove_attribute(Residue self, ObjectKey a0)
8723 return _IMP_atom.Residue_remove_attribute(self, *args)
8726 def has_attribute(self, *args):
8728 has_attribute(Residue self, FloatKey a0) -> bool
8729 has_attribute(Residue self, IntKey a0) -> bool
8730 has_attribute(Residue self, StringKey a0) -> bool
8731 has_attribute(Residue self, ParticleIndexKey a0) -> bool
8732 has_attribute(Residue self, ObjectKey a0) -> bool
8734 return _IMP_atom.Residue_has_attribute(self, *args)
8737 def get_derivative(self, a0):
8738 """get_derivative(Residue self, FloatKey a0) -> double"""
8739 return _IMP_atom.Residue_get_derivative(self, a0)
8743 """get_name(Residue self) -> std::string"""
8744 return _IMP_atom.Residue_get_name(self)
8747 def clear_caches(self):
8748 """clear_caches(Residue self)"""
8749 return _IMP_atom.Residue_clear_caches(self)
8752 def set_name(self, a0):
8753 """set_name(Residue self, std::string a0)"""
8754 return _IMP_atom.Residue_set_name(self, a0)
8758 """set_check_level(Residue self, IMP::CheckLevel a0)"""
8759 return _IMP_atom.Residue_set_check_level(self, a0)
8762 def add_to_derivative(self, a0, a1, a2):
8763 """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8764 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
8767 def set_is_optimized(self, a0, a1):
8768 """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
8769 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
8772 def get_is_optimized(self, a0):
8773 """get_is_optimized(Residue self, FloatKey a0) -> bool"""
8774 return _IMP_atom.Residue_get_is_optimized(self, a0)
8778 """get_check_level(Residue self) -> IMP::CheckLevel"""
8779 return _IMP_atom.Residue_get_check_level(self)
8782 def __eq__(self, *args):
8784 __eq__(Residue self, Residue o) -> bool
8785 __eq__(Residue self, Particle d) -> bool
8787 return _IMP_atom.Residue___eq__(self, *args)
8790 def __ne__(self, *args):
8792 __ne__(Residue self, Residue o) -> bool
8793 __ne__(Residue self, Particle d) -> bool
8795 return _IMP_atom.Residue___ne__(self, *args)
8798 def __le__(self, *args):
8800 __le__(Residue self, Residue o) -> bool
8801 __le__(Residue self, Particle d) -> bool
8803 return _IMP_atom.Residue___le__(self, *args)
8806 def __lt__(self, *args):
8808 __lt__(Residue self, Residue o) -> bool
8809 __lt__(Residue self, Particle d) -> bool
8811 return _IMP_atom.Residue___lt__(self, *args)
8814 def __ge__(self, *args):
8816 __ge__(Residue self, Residue o) -> bool
8817 __ge__(Residue self, Particle d) -> bool
8819 return _IMP_atom.Residue___ge__(self, *args)
8822 def __gt__(self, *args):
8824 __gt__(Residue self, Residue o) -> bool
8825 __gt__(Residue self, Particle d) -> bool
8827 return _IMP_atom.Residue___gt__(self, *args)
8831 """__hash__(Residue self) -> std::size_t"""
8832 return _IMP_atom.Residue___hash__(self)
8836 """__str__(Residue self) -> std::string"""
8837 return _IMP_atom.Residue___str__(self)
8841 """__repr__(Residue self) -> std::string"""
8842 return _IMP_atom.Residue___repr__(self)
8844 __swig_destroy__ = _IMP_atom.delete_Residue
8845 __del__ =
lambda self:
None
8846 Residue_swigregister = _IMP_atom.Residue_swigregister
8847 Residue_swigregister(Residue)
8884 def Residue_setup_particle(*args):
8886 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8887 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8888 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8889 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8890 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8891 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8892 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8893 Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8895 return _IMP_atom.Residue_setup_particle(*args)
8897 def Residue_get_is_setup(*args):
8899 get_is_setup(_ParticleAdaptor p) -> bool
8900 Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
8902 return _IMP_atom.Residue_get_is_setup(*args)
8904 def Residue_get_index_key():
8905 """Residue_get_index_key() -> IntKey"""
8906 return _IMP_atom.Residue_get_index_key()
8908 def Residue_get_residue_type_key():
8909 """Residue_get_residue_type_key() -> IntKey"""
8910 return _IMP_atom.Residue_get_residue_type_key()
8912 def Residue_get_insertion_code_key():
8913 """Residue_get_insertion_code_key() -> IntKey"""
8914 return _IMP_atom.Residue_get_insertion_code_key()
8918 """get_next_residue(Residue rd) -> Hierarchy"""
8919 return _IMP_atom.get_next_residue(rd)
8922 """get_previous_residue(Residue rd) -> Hierarchy"""
8923 return _IMP_atom.get_previous_residue(rd)
8926 """get_one_letter_code(ResidueType c) -> char"""
8927 return _IMP_atom.get_one_letter_code(c)
8928 BALLS = _IMP_atom.BALLS
8929 DENSITIES = _IMP_atom.DENSITIES
8930 class Representation(Hierarchy):
8931 """Proxy of C++ IMP::atom::Representation class."""
8933 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8935 def setup_particle(*args):
8937 setup_particle(Model m, ParticleIndex pi) -> Representation
8938 setup_particle(_ParticleAdaptor decorator) -> Representation
8939 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
8940 setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
8941 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
8942 setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
8944 return _IMP_atom.Representation_setup_particle(*args)
8946 setup_particle = staticmethod(setup_particle)
8948 def __init__(self, *args):
8950 __init__(IMP::atom::Representation self) -> Representation
8951 __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
8952 __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
8954 this = _IMP_atom.new_Representation(*args)
8956 self.this.append(this)
8957 except __builtin__.Exception:
8960 def show(self, *args):
8962 show(Representation self, _ostream out)
8963 show(Representation self)
8965 return _IMP_atom.Representation_show(self, *args)
8968 def get_is_setup(*args):
8970 get_is_setup(_ParticleAdaptor p) -> bool
8971 get_is_setup(Model m, ParticleIndex pi) -> bool
8973 return _IMP_atom.Representation_get_is_setup(*args)
8975 get_is_setup = staticmethod(get_is_setup)
8979 get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
8980 get_representation(Representation self, double resolution) -> Hierarchy
8982 return _IMP_atom.Representation_get_representation(self, *args)
8985 def get_representations(self, *args):
8987 get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
8988 get_representations(Representation self) -> IMP::atom::Hierarchies
8990 return _IMP_atom.Representation_get_representations(self, *args)
8993 def add_representation(self, *args):
8995 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
8996 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
8997 add_representation(Representation self, _ParticleIndexAdaptor rep)
8999 return _IMP_atom.Representation_add_representation(self, *args)
9002 def get_resolutions(self, *args):
9004 get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9005 get_resolutions(Representation self) -> IMP::Floats
9007 return _IMP_atom.Representation_get_resolutions(self, *args)
9010 def update_parents(self):
9011 """update_parents(Representation self)"""
9012 return _IMP_atom.Representation_update_parents(self)
9015 def add_attribute(self, *args):
9017 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9018 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9019 add_attribute(Representation self, IntKey a0, IMP::Int a1)
9020 add_attribute(Representation self, StringKey a0, IMP::String a1)
9021 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9022 add_attribute(Representation self, ObjectKey a0, Object a1)
9024 return _IMP_atom.Representation_add_attribute(self, *args)
9027 def get_value(self, *args):
9029 get_value(Representation self, FloatKey a0) -> IMP::Float
9030 get_value(Representation self, IntKey a0) -> IMP::Int
9031 get_value(Representation self, StringKey a0) -> IMP::String
9032 get_value(Representation self, ParticleIndexKey a0) -> Particle
9033 get_value(Representation self, ObjectKey a0) -> Object
9035 return _IMP_atom.Representation_get_value(self, *args)
9038 def set_value(self, *args):
9040 set_value(Representation self, FloatKey a0, IMP::Float a1)
9041 set_value(Representation self, IntKey a0, IMP::Int a1)
9042 set_value(Representation self, StringKey a0, IMP::String a1)
9043 set_value(Representation self, ParticleIndexKey a0, Particle a1)
9044 set_value(Representation self, ObjectKey a0, Object a1)
9046 return _IMP_atom.Representation_set_value(self, *args)
9049 def remove_attribute(self, *args):
9051 remove_attribute(Representation self, FloatKey a0)
9052 remove_attribute(Representation self, IntKey a0)
9053 remove_attribute(Representation self, StringKey a0)
9054 remove_attribute(Representation self, ParticleIndexKey a0)
9055 remove_attribute(Representation self, ObjectKey a0)
9057 return _IMP_atom.Representation_remove_attribute(self, *args)
9060 def has_attribute(self, *args):
9062 has_attribute(Representation self, FloatKey a0) -> bool
9063 has_attribute(Representation self, IntKey a0) -> bool
9064 has_attribute(Representation self, StringKey a0) -> bool
9065 has_attribute(Representation self, ParticleIndexKey a0) -> bool
9066 has_attribute(Representation self, ObjectKey a0) -> bool
9068 return _IMP_atom.Representation_has_attribute(self, *args)
9071 def get_derivative(self, a0):
9072 """get_derivative(Representation self, FloatKey a0) -> double"""
9073 return _IMP_atom.Representation_get_derivative(self, a0)
9077 """get_name(Representation self) -> std::string"""
9078 return _IMP_atom.Representation_get_name(self)
9081 def clear_caches(self):
9082 """clear_caches(Representation self)"""
9083 return _IMP_atom.Representation_clear_caches(self)
9086 def set_name(self, a0):
9087 """set_name(Representation self, std::string a0)"""
9088 return _IMP_atom.Representation_set_name(self, a0)
9092 """set_check_level(Representation self, IMP::CheckLevel a0)"""
9093 return _IMP_atom.Representation_set_check_level(self, a0)
9096 def add_to_derivative(self, a0, a1, a2):
9097 """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9098 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9101 def set_is_optimized(self, a0, a1):
9102 """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9103 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9106 def get_is_optimized(self, a0):
9107 """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9108 return _IMP_atom.Representation_get_is_optimized(self, a0)
9112 """get_check_level(Representation self) -> IMP::CheckLevel"""
9113 return _IMP_atom.Representation_get_check_level(self)
9116 def __eq__(self, *args):
9118 __eq__(Representation self, Representation o) -> bool
9119 __eq__(Representation self, Particle d) -> bool
9121 return _IMP_atom.Representation___eq__(self, *args)
9124 def __ne__(self, *args):
9126 __ne__(Representation self, Representation o) -> bool
9127 __ne__(Representation self, Particle d) -> bool
9129 return _IMP_atom.Representation___ne__(self, *args)
9132 def __le__(self, *args):
9134 __le__(Representation self, Representation o) -> bool
9135 __le__(Representation self, Particle d) -> bool
9137 return _IMP_atom.Representation___le__(self, *args)
9140 def __lt__(self, *args):
9142 __lt__(Representation self, Representation o) -> bool
9143 __lt__(Representation self, Particle d) -> bool
9145 return _IMP_atom.Representation___lt__(self, *args)
9148 def __ge__(self, *args):
9150 __ge__(Representation self, Representation o) -> bool
9151 __ge__(Representation self, Particle d) -> bool
9153 return _IMP_atom.Representation___ge__(self, *args)
9156 def __gt__(self, *args):
9158 __gt__(Representation self, Representation o) -> bool
9159 __gt__(Representation self, Particle d) -> bool
9161 return _IMP_atom.Representation___gt__(self, *args)
9165 """__hash__(Representation self) -> std::size_t"""
9166 return _IMP_atom.Representation___hash__(self)
9170 """__str__(Representation self) -> std::string"""
9171 return _IMP_atom.Representation___str__(self)
9175 """__repr__(Representation self) -> std::string"""
9176 return _IMP_atom.Representation___repr__(self)
9178 __swig_destroy__ = _IMP_atom.delete_Representation
9179 __del__ =
lambda self:
None
9180 Representation_swigregister = _IMP_atom.Representation_swigregister
9181 Representation_swigregister(Representation)
9182 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9184 def Representation_setup_particle(*args):
9186 setup_particle(Model m, ParticleIndex pi) -> Representation
9187 setup_particle(_ParticleAdaptor decorator) -> Representation
9188 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9189 setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9190 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9191 Representation_setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9193 return _IMP_atom.Representation_setup_particle(*args)
9195 def Representation_get_is_setup(*args):
9197 get_is_setup(_ParticleAdaptor p) -> bool
9198 Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9200 return _IMP_atom.Representation_get_is_setup(*args)
9205 get_resolution(Model m, ParticleIndex pi) -> double
9206 get_resolution(Hierarchy h) -> double
9208 return _IMP_atom.get_resolution(*args)
9212 get_representation(Hierarchy h, bool nothrow=False) -> Representation
9213 get_representation(Hierarchy h) -> Representation
9215 return _IMP_atom.get_representation(h, nothrow)
9219 show_with_representations(Hierarchy h, _ostream out)
9220 show_with_representations(Hierarchy h)
9222 return _IMP_atom.show_with_representations(*args)
9223 class State(Hierarchy):
9224 """Proxy of C++ IMP::atom::State class."""
9226 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9228 def setup_particle(*args):
9230 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9231 setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9232 setup_particle(Model m, ParticleIndex pi, State other) -> State
9233 setup_particle(_ParticleAdaptor decorator, State other) -> State
9235 return _IMP_atom.State_setup_particle(*args)
9237 setup_particle = staticmethod(setup_particle)
9239 def __init__(self, *args):
9241 __init__(IMP::atom::State self) -> State
9242 __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9243 __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9245 this = _IMP_atom.new_State(*args)
9247 self.this.append(this)
9248 except __builtin__.Exception:
9251 def show(self, *args):
9253 show(State self, _ostream out)
9256 return _IMP_atom.State_show(self, *args)
9259 def get_is_setup(*args):
9261 get_is_setup(_ParticleAdaptor p) -> bool
9262 get_is_setup(Model m, ParticleIndex pi) -> bool
9264 return _IMP_atom.State_get_is_setup(*args)
9266 get_is_setup = staticmethod(get_is_setup)
9269 """get_state_index(State self) -> unsigned int"""
9270 return _IMP_atom.State_get_state_index(self)
9273 def add_attribute(self, *args):
9275 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9276 add_attribute(State self, FloatKey a0, IMP::Float a1)
9277 add_attribute(State self, IntKey a0, IMP::Int a1)
9278 add_attribute(State self, StringKey a0, IMP::String a1)
9279 add_attribute(State self, ParticleIndexKey a0, Particle a1)
9280 add_attribute(State self, ObjectKey a0, Object a1)
9282 return _IMP_atom.State_add_attribute(self, *args)
9285 def get_value(self, *args):
9287 get_value(State self, FloatKey a0) -> IMP::Float
9288 get_value(State self, IntKey a0) -> IMP::Int
9289 get_value(State self, StringKey a0) -> IMP::String
9290 get_value(State self, ParticleIndexKey a0) -> Particle
9291 get_value(State self, ObjectKey a0) -> Object
9293 return _IMP_atom.State_get_value(self, *args)
9296 def set_value(self, *args):
9298 set_value(State self, FloatKey a0, IMP::Float a1)
9299 set_value(State self, IntKey a0, IMP::Int a1)
9300 set_value(State self, StringKey a0, IMP::String a1)
9301 set_value(State self, ParticleIndexKey a0, Particle a1)
9302 set_value(State self, ObjectKey a0, Object a1)
9304 return _IMP_atom.State_set_value(self, *args)
9307 def remove_attribute(self, *args):
9309 remove_attribute(State self, FloatKey a0)
9310 remove_attribute(State self, IntKey a0)
9311 remove_attribute(State self, StringKey a0)
9312 remove_attribute(State self, ParticleIndexKey a0)
9313 remove_attribute(State self, ObjectKey a0)
9315 return _IMP_atom.State_remove_attribute(self, *args)
9318 def has_attribute(self, *args):
9320 has_attribute(State self, FloatKey a0) -> bool
9321 has_attribute(State self, IntKey a0) -> bool
9322 has_attribute(State self, StringKey a0) -> bool
9323 has_attribute(State self, ParticleIndexKey a0) -> bool
9324 has_attribute(State self, ObjectKey a0) -> bool
9326 return _IMP_atom.State_has_attribute(self, *args)
9329 def get_derivative(self, a0):
9330 """get_derivative(State self, FloatKey a0) -> double"""
9331 return _IMP_atom.State_get_derivative(self, a0)
9335 """get_name(State self) -> std::string"""
9336 return _IMP_atom.State_get_name(self)
9339 def clear_caches(self):
9340 """clear_caches(State self)"""
9341 return _IMP_atom.State_clear_caches(self)
9344 def set_name(self, a0):
9345 """set_name(State self, std::string a0)"""
9346 return _IMP_atom.State_set_name(self, a0)
9350 """set_check_level(State self, IMP::CheckLevel a0)"""
9351 return _IMP_atom.State_set_check_level(self, a0)
9354 def add_to_derivative(self, a0, a1, a2):
9355 """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9356 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9359 def set_is_optimized(self, a0, a1):
9360 """set_is_optimized(State self, FloatKey a0, bool a1)"""
9361 return _IMP_atom.State_set_is_optimized(self, a0, a1)
9364 def get_is_optimized(self, a0):
9365 """get_is_optimized(State self, FloatKey a0) -> bool"""
9366 return _IMP_atom.State_get_is_optimized(self, a0)
9370 """get_check_level(State self) -> IMP::CheckLevel"""
9371 return _IMP_atom.State_get_check_level(self)
9374 def __eq__(self, *args):
9376 __eq__(State self, State o) -> bool
9377 __eq__(State self, Particle d) -> bool
9379 return _IMP_atom.State___eq__(self, *args)
9382 def __ne__(self, *args):
9384 __ne__(State self, State o) -> bool
9385 __ne__(State self, Particle d) -> bool
9387 return _IMP_atom.State___ne__(self, *args)
9390 def __le__(self, *args):
9392 __le__(State self, State o) -> bool
9393 __le__(State self, Particle d) -> bool
9395 return _IMP_atom.State___le__(self, *args)
9398 def __lt__(self, *args):
9400 __lt__(State self, State o) -> bool
9401 __lt__(State self, Particle d) -> bool
9403 return _IMP_atom.State___lt__(self, *args)
9406 def __ge__(self, *args):
9408 __ge__(State self, State o) -> bool
9409 __ge__(State self, Particle d) -> bool
9411 return _IMP_atom.State___ge__(self, *args)
9414 def __gt__(self, *args):
9416 __gt__(State self, State o) -> bool
9417 __gt__(State self, Particle d) -> bool
9419 return _IMP_atom.State___gt__(self, *args)
9423 """__hash__(State self) -> std::size_t"""
9424 return _IMP_atom.State___hash__(self)
9428 """__str__(State self) -> std::string"""
9429 return _IMP_atom.State___str__(self)
9433 """__repr__(State self) -> std::string"""
9434 return _IMP_atom.State___repr__(self)
9436 __swig_destroy__ = _IMP_atom.delete_State
9437 __del__ =
lambda self:
None
9438 State_swigregister = _IMP_atom.State_swigregister
9439 State_swigregister(State)
9441 def State_setup_particle(*args):
9443 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9444 setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9445 setup_particle(Model m, ParticleIndex pi, State other) -> State
9446 State_setup_particle(_ParticleAdaptor decorator, State other) -> State
9448 return _IMP_atom.State_setup_particle(*args)
9450 def State_get_is_setup(*args):
9452 get_is_setup(_ParticleAdaptor p) -> bool
9453 State_get_is_setup(Model m, ParticleIndex pi) -> bool
9455 return _IMP_atom.State_get_is_setup(*args)
9459 """get_state_index(Hierarchy h) -> int"""
9460 return _IMP_atom.get_state_index(h)
9463 """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9464 return _IMP_atom.get_phi_dihedral_atoms(rd)
9467 """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9468 return _IMP_atom.get_psi_dihedral_atoms(rd)
9469 class Molecule(Hierarchy):
9470 """Proxy of C++ IMP::atom::Molecule class."""
9472 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9474 def __init__(self, *args):
9476 __init__(IMP::atom::Molecule self) -> Molecule
9477 __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
9478 __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
9480 this = _IMP_atom.new_Molecule(*args)
9482 self.this.append(this)
9483 except __builtin__.Exception:
9486 def show(self, *args):
9488 show(Molecule self, _ostream out)
9491 return _IMP_atom.Molecule_show(self, *args)
9494 def setup_particle(*args):
9496 setup_particle(Model m, ParticleIndex pi) -> Molecule
9497 setup_particle(_ParticleAdaptor decorator) -> Molecule
9498 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9499 setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9501 return _IMP_atom.Molecule_setup_particle(*args)
9503 setup_particle = staticmethod(setup_particle)
9505 def get_is_setup(*args):
9507 get_is_setup(_ParticleAdaptor p) -> bool
9508 get_is_setup(Model m, ParticleIndex pi) -> bool
9510 return _IMP_atom.Molecule_get_is_setup(*args)
9512 get_is_setup = staticmethod(get_is_setup)
9514 def add_attribute(self, *args):
9516 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9517 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9518 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9519 add_attribute(Molecule self, StringKey a0, IMP::String a1)
9520 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9521 add_attribute(Molecule self, ObjectKey a0, Object a1)
9523 return _IMP_atom.Molecule_add_attribute(self, *args)
9526 def get_value(self, *args):
9528 get_value(Molecule self, FloatKey a0) -> IMP::Float
9529 get_value(Molecule self, IntKey a0) -> IMP::Int
9530 get_value(Molecule self, StringKey a0) -> IMP::String
9531 get_value(Molecule self, ParticleIndexKey a0) -> Particle
9532 get_value(Molecule self, ObjectKey a0) -> Object
9534 return _IMP_atom.Molecule_get_value(self, *args)
9537 def set_value(self, *args):
9539 set_value(Molecule self, FloatKey a0, IMP::Float a1)
9540 set_value(Molecule self, IntKey a0, IMP::Int a1)
9541 set_value(Molecule self, StringKey a0, IMP::String a1)
9542 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9543 set_value(Molecule self, ObjectKey a0, Object a1)
9545 return _IMP_atom.Molecule_set_value(self, *args)
9548 def remove_attribute(self, *args):
9550 remove_attribute(Molecule self, FloatKey a0)
9551 remove_attribute(Molecule self, IntKey a0)
9552 remove_attribute(Molecule self, StringKey a0)
9553 remove_attribute(Molecule self, ParticleIndexKey a0)
9554 remove_attribute(Molecule self, ObjectKey a0)
9556 return _IMP_atom.Molecule_remove_attribute(self, *args)
9559 def has_attribute(self, *args):
9561 has_attribute(Molecule self, FloatKey a0) -> bool
9562 has_attribute(Molecule self, IntKey a0) -> bool
9563 has_attribute(Molecule self, StringKey a0) -> bool
9564 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9565 has_attribute(Molecule self, ObjectKey a0) -> bool
9567 return _IMP_atom.Molecule_has_attribute(self, *args)
9570 def get_derivative(self, a0):
9571 """get_derivative(Molecule self, FloatKey a0) -> double"""
9572 return _IMP_atom.Molecule_get_derivative(self, a0)
9576 """get_name(Molecule self) -> std::string"""
9577 return _IMP_atom.Molecule_get_name(self)
9580 def clear_caches(self):
9581 """clear_caches(Molecule self)"""
9582 return _IMP_atom.Molecule_clear_caches(self)
9585 def set_name(self, a0):
9586 """set_name(Molecule self, std::string a0)"""
9587 return _IMP_atom.Molecule_set_name(self, a0)
9591 """set_check_level(Molecule self, IMP::CheckLevel a0)"""
9592 return _IMP_atom.Molecule_set_check_level(self, a0)
9595 def add_to_derivative(self, a0, a1, a2):
9596 """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9597 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9600 def set_is_optimized(self, a0, a1):
9601 """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9602 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9605 def get_is_optimized(self, a0):
9606 """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9607 return _IMP_atom.Molecule_get_is_optimized(self, a0)
9611 """get_check_level(Molecule self) -> IMP::CheckLevel"""
9612 return _IMP_atom.Molecule_get_check_level(self)
9615 def __eq__(self, *args):
9617 __eq__(Molecule self, Molecule o) -> bool
9618 __eq__(Molecule self, Particle d) -> bool
9620 return _IMP_atom.Molecule___eq__(self, *args)
9623 def __ne__(self, *args):
9625 __ne__(Molecule self, Molecule o) -> bool
9626 __ne__(Molecule self, Particle d) -> bool
9628 return _IMP_atom.Molecule___ne__(self, *args)
9631 def __le__(self, *args):
9633 __le__(Molecule self, Molecule o) -> bool
9634 __le__(Molecule self, Particle d) -> bool
9636 return _IMP_atom.Molecule___le__(self, *args)
9639 def __lt__(self, *args):
9641 __lt__(Molecule self, Molecule o) -> bool
9642 __lt__(Molecule self, Particle d) -> bool
9644 return _IMP_atom.Molecule___lt__(self, *args)
9647 def __ge__(self, *args):
9649 __ge__(Molecule self, Molecule o) -> bool
9650 __ge__(Molecule self, Particle d) -> bool
9652 return _IMP_atom.Molecule___ge__(self, *args)
9655 def __gt__(self, *args):
9657 __gt__(Molecule self, Molecule o) -> bool
9658 __gt__(Molecule self, Particle d) -> bool
9660 return _IMP_atom.Molecule___gt__(self, *args)
9664 """__hash__(Molecule self) -> std::size_t"""
9665 return _IMP_atom.Molecule___hash__(self)
9669 """__str__(Molecule self) -> std::string"""
9670 return _IMP_atom.Molecule___str__(self)
9674 """__repr__(Molecule self) -> std::string"""
9675 return _IMP_atom.Molecule___repr__(self)
9677 __swig_destroy__ = _IMP_atom.delete_Molecule
9678 __del__ =
lambda self:
None
9679 Molecule_swigregister = _IMP_atom.Molecule_swigregister
9680 Molecule_swigregister(Molecule)
9682 def Molecule_setup_particle(*args):
9684 setup_particle(Model m, ParticleIndex pi) -> Molecule
9685 setup_particle(_ParticleAdaptor decorator) -> Molecule
9686 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9687 Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9689 return _IMP_atom.Molecule_setup_particle(*args)
9691 def Molecule_get_is_setup(*args):
9693 get_is_setup(_ParticleAdaptor p) -> bool
9694 Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
9696 return _IMP_atom.Molecule_get_is_setup(*args)
9700 """get_molecule_name(Hierarchy h) -> std::string"""
9701 return _IMP_atom.get_molecule_name(h)
9702 class Copy(Molecule):
9703 """Proxy of C++ IMP::atom::Copy class."""
9705 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9707 def get_copy_index_key():
9708 """get_copy_index_key() -> IntKey"""
9709 return _IMP_atom.Copy_get_copy_index_key()
9711 get_copy_index_key = staticmethod(get_copy_index_key)
9713 def __init__(self, *args):
9715 __init__(IMP::atom::Copy self) -> Copy
9716 __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
9717 __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
9719 this = _IMP_atom.new_Copy(*args)
9721 self.this.append(this)
9722 except __builtin__.Exception:
9725 def show(self, *args):
9727 show(Copy self, _ostream out)
9730 return _IMP_atom.Copy_show(self, *args)
9733 def setup_particle(*args):
9735 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9736 setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
9738 return _IMP_atom.Copy_setup_particle(*args)
9740 setup_particle = staticmethod(setup_particle)
9742 def get_is_setup(*args):
9744 get_is_setup(_ParticleAdaptor p) -> bool
9745 get_is_setup(Model m, ParticleIndex pi) -> bool
9747 return _IMP_atom.Copy_get_is_setup(*args)
9749 get_is_setup = staticmethod(get_is_setup)
9752 """get_copy_index(Copy self) -> int"""
9753 return _IMP_atom.Copy_get_copy_index(self)
9756 def add_attribute(self, *args):
9758 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
9759 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
9760 add_attribute(Copy self, IntKey a0, IMP::Int a1)
9761 add_attribute(Copy self, StringKey a0, IMP::String a1)
9762 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
9763 add_attribute(Copy self, ObjectKey a0, Object a1)
9765 return _IMP_atom.Copy_add_attribute(self, *args)
9768 def get_value(self, *args):
9770 get_value(Copy self, FloatKey a0) -> IMP::Float
9771 get_value(Copy self, IntKey a0) -> IMP::Int
9772 get_value(Copy self, StringKey a0) -> IMP::String
9773 get_value(Copy self, ParticleIndexKey a0) -> Particle
9774 get_value(Copy self, ObjectKey a0) -> Object
9776 return _IMP_atom.Copy_get_value(self, *args)
9779 def set_value(self, *args):
9781 set_value(Copy self, FloatKey a0, IMP::Float a1)
9782 set_value(Copy self, IntKey a0, IMP::Int a1)
9783 set_value(Copy self, StringKey a0, IMP::String a1)
9784 set_value(Copy self, ParticleIndexKey a0, Particle a1)
9785 set_value(Copy self, ObjectKey a0, Object a1)
9787 return _IMP_atom.Copy_set_value(self, *args)
9790 def remove_attribute(self, *args):
9792 remove_attribute(Copy self, FloatKey a0)
9793 remove_attribute(Copy self, IntKey a0)
9794 remove_attribute(Copy self, StringKey a0)
9795 remove_attribute(Copy self, ParticleIndexKey a0)
9796 remove_attribute(Copy self, ObjectKey a0)
9798 return _IMP_atom.Copy_remove_attribute(self, *args)
9801 def has_attribute(self, *args):
9803 has_attribute(Copy self, FloatKey a0) -> bool
9804 has_attribute(Copy self, IntKey a0) -> bool
9805 has_attribute(Copy self, StringKey a0) -> bool
9806 has_attribute(Copy self, ParticleIndexKey a0) -> bool
9807 has_attribute(Copy self, ObjectKey a0) -> bool
9809 return _IMP_atom.Copy_has_attribute(self, *args)
9812 def get_derivative(self, a0):
9813 """get_derivative(Copy self, FloatKey a0) -> double"""
9814 return _IMP_atom.Copy_get_derivative(self, a0)
9818 """get_name(Copy self) -> std::string"""
9819 return _IMP_atom.Copy_get_name(self)
9822 def clear_caches(self):
9823 """clear_caches(Copy self)"""
9824 return _IMP_atom.Copy_clear_caches(self)
9827 def set_name(self, a0):
9828 """set_name(Copy self, std::string a0)"""
9829 return _IMP_atom.Copy_set_name(self, a0)
9833 """set_check_level(Copy self, IMP::CheckLevel a0)"""
9834 return _IMP_atom.Copy_set_check_level(self, a0)
9837 def add_to_derivative(self, a0, a1, a2):
9838 """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9839 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
9842 def set_is_optimized(self, a0, a1):
9843 """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
9844 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
9847 def get_is_optimized(self, a0):
9848 """get_is_optimized(Copy self, FloatKey a0) -> bool"""
9849 return _IMP_atom.Copy_get_is_optimized(self, a0)
9853 """get_check_level(Copy self) -> IMP::CheckLevel"""
9854 return _IMP_atom.Copy_get_check_level(self)
9857 def __eq__(self, *args):
9859 __eq__(Copy self, Copy o) -> bool
9860 __eq__(Copy self, Particle d) -> bool
9862 return _IMP_atom.Copy___eq__(self, *args)
9865 def __ne__(self, *args):
9867 __ne__(Copy self, Copy o) -> bool
9868 __ne__(Copy self, Particle d) -> bool
9870 return _IMP_atom.Copy___ne__(self, *args)
9873 def __le__(self, *args):
9875 __le__(Copy self, Copy o) -> bool
9876 __le__(Copy self, Particle d) -> bool
9878 return _IMP_atom.Copy___le__(self, *args)
9881 def __lt__(self, *args):
9883 __lt__(Copy self, Copy o) -> bool
9884 __lt__(Copy self, Particle d) -> bool
9886 return _IMP_atom.Copy___lt__(self, *args)
9889 def __ge__(self, *args):
9891 __ge__(Copy self, Copy o) -> bool
9892 __ge__(Copy self, Particle d) -> bool
9894 return _IMP_atom.Copy___ge__(self, *args)
9897 def __gt__(self, *args):
9899 __gt__(Copy self, Copy o) -> bool
9900 __gt__(Copy self, Particle d) -> bool
9902 return _IMP_atom.Copy___gt__(self, *args)
9906 """__hash__(Copy self) -> std::size_t"""
9907 return _IMP_atom.Copy___hash__(self)
9911 """__str__(Copy self) -> std::string"""
9912 return _IMP_atom.Copy___str__(self)
9916 """__repr__(Copy self) -> std::string"""
9917 return _IMP_atom.Copy___repr__(self)
9919 __swig_destroy__ = _IMP_atom.delete_Copy
9920 __del__ =
lambda self:
None
9921 Copy_swigregister = _IMP_atom.Copy_swigregister
9922 Copy_swigregister(Copy)
9924 def Copy_get_copy_index_key():
9925 """Copy_get_copy_index_key() -> IntKey"""
9926 return _IMP_atom.Copy_get_copy_index_key()
9928 def Copy_setup_particle(*args):
9930 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
9931 Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
9933 return _IMP_atom.Copy_setup_particle(*args)
9935 def Copy_get_is_setup(*args):
9937 get_is_setup(_ParticleAdaptor p) -> bool
9938 Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
9940 return _IMP_atom.Copy_get_is_setup(*args)
9944 """get_copy_index(Hierarchy h) -> int"""
9945 return _IMP_atom.get_copy_index(h)
9946 class Selection(IMP._ParticleIndexesAdaptor):
9947 """Proxy of C++ IMP::atom::Selection class."""
9949 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9950 NONE = _IMP_atom.Selection_NONE
9951 C = _IMP_atom.Selection_C
9952 N = _IMP_atom.Selection_N
9954 def __init__(self, *args):
9956 __init__(IMP::atom::Selection self) -> Selection
9957 __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
9958 __init__(IMP::atom::Selection self, Particle h) -> Selection
9959 __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
9960 __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
9962 this = _IMP_atom.new_Selection(*args)
9964 self.this.append(this)
9965 except __builtin__.Exception:
9968 def create_clone(self):
9969 """create_clone(Selection self) -> Selection"""
9970 return _IMP_atom.Selection_create_clone(self)
9973 def get_hierarchies(self):
9974 """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
9975 return _IMP_atom.Selection_get_hierarchies(self)
9978 def set_molecules(self, mols):
9979 """set_molecules(Selection self, IMP::Strings mols)"""
9980 return _IMP_atom.Selection_set_molecules(self, mols)
9983 def set_resolution(self, r):
9984 """set_resolution(Selection self, double r)"""
9985 return _IMP_atom.Selection_set_resolution(self, r)
9988 def set_representation_type(self, t):
9989 """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
9990 return _IMP_atom.Selection_set_representation_type(self, t)
9993 def set_state_index(self, state):
9994 """set_state_index(Selection self, int state)"""
9995 return _IMP_atom.Selection_set_state_index(self, state)
9998 def set_state_indexes(self, states):
9999 """set_state_indexes(Selection self, IMP::Ints states)"""
10000 return _IMP_atom.Selection_set_state_indexes(self, states)
10003 def set_terminus(self, t):
10004 """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10005 return _IMP_atom.Selection_set_terminus(self, t)
10008 def set_element(self, e):
10009 """set_element(Selection self, IMP::atom::Element e)"""
10010 return _IMP_atom.Selection_set_element(self, e)
10013 def set_chain_ids(self, chains):
10014 """set_chain_ids(Selection self, IMP::Strings chains)"""
10015 return _IMP_atom.Selection_set_chain_ids(self, chains)
10018 def set_chains(self, chains):
10019 """set_chains(Selection self, IMP::Strings chains)"""
10020 return _IMP_atom.Selection_set_chains(self, chains)
10023 def set_residue_indexes(self, indexes):
10024 """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10025 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10028 def set_atom_types(self, types):
10029 """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10030 return _IMP_atom.Selection_set_atom_types(self, types)
10033 def set_residue_types(self, types):
10034 """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10035 return _IMP_atom.Selection_set_residue_types(self, types)
10038 def set_domains(self, names):
10039 """set_domains(Selection self, IMP::Strings names)"""
10040 return _IMP_atom.Selection_set_domains(self, names)
10043 def set_molecule(self, mol):
10044 """set_molecule(Selection self, std::string mol)"""
10045 return _IMP_atom.Selection_set_molecule(self, mol)
10048 def set_chain_id(self, c):
10049 """set_chain_id(Selection self, std::string c)"""
10050 return _IMP_atom.Selection_set_chain_id(self, c)
10053 def set_chain(self, c):
10054 """set_chain(Selection self, std::string c)"""
10055 return _IMP_atom.Selection_set_chain(self, c)
10058 def set_residue_index(self, i):
10059 """set_residue_index(Selection self, int i)"""
10060 return _IMP_atom.Selection_set_residue_index(self, i)
10063 def set_atom_type(self, types):
10064 """set_atom_type(Selection self, AtomType types)"""
10065 return _IMP_atom.Selection_set_atom_type(self, types)
10068 def set_residue_type(self, type):
10069 """set_residue_type(Selection self, ResidueType type)"""
10070 return _IMP_atom.Selection_set_residue_type(self, type)
10073 def set_domain(self, name):
10074 """set_domain(Selection self, std::string name)"""
10075 return _IMP_atom.Selection_set_domain(self, name)
10078 def set_copy_index(self, copy):
10079 """set_copy_index(Selection self, unsigned int copy)"""
10080 return _IMP_atom.Selection_set_copy_index(self, copy)
10083 def set_copy_indexes(self, copies):
10084 """set_copy_indexes(Selection self, IMP::Ints copies)"""
10085 return _IMP_atom.Selection_set_copy_indexes(self, copies)
10088 def set_particle_type(self, t):
10089 """set_particle_type(Selection self, ParticleType t)"""
10090 return _IMP_atom.Selection_set_particle_type(self, t)
10093 def set_particle_types(self, t):
10094 """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10095 return _IMP_atom.Selection_set_particle_types(self, t)
10098 def set_hierarchy_types(self, types):
10099 """set_hierarchy_types(Selection self, IMP::Ints types)"""
10100 return _IMP_atom.Selection_set_hierarchy_types(self, types)
10103 def set_intersection(self, s):
10104 """set_intersection(Selection self, Selection s)"""
10105 return _IMP_atom.Selection_set_intersection(self, s)
10108 def set_union(self, s):
10109 """set_union(Selection self, Selection s)"""
10110 return _IMP_atom.Selection_set_union(self, s)
10113 def set_symmetric_difference(self, s):
10114 """set_symmetric_difference(Selection self, Selection s)"""
10115 return _IMP_atom.Selection_set_symmetric_difference(self, s)
10118 def set_difference(self, s):
10119 """set_difference(Selection self, Selection s)"""
10120 return _IMP_atom.Selection_set_difference(self, s)
10123 def get_selected_particles(self, with_representation=True):
10125 get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10126 get_selected_particles(Selection self) -> IMP::ParticlesTemp
10128 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10131 def get_selected_particle_indexes(self, with_representation=True):
10133 get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10134 get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10136 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10139 def show(self, *args):
10141 show(Selection self, _ostream out)
10142 show(Selection self)
10144 return _IMP_atom.Selection_show(self, *args)
10148 """__str__(Selection self) -> std::string"""
10149 return _IMP_atom.Selection___str__(self)
10152 def __repr__(self):
10153 """__repr__(Selection self) -> std::string"""
10154 return _IMP_atom.Selection___repr__(self)
10157 def __init__(self, hierarchy=None,
10158 hierarchies=
None, **params):
10159 if hierarchy
and hierarchies:
10160 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
10162 this = _IMP_atom.new_Selection(hierarchy)
10163 try: self.this.append(this)
10164 except: self.this = this
10166 this = _IMP_atom.new_Selection(hierarchies)
10167 try: self.this.append(this)
10168 except: self.this = this
10170 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
10171 for k
in params.keys():
10172 eval(
"self.set_%s(params[k])"%k)
10174 def union(self, s):
10175 news = self.create_clone()
10176 news.union_update(s)
10178 def intersection(self, s):
10179 news = self.create_clone()
10180 news.intersection_update(s)
10182 def symmetric_difference(self, s):
10183 news = self.create_clone()
10184 news.symmetric_difference_update(s)
10186 def difference(self, s):
10187 news = self.create_clone()
10188 news.difference_update(s)
10190 def union_update(self, s):
10193 def intersection_update(self, s):
10194 self.set_intersection(s)
10196 def symmetric_difference_update(self, s):
10197 self.set_symmetric_difference(s)
10199 def difference_update(self, s):
10200 self.set_difference(s)
10203 __and__ = intersection
10204 __xor__ = symmetric_difference
10205 __sub__ = difference
10206 __ior__ = union_update
10207 __iand__ = intersection_update
10208 __ixor__ = symmetric_difference_update
10209 __isub__ = difference_update
10211 __swig_destroy__ = _IMP_atom.delete_Selection
10212 __del__ =
lambda self:
None
10213 Selection_swigregister = _IMP_atom.Selection_swigregister
10214 Selection_swigregister(Selection)
10219 create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10220 create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10222 return _IMP_atom.create_distance_restraint(*args)
10226 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10227 create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10228 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10229 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10231 return _IMP_atom.create_connectivity_restraint(*args)
10235 create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10236 create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10237 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10238 create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10240 return _IMP_atom.create_internal_connectivity_restraint(*args)
10244 create_cover(Selection s, std::string name) -> XYZR
10245 create_cover(Selection s) -> XYZR
10247 return _IMP_atom.create_cover(*args)
10251 get_mass(ResidueType c) -> double
10252 get_mass(Selection s) -> double
10254 return _IMP_atom.get_mass(*args)
10257 """get_volume(Selection s) -> double"""
10258 return _IMP_atom.get_volume(s)
10261 """get_surface_area(Selection s) -> double"""
10262 return _IMP_atom.get_surface_area(s)
10266 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10267 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10268 get_leaves(Selection h) -> IMP::atom::Hierarchies
10270 return _IMP_atom.get_leaves(*args)
10272 """Proxy of C++ IMP::atom::SelectionGeometry class."""
10274 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10276 def __init__(self, *args):
10278 __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10279 __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10281 this = _IMP_atom.new_SelectionGeometry(*args)
10283 self.this.append(this)
10284 except __builtin__.Exception:
10287 def get_version_info(self):
10288 """get_version_info(SelectionGeometry self) -> VersionInfo"""
10289 return _IMP_atom.SelectionGeometry_get_version_info(self)
10293 """__str__(SelectionGeometry self) -> std::string"""
10294 return _IMP_atom.SelectionGeometry___str__(self)
10297 def __repr__(self):
10298 """__repr__(SelectionGeometry self) -> std::string"""
10299 return _IMP_atom.SelectionGeometry___repr__(self)
10304 return _object_cast_to_SelectionGeometry(o)
10306 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10307 SelectionGeometry_swigregister(SelectionGeometry)
10312 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10313 get_rmsd(Selection s0, Selection s1) -> double
10315 return _IMP_atom.get_rmsd(*args)
10319 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10320 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10322 return _IMP_atom.get_rmsd_transforming_first(*args)
10325 """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10326 return _IMP_atom.get_placement_score(source, target)
10329 """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"""
10330 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10333 """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"""
10334 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10338 get_radius_of_gyration(Selection s) -> double
10339 get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10340 get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10342 return _IMP_atom.get_radius_of_gyration(*args)
10344 """Proxy of C++ IMP::atom::ForceFieldParameters class."""
10346 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10348 def __init__(self):
10349 """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10350 this = _IMP_atom.new_ForceFieldParameters()
10352 self.this.append(this)
10353 except __builtin__.Exception:
10356 def get_radius(self, atom):
10357 """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10358 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10361 def get_epsilon(self, atom):
10362 """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10363 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10368 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10369 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10370 add_radii(ForceFieldParameters self, Hierarchy mhd)
10372 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10375 def add_well_depths(self, mhd):
10376 """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10377 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10381 """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10382 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10384 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10385 __del__ =
lambda self:
None
10388 """__str__(ForceFieldParameters self) -> std::string"""
10389 return _IMP_atom.ForceFieldParameters___str__(self)
10392 def __repr__(self):
10393 """__repr__(ForceFieldParameters self) -> std::string"""
10394 return _IMP_atom.ForceFieldParameters___repr__(self)
10399 return _object_cast_to_ForceFieldParameters(o)
10401 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10402 ForceFieldParameters_swigregister(ForceFieldParameters)
10404 class CHARMMAtomTopology(object):
10405 """Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10407 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10409 def __init__(self, *args):
10411 __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10412 __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10414 this = _IMP_atom.new_CHARMMAtomTopology(*args)
10416 self.this.append(this)
10417 except __builtin__.Exception:
10420 def get_name(self):
10421 """get_name(CHARMMAtomTopology self) -> std::string"""
10422 return _IMP_atom.CHARMMAtomTopology_get_name(self)
10425 def get_charmm_type(self):
10426 """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10427 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10430 def get_charge(self):
10431 """get_charge(CHARMMAtomTopology self) -> double"""
10432 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10435 def set_charmm_type(self, charmm_type):
10436 """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10437 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10440 def set_charge(self, charge):
10441 """set_charge(CHARMMAtomTopology self, double charge)"""
10442 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10445 def show(self, *args):
10447 show(CHARMMAtomTopology self, _ostream out)
10448 show(CHARMMAtomTopology self)
10450 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10454 """__str__(CHARMMAtomTopology self) -> std::string"""
10455 return _IMP_atom.CHARMMAtomTopology___str__(self)
10458 def __repr__(self):
10459 """__repr__(CHARMMAtomTopology self) -> std::string"""
10460 return _IMP_atom.CHARMMAtomTopology___repr__(self)
10462 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10463 __del__ =
lambda self:
None
10464 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
10465 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10467 class CHARMMBondEndpoint(object):
10468 """Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
10470 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10472 def __init__(self, atom_name, residue=None):
10474 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
10475 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
10477 this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
10479 self.this.append(this)
10480 except __builtin__.Exception:
10483 def get_atom_name(self):
10484 """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10485 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10488 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10489 """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"""
10490 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10493 def show(self, *args):
10495 show(CHARMMBondEndpoint self, _ostream out)
10496 show(CHARMMBondEndpoint self)
10498 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10502 """__str__(CHARMMBondEndpoint self) -> std::string"""
10503 return _IMP_atom.CHARMMBondEndpoint___str__(self)
10506 def __repr__(self):
10507 """__repr__(CHARMMBondEndpoint self) -> std::string"""
10508 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10510 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10511 __del__ =
lambda self:
None
10512 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
10513 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10515 class CHARMMDihedral(object):
10516 """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class."""
10518 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10519 __repr__ = _swig_repr
10521 def __init__(self, atoms):
10522 """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10523 this = _IMP_atom.new_CHARMMDihedral(atoms)
10525 self.this.append(this)
10526 except __builtin__.Exception:
10529 def get_endpoint(self, i):
10530 """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10531 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10534 def get_contains_atom(self, name):
10535 """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10536 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10539 def show(self, *args):
10541 show(CHARMMDihedral self, _ostream out)
10542 show(CHARMMDihedral self)
10544 return _IMP_atom.CHARMMDihedral_show(self, *args)
10546 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10547 __del__ =
lambda self:
None
10548 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
10549 CHARMMDihedral_swigregister(CHARMMDihedral)
10551 class CHARMMInternalCoordinate(CHARMMDihedral):
10552 """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
10554 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10556 def __init__(self, *args):
10558 __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10559 __init__(IMP::atom::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
10561 this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
10563 self.this.append(this)
10564 except __builtin__.Exception:
10567 def get_first_distance(self):
10568 """get_first_distance(CHARMMInternalCoordinate self) -> float"""
10569 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10572 def get_second_distance(self):
10573 """get_second_distance(CHARMMInternalCoordinate self) -> float"""
10574 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10577 def get_first_angle(self):
10578 """get_first_angle(CHARMMInternalCoordinate self) -> float"""
10579 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10582 def get_second_angle(self):
10583 """get_second_angle(CHARMMInternalCoordinate self) -> float"""
10584 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10588 """get_dihedral(CHARMMInternalCoordinate self) -> float"""
10589 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10592 def get_improper(self):
10593 """get_improper(CHARMMInternalCoordinate self) -> bool"""
10594 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10597 def show(self, *args):
10599 show(CHARMMInternalCoordinate self, _ostream out)
10600 show(CHARMMInternalCoordinate self)
10602 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10606 """__str__(CHARMMInternalCoordinate self) -> std::string"""
10607 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10610 def __repr__(self):
10611 """__repr__(CHARMMInternalCoordinate self) -> std::string"""
10612 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10614 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10615 __del__ =
lambda self:
None
10616 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
10617 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10619 class CHARMMResidueTopologyBase(
IMP.Object):
10620 """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
10622 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10624 def __init__(self, *args, **kwargs):
10625 raise AttributeError(
"No constructor defined")
10627 def get_type(self):
10628 """get_type(CHARMMResidueTopologyBase self) -> std::string"""
10629 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10632 def get_number_of_atoms(self):
10633 """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10634 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10637 def add_atom(self, atom):
10638 """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10639 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
10644 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
10645 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
10646 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
10648 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
10651 def get_number_of_bonds(self):
10652 """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
10653 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
10656 def add_bond(self, bond):
10657 """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
10658 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
10661 def get_number_of_angles(self):
10662 """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
10663 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
10666 def add_angle(self, bond):
10667 """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
10668 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
10671 def get_number_of_dihedrals(self):
10672 """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
10673 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
10676 def add_dihedral(self, bond):
10677 """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10678 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
10681 def get_number_of_impropers(self):
10682 """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
10683 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
10686 def add_improper(self, bond):
10687 """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
10688 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
10691 def get_number_of_internal_coordinates(self):
10692 """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
10693 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
10696 def add_internal_coordinate(self, ic):
10697 """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
10698 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
10701 def get_internal_coordinate(self, index):
10702 """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
10703 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
10707 """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
10708 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
10712 """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
10713 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
10717 """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10718 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
10721 def get_improper(self, index):
10722 """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
10723 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
10726 def get_version_info(self):
10727 """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
10728 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
10732 """__str__(CHARMMResidueTopologyBase self) -> std::string"""
10733 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
10736 def __repr__(self):
10737 """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
10738 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
10743 return _object_cast_to_CHARMMResidueTopologyBase(o)
10745 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
10746 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
10748 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
10749 """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
10751 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10753 def __init__(self, *args):
10755 __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
10756 __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
10758 this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
10760 self.this.append(this)
10761 except __builtin__.Exception:
10764 def remove_atom(self, name):
10765 """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
10766 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
10769 def set_default_first_patch(self, patch):
10770 """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10771 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
10774 def set_default_last_patch(self, patch):
10775 """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
10776 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
10779 def get_default_first_patch(self):
10780 """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
10781 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
10784 def get_default_last_patch(self):
10785 """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
10786 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
10790 """__str__(CHARMMIdealResidueTopology self) -> std::string"""
10791 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
10794 def __repr__(self):
10795 """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
10796 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
10801 return _object_cast_to_CHARMMIdealResidueTopology(o)
10803 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
10804 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
10806 class CHARMMPatch(CHARMMResidueTopologyBase):
10807 """Proxy of C++ IMP::atom::CHARMMPatch class."""
10809 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10811 def __init__(self, type):
10812 """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
10813 this = _IMP_atom.new_CHARMMPatch(type)
10815 self.this.append(this)
10816 except __builtin__.Exception:
10819 def add_removed_atom(self, name):
10820 """add_removed_atom(CHARMMPatch self, std::string name)"""
10821 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
10824 def get_number_of_removed_atoms(self):
10825 """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
10826 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
10829 def get_removed_atom(self, i):
10830 """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
10831 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
10834 def apply(self, *args):
10836 apply(CHARMMPatch self, CHARMMResidueTopology res)
10837 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
10839 return _IMP_atom.CHARMMPatch_apply(self, *args)
10843 """__str__(CHARMMPatch self) -> std::string"""
10844 return _IMP_atom.CHARMMPatch___str__(self)
10847 def __repr__(self):
10848 """__repr__(CHARMMPatch self) -> std::string"""
10849 return _IMP_atom.CHARMMPatch___repr__(self)
10854 return _object_cast_to_CHARMMPatch(o)
10856 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
10857 CHARMMPatch_swigregister(CHARMMPatch)
10859 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
10860 """Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
10862 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10864 def __init__(self, *args):
10866 __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
10867 __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
10869 this = _IMP_atom.new_CHARMMResidueTopology(*args)
10871 self.this.append(this)
10872 except __builtin__.Exception:
10875 def get_patched(self):
10876 """get_patched(CHARMMResidueTopology self) -> bool"""
10877 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
10880 def set_patched(self, patched):
10881 """set_patched(CHARMMResidueTopology self, bool patched)"""
10882 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
10886 """__str__(CHARMMResidueTopology self) -> std::string"""
10887 return _IMP_atom.CHARMMResidueTopology___str__(self)
10890 def __repr__(self):
10891 """__repr__(CHARMMResidueTopology self) -> std::string"""
10892 return _IMP_atom.CHARMMResidueTopology___repr__(self)
10897 return _object_cast_to_CHARMMResidueTopology(o)
10899 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
10900 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
10902 class CHARMMAtom(Atom):
10903 """Proxy of C++ IMP::atom::CHARMMAtom class."""
10905 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10907 def __init__(self, *args):
10909 __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
10910 __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
10911 __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
10913 this = _IMP_atom.new_CHARMMAtom(*args)
10915 self.this.append(this)
10916 except __builtin__.Exception:
10919 def show(self, *args):
10921 show(CHARMMAtom self, _ostream out)
10922 show(CHARMMAtom self)
10924 return _IMP_atom.CHARMMAtom_show(self, *args)
10927 def setup_particle(*args):
10929 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
10930 setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
10932 return _IMP_atom.CHARMMAtom_setup_particle(*args)
10934 setup_particle = staticmethod(setup_particle)
10936 def get_charmm_type(self):
10937 """get_charmm_type(CHARMMAtom self) -> IMP::String"""
10938 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
10941 def set_charmm_type(self, t):
10942 """set_charmm_type(CHARMMAtom self, IMP::String t)"""
10943 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
10946 def get_is_setup(*args):
10948 get_is_setup(_ParticleAdaptor p) -> bool
10949 get_is_setup(Model m, ParticleIndex pi) -> bool
10951 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
10953 get_is_setup = staticmethod(get_is_setup)
10955 def get_charmm_type_key():
10956 """get_charmm_type_key() -> StringKey"""
10957 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
10959 get_charmm_type_key = staticmethod(get_charmm_type_key)
10961 def add_attribute(self, *args):
10963 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
10964 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10965 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
10966 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
10967 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10968 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
10970 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
10973 def get_value(self, *args):
10975 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
10976 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
10977 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
10978 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
10979 get_value(CHARMMAtom self, ObjectKey a0) -> Object
10981 return _IMP_atom.CHARMMAtom_get_value(self, *args)
10984 def set_value(self, *args):
10986 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
10987 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
10988 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
10989 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
10990 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
10992 return _IMP_atom.CHARMMAtom_set_value(self, *args)
10995 def remove_attribute(self, *args):
10997 remove_attribute(CHARMMAtom self, FloatKey a0)
10998 remove_attribute(CHARMMAtom self, IntKey a0)
10999 remove_attribute(CHARMMAtom self, StringKey a0)
11000 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11001 remove_attribute(CHARMMAtom self, ObjectKey a0)
11003 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11006 def has_attribute(self, *args):
11008 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11009 has_attribute(CHARMMAtom self, IntKey a0) -> bool
11010 has_attribute(CHARMMAtom self, StringKey a0) -> bool
11011 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11012 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11014 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11017 def get_derivative(self, a0):
11018 """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11019 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11022 def get_name(self):
11023 """get_name(CHARMMAtom self) -> std::string"""
11024 return _IMP_atom.CHARMMAtom_get_name(self)
11027 def clear_caches(self):
11028 """clear_caches(CHARMMAtom self)"""
11029 return _IMP_atom.CHARMMAtom_clear_caches(self)
11032 def set_name(self, a0):
11033 """set_name(CHARMMAtom self, std::string a0)"""
11034 return _IMP_atom.CHARMMAtom_set_name(self, a0)
11038 """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11039 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11042 def add_to_derivative(self, a0, a1, a2):
11043 """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11044 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11047 def set_is_optimized(self, a0, a1):
11048 """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11049 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11052 def get_is_optimized(self, a0):
11053 """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11054 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11058 """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11059 return _IMP_atom.CHARMMAtom_get_check_level(self)
11062 def __eq__(self, *args):
11064 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11065 __eq__(CHARMMAtom self, Particle d) -> bool
11067 return _IMP_atom.CHARMMAtom___eq__(self, *args)
11070 def __ne__(self, *args):
11072 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11073 __ne__(CHARMMAtom self, Particle d) -> bool
11075 return _IMP_atom.CHARMMAtom___ne__(self, *args)
11078 def __le__(self, *args):
11080 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11081 __le__(CHARMMAtom self, Particle d) -> bool
11083 return _IMP_atom.CHARMMAtom___le__(self, *args)
11086 def __lt__(self, *args):
11088 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11089 __lt__(CHARMMAtom self, Particle d) -> bool
11091 return _IMP_atom.CHARMMAtom___lt__(self, *args)
11094 def __ge__(self, *args):
11096 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11097 __ge__(CHARMMAtom self, Particle d) -> bool
11099 return _IMP_atom.CHARMMAtom___ge__(self, *args)
11102 def __gt__(self, *args):
11104 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11105 __gt__(CHARMMAtom self, Particle d) -> bool
11107 return _IMP_atom.CHARMMAtom___gt__(self, *args)
11110 def __hash__(self):
11111 """__hash__(CHARMMAtom self) -> std::size_t"""
11112 return _IMP_atom.CHARMMAtom___hash__(self)
11116 """__str__(CHARMMAtom self) -> std::string"""
11117 return _IMP_atom.CHARMMAtom___str__(self)
11120 def __repr__(self):
11121 """__repr__(CHARMMAtom self) -> std::string"""
11122 return _IMP_atom.CHARMMAtom___repr__(self)
11124 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11125 __del__ =
lambda self:
None
11126 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11127 CHARMMAtom_swigregister(CHARMMAtom)
11129 def CHARMMAtom_setup_particle(*args):
11131 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11132 CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11134 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11136 def CHARMMAtom_get_is_setup(*args):
11138 get_is_setup(_ParticleAdaptor p) -> bool
11139 CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11141 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11143 def CHARMMAtom_get_charmm_type_key():
11144 """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11145 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11149 """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11150 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11153 """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11154 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11155 class CHARMMBondParameters(object):
11156 """Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11158 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11159 force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11160 ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11162 def __init__(self):
11163 """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11164 this = _IMP_atom.new_CHARMMBondParameters()
11166 self.this.append(this)
11167 except __builtin__.Exception:
11170 def show(self, *args):
11172 show(CHARMMBondParameters self, _ostream out)
11173 show(CHARMMBondParameters self)
11175 return _IMP_atom.CHARMMBondParameters_show(self, *args)
11179 """__str__(CHARMMBondParameters self) -> std::string"""
11180 return _IMP_atom.CHARMMBondParameters___str__(self)
11183 def __repr__(self):
11184 """__repr__(CHARMMBondParameters self) -> std::string"""
11185 return _IMP_atom.CHARMMBondParameters___repr__(self)
11187 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11188 __del__ =
lambda self:
None
11189 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11190 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11192 class CHARMMDihedralParameters(object):
11193 """Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11195 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11196 force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11197 multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11198 ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11200 def __init__(self):
11201 """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11202 this = _IMP_atom.new_CHARMMDihedralParameters()
11204 self.this.append(this)
11205 except __builtin__.Exception:
11208 def show(self, *args):
11210 show(CHARMMDihedralParameters self, _ostream out)
11211 show(CHARMMDihedralParameters self)
11213 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11217 """__str__(CHARMMDihedralParameters self) -> std::string"""
11218 return _IMP_atom.CHARMMDihedralParameters___str__(self)
11221 def __repr__(self):
11222 """__repr__(CHARMMDihedralParameters self) -> std::string"""
11223 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11225 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11226 __del__ =
lambda self:
None
11227 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11228 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11230 class CHARMMParameters(ForceFieldParameters):
11231 """Proxy of C++ IMP::atom::CHARMMParameters class."""
11233 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11235 def __init__(self, *args):
11237 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11238 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11239 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11241 this = _IMP_atom.new_CHARMMParameters(*args)
11243 self.this.append(this)
11244 except __builtin__.Exception:
11247 def add_residue_topology(self, res):
11248 """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11249 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11252 def get_residue_topology(self, type):
11253 """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11254 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11257 def add_patch(self, patch):
11258 """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11259 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11262 def get_patch(self, name):
11263 """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11264 return _IMP_atom.CHARMMParameters_get_patch(self, name)
11267 def create_topology(self, hierarchy):
11268 """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11269 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11272 def get_bond_parameters(self, type1, type2):
11273 """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11274 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11277 def get_angle_parameters(self, type1, type2, type3):
11278 """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11279 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11282 def get_dihedral_parameters(self, type1, type2, type3, type4):
11283 """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11284 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11287 def get_improper_parameters(self, type1, type2, type3, type4):
11288 """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11289 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11292 def create_angles(self, bonds):
11293 """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11294 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11297 def create_dihedrals(self, bonds):
11298 """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11299 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11302 def get_version_info(self):
11303 """get_version_info(CHARMMParameters self) -> VersionInfo"""
11304 return _IMP_atom.CHARMMParameters_get_version_info(self)
11308 """__str__(CHARMMParameters self) -> std::string"""
11309 return _IMP_atom.CHARMMParameters___str__(self)
11312 def __repr__(self):
11313 """__repr__(CHARMMParameters self) -> std::string"""
11314 return _IMP_atom.CHARMMParameters___repr__(self)
11319 return _object_cast_to_CHARMMParameters(o)
11321 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11322 CHARMMParameters_swigregister(CHARMMParameters)
11326 """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11327 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11330 """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11331 return _IMP_atom.get_all_atom_CHARMM_parameters()
11333 """Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11335 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11337 def remove_residue(self, d):
11338 """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11339 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11342 def remove_residues(self, d):
11343 """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11344 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11347 def set_residues(self, ps):
11348 """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11349 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11352 def set_residues_order(self, objs):
11353 """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11354 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11357 def add_residue(self, obj):
11358 """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11359 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11362 def add_residues(self, objs):
11363 """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11364 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11367 def clear_residues(self):
11368 """clear_residues(CHARMMSegmentTopology self)"""
11369 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11372 def get_number_of_residues(self):
11373 """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11374 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11377 def get_has_residues(self):
11378 """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11379 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11383 """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11384 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11387 def get_residues(self):
11388 """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11389 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11392 def reserve_residues(self, sz):
11393 """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11394 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11397 def get_version_info(self):
11398 """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11399 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11402 def __init__(self, *args):
11404 __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11405 __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11407 this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11409 self.this.append(this)
11410 except __builtin__.Exception:
11413 def apply_default_patches(self, ff):
11414 """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11415 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11419 """__str__(CHARMMSegmentTopology self) -> std::string"""
11420 return _IMP_atom.CHARMMSegmentTopology___str__(self)
11423 def __repr__(self):
11424 """__repr__(CHARMMSegmentTopology self) -> std::string"""
11425 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11430 return _object_cast_to_CHARMMSegmentTopology(o)
11432 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
11433 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11436 """Proxy of C++ IMP::atom::CHARMMTopology class."""
11438 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11440 def __init__(self, *args):
11442 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
11443 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
11445 this = _IMP_atom.new_CHARMMTopology(*args)
11447 self.this.append(this)
11448 except __builtin__.Exception:
11451 def get_parameters(self):
11452 """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11453 return _IMP_atom.CHARMMTopology_get_parameters(self)
11456 def add_sequence(self, sequence):
11457 """add_sequence(CHARMMTopology self, std::string sequence)"""
11458 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11461 def apply_default_patches(self):
11462 """apply_default_patches(CHARMMTopology self)"""
11463 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11466 def create_hierarchy(self, model):
11467 """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11468 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11471 def add_atom_types(self, hierarchy):
11472 """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11473 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11476 def add_coordinates(self, hierarchy):
11477 """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11478 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11481 def add_missing_atoms(self, hierarchy):
11482 """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11483 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11486 def setup_hierarchy(self, hierarchy):
11487 """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11488 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11491 def add_charges(self, hierarchy):
11492 """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11493 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11497 """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11498 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11501 def add_dihedrals(self, hierarchy):
11502 """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11503 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11506 def add_impropers(self, hierarchy):
11507 """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11508 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11511 def remove_segment(self, d):
11512 """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11513 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11516 def remove_segments(self, d):
11517 """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11518 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11521 def set_segments(self, ps):
11522 """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11523 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11526 def set_segments_order(self, objs):
11527 """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11528 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11531 def add_segment(self, obj):
11532 """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11533 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11536 def add_segments(self, objs):
11537 """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11538 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11541 def clear_segments(self):
11542 """clear_segments(CHARMMTopology self)"""
11543 return _IMP_atom.CHARMMTopology_clear_segments(self)
11546 def get_number_of_segments(self):
11547 """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11548 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11551 def get_has_segments(self):
11552 """get_has_segments(CHARMMTopology self) -> bool"""
11553 return _IMP_atom.CHARMMTopology_get_has_segments(self)
11557 """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11558 return _IMP_atom.CHARMMTopology_get_segment(self, i)
11561 def get_segments(self):
11562 """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11563 return _IMP_atom.CHARMMTopology_get_segments(self)
11566 def reserve_segments(self, sz):
11567 """reserve_segments(CHARMMTopology self, unsigned int sz)"""
11568 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11571 def get_version_info(self):
11572 """get_version_info(CHARMMTopology self) -> VersionInfo"""
11573 return _IMP_atom.CHARMMTopology_get_version_info(self)
11577 """__str__(CHARMMTopology self) -> std::string"""
11578 return _IMP_atom.CHARMMTopology___str__(self)
11581 def __repr__(self):
11582 """__repr__(CHARMMTopology self) -> std::string"""
11583 return _IMP_atom.CHARMMTopology___repr__(self)
11588 return _object_cast_to_CHARMMTopology(o)
11590 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
11591 CHARMMTopology_swigregister(CHARMMTopology)
11594 """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
11596 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11598 def __init__(self, *args):
11600 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11601 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11603 this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
11605 self.this.append(this)
11606 except __builtin__.Exception:
11609 def get_pair_filter(self):
11610 """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11611 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11614 def get_full_pair_filter(self):
11615 """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11616 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11619 def do_get_inputs(self):
11620 """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11621 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11624 def get_version_info(self):
11625 """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11626 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11630 """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11631 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11634 def __repr__(self):
11635 """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11636 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11641 return _object_cast_to_CHARMMStereochemistryRestraint(o)
11643 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
11644 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11649 add_bonds(Hierarchy d, ForceFieldParameters ffp)
11650 add_bonds(Hierarchy d)
11652 return _IMP_atom.add_bonds(*args)
11656 add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
11657 add_radii(Hierarchy d, ForceFieldParameters ffp)
11658 add_radii(Hierarchy d)
11660 return _IMP_atom.add_radii(*args)
11661 ALBER = _IMP_atom.ALBER
11662 HARPAZ = _IMP_atom.HARPAZ
11663 ANDERSSON = _IMP_atom.ANDERSSON
11664 TSAI = _IMP_atom.TSAI
11665 QUILLIN = _IMP_atom.QUILLIN
11666 SQUIRE = _IMP_atom.SQUIRE
11669 """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
11670 return _IMP_atom.get_protein_density_from_reference(densityReference)
11674 get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
11675 get_volume_from_mass(double m) -> double
11677 return _IMP_atom.get_volume_from_mass(*args)
11681 get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
11682 get_mass_from_volume(double v) -> double
11684 return _IMP_atom.get_mass_from_volume(*args)
11687 """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
11688 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
11691 """get_volume_from_residue_type(ResidueType rt) -> double"""
11692 return _IMP_atom.get_volume_from_residue_type(rt)
11695 """get_molarity(double n, double volume) -> double"""
11696 return _IMP_atom.get_molarity(n, volume)
11698 def get_kd(na, nb, nab, volume):
11699 """get_kd(double na, double nb, double nab, double volume) -> double"""
11700 return _IMP_atom.get_kd(na, nb, nab, volume)
11703 """get_einstein_diffusion_coefficient(double r) -> double"""
11704 return _IMP_atom.get_einstein_diffusion_coefficient(r)
11707 """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
11708 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r)
11712 get_diffusion_length(double D, double t) -> double
11713 get_diffusion_length(double D, double force, double t, double temp=273) -> double
11714 get_diffusion_length(double D, double force, double t) -> double
11716 return _IMP_atom.get_diffusion_length(*args)
11719 """get_diffusion_angle(double D, double dtfs) -> double"""
11720 return _IMP_atom.get_diffusion_angle(D, dtfs)
11723 """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
11724 return _IMP_atom.get_diffusion_coefficient(displacements, dt)
11727 """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
11728 return _IMP_atom.get_rotational_diffusion_coefficient(displacements, dt)
11730 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
11731 """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
11732 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
11735 """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
11736 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
11739 """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
11740 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
11742 """Proxy of C++ IMP::atom::EzRestraint class."""
11744 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11746 def __init__(self, m, ps):
11747 """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
11748 this = _IMP_atom.new_EzRestraint(m, ps)
11750 self.this.append(this)
11751 except __builtin__.Exception:
11754 def get_version_info(self):
11755 """get_version_info(EzRestraint self) -> VersionInfo"""
11756 return _IMP_atom.EzRestraint_get_version_info(self)
11760 """__str__(EzRestraint self) -> std::string"""
11761 return _IMP_atom.EzRestraint___str__(self)
11764 def __repr__(self):
11765 """__repr__(EzRestraint self) -> std::string"""
11766 return _IMP_atom.EzRestraint___repr__(self)
11771 return _object_cast_to_EzRestraint(o)
11773 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
11774 EzRestraint_swigregister(EzRestraint)
11779 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
11780 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
11781 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
11782 create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
11783 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
11785 return _IMP_atom.create_protein(*args)
11789 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
11790 create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
11791 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
11792 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
11794 return _IMP_atom.create_simplified_along_backbone(*args)
11797 """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11798 return _IMP_atom.create_simplified_from_volume(h, resolution)
11801 """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
11802 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
11804 def get_residue_indexes(h):
11805 """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
11806 return _IMP_atom.get_residue_indexes(h)
11808 def get_residue_type(*args):
11810 get_residue_type(char c) -> ResidueType
11811 get_residue_type(Hierarchy h) -> ResidueType
11813 return _IMP_atom.get_residue_type(*args)
11815 def get_atom_type(h):
11816 """get_atom_type(Hierarchy h) -> AtomType"""
11817 return _IMP_atom.get_atom_type(h)
11819 def get_domain_name(h):
11820 """get_domain_name(Hierarchy h) -> std::string"""
11821 return _IMP_atom.get_domain_name(h)
11825 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
11826 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
11827 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
11829 return _IMP_atom.create_excluded_volume_restraint(*args)
11833 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
11834 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
11835 setup_as_approximation(Hierarchy h, double resolution=-1)
11836 setup_as_approximation(Hierarchy h)
11838 return _IMP_atom.setup_as_approximation(*args)
11839 class _HierarchyTreeVertexIndex(object):
11840 """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
11842 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11843 __repr__ = _swig_repr
11845 def __init__(self):
11846 """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
11847 this = _IMP_atom.new__HierarchyTreeVertexIndex()
11849 self.this.append(this)
11850 except __builtin__.Exception:
11852 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
11853 __del__ =
lambda self:
None
11854 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
11855 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
11858 def show_as_graphviz(name, out):
11859 """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
11860 return _IMP_atom.show_as_graphviz(name, out)
11862 def get_vertex_index(g):
11863 """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
11864 return _IMP_atom.get_vertex_index(g)
11867 """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
11868 return _IMP_atom.get_hierarchy_tree(h)
11870 """Proxy of C++ IMP::atom::HierarchyGeometry class."""
11872 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11874 def __init__(self, d, resolution=0):
11876 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
11877 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
11879 this = _IMP_atom.new_HierarchyGeometry(d, resolution)
11881 self.this.append(this)
11882 except __builtin__.Exception:
11885 def get_version_info(self):
11886 """get_version_info(HierarchyGeometry self) -> VersionInfo"""
11887 return _IMP_atom.HierarchyGeometry_get_version_info(self)
11891 """__str__(HierarchyGeometry self) -> std::string"""
11892 return _IMP_atom.HierarchyGeometry___str__(self)
11895 def __repr__(self):
11896 """__repr__(HierarchyGeometry self) -> std::string"""
11897 return _IMP_atom.HierarchyGeometry___repr__(self)
11902 return _object_cast_to_HierarchyGeometry(o)
11904 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
11905 HierarchyGeometry_swigregister(HierarchyGeometry)
11908 """Proxy of C++ IMP::atom::HierarchiesGeometry class."""
11910 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11912 def __init__(self, sc, resolution=-1):
11914 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
11915 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
11917 this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
11919 self.this.append(this)
11920 except __builtin__.Exception:
11923 def get_version_info(self):
11924 """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
11925 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
11929 """__str__(HierarchiesGeometry self) -> std::string"""
11930 return _IMP_atom.HierarchiesGeometry___str__(self)
11933 def __repr__(self):
11934 """__repr__(HierarchiesGeometry self) -> std::string"""
11935 return _IMP_atom.HierarchiesGeometry___repr__(self)
11940 return _object_cast_to_HierarchiesGeometry(o)
11942 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
11943 HierarchiesGeometry_swigregister(HierarchiesGeometry)
11948 transform(Hierarchy h, Transformation3D tr)
11949 transform(Hierarchy h, Transformation3D tr)
11951 return _IMP_atom.transform(*args)
11952 class DopePairScore(_ADopeBase):
11953 """Proxy of C++ IMP::atom::DopePairScore class."""
11955 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11957 def __init__(self, *args):
11959 __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
11960 __init__(IMP::atom::DopePairScore self) -> DopePairScore
11961 __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
11963 this = _IMP_atom.new_DopePairScore(*args)
11965 self.this.append(this)
11966 except __builtin__.Exception:
11970 """__str__(DopePairScore self) -> std::string"""
11971 return _IMP_atom.DopePairScore___str__(self)
11974 def __repr__(self):
11975 """__repr__(DopePairScore self) -> std::string"""
11976 return _IMP_atom.DopePairScore___repr__(self)
11981 return _object_cast_to_DopePairScore(o)
11983 __swig_destroy__ = _IMP_atom.delete_DopePairScore
11984 __del__ =
lambda self:
None
11985 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
11986 DopePairScore_swigregister(DopePairScore)
11990 """add_dope_score_data(Hierarchy h)"""
11991 return _IMP_atom.add_dope_score_data(h)
11992 class OrientedSoapPairScore(_OrientedSoapBase):
11993 """Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
11995 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11997 def __init__(self, library):
11998 """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
11999 this = _IMP_atom.new_OrientedSoapPairScore(library)
12001 self.this.append(this)
12002 except __builtin__.Exception:
12005 def get_pair_filter(self):
12006 """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12007 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12011 """__str__(OrientedSoapPairScore self) -> std::string"""
12012 return _IMP_atom.OrientedSoapPairScore___str__(self)
12015 def __repr__(self):
12016 """__repr__(OrientedSoapPairScore self) -> std::string"""
12017 return _IMP_atom.OrientedSoapPairScore___repr__(self)
12022 return _object_cast_to_OrientedSoapPairScore(o)
12024 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12025 __del__ =
lambda self:
None
12026 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12027 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12030 """Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12032 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12034 def __init__(self):
12035 """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12036 this = _IMP_atom.new_SameResiduePairFilter()
12038 self.this.append(this)
12039 except __builtin__.Exception:
12042 def do_get_inputs(self, m, pis):
12043 """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12044 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12047 def get_value(self, *args):
12049 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12050 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12052 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12055 def get_value_index(self, *args):
12057 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12058 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12060 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12063 def get_version_info(self):
12064 """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12065 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12069 """__str__(SameResiduePairFilter self) -> std::string"""
12070 return _IMP_atom.SameResiduePairFilter___str__(self)
12073 def __repr__(self):
12074 """__repr__(SameResiduePairFilter self) -> std::string"""
12075 return _IMP_atom.SameResiduePairFilter___repr__(self)
12080 return _object_cast_to_SameResiduePairFilter(o)
12082 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12083 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12086 """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12088 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12090 def __init__(self, m, pis):
12091 """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12092 this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12094 self.this.append(this)
12095 except __builtin__.Exception:
12098 def set_particles(self, pis):
12099 """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12100 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12103 def remove_rigid_motion(self):
12104 """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12105 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12108 def get_version_info(self):
12109 """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12110 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12114 """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12115 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12118 def __repr__(self):
12119 """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12120 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12125 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12127 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12128 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12131 """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12133 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12135 def __init__(self, pis, temperature, tau):
12136 """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12137 this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12139 self.this.append(this)
12140 except __builtin__.Exception:
12143 def set_particles(self, pis):
12144 """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12145 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12148 def get_temperature(self):
12149 """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12150 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12154 """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12155 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12158 def set_temperature(self, temperature):
12159 """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12160 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12163 def set_tau(self, tau):
12164 """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12165 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12168 def rescale_velocities(self):
12169 """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12170 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12173 def get_version_info(self):
12174 """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12175 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12179 """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12180 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12183 def __repr__(self):
12184 """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12185 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12190 return _object_cast_to_BerendsenThermostatOptimizerState(o)
12192 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12193 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12196 """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12198 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12200 def __init__(self, m, pis, temperature, gamma):
12201 """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12202 this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12204 self.this.append(this)
12205 except __builtin__.Exception:
12208 def set_particles(self, pis):
12209 """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12210 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12213 def get_temperature(self):
12214 """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12215 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12218 def get_gamma(self):
12219 """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12220 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12223 def set_temperature(self, temperature):
12224 """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12225 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12228 def set_gamma(self, gamma):
12229 """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12230 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12233 def rescale_velocities(self):
12234 """rescale_velocities(LangevinThermostatOptimizerState self)"""
12235 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12238 def get_version_info(self):
12239 """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12240 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12244 """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12245 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12248 def __repr__(self):
12249 """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12250 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12255 return _object_cast_to_LangevinThermostatOptimizerState(o)
12257 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12258 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12261 """Proxy of C++ IMP::atom::PDBSelector class."""
12263 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12265 def __init__(self, name):
12266 """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12267 if self.__class__ == PDBSelector:
12271 this = _IMP_atom.new_PDBSelector(_self, name)
12273 self.this.append(this)
12274 except __builtin__.Exception:
12277 if self.__class__ != PDBSelector:
12278 _director_objects.register(self)
12283 def get_is_selected(self, pdb_line):
12284 """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12285 return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12287 __swig_destroy__ = _IMP_atom.delete_PDBSelector
12288 __del__ =
lambda self:
None
12291 """__str__(PDBSelector self) -> std::string"""
12292 return _IMP_atom.PDBSelector___str__(self)
12295 def __repr__(self):
12296 """__repr__(PDBSelector self) -> std::string"""
12297 return _IMP_atom.PDBSelector___repr__(self)
12302 return _object_cast_to_PDBSelector(o)
12305 def get_type_name(self):
12306 return self.__class__.__name__
12307 def do_show(self, out):
12309 def get_version_info(self):
12310 if"IMP::atom" ==
"IMP":
12311 return VersionInfo(self.__module__,
12312 __import__(self.__module__).get_module_version())
12315 __import__(self.__module__).get_module_version())
12318 return _object_cast_to_PDBSelector(o)
12321 def __and__(self, s):
12322 return AndPDBSelector(self, s)
12323 def __or__(self, s):
12324 return OrPDBSelector(self, s)
12325 def __xor__(self, s):
12326 return XorPDBSelector(self, s)
12327 def __invert__(self):
12328 return NotPDBSelector(self)
12329 def __sub__(self, s):
12330 return AndPDBSelector(self, NotPDBSelector(s))
12332 def __disown__(self):
12334 _IMP_atom.disown_PDBSelector(self)
12335 return weakref_proxy(self)
12337 def do_destroy(self):
12338 """do_destroy(PDBSelector self)"""
12339 return _IMP_atom.PDBSelector_do_destroy(self)
12341 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12342 PDBSelector_swigregister(PDBSelector)
12344 class NonAlternativePDBSelector(PDBSelector):
12345 """Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12347 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12349 def __init__(self, *args):
12351 __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12352 __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12354 this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12356 self.this.append(this)
12357 except __builtin__.Exception:
12360 def get_version_info(self):
12361 """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12362 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12366 """__str__(NonAlternativePDBSelector self) -> std::string"""
12367 return _IMP_atom.NonAlternativePDBSelector___str__(self)
12370 def __repr__(self):
12371 """__repr__(NonAlternativePDBSelector self) -> std::string"""
12372 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12377 return _object_cast_to_NonAlternativePDBSelector(o)
12379 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
12380 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12382 class ATOMPDBSelector(NonAlternativePDBSelector):
12383 """Proxy of C++ IMP::atom::ATOMPDBSelector class."""
12385 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12387 def __init__(self, *args):
12389 __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
12390 __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
12392 this = _IMP_atom.new_ATOMPDBSelector(*args)
12394 self.this.append(this)
12395 except __builtin__.Exception:
12399 """__str__(ATOMPDBSelector self) -> std::string"""
12400 return _IMP_atom.ATOMPDBSelector___str__(self)
12403 def __repr__(self):
12404 """__repr__(ATOMPDBSelector self) -> std::string"""
12405 return _IMP_atom.ATOMPDBSelector___repr__(self)
12410 return _object_cast_to_ATOMPDBSelector(o)
12412 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
12413 ATOMPDBSelector_swigregister(ATOMPDBSelector)
12415 class CAlphaPDBSelector(NonAlternativePDBSelector):
12416 """Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
12418 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12420 def __init__(self, *args):
12422 __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
12423 __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
12425 this = _IMP_atom.new_CAlphaPDBSelector(*args)
12427 self.this.append(this)
12428 except __builtin__.Exception:
12432 """__str__(CAlphaPDBSelector self) -> std::string"""
12433 return _IMP_atom.CAlphaPDBSelector___str__(self)
12436 def __repr__(self):
12437 """__repr__(CAlphaPDBSelector self) -> std::string"""
12438 return _IMP_atom.CAlphaPDBSelector___repr__(self)
12443 return _object_cast_to_CAlphaPDBSelector(o)
12445 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
12446 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12448 class CBetaPDBSelector(NonAlternativePDBSelector):
12449 """Proxy of C++ IMP::atom::CBetaPDBSelector class."""
12451 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12453 def __init__(self, *args):
12455 __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
12456 __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
12458 this = _IMP_atom.new_CBetaPDBSelector(*args)
12460 self.this.append(this)
12461 except __builtin__.Exception:
12465 """__str__(CBetaPDBSelector self) -> std::string"""
12466 return _IMP_atom.CBetaPDBSelector___str__(self)
12469 def __repr__(self):
12470 """__repr__(CBetaPDBSelector self) -> std::string"""
12471 return _IMP_atom.CBetaPDBSelector___repr__(self)
12476 return _object_cast_to_CBetaPDBSelector(o)
12478 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
12479 CBetaPDBSelector_swigregister(CBetaPDBSelector)
12481 class AtomTypePDBSelector(PDBSelector):
12482 """Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
12484 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12486 def __init__(self, *args):
12488 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
12489 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
12491 this = _IMP_atom.new_AtomTypePDBSelector(*args)
12493 self.this.append(this)
12494 except __builtin__.Exception:
12497 def get_version_info(self):
12498 """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12499 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12503 """__str__(AtomTypePDBSelector self) -> std::string"""
12504 return _IMP_atom.AtomTypePDBSelector___str__(self)
12507 def __repr__(self):
12508 """__repr__(AtomTypePDBSelector self) -> std::string"""
12509 return _IMP_atom.AtomTypePDBSelector___repr__(self)
12514 return _object_cast_to_AtomTypePDBSelector(o)
12516 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
12517 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12519 class ResidueTypePDBSelector(PDBSelector):
12520 """Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
12522 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12524 def __init__(self, *args):
12526 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
12527 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
12529 this = _IMP_atom.new_ResidueTypePDBSelector(*args)
12531 self.this.append(this)
12532 except __builtin__.Exception:
12535 def get_version_info(self):
12536 """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12537 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12541 """__str__(ResidueTypePDBSelector self) -> std::string"""
12542 return _IMP_atom.ResidueTypePDBSelector___str__(self)
12545 def __repr__(self):
12546 """__repr__(ResidueTypePDBSelector self) -> std::string"""
12547 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12552 return _object_cast_to_ResidueTypePDBSelector(o)
12554 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
12555 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12557 class CPDBSelector(NonAlternativePDBSelector):
12558 """Proxy of C++ IMP::atom::CPDBSelector class."""
12560 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12562 def __init__(self, *args):
12564 __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
12565 __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
12567 this = _IMP_atom.new_CPDBSelector(*args)
12569 self.this.append(this)
12570 except __builtin__.Exception:
12574 """__str__(CPDBSelector self) -> std::string"""
12575 return _IMP_atom.CPDBSelector___str__(self)
12578 def __repr__(self):
12579 """__repr__(CPDBSelector self) -> std::string"""
12580 return _IMP_atom.CPDBSelector___repr__(self)
12585 return _object_cast_to_CPDBSelector(o)
12587 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
12588 CPDBSelector_swigregister(CPDBSelector)
12590 class NPDBSelector(NonAlternativePDBSelector):
12591 """Proxy of C++ IMP::atom::NPDBSelector class."""
12593 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12595 def __init__(self, *args):
12597 __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
12598 __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
12600 this = _IMP_atom.new_NPDBSelector(*args)
12602 self.this.append(this)
12603 except __builtin__.Exception:
12607 """__str__(NPDBSelector self) -> std::string"""
12608 return _IMP_atom.NPDBSelector___str__(self)
12611 def __repr__(self):
12612 """__repr__(NPDBSelector self) -> std::string"""
12613 return _IMP_atom.NPDBSelector___repr__(self)
12618 return _object_cast_to_NPDBSelector(o)
12620 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
12621 NPDBSelector_swigregister(NPDBSelector)
12623 class AllPDBSelector(PDBSelector):
12624 """Proxy of C++ IMP::atom::AllPDBSelector class."""
12626 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12628 def __init__(self, *args):
12630 __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
12631 __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
12633 this = _IMP_atom.new_AllPDBSelector(*args)
12635 self.this.append(this)
12636 except __builtin__.Exception:
12639 def get_version_info(self):
12640 """get_version_info(AllPDBSelector self) -> VersionInfo"""
12641 return _IMP_atom.AllPDBSelector_get_version_info(self)
12645 """__str__(AllPDBSelector self) -> std::string"""
12646 return _IMP_atom.AllPDBSelector___str__(self)
12649 def __repr__(self):
12650 """__repr__(AllPDBSelector self) -> std::string"""
12651 return _IMP_atom.AllPDBSelector___repr__(self)
12656 return _object_cast_to_AllPDBSelector(o)
12658 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
12659 AllPDBSelector_swigregister(AllPDBSelector)
12661 class ChainPDBSelector(NonAlternativePDBSelector):
12662 """Proxy of C++ IMP::atom::ChainPDBSelector class."""
12664 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12666 def __init__(self, *args):
12668 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
12669 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
12671 this = _IMP_atom.new_ChainPDBSelector(*args)
12673 self.this.append(this)
12674 except __builtin__.Exception:
12678 """__str__(ChainPDBSelector self) -> std::string"""
12679 return _IMP_atom.ChainPDBSelector___str__(self)
12682 def __repr__(self):
12683 """__repr__(ChainPDBSelector self) -> std::string"""
12684 return _IMP_atom.ChainPDBSelector___repr__(self)
12689 return _object_cast_to_ChainPDBSelector(o)
12691 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
12692 ChainPDBSelector_swigregister(ChainPDBSelector)
12694 class WaterPDBSelector(NonAlternativePDBSelector):
12695 """Proxy of C++ IMP::atom::WaterPDBSelector class."""
12697 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12699 def __init__(self, *args):
12701 __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
12702 __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
12704 this = _IMP_atom.new_WaterPDBSelector(*args)
12706 self.this.append(this)
12707 except __builtin__.Exception:
12711 """__str__(WaterPDBSelector self) -> std::string"""
12712 return _IMP_atom.WaterPDBSelector___str__(self)
12715 def __repr__(self):
12716 """__repr__(WaterPDBSelector self) -> std::string"""
12717 return _IMP_atom.WaterPDBSelector___repr__(self)
12722 return _object_cast_to_WaterPDBSelector(o)
12724 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
12725 WaterPDBSelector_swigregister(WaterPDBSelector)
12727 class HydrogenPDBSelector(NonAlternativePDBSelector):
12728 """Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
12730 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12732 def __init__(self, *args):
12734 __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
12735 __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
12737 this = _IMP_atom.new_HydrogenPDBSelector(*args)
12739 self.this.append(this)
12740 except __builtin__.Exception:
12744 """__str__(HydrogenPDBSelector self) -> std::string"""
12745 return _IMP_atom.HydrogenPDBSelector___str__(self)
12748 def __repr__(self):
12749 """__repr__(HydrogenPDBSelector self) -> std::string"""
12750 return _IMP_atom.HydrogenPDBSelector___repr__(self)
12755 return _object_cast_to_HydrogenPDBSelector(o)
12757 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
12758 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
12760 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
12761 """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
12763 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12765 def __init__(self, *args):
12767 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
12768 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
12770 this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
12772 self.this.append(this)
12773 except __builtin__.Exception:
12777 """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12778 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
12781 def __repr__(self):
12782 """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
12783 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
12788 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
12790 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
12791 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
12793 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
12794 """Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
12796 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12798 def __init__(self, *args):
12800 __init__(IMP::atom::NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
12801 __init__(IMP::atom::NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
12803 this = _IMP_atom.new_NonHydrogenPDBSelector(*args)
12805 self.this.append(this)
12806 except __builtin__.Exception:
12810 """__str__(NonHydrogenPDBSelector self) -> std::string"""
12811 return _IMP_atom.NonHydrogenPDBSelector___str__(self)
12814 def __repr__(self):
12815 """__repr__(NonHydrogenPDBSelector self) -> std::string"""
12816 return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
12821 return _object_cast_to_NonHydrogenPDBSelector(o)
12823 NonHydrogenPDBSelector_swigregister = _IMP_atom.NonHydrogenPDBSelector_swigregister
12824 NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
12826 class NonWaterPDBSelector(NonAlternativePDBSelector):
12827 """Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
12829 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12831 def __init__(self, *args):
12833 __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
12834 __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
12836 this = _IMP_atom.new_NonWaterPDBSelector(*args)
12838 self.this.append(this)
12839 except __builtin__.Exception:
12843 """__str__(NonWaterPDBSelector self) -> std::string"""
12844 return _IMP_atom.NonWaterPDBSelector___str__(self)
12847 def __repr__(self):
12848 """__repr__(NonWaterPDBSelector self) -> std::string"""
12849 return _IMP_atom.NonWaterPDBSelector___repr__(self)
12854 return _object_cast_to_NonWaterPDBSelector(o)
12856 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
12857 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
12859 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
12860 """Proxy of C++ IMP::atom::BackbonePDBSelector class."""
12862 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12864 def __init__(self, *args):
12866 __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
12867 __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
12869 this = _IMP_atom.new_BackbonePDBSelector(*args)
12871 self.this.append(this)
12872 except __builtin__.Exception:
12876 """__str__(BackbonePDBSelector self) -> std::string"""
12877 return _IMP_atom.BackbonePDBSelector___str__(self)
12880 def __repr__(self):
12881 """__repr__(BackbonePDBSelector self) -> std::string"""
12882 return _IMP_atom.BackbonePDBSelector___repr__(self)
12887 return _object_cast_to_BackbonePDBSelector(o)
12889 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
12890 BackbonePDBSelector_swigregister(BackbonePDBSelector)
12892 class PPDBSelector(NonAlternativePDBSelector):
12893 """Proxy of C++ IMP::atom::PPDBSelector class."""
12895 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12897 def __init__(self, *args):
12899 __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
12900 __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
12902 this = _IMP_atom.new_PPDBSelector(*args)
12904 self.this.append(this)
12905 except __builtin__.Exception:
12909 """__str__(PPDBSelector self) -> std::string"""
12910 return _IMP_atom.PPDBSelector___str__(self)
12913 def __repr__(self):
12914 """__repr__(PPDBSelector self) -> std::string"""
12915 return _IMP_atom.PPDBSelector___repr__(self)
12920 return _object_cast_to_PPDBSelector(o)
12922 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
12923 PPDBSelector_swigregister(PPDBSelector)
12925 class AndPDBSelector(PDBSelector):
12926 """Proxy of C++ IMP::atom::AndPDBSelector class."""
12928 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12930 def get_version_info(self):
12931 """get_version_info(AndPDBSelector self) -> VersionInfo"""
12932 return _IMP_atom.AndPDBSelector_get_version_info(self)
12935 def __init__(self, a, b):
12936 """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
12937 this = _IMP_atom.new_AndPDBSelector(a, b)
12939 self.this.append(this)
12940 except __builtin__.Exception:
12944 """__str__(AndPDBSelector self) -> std::string"""
12945 return _IMP_atom.AndPDBSelector___str__(self)
12948 def __repr__(self):
12949 """__repr__(AndPDBSelector self) -> std::string"""
12950 return _IMP_atom.AndPDBSelector___repr__(self)
12955 return _object_cast_to_AndPDBSelector(o)
12957 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
12958 AndPDBSelector_swigregister(AndPDBSelector)
12960 class OrPDBSelector(PDBSelector):
12961 """Proxy of C++ IMP::atom::OrPDBSelector class."""
12963 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12965 def get_version_info(self):
12966 """get_version_info(OrPDBSelector self) -> VersionInfo"""
12967 return _IMP_atom.OrPDBSelector_get_version_info(self)
12970 def __init__(self, a, b):
12971 """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
12972 this = _IMP_atom.new_OrPDBSelector(a, b)
12974 self.this.append(this)
12975 except __builtin__.Exception:
12979 """__str__(OrPDBSelector self) -> std::string"""
12980 return _IMP_atom.OrPDBSelector___str__(self)
12983 def __repr__(self):
12984 """__repr__(OrPDBSelector self) -> std::string"""
12985 return _IMP_atom.OrPDBSelector___repr__(self)
12990 return _object_cast_to_OrPDBSelector(o)
12992 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
12993 OrPDBSelector_swigregister(OrPDBSelector)
12995 class XorPDBSelector(PDBSelector):
12996 """Proxy of C++ IMP::atom::XorPDBSelector class."""
12998 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13000 def get_version_info(self):
13001 """get_version_info(XorPDBSelector self) -> VersionInfo"""
13002 return _IMP_atom.XorPDBSelector_get_version_info(self)
13005 def __init__(self, a, b):
13006 """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13007 this = _IMP_atom.new_XorPDBSelector(a, b)
13009 self.this.append(this)
13010 except __builtin__.Exception:
13014 """__str__(XorPDBSelector self) -> std::string"""
13015 return _IMP_atom.XorPDBSelector___str__(self)
13018 def __repr__(self):
13019 """__repr__(XorPDBSelector self) -> std::string"""
13020 return _IMP_atom.XorPDBSelector___repr__(self)
13025 return _object_cast_to_XorPDBSelector(o)
13027 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13028 XorPDBSelector_swigregister(XorPDBSelector)
13030 class NotPDBSelector(PDBSelector):
13031 """Proxy of C++ IMP::atom::NotPDBSelector class."""
13033 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13035 def get_version_info(self):
13036 """get_version_info(NotPDBSelector self) -> VersionInfo"""
13037 return _IMP_atom.NotPDBSelector_get_version_info(self)
13040 def __init__(self, a):
13041 """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13042 this = _IMP_atom.new_NotPDBSelector(a)
13044 self.this.append(this)
13045 except __builtin__.Exception:
13049 """__str__(NotPDBSelector self) -> std::string"""
13050 return _IMP_atom.NotPDBSelector___str__(self)
13053 def __repr__(self):
13054 """__repr__(NotPDBSelector self) -> std::string"""
13055 return _IMP_atom.NotPDBSelector___repr__(self)
13060 return _object_cast_to_NotPDBSelector(o)
13062 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13063 NotPDBSelector_swigregister(NotPDBSelector)
13066 def get_default_pdb_selector():
13067 """get_default_pdb_selector() -> PDBSelector"""
13068 return _IMP_atom.get_default_pdb_selector()
13072 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13073 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13074 read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13075 read_pdb(TextInput input, Model model) -> Hierarchy
13076 read_pdb(TextInput input, int model, Hierarchy h)
13078 return _IMP_atom.read_pdb(*args)
13082 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13083 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13084 read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13086 return _IMP_atom.read_multimodel_pdb(*args)
13090 write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13091 write_pdb(Selection mhd, TextOutput out)
13093 return _IMP_atom.write_pdb(mhd, out, model)
13097 write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13098 write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13100 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13103 """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13104 return _IMP_atom.write_multimodel_pdb(mhd, out)
13106 def get_pdb_string(*args):
13108 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00, double tempFactor=0.00, IMP::atom::Element e) -> std::string
13109 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00, double tempFactor=0.00) -> std::string
13110 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occupancy=1.00) -> std::string
13111 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13112 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13113 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13114 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13115 get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13116 get_pdb_string(Vector3D v, int index=-1) -> std::string
13117 get_pdb_string(Vector3D v) -> std::string
13119 return _IMP_atom.get_pdb_string(*args)
13121 def get_pdb_conect_record_string(arg1, arg2):
13122 """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13123 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13125 """Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13127 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13129 def __init__(self, *args):
13131 __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13132 __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13134 this = _IMP_atom.new_WritePDBOptimizerState(*args)
13136 self.this.append(this)
13137 except __builtin__.Exception:
13140 def get_version_info(self):
13141 """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13142 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13146 """__str__(WritePDBOptimizerState self) -> std::string"""
13147 return _IMP_atom.WritePDBOptimizerState___str__(self)
13150 def __repr__(self):
13151 """__repr__(WritePDBOptimizerState self) -> std::string"""
13152 return _IMP_atom.WritePDBOptimizerState___repr__(self)
13157 return _object_cast_to_WritePDBOptimizerState(o)
13159 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13160 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13164 """get_kt(double T) -> double"""
13165 return _IMP_atom.get_kt(T)
13167 """Proxy of C++ IMP::atom::CAAngleRestraint class."""
13169 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13171 def __init__(self, m, p1, p2, p3, phi0, score):
13172 """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13173 this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13175 self.this.append(this)
13176 except __builtin__.Exception:
13179 def do_get_inputs(self):
13180 """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13181 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13184 def get_version_info(self):
13185 """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13186 return _IMP_atom.CAAngleRestraint_get_version_info(self)
13190 """__str__(CAAngleRestraint self) -> std::string"""
13191 return _IMP_atom.CAAngleRestraint___str__(self)
13194 def __repr__(self):
13195 """__repr__(CAAngleRestraint self) -> std::string"""
13196 return _IMP_atom.CAAngleRestraint___repr__(self)
13201 return _object_cast_to_CAAngleRestraint(o)
13203 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13204 CAAngleRestraint_swigregister(CAAngleRestraint)
13207 """Proxy of C++ IMP::atom::CADihedralRestraint class."""
13209 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13211 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13212 """__init__(IMP::atom::CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
13213 this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13215 self.this.append(this)
13216 except __builtin__.Exception:
13219 def do_get_inputs(self):
13220 """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13221 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13224 def get_version_info(self):
13225 """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13226 return _IMP_atom.CADihedralRestraint_get_version_info(self)
13230 """__str__(CADihedralRestraint self) -> std::string"""
13231 return _IMP_atom.CADihedralRestraint___str__(self)
13234 def __repr__(self):
13235 """__repr__(CADihedralRestraint self) -> std::string"""
13236 return _IMP_atom.CADihedralRestraint___repr__(self)
13241 return _object_cast_to_CADihedralRestraint(o)
13243 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13244 CADihedralRestraint_swigregister(CADihedralRestraint)
13247 """Proxy of C++ IMP::atom::StructureSource class."""
13249 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13251 def get_source_id(self):
13252 """get_source_id(StructureSource self) -> std::string"""
13253 return _IMP_atom.StructureSource_get_source_id(self)
13256 def get_source_chain_id(self):
13257 """get_source_chain_id(StructureSource self) -> std::string"""
13258 return _IMP_atom.StructureSource_get_source_chain_id(self)
13261 def set_source_id(self, source_id):
13262 """set_source_id(StructureSource self, std::string source_id)"""
13263 return _IMP_atom.StructureSource_set_source_id(self, source_id)
13266 def set_source_chain_id(self, source_chain_id):
13267 """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13268 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13271 def __init__(self, *args):
13273 __init__(IMP::atom::StructureSource self) -> StructureSource
13274 __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13275 __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13277 this = _IMP_atom.new_StructureSource(*args)
13279 self.this.append(this)
13280 except __builtin__.Exception:
13283 def get_is_setup(*args):
13285 get_is_setup(Model m, ParticleIndex pi) -> bool
13286 get_is_setup(_ParticleAdaptor p) -> bool
13288 return _IMP_atom.StructureSource_get_is_setup(*args)
13290 get_is_setup = staticmethod(get_is_setup)
13292 def show(self, *args):
13294 show(StructureSource self, _ostream out)
13295 show(StructureSource self)
13297 return _IMP_atom.StructureSource_show(self, *args)
13300 def setup_particle(*args):
13302 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13303 setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13305 return _IMP_atom.StructureSource_setup_particle(*args)
13307 setup_particle = staticmethod(setup_particle)
13309 def add_attribute(self, *args):
13311 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13312 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13313 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13314 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13315 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13316 add_attribute(StructureSource self, ObjectKey a0, Object a1)
13318 return _IMP_atom.StructureSource_add_attribute(self, *args)
13321 def get_value(self, *args):
13323 get_value(StructureSource self, FloatKey a0) -> IMP::Float
13324 get_value(StructureSource self, IntKey a0) -> IMP::Int
13325 get_value(StructureSource self, StringKey a0) -> IMP::String
13326 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13327 get_value(StructureSource self, ObjectKey a0) -> Object
13329 return _IMP_atom.StructureSource_get_value(self, *args)
13332 def set_value(self, *args):
13334 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13335 set_value(StructureSource self, IntKey a0, IMP::Int a1)
13336 set_value(StructureSource self, StringKey a0, IMP::String a1)
13337 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13338 set_value(StructureSource self, ObjectKey a0, Object a1)
13340 return _IMP_atom.StructureSource_set_value(self, *args)
13343 def remove_attribute(self, *args):
13345 remove_attribute(StructureSource self, FloatKey a0)
13346 remove_attribute(StructureSource self, IntKey a0)
13347 remove_attribute(StructureSource self, StringKey a0)
13348 remove_attribute(StructureSource self, ParticleIndexKey a0)
13349 remove_attribute(StructureSource self, ObjectKey a0)
13351 return _IMP_atom.StructureSource_remove_attribute(self, *args)
13354 def has_attribute(self, *args):
13356 has_attribute(StructureSource self, FloatKey a0) -> bool
13357 has_attribute(StructureSource self, IntKey a0) -> bool
13358 has_attribute(StructureSource self, StringKey a0) -> bool
13359 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13360 has_attribute(StructureSource self, ObjectKey a0) -> bool
13362 return _IMP_atom.StructureSource_has_attribute(self, *args)
13365 def get_derivative(self, a0):
13366 """get_derivative(StructureSource self, FloatKey a0) -> double"""
13367 return _IMP_atom.StructureSource_get_derivative(self, a0)
13370 def get_name(self):
13371 """get_name(StructureSource self) -> std::string"""
13372 return _IMP_atom.StructureSource_get_name(self)
13375 def clear_caches(self):
13376 """clear_caches(StructureSource self)"""
13377 return _IMP_atom.StructureSource_clear_caches(self)
13380 def set_name(self, a0):
13381 """set_name(StructureSource self, std::string a0)"""
13382 return _IMP_atom.StructureSource_set_name(self, a0)
13386 """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13387 return _IMP_atom.StructureSource_set_check_level(self, a0)
13390 def add_to_derivative(self, a0, a1, a2):
13391 """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13392 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13395 def set_is_optimized(self, a0, a1):
13396 """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13397 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13400 def get_is_optimized(self, a0):
13401 """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13402 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13406 """get_check_level(StructureSource self) -> IMP::CheckLevel"""
13407 return _IMP_atom.StructureSource_get_check_level(self)
13410 def __eq__(self, *args):
13412 __eq__(StructureSource self, StructureSource o) -> bool
13413 __eq__(StructureSource self, Particle d) -> bool
13415 return _IMP_atom.StructureSource___eq__(self, *args)
13418 def __ne__(self, *args):
13420 __ne__(StructureSource self, StructureSource o) -> bool
13421 __ne__(StructureSource self, Particle d) -> bool
13423 return _IMP_atom.StructureSource___ne__(self, *args)
13426 def __le__(self, *args):
13428 __le__(StructureSource self, StructureSource o) -> bool
13429 __le__(StructureSource self, Particle d) -> bool
13431 return _IMP_atom.StructureSource___le__(self, *args)
13434 def __lt__(self, *args):
13436 __lt__(StructureSource self, StructureSource o) -> bool
13437 __lt__(StructureSource self, Particle d) -> bool
13439 return _IMP_atom.StructureSource___lt__(self, *args)
13442 def __ge__(self, *args):
13444 __ge__(StructureSource self, StructureSource o) -> bool
13445 __ge__(StructureSource self, Particle d) -> bool
13447 return _IMP_atom.StructureSource___ge__(self, *args)
13450 def __gt__(self, *args):
13452 __gt__(StructureSource self, StructureSource o) -> bool
13453 __gt__(StructureSource self, Particle d) -> bool
13455 return _IMP_atom.StructureSource___gt__(self, *args)
13458 def __hash__(self):
13459 """__hash__(StructureSource self) -> std::size_t"""
13460 return _IMP_atom.StructureSource___hash__(self)
13464 """__str__(StructureSource self) -> std::string"""
13465 return _IMP_atom.StructureSource___str__(self)
13468 def __repr__(self):
13469 """__repr__(StructureSource self) -> std::string"""
13470 return _IMP_atom.StructureSource___repr__(self)
13472 __swig_destroy__ = _IMP_atom.delete_StructureSource
13473 __del__ =
lambda self:
None
13474 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
13475 StructureSource_swigregister(StructureSource)
13477 def StructureSource_get_is_setup(*args):
13479 get_is_setup(Model m, ParticleIndex pi) -> bool
13480 StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
13482 return _IMP_atom.StructureSource_get_is_setup(*args)
13484 def StructureSource_setup_particle(*args):
13486 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13487 StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13489 return _IMP_atom.StructureSource_setup_particle(*args)
13492 def __lshift__(*args):
13494 __lshift__(_ostream out, Bonded n) -> _ostream
13495 __lshift__(_ostream out, Bond n) -> _ostream
13496 __lshift__(_ostream out, Hierarchy n) -> _ostream
13497 __lshift__(_ostream out, Angle n) -> _ostream
13498 __lshift__(_ostream out, Dihedral n) -> _ostream
13499 __lshift__(_ostream out, CenterOfMass n) -> _ostream
13500 __lshift__(_ostream out, Diffusion n) -> _ostream
13501 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13502 __lshift__(_ostream out, TAMDParticle n) -> _ostream
13503 __lshift__(_ostream out, Chain n) -> _ostream
13504 __lshift__(_ostream out, Charged n) -> _ostream
13505 __lshift__(_ostream out, Domain n) -> _ostream
13506 __lshift__(_ostream out, LennardJones n) -> _ostream
13507 __lshift__(_ostream out, Fragment n) -> _ostream
13508 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13509 __lshift__(_ostream out, Atom n) -> _ostream
13510 __lshift__(_ostream out, Residue n) -> _ostream
13511 __lshift__(_ostream out, Representation n) -> _ostream
13512 __lshift__(_ostream out, State n) -> _ostream
13513 __lshift__(_ostream out, Molecule n) -> _ostream
13514 __lshift__(_ostream out, Copy n) -> _ostream
13515 __lshift__(_ostream out, StructureSource n) -> _ostream
13517 return _IMP_atom.__lshift__(*args)
13519 """Proxy of C++ IMP::atom::HelixRestraint class."""
13521 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13523 def __init__(self, rs, ideal=True):
13525 __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint
13526 __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs) -> HelixRestraint
13528 this = _IMP_atom.new_HelixRestraint(rs, ideal)
13530 self.this.append(this)
13531 except __builtin__.Exception:
13534 def get_number_of_bonds(self):
13535 """get_number_of_bonds(HelixRestraint self) -> int"""
13536 return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
13539 def get_number_of_dihedrals(self):
13540 """get_number_of_dihedrals(HelixRestraint self) -> int"""
13541 return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
13544 def do_get_inputs(self):
13545 """do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
13546 return _IMP_atom.HelixRestraint_do_get_inputs(self)
13549 def get_version_info(self):
13550 """get_version_info(HelixRestraint self) -> VersionInfo"""
13551 return _IMP_atom.HelixRestraint_get_version_info(self)
13555 """__str__(HelixRestraint self) -> std::string"""
13556 return _IMP_atom.HelixRestraint___str__(self)
13559 def __repr__(self):
13560 """__repr__(HelixRestraint self) -> std::string"""
13561 return _IMP_atom.HelixRestraint___repr__(self)
13566 return _object_cast_to_HelixRestraint(o)
13568 HelixRestraint_swigregister = _IMP_atom.HelixRestraint_swigregister
13569 HelixRestraint_swigregister(HelixRestraint)
13574 show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
13575 show_molecular_hierarchy(Hierarchy h) -> _ostream
13577 return _IMP_atom.show_molecular_hierarchy(*args)
13578 class CHARMMBond(object):
13579 """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class."""
13581 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13582 __repr__ = _swig_repr
13584 def __init__(self, atoms):
13585 """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
13586 this = _IMP_atom.new_CHARMMBond(atoms)
13588 self.this.append(this)
13589 except __builtin__.Exception:
13592 def get_endpoint(self, i):
13593 """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13594 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13597 def get_contains_atom(self, name):
13598 """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13599 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13602 def show(self, *args):
13604 show(CHARMMBond self, _ostream out)
13605 show(CHARMMBond self)
13607 return _IMP_atom.CHARMMBond_show(self, *args)
13609 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13610 __del__ =
lambda self:
None
13611 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
13612 CHARMMBond_swigregister(CHARMMBond)
13614 class CHARMMAngle(object):
13615 """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class."""
13617 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13618 __repr__ = _swig_repr
13620 def __init__(self, atoms):
13621 """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
13622 this = _IMP_atom.new_CHARMMAngle(atoms)
13624 self.this.append(this)
13625 except __builtin__.Exception:
13628 def get_endpoint(self, i):
13629 """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13630 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13633 def get_contains_atom(self, name):
13634 """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13635 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13638 def show(self, *args):
13640 show(CHARMMAngle self, _ostream out)
13641 show(CHARMMAngle self)
13643 return _IMP_atom.CHARMMAngle_show(self, *args)
13645 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13646 __del__ =
lambda self:
None
13647 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
13648 CHARMMAngle_swigregister(CHARMMAngle)
13651 def _get_native_overlap_cpp(m1, m2, threshold):
13652 """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13653 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13655 def _get_drmsd_cpp(m0, m1):
13656 """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13657 return _IMP_atom._get_drmsd_cpp(m0, m1)
13659 def _get_drmsd_Q_cpp(m0, m1, threshold):
13660 """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13661 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13663 def _get_drms_cpp(m1, m2):
13664 """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13665 return _IMP_atom._get_drms_cpp(m1, m2)
13667 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13668 """_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"""
13669 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13672 va= [IMP.algebra.get_vector(x)
for x
in a]
13673 vb= [IMP.algebra.get_vector(x)
for x
in b]
13674 return _get_native_overlap_cpp(va, vb, d)
13677 va= [IMP.algebra.get_vector(x)
for x
in a]
13678 vb= [IMP.algebra.get_vector(x)
for x
in b]
13679 return _get_drmsd_cpp(va, vb)
13682 va= [IMP.algebra.get_vector(x)
for x
in a]
13683 vb= [IMP.algebra.get_vector(x)
for x
in b]
13684 return _get_drms_cpp(va, vb)
13687 va= [IMP.algebra.get_vector(x)
for x
in a]
13688 vb= [IMP.algebra.get_vector(x)
for x
in b]
13689 return _get_drmsd_Q_cpp(va, vb, t)
13692 va= [IMP.algebra.get_vector(x)
for x
in a]
13693 vb= [IMP.algebra.get_vector(x)
for x
in b]
13695 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13699 def get_module_version():
13700 """get_module_version() -> std::string const"""
13701 return _IMP_atom.get_module_version()
13704 """get_example_path(std::string fname) -> std::string"""
13705 return _IMP_atom.get_example_path(fname)
13708 """get_data_path(std::string fname) -> std::string"""
13709 return _IMP_atom.get_data_path(fname)
13711 from .
import _version_check
13712 _version_check.check_version(get_module_version())
13713 __version__ = get_module_version()
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
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.
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)
double get_einstein_rotational_diffusion_coefficient(double r)
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"))
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.
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)
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.
double get_kd(double na, double nb, double nab, double volume)
double get_diffusion_angle(double D, double dtfs)
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.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &displacements, double dt)
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.
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.
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)
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.
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_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())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
double get_diffusion_length(double D, double t)
double get_einstein_diffusion_coefficient(double r)
A restraint is a term in an IMP ScoringFunction.
A decorator for a particle with x,y,z coordinates and a radius.