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_NUMPY = _IMP_atom.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
250 def register(self, obj):
251 """Take a reference to a director object; will only work for
252 refcounted C++ classes"""
253 if hasattr(obj,
'get_ref_count'):
254 self._objects.append(obj)
256 """Only drop our reference and allow cleanup by Python if no other
257 Python references exist (we hold 3 references: one in self._objects,
258 one in x, and one in the argument list for getrefcount) *and* no
259 other C++ references exist (the Python object always holds one)"""
260 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
261 or x.get_ref_count() > 1]
265 def get_object_count(self):
266 """Get number of director objects (useful for testing only)"""
267 return len(self._objects)
268 _director_objects = _DirectorObjects()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_atom._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_atom._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_atom.IMP_C_OPEN_BINARY
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_atom.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_atom.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_atom.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
329 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
330 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
331 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
332 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
333 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
334 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
335 IMP_CORE_HAS_NUMPY = _IMP_atom.IMP_CORE_HAS_NUMPY
336 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
338 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
339 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
341 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
342 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
343 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
344 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
345 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
348 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
349 IMP_CONTAINER_HAS_NUMPY = _IMP_atom.IMP_CONTAINER_HAS_NUMPY
350 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_atom.IMP_CONTAINER_HAS_PYTHON_IHM
351 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_atom.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
352 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_atom.IMP_CONTAINER_HAS_ROBIN_MAP
353 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
355 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
356 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
357 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
358 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
359 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
360 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
361 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
362 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
363 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
364 IMP_ATOM_HAS_NUMPY = _IMP_atom.IMP_ATOM_HAS_NUMPY
365 IMP_ATOM_HAS_PYTHON_IHM = _IMP_atom.IMP_ATOM_HAS_PYTHON_IHM
366 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
367 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
368 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
369 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
370 IMP_CHAIN_TYPE_INDEX = _IMP_atom.IMP_CHAIN_TYPE_INDEX
372 """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class."""
374 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
375 __repr__ = _swig_repr
378 """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
379 this = _IMP_atom.new_HierarchyTree()
381 self.this.append(this)
382 except __builtin__.Exception:
386 """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
387 return _IMP_atom.HierarchyTree_get_graph(self)
391 """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
392 return _IMP_atom.HierarchyTree_get_vertices(self)
395 def get_vertex_name(self, i):
396 """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
397 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
400 def get_in_neighbors(self, v):
401 """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"""
402 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
405 def get_out_neighbors(self, v):
406 """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"""
407 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
412 show_graphviz(HierarchyTree self, _ostream out)
413 show_graphviz(HierarchyTree self)
415 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
418 def get_graphviz_string(self):
419 """get_graphviz_string(HierarchyTree self) -> std::string"""
420 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
423 def add_edge(self, v0, v1):
424 """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)"""
425 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
428 def add_vertex(self, l):
429 """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
430 return _IMP_atom.HierarchyTree_add_vertex(self, l)
433 def remove_vertex(self, l):
434 """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
435 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
437 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
438 __del__ =
lambda self:
None
439 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
440 HierarchyTree_swigregister(HierarchyTree)
443 _value_types.append(
"HierarchyTree")
446 _object_types.append(
"PDBSelector")
449 def _object_cast_to_PDBSelector(o):
450 """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
451 return _IMP_atom._object_cast_to_PDBSelector(o)
454 return [Angle(x)
for x
in l]
455 _plural_types.append(
"Angles")
458 _value_types.append(
"Angle")
462 return [Atom(x)
for x
in l]
463 _plural_types.append(
"Atoms")
466 _value_types.append(
"Atom")
470 return [Bond(x)
for x
in l]
471 _plural_types.append(
"Bonds")
474 _value_types.append(
"Bond")
478 return [Bonded(x)
for x
in l]
479 _plural_types.append(
"Bondeds")
482 _value_types.append(
"Bonded")
485 def CHARMMAtomList(l=[]):
486 return [CHARMMAtom(x)
for x
in l]
487 _plural_types.append(
"CHARMMAtomList")
490 _value_types.append(
"CHARMMAtom")
494 return [Chain(x)
for x
in l]
495 _plural_types.append(
"Chains")
498 _value_types.append(
"Chain")
501 def CenterOfMasses(l=[]):
502 return [CenterOfMass(x)
for x
in l]
503 _plural_types.append(
"CenterOfMasses")
506 _value_types.append(
"CenterOfMass")
510 return [Charged(x)
for x
in l]
511 _plural_types.append(
"Chargeds")
514 _value_types.append(
"Charged")
517 def Diffusions(l=[]):
518 return [Diffusion(x)
for x
in l]
519 _plural_types.append(
"Diffusions")
522 _value_types.append(
"Diffusion")
525 def RigidBodyDiffusions(l=[]):
526 return [RigidBodyDiffusion(x)
for x
in l]
527 _plural_types.append(
"RigidBodyDiffusions")
530 _value_types.append(
"RigidBodyDiffusion")
533 def TAMDParticles(l=[]):
534 return [TAMDParticle(x)
for x
in l]
535 _plural_types.append(
"TAMDParticles")
538 _value_types.append(
"TAMDParticle")
541 def TAMDCentroids(l=[]):
542 return [TAMDCentroid(x)
for x
in l]
543 _plural_types.append(
"TAMDCentroids")
546 _value_types.append(
"TAMDCentroid")
550 return [Dihedral(x)
for x
in l]
551 _plural_types.append(
"Dihedrals")
554 _value_types.append(
"Dihedral")
558 return [Domain(x)
for x
in l]
559 _plural_types.append(
"Domains")
562 _value_types.append(
"Domain")
566 return [Fragment(x)
for x
in l]
567 _plural_types.append(
"Fragments")
570 _value_types.append(
"Fragment")
573 def Hierarchies(l=[]):
574 return [Hierarchy(x)
for x
in l]
575 _plural_types.append(
"Hierarchies")
578 _value_types.append(
"Hierarchy")
581 def LennardJonesList(l=[]):
582 return [LennardJones(x)
for x
in l]
583 _plural_types.append(
"LennardJonesList")
586 _value_types.append(
"LennardJones")
590 return [Mass(x)
for x
in l]
591 _plural_types.append(
"Masses")
594 _value_types.append(
"Mass")
597 def LinearVelocities(l=[]):
598 return [LinearVelocity(x)
for x
in l]
599 _plural_types.append(
"LinearVelocities")
602 _value_types.append(
"LinearVelocity")
605 def AngularVelocities(l=[]):
606 return [AngularVelocity(x)
for x
in l]
607 _plural_types.append(
"AngularVelocities")
610 _value_types.append(
"AngularVelocity")
614 return [Molecule(x)
for x
in l]
615 _plural_types.append(
"Molecules")
618 _value_types.append(
"Molecule")
622 return [Residue(x)
for x
in l]
623 _plural_types.append(
"Residues")
626 _value_types.append(
"Residue")
629 def Representations(l=[]):
630 return [Representation(x)
for x
in l]
631 _plural_types.append(
"Representations")
634 _value_types.append(
"Representation")
638 return [State(x)
for x
in l]
639 _plural_types.append(
"States")
642 _value_types.append(
"State")
646 return [Copy(x)
for x
in l]
647 _plural_types.append(
"Copies")
650 _value_types.append(
"Copy")
653 def SecondaryStructureResidues(l=[]):
654 return [SecondaryStructureResidue(x)
for x
in l]
655 _plural_types.append(
"SecondaryStructureResidues")
658 _value_types.append(
"SecondaryStructureResidue")
661 def StructureSources(l=[]):
662 return [StructureSource(x)
for x
in l]
663 _plural_types.append(
"StructureSources")
666 _value_types.append(
"StructureSource")
669 _object_types.append(
"Simulator")
672 def _object_cast_to_Simulator(o):
673 """_object_cast_to_Simulator(Object o) -> Simulator"""
674 return _IMP_atom._object_cast_to_Simulator(o)
676 _object_types.append(
"ATOMPDBSelector")
679 def _object_cast_to_ATOMPDBSelector(o):
680 """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
681 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
683 _object_types.append(
"AllMol2Selector")
686 def _object_cast_to_AllMol2Selector(o):
687 """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
688 return _IMP_atom._object_cast_to_AllMol2Selector(o)
690 _object_types.append(
"AllPDBSelector")
693 def _object_cast_to_AllPDBSelector(o):
694 """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
695 return _IMP_atom._object_cast_to_AllPDBSelector(o)
697 _object_types.append(
"AndPDBSelector")
700 def _object_cast_to_AndPDBSelector(o):
701 """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
702 return _IMP_atom._object_cast_to_AndPDBSelector(o)
704 _object_types.append(
"XorPDBSelector")
707 def _object_cast_to_XorPDBSelector(o):
708 """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
709 return _IMP_atom._object_cast_to_XorPDBSelector(o)
711 _object_types.append(
"ResidueTypePDBSelector")
714 def _object_cast_to_ResidueTypePDBSelector(o):
715 """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
716 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
718 _object_types.append(
"AtomTypePDBSelector")
721 def _object_cast_to_AtomTypePDBSelector(o):
722 """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
723 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
725 _object_types.append(
"AngleSingletonScore")
728 def _object_cast_to_AngleSingletonScore(o):
729 """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
730 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
732 _object_types.append(
"BondEndpointsRefiner")
735 def _object_cast_to_BondEndpointsRefiner(o):
736 """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
737 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
739 _object_types.append(
"BondPairContainer")
742 def _object_cast_to_BondPairContainer(o):
743 """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
744 return _IMP_atom._object_cast_to_BondPairContainer(o)
746 _object_types.append(
"BondSingletonScore")
749 def _object_cast_to_BondSingletonScore(o):
750 """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
751 return _IMP_atom._object_cast_to_BondSingletonScore(o)
753 _object_types.append(
"BondedPairFilter")
756 def _object_cast_to_BondedPairFilter(o):
757 """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
758 return _IMP_atom._object_cast_to_BondedPairFilter(o)
760 _object_types.append(
"BrownianDynamics")
763 def _object_cast_to_BrownianDynamics(o):
764 """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
765 return _IMP_atom._object_cast_to_BrownianDynamics(o)
767 _object_types.append(
"BrownianDynamicsTAMD")
770 def _object_cast_to_BrownianDynamicsTAMD(o):
771 """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
772 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
774 _object_types.append(
"CAlphaPDBSelector")
777 def _object_cast_to_CAlphaPDBSelector(o):
778 """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
779 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
781 _object_types.append(
"CBetaPDBSelector")
784 def _object_cast_to_CBetaPDBSelector(o):
785 """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
786 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
788 _object_types.append(
"BackbonePDBSelector")
791 def _object_cast_to_BackbonePDBSelector(o):
792 """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
793 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
795 _object_types.append(
"CHARMMParameters")
798 def _object_cast_to_CHARMMParameters(o):
799 """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
800 return _IMP_atom._object_cast_to_CHARMMParameters(o)
802 _object_types.append(
"CHARMMResidueTopology")
805 def _object_cast_to_CHARMMResidueTopology(o):
806 """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
807 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
809 _object_types.append(
"CHARMMSegmentTopology")
812 def _object_cast_to_CHARMMSegmentTopology(o):
813 """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
814 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
816 _object_types.append(
"CHARMMStereochemistryRestraint")
819 def _object_cast_to_CHARMMStereochemistryRestraint(o):
820 """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
821 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
823 _object_types.append(
"CHARMMTopology")
826 def _object_cast_to_CHARMMTopology(o):
827 """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
828 return _IMP_atom._object_cast_to_CHARMMTopology(o)
830 _object_types.append(
"CPDBSelector")
833 def _object_cast_to_CPDBSelector(o):
834 """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
835 return _IMP_atom._object_cast_to_CPDBSelector(o)
837 _object_types.append(
"ChainPDBSelector")
840 def _object_cast_to_ChainPDBSelector(o):
841 """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
842 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
844 _object_types.append(
"CoulombPairScore")
847 def _object_cast_to_CoulombPairScore(o):
848 """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
849 return _IMP_atom._object_cast_to_CoulombPairScore(o)
851 _object_types.append(
"CoverBond")
854 def _object_cast_to_CoverBond(o):
855 """_object_cast_to_CoverBond(Object o) -> CoverBond"""
856 return _IMP_atom._object_cast_to_CoverBond(o)
858 _object_types.append(
"DihedralSingletonScore")
861 def _object_cast_to_DihedralSingletonScore(o):
862 """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
863 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
865 _object_types.append(
"DopePairScore")
868 def _object_cast_to_DopePairScore(o):
869 """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
870 return _IMP_atom._object_cast_to_DopePairScore(o)
872 _object_types.append(
"LoopStatisticalPairScore")
875 def _object_cast_to_LoopStatisticalPairScore(o):
876 """_object_cast_to_LoopStatisticalPairScore(Object o) -> LoopStatisticalPairScore"""
877 return _IMP_atom._object_cast_to_LoopStatisticalPairScore(o)
879 _object_types.append(
"OrientedSoapPairScore")
882 def _object_cast_to_OrientedSoapPairScore(o):
883 """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
884 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
886 _object_types.append(
"EzRestraint")
889 def _object_cast_to_EzRestraint(o):
890 """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
891 return _IMP_atom._object_cast_to_EzRestraint(o)
893 _object_types.append(
"ForceFieldParameters")
896 def _object_cast_to_ForceFieldParameters(o):
897 """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
898 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
900 _object_types.append(
"ForceSwitch")
903 def _object_cast_to_ForceSwitch(o):
904 """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
905 return _IMP_atom._object_cast_to_ForceSwitch(o)
907 _object_types.append(
"HydrogenPDBSelector")
910 def _object_cast_to_HydrogenPDBSelector(o):
911 """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
912 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
914 _object_types.append(
"ImproperSingletonScore")
917 def _object_cast_to_ImproperSingletonScore(o):
918 """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
919 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
921 _object_types.append(
"LennardJonesPairScore")
924 def _object_cast_to_LennardJonesPairScore(o):
925 """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
926 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
928 _object_types.append(
"Mol2Selector")
931 def _object_cast_to_Mol2Selector(o):
932 """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
933 return _IMP_atom._object_cast_to_Mol2Selector(o)
935 _object_types.append(
"MolecularDynamics")
938 def _object_cast_to_MolecularDynamics(o):
939 """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
940 return _IMP_atom._object_cast_to_MolecularDynamics(o)
942 _object_types.append(
"NPDBSelector")
945 def _object_cast_to_NPDBSelector(o):
946 """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
947 return _IMP_atom._object_cast_to_NPDBSelector(o)
949 _object_types.append(
"NonAlternativePDBSelector")
952 def _object_cast_to_NonAlternativePDBSelector(o):
953 """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
954 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
956 _object_types.append(
"NonHydrogenMol2Selector")
959 def _object_cast_to_NonHydrogenMol2Selector(o):
960 """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
961 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
963 _object_types.append(
"NonHydrogenPDBSelector")
966 def _object_cast_to_NonHydrogenPDBSelector(o):
967 """_object_cast_to_NonHydrogenPDBSelector(Object o) -> NonHydrogenPDBSelector"""
968 return _IMP_atom._object_cast_to_NonHydrogenPDBSelector(o)
970 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
973 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
974 """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
975 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
977 _object_types.append(
"NonWaterPDBSelector")
980 def _object_cast_to_NonWaterPDBSelector(o):
981 """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
982 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
984 _object_types.append(
"NotPDBSelector")
987 def _object_cast_to_NotPDBSelector(o):
988 """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
989 return _IMP_atom._object_cast_to_NotPDBSelector(o)
991 _object_types.append(
"OrPDBSelector")
994 def _object_cast_to_OrPDBSelector(o):
995 """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
996 return _IMP_atom._object_cast_to_OrPDBSelector(o)
998 _object_types.append(
"PPDBSelector")
1001 def _object_cast_to_PPDBSelector(o):
1002 """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1003 return _IMP_atom._object_cast_to_PPDBSelector(o)
1005 _object_types.append(
"ProteinLigandAtomPairScore")
1008 def _object_cast_to_ProteinLigandAtomPairScore(o):
1009 """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1010 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1012 _object_types.append(
"ProteinLigandRestraint")
1015 def _object_cast_to_ProteinLigandRestraint(o):
1016 """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1017 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1019 _object_types.append(
"SameResiduePairFilter")
1022 def _object_cast_to_SameResiduePairFilter(o):
1023 """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1024 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1026 _object_types.append(
"SoapPairFilter")
1029 def _object_cast_to_SoapPairFilter(o):
1030 """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1031 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1033 _object_types.append(
"SmoothingFunction")
1036 def _object_cast_to_SmoothingFunction(o):
1037 """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1038 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1040 _object_types.append(
"StereochemistryPairFilter")
1043 def _object_cast_to_StereochemistryPairFilter(o):
1044 """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1045 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1047 _object_types.append(
"VelocityScalingOptimizerState")
1050 def _object_cast_to_VelocityScalingOptimizerState(o):
1051 """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1052 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1054 _object_types.append(
"WaterPDBSelector")
1057 def _object_cast_to_WaterPDBSelector(o):
1058 """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1059 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1061 _object_types.append(
"WritePDBOptimizerState")
1064 def _object_cast_to_WritePDBOptimizerState(o):
1065 """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1066 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1069 _plural_types.append(
"AtomTypes")
1070 _value_types.append(
"AtomType")
1073 CHARMMAtomTopologies=list
1074 _plural_types.append(
"CHARMMAtomTopologies")
1075 _value_types.append(
"CHARMMAtomTopology")
1078 CHARMMBondEndpoints=list
1079 _plural_types.append(
"CHARMMBondEndpoints")
1080 _value_types.append(
"CHARMMBondEndpoint")
1083 CHARMMBondParametersList=list
1084 _plural_types.append(
"CHARMMBondParametersList")
1085 _value_types.append(
"CHARMMBondParameters")
1088 CHARMMDihedralParametersList=list
1089 _plural_types.append(
"CHARMMDihedralParametersList")
1090 _value_types.append(
"CHARMMDihedralParameters")
1093 _object_types.append(
"CHARMMIdealResidueTopology")
1096 def _object_cast_to_CHARMMIdealResidueTopology(o):
1097 """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1098 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1100 CHARMMInternalCoordinates=list
1101 _plural_types.append(
"CHARMMInternalCoordinates")
1102 _value_types.append(
"CHARMMInternalCoordinate")
1105 _object_types.append(
"CHARMMPatch")
1108 def _object_cast_to_CHARMMPatch(o):
1109 """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1110 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1112 _object_types.append(
"CHARMMResidueTopologyBase")
1115 def _object_cast_to_CHARMMResidueTopologyBase(o):
1116 """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1117 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1120 _plural_types.append(
"ResidueTypes")
1121 _value_types.append(
"ResidueType")
1125 _plural_types.append(
"ChainTypes")
1126 _value_types.append(
"ChainType")
1130 _plural_types.append(
"Selections")
1131 _value_types.append(
"Selection")
1134 _object_types.append(
"RemoveRigidMotionOptimizerState")
1137 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1138 """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1139 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1141 _object_types.append(
"BerendsenThermostatOptimizerState")
1144 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1145 """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1146 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1148 _object_types.append(
"LangevinThermostatOptimizerState")
1151 def _object_cast_to_LangevinThermostatOptimizerState(o):
1152 """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1153 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1155 _object_types.append(
"SelectionGeometry")
1158 def _object_cast_to_SelectionGeometry(o):
1159 """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1160 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1162 _object_types.append(
"HierarchyGeometry")
1165 def _object_cast_to_HierarchyGeometry(o):
1166 """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1167 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1169 _object_types.append(
"HierarchiesGeometry")
1172 def _object_cast_to_HierarchiesGeometry(o):
1173 """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1174 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1176 _object_types.append(
"BondGeometry")
1179 def _object_cast_to_BondGeometry(o):
1180 """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1181 return _IMP_atom._object_cast_to_BondGeometry(o)
1183 _object_types.append(
"BondsGeometry")
1186 def _object_cast_to_BondsGeometry(o):
1187 """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1188 return _IMP_atom._object_cast_to_BondsGeometry(o)
1190 _object_types.append(
"CAAngleRestraint")
1193 def _object_cast_to_CAAngleRestraint(o):
1194 """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1195 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1197 _object_types.append(
"CADihedralRestraint")
1200 def _object_cast_to_CADihedralRestraint(o):
1201 """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1202 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1204 _object_types.append(
"HelixRestraint")
1207 def _object_cast_to_HelixRestraint(o):
1208 """_object_cast_to_HelixRestraint(Object o) -> HelixRestraint"""
1209 return _IMP_atom._object_cast_to_HelixRestraint(o)
1211 CHARMMDihedrals=list
1212 _plural_types.append(
"CHARMMDihedrals")
1213 _value_types.append(
"CHARMMDihedral")
1217 _plural_types.append(
"CHARMMBonds")
1218 _value_types.append(
"CHARMMBond")
1222 _plural_types.append(
"CHARMMAngles")
1223 _value_types.append(
"CHARMMAngle")
1226 """Proxy of C++ IMP::atom::Bond class."""
1228 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1230 def __init__(self, *args):
1232 __init__(IMP::atom::Bond self) -> Bond
1233 __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1234 __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1236 this = _IMP_atom.new_Bond(*args)
1238 self.this.append(this)
1239 except __builtin__.Exception:
1242 def show(self, *args):
1244 show(Bond self, _ostream out)
1247 return _IMP_atom.Bond_show(self, *args)
1250 def get_is_setup(*args):
1252 get_is_setup(_ParticleAdaptor p) -> bool
1253 get_is_setup(Model m, ParticleIndex pi) -> bool
1255 return _IMP_atom.Bond_get_is_setup(*args)
1257 get_is_setup = staticmethod(get_is_setup)
1258 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1259 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1260 SINGLE = _IMP_atom.Bond_SINGLE
1261 DOUBLE = _IMP_atom.Bond_DOUBLE
1262 TRIPLE = _IMP_atom.Bond_TRIPLE
1263 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1264 SALT = _IMP_atom.Bond_SALT
1265 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1266 AMIDE = _IMP_atom.Bond_AMIDE
1267 AROMATIC = _IMP_atom.Bond_AROMATIC
1269 def get_bonded(self, i):
1270 """get_bonded(Bond self, unsigned int i) -> Bonded"""
1271 return _IMP_atom.Bond_get_bonded(self, i)
1275 """get_type(Bond self) -> IMP::Int"""
1276 return _IMP_atom.Bond_get_type(self)
1279 def set_type(self, t):
1280 """set_type(Bond self, IMP::Int t)"""
1281 return _IMP_atom.Bond_set_type(self, t)
1285 """get_order(Bond self) -> IMP::Int"""
1286 return _IMP_atom.Bond_get_order(self)
1289 def set_order(self, t):
1290 """set_order(Bond self, IMP::Int t)"""
1291 return _IMP_atom.Bond_set_order(self, t)
1294 def get_length(self):
1295 """get_length(Bond self) -> IMP::Float"""
1296 return _IMP_atom.Bond_get_length(self)
1299 def set_length(self, t):
1300 """set_length(Bond self, IMP::Float t)"""
1301 return _IMP_atom.Bond_set_length(self, t)
1304 def get_stiffness(self):
1305 """get_stiffness(Bond self) -> IMP::Float"""
1306 return _IMP_atom.Bond_get_stiffness(self)
1309 def set_stiffness(self, t):
1310 """set_stiffness(Bond self, IMP::Float t)"""
1311 return _IMP_atom.Bond_set_stiffness(self, t)
1314 def get_length_key():
1315 """get_length_key() -> FloatKey"""
1316 return _IMP_atom.Bond_get_length_key()
1318 get_length_key = staticmethod(get_length_key)
1320 def add_attribute(self, *args):
1322 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1323 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1324 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1325 add_attribute(Bond self, FloatsKey a0, IMP::Floats a1)
1326 add_attribute(Bond self, IntsKey a0, IMP::Ints a1)
1327 add_attribute(Bond self, StringKey a0, IMP::String a1)
1328 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1329 add_attribute(Bond self, ObjectKey a0, Object a1)
1331 return _IMP_atom.Bond_add_attribute(self, *args)
1334 def get_value(self, *args):
1336 get_value(Bond self, FloatKey a0) -> IMP::Float
1337 get_value(Bond self, IntKey a0) -> IMP::Int
1338 get_value(Bond self, FloatsKey a0) -> IMP::Floats
1339 get_value(Bond self, IntsKey a0) -> IMP::Ints
1340 get_value(Bond self, StringKey a0) -> IMP::String
1341 get_value(Bond self, ParticleIndexKey a0) -> Particle
1342 get_value(Bond self, ObjectKey a0) -> Object
1344 return _IMP_atom.Bond_get_value(self, *args)
1347 def set_value(self, *args):
1349 set_value(Bond self, FloatKey a0, IMP::Float a1)
1350 set_value(Bond self, IntKey a0, IMP::Int a1)
1351 set_value(Bond self, FloatsKey a0, IMP::Floats a1)
1352 set_value(Bond self, IntsKey a0, IMP::Ints a1)
1353 set_value(Bond self, StringKey a0, IMP::String a1)
1354 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1355 set_value(Bond self, ObjectKey a0, Object a1)
1357 return _IMP_atom.Bond_set_value(self, *args)
1360 def remove_attribute(self, *args):
1362 remove_attribute(Bond self, FloatKey a0)
1363 remove_attribute(Bond self, IntKey a0)
1364 remove_attribute(Bond self, FloatsKey a0)
1365 remove_attribute(Bond self, IntsKey a0)
1366 remove_attribute(Bond self, StringKey a0)
1367 remove_attribute(Bond self, ParticleIndexKey a0)
1368 remove_attribute(Bond self, ObjectKey a0)
1370 return _IMP_atom.Bond_remove_attribute(self, *args)
1373 def has_attribute(self, *args):
1375 has_attribute(Bond self, FloatKey a0) -> bool
1376 has_attribute(Bond self, IntKey a0) -> bool
1377 has_attribute(Bond self, FloatsKey a0) -> bool
1378 has_attribute(Bond self, IntsKey a0) -> bool
1379 has_attribute(Bond self, StringKey a0) -> bool
1380 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1381 has_attribute(Bond self, ObjectKey a0) -> bool
1383 return _IMP_atom.Bond_has_attribute(self, *args)
1386 def get_derivative(self, a0):
1387 """get_derivative(Bond self, FloatKey a0) -> double"""
1388 return _IMP_atom.Bond_get_derivative(self, a0)
1392 """get_name(Bond self) -> std::string"""
1393 return _IMP_atom.Bond_get_name(self)
1396 def clear_caches(self):
1397 """clear_caches(Bond self)"""
1398 return _IMP_atom.Bond_clear_caches(self)
1401 def set_name(self, a0):
1402 """set_name(Bond self, std::string a0)"""
1403 return _IMP_atom.Bond_set_name(self, a0)
1407 """set_check_level(Bond self, IMP::CheckLevel a0)"""
1408 return _IMP_atom.Bond_set_check_level(self, a0)
1411 def add_to_derivative(self, a0, a1, a2):
1412 """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1413 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1416 def set_is_optimized(self, a0, a1):
1417 """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1418 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1421 def get_is_optimized(self, a0):
1422 """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1423 return _IMP_atom.Bond_get_is_optimized(self, a0)
1427 """get_check_level(Bond self) -> IMP::CheckLevel"""
1428 return _IMP_atom.Bond_get_check_level(self)
1431 def __eq__(self, *args):
1433 __eq__(Bond self, Bond o) -> bool
1434 __eq__(Bond self, Particle d) -> bool
1436 return _IMP_atom.Bond___eq__(self, *args)
1439 def __ne__(self, *args):
1441 __ne__(Bond self, Bond o) -> bool
1442 __ne__(Bond self, Particle d) -> bool
1444 return _IMP_atom.Bond___ne__(self, *args)
1447 def __le__(self, *args):
1449 __le__(Bond self, Bond o) -> bool
1450 __le__(Bond self, Particle d) -> bool
1452 return _IMP_atom.Bond___le__(self, *args)
1455 def __lt__(self, *args):
1457 __lt__(Bond self, Bond o) -> bool
1458 __lt__(Bond self, Particle d) -> bool
1460 return _IMP_atom.Bond___lt__(self, *args)
1463 def __ge__(self, *args):
1465 __ge__(Bond self, Bond o) -> bool
1466 __ge__(Bond self, Particle d) -> bool
1468 return _IMP_atom.Bond___ge__(self, *args)
1471 def __gt__(self, *args):
1473 __gt__(Bond self, Bond o) -> bool
1474 __gt__(Bond self, Particle d) -> bool
1476 return _IMP_atom.Bond___gt__(self, *args)
1480 """__hash__(Bond self) -> std::size_t"""
1481 return _IMP_atom.Bond___hash__(self)
1485 """__str__(Bond self) -> std::string"""
1486 return _IMP_atom.Bond___str__(self)
1490 """__repr__(Bond self) -> std::string"""
1491 return _IMP_atom.Bond___repr__(self)
1493 __swig_destroy__ = _IMP_atom.delete_Bond
1494 __del__ =
lambda self:
None
1495 Bond_swigregister = _IMP_atom.Bond_swigregister
1496 Bond_swigregister(Bond)
1498 def Bond_get_is_setup(*args):
1500 get_is_setup(_ParticleAdaptor p) -> bool
1501 Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1503 return _IMP_atom.Bond_get_is_setup(*args)
1505 def Bond_get_length_key():
1506 """Bond_get_length_key() -> FloatKey"""
1507 return _IMP_atom.Bond_get_length_key()
1510 """Proxy of C++ IMP::atom::Bonded class."""
1512 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1514 def __init__(self, *args):
1516 __init__(IMP::atom::Bonded self) -> Bonded
1517 __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1518 __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1520 this = _IMP_atom.new_Bonded(*args)
1522 self.this.append(this)
1523 except __builtin__.Exception:
1526 def show(self, *args):
1528 show(Bonded self, _ostream out)
1531 return _IMP_atom.Bonded_show(self, *args)
1534 def setup_particle(*args):
1536 setup_particle(Model m, ParticleIndex pi) -> Bonded
1537 setup_particle(_ParticleAdaptor decorator) -> Bonded
1539 return _IMP_atom.Bonded_setup_particle(*args)
1541 setup_particle = staticmethod(setup_particle)
1543 def get_is_setup(*args):
1545 get_is_setup(_ParticleAdaptor p) -> bool
1546 get_is_setup(Model m, ParticleIndex pi) -> bool
1548 return _IMP_atom.Bonded_get_is_setup(*args)
1550 get_is_setup = staticmethod(get_is_setup)
1552 def get_number_of_bonds(self):
1553 """get_number_of_bonds(Bonded self) -> unsigned int"""
1554 return _IMP_atom.Bonded_get_number_of_bonds(self)
1557 def get_bond_indexes(self):
1558 """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1559 return _IMP_atom.Bonded_get_bond_indexes(self)
1563 """get_bond(Bonded self, unsigned int i) -> Bond"""
1564 return _IMP_atom.Bonded_get_bond(self, i)
1567 def get_bonded(self, i):
1568 """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1569 return _IMP_atom.Bonded_get_bonded(self, i)
1572 def add_attribute(self, *args):
1574 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1575 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1576 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1577 add_attribute(Bonded self, FloatsKey a0, IMP::Floats a1)
1578 add_attribute(Bonded self, IntsKey a0, IMP::Ints a1)
1579 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1580 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1581 add_attribute(Bonded self, ObjectKey a0, Object a1)
1583 return _IMP_atom.Bonded_add_attribute(self, *args)
1586 def get_value(self, *args):
1588 get_value(Bonded self, FloatKey a0) -> IMP::Float
1589 get_value(Bonded self, IntKey a0) -> IMP::Int
1590 get_value(Bonded self, FloatsKey a0) -> IMP::Floats
1591 get_value(Bonded self, IntsKey a0) -> IMP::Ints
1592 get_value(Bonded self, StringKey a0) -> IMP::String
1593 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1594 get_value(Bonded self, ObjectKey a0) -> Object
1596 return _IMP_atom.Bonded_get_value(self, *args)
1599 def set_value(self, *args):
1601 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1602 set_value(Bonded self, IntKey a0, IMP::Int a1)
1603 set_value(Bonded self, FloatsKey a0, IMP::Floats a1)
1604 set_value(Bonded self, IntsKey a0, IMP::Ints a1)
1605 set_value(Bonded self, StringKey a0, IMP::String a1)
1606 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1607 set_value(Bonded self, ObjectKey a0, Object a1)
1609 return _IMP_atom.Bonded_set_value(self, *args)
1612 def remove_attribute(self, *args):
1614 remove_attribute(Bonded self, FloatKey a0)
1615 remove_attribute(Bonded self, IntKey a0)
1616 remove_attribute(Bonded self, FloatsKey a0)
1617 remove_attribute(Bonded self, IntsKey a0)
1618 remove_attribute(Bonded self, StringKey a0)
1619 remove_attribute(Bonded self, ParticleIndexKey a0)
1620 remove_attribute(Bonded self, ObjectKey a0)
1622 return _IMP_atom.Bonded_remove_attribute(self, *args)
1625 def has_attribute(self, *args):
1627 has_attribute(Bonded self, FloatKey a0) -> bool
1628 has_attribute(Bonded self, IntKey a0) -> bool
1629 has_attribute(Bonded self, FloatsKey a0) -> bool
1630 has_attribute(Bonded self, IntsKey a0) -> bool
1631 has_attribute(Bonded self, StringKey a0) -> bool
1632 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1633 has_attribute(Bonded self, ObjectKey a0) -> bool
1635 return _IMP_atom.Bonded_has_attribute(self, *args)
1638 def get_derivative(self, a0):
1639 """get_derivative(Bonded self, FloatKey a0) -> double"""
1640 return _IMP_atom.Bonded_get_derivative(self, a0)
1644 """get_name(Bonded self) -> std::string"""
1645 return _IMP_atom.Bonded_get_name(self)
1648 def clear_caches(self):
1649 """clear_caches(Bonded self)"""
1650 return _IMP_atom.Bonded_clear_caches(self)
1653 def set_name(self, a0):
1654 """set_name(Bonded self, std::string a0)"""
1655 return _IMP_atom.Bonded_set_name(self, a0)
1659 """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1660 return _IMP_atom.Bonded_set_check_level(self, a0)
1663 def add_to_derivative(self, a0, a1, a2):
1664 """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1665 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1668 def set_is_optimized(self, a0, a1):
1669 """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1670 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1673 def get_is_optimized(self, a0):
1674 """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1675 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1679 """get_check_level(Bonded self) -> IMP::CheckLevel"""
1680 return _IMP_atom.Bonded_get_check_level(self)
1683 def __eq__(self, *args):
1685 __eq__(Bonded self, Bonded o) -> bool
1686 __eq__(Bonded self, Particle d) -> bool
1688 return _IMP_atom.Bonded___eq__(self, *args)
1691 def __ne__(self, *args):
1693 __ne__(Bonded self, Bonded o) -> bool
1694 __ne__(Bonded self, Particle d) -> bool
1696 return _IMP_atom.Bonded___ne__(self, *args)
1699 def __le__(self, *args):
1701 __le__(Bonded self, Bonded o) -> bool
1702 __le__(Bonded self, Particle d) -> bool
1704 return _IMP_atom.Bonded___le__(self, *args)
1707 def __lt__(self, *args):
1709 __lt__(Bonded self, Bonded o) -> bool
1710 __lt__(Bonded self, Particle d) -> bool
1712 return _IMP_atom.Bonded___lt__(self, *args)
1715 def __ge__(self, *args):
1717 __ge__(Bonded self, Bonded o) -> bool
1718 __ge__(Bonded self, Particle d) -> bool
1720 return _IMP_atom.Bonded___ge__(self, *args)
1723 def __gt__(self, *args):
1725 __gt__(Bonded self, Bonded o) -> bool
1726 __gt__(Bonded self, Particle d) -> bool
1728 return _IMP_atom.Bonded___gt__(self, *args)
1732 """__hash__(Bonded self) -> std::size_t"""
1733 return _IMP_atom.Bonded___hash__(self)
1737 """__str__(Bonded self) -> std::string"""
1738 return _IMP_atom.Bonded___str__(self)
1742 """__repr__(Bonded self) -> std::string"""
1743 return _IMP_atom.Bonded___repr__(self)
1745 __swig_destroy__ = _IMP_atom.delete_Bonded
1746 __del__ =
lambda self:
None
1747 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1748 Bonded_swigregister(Bonded)
1750 def Bonded_setup_particle(*args):
1752 setup_particle(Model m, ParticleIndex pi) -> Bonded
1753 Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1755 return _IMP_atom.Bonded_setup_particle(*args)
1757 def Bonded_get_is_setup(*args):
1759 get_is_setup(_ParticleAdaptor p) -> bool
1760 Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1762 return _IMP_atom.Bonded_get_is_setup(*args)
1767 create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1768 create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1770 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1774 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1775 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1777 return _IMP_atom.create_bond(*args)
1780 """destroy_bond(Bond b)"""
1781 return _IMP_atom.destroy_bond(b)
1784 """get_bond(Bonded a, Bonded b) -> Bond"""
1785 return _IMP_atom.get_bond(a, b)
1787 """Proxy of C++ IMP::atom::BondGeometry class."""
1789 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1791 def __init__(self, *args):
1793 __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1794 __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1796 this = _IMP_atom.new_BondGeometry(*args)
1798 self.this.append(this)
1799 except __builtin__.Exception:
1802 def get_version_info(self):
1803 """get_version_info(BondGeometry self) -> VersionInfo"""
1804 return _IMP_atom.BondGeometry_get_version_info(self)
1808 """__str__(BondGeometry self) -> std::string"""
1809 return _IMP_atom.BondGeometry___str__(self)
1813 """__repr__(BondGeometry self) -> std::string"""
1814 return _IMP_atom.BondGeometry___repr__(self)
1819 return _object_cast_to_BondGeometry(o)
1821 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1822 BondGeometry_swigregister(BondGeometry)
1825 """Proxy of C++ IMP::atom::BondsGeometry class."""
1827 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1829 def __init__(self, sc):
1830 """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1831 this = _IMP_atom.new_BondsGeometry(sc)
1833 self.this.append(this)
1834 except __builtin__.Exception:
1837 def get_version_info(self):
1838 """get_version_info(BondsGeometry self) -> VersionInfo"""
1839 return _IMP_atom.BondsGeometry_get_version_info(self)
1843 """__str__(BondsGeometry self) -> std::string"""
1844 return _IMP_atom.BondsGeometry___str__(self)
1848 """__repr__(BondsGeometry self) -> std::string"""
1849 return _IMP_atom.BondsGeometry___repr__(self)
1854 return _object_cast_to_BondsGeometry(o)
1856 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1857 BondsGeometry_swigregister(BondsGeometry)
1860 """Proxy of C++ IMP::atom::Hierarchy class."""
1862 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1864 def __init__(self, *args):
1866 __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1867 __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1868 __init__(IMP::atom::Hierarchy self) -> Hierarchy
1869 __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1871 this = _IMP_atom.new_Hierarchy(*args)
1873 self.this.append(this)
1874 except __builtin__.Exception:
1877 def setup_particle(*args):
1879 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1880 setup_particle(Particle p) -> Hierarchy
1881 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1882 setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1884 return _IMP_atom.Hierarchy_setup_particle(*args)
1886 setup_particle = staticmethod(setup_particle)
1888 def get_is_setup(*args):
1890 get_is_setup(Particle p) -> bool
1891 get_is_setup(Model m, ParticleIndex p) -> bool
1893 return _IMP_atom.Hierarchy_get_is_setup(*args)
1895 get_is_setup = staticmethod(get_is_setup)
1897 def get_is_valid(self, print_info=False):
1899 get_is_valid(Hierarchy self, bool print_info=False) -> bool
1900 get_is_valid(Hierarchy self) -> bool
1902 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
1905 def add_child(self, o):
1906 """add_child(Hierarchy self, Hierarchy o)"""
1907 return _IMP_atom.Hierarchy_add_child(self, o)
1910 def get_child(self, i):
1911 """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
1912 return _IMP_atom.Hierarchy_get_child(self, i)
1915 def get_children(self):
1916 """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
1917 return _IMP_atom.Hierarchy_get_children(self)
1920 def get_parent(self):
1921 """get_parent(Hierarchy self) -> Hierarchy"""
1922 return _IMP_atom.Hierarchy_get_parent(self)
1926 """get_traits() -> HierarchyTraits"""
1927 return _IMP_atom.Hierarchy_get_traits()
1929 get_traits = staticmethod(get_traits)
1931 def show(self, *args):
1933 show(Hierarchy self, _ostream out, std::string delimiter)
1934 show(Hierarchy self, _ostream out)
1935 show(Hierarchy self)
1937 return _IMP_atom.Hierarchy_show(self, *args)
1940 def add_attribute(self, *args):
1942 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
1943 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
1944 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
1945 add_attribute(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1946 add_attribute(Hierarchy self, IntsKey a0, IMP::Ints a1)
1947 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
1948 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
1949 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
1951 return _IMP_atom.Hierarchy_add_attribute(self, *args)
1954 def get_value(self, *args):
1956 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
1957 get_value(Hierarchy self, IntKey a0) -> IMP::Int
1958 get_value(Hierarchy self, FloatsKey a0) -> IMP::Floats
1959 get_value(Hierarchy self, IntsKey a0) -> IMP::Ints
1960 get_value(Hierarchy self, StringKey a0) -> IMP::String
1961 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
1962 get_value(Hierarchy self, ObjectKey a0) -> Object
1964 return _IMP_atom.Hierarchy_get_value(self, *args)
1967 def set_value(self, *args):
1969 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
1970 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
1971 set_value(Hierarchy self, FloatsKey a0, IMP::Floats a1)
1972 set_value(Hierarchy self, IntsKey a0, IMP::Ints a1)
1973 set_value(Hierarchy self, StringKey a0, IMP::String a1)
1974 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
1975 set_value(Hierarchy self, ObjectKey a0, Object a1)
1977 return _IMP_atom.Hierarchy_set_value(self, *args)
1980 def remove_attribute(self, *args):
1982 remove_attribute(Hierarchy self, FloatKey a0)
1983 remove_attribute(Hierarchy self, IntKey a0)
1984 remove_attribute(Hierarchy self, FloatsKey a0)
1985 remove_attribute(Hierarchy self, IntsKey a0)
1986 remove_attribute(Hierarchy self, StringKey a0)
1987 remove_attribute(Hierarchy self, ParticleIndexKey a0)
1988 remove_attribute(Hierarchy self, ObjectKey a0)
1990 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
1993 def has_attribute(self, *args):
1995 has_attribute(Hierarchy self, FloatKey a0) -> bool
1996 has_attribute(Hierarchy self, IntKey a0) -> bool
1997 has_attribute(Hierarchy self, FloatsKey a0) -> bool
1998 has_attribute(Hierarchy self, IntsKey a0) -> bool
1999 has_attribute(Hierarchy self, StringKey a0) -> bool
2000 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2001 has_attribute(Hierarchy self, ObjectKey a0) -> bool
2003 return _IMP_atom.Hierarchy_has_attribute(self, *args)
2006 def get_derivative(self, a0):
2007 """get_derivative(Hierarchy self, FloatKey a0) -> double"""
2008 return _IMP_atom.Hierarchy_get_derivative(self, a0)
2012 """get_name(Hierarchy self) -> std::string"""
2013 return _IMP_atom.Hierarchy_get_name(self)
2016 def clear_caches(self):
2017 """clear_caches(Hierarchy self)"""
2018 return _IMP_atom.Hierarchy_clear_caches(self)
2021 def set_name(self, a0):
2022 """set_name(Hierarchy self, std::string a0)"""
2023 return _IMP_atom.Hierarchy_set_name(self, a0)
2027 """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2028 return _IMP_atom.Hierarchy_set_check_level(self, a0)
2031 def add_to_derivative(self, a0, a1, a2):
2032 """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2033 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2036 def set_is_optimized(self, a0, a1):
2037 """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2038 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2041 def get_is_optimized(self, a0):
2042 """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2043 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2047 """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2048 return _IMP_atom.Hierarchy_get_check_level(self)
2051 def __eq__(self, *args):
2053 __eq__(Hierarchy self, Hierarchy o) -> bool
2054 __eq__(Hierarchy self, Particle d) -> bool
2056 return _IMP_atom.Hierarchy___eq__(self, *args)
2059 def __ne__(self, *args):
2061 __ne__(Hierarchy self, Hierarchy o) -> bool
2062 __ne__(Hierarchy self, Particle d) -> bool
2064 return _IMP_atom.Hierarchy___ne__(self, *args)
2067 def __le__(self, *args):
2069 __le__(Hierarchy self, Hierarchy o) -> bool
2070 __le__(Hierarchy self, Particle d) -> bool
2072 return _IMP_atom.Hierarchy___le__(self, *args)
2075 def __lt__(self, *args):
2077 __lt__(Hierarchy self, Hierarchy o) -> bool
2078 __lt__(Hierarchy self, Particle d) -> bool
2080 return _IMP_atom.Hierarchy___lt__(self, *args)
2083 def __ge__(self, *args):
2085 __ge__(Hierarchy self, Hierarchy o) -> bool
2086 __ge__(Hierarchy self, Particle d) -> bool
2088 return _IMP_atom.Hierarchy___ge__(self, *args)
2091 def __gt__(self, *args):
2093 __gt__(Hierarchy self, Hierarchy o) -> bool
2094 __gt__(Hierarchy self, Particle d) -> bool
2096 return _IMP_atom.Hierarchy___gt__(self, *args)
2100 """__hash__(Hierarchy self) -> std::size_t"""
2101 return _IMP_atom.Hierarchy___hash__(self)
2105 """__str__(Hierarchy self) -> std::string"""
2106 return _IMP_atom.Hierarchy___str__(self)
2110 """__repr__(Hierarchy self) -> std::string"""
2111 return _IMP_atom.Hierarchy___repr__(self)
2113 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2114 __del__ =
lambda self:
None
2115 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2116 Hierarchy_swigregister(Hierarchy)
2118 def Hierarchy_setup_particle(*args):
2120 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2121 setup_particle(Particle p) -> Hierarchy
2122 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2123 Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2125 return _IMP_atom.Hierarchy_setup_particle(*args)
2127 def Hierarchy_get_is_setup(*args):
2129 get_is_setup(Particle p) -> bool
2130 Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2132 return _IMP_atom.Hierarchy_get_is_setup(*args)
2134 def Hierarchy_get_traits():
2135 """Hierarchy_get_traits() -> HierarchyTraits"""
2136 return _IMP_atom.Hierarchy_get_traits()
2138 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2139 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2140 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2141 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2142 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2143 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2144 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2145 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2146 MASS_TYPE = _IMP_atom.MASS_TYPE
2147 STATE_TYPE = _IMP_atom.STATE_TYPE
2149 def get_by_type(mhd, t):
2150 """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2151 return _IMP_atom.get_by_type(mhd, t)
2153 def create_fragment(ps):
2154 """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2155 return _IMP_atom.create_fragment(ps)
2157 def get_internal_bonds(mhd):
2158 """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2159 return _IMP_atom.get_internal_bonds(mhd)
2162 """get_root(Hierarchy h) -> Hierarchy"""
2163 return _IMP_atom.get_root(h)
2167 show(Hierarchy h, _ostream out)
2170 return _IMP_atom.show(*args)
2174 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2175 create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2176 create_rigid_body(Hierarchy h) -> RigidBody
2178 return _IMP_atom.create_rigid_body(*args)
2181 """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2182 return _IMP_atom.create_compatible_rigid_body(h, reference)
2184 def get_is_heterogen(h):
2185 """get_is_heterogen(Hierarchy h) -> bool"""
2186 return _IMP_atom.get_is_heterogen(h)
2189 """create_clone(Hierarchy d) -> Hierarchy"""
2190 return _IMP_atom.create_clone(d)
2192 def create_clone_one(d):
2193 """create_clone_one(Hierarchy d) -> Hierarchy"""
2194 return _IMP_atom.create_clone_one(d)
2197 """destroy(Hierarchy d)"""
2198 return _IMP_atom.destroy(d)
2200 def get_bounding_box(h):
2201 """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2202 return _IMP_atom.get_bounding_box(h)
2204 def get_bounding_sphere(h):
2205 """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2206 return _IMP_atom.get_bounding_sphere(h)
2208 """Proxy of C++ IMP::atom::Angle class."""
2210 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2212 def __init__(self, *args):
2214 __init__(IMP::atom::Angle self) -> Angle
2215 __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2216 __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2218 this = _IMP_atom.new_Angle(*args)
2220 self.this.append(this)
2221 except __builtin__.Exception:
2224 def show(self, *args):
2226 show(Angle self, _ostream out)
2229 return _IMP_atom.Angle_show(self, *args)
2232 def setup_particle(*args):
2234 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2235 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2237 return _IMP_atom.Angle_setup_particle(*args)
2239 setup_particle = staticmethod(setup_particle)
2241 def get_is_setup(*args):
2243 get_is_setup(_ParticleAdaptor p) -> bool
2244 get_is_setup(Model m, ParticleIndex pi) -> bool
2246 return _IMP_atom.Angle_get_is_setup(*args)
2248 get_is_setup = staticmethod(get_is_setup)
2250 def get_particle(self, *args):
2252 get_particle(Angle self) -> Particle
2253 get_particle(Angle self, unsigned int i) -> Particle
2255 return _IMP_atom.Angle_get_particle(self, *args)
2258 def get_ideal(self):
2259 """get_ideal(Angle self) -> IMP::Float"""
2260 return _IMP_atom.Angle_get_ideal(self)
2263 def set_ideal(self, t):
2264 """set_ideal(Angle self, IMP::Float t)"""
2265 return _IMP_atom.Angle_set_ideal(self, t)
2268 def get_stiffness(self):
2269 """get_stiffness(Angle self) -> IMP::Float"""
2270 return _IMP_atom.Angle_get_stiffness(self)
2273 def set_stiffness(self, t):
2274 """set_stiffness(Angle self, IMP::Float t)"""
2275 return _IMP_atom.Angle_set_stiffness(self, t)
2278 def get_particle_key(i):
2279 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2280 return _IMP_atom.Angle_get_particle_key(i)
2282 get_particle_key = staticmethod(get_particle_key)
2284 def get_ideal_key():
2285 """get_ideal_key() -> FloatKey"""
2286 return _IMP_atom.Angle_get_ideal_key()
2288 get_ideal_key = staticmethod(get_ideal_key)
2290 def get_stiffness_key():
2291 """get_stiffness_key() -> FloatKey"""
2292 return _IMP_atom.Angle_get_stiffness_key()
2294 get_stiffness_key = staticmethod(get_stiffness_key)
2296 def add_attribute(self, *args):
2298 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2299 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2300 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2301 add_attribute(Angle self, FloatsKey a0, IMP::Floats a1)
2302 add_attribute(Angle self, IntsKey a0, IMP::Ints a1)
2303 add_attribute(Angle self, StringKey a0, IMP::String a1)
2304 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2305 add_attribute(Angle self, ObjectKey a0, Object a1)
2307 return _IMP_atom.Angle_add_attribute(self, *args)
2310 def get_value(self, *args):
2312 get_value(Angle self, FloatKey a0) -> IMP::Float
2313 get_value(Angle self, IntKey a0) -> IMP::Int
2314 get_value(Angle self, FloatsKey a0) -> IMP::Floats
2315 get_value(Angle self, IntsKey a0) -> IMP::Ints
2316 get_value(Angle self, StringKey a0) -> IMP::String
2317 get_value(Angle self, ParticleIndexKey a0) -> Particle
2318 get_value(Angle self, ObjectKey a0) -> Object
2320 return _IMP_atom.Angle_get_value(self, *args)
2323 def set_value(self, *args):
2325 set_value(Angle self, FloatKey a0, IMP::Float a1)
2326 set_value(Angle self, IntKey a0, IMP::Int a1)
2327 set_value(Angle self, FloatsKey a0, IMP::Floats a1)
2328 set_value(Angle self, IntsKey a0, IMP::Ints a1)
2329 set_value(Angle self, StringKey a0, IMP::String a1)
2330 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2331 set_value(Angle self, ObjectKey a0, Object a1)
2333 return _IMP_atom.Angle_set_value(self, *args)
2336 def remove_attribute(self, *args):
2338 remove_attribute(Angle self, FloatKey a0)
2339 remove_attribute(Angle self, IntKey a0)
2340 remove_attribute(Angle self, FloatsKey a0)
2341 remove_attribute(Angle self, IntsKey a0)
2342 remove_attribute(Angle self, StringKey a0)
2343 remove_attribute(Angle self, ParticleIndexKey a0)
2344 remove_attribute(Angle self, ObjectKey a0)
2346 return _IMP_atom.Angle_remove_attribute(self, *args)
2349 def has_attribute(self, *args):
2351 has_attribute(Angle self, FloatKey a0) -> bool
2352 has_attribute(Angle self, IntKey a0) -> bool
2353 has_attribute(Angle self, FloatsKey a0) -> bool
2354 has_attribute(Angle self, IntsKey a0) -> bool
2355 has_attribute(Angle self, StringKey a0) -> bool
2356 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2357 has_attribute(Angle self, ObjectKey a0) -> bool
2359 return _IMP_atom.Angle_has_attribute(self, *args)
2362 def get_derivative(self, a0):
2363 """get_derivative(Angle self, FloatKey a0) -> double"""
2364 return _IMP_atom.Angle_get_derivative(self, a0)
2368 """get_name(Angle self) -> std::string"""
2369 return _IMP_atom.Angle_get_name(self)
2372 def clear_caches(self):
2373 """clear_caches(Angle self)"""
2374 return _IMP_atom.Angle_clear_caches(self)
2377 def set_name(self, a0):
2378 """set_name(Angle self, std::string a0)"""
2379 return _IMP_atom.Angle_set_name(self, a0)
2383 """set_check_level(Angle self, IMP::CheckLevel a0)"""
2384 return _IMP_atom.Angle_set_check_level(self, a0)
2387 def add_to_derivative(self, a0, a1, a2):
2388 """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2389 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2392 def set_is_optimized(self, a0, a1):
2393 """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2394 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2397 def get_is_optimized(self, a0):
2398 """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2399 return _IMP_atom.Angle_get_is_optimized(self, a0)
2403 """get_check_level(Angle self) -> IMP::CheckLevel"""
2404 return _IMP_atom.Angle_get_check_level(self)
2407 def __eq__(self, *args):
2409 __eq__(Angle self, Angle o) -> bool
2410 __eq__(Angle self, Particle d) -> bool
2412 return _IMP_atom.Angle___eq__(self, *args)
2415 def __ne__(self, *args):
2417 __ne__(Angle self, Angle o) -> bool
2418 __ne__(Angle self, Particle d) -> bool
2420 return _IMP_atom.Angle___ne__(self, *args)
2423 def __le__(self, *args):
2425 __le__(Angle self, Angle o) -> bool
2426 __le__(Angle self, Particle d) -> bool
2428 return _IMP_atom.Angle___le__(self, *args)
2431 def __lt__(self, *args):
2433 __lt__(Angle self, Angle o) -> bool
2434 __lt__(Angle self, Particle d) -> bool
2436 return _IMP_atom.Angle___lt__(self, *args)
2439 def __ge__(self, *args):
2441 __ge__(Angle self, Angle o) -> bool
2442 __ge__(Angle self, Particle d) -> bool
2444 return _IMP_atom.Angle___ge__(self, *args)
2447 def __gt__(self, *args):
2449 __gt__(Angle self, Angle o) -> bool
2450 __gt__(Angle self, Particle d) -> bool
2452 return _IMP_atom.Angle___gt__(self, *args)
2456 """__hash__(Angle self) -> std::size_t"""
2457 return _IMP_atom.Angle___hash__(self)
2461 """__str__(Angle self) -> std::string"""
2462 return _IMP_atom.Angle___str__(self)
2466 """__repr__(Angle self) -> std::string"""
2467 return _IMP_atom.Angle___repr__(self)
2469 __swig_destroy__ = _IMP_atom.delete_Angle
2470 __del__ =
lambda self:
None
2471 Angle_swigregister = _IMP_atom.Angle_swigregister
2472 Angle_swigregister(Angle)
2474 def Angle_setup_particle(*args):
2476 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2477 Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2479 return _IMP_atom.Angle_setup_particle(*args)
2481 def Angle_get_is_setup(*args):
2483 get_is_setup(_ParticleAdaptor p) -> bool
2484 Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2486 return _IMP_atom.Angle_get_is_setup(*args)
2488 def Angle_get_particle_key(i):
2489 """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2490 return _IMP_atom.Angle_get_particle_key(i)
2492 def Angle_get_ideal_key():
2493 """Angle_get_ideal_key() -> FloatKey"""
2494 return _IMP_atom.Angle_get_ideal_key()
2496 def Angle_get_stiffness_key():
2497 """Angle_get_stiffness_key() -> FloatKey"""
2498 return _IMP_atom.Angle_get_stiffness_key()
2501 """Proxy of C++ IMP::atom::Dihedral class."""
2503 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2505 def __init__(self, *args):
2507 __init__(IMP::atom::Dihedral self) -> Dihedral
2508 __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2509 __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2511 this = _IMP_atom.new_Dihedral(*args)
2513 self.this.append(this)
2514 except __builtin__.Exception:
2517 def show(self, *args):
2519 show(Dihedral self, _ostream out)
2522 return _IMP_atom.Dihedral_show(self, *args)
2525 def setup_particle(*args):
2527 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2528 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2530 return _IMP_atom.Dihedral_setup_particle(*args)
2532 setup_particle = staticmethod(setup_particle)
2534 def get_is_setup(*args):
2536 get_is_setup(_ParticleAdaptor p) -> bool
2537 get_is_setup(Model m, ParticleIndex pi) -> bool
2539 return _IMP_atom.Dihedral_get_is_setup(*args)
2541 get_is_setup = staticmethod(get_is_setup)
2543 def get_particle(self, *args):
2545 get_particle(Dihedral self) -> Particle
2546 get_particle(Dihedral self, unsigned int i) -> Particle
2548 return _IMP_atom.Dihedral_get_particle(self, *args)
2551 def get_ideal(self):
2552 """get_ideal(Dihedral self) -> IMP::Float"""
2553 return _IMP_atom.Dihedral_get_ideal(self)
2556 def set_ideal(self, t):
2557 """set_ideal(Dihedral self, IMP::Float t)"""
2558 return _IMP_atom.Dihedral_set_ideal(self, t)
2561 def get_multiplicity(self):
2562 """get_multiplicity(Dihedral self) -> IMP::Int"""
2563 return _IMP_atom.Dihedral_get_multiplicity(self)
2566 def set_multiplicity(self, t):
2567 """set_multiplicity(Dihedral self, IMP::Int t)"""
2568 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2571 def get_stiffness(self):
2572 """get_stiffness(Dihedral self) -> IMP::Float"""
2573 return _IMP_atom.Dihedral_get_stiffness(self)
2576 def set_stiffness(self, t):
2577 """set_stiffness(Dihedral self, IMP::Float t)"""
2578 return _IMP_atom.Dihedral_set_stiffness(self, t)
2581 def get_particle_key(i):
2582 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2583 return _IMP_atom.Dihedral_get_particle_key(i)
2585 get_particle_key = staticmethod(get_particle_key)
2587 def get_ideal_key():
2588 """get_ideal_key() -> FloatKey"""
2589 return _IMP_atom.Dihedral_get_ideal_key()
2591 get_ideal_key = staticmethod(get_ideal_key)
2593 def get_multiplicity_key():
2594 """get_multiplicity_key() -> IntKey"""
2595 return _IMP_atom.Dihedral_get_multiplicity_key()
2597 get_multiplicity_key = staticmethod(get_multiplicity_key)
2599 def get_stiffness_key():
2600 """get_stiffness_key() -> FloatKey"""
2601 return _IMP_atom.Dihedral_get_stiffness_key()
2603 get_stiffness_key = staticmethod(get_stiffness_key)
2605 def add_attribute(self, *args):
2607 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2608 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2609 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2610 add_attribute(Dihedral self, FloatsKey a0, IMP::Floats a1)
2611 add_attribute(Dihedral self, IntsKey a0, IMP::Ints a1)
2612 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2613 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2614 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2616 return _IMP_atom.Dihedral_add_attribute(self, *args)
2619 def get_value(self, *args):
2621 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2622 get_value(Dihedral self, IntKey a0) -> IMP::Int
2623 get_value(Dihedral self, FloatsKey a0) -> IMP::Floats
2624 get_value(Dihedral self, IntsKey a0) -> IMP::Ints
2625 get_value(Dihedral self, StringKey a0) -> IMP::String
2626 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2627 get_value(Dihedral self, ObjectKey a0) -> Object
2629 return _IMP_atom.Dihedral_get_value(self, *args)
2632 def set_value(self, *args):
2634 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2635 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2636 set_value(Dihedral self, FloatsKey a0, IMP::Floats a1)
2637 set_value(Dihedral self, IntsKey a0, IMP::Ints a1)
2638 set_value(Dihedral self, StringKey a0, IMP::String a1)
2639 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2640 set_value(Dihedral self, ObjectKey a0, Object a1)
2642 return _IMP_atom.Dihedral_set_value(self, *args)
2645 def remove_attribute(self, *args):
2647 remove_attribute(Dihedral self, FloatKey a0)
2648 remove_attribute(Dihedral self, IntKey a0)
2649 remove_attribute(Dihedral self, FloatsKey a0)
2650 remove_attribute(Dihedral self, IntsKey a0)
2651 remove_attribute(Dihedral self, StringKey a0)
2652 remove_attribute(Dihedral self, ParticleIndexKey a0)
2653 remove_attribute(Dihedral self, ObjectKey a0)
2655 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2658 def has_attribute(self, *args):
2660 has_attribute(Dihedral self, FloatKey a0) -> bool
2661 has_attribute(Dihedral self, IntKey a0) -> bool
2662 has_attribute(Dihedral self, FloatsKey a0) -> bool
2663 has_attribute(Dihedral self, IntsKey a0) -> bool
2664 has_attribute(Dihedral self, StringKey a0) -> bool
2665 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2666 has_attribute(Dihedral self, ObjectKey a0) -> bool
2668 return _IMP_atom.Dihedral_has_attribute(self, *args)
2671 def get_derivative(self, a0):
2672 """get_derivative(Dihedral self, FloatKey a0) -> double"""
2673 return _IMP_atom.Dihedral_get_derivative(self, a0)
2677 """get_name(Dihedral self) -> std::string"""
2678 return _IMP_atom.Dihedral_get_name(self)
2681 def clear_caches(self):
2682 """clear_caches(Dihedral self)"""
2683 return _IMP_atom.Dihedral_clear_caches(self)
2686 def set_name(self, a0):
2687 """set_name(Dihedral self, std::string a0)"""
2688 return _IMP_atom.Dihedral_set_name(self, a0)
2692 """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2693 return _IMP_atom.Dihedral_set_check_level(self, a0)
2696 def add_to_derivative(self, a0, a1, a2):
2697 """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2698 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2701 def set_is_optimized(self, a0, a1):
2702 """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2703 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2706 def get_is_optimized(self, a0):
2707 """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2708 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2712 """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2713 return _IMP_atom.Dihedral_get_check_level(self)
2716 def __eq__(self, *args):
2718 __eq__(Dihedral self, Dihedral o) -> bool
2719 __eq__(Dihedral self, Particle d) -> bool
2721 return _IMP_atom.Dihedral___eq__(self, *args)
2724 def __ne__(self, *args):
2726 __ne__(Dihedral self, Dihedral o) -> bool
2727 __ne__(Dihedral self, Particle d) -> bool
2729 return _IMP_atom.Dihedral___ne__(self, *args)
2732 def __le__(self, *args):
2734 __le__(Dihedral self, Dihedral o) -> bool
2735 __le__(Dihedral self, Particle d) -> bool
2737 return _IMP_atom.Dihedral___le__(self, *args)
2740 def __lt__(self, *args):
2742 __lt__(Dihedral self, Dihedral o) -> bool
2743 __lt__(Dihedral self, Particle d) -> bool
2745 return _IMP_atom.Dihedral___lt__(self, *args)
2748 def __ge__(self, *args):
2750 __ge__(Dihedral self, Dihedral o) -> bool
2751 __ge__(Dihedral self, Particle d) -> bool
2753 return _IMP_atom.Dihedral___ge__(self, *args)
2756 def __gt__(self, *args):
2758 __gt__(Dihedral self, Dihedral o) -> bool
2759 __gt__(Dihedral self, Particle d) -> bool
2761 return _IMP_atom.Dihedral___gt__(self, *args)
2765 """__hash__(Dihedral self) -> std::size_t"""
2766 return _IMP_atom.Dihedral___hash__(self)
2770 """__str__(Dihedral self) -> std::string"""
2771 return _IMP_atom.Dihedral___str__(self)
2775 """__repr__(Dihedral self) -> std::string"""
2776 return _IMP_atom.Dihedral___repr__(self)
2778 __swig_destroy__ = _IMP_atom.delete_Dihedral
2779 __del__ =
lambda self:
None
2780 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2781 Dihedral_swigregister(Dihedral)
2783 def Dihedral_setup_particle(*args):
2785 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2786 Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2788 return _IMP_atom.Dihedral_setup_particle(*args)
2790 def Dihedral_get_is_setup(*args):
2792 get_is_setup(_ParticleAdaptor p) -> bool
2793 Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2795 return _IMP_atom.Dihedral_get_is_setup(*args)
2797 def Dihedral_get_particle_key(i):
2798 """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2799 return _IMP_atom.Dihedral_get_particle_key(i)
2801 def Dihedral_get_ideal_key():
2802 """Dihedral_get_ideal_key() -> FloatKey"""
2803 return _IMP_atom.Dihedral_get_ideal_key()
2805 def Dihedral_get_multiplicity_key():
2806 """Dihedral_get_multiplicity_key() -> IntKey"""
2807 return _IMP_atom.Dihedral_get_multiplicity_key()
2809 def Dihedral_get_stiffness_key():
2810 """Dihedral_get_stiffness_key() -> FloatKey"""
2811 return _IMP_atom.Dihedral_get_stiffness_key()
2814 """Proxy of C++ IMP::atom::SmoothingFunction class."""
2816 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2818 def __init__(self, *args, **kwargs):
2819 raise AttributeError(
"No constructor defined - class is abstract")
2821 def __call__(self, *args):
2823 __call__(SmoothingFunction self, double score, double distance) -> double
2824 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2826 return _IMP_atom.SmoothingFunction___call__(self, *args)
2828 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2829 __del__ =
lambda self:
None
2832 """__str__(SmoothingFunction self) -> std::string"""
2833 return _IMP_atom.SmoothingFunction___str__(self)
2837 """__repr__(SmoothingFunction self) -> std::string"""
2838 return _IMP_atom.SmoothingFunction___repr__(self)
2843 return _object_cast_to_SmoothingFunction(o)
2845 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2846 SmoothingFunction_swigregister(SmoothingFunction)
2848 class ForceSwitch(SmoothingFunction):
2849 """Proxy of C++ IMP::atom::ForceSwitch class."""
2851 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2853 def __init__(self, min_distance, max_distance):
2854 """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2855 this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2857 self.this.append(this)
2858 except __builtin__.Exception:
2861 def __call__(self, *args):
2863 __call__(ForceSwitch self, double score, double distance) -> double
2864 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
2866 return _IMP_atom.ForceSwitch___call__(self, *args)
2869 def get_version_info(self):
2870 """get_version_info(ForceSwitch self) -> VersionInfo"""
2871 return _IMP_atom.ForceSwitch_get_version_info(self)
2875 """__str__(ForceSwitch self) -> std::string"""
2876 return _IMP_atom.ForceSwitch___str__(self)
2880 """__repr__(ForceSwitch self) -> std::string"""
2881 return _IMP_atom.ForceSwitch___repr__(self)
2886 return _object_cast_to_ForceSwitch(o)
2888 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
2889 ForceSwitch_swigregister(ForceSwitch)
2892 """Proxy of C++ IMP::atom::AngleSingletonScore class."""
2894 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2896 def __init__(self, f):
2897 """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
2898 this = _IMP_atom.new_AngleSingletonScore(f)
2900 self.this.append(this)
2901 except __builtin__.Exception:
2904 def do_get_inputs(self, m, pis):
2905 """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2906 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
2909 def get_version_info(self):
2910 """get_version_info(AngleSingletonScore self) -> VersionInfo"""
2911 return _IMP_atom.AngleSingletonScore_get_version_info(self)
2915 """__str__(AngleSingletonScore self) -> std::string"""
2916 return _IMP_atom.AngleSingletonScore___str__(self)
2920 """__repr__(AngleSingletonScore self) -> std::string"""
2921 return _IMP_atom.AngleSingletonScore___repr__(self)
2926 return _object_cast_to_AngleSingletonScore(o)
2928 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
2929 AngleSingletonScore_swigregister(AngleSingletonScore)
2932 """Proxy of C++ IMP::atom::BondEndpointsRefiner class."""
2934 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2937 """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
2938 this = _IMP_atom.new_BondEndpointsRefiner()
2940 self.this.append(this)
2941 except __builtin__.Exception:
2944 def do_get_inputs(self, m, pis):
2945 """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2946 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
2949 def get_version_info(self):
2950 """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
2951 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
2955 """__str__(BondEndpointsRefiner self) -> std::string"""
2956 return _IMP_atom.BondEndpointsRefiner___str__(self)
2960 """__repr__(BondEndpointsRefiner self) -> std::string"""
2961 return _IMP_atom.BondEndpointsRefiner___repr__(self)
2966 return _object_cast_to_BondEndpointsRefiner(o)
2968 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
2969 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
2972 """Proxy of C++ IMP::atom::BondPairContainer class."""
2974 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2976 def __init__(self, sc):
2977 """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
2978 this = _IMP_atom.new_BondPairContainer(sc)
2980 self.this.append(this)
2981 except __builtin__.Exception:
2984 def do_get_inputs(self):
2985 """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
2986 return _IMP_atom.BondPairContainer_do_get_inputs(self)
2989 def do_apply(self, sm):
2990 """do_apply(BondPairContainer self, PairModifier sm)"""
2991 return _IMP_atom.BondPairContainer_do_apply(self, sm)
2994 def get_version_info(self):
2995 """get_version_info(BondPairContainer self) -> VersionInfo"""
2996 return _IMP_atom.BondPairContainer_get_version_info(self)
3000 """__str__(BondPairContainer self) -> std::string"""
3001 return _IMP_atom.BondPairContainer___str__(self)
3005 """__repr__(BondPairContainer self) -> std::string"""
3006 return _IMP_atom.BondPairContainer___repr__(self)
3011 return _object_cast_to_BondPairContainer(o)
3013 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
3014 BondPairContainer_swigregister(BondPairContainer)
3017 """Proxy of C++ IMP::atom::BondSingletonScore class."""
3019 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3021 def __init__(self, f):
3022 """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
3023 this = _IMP_atom.new_BondSingletonScore(f)
3025 self.this.append(this)
3026 except __builtin__.Exception:
3029 def get_unary_function(self):
3030 """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
3031 return _IMP_atom.BondSingletonScore_get_unary_function(self)
3034 def do_get_inputs(self, m, pis):
3035 """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3036 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
3039 def get_version_info(self):
3040 """get_version_info(BondSingletonScore self) -> VersionInfo"""
3041 return _IMP_atom.BondSingletonScore_get_version_info(self)
3045 """__str__(BondSingletonScore self) -> std::string"""
3046 return _IMP_atom.BondSingletonScore___str__(self)
3050 """__repr__(BondSingletonScore self) -> std::string"""
3051 return _IMP_atom.BondSingletonScore___repr__(self)
3056 return _object_cast_to_BondSingletonScore(o)
3058 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
3059 BondSingletonScore_swigregister(BondSingletonScore)
3062 """Proxy of C++ IMP::atom::DihedralSingletonScore class."""
3064 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3067 """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
3068 this = _IMP_atom.new_DihedralSingletonScore()
3070 self.this.append(this)
3071 except __builtin__.Exception:
3074 def do_get_inputs(self, m, pis):
3075 """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3076 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3079 def get_version_info(self):
3080 """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3081 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3085 """__str__(DihedralSingletonScore self) -> std::string"""
3086 return _IMP_atom.DihedralSingletonScore___str__(self)
3090 """__repr__(DihedralSingletonScore self) -> std::string"""
3091 return _IMP_atom.DihedralSingletonScore___repr__(self)
3096 return _object_cast_to_DihedralSingletonScore(o)
3098 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3099 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3102 """Proxy of C++ IMP::atom::ImproperSingletonScore class."""
3104 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3106 def __init__(self, f):
3107 """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3108 this = _IMP_atom.new_ImproperSingletonScore(f)
3110 self.this.append(this)
3111 except __builtin__.Exception:
3114 def do_get_inputs(self, m, pis):
3115 """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3116 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3119 def get_version_info(self):
3120 """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3121 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3125 """__str__(ImproperSingletonScore self) -> std::string"""
3126 return _IMP_atom.ImproperSingletonScore___str__(self)
3130 """__repr__(ImproperSingletonScore self) -> std::string"""
3131 return _IMP_atom.ImproperSingletonScore___repr__(self)
3136 return _object_cast_to_ImproperSingletonScore(o)
3138 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3139 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3142 """Proxy of C++ IMP::atom::CenterOfMass class."""
3144 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3146 def get_constraint(self):
3147 """get_constraint(CenterOfMass self) -> Constraint"""
3148 return _IMP_atom.CenterOfMass_get_constraint(self)
3152 """get_mass(CenterOfMass self) -> IMP::Float"""
3153 return _IMP_atom.CenterOfMass_get_mass(self)
3156 def get_coordinate(self, i):
3157 """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3158 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3161 def get_coordinates(self):
3162 """get_coordinates(CenterOfMass self) -> Vector3D"""
3163 return _IMP_atom.CenterOfMass_get_coordinates(self)
3166 def __init__(self, *args):
3168 __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3169 __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3170 __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3172 this = _IMP_atom.new_CenterOfMass(*args)
3174 self.this.append(this)
3175 except __builtin__.Exception:
3178 def show(self, *args):
3180 show(CenterOfMass self, _ostream out)
3181 show(CenterOfMass self)
3183 return _IMP_atom.CenterOfMass_show(self, *args)
3186 def setup_particle(*args):
3188 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3189 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3190 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3191 setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3193 return _IMP_atom.CenterOfMass_setup_particle(*args)
3195 setup_particle = staticmethod(setup_particle)
3197 def get_is_setup(*args):
3199 get_is_setup(_ParticleAdaptor p) -> bool
3200 get_is_setup(Model m, ParticleIndex pi) -> bool
3202 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3204 get_is_setup = staticmethod(get_is_setup)
3206 def add_attribute(self, *args):
3208 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3209 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3210 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3211 add_attribute(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3212 add_attribute(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3213 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3214 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3215 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3217 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3220 def get_value(self, *args):
3222 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3223 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3224 get_value(CenterOfMass self, FloatsKey a0) -> IMP::Floats
3225 get_value(CenterOfMass self, IntsKey a0) -> IMP::Ints
3226 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3227 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3228 get_value(CenterOfMass self, ObjectKey a0) -> Object
3230 return _IMP_atom.CenterOfMass_get_value(self, *args)
3233 def set_value(self, *args):
3235 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3236 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3237 set_value(CenterOfMass self, FloatsKey a0, IMP::Floats a1)
3238 set_value(CenterOfMass self, IntsKey a0, IMP::Ints a1)
3239 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3240 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3241 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3243 return _IMP_atom.CenterOfMass_set_value(self, *args)
3246 def remove_attribute(self, *args):
3248 remove_attribute(CenterOfMass self, FloatKey a0)
3249 remove_attribute(CenterOfMass self, IntKey a0)
3250 remove_attribute(CenterOfMass self, FloatsKey a0)
3251 remove_attribute(CenterOfMass self, IntsKey a0)
3252 remove_attribute(CenterOfMass self, StringKey a0)
3253 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3254 remove_attribute(CenterOfMass self, ObjectKey a0)
3256 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3259 def has_attribute(self, *args):
3261 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3262 has_attribute(CenterOfMass self, IntKey a0) -> bool
3263 has_attribute(CenterOfMass self, FloatsKey a0) -> bool
3264 has_attribute(CenterOfMass self, IntsKey a0) -> bool
3265 has_attribute(CenterOfMass self, StringKey a0) -> bool
3266 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3267 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3269 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3272 def get_derivative(self, a0):
3273 """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3274 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3278 """get_name(CenterOfMass self) -> std::string"""
3279 return _IMP_atom.CenterOfMass_get_name(self)
3282 def clear_caches(self):
3283 """clear_caches(CenterOfMass self)"""
3284 return _IMP_atom.CenterOfMass_clear_caches(self)
3287 def set_name(self, a0):
3288 """set_name(CenterOfMass self, std::string a0)"""
3289 return _IMP_atom.CenterOfMass_set_name(self, a0)
3293 """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3294 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3297 def add_to_derivative(self, a0, a1, a2):
3298 """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3299 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3302 def set_is_optimized(self, a0, a1):
3303 """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3304 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3307 def get_is_optimized(self, a0):
3308 """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3309 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3313 """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3314 return _IMP_atom.CenterOfMass_get_check_level(self)
3317 def __eq__(self, *args):
3319 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3320 __eq__(CenterOfMass self, Particle d) -> bool
3322 return _IMP_atom.CenterOfMass___eq__(self, *args)
3325 def __ne__(self, *args):
3327 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3328 __ne__(CenterOfMass self, Particle d) -> bool
3330 return _IMP_atom.CenterOfMass___ne__(self, *args)
3333 def __le__(self, *args):
3335 __le__(CenterOfMass self, CenterOfMass o) -> bool
3336 __le__(CenterOfMass self, Particle d) -> bool
3338 return _IMP_atom.CenterOfMass___le__(self, *args)
3341 def __lt__(self, *args):
3343 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3344 __lt__(CenterOfMass self, Particle d) -> bool
3346 return _IMP_atom.CenterOfMass___lt__(self, *args)
3349 def __ge__(self, *args):
3351 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3352 __ge__(CenterOfMass self, Particle d) -> bool
3354 return _IMP_atom.CenterOfMass___ge__(self, *args)
3357 def __gt__(self, *args):
3359 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3360 __gt__(CenterOfMass self, Particle d) -> bool
3362 return _IMP_atom.CenterOfMass___gt__(self, *args)
3366 """__hash__(CenterOfMass self) -> std::size_t"""
3367 return _IMP_atom.CenterOfMass___hash__(self)
3371 """__str__(CenterOfMass self) -> std::string"""
3372 return _IMP_atom.CenterOfMass___str__(self)
3376 """__repr__(CenterOfMass self) -> std::string"""
3377 return _IMP_atom.CenterOfMass___repr__(self)
3379 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3380 __del__ =
lambda self:
None
3381 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3382 CenterOfMass_swigregister(CenterOfMass)
3384 def CenterOfMass_setup_particle(*args):
3386 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3387 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3388 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3389 CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3391 return _IMP_atom.CenterOfMass_setup_particle(*args)
3393 def CenterOfMass_get_is_setup(*args):
3395 get_is_setup(_ParticleAdaptor p) -> bool
3396 CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3398 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3401 """Proxy of C++ IMP::atom::CoverBond class."""
3403 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3406 """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3407 this = _IMP_atom.new_CoverBond()
3409 self.this.append(this)
3410 except __builtin__.Exception:
3413 def do_get_inputs(self, m, pis):
3414 """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3415 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3418 def do_get_outputs(self, m, pis):
3419 """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3420 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3423 def get_version_info(self):
3424 """get_version_info(CoverBond self) -> VersionInfo"""
3425 return _IMP_atom.CoverBond_get_version_info(self)
3429 """__str__(CoverBond self) -> std::string"""
3430 return _IMP_atom.CoverBond___str__(self)
3434 """__repr__(CoverBond self) -> std::string"""
3435 return _IMP_atom.CoverBond___repr__(self)
3440 return _object_cast_to_CoverBond(o)
3442 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3443 CoverBond_swigregister(CoverBond)
3446 """Proxy of C++ IMP::atom::Simulator class."""
3448 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3450 def __init__(self, *args):
3452 __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3453 __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3454 __init__(IMP::atom::Simulator self, Model m) -> Simulator
3456 if self.__class__ == Simulator:
3460 this = _IMP_atom.new_Simulator(_self, *args)
3462 self.this.append(this)
3463 except __builtin__.Exception:
3466 if self.__class__ != Simulator:
3467 _director_objects.register(self)
3472 def simulate(self, time_in_fs):
3473 """simulate(Simulator self, double time_in_fs) -> double"""
3474 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3477 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3479 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3480 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3481 simulate_wave(Simulator self, double time_in_fs) -> double
3483 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3486 def get_temperature(self):
3487 """get_temperature(Simulator self) -> double"""
3488 return _IMP_atom.Simulator_get_temperature(self)
3491 def set_temperature(self, d):
3492 """set_temperature(Simulator self, double d)"""
3493 return _IMP_atom.Simulator_set_temperature(self, d)
3496 def set_maximum_time_step(self, ts):
3497 """set_maximum_time_step(Simulator self, double ts)"""
3498 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3501 def get_maximum_time_step(self):
3502 """get_maximum_time_step(Simulator self) -> double"""
3503 return _IMP_atom.Simulator_get_maximum_time_step(self)
3506 def get_last_time_step(self):
3507 """get_last_time_step(Simulator self) -> double"""
3508 return _IMP_atom.Simulator_get_last_time_step(self)
3511 def set_time_step(self, ts):
3512 """set_time_step(Simulator self, double ts)"""
3513 return _IMP_atom.Simulator_set_time_step(self, ts)
3517 """get_kt(Simulator self) -> double"""
3518 return _IMP_atom.Simulator_get_kt(self)
3521 def get_current_time(self):
3522 """get_current_time(Simulator self) -> double"""
3523 return _IMP_atom.Simulator_get_current_time(self)
3526 def set_current_time(self, ct):
3527 """set_current_time(Simulator self, double ct)"""
3528 return _IMP_atom.Simulator_set_current_time(self, ct)
3531 def get_simulation_particles(self):
3532 """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3533 return _IMP_atom.Simulator_get_simulation_particles(self)
3536 def get_simulation_particle_indexes(self):
3537 """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3538 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3541 def remove_particle(self, d):
3542 """remove_particle(Simulator self, Particle d)"""
3543 return _IMP_atom.Simulator_remove_particle(self, d)
3546 def remove_particles(self, d):
3547 """remove_particles(Simulator self, IMP::Particles const & d)"""
3548 return _IMP_atom.Simulator_remove_particles(self, d)
3551 def set_particles(self, ps):
3552 """set_particles(Simulator self, IMP::Particles const & ps)"""
3553 return _IMP_atom.Simulator_set_particles(self, ps)
3556 def set_particles_order(self, objs):
3557 """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3558 return _IMP_atom.Simulator_set_particles_order(self, objs)
3562 """add_particle(Simulator self, Particle obj) -> unsigned int"""
3563 return _IMP_atom.Simulator_add_particle(self, obj)
3567 """add_particles(Simulator self, IMP::Particles const & objs)"""
3568 return _IMP_atom.Simulator_add_particles(self, objs)
3571 def clear_particles(self):
3572 """clear_particles(Simulator self)"""
3573 return _IMP_atom.Simulator_clear_particles(self)
3576 def get_number_of_particles(self):
3577 """get_number_of_particles(Simulator self) -> unsigned int"""
3578 return _IMP_atom.Simulator_get_number_of_particles(self)
3581 def get_has_particles(self):
3582 """get_has_particles(Simulator self) -> bool"""
3583 return _IMP_atom.Simulator_get_has_particles(self)
3586 def get_particle(self, i):
3587 """get_particle(Simulator self, unsigned int i) -> Particle"""
3588 return _IMP_atom.Simulator_get_particle(self, i)
3592 """get_particles(Simulator self) -> IMP::Particles"""
3593 return _IMP_atom.Simulator_get_particles(self)
3596 def reserve_particles(self, sz):
3597 """reserve_particles(Simulator self, unsigned int sz)"""
3598 return _IMP_atom.Simulator_reserve_particles(self, sz)
3601 def do_optimize(self, max_steps):
3602 """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3603 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3606 def setup(self, arg0):
3607 """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3608 return _IMP_atom.Simulator_setup(self, arg0)
3611 def do_step(self, sc, dt):
3612 """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3613 return _IMP_atom.Simulator_do_step(self, sc, dt)
3616 def get_is_simulation_particle(self, p):
3617 """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3618 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3621 def do_simulate(self, time):
3622 """do_simulate(Simulator self, double time) -> double"""
3623 return _IMP_atom.Simulator_do_simulate(self, time)
3626 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3628 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3629 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3630 do_simulate_wave(Simulator self, double time_in_fs) -> double
3632 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3636 """__str__(Simulator self) -> std::string"""
3637 return _IMP_atom.Simulator___str__(self)
3641 """__repr__(Simulator self) -> std::string"""
3642 return _IMP_atom.Simulator___repr__(self)
3647 return _object_cast_to_Simulator(o)
3650 def get_type_name(self):
3651 return self.__class__.__name__
3652 def do_show(self, out):
3654 def get_version_info(self):
3655 if"IMP::atom" ==
"IMP":
3656 return VersionInfo(self.__module__,
3663 return _object_cast_to_Simulator(o)
3665 __swig_destroy__ = _IMP_atom.delete_Simulator
3666 __del__ =
lambda self:
None
3667 def __disown__(self):
3669 _IMP_atom.disown_Simulator(self)
3670 return weakref_proxy(self)
3672 def do_destroy(self):
3673 """do_destroy(Simulator self)"""
3674 return _IMP_atom.Simulator_do_destroy(self)
3677 def handle_set_has_required_score_states(self, arg0):
3678 """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3679 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3682 def do_get_inputs(self):
3683 """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3684 return _IMP_atom.Simulator_do_get_inputs(self)
3687 def do_get_outputs(self):
3688 """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3689 return _IMP_atom.Simulator_do_get_outputs(self)
3692 def do_get_interactions(self):
3693 """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3694 return _IMP_atom.Simulator_do_get_interactions(self)
3696 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3697 Simulator_swigregister(Simulator)
3699 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3700 class BrownianDynamics(Simulator):
3701 """Proxy of C++ IMP::atom::BrownianDynamics class."""
3703 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3705 def __init__(self, *args):
3707 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=10000) -> BrownianDynamics
3708 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3709 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3710 __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3712 this = _IMP_atom.new_BrownianDynamics(*args)
3714 self.this.append(this)
3715 except __builtin__.Exception:
3718 def set_maximum_move(self, ms_in_A):
3719 """set_maximum_move(BrownianDynamics self, double ms_in_A)"""
3720 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms_in_A)
3723 def set_use_stochastic_runge_kutta(self, tf):
3724 """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3725 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3728 def get_version_info(self):
3729 """get_version_info(BrownianDynamics self) -> VersionInfo"""
3730 return _IMP_atom.BrownianDynamics_get_version_info(self)
3734 """__str__(BrownianDynamics self) -> std::string"""
3735 return _IMP_atom.BrownianDynamics___str__(self)
3739 """__repr__(BrownianDynamics self) -> std::string"""
3740 return _IMP_atom.BrownianDynamics___repr__(self)
3745 return _object_cast_to_BrownianDynamics(o)
3747 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3748 BrownianDynamics_swigregister(BrownianDynamics)
3752 """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3753 return _IMP_atom.get_maximum_time_step_estimate(bd)
3755 def get_harmonic_sigma(D, f):
3756 """get_harmonic_sigma(double D, double f) -> double"""
3757 return _IMP_atom.get_harmonic_sigma(D, f)
3758 class BrownianDynamicsTAMD(BrownianDynamics):
3759 """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class."""
3761 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3763 def __init__(self, *args):
3765 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3766 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3767 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3769 this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3771 self.this.append(this)
3772 except __builtin__.Exception:
3776 """__str__(BrownianDynamicsTAMD self) -> std::string"""
3777 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3781 """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3782 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3787 return _object_cast_to_BrownianDynamicsTAMD(o)
3789 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3790 __del__ =
lambda self:
None
3791 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3792 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3795 """Proxy of C++ IMP::atom::Diffusion class."""
3797 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3799 def __init__(self, *args):
3801 __init__(IMP::atom::Diffusion self) -> Diffusion
3802 __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3803 __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3805 this = _IMP_atom.new_Diffusion(*args)
3807 self.this.append(this)
3808 except __builtin__.Exception:
3811 def show(self, *args):
3813 show(Diffusion self, _ostream out)
3814 show(Diffusion self)
3816 return _IMP_atom.Diffusion_show(self, *args)
3819 def setup_particle(*args):
3821 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3822 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3823 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3824 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3825 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3826 setup_particle(_ParticleAdaptor decorator) -> Diffusion
3828 return _IMP_atom.Diffusion_setup_particle(*args)
3830 setup_particle = staticmethod(setup_particle)
3832 def get_is_setup(*args):
3834 get_is_setup(_ParticleAdaptor p) -> bool
3835 get_is_setup(Model m, ParticleIndex p) -> bool
3837 return _IMP_atom.Diffusion_get_is_setup(*args)
3839 get_is_setup = staticmethod(get_is_setup)
3841 def set_diffusion_coefficient(self, d):
3842 """set_diffusion_coefficient(Diffusion self, double d)"""
3843 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3847 """get_diffusion_coefficient(Diffusion self) -> double"""
3848 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3851 def get_diffusion_coefficient_key():
3852 """get_diffusion_coefficient_key() -> FloatKey"""
3853 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3855 get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3857 def add_attribute(self, *args):
3859 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3860 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3861 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3862 add_attribute(Diffusion self, FloatsKey a0, IMP::Floats a1)
3863 add_attribute(Diffusion self, IntsKey a0, IMP::Ints a1)
3864 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3865 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3866 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3868 return _IMP_atom.Diffusion_add_attribute(self, *args)
3871 def get_value(self, *args):
3873 get_value(Diffusion self, FloatKey a0) -> IMP::Float
3874 get_value(Diffusion self, IntKey a0) -> IMP::Int
3875 get_value(Diffusion self, FloatsKey a0) -> IMP::Floats
3876 get_value(Diffusion self, IntsKey a0) -> IMP::Ints
3877 get_value(Diffusion self, StringKey a0) -> IMP::String
3878 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
3879 get_value(Diffusion self, ObjectKey a0) -> Object
3881 return _IMP_atom.Diffusion_get_value(self, *args)
3884 def set_value(self, *args):
3886 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
3887 set_value(Diffusion self, IntKey a0, IMP::Int a1)
3888 set_value(Diffusion self, FloatsKey a0, IMP::Floats a1)
3889 set_value(Diffusion self, IntsKey a0, IMP::Ints a1)
3890 set_value(Diffusion self, StringKey a0, IMP::String a1)
3891 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
3892 set_value(Diffusion self, ObjectKey a0, Object a1)
3894 return _IMP_atom.Diffusion_set_value(self, *args)
3897 def remove_attribute(self, *args):
3899 remove_attribute(Diffusion self, FloatKey a0)
3900 remove_attribute(Diffusion self, IntKey a0)
3901 remove_attribute(Diffusion self, FloatsKey a0)
3902 remove_attribute(Diffusion self, IntsKey a0)
3903 remove_attribute(Diffusion self, StringKey a0)
3904 remove_attribute(Diffusion self, ParticleIndexKey a0)
3905 remove_attribute(Diffusion self, ObjectKey a0)
3907 return _IMP_atom.Diffusion_remove_attribute(self, *args)
3910 def has_attribute(self, *args):
3912 has_attribute(Diffusion self, FloatKey a0) -> bool
3913 has_attribute(Diffusion self, IntKey a0) -> bool
3914 has_attribute(Diffusion self, FloatsKey a0) -> bool
3915 has_attribute(Diffusion self, IntsKey a0) -> bool
3916 has_attribute(Diffusion self, StringKey a0) -> bool
3917 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
3918 has_attribute(Diffusion self, ObjectKey a0) -> bool
3920 return _IMP_atom.Diffusion_has_attribute(self, *args)
3923 def get_derivative(self, a0):
3924 """get_derivative(Diffusion self, FloatKey a0) -> double"""
3925 return _IMP_atom.Diffusion_get_derivative(self, a0)
3929 """get_name(Diffusion self) -> std::string"""
3930 return _IMP_atom.Diffusion_get_name(self)
3933 def clear_caches(self):
3934 """clear_caches(Diffusion self)"""
3935 return _IMP_atom.Diffusion_clear_caches(self)
3938 def set_name(self, a0):
3939 """set_name(Diffusion self, std::string a0)"""
3940 return _IMP_atom.Diffusion_set_name(self, a0)
3944 """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
3945 return _IMP_atom.Diffusion_set_check_level(self, a0)
3948 def add_to_derivative(self, a0, a1, a2):
3949 """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3950 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
3953 def set_is_optimized(self, a0, a1):
3954 """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
3955 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
3958 def get_is_optimized(self, a0):
3959 """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
3960 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
3964 """get_check_level(Diffusion self) -> IMP::CheckLevel"""
3965 return _IMP_atom.Diffusion_get_check_level(self)
3968 def __eq__(self, *args):
3970 __eq__(Diffusion self, Diffusion o) -> bool
3971 __eq__(Diffusion self, Particle d) -> bool
3973 return _IMP_atom.Diffusion___eq__(self, *args)
3976 def __ne__(self, *args):
3978 __ne__(Diffusion self, Diffusion o) -> bool
3979 __ne__(Diffusion self, Particle d) -> bool
3981 return _IMP_atom.Diffusion___ne__(self, *args)
3984 def __le__(self, *args):
3986 __le__(Diffusion self, Diffusion o) -> bool
3987 __le__(Diffusion self, Particle d) -> bool
3989 return _IMP_atom.Diffusion___le__(self, *args)
3992 def __lt__(self, *args):
3994 __lt__(Diffusion self, Diffusion o) -> bool
3995 __lt__(Diffusion self, Particle d) -> bool
3997 return _IMP_atom.Diffusion___lt__(self, *args)
4000 def __ge__(self, *args):
4002 __ge__(Diffusion self, Diffusion o) -> bool
4003 __ge__(Diffusion self, Particle d) -> bool
4005 return _IMP_atom.Diffusion___ge__(self, *args)
4008 def __gt__(self, *args):
4010 __gt__(Diffusion self, Diffusion o) -> bool
4011 __gt__(Diffusion self, Particle d) -> bool
4013 return _IMP_atom.Diffusion___gt__(self, *args)
4017 """__hash__(Diffusion self) -> std::size_t"""
4018 return _IMP_atom.Diffusion___hash__(self)
4022 """__str__(Diffusion self) -> std::string"""
4023 return _IMP_atom.Diffusion___str__(self)
4027 """__repr__(Diffusion self) -> std::string"""
4028 return _IMP_atom.Diffusion___repr__(self)
4030 __swig_destroy__ = _IMP_atom.delete_Diffusion
4031 __del__ =
lambda self:
None
4032 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
4033 Diffusion_swigregister(Diffusion)
4035 def Diffusion_setup_particle(*args):
4037 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
4038 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
4039 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
4040 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
4041 setup_particle(Model m, ParticleIndex pi) -> Diffusion
4042 Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
4044 return _IMP_atom.Diffusion_setup_particle(*args)
4046 def Diffusion_get_is_setup(*args):
4048 get_is_setup(_ParticleAdaptor p) -> bool
4049 Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4051 return _IMP_atom.Diffusion_get_is_setup(*args)
4053 def Diffusion_get_diffusion_coefficient_key():
4054 """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
4055 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
4058 def get_diffusion_coefficient_from_cm2_per_second(din):
4059 """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
4060 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
4061 class RigidBodyDiffusion(Diffusion):
4062 """Proxy of C++ IMP::atom::RigidBodyDiffusion class."""
4064 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4066 def __init__(self, *args):
4068 __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
4069 __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
4070 __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
4072 this = _IMP_atom.new_RigidBodyDiffusion(*args)
4074 self.this.append(this)
4075 except __builtin__.Exception:
4078 def show(self, *args):
4080 show(RigidBodyDiffusion self, _ostream out)
4081 show(RigidBodyDiffusion self)
4083 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
4086 def setup_particle(*args):
4088 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4089 setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4091 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4093 setup_particle = staticmethod(setup_particle)
4096 """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4097 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4100 def set_rotational_diffusion_coefficient(self, d):
4101 """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4102 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4105 def get_is_setup(*args):
4107 get_is_setup(_ParticleAdaptor p) -> bool
4108 get_is_setup(Model m, ParticleIndex p) -> bool
4110 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4112 get_is_setup = staticmethod(get_is_setup)
4114 def get_rotational_diffusion_coefficient_key():
4115 """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4116 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4118 get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4120 def add_attribute(self, *args):
4122 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4123 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4124 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4125 add_attribute(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4126 add_attribute(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4127 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4128 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4129 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4131 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4134 def get_value(self, *args):
4136 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4137 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4138 get_value(RigidBodyDiffusion self, FloatsKey a0) -> IMP::Floats
4139 get_value(RigidBodyDiffusion self, IntsKey a0) -> IMP::Ints
4140 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4141 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4142 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4144 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4147 def set_value(self, *args):
4149 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4150 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4151 set_value(RigidBodyDiffusion self, FloatsKey a0, IMP::Floats a1)
4152 set_value(RigidBodyDiffusion self, IntsKey a0, IMP::Ints a1)
4153 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4154 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4155 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4157 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4160 def remove_attribute(self, *args):
4162 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4163 remove_attribute(RigidBodyDiffusion self, IntKey a0)
4164 remove_attribute(RigidBodyDiffusion self, FloatsKey a0)
4165 remove_attribute(RigidBodyDiffusion self, IntsKey a0)
4166 remove_attribute(RigidBodyDiffusion self, StringKey a0)
4167 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4168 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4170 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4173 def has_attribute(self, *args):
4175 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4176 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4177 has_attribute(RigidBodyDiffusion self, FloatsKey a0) -> bool
4178 has_attribute(RigidBodyDiffusion self, IntsKey a0) -> bool
4179 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4180 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4181 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4183 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4186 def get_derivative(self, a0):
4187 """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4188 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4192 """get_name(RigidBodyDiffusion self) -> std::string"""
4193 return _IMP_atom.RigidBodyDiffusion_get_name(self)
4196 def clear_caches(self):
4197 """clear_caches(RigidBodyDiffusion self)"""
4198 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4201 def set_name(self, a0):
4202 """set_name(RigidBodyDiffusion self, std::string a0)"""
4203 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4207 """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4208 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4211 def add_to_derivative(self, a0, a1, a2):
4212 """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4213 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4216 def set_is_optimized(self, a0, a1):
4217 """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4218 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4221 def get_is_optimized(self, a0):
4222 """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4223 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4227 """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4228 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4231 def __eq__(self, *args):
4233 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4234 __eq__(RigidBodyDiffusion self, Particle d) -> bool
4236 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4239 def __ne__(self, *args):
4241 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4242 __ne__(RigidBodyDiffusion self, Particle d) -> bool
4244 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4247 def __le__(self, *args):
4249 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4250 __le__(RigidBodyDiffusion self, Particle d) -> bool
4252 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4255 def __lt__(self, *args):
4257 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4258 __lt__(RigidBodyDiffusion self, Particle d) -> bool
4260 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4263 def __ge__(self, *args):
4265 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4266 __ge__(RigidBodyDiffusion self, Particle d) -> bool
4268 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4271 def __gt__(self, *args):
4273 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4274 __gt__(RigidBodyDiffusion self, Particle d) -> bool
4276 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4280 """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4281 return _IMP_atom.RigidBodyDiffusion___hash__(self)
4285 """__str__(RigidBodyDiffusion self) -> std::string"""
4286 return _IMP_atom.RigidBodyDiffusion___str__(self)
4290 """__repr__(RigidBodyDiffusion self) -> std::string"""
4291 return _IMP_atom.RigidBodyDiffusion___repr__(self)
4293 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4294 __del__ =
lambda self:
None
4295 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4296 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4298 def RigidBodyDiffusion_setup_particle(*args):
4300 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4301 RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4303 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4305 def RigidBodyDiffusion_get_is_setup(*args):
4307 get_is_setup(_ParticleAdaptor p) -> bool
4308 RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4310 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4312 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4313 """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4314 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4317 """Proxy of C++ IMP::atom::TAMDParticle class."""
4319 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4321 def __init__(self, *args):
4323 __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4324 __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4325 __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4327 this = _IMP_atom.new_TAMDParticle(*args)
4329 self.this.append(this)
4330 except __builtin__.Exception:
4333 def show(self, *args):
4335 show(TAMDParticle self, _ostream out)
4336 show(TAMDParticle self)
4338 return _IMP_atom.TAMDParticle_show(self, *args)
4341 def setup_particle(*args):
4343 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4344 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4345 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4346 setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4348 return _IMP_atom.TAMDParticle_setup_particle(*args)
4350 setup_particle = staticmethod(setup_particle)
4352 def get_is_setup(*args):
4354 get_is_setup(_ParticleAdaptor p) -> bool
4355 get_is_setup(Model m, ParticleIndex p) -> bool
4357 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4359 get_is_setup = staticmethod(get_is_setup)
4361 def get_reference_particle_index(self):
4362 """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4363 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4366 def set_temperature_scale_factor(self, tsf):
4367 """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4368 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4371 def get_temperature_scale_factor(self):
4372 """get_temperature_scale_factor(TAMDParticle self) -> double"""
4373 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4376 def set_friction_scale_factor(self, tsf):
4377 """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4378 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4381 def get_friction_scale_factor(self):
4382 """get_friction_scale_factor(TAMDParticle self) -> double"""
4383 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4386 def update_coordinates_from_ref(self):
4387 """update_coordinates_from_ref(TAMDParticle self)"""
4388 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4391 def get_temperature_scale_factor_key():
4392 """get_temperature_scale_factor_key() -> FloatKey"""
4393 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4395 get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4397 def get_friction_scale_factor_key():
4398 """get_friction_scale_factor_key() -> FloatKey"""
4399 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4401 get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4403 def get_reference_particle_index_key():
4404 """get_reference_particle_index_key() -> ParticleIndexKey"""
4405 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4407 get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4409 def add_attribute(self, *args):
4411 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4412 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4413 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4414 add_attribute(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4415 add_attribute(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4416 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4417 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4418 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4420 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4423 def get_value(self, *args):
4425 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4426 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4427 get_value(TAMDParticle self, FloatsKey a0) -> IMP::Floats
4428 get_value(TAMDParticle self, IntsKey a0) -> IMP::Ints
4429 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4430 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4431 get_value(TAMDParticle self, ObjectKey a0) -> Object
4433 return _IMP_atom.TAMDParticle_get_value(self, *args)
4436 def set_value(self, *args):
4438 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4439 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4440 set_value(TAMDParticle self, FloatsKey a0, IMP::Floats a1)
4441 set_value(TAMDParticle self, IntsKey a0, IMP::Ints a1)
4442 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4443 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4444 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4446 return _IMP_atom.TAMDParticle_set_value(self, *args)
4449 def remove_attribute(self, *args):
4451 remove_attribute(TAMDParticle self, FloatKey a0)
4452 remove_attribute(TAMDParticle self, IntKey a0)
4453 remove_attribute(TAMDParticle self, FloatsKey a0)
4454 remove_attribute(TAMDParticle self, IntsKey a0)
4455 remove_attribute(TAMDParticle self, StringKey a0)
4456 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4457 remove_attribute(TAMDParticle self, ObjectKey a0)
4459 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4462 def has_attribute(self, *args):
4464 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4465 has_attribute(TAMDParticle self, IntKey a0) -> bool
4466 has_attribute(TAMDParticle self, FloatsKey a0) -> bool
4467 has_attribute(TAMDParticle self, IntsKey a0) -> bool
4468 has_attribute(TAMDParticle self, StringKey a0) -> bool
4469 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4470 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4472 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4475 def get_derivative(self, a0):
4476 """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4477 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4481 """get_name(TAMDParticle self) -> std::string"""
4482 return _IMP_atom.TAMDParticle_get_name(self)
4485 def clear_caches(self):
4486 """clear_caches(TAMDParticle self)"""
4487 return _IMP_atom.TAMDParticle_clear_caches(self)
4490 def set_name(self, a0):
4491 """set_name(TAMDParticle self, std::string a0)"""
4492 return _IMP_atom.TAMDParticle_set_name(self, a0)
4496 """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4497 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4500 def add_to_derivative(self, a0, a1, a2):
4501 """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4502 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4505 def set_is_optimized(self, a0, a1):
4506 """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4507 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4510 def get_is_optimized(self, a0):
4511 """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4512 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4516 """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4517 return _IMP_atom.TAMDParticle_get_check_level(self)
4520 def __eq__(self, *args):
4522 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4523 __eq__(TAMDParticle self, Particle d) -> bool
4525 return _IMP_atom.TAMDParticle___eq__(self, *args)
4528 def __ne__(self, *args):
4530 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4531 __ne__(TAMDParticle self, Particle d) -> bool
4533 return _IMP_atom.TAMDParticle___ne__(self, *args)
4536 def __le__(self, *args):
4538 __le__(TAMDParticle self, TAMDParticle o) -> bool
4539 __le__(TAMDParticle self, Particle d) -> bool
4541 return _IMP_atom.TAMDParticle___le__(self, *args)
4544 def __lt__(self, *args):
4546 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4547 __lt__(TAMDParticle self, Particle d) -> bool
4549 return _IMP_atom.TAMDParticle___lt__(self, *args)
4552 def __ge__(self, *args):
4554 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4555 __ge__(TAMDParticle self, Particle d) -> bool
4557 return _IMP_atom.TAMDParticle___ge__(self, *args)
4560 def __gt__(self, *args):
4562 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4563 __gt__(TAMDParticle self, Particle d) -> bool
4565 return _IMP_atom.TAMDParticle___gt__(self, *args)
4569 """__hash__(TAMDParticle self) -> std::size_t"""
4570 return _IMP_atom.TAMDParticle___hash__(self)
4574 """__str__(TAMDParticle self) -> std::string"""
4575 return _IMP_atom.TAMDParticle___str__(self)
4579 """__repr__(TAMDParticle self) -> std::string"""
4580 return _IMP_atom.TAMDParticle___repr__(self)
4582 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4583 __del__ =
lambda self:
None
4584 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4585 TAMDParticle_swigregister(TAMDParticle)
4587 def TAMDParticle_setup_particle(*args):
4589 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4590 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4591 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4592 TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4594 return _IMP_atom.TAMDParticle_setup_particle(*args)
4596 def TAMDParticle_get_is_setup(*args):
4598 get_is_setup(_ParticleAdaptor p) -> bool
4599 TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4601 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4603 def TAMDParticle_get_temperature_scale_factor_key():
4604 """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4605 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4607 def TAMDParticle_get_friction_scale_factor_key():
4608 """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4609 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4611 def TAMDParticle_get_reference_particle_index_key():
4612 """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4613 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4615 class Chain(Hierarchy):
4616 """Proxy of C++ IMP::atom::Chain class."""
4618 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4620 def __init__(self, *args):
4622 __init__(IMP::atom::Chain self) -> Chain
4623 __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4624 __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4626 this = _IMP_atom.new_Chain(*args)
4628 self.this.append(this)
4629 except __builtin__.Exception:
4632 def show(self, *args):
4634 show(Chain self, _ostream out)
4637 return _IMP_atom.Chain_show(self, *args)
4640 def setup_particle(*args):
4642 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4643 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4644 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4645 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4646 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4647 setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4649 return _IMP_atom.Chain_setup_particle(*args)
4651 setup_particle = staticmethod(setup_particle)
4653 def get_is_setup(*args):
4655 get_is_setup(_ParticleAdaptor p) -> bool
4656 get_is_setup(Model m, ParticleIndex pi) -> bool
4658 return _IMP_atom.Chain_get_is_setup(*args)
4660 get_is_setup = staticmethod(get_is_setup)
4663 """get_id(Chain self) -> std::string"""
4664 return _IMP_atom.Chain_get_id(self)
4667 def set_id(self, c):
4668 """set_id(Chain self, std::string c)"""
4669 return _IMP_atom.Chain_set_id(self, c)
4672 def get_sequence(self):
4673 """get_sequence(Chain self) -> std::string"""
4674 return _IMP_atom.Chain_get_sequence(self)
4677 def set_sequence(self, sequence):
4678 """set_sequence(Chain self, std::string sequence)"""
4679 return _IMP_atom.Chain_set_sequence(self, sequence)
4682 def get_chain_type(self):
4683 """get_chain_type(Chain self) -> ChainType"""
4684 return _IMP_atom.Chain_get_chain_type(self)
4687 def set_chain_type(self, t):
4688 """set_chain_type(Chain self, ChainType t)"""
4689 return _IMP_atom.Chain_set_chain_type(self, t)
4693 """get_id_key() -> StringKey"""
4694 return _IMP_atom.Chain_get_id_key()
4696 get_id_key = staticmethod(get_id_key)
4698 def get_sequence_key():
4699 """get_sequence_key() -> StringKey"""
4700 return _IMP_atom.Chain_get_sequence_key()
4702 get_sequence_key = staticmethod(get_sequence_key)
4704 def get_chain_type_key():
4705 """get_chain_type_key() -> IntKey"""
4706 return _IMP_atom.Chain_get_chain_type_key()
4708 get_chain_type_key = staticmethod(get_chain_type_key)
4710 def add_attribute(self, *args):
4712 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4713 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4714 add_attribute(Chain self, IntKey a0, IMP::Int a1)
4715 add_attribute(Chain self, FloatsKey a0, IMP::Floats a1)
4716 add_attribute(Chain self, IntsKey a0, IMP::Ints a1)
4717 add_attribute(Chain self, StringKey a0, IMP::String a1)
4718 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4719 add_attribute(Chain self, ObjectKey a0, Object a1)
4721 return _IMP_atom.Chain_add_attribute(self, *args)
4724 def get_value(self, *args):
4726 get_value(Chain self, FloatKey a0) -> IMP::Float
4727 get_value(Chain self, IntKey a0) -> IMP::Int
4728 get_value(Chain self, FloatsKey a0) -> IMP::Floats
4729 get_value(Chain self, IntsKey a0) -> IMP::Ints
4730 get_value(Chain self, StringKey a0) -> IMP::String
4731 get_value(Chain self, ParticleIndexKey a0) -> Particle
4732 get_value(Chain self, ObjectKey a0) -> Object
4734 return _IMP_atom.Chain_get_value(self, *args)
4737 def set_value(self, *args):
4739 set_value(Chain self, FloatKey a0, IMP::Float a1)
4740 set_value(Chain self, IntKey a0, IMP::Int a1)
4741 set_value(Chain self, FloatsKey a0, IMP::Floats a1)
4742 set_value(Chain self, IntsKey a0, IMP::Ints a1)
4743 set_value(Chain self, StringKey a0, IMP::String a1)
4744 set_value(Chain self, ParticleIndexKey a0, Particle a1)
4745 set_value(Chain self, ObjectKey a0, Object a1)
4747 return _IMP_atom.Chain_set_value(self, *args)
4750 def remove_attribute(self, *args):
4752 remove_attribute(Chain self, FloatKey a0)
4753 remove_attribute(Chain self, IntKey a0)
4754 remove_attribute(Chain self, FloatsKey a0)
4755 remove_attribute(Chain self, IntsKey a0)
4756 remove_attribute(Chain self, StringKey a0)
4757 remove_attribute(Chain self, ParticleIndexKey a0)
4758 remove_attribute(Chain self, ObjectKey a0)
4760 return _IMP_atom.Chain_remove_attribute(self, *args)
4763 def has_attribute(self, *args):
4765 has_attribute(Chain self, FloatKey a0) -> bool
4766 has_attribute(Chain self, IntKey a0) -> bool
4767 has_attribute(Chain self, FloatsKey a0) -> bool
4768 has_attribute(Chain self, IntsKey a0) -> bool
4769 has_attribute(Chain self, StringKey a0) -> bool
4770 has_attribute(Chain self, ParticleIndexKey a0) -> bool
4771 has_attribute(Chain self, ObjectKey a0) -> bool
4773 return _IMP_atom.Chain_has_attribute(self, *args)
4776 def get_derivative(self, a0):
4777 """get_derivative(Chain self, FloatKey a0) -> double"""
4778 return _IMP_atom.Chain_get_derivative(self, a0)
4782 """get_name(Chain self) -> std::string"""
4783 return _IMP_atom.Chain_get_name(self)
4786 def clear_caches(self):
4787 """clear_caches(Chain self)"""
4788 return _IMP_atom.Chain_clear_caches(self)
4791 def set_name(self, a0):
4792 """set_name(Chain self, std::string a0)"""
4793 return _IMP_atom.Chain_set_name(self, a0)
4797 """set_check_level(Chain self, IMP::CheckLevel a0)"""
4798 return _IMP_atom.Chain_set_check_level(self, a0)
4801 def add_to_derivative(self, a0, a1, a2):
4802 """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4803 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4806 def set_is_optimized(self, a0, a1):
4807 """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4808 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4811 def get_is_optimized(self, a0):
4812 """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4813 return _IMP_atom.Chain_get_is_optimized(self, a0)
4817 """get_check_level(Chain self) -> IMP::CheckLevel"""
4818 return _IMP_atom.Chain_get_check_level(self)
4821 def __eq__(self, *args):
4823 __eq__(Chain self, Chain o) -> bool
4824 __eq__(Chain self, Particle d) -> bool
4826 return _IMP_atom.Chain___eq__(self, *args)
4829 def __ne__(self, *args):
4831 __ne__(Chain self, Chain o) -> bool
4832 __ne__(Chain self, Particle d) -> bool
4834 return _IMP_atom.Chain___ne__(self, *args)
4837 def __le__(self, *args):
4839 __le__(Chain self, Chain o) -> bool
4840 __le__(Chain self, Particle d) -> bool
4842 return _IMP_atom.Chain___le__(self, *args)
4845 def __lt__(self, *args):
4847 __lt__(Chain self, Chain o) -> bool
4848 __lt__(Chain self, Particle d) -> bool
4850 return _IMP_atom.Chain___lt__(self, *args)
4853 def __ge__(self, *args):
4855 __ge__(Chain self, Chain o) -> bool
4856 __ge__(Chain self, Particle d) -> bool
4858 return _IMP_atom.Chain___ge__(self, *args)
4861 def __gt__(self, *args):
4863 __gt__(Chain self, Chain o) -> bool
4864 __gt__(Chain self, Particle d) -> bool
4866 return _IMP_atom.Chain___gt__(self, *args)
4870 """__hash__(Chain self) -> std::size_t"""
4871 return _IMP_atom.Chain___hash__(self)
4875 """__str__(Chain self) -> std::string"""
4876 return _IMP_atom.Chain___str__(self)
4880 """__repr__(Chain self) -> std::string"""
4881 return _IMP_atom.Chain___repr__(self)
4883 __swig_destroy__ = _IMP_atom.delete_Chain
4884 __del__ =
lambda self:
None
4885 Chain_swigregister = _IMP_atom.Chain_swigregister
4886 Chain_swigregister(Chain)
4887 cvar = _IMP_atom.cvar
4888 UnknownChainType = cvar.UnknownChainType
4889 DPolypeptide = cvar.DPolypeptide
4890 LPolypeptide = cvar.LPolypeptide
4891 Polydeoxyribonucleotide = cvar.Polydeoxyribonucleotide
4892 Polyribonucleotide = cvar.Polyribonucleotide
4893 DPolysaccharide = cvar.DPolysaccharide
4894 LPolysaccharide = cvar.LPolysaccharide
4895 Protein = cvar.Protein
4899 def Chain_setup_particle(*args):
4901 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4902 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4903 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4904 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4905 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4906 Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4908 return _IMP_atom.Chain_setup_particle(*args)
4910 def Chain_get_is_setup(*args):
4912 get_is_setup(_ParticleAdaptor p) -> bool
4913 Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4915 return _IMP_atom.Chain_get_is_setup(*args)
4917 def Chain_get_id_key():
4918 """Chain_get_id_key() -> StringKey"""
4919 return _IMP_atom.Chain_get_id_key()
4921 def Chain_get_sequence_key():
4922 """Chain_get_sequence_key() -> StringKey"""
4923 return _IMP_atom.Chain_get_sequence_key()
4925 def Chain_get_chain_type_key():
4926 """Chain_get_chain_type_key() -> IntKey"""
4927 return _IMP_atom.Chain_get_chain_type_key()
4931 """get_chain(Hierarchy h) -> Chain"""
4932 return _IMP_atom.get_chain(h)
4935 """get_chain_id(Hierarchy h) -> std::string"""
4936 return _IMP_atom.get_chain_id(h)
4938 """Proxy of C++ IMP::atom::Charged class."""
4940 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4942 def __init__(self, *args):
4944 __init__(IMP::atom::Charged self) -> Charged
4945 __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4946 __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4948 this = _IMP_atom.new_Charged(*args)
4950 self.this.append(this)
4951 except __builtin__.Exception:
4954 def show(self, *args):
4956 show(Charged self, _ostream out)
4959 return _IMP_atom.Charged_show(self, *args)
4962 def setup_particle(*args):
4964 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
4965 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
4966 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
4967 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
4969 return _IMP_atom.Charged_setup_particle(*args)
4971 setup_particle = staticmethod(setup_particle)
4973 def get_charge(self):
4974 """get_charge(Charged self) -> IMP::Float"""
4975 return _IMP_atom.Charged_get_charge(self)
4978 def set_charge(self, t):
4979 """set_charge(Charged self, IMP::Float t)"""
4980 return _IMP_atom.Charged_set_charge(self, t)
4983 def get_is_setup(*args):
4985 get_is_setup(_ParticleAdaptor p) -> bool
4986 get_is_setup(Model m, ParticleIndex pi) -> bool
4988 return _IMP_atom.Charged_get_is_setup(*args)
4990 get_is_setup = staticmethod(get_is_setup)
4992 def get_charge_key():
4993 """get_charge_key() -> FloatKey"""
4994 return _IMP_atom.Charged_get_charge_key()
4996 get_charge_key = staticmethod(get_charge_key)
4998 def add_attribute(self, *args):
5000 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
5001 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
5002 add_attribute(Charged self, IntKey a0, IMP::Int a1)
5003 add_attribute(Charged self, FloatsKey a0, IMP::Floats a1)
5004 add_attribute(Charged self, IntsKey a0, IMP::Ints a1)
5005 add_attribute(Charged self, StringKey a0, IMP::String a1)
5006 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
5007 add_attribute(Charged self, ObjectKey a0, Object a1)
5009 return _IMP_atom.Charged_add_attribute(self, *args)
5012 def get_value(self, *args):
5014 get_value(Charged self, FloatKey a0) -> IMP::Float
5015 get_value(Charged self, IntKey a0) -> IMP::Int
5016 get_value(Charged self, FloatsKey a0) -> IMP::Floats
5017 get_value(Charged self, IntsKey a0) -> IMP::Ints
5018 get_value(Charged self, StringKey a0) -> IMP::String
5019 get_value(Charged self, ParticleIndexKey a0) -> Particle
5020 get_value(Charged self, ObjectKey a0) -> Object
5022 return _IMP_atom.Charged_get_value(self, *args)
5025 def set_value(self, *args):
5027 set_value(Charged self, FloatKey a0, IMP::Float a1)
5028 set_value(Charged self, IntKey a0, IMP::Int a1)
5029 set_value(Charged self, FloatsKey a0, IMP::Floats a1)
5030 set_value(Charged self, IntsKey a0, IMP::Ints a1)
5031 set_value(Charged self, StringKey a0, IMP::String a1)
5032 set_value(Charged self, ParticleIndexKey a0, Particle a1)
5033 set_value(Charged self, ObjectKey a0, Object a1)
5035 return _IMP_atom.Charged_set_value(self, *args)
5038 def remove_attribute(self, *args):
5040 remove_attribute(Charged self, FloatKey a0)
5041 remove_attribute(Charged self, IntKey a0)
5042 remove_attribute(Charged self, FloatsKey a0)
5043 remove_attribute(Charged self, IntsKey a0)
5044 remove_attribute(Charged self, StringKey a0)
5045 remove_attribute(Charged self, ParticleIndexKey a0)
5046 remove_attribute(Charged self, ObjectKey a0)
5048 return _IMP_atom.Charged_remove_attribute(self, *args)
5051 def has_attribute(self, *args):
5053 has_attribute(Charged self, FloatKey a0) -> bool
5054 has_attribute(Charged self, IntKey a0) -> bool
5055 has_attribute(Charged self, FloatsKey a0) -> bool
5056 has_attribute(Charged self, IntsKey a0) -> bool
5057 has_attribute(Charged self, StringKey a0) -> bool
5058 has_attribute(Charged self, ParticleIndexKey a0) -> bool
5059 has_attribute(Charged self, ObjectKey a0) -> bool
5061 return _IMP_atom.Charged_has_attribute(self, *args)
5064 def get_derivative(self, a0):
5065 """get_derivative(Charged self, FloatKey a0) -> double"""
5066 return _IMP_atom.Charged_get_derivative(self, a0)
5070 """get_name(Charged self) -> std::string"""
5071 return _IMP_atom.Charged_get_name(self)
5074 def clear_caches(self):
5075 """clear_caches(Charged self)"""
5076 return _IMP_atom.Charged_clear_caches(self)
5079 def set_name(self, a0):
5080 """set_name(Charged self, std::string a0)"""
5081 return _IMP_atom.Charged_set_name(self, a0)
5085 """set_check_level(Charged self, IMP::CheckLevel a0)"""
5086 return _IMP_atom.Charged_set_check_level(self, a0)
5089 def add_to_derivative(self, a0, a1, a2):
5090 """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5091 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
5094 def set_is_optimized(self, a0, a1):
5095 """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
5096 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
5099 def get_is_optimized(self, a0):
5100 """get_is_optimized(Charged self, FloatKey a0) -> bool"""
5101 return _IMP_atom.Charged_get_is_optimized(self, a0)
5105 """get_check_level(Charged self) -> IMP::CheckLevel"""
5106 return _IMP_atom.Charged_get_check_level(self)
5109 def __eq__(self, *args):
5111 __eq__(Charged self, Charged o) -> bool
5112 __eq__(Charged self, Particle d) -> bool
5114 return _IMP_atom.Charged___eq__(self, *args)
5117 def __ne__(self, *args):
5119 __ne__(Charged self, Charged o) -> bool
5120 __ne__(Charged self, Particle d) -> bool
5122 return _IMP_atom.Charged___ne__(self, *args)
5125 def __le__(self, *args):
5127 __le__(Charged self, Charged o) -> bool
5128 __le__(Charged self, Particle d) -> bool
5130 return _IMP_atom.Charged___le__(self, *args)
5133 def __lt__(self, *args):
5135 __lt__(Charged self, Charged o) -> bool
5136 __lt__(Charged self, Particle d) -> bool
5138 return _IMP_atom.Charged___lt__(self, *args)
5141 def __ge__(self, *args):
5143 __ge__(Charged self, Charged o) -> bool
5144 __ge__(Charged self, Particle d) -> bool
5146 return _IMP_atom.Charged___ge__(self, *args)
5149 def __gt__(self, *args):
5151 __gt__(Charged self, Charged o) -> bool
5152 __gt__(Charged self, Particle d) -> bool
5154 return _IMP_atom.Charged___gt__(self, *args)
5158 """__hash__(Charged self) -> std::size_t"""
5159 return _IMP_atom.Charged___hash__(self)
5163 """__str__(Charged self) -> std::string"""
5164 return _IMP_atom.Charged___str__(self)
5168 """__repr__(Charged self) -> std::string"""
5169 return _IMP_atom.Charged___repr__(self)
5171 __swig_destroy__ = _IMP_atom.delete_Charged
5172 __del__ =
lambda self:
None
5173 Charged_swigregister = _IMP_atom.Charged_swigregister
5174 Charged_swigregister(Charged)
5176 def Charged_setup_particle(*args):
5178 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5179 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5180 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5181 Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5183 return _IMP_atom.Charged_setup_particle(*args)
5185 def Charged_get_is_setup(*args):
5187 get_is_setup(_ParticleAdaptor p) -> bool
5188 Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5190 return _IMP_atom.Charged_get_is_setup(*args)
5192 def Charged_get_charge_key():
5193 """Charged_get_charge_key() -> FloatKey"""
5194 return _IMP_atom.Charged_get_charge_key()
5197 """Proxy of C++ IMP::atom::CoulombPairScore class."""
5199 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5201 def __init__(self, f):
5202 """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5203 this = _IMP_atom.new_CoulombPairScore(f)
5205 self.this.append(this)
5206 except __builtin__.Exception:
5209 def set_relative_dielectric(self, relative_dielectric):
5210 """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5211 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5214 def get_relative_dielectric(self):
5215 """get_relative_dielectric(CoulombPairScore self) -> double"""
5216 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5219 def do_get_inputs(self, m, pis):
5220 """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5221 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5224 def get_version_info(self):
5225 """get_version_info(CoulombPairScore self) -> VersionInfo"""
5226 return _IMP_atom.CoulombPairScore_get_version_info(self)
5230 """__str__(CoulombPairScore self) -> std::string"""
5231 return _IMP_atom.CoulombPairScore___str__(self)
5235 """__repr__(CoulombPairScore self) -> std::string"""
5236 return _IMP_atom.CoulombPairScore___repr__(self)
5241 return _object_cast_to_CoulombPairScore(o)
5243 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5244 CoulombPairScore_swigregister(CoulombPairScore)
5246 class Domain(Hierarchy):
5247 """Proxy of C++ IMP::atom::Domain class."""
5249 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5251 def set_index_range(self, ir):
5252 """set_index_range(Domain self, IMP::IntRange ir)"""
5253 return _IMP_atom.Domain_set_index_range(self, ir)
5256 def get_index_range(self):
5257 """get_index_range(Domain self) -> IMP::IntRange"""
5258 return _IMP_atom.Domain_get_index_range(self)
5261 def __init__(self, *args):
5263 __init__(IMP::atom::Domain self) -> Domain
5264 __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5265 __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5267 this = _IMP_atom.new_Domain(*args)
5269 self.this.append(this)
5270 except __builtin__.Exception:
5273 def get_is_setup(*args):
5275 get_is_setup(Model m, ParticleIndex pi) -> bool
5276 get_is_setup(_ParticleAdaptor p) -> bool
5278 return _IMP_atom.Domain_get_is_setup(*args)
5280 get_is_setup = staticmethod(get_is_setup)
5282 def show(self, *args):
5284 show(Domain self, _ostream out)
5287 return _IMP_atom.Domain_show(self, *args)
5290 def setup_particle(*args):
5292 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5293 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5294 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5295 setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5297 return _IMP_atom.Domain_setup_particle(*args)
5299 setup_particle = staticmethod(setup_particle)
5301 def add_attribute(self, *args):
5303 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5304 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5305 add_attribute(Domain self, IntKey a0, IMP::Int a1)
5306 add_attribute(Domain self, FloatsKey a0, IMP::Floats a1)
5307 add_attribute(Domain self, IntsKey a0, IMP::Ints a1)
5308 add_attribute(Domain self, StringKey a0, IMP::String a1)
5309 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5310 add_attribute(Domain self, ObjectKey a0, Object a1)
5312 return _IMP_atom.Domain_add_attribute(self, *args)
5315 def get_value(self, *args):
5317 get_value(Domain self, FloatKey a0) -> IMP::Float
5318 get_value(Domain self, IntKey a0) -> IMP::Int
5319 get_value(Domain self, FloatsKey a0) -> IMP::Floats
5320 get_value(Domain self, IntsKey a0) -> IMP::Ints
5321 get_value(Domain self, StringKey a0) -> IMP::String
5322 get_value(Domain self, ParticleIndexKey a0) -> Particle
5323 get_value(Domain self, ObjectKey a0) -> Object
5325 return _IMP_atom.Domain_get_value(self, *args)
5328 def set_value(self, *args):
5330 set_value(Domain self, FloatKey a0, IMP::Float a1)
5331 set_value(Domain self, IntKey a0, IMP::Int a1)
5332 set_value(Domain self, FloatsKey a0, IMP::Floats a1)
5333 set_value(Domain self, IntsKey a0, IMP::Ints a1)
5334 set_value(Domain self, StringKey a0, IMP::String a1)
5335 set_value(Domain self, ParticleIndexKey a0, Particle a1)
5336 set_value(Domain self, ObjectKey a0, Object a1)
5338 return _IMP_atom.Domain_set_value(self, *args)
5341 def remove_attribute(self, *args):
5343 remove_attribute(Domain self, FloatKey a0)
5344 remove_attribute(Domain self, IntKey a0)
5345 remove_attribute(Domain self, FloatsKey a0)
5346 remove_attribute(Domain self, IntsKey a0)
5347 remove_attribute(Domain self, StringKey a0)
5348 remove_attribute(Domain self, ParticleIndexKey a0)
5349 remove_attribute(Domain self, ObjectKey a0)
5351 return _IMP_atom.Domain_remove_attribute(self, *args)
5354 def has_attribute(self, *args):
5356 has_attribute(Domain self, FloatKey a0) -> bool
5357 has_attribute(Domain self, IntKey a0) -> bool
5358 has_attribute(Domain self, FloatsKey a0) -> bool
5359 has_attribute(Domain self, IntsKey a0) -> bool
5360 has_attribute(Domain self, StringKey a0) -> bool
5361 has_attribute(Domain self, ParticleIndexKey a0) -> bool
5362 has_attribute(Domain self, ObjectKey a0) -> bool
5364 return _IMP_atom.Domain_has_attribute(self, *args)
5367 def get_derivative(self, a0):
5368 """get_derivative(Domain self, FloatKey a0) -> double"""
5369 return _IMP_atom.Domain_get_derivative(self, a0)
5373 """get_name(Domain self) -> std::string"""
5374 return _IMP_atom.Domain_get_name(self)
5377 def clear_caches(self):
5378 """clear_caches(Domain self)"""
5379 return _IMP_atom.Domain_clear_caches(self)
5382 def set_name(self, a0):
5383 """set_name(Domain self, std::string a0)"""
5384 return _IMP_atom.Domain_set_name(self, a0)
5388 """set_check_level(Domain self, IMP::CheckLevel a0)"""
5389 return _IMP_atom.Domain_set_check_level(self, a0)
5392 def add_to_derivative(self, a0, a1, a2):
5393 """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5394 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5397 def set_is_optimized(self, a0, a1):
5398 """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5399 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5402 def get_is_optimized(self, a0):
5403 """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5404 return _IMP_atom.Domain_get_is_optimized(self, a0)
5408 """get_check_level(Domain self) -> IMP::CheckLevel"""
5409 return _IMP_atom.Domain_get_check_level(self)
5412 def __eq__(self, *args):
5414 __eq__(Domain self, Domain o) -> bool
5415 __eq__(Domain self, Particle d) -> bool
5417 return _IMP_atom.Domain___eq__(self, *args)
5420 def __ne__(self, *args):
5422 __ne__(Domain self, Domain o) -> bool
5423 __ne__(Domain self, Particle d) -> bool
5425 return _IMP_atom.Domain___ne__(self, *args)
5428 def __le__(self, *args):
5430 __le__(Domain self, Domain o) -> bool
5431 __le__(Domain self, Particle d) -> bool
5433 return _IMP_atom.Domain___le__(self, *args)
5436 def __lt__(self, *args):
5438 __lt__(Domain self, Domain o) -> bool
5439 __lt__(Domain self, Particle d) -> bool
5441 return _IMP_atom.Domain___lt__(self, *args)
5444 def __ge__(self, *args):
5446 __ge__(Domain self, Domain o) -> bool
5447 __ge__(Domain self, Particle d) -> bool
5449 return _IMP_atom.Domain___ge__(self, *args)
5452 def __gt__(self, *args):
5454 __gt__(Domain self, Domain o) -> bool
5455 __gt__(Domain self, Particle d) -> bool
5457 return _IMP_atom.Domain___gt__(self, *args)
5461 """__hash__(Domain self) -> std::size_t"""
5462 return _IMP_atom.Domain___hash__(self)
5466 """__str__(Domain self) -> std::string"""
5467 return _IMP_atom.Domain___str__(self)
5471 """__repr__(Domain self) -> std::string"""
5472 return _IMP_atom.Domain___repr__(self)
5474 __swig_destroy__ = _IMP_atom.delete_Domain
5475 __del__ =
lambda self:
None
5476 Domain_swigregister = _IMP_atom.Domain_swigregister
5477 Domain_swigregister(Domain)
5479 def Domain_get_is_setup(*args):
5481 get_is_setup(Model m, ParticleIndex pi) -> bool
5482 Domain_get_is_setup(_ParticleAdaptor p) -> bool
5484 return _IMP_atom.Domain_get_is_setup(*args)
5486 def Domain_setup_particle(*args):
5488 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5489 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5490 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5491 Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5493 return _IMP_atom.Domain_setup_particle(*args)
5496 """Proxy of C++ IMP::atom::LennardJones class."""
5498 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5500 def __init__(self, *args):
5502 __init__(IMP::atom::LennardJones self) -> LennardJones
5503 __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5504 __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5506 this = _IMP_atom.new_LennardJones(*args)
5508 self.this.append(this)
5509 except __builtin__.Exception:
5512 def show(self, *args):
5514 show(LennardJones self, _ostream out)
5515 show(LennardJones self)
5517 return _IMP_atom.LennardJones_show(self, *args)
5520 def setup_particle(*args):
5522 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5523 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5524 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5525 setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5527 return _IMP_atom.LennardJones_setup_particle(*args)
5529 setup_particle = staticmethod(setup_particle)
5531 def get_well_depth(self):
5532 """get_well_depth(LennardJones self) -> IMP::Float"""
5533 return _IMP_atom.LennardJones_get_well_depth(self)
5536 def set_well_depth(self, well_depth):
5537 """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5538 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5541 def get_is_setup(*args):
5543 get_is_setup(_ParticleAdaptor p) -> bool
5544 get_is_setup(Model m, ParticleIndex pi) -> bool
5546 return _IMP_atom.LennardJones_get_is_setup(*args)
5548 get_is_setup = staticmethod(get_is_setup)
5550 def get_well_depth_key():
5551 """get_well_depth_key() -> FloatKey"""
5552 return _IMP_atom.LennardJones_get_well_depth_key()
5554 get_well_depth_key = staticmethod(get_well_depth_key)
5556 def add_attribute(self, *args):
5558 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5559 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5560 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5561 add_attribute(LennardJones self, FloatsKey a0, IMP::Floats a1)
5562 add_attribute(LennardJones self, IntsKey a0, IMP::Ints a1)
5563 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5564 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5565 add_attribute(LennardJones self, ObjectKey a0, Object a1)
5567 return _IMP_atom.LennardJones_add_attribute(self, *args)
5570 def get_value(self, *args):
5572 get_value(LennardJones self, FloatKey a0) -> IMP::Float
5573 get_value(LennardJones self, IntKey a0) -> IMP::Int
5574 get_value(LennardJones self, FloatsKey a0) -> IMP::Floats
5575 get_value(LennardJones self, IntsKey a0) -> IMP::Ints
5576 get_value(LennardJones self, StringKey a0) -> IMP::String
5577 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5578 get_value(LennardJones self, ObjectKey a0) -> Object
5580 return _IMP_atom.LennardJones_get_value(self, *args)
5583 def set_value(self, *args):
5585 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5586 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5587 set_value(LennardJones self, FloatsKey a0, IMP::Floats a1)
5588 set_value(LennardJones self, IntsKey a0, IMP::Ints a1)
5589 set_value(LennardJones self, StringKey a0, IMP::String a1)
5590 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5591 set_value(LennardJones self, ObjectKey a0, Object a1)
5593 return _IMP_atom.LennardJones_set_value(self, *args)
5596 def remove_attribute(self, *args):
5598 remove_attribute(LennardJones self, FloatKey a0)
5599 remove_attribute(LennardJones self, IntKey a0)
5600 remove_attribute(LennardJones self, FloatsKey a0)
5601 remove_attribute(LennardJones self, IntsKey a0)
5602 remove_attribute(LennardJones self, StringKey a0)
5603 remove_attribute(LennardJones self, ParticleIndexKey a0)
5604 remove_attribute(LennardJones self, ObjectKey a0)
5606 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5609 def has_attribute(self, *args):
5611 has_attribute(LennardJones self, FloatKey a0) -> bool
5612 has_attribute(LennardJones self, IntKey a0) -> bool
5613 has_attribute(LennardJones self, FloatsKey a0) -> bool
5614 has_attribute(LennardJones self, IntsKey a0) -> bool
5615 has_attribute(LennardJones self, StringKey a0) -> bool
5616 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5617 has_attribute(LennardJones self, ObjectKey a0) -> bool
5619 return _IMP_atom.LennardJones_has_attribute(self, *args)
5622 def get_derivative(self, a0):
5623 """get_derivative(LennardJones self, FloatKey a0) -> double"""
5624 return _IMP_atom.LennardJones_get_derivative(self, a0)
5628 """get_name(LennardJones self) -> std::string"""
5629 return _IMP_atom.LennardJones_get_name(self)
5632 def clear_caches(self):
5633 """clear_caches(LennardJones self)"""
5634 return _IMP_atom.LennardJones_clear_caches(self)
5637 def set_name(self, a0):
5638 """set_name(LennardJones self, std::string a0)"""
5639 return _IMP_atom.LennardJones_set_name(self, a0)
5643 """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5644 return _IMP_atom.LennardJones_set_check_level(self, a0)
5647 def add_to_derivative(self, a0, a1, a2):
5648 """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5649 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5652 def set_is_optimized(self, a0, a1):
5653 """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5654 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5657 def get_is_optimized(self, a0):
5658 """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5659 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5663 """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5664 return _IMP_atom.LennardJones_get_check_level(self)
5667 def __eq__(self, *args):
5669 __eq__(LennardJones self, LennardJones o) -> bool
5670 __eq__(LennardJones self, Particle d) -> bool
5672 return _IMP_atom.LennardJones___eq__(self, *args)
5675 def __ne__(self, *args):
5677 __ne__(LennardJones self, LennardJones o) -> bool
5678 __ne__(LennardJones self, Particle d) -> bool
5680 return _IMP_atom.LennardJones___ne__(self, *args)
5683 def __le__(self, *args):
5685 __le__(LennardJones self, LennardJones o) -> bool
5686 __le__(LennardJones self, Particle d) -> bool
5688 return _IMP_atom.LennardJones___le__(self, *args)
5691 def __lt__(self, *args):
5693 __lt__(LennardJones self, LennardJones o) -> bool
5694 __lt__(LennardJones self, Particle d) -> bool
5696 return _IMP_atom.LennardJones___lt__(self, *args)
5699 def __ge__(self, *args):
5701 __ge__(LennardJones self, LennardJones o) -> bool
5702 __ge__(LennardJones self, Particle d) -> bool
5704 return _IMP_atom.LennardJones___ge__(self, *args)
5707 def __gt__(self, *args):
5709 __gt__(LennardJones self, LennardJones o) -> bool
5710 __gt__(LennardJones self, Particle d) -> bool
5712 return _IMP_atom.LennardJones___gt__(self, *args)
5716 """__hash__(LennardJones self) -> std::size_t"""
5717 return _IMP_atom.LennardJones___hash__(self)
5721 """__str__(LennardJones self) -> std::string"""
5722 return _IMP_atom.LennardJones___str__(self)
5726 """__repr__(LennardJones self) -> std::string"""
5727 return _IMP_atom.LennardJones___repr__(self)
5729 __swig_destroy__ = _IMP_atom.delete_LennardJones
5730 __del__ =
lambda self:
None
5731 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5732 LennardJones_swigregister(LennardJones)
5734 def LennardJones_setup_particle(*args):
5736 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5737 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5738 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5739 LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5741 return _IMP_atom.LennardJones_setup_particle(*args)
5743 def LennardJones_get_is_setup(*args):
5745 get_is_setup(_ParticleAdaptor p) -> bool
5746 LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5748 return _IMP_atom.LennardJones_get_is_setup(*args)
5750 def LennardJones_get_well_depth_key():
5751 """LennardJones_get_well_depth_key() -> FloatKey"""
5752 return _IMP_atom.LennardJones_get_well_depth_key()
5755 """Proxy of C++ IMP::atom::LennardJonesPairScore class."""
5757 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5759 def __init__(self, f):
5760 """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5761 this = _IMP_atom.new_LennardJonesPairScore(f)
5763 self.this.append(this)
5764 except __builtin__.Exception:
5767 def set_repulsive_weight(self, repulsive_weight):
5768 """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5769 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5772 def get_repulsive_weight(self):
5773 """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5774 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5777 def set_attractive_weight(self, attractive_weight):
5778 """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5779 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5782 def get_attractive_weight(self):
5783 """get_attractive_weight(LennardJonesPairScore self) -> double"""
5784 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5787 def do_get_inputs(self, m, pis):
5788 """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5789 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5792 def get_version_info(self):
5793 """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5794 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5798 """__str__(LennardJonesPairScore self) -> std::string"""
5799 return _IMP_atom.LennardJonesPairScore___str__(self)
5803 """__repr__(LennardJonesPairScore self) -> std::string"""
5804 return _IMP_atom.LennardJonesPairScore___repr__(self)
5809 return _object_cast_to_LennardJonesPairScore(o)
5811 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5812 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5815 """Proxy of C++ IMP::atom::LinearVelocity class."""
5817 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5819 def __init__(self, *args):
5821 __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5822 __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5823 __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5825 this = _IMP_atom.new_LinearVelocity(*args)
5827 self.this.append(this)
5828 except __builtin__.Exception:
5831 def get_is_setup(*args):
5833 get_is_setup(Model m, ParticleIndex pi) -> bool
5834 get_is_setup(_ParticleAdaptor p) -> bool
5836 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5838 get_is_setup = staticmethod(get_is_setup)
5840 def show(self, *args):
5842 show(LinearVelocity self, _ostream out)
5843 show(LinearVelocity self)
5845 return _IMP_atom.LinearVelocity_show(self, *args)
5848 def setup_particle(*args):
5850 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5851 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5852 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5853 setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5855 return _IMP_atom.LinearVelocity_setup_particle(*args)
5857 setup_particle = staticmethod(setup_particle)
5859 def set_velocity(self, v):
5860 """set_velocity(LinearVelocity self, Vector3D v)"""
5861 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5864 def get_velocity(self):
5865 """get_velocity(LinearVelocity self) -> Vector3D"""
5866 return _IMP_atom.LinearVelocity_get_velocity(self)
5869 def add_attribute(self, *args):
5871 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5872 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5873 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5874 add_attribute(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5875 add_attribute(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5876 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5877 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5878 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5880 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5883 def get_value(self, *args):
5885 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5886 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5887 get_value(LinearVelocity self, FloatsKey a0) -> IMP::Floats
5888 get_value(LinearVelocity self, IntsKey a0) -> IMP::Ints
5889 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5890 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5891 get_value(LinearVelocity self, ObjectKey a0) -> Object
5893 return _IMP_atom.LinearVelocity_get_value(self, *args)
5896 def set_value(self, *args):
5898 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5899 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5900 set_value(LinearVelocity self, FloatsKey a0, IMP::Floats a1)
5901 set_value(LinearVelocity self, IntsKey a0, IMP::Ints a1)
5902 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5903 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5904 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5906 return _IMP_atom.LinearVelocity_set_value(self, *args)
5909 def remove_attribute(self, *args):
5911 remove_attribute(LinearVelocity self, FloatKey a0)
5912 remove_attribute(LinearVelocity self, IntKey a0)
5913 remove_attribute(LinearVelocity self, FloatsKey a0)
5914 remove_attribute(LinearVelocity self, IntsKey a0)
5915 remove_attribute(LinearVelocity self, StringKey a0)
5916 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5917 remove_attribute(LinearVelocity self, ObjectKey a0)
5919 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5922 def has_attribute(self, *args):
5924 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5925 has_attribute(LinearVelocity self, IntKey a0) -> bool
5926 has_attribute(LinearVelocity self, FloatsKey a0) -> bool
5927 has_attribute(LinearVelocity self, IntsKey a0) -> bool
5928 has_attribute(LinearVelocity self, StringKey a0) -> bool
5929 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5930 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5932 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5935 def get_derivative(self, a0):
5936 """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5937 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5941 """get_name(LinearVelocity self) -> std::string"""
5942 return _IMP_atom.LinearVelocity_get_name(self)
5945 def clear_caches(self):
5946 """clear_caches(LinearVelocity self)"""
5947 return _IMP_atom.LinearVelocity_clear_caches(self)
5950 def set_name(self, a0):
5951 """set_name(LinearVelocity self, std::string a0)"""
5952 return _IMP_atom.LinearVelocity_set_name(self, a0)
5956 """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5957 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5960 def add_to_derivative(self, a0, a1, a2):
5961 """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5962 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5965 def set_is_optimized(self, a0, a1):
5966 """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5967 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5970 def get_is_optimized(self, a0):
5971 """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5972 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5976 """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5977 return _IMP_atom.LinearVelocity_get_check_level(self)
5980 def __eq__(self, *args):
5982 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5983 __eq__(LinearVelocity self, Particle d) -> bool
5985 return _IMP_atom.LinearVelocity___eq__(self, *args)
5988 def __ne__(self, *args):
5990 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5991 __ne__(LinearVelocity self, Particle d) -> bool
5993 return _IMP_atom.LinearVelocity___ne__(self, *args)
5996 def __le__(self, *args):
5998 __le__(LinearVelocity self, LinearVelocity o) -> bool
5999 __le__(LinearVelocity self, Particle d) -> bool
6001 return _IMP_atom.LinearVelocity___le__(self, *args)
6004 def __lt__(self, *args):
6006 __lt__(LinearVelocity self, LinearVelocity o) -> bool
6007 __lt__(LinearVelocity self, Particle d) -> bool
6009 return _IMP_atom.LinearVelocity___lt__(self, *args)
6012 def __ge__(self, *args):
6014 __ge__(LinearVelocity self, LinearVelocity o) -> bool
6015 __ge__(LinearVelocity self, Particle d) -> bool
6017 return _IMP_atom.LinearVelocity___ge__(self, *args)
6020 def __gt__(self, *args):
6022 __gt__(LinearVelocity self, LinearVelocity o) -> bool
6023 __gt__(LinearVelocity self, Particle d) -> bool
6025 return _IMP_atom.LinearVelocity___gt__(self, *args)
6029 """__hash__(LinearVelocity self) -> std::size_t"""
6030 return _IMP_atom.LinearVelocity___hash__(self)
6034 """__str__(LinearVelocity self) -> std::string"""
6035 return _IMP_atom.LinearVelocity___str__(self)
6039 """__repr__(LinearVelocity self) -> std::string"""
6040 return _IMP_atom.LinearVelocity___repr__(self)
6042 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
6043 __del__ =
lambda self:
None
6044 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
6045 LinearVelocity_swigregister(LinearVelocity)
6047 def LinearVelocity_get_is_setup(*args):
6049 get_is_setup(Model m, ParticleIndex pi) -> bool
6050 LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6052 return _IMP_atom.LinearVelocity_get_is_setup(*args)
6054 def LinearVelocity_setup_particle(*args):
6056 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
6057 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
6058 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
6059 LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
6061 return _IMP_atom.LinearVelocity_setup_particle(*args)
6064 """Proxy of C++ IMP::atom::AngularVelocity class."""
6066 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6068 def __init__(self, *args):
6070 __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
6071 __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
6072 __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
6074 this = _IMP_atom.new_AngularVelocity(*args)
6076 self.this.append(this)
6077 except __builtin__.Exception:
6080 def get_is_setup(*args):
6082 get_is_setup(Model m, ParticleIndex pi) -> bool
6083 get_is_setup(_ParticleAdaptor p) -> bool
6085 return _IMP_atom.AngularVelocity_get_is_setup(*args)
6087 get_is_setup = staticmethod(get_is_setup)
6089 def show(self, *args):
6091 show(AngularVelocity self, _ostream out)
6092 show(AngularVelocity self)
6094 return _IMP_atom.AngularVelocity_show(self, *args)
6097 def setup_particle(*args):
6099 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6100 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6101 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6102 setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6104 return _IMP_atom.AngularVelocity_setup_particle(*args)
6106 setup_particle = staticmethod(setup_particle)
6108 def set_velocity(self, v):
6109 """set_velocity(AngularVelocity self, Vector4D v)"""
6110 return _IMP_atom.AngularVelocity_set_velocity(self, v)
6113 def get_velocity(self):
6114 """get_velocity(AngularVelocity self) -> Vector4D"""
6115 return _IMP_atom.AngularVelocity_get_velocity(self)
6118 def add_attribute(self, *args):
6120 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
6121 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
6122 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
6123 add_attribute(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
6124 add_attribute(AngularVelocity self, IntsKey a0, IMP::Ints a1)
6125 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
6126 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6127 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
6129 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
6132 def get_value(self, *args):
6134 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
6135 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
6136 get_value(AngularVelocity self, FloatsKey a0) -> IMP::Floats
6137 get_value(AngularVelocity self, IntsKey a0) -> IMP::Ints
6138 get_value(AngularVelocity self, StringKey a0) -> IMP::String
6139 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
6140 get_value(AngularVelocity self, ObjectKey a0) -> Object
6142 return _IMP_atom.AngularVelocity_get_value(self, *args)
6145 def set_value(self, *args):
6147 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
6148 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
6149 set_value(AngularVelocity self, FloatsKey a0, IMP::Floats a1)
6150 set_value(AngularVelocity self, IntsKey a0, IMP::Ints a1)
6151 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
6152 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6153 set_value(AngularVelocity self, ObjectKey a0, Object a1)
6155 return _IMP_atom.AngularVelocity_set_value(self, *args)
6158 def remove_attribute(self, *args):
6160 remove_attribute(AngularVelocity self, FloatKey a0)
6161 remove_attribute(AngularVelocity self, IntKey a0)
6162 remove_attribute(AngularVelocity self, FloatsKey a0)
6163 remove_attribute(AngularVelocity self, IntsKey a0)
6164 remove_attribute(AngularVelocity self, StringKey a0)
6165 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
6166 remove_attribute(AngularVelocity self, ObjectKey a0)
6168 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
6171 def has_attribute(self, *args):
6173 has_attribute(AngularVelocity self, FloatKey a0) -> bool
6174 has_attribute(AngularVelocity self, IntKey a0) -> bool
6175 has_attribute(AngularVelocity self, FloatsKey a0) -> bool
6176 has_attribute(AngularVelocity self, IntsKey a0) -> bool
6177 has_attribute(AngularVelocity self, StringKey a0) -> bool
6178 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6179 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6181 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6184 def get_derivative(self, a0):
6185 """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6186 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6190 """get_name(AngularVelocity self) -> std::string"""
6191 return _IMP_atom.AngularVelocity_get_name(self)
6194 def clear_caches(self):
6195 """clear_caches(AngularVelocity self)"""
6196 return _IMP_atom.AngularVelocity_clear_caches(self)
6199 def set_name(self, a0):
6200 """set_name(AngularVelocity self, std::string a0)"""
6201 return _IMP_atom.AngularVelocity_set_name(self, a0)
6205 """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6206 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6209 def add_to_derivative(self, a0, a1, a2):
6210 """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6211 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6214 def set_is_optimized(self, a0, a1):
6215 """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6216 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6219 def get_is_optimized(self, a0):
6220 """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6221 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6225 """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6226 return _IMP_atom.AngularVelocity_get_check_level(self)
6229 def __eq__(self, *args):
6231 __eq__(AngularVelocity self, AngularVelocity o) -> bool
6232 __eq__(AngularVelocity self, Particle d) -> bool
6234 return _IMP_atom.AngularVelocity___eq__(self, *args)
6237 def __ne__(self, *args):
6239 __ne__(AngularVelocity self, AngularVelocity o) -> bool
6240 __ne__(AngularVelocity self, Particle d) -> bool
6242 return _IMP_atom.AngularVelocity___ne__(self, *args)
6245 def __le__(self, *args):
6247 __le__(AngularVelocity self, AngularVelocity o) -> bool
6248 __le__(AngularVelocity self, Particle d) -> bool
6250 return _IMP_atom.AngularVelocity___le__(self, *args)
6253 def __lt__(self, *args):
6255 __lt__(AngularVelocity self, AngularVelocity o) -> bool
6256 __lt__(AngularVelocity self, Particle d) -> bool
6258 return _IMP_atom.AngularVelocity___lt__(self, *args)
6261 def __ge__(self, *args):
6263 __ge__(AngularVelocity self, AngularVelocity o) -> bool
6264 __ge__(AngularVelocity self, Particle d) -> bool
6266 return _IMP_atom.AngularVelocity___ge__(self, *args)
6269 def __gt__(self, *args):
6271 __gt__(AngularVelocity self, AngularVelocity o) -> bool
6272 __gt__(AngularVelocity self, Particle d) -> bool
6274 return _IMP_atom.AngularVelocity___gt__(self, *args)
6278 """__hash__(AngularVelocity self) -> std::size_t"""
6279 return _IMP_atom.AngularVelocity___hash__(self)
6283 """__str__(AngularVelocity self) -> std::string"""
6284 return _IMP_atom.AngularVelocity___str__(self)
6288 """__repr__(AngularVelocity self) -> std::string"""
6289 return _IMP_atom.AngularVelocity___repr__(self)
6291 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6292 __del__ =
lambda self:
None
6293 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6294 AngularVelocity_swigregister(AngularVelocity)
6296 def AngularVelocity_get_is_setup(*args):
6298 get_is_setup(Model m, ParticleIndex pi) -> bool
6299 AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6301 return _IMP_atom.AngularVelocity_get_is_setup(*args)
6303 def AngularVelocity_setup_particle(*args):
6305 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6306 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6307 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6308 AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6310 return _IMP_atom.AngularVelocity_setup_particle(*args)
6312 class MolecularDynamics(Simulator):
6313 """Proxy of C++ IMP::atom::MolecularDynamics class."""
6315 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6317 def __init__(self, m):
6318 """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6319 this = _IMP_atom.new_MolecularDynamics(m)
6321 self.this.append(this)
6322 except __builtin__.Exception:
6325 def get_kinetic_energy(self):
6326 """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6327 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6330 def get_kinetic_temperature(self, ekinetic):
6331 """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6332 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6335 def set_velocity_cap(self, velocity_cap):
6336 """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6337 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6340 def assign_velocities(self, temperature):
6341 """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6342 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6345 def setup(self, ps):
6346 """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6347 return _IMP_atom.MolecularDynamics_setup(self, ps)
6350 def do_step(self, sc, dt):
6351 """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6352 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6355 def get_is_simulation_particle(self, p):
6356 """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6357 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6360 def get_version_info(self):
6361 """get_version_info(MolecularDynamics self) -> VersionInfo"""
6362 return _IMP_atom.MolecularDynamics_get_version_info(self)
6366 """__str__(MolecularDynamics self) -> std::string"""
6367 return _IMP_atom.MolecularDynamics___str__(self)
6371 """__repr__(MolecularDynamics self) -> std::string"""
6372 return _IMP_atom.MolecularDynamics___repr__(self)
6377 return _object_cast_to_MolecularDynamics(o)
6379 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6380 MolecularDynamics_swigregister(MolecularDynamics)
6383 """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class."""
6385 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6387 def __init__(self, m, pis, temperature):
6388 """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6389 this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6391 self.this.append(this)
6392 except __builtin__.Exception:
6395 def set_particles(self, pis):
6396 """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6397 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6400 def set_temperature(self, temperature):
6401 """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6402 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6405 def rescale_velocities(self):
6406 """rescale_velocities(VelocityScalingOptimizerState self)"""
6407 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6410 def get_version_info(self):
6411 """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6412 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6416 """__str__(VelocityScalingOptimizerState self) -> std::string"""
6417 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6421 """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6422 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6427 return _object_cast_to_VelocityScalingOptimizerState(o)
6429 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6430 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6432 class Fragment(Hierarchy):
6433 """Proxy of C++ IMP::atom::Fragment class."""
6435 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6437 def set_residue_indexes(self, o):
6438 """set_residue_indexes(Fragment self, IMP::Ints o)"""
6439 return _IMP_atom.Fragment_set_residue_indexes(self, o)
6442 def get_residue_indexes(self):
6443 """get_residue_indexes(Fragment self) -> IMP::Ints"""
6444 return _IMP_atom.Fragment_get_residue_indexes(self)
6447 def get_contains_residue(self, rindex):
6448 """get_contains_residue(Fragment self, int rindex) -> bool"""
6449 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6452 def __init__(self, *args):
6454 __init__(IMP::atom::Fragment self) -> Fragment
6455 __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6456 __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6458 this = _IMP_atom.new_Fragment(*args)
6460 self.this.append(this)
6461 except __builtin__.Exception:
6464 def get_is_setup(*args):
6466 get_is_setup(Model m, ParticleIndex pi) -> bool
6467 get_is_setup(_ParticleAdaptor p) -> bool
6469 return _IMP_atom.Fragment_get_is_setup(*args)
6471 get_is_setup = staticmethod(get_is_setup)
6473 def show(self, *args):
6475 show(Fragment self, _ostream out)
6478 return _IMP_atom.Fragment_show(self, *args)
6481 def setup_particle(*args):
6483 setup_particle(Model m, ParticleIndex pi) -> Fragment
6484 setup_particle(_ParticleAdaptor decorator) -> Fragment
6485 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6486 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6487 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6488 setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6490 return _IMP_atom.Fragment_setup_particle(*args)
6492 setup_particle = staticmethod(setup_particle)
6494 def add_attribute(self, *args):
6496 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6497 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6498 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6499 add_attribute(Fragment self, FloatsKey a0, IMP::Floats a1)
6500 add_attribute(Fragment self, IntsKey a0, IMP::Ints a1)
6501 add_attribute(Fragment self, StringKey a0, IMP::String a1)
6502 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6503 add_attribute(Fragment self, ObjectKey a0, Object a1)
6505 return _IMP_atom.Fragment_add_attribute(self, *args)
6508 def get_value(self, *args):
6510 get_value(Fragment self, FloatKey a0) -> IMP::Float
6511 get_value(Fragment self, IntKey a0) -> IMP::Int
6512 get_value(Fragment self, FloatsKey a0) -> IMP::Floats
6513 get_value(Fragment self, IntsKey a0) -> IMP::Ints
6514 get_value(Fragment self, StringKey a0) -> IMP::String
6515 get_value(Fragment self, ParticleIndexKey a0) -> Particle
6516 get_value(Fragment self, ObjectKey a0) -> Object
6518 return _IMP_atom.Fragment_get_value(self, *args)
6521 def set_value(self, *args):
6523 set_value(Fragment self, FloatKey a0, IMP::Float a1)
6524 set_value(Fragment self, IntKey a0, IMP::Int a1)
6525 set_value(Fragment self, FloatsKey a0, IMP::Floats a1)
6526 set_value(Fragment self, IntsKey a0, IMP::Ints a1)
6527 set_value(Fragment self, StringKey a0, IMP::String a1)
6528 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6529 set_value(Fragment self, ObjectKey a0, Object a1)
6531 return _IMP_atom.Fragment_set_value(self, *args)
6534 def remove_attribute(self, *args):
6536 remove_attribute(Fragment self, FloatKey a0)
6537 remove_attribute(Fragment self, IntKey a0)
6538 remove_attribute(Fragment self, FloatsKey a0)
6539 remove_attribute(Fragment self, IntsKey a0)
6540 remove_attribute(Fragment self, StringKey a0)
6541 remove_attribute(Fragment self, ParticleIndexKey a0)
6542 remove_attribute(Fragment self, ObjectKey a0)
6544 return _IMP_atom.Fragment_remove_attribute(self, *args)
6547 def has_attribute(self, *args):
6549 has_attribute(Fragment self, FloatKey a0) -> bool
6550 has_attribute(Fragment self, IntKey a0) -> bool
6551 has_attribute(Fragment self, FloatsKey a0) -> bool
6552 has_attribute(Fragment self, IntsKey a0) -> bool
6553 has_attribute(Fragment self, StringKey a0) -> bool
6554 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6555 has_attribute(Fragment self, ObjectKey a0) -> bool
6557 return _IMP_atom.Fragment_has_attribute(self, *args)
6560 def get_derivative(self, a0):
6561 """get_derivative(Fragment self, FloatKey a0) -> double"""
6562 return _IMP_atom.Fragment_get_derivative(self, a0)
6566 """get_name(Fragment self) -> std::string"""
6567 return _IMP_atom.Fragment_get_name(self)
6570 def clear_caches(self):
6571 """clear_caches(Fragment self)"""
6572 return _IMP_atom.Fragment_clear_caches(self)
6575 def set_name(self, a0):
6576 """set_name(Fragment self, std::string a0)"""
6577 return _IMP_atom.Fragment_set_name(self, a0)
6581 """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6582 return _IMP_atom.Fragment_set_check_level(self, a0)
6585 def add_to_derivative(self, a0, a1, a2):
6586 """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6587 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6590 def set_is_optimized(self, a0, a1):
6591 """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6592 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6595 def get_is_optimized(self, a0):
6596 """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6597 return _IMP_atom.Fragment_get_is_optimized(self, a0)
6601 """get_check_level(Fragment self) -> IMP::CheckLevel"""
6602 return _IMP_atom.Fragment_get_check_level(self)
6605 def __eq__(self, *args):
6607 __eq__(Fragment self, Fragment o) -> bool
6608 __eq__(Fragment self, Particle d) -> bool
6610 return _IMP_atom.Fragment___eq__(self, *args)
6613 def __ne__(self, *args):
6615 __ne__(Fragment self, Fragment o) -> bool
6616 __ne__(Fragment self, Particle d) -> bool
6618 return _IMP_atom.Fragment___ne__(self, *args)
6621 def __le__(self, *args):
6623 __le__(Fragment self, Fragment o) -> bool
6624 __le__(Fragment self, Particle d) -> bool
6626 return _IMP_atom.Fragment___le__(self, *args)
6629 def __lt__(self, *args):
6631 __lt__(Fragment self, Fragment o) -> bool
6632 __lt__(Fragment self, Particle d) -> bool
6634 return _IMP_atom.Fragment___lt__(self, *args)
6637 def __ge__(self, *args):
6639 __ge__(Fragment self, Fragment o) -> bool
6640 __ge__(Fragment self, Particle d) -> bool
6642 return _IMP_atom.Fragment___ge__(self, *args)
6645 def __gt__(self, *args):
6647 __gt__(Fragment self, Fragment o) -> bool
6648 __gt__(Fragment self, Particle d) -> bool
6650 return _IMP_atom.Fragment___gt__(self, *args)
6654 """__hash__(Fragment self) -> std::size_t"""
6655 return _IMP_atom.Fragment___hash__(self)
6659 """__str__(Fragment self) -> std::string"""
6660 return _IMP_atom.Fragment___str__(self)
6664 """__repr__(Fragment self) -> std::string"""
6665 return _IMP_atom.Fragment___repr__(self)
6667 __swig_destroy__ = _IMP_atom.delete_Fragment
6668 __del__ =
lambda self:
None
6669 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6670 Fragment_swigregister(Fragment)
6672 def Fragment_get_is_setup(*args):
6674 get_is_setup(Model m, ParticleIndex pi) -> bool
6675 Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6677 return _IMP_atom.Fragment_get_is_setup(*args)
6679 def Fragment_setup_particle(*args):
6681 setup_particle(Model m, ParticleIndex pi) -> Fragment
6682 setup_particle(_ParticleAdaptor decorator) -> Fragment
6683 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6684 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6685 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6686 Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6688 return _IMP_atom.Fragment_setup_particle(*args)
6691 """Proxy of C++ IMP::atom::StereochemistryPairFilter class."""
6693 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6696 """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6697 this = _IMP_atom.new_StereochemistryPairFilter()
6699 self.this.append(this)
6700 except __builtin__.Exception:
6703 def set_bonds(self, bonds):
6704 """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6705 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6708 def set_angles(self, angles):
6709 """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6710 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6713 def set_dihedrals(self, dihedrals):
6714 """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6715 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6718 def do_get_inputs(self, m, pis):
6719 """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6720 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6723 def get_value(self, *args):
6725 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6726 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6728 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6731 def get_value_index(self, *args):
6733 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6734 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6736 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6739 def get_version_info(self):
6740 """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6741 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6745 """__str__(StereochemistryPairFilter self) -> std::string"""
6746 return _IMP_atom.StereochemistryPairFilter___str__(self)
6750 """__repr__(StereochemistryPairFilter self) -> std::string"""
6751 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6756 return _object_cast_to_StereochemistryPairFilter(o)
6758 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6759 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6762 """Proxy of C++ IMP::atom::SoapPairFilter class."""
6764 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6766 def __init__(self, library):
6767 """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6768 this = _IMP_atom.new_SoapPairFilter(library)
6770 self.this.append(this)
6771 except __builtin__.Exception:
6774 def do_get_inputs(self, m, pis):
6775 """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6776 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6779 def get_value(self, *args):
6781 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6782 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6784 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6787 def get_value_index(self, *args):
6789 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6790 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6792 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6795 def get_version_info(self):
6796 """get_version_info(SoapPairFilter self) -> VersionInfo"""
6797 return _IMP_atom.SoapPairFilter_get_version_info(self)
6801 """__str__(SoapPairFilter self) -> std::string"""
6802 return _IMP_atom.SoapPairFilter___str__(self)
6806 """__repr__(SoapPairFilter self) -> std::string"""
6807 return _IMP_atom.SoapPairFilter___repr__(self)
6812 return _object_cast_to_SoapPairFilter(o)
6814 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6815 SoapPairFilter_swigregister(SoapPairFilter)
6818 """Proxy of C++ IMP::atom::Mass class."""
6820 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6823 """get_mass(Mass self) -> IMP::Float"""
6824 return _IMP_atom.Mass_get_mass(self)
6827 def set_mass(self, d):
6828 """set_mass(Mass self, IMP::Float d)"""
6829 return _IMP_atom.Mass_set_mass(self, d)
6832 def __init__(self, *args):
6834 __init__(IMP::atom::Mass self) -> Mass
6835 __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6836 __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6838 this = _IMP_atom.new_Mass(*args)
6840 self.this.append(this)
6841 except __builtin__.Exception:
6844 def get_is_setup(*args):
6846 get_is_setup(Model m, ParticleIndex pi) -> bool
6847 get_is_setup(_ParticleAdaptor p) -> bool
6849 return _IMP_atom.Mass_get_is_setup(*args)
6851 get_is_setup = staticmethod(get_is_setup)
6853 def show(self, *args):
6855 show(Mass self, _ostream out)
6858 return _IMP_atom.Mass_show(self, *args)
6861 def setup_particle(*args):
6863 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6864 setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6865 setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
6866 setup_particle(_ParticleAdaptor decorator, Mass other) -> Mass
6868 return _IMP_atom.Mass_setup_particle(*args)
6870 setup_particle = staticmethod(setup_particle)
6873 """get_mass_key() -> FloatKey"""
6874 return _IMP_atom.Mass_get_mass_key()
6876 get_mass_key = staticmethod(get_mass_key)
6878 def add_attribute(self, *args):
6880 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6881 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6882 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6883 add_attribute(Mass self, FloatsKey a0, IMP::Floats a1)
6884 add_attribute(Mass self, IntsKey a0, IMP::Ints a1)
6885 add_attribute(Mass self, StringKey a0, IMP::String a1)
6886 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6887 add_attribute(Mass self, ObjectKey a0, Object a1)
6889 return _IMP_atom.Mass_add_attribute(self, *args)
6892 def get_value(self, *args):
6894 get_value(Mass self, FloatKey a0) -> IMP::Float
6895 get_value(Mass self, IntKey a0) -> IMP::Int
6896 get_value(Mass self, FloatsKey a0) -> IMP::Floats
6897 get_value(Mass self, IntsKey a0) -> IMP::Ints
6898 get_value(Mass self, StringKey a0) -> IMP::String
6899 get_value(Mass self, ParticleIndexKey a0) -> Particle
6900 get_value(Mass self, ObjectKey a0) -> Object
6902 return _IMP_atom.Mass_get_value(self, *args)
6905 def set_value(self, *args):
6907 set_value(Mass self, FloatKey a0, IMP::Float a1)
6908 set_value(Mass self, IntKey a0, IMP::Int a1)
6909 set_value(Mass self, FloatsKey a0, IMP::Floats a1)
6910 set_value(Mass self, IntsKey a0, IMP::Ints a1)
6911 set_value(Mass self, StringKey a0, IMP::String a1)
6912 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6913 set_value(Mass self, ObjectKey a0, Object a1)
6915 return _IMP_atom.Mass_set_value(self, *args)
6918 def remove_attribute(self, *args):
6920 remove_attribute(Mass self, FloatKey a0)
6921 remove_attribute(Mass self, IntKey a0)
6922 remove_attribute(Mass self, FloatsKey a0)
6923 remove_attribute(Mass self, IntsKey a0)
6924 remove_attribute(Mass self, StringKey a0)
6925 remove_attribute(Mass self, ParticleIndexKey a0)
6926 remove_attribute(Mass self, ObjectKey a0)
6928 return _IMP_atom.Mass_remove_attribute(self, *args)
6931 def has_attribute(self, *args):
6933 has_attribute(Mass self, FloatKey a0) -> bool
6934 has_attribute(Mass self, IntKey a0) -> bool
6935 has_attribute(Mass self, FloatsKey a0) -> bool
6936 has_attribute(Mass self, IntsKey a0) -> bool
6937 has_attribute(Mass self, StringKey a0) -> bool
6938 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6939 has_attribute(Mass self, ObjectKey a0) -> bool
6941 return _IMP_atom.Mass_has_attribute(self, *args)
6944 def get_derivative(self, a0):
6945 """get_derivative(Mass self, FloatKey a0) -> double"""
6946 return _IMP_atom.Mass_get_derivative(self, a0)
6950 """get_name(Mass self) -> std::string"""
6951 return _IMP_atom.Mass_get_name(self)
6954 def clear_caches(self):
6955 """clear_caches(Mass self)"""
6956 return _IMP_atom.Mass_clear_caches(self)
6959 def set_name(self, a0):
6960 """set_name(Mass self, std::string a0)"""
6961 return _IMP_atom.Mass_set_name(self, a0)
6965 """set_check_level(Mass self, IMP::CheckLevel a0)"""
6966 return _IMP_atom.Mass_set_check_level(self, a0)
6969 def add_to_derivative(self, a0, a1, a2):
6970 """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6971 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6974 def set_is_optimized(self, a0, a1):
6975 """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6976 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6979 def get_is_optimized(self, a0):
6980 """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6981 return _IMP_atom.Mass_get_is_optimized(self, a0)
6985 """get_check_level(Mass self) -> IMP::CheckLevel"""
6986 return _IMP_atom.Mass_get_check_level(self)
6989 def __eq__(self, *args):
6991 __eq__(Mass self, Mass o) -> bool
6992 __eq__(Mass self, Particle d) -> bool
6994 return _IMP_atom.Mass___eq__(self, *args)
6997 def __ne__(self, *args):
6999 __ne__(Mass self, Mass o) -> bool
7000 __ne__(Mass self, Particle d) -> bool
7002 return _IMP_atom.Mass___ne__(self, *args)
7005 def __le__(self, *args):
7007 __le__(Mass self, Mass o) -> bool
7008 __le__(Mass self, Particle d) -> bool
7010 return _IMP_atom.Mass___le__(self, *args)
7013 def __lt__(self, *args):
7015 __lt__(Mass self, Mass o) -> bool
7016 __lt__(Mass self, Particle d) -> bool
7018 return _IMP_atom.Mass___lt__(self, *args)
7021 def __ge__(self, *args):
7023 __ge__(Mass self, Mass o) -> bool
7024 __ge__(Mass self, Particle d) -> bool
7026 return _IMP_atom.Mass___ge__(self, *args)
7029 def __gt__(self, *args):
7031 __gt__(Mass self, Mass o) -> bool
7032 __gt__(Mass self, Particle d) -> bool
7034 return _IMP_atom.Mass___gt__(self, *args)
7038 """__hash__(Mass self) -> std::size_t"""
7039 return _IMP_atom.Mass___hash__(self)
7043 """__str__(Mass self) -> std::string"""
7044 return _IMP_atom.Mass___str__(self)
7048 """__repr__(Mass self) -> std::string"""
7049 return _IMP_atom.Mass___repr__(self)
7051 __swig_destroy__ = _IMP_atom.delete_Mass
7052 __del__ =
lambda self:
None
7053 Mass_swigregister = _IMP_atom.Mass_swigregister
7054 Mass_swigregister(Mass)
7056 def Mass_get_is_setup(*args):
7058 get_is_setup(Model m, ParticleIndex pi) -> bool
7059 Mass_get_is_setup(_ParticleAdaptor p) -> bool
7061 return _IMP_atom.Mass_get_is_setup(*args)
7063 def Mass_setup_particle(*args):
7065 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
7066 setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
7067 setup_particle(Model m, ParticleIndex pi, Mass other) -> Mass
7068 Mass_setup_particle(_ParticleAdaptor decorator, Mass other) -> Mass
7070 return _IMP_atom.Mass_setup_particle(*args)
7072 def Mass_get_mass_key():
7073 """Mass_get_mass_key() -> FloatKey"""
7074 return _IMP_atom.Mass_get_mass_key()
7077 """Proxy of C++ IMP::atom::BondedPairFilter class."""
7079 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7082 """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
7083 this = _IMP_atom.new_BondedPairFilter()
7085 self.this.append(this)
7086 except __builtin__.Exception:
7089 def do_get_inputs(self, m, pis):
7090 """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7091 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
7094 def get_value(self, *args):
7096 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
7097 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
7099 return _IMP_atom.BondedPairFilter_get_value(self, *args)
7102 def get_value_index(self, *args):
7104 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
7105 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
7107 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
7110 def get_version_info(self):
7111 """get_version_info(BondedPairFilter self) -> VersionInfo"""
7112 return _IMP_atom.BondedPairFilter_get_version_info(self)
7116 """__str__(BondedPairFilter self) -> std::string"""
7117 return _IMP_atom.BondedPairFilter___str__(self)
7121 """__repr__(BondedPairFilter self) -> std::string"""
7122 return _IMP_atom.BondedPairFilter___repr__(self)
7127 return _object_cast_to_BondedPairFilter(o)
7129 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
7130 BondedPairFilter_swigregister(BondedPairFilter)
7133 """Proxy of C++ IMP::atom::Mol2Selector class."""
7135 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7137 def __init__(self, *args, **kwargs):
7138 raise AttributeError(
"No constructor defined - class is abstract")
7140 def get_is_selected(self, atom_line):
7141 """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
7142 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
7144 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
7145 __del__ =
lambda self:
None
7148 """__str__(Mol2Selector self) -> std::string"""
7149 return _IMP_atom.Mol2Selector___str__(self)
7153 """__repr__(Mol2Selector self) -> std::string"""
7154 return _IMP_atom.Mol2Selector___repr__(self)
7159 return _object_cast_to_Mol2Selector(o)
7161 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
7162 Mol2Selector_swigregister(Mol2Selector)
7164 class AllMol2Selector(Mol2Selector):
7165 """Proxy of C++ IMP::atom::AllMol2Selector class."""
7167 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7170 """__str__(AllMol2Selector self) -> std::string"""
7171 return _IMP_atom.AllMol2Selector___str__(self)
7175 """__repr__(AllMol2Selector self) -> std::string"""
7176 return _IMP_atom.AllMol2Selector___repr__(self)
7181 return _object_cast_to_AllMol2Selector(o)
7185 """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
7186 this = _IMP_atom.new_AllMol2Selector()
7188 self.this.append(this)
7189 except __builtin__.Exception:
7191 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
7192 __del__ =
lambda self:
None
7193 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
7194 AllMol2Selector_swigregister(AllMol2Selector)
7196 class NonHydrogenMol2Selector(Mol2Selector):
7197 """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class."""
7199 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7202 """__str__(NonHydrogenMol2Selector self) -> std::string"""
7203 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
7207 """__repr__(NonHydrogenMol2Selector self) -> std::string"""
7208 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
7213 return _object_cast_to_NonHydrogenMol2Selector(o)
7217 """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
7218 this = _IMP_atom.new_NonHydrogenMol2Selector()
7220 self.this.append(this)
7221 except __builtin__.Exception:
7223 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
7224 __del__ =
lambda self:
None
7225 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
7226 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7229 def read_mol2(mol2_file, model, mol2sel=None):
7231 read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7232 read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7234 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7237 """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7238 return _IMP_atom.write_mol2(rhd, file_name)
7240 """Proxy of C++ IMP::atom::SecondaryStructureResidue class."""
7242 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7244 def __init__(self, *args):
7246 __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7247 __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7248 __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7250 this = _IMP_atom.new_SecondaryStructureResidue(*args)
7252 self.this.append(this)
7253 except __builtin__.Exception:
7256 def show(self, *args):
7258 show(SecondaryStructureResidue self, _ostream out)
7259 show(SecondaryStructureResidue self)
7261 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7264 def setup_particle(*args):
7266 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7267 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7268 setup_particle(Particle res_p) -> SecondaryStructureResidue
7270 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7272 setup_particle = staticmethod(setup_particle)
7274 def get_is_setup(*args):
7276 get_is_setup(_ParticleAdaptor p) -> bool
7277 get_is_setup(Model m, ParticleIndex pi) -> bool
7279 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7281 get_is_setup = staticmethod(get_is_setup)
7283 def get_particle(self):
7284 """get_particle(SecondaryStructureResidue self) -> Particle"""
7285 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7288 def get_all_probabilities(self):
7289 """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7290 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7293 def get_prob_helix(self):
7294 """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7295 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7298 def set_prob_helix(self, t):
7299 """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7300 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7303 def get_prob_strand(self):
7304 """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7305 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7308 def set_prob_strand(self, t):
7309 """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7310 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7313 def get_prob_coil(self):
7314 """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7315 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7318 def set_prob_coil(self, t):
7319 """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7320 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7323 def get_prob_helix_key():
7324 """get_prob_helix_key() -> FloatKey"""
7325 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7327 get_prob_helix_key = staticmethod(get_prob_helix_key)
7329 def get_prob_strand_key():
7330 """get_prob_strand_key() -> FloatKey"""
7331 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7333 get_prob_strand_key = staticmethod(get_prob_strand_key)
7335 def get_prob_coil_key():
7336 """get_prob_coil_key() -> FloatKey"""
7337 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7339 get_prob_coil_key = staticmethod(get_prob_coil_key)
7341 def add_attribute(self, *args):
7343 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7344 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7345 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7346 add_attribute(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7347 add_attribute(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7348 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7349 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7350 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7352 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7355 def get_value(self, *args):
7357 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7358 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7359 get_value(SecondaryStructureResidue self, FloatsKey a0) -> IMP::Floats
7360 get_value(SecondaryStructureResidue self, IntsKey a0) -> IMP::Ints
7361 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7362 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7363 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7365 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7368 def set_value(self, *args):
7370 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7371 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7372 set_value(SecondaryStructureResidue self, FloatsKey a0, IMP::Floats a1)
7373 set_value(SecondaryStructureResidue self, IntsKey a0, IMP::Ints a1)
7374 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7375 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7376 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7378 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7381 def remove_attribute(self, *args):
7383 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7384 remove_attribute(SecondaryStructureResidue self, IntKey a0)
7385 remove_attribute(SecondaryStructureResidue self, FloatsKey a0)
7386 remove_attribute(SecondaryStructureResidue self, IntsKey a0)
7387 remove_attribute(SecondaryStructureResidue self, StringKey a0)
7388 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7389 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7391 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7394 def has_attribute(self, *args):
7396 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7397 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7398 has_attribute(SecondaryStructureResidue self, FloatsKey a0) -> bool
7399 has_attribute(SecondaryStructureResidue self, IntsKey a0) -> bool
7400 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7401 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7402 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7404 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7407 def get_derivative(self, a0):
7408 """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7409 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7413 """get_name(SecondaryStructureResidue self) -> std::string"""
7414 return _IMP_atom.SecondaryStructureResidue_get_name(self)
7417 def clear_caches(self):
7418 """clear_caches(SecondaryStructureResidue self)"""
7419 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7422 def set_name(self, a0):
7423 """set_name(SecondaryStructureResidue self, std::string a0)"""
7424 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7428 """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7429 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7432 def add_to_derivative(self, a0, a1, a2):
7433 """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7434 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7437 def set_is_optimized(self, a0, a1):
7438 """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7439 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7442 def get_is_optimized(self, a0):
7443 """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7444 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7448 """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7449 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7452 def __eq__(self, *args):
7454 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7455 __eq__(SecondaryStructureResidue self, Particle d) -> bool
7457 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7460 def __ne__(self, *args):
7462 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7463 __ne__(SecondaryStructureResidue self, Particle d) -> bool
7465 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7468 def __le__(self, *args):
7470 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7471 __le__(SecondaryStructureResidue self, Particle d) -> bool
7473 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7476 def __lt__(self, *args):
7478 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7479 __lt__(SecondaryStructureResidue self, Particle d) -> bool
7481 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7484 def __ge__(self, *args):
7486 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7487 __ge__(SecondaryStructureResidue self, Particle d) -> bool
7489 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7492 def __gt__(self, *args):
7494 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7495 __gt__(SecondaryStructureResidue self, Particle d) -> bool
7497 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7501 """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7502 return _IMP_atom.SecondaryStructureResidue___hash__(self)
7506 """__str__(SecondaryStructureResidue self) -> std::string"""
7507 return _IMP_atom.SecondaryStructureResidue___str__(self)
7511 """__repr__(SecondaryStructureResidue self) -> std::string"""
7512 return _IMP_atom.SecondaryStructureResidue___repr__(self)
7514 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7515 __del__ =
lambda self:
None
7516 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7517 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7519 def SecondaryStructureResidue_setup_particle(*args):
7521 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7522 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7523 SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7525 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7527 def SecondaryStructureResidue_get_is_setup(*args):
7529 get_is_setup(_ParticleAdaptor p) -> bool
7530 SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7532 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7534 def SecondaryStructureResidue_get_prob_helix_key():
7535 """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7536 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7538 def SecondaryStructureResidue_get_prob_strand_key():
7539 """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7540 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7542 def SecondaryStructureResidue_get_prob_coil_key():
7543 """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7544 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7549 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7550 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7552 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7556 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
7557 setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7559 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7562 """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7563 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7565 def read_psipred(*args):
7567 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7568 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7570 return _IMP_atom.read_psipred(*args)
7572 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class."""
7574 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7575 __repr__ = _swig_repr
7577 def __init__(self, *args):
7579 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7580 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7582 this = _IMP_atom.new__ADopeBase(*args)
7584 self.this.append(this)
7585 except __builtin__.Exception:
7588 def do_get_inputs(self, m, pis):
7589 """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7590 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7593 def get_score_functor(self):
7594 """get_score_functor(_ADopeBase self) -> Dope"""
7595 return _IMP_atom._ADopeBase_get_score_functor(self)
7598 def get_version_info(self):
7599 """get_version_info(_ADopeBase self) -> VersionInfo"""
7600 return _IMP_atom._ADopeBase_get_version_info(self)
7602 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7603 _ADopeBase_swigregister(_ADopeBase)
7606 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class."""
7608 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7609 __repr__ = _swig_repr
7611 def __init__(self, *args):
7613 __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
7614 __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
7616 this = _IMP_atom.new__BDopeBase(*args)
7618 self.this.append(this)
7619 except __builtin__.Exception:
7622 def do_get_inputs(self, m, pis):
7623 """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7624 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7627 def get_score_functor(self):
7628 """get_score_functor(_BDopeBase self) -> _DopeBase"""
7629 return _IMP_atom._BDopeBase_get_score_functor(self)
7632 def get_version_info(self):
7633 """get_version_info(_BDopeBase self) -> VersionInfo"""
7634 return _IMP_atom._BDopeBase_get_version_info(self)
7636 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7637 _BDopeBase_swigregister(_BDopeBase)
7640 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> class."""
7642 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7643 __repr__ = _swig_repr
7645 def __init__(self, *args):
7647 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> self, LoopStatistical t0, std::string name) -> _ALoopStatisticalBase
7648 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::LoopStatistical)> self, LoopStatistical t0) -> _ALoopStatisticalBase
7650 this = _IMP_atom.new__ALoopStatisticalBase(*args)
7652 self.this.append(this)
7653 except __builtin__.Exception:
7656 def do_get_inputs(self, m, pis):
7657 """do_get_inputs(_ALoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7658 return _IMP_atom._ALoopStatisticalBase_do_get_inputs(self, m, pis)
7661 def get_score_functor(self):
7662 """get_score_functor(_ALoopStatisticalBase self) -> LoopStatistical"""
7663 return _IMP_atom._ALoopStatisticalBase_get_score_functor(self)
7666 def get_version_info(self):
7667 """get_version_info(_ALoopStatisticalBase self) -> VersionInfo"""
7668 return _IMP_atom._ALoopStatisticalBase_get_version_info(self)
7670 _ALoopStatisticalBase_swigregister = _IMP_atom._ALoopStatisticalBase_swigregister
7671 _ALoopStatisticalBase_swigregister(_ALoopStatisticalBase)
7674 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> class."""
7676 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7677 __repr__ = _swig_repr
7679 def __init__(self, *args):
7681 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BLoopStatisticalBase
7682 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::LoopStatisticalType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >::DistanceScore const & t0) -> _BLoopStatisticalBase
7684 this = _IMP_atom.new__BLoopStatisticalBase(*args)
7686 self.this.append(this)
7687 except __builtin__.Exception:
7690 def do_get_inputs(self, m, pis):
7691 """do_get_inputs(_BLoopStatisticalBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7692 return _IMP_atom._BLoopStatisticalBase_do_get_inputs(self, m, pis)
7695 def get_score_functor(self):
7696 """get_score_functor(_BLoopStatisticalBase self) -> _LoopStatisticalBase"""
7697 return _IMP_atom._BLoopStatisticalBase_get_score_functor(self)
7700 def get_version_info(self):
7701 """get_version_info(_BLoopStatisticalBase self) -> VersionInfo"""
7702 return _IMP_atom._BLoopStatisticalBase_get_version_info(self)
7704 _BLoopStatisticalBase_swigregister = _IMP_atom._BLoopStatisticalBase_swigregister
7705 _BLoopStatisticalBase_swigregister(_BLoopStatisticalBase)
7708 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class."""
7710 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7711 __repr__ = _swig_repr
7713 def __init__(self, *args):
7715 __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
7716 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7718 this = _IMP_atom.new__OrientedSoapBase(*args)
7720 self.this.append(this)
7721 except __builtin__.Exception:
7724 def do_get_inputs(self, m, pis):
7725 """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7726 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7729 def get_score_functor(self):
7730 """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7731 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7734 def get_version_info(self):
7735 """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7736 return _IMP_atom._OrientedSoapBase_get_version_info(self)
7738 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7739 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7742 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class."""
7744 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7745 __repr__ = _swig_repr
7747 def __init__(self, *args):
7749 __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
7750 __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
7752 this = _IMP_atom.new__SPSFTB(*args)
7754 self.this.append(this)
7755 except __builtin__.Exception:
7758 def do_get_inputs(self, m, pis):
7759 """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7760 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7763 def get_score_functor(self):
7764 """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7765 return _IMP_atom._SPSFTB_get_score_functor(self)
7768 def get_version_info(self):
7769 """get_version_info(_SPSFTB self) -> VersionInfo"""
7770 return _IMP_atom._SPSFTB_get_version_info(self)
7772 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7773 _SPSFTB_swigregister(_SPSFTB)
7775 class _SPSTF(_SPSFTB):
7776 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class."""
7778 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7779 __repr__ = _swig_repr
7781 def __init__(self, *args):
7783 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7784 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7786 this = _IMP_atom.new__SPSTF(*args)
7788 self.this.append(this)
7789 except __builtin__.Exception:
7791 __swig_destroy__ = _IMP_atom.delete__SPSTF
7792 __del__ =
lambda self:
None
7793 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7794 _SPSTF_swigregister(_SPSTF)
7796 class _SPSFT(_BDopeBase):
7797 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class."""
7799 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7800 __repr__ = _swig_repr
7802 def __init__(self, *args):
7804 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7805 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7807 this = _IMP_atom.new__SPSFT(*args)
7809 self.this.append(this)
7810 except __builtin__.Exception:
7812 __swig_destroy__ = _IMP_atom.delete__SPSFT
7813 __del__ =
lambda self:
None
7814 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7815 _SPSFT_swigregister(_SPSFT)
7817 class _SPSFTL(_BLoopStatisticalBase):
7818 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> class."""
7820 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7821 __repr__ = _swig_repr
7823 def __init__(self, *args):
7825 __init__(IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFTL
7826 __init__(IMP::core::StatisticalPairScore<(IMP::atom::LoopStatisticalType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFTL
7828 this = _IMP_atom.new__SPSFTL(*args)
7830 self.this.append(this)
7831 except __builtin__.Exception:
7833 __swig_destroy__ = _IMP_atom.delete__SPSFTL
7834 __del__ =
lambda self:
None
7835 _SPSFTL_swigregister = _IMP_atom._SPSFTL_swigregister
7836 _SPSFTL_swigregister(_SPSFTL)
7838 class ProteinLigandAtomPairScore(_SPSTF):
7839 """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class."""
7841 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7843 def __init__(self, *args):
7845 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7846 __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7847 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7849 this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7851 self.this.append(this)
7852 except __builtin__.Exception:
7855 def get_maximum_distance(self):
7856 """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7857 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7861 """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7862 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7866 """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7867 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7872 return _object_cast_to_ProteinLigandAtomPairScore(o)
7874 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7875 __del__ =
lambda self:
None
7876 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7877 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7880 """Proxy of C++ IMP::atom::ProteinLigandRestraint class."""
7882 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7884 def __init__(self, *args):
7886 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7887 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7888 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7890 this = _IMP_atom.new_ProteinLigandRestraint(*args)
7892 self.this.append(this)
7893 except __builtin__.Exception:
7897 """__str__(ProteinLigandRestraint self) -> std::string"""
7898 return _IMP_atom.ProteinLigandRestraint___str__(self)
7902 """__repr__(ProteinLigandRestraint self) -> std::string"""
7903 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7908 return _object_cast_to_ProteinLigandRestraint(o)
7910 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7911 __del__ =
lambda self:
None
7912 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7913 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7917 """add_protein_ligand_score_data(Hierarchy h)"""
7918 return _IMP_atom.add_protein_ligand_score_data(h)
7919 class AtomType(IMP._Value):
7920 """Proxy of C++ IMP::Key<(8974343)> class."""
7922 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7924 def __init__(self, *args):
7926 __init__(IMP::Key<(8974343)> self) -> AtomType
7927 __init__(IMP::Key<(8974343)> self, std::string const & c, bool is_implicit_add_permitted=True) -> AtomType
7928 __init__(IMP::Key<(8974343)> self, std::string const & c) -> AtomType
7929 __init__(IMP::Key<(8974343)> self, unsigned int i) -> AtomType
7931 this = _IMP_atom.new_AtomType(*args)
7933 self.this.append(this)
7934 except __builtin__.Exception:
7938 """add_key(std::string sc) -> unsigned int"""
7939 return _IMP_atom.AtomType_add_key(sc)
7941 add_key = staticmethod(add_key)
7943 def get_key_exists(sc):
7944 """get_key_exists(std::string sc) -> bool"""
7945 return _IMP_atom.AtomType_get_key_exists(sc)
7947 get_key_exists = staticmethod(get_key_exists)
7949 def get_string(self):
7950 """get_string(AtomType self) -> std::string const"""
7951 return _IMP_atom.AtomType_get_string(self)
7954 def __cmp__(self, o):
7955 """__cmp__(AtomType self, AtomType o) -> int"""
7956 return _IMP_atom.AtomType___cmp__(self, o)
7959 def __eq__(self, o):
7960 """__eq__(AtomType self, AtomType o) -> bool"""
7961 return _IMP_atom.AtomType___eq__(self, o)
7964 def __ne__(self, o):
7965 """__ne__(AtomType self, AtomType o) -> bool"""
7966 return _IMP_atom.AtomType___ne__(self, o)
7969 def __lt__(self, o):
7970 """__lt__(AtomType self, AtomType o) -> bool"""
7971 return _IMP_atom.AtomType___lt__(self, o)
7974 def __gt__(self, o):
7975 """__gt__(AtomType self, AtomType o) -> bool"""
7976 return _IMP_atom.AtomType___gt__(self, o)
7979 def __ge__(self, o):
7980 """__ge__(AtomType self, AtomType o) -> bool"""
7981 return _IMP_atom.AtomType___ge__(self, o)
7984 def __le__(self, o):
7985 """__le__(AtomType self, AtomType o) -> bool"""
7986 return _IMP_atom.AtomType___le__(self, o)
7990 """__hash__(AtomType self) -> std::size_t"""
7991 return _IMP_atom.AtomType___hash__(self)
7994 def show(self, *args):
7996 show(AtomType self, _ostream out)
7999 return _IMP_atom.AtomType_show(self, *args)
8002 def add_alias(old_key, new_name):
8003 """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
8004 return _IMP_atom.AtomType_add_alias(old_key, new_name)
8006 add_alias = staticmethod(add_alias)
8008 def get_number_of_keys():
8009 """get_number_of_keys() -> unsigned int"""
8010 return _IMP_atom.AtomType_get_number_of_keys()
8012 get_number_of_keys = staticmethod(get_number_of_keys)
8015 """get_index(AtomType self) -> unsigned int"""
8016 return _IMP_atom.AtomType_get_index(self)
8020 """show_all(_ostream out)"""
8021 return _IMP_atom.AtomType_show_all(out)
8023 show_all = staticmethod(show_all)
8025 def get_all_strings():
8026 """get_all_strings() -> IMP::Vector< std::string >"""
8027 return _IMP_atom.AtomType_get_all_strings()
8029 get_all_strings = staticmethod(get_all_strings)
8031 def get_number_unique():
8032 """get_number_unique() -> unsigned int"""
8033 return _IMP_atom.AtomType_get_number_unique()
8035 get_number_unique = staticmethod(get_number_unique)
8038 """__str__(AtomType self) -> std::string"""
8039 return _IMP_atom.AtomType___str__(self)
8043 """__repr__(AtomType self) -> std::string"""
8044 return _IMP_atom.AtomType___repr__(self)
8046 __swig_destroy__ = _IMP_atom.delete_AtomType
8047 __del__ =
lambda self:
None
8048 AtomType_swigregister = _IMP_atom.AtomType_swigregister
8049 AtomType_swigregister(AtomType)
8051 def AtomType_add_key(sc):
8052 """AtomType_add_key(std::string sc) -> unsigned int"""
8053 return _IMP_atom.AtomType_add_key(sc)
8055 def AtomType_get_key_exists(sc):
8056 """AtomType_get_key_exists(std::string sc) -> bool"""
8057 return _IMP_atom.AtomType_get_key_exists(sc)
8059 def AtomType_add_alias(old_key, new_name):
8060 """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
8061 return _IMP_atom.AtomType_add_alias(old_key, new_name)
8063 def AtomType_get_number_of_keys():
8064 """AtomType_get_number_of_keys() -> unsigned int"""
8065 return _IMP_atom.AtomType_get_number_of_keys()
8067 def AtomType_show_all(out):
8068 """AtomType_show_all(_ostream out)"""
8069 return _IMP_atom.AtomType_show_all(out)
8071 def AtomType_get_all_strings():
8072 """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
8073 return _IMP_atom.AtomType_get_all_strings()
8075 def AtomType_get_number_unique():
8076 """AtomType_get_number_unique() -> unsigned int"""
8077 return _IMP_atom.AtomType_get_number_unique()
8079 class ResidueType(IMP._Value):
8080 """Proxy of C++ IMP::Key<(90784334)> class."""
8082 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8084 def __init__(self, *args):
8086 __init__(IMP::Key<(90784334)> self) -> ResidueType
8087 __init__(IMP::Key<(90784334)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ResidueType
8088 __init__(IMP::Key<(90784334)> self, std::string const & c) -> ResidueType
8089 __init__(IMP::Key<(90784334)> self, unsigned int i) -> ResidueType
8091 this = _IMP_atom.new_ResidueType(*args)
8093 self.this.append(this)
8094 except __builtin__.Exception:
8098 """add_key(std::string sc) -> unsigned int"""
8099 return _IMP_atom.ResidueType_add_key(sc)
8101 add_key = staticmethod(add_key)
8103 def get_key_exists(sc):
8104 """get_key_exists(std::string sc) -> bool"""
8105 return _IMP_atom.ResidueType_get_key_exists(sc)
8107 get_key_exists = staticmethod(get_key_exists)
8109 def get_string(self):
8110 """get_string(ResidueType self) -> std::string const"""
8111 return _IMP_atom.ResidueType_get_string(self)
8114 def __cmp__(self, o):
8115 """__cmp__(ResidueType self, ResidueType o) -> int"""
8116 return _IMP_atom.ResidueType___cmp__(self, o)
8119 def __eq__(self, o):
8120 """__eq__(ResidueType self, ResidueType o) -> bool"""
8121 return _IMP_atom.ResidueType___eq__(self, o)
8124 def __ne__(self, o):
8125 """__ne__(ResidueType self, ResidueType o) -> bool"""
8126 return _IMP_atom.ResidueType___ne__(self, o)
8129 def __lt__(self, o):
8130 """__lt__(ResidueType self, ResidueType o) -> bool"""
8131 return _IMP_atom.ResidueType___lt__(self, o)
8134 def __gt__(self, o):
8135 """__gt__(ResidueType self, ResidueType o) -> bool"""
8136 return _IMP_atom.ResidueType___gt__(self, o)
8139 def __ge__(self, o):
8140 """__ge__(ResidueType self, ResidueType o) -> bool"""
8141 return _IMP_atom.ResidueType___ge__(self, o)
8144 def __le__(self, o):
8145 """__le__(ResidueType self, ResidueType o) -> bool"""
8146 return _IMP_atom.ResidueType___le__(self, o)
8150 """__hash__(ResidueType self) -> std::size_t"""
8151 return _IMP_atom.ResidueType___hash__(self)
8154 def show(self, *args):
8156 show(ResidueType self, _ostream out)
8157 show(ResidueType self)
8159 return _IMP_atom.ResidueType_show(self, *args)
8162 def add_alias(old_key, new_name):
8163 """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8164 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8166 add_alias = staticmethod(add_alias)
8168 def get_number_of_keys():
8169 """get_number_of_keys() -> unsigned int"""
8170 return _IMP_atom.ResidueType_get_number_of_keys()
8172 get_number_of_keys = staticmethod(get_number_of_keys)
8175 """get_index(ResidueType self) -> unsigned int"""
8176 return _IMP_atom.ResidueType_get_index(self)
8180 """show_all(_ostream out)"""
8181 return _IMP_atom.ResidueType_show_all(out)
8183 show_all = staticmethod(show_all)
8185 def get_all_strings():
8186 """get_all_strings() -> IMP::Vector< std::string >"""
8187 return _IMP_atom.ResidueType_get_all_strings()
8189 get_all_strings = staticmethod(get_all_strings)
8191 def get_number_unique():
8192 """get_number_unique() -> unsigned int"""
8193 return _IMP_atom.ResidueType_get_number_unique()
8195 get_number_unique = staticmethod(get_number_unique)
8198 """__str__(ResidueType self) -> std::string"""
8199 return _IMP_atom.ResidueType___str__(self)
8203 """__repr__(ResidueType self) -> std::string"""
8204 return _IMP_atom.ResidueType___repr__(self)
8206 __swig_destroy__ = _IMP_atom.delete_ResidueType
8207 __del__ =
lambda self:
None
8208 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
8209 ResidueType_swigregister(ResidueType)
8211 def ResidueType_add_key(sc):
8212 """ResidueType_add_key(std::string sc) -> unsigned int"""
8213 return _IMP_atom.ResidueType_add_key(sc)
8215 def ResidueType_get_key_exists(sc):
8216 """ResidueType_get_key_exists(std::string sc) -> bool"""
8217 return _IMP_atom.ResidueType_get_key_exists(sc)
8219 def ResidueType_add_alias(old_key, new_name):
8220 """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8221 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8223 def ResidueType_get_number_of_keys():
8224 """ResidueType_get_number_of_keys() -> unsigned int"""
8225 return _IMP_atom.ResidueType_get_number_of_keys()
8227 def ResidueType_show_all(out):
8228 """ResidueType_show_all(_ostream out)"""
8229 return _IMP_atom.ResidueType_show_all(out)
8231 def ResidueType_get_all_strings():
8232 """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
8233 return _IMP_atom.ResidueType_get_all_strings()
8235 def ResidueType_get_number_unique():
8236 """ResidueType_get_number_unique() -> unsigned int"""
8237 return _IMP_atom.ResidueType_get_number_unique()
8239 class ChainType(IMP._Value):
8240 """Proxy of C++ IMP::Key<(90784336)> class."""
8242 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8244 def __init__(self, *args):
8246 __init__(IMP::Key<(90784336)> self) -> ChainType
8247 __init__(IMP::Key<(90784336)> self, std::string const & c, bool is_implicit_add_permitted=True) -> ChainType
8248 __init__(IMP::Key<(90784336)> self, std::string const & c) -> ChainType
8249 __init__(IMP::Key<(90784336)> self, unsigned int i) -> ChainType
8251 this = _IMP_atom.new_ChainType(*args)
8253 self.this.append(this)
8254 except __builtin__.Exception:
8258 """add_key(std::string sc) -> unsigned int"""
8259 return _IMP_atom.ChainType_add_key(sc)
8261 add_key = staticmethod(add_key)
8263 def get_key_exists(sc):
8264 """get_key_exists(std::string sc) -> bool"""
8265 return _IMP_atom.ChainType_get_key_exists(sc)
8267 get_key_exists = staticmethod(get_key_exists)
8269 def get_string(self):
8270 """get_string(ChainType self) -> std::string const"""
8271 return _IMP_atom.ChainType_get_string(self)
8274 def __cmp__(self, o):
8275 """__cmp__(ChainType self, ChainType o) -> int"""
8276 return _IMP_atom.ChainType___cmp__(self, o)
8279 def __eq__(self, o):
8280 """__eq__(ChainType self, ChainType o) -> bool"""
8281 return _IMP_atom.ChainType___eq__(self, o)
8284 def __ne__(self, o):
8285 """__ne__(ChainType self, ChainType o) -> bool"""
8286 return _IMP_atom.ChainType___ne__(self, o)
8289 def __lt__(self, o):
8290 """__lt__(ChainType self, ChainType o) -> bool"""
8291 return _IMP_atom.ChainType___lt__(self, o)
8294 def __gt__(self, o):
8295 """__gt__(ChainType self, ChainType o) -> bool"""
8296 return _IMP_atom.ChainType___gt__(self, o)
8299 def __ge__(self, o):
8300 """__ge__(ChainType self, ChainType o) -> bool"""
8301 return _IMP_atom.ChainType___ge__(self, o)
8304 def __le__(self, o):
8305 """__le__(ChainType self, ChainType o) -> bool"""
8306 return _IMP_atom.ChainType___le__(self, o)
8310 """__hash__(ChainType self) -> std::size_t"""
8311 return _IMP_atom.ChainType___hash__(self)
8314 def show(self, *args):
8316 show(ChainType self, _ostream out)
8317 show(ChainType self)
8319 return _IMP_atom.ChainType_show(self, *args)
8322 def add_alias(old_key, new_name):
8323 """add_alias(ChainType old_key, std::string new_name) -> ChainType"""
8324 return _IMP_atom.ChainType_add_alias(old_key, new_name)
8326 add_alias = staticmethod(add_alias)
8328 def get_number_of_keys():
8329 """get_number_of_keys() -> unsigned int"""
8330 return _IMP_atom.ChainType_get_number_of_keys()
8332 get_number_of_keys = staticmethod(get_number_of_keys)
8335 """get_index(ChainType self) -> unsigned int"""
8336 return _IMP_atom.ChainType_get_index(self)
8340 """show_all(_ostream out)"""
8341 return _IMP_atom.ChainType_show_all(out)
8343 show_all = staticmethod(show_all)
8345 def get_all_strings():
8346 """get_all_strings() -> IMP::Vector< std::string >"""
8347 return _IMP_atom.ChainType_get_all_strings()
8349 get_all_strings = staticmethod(get_all_strings)
8351 def get_number_unique():
8352 """get_number_unique() -> unsigned int"""
8353 return _IMP_atom.ChainType_get_number_unique()
8355 get_number_unique = staticmethod(get_number_unique)
8358 """__str__(ChainType self) -> std::string"""
8359 return _IMP_atom.ChainType___str__(self)
8363 """__repr__(ChainType self) -> std::string"""
8364 return _IMP_atom.ChainType___repr__(self)
8366 __swig_destroy__ = _IMP_atom.delete_ChainType
8367 __del__ =
lambda self:
None
8368 ChainType_swigregister = _IMP_atom.ChainType_swigregister
8369 ChainType_swigregister(ChainType)
8371 def ChainType_add_key(sc):
8372 """ChainType_add_key(std::string sc) -> unsigned int"""
8373 return _IMP_atom.ChainType_add_key(sc)
8375 def ChainType_get_key_exists(sc):
8376 """ChainType_get_key_exists(std::string sc) -> bool"""
8377 return _IMP_atom.ChainType_get_key_exists(sc)
8379 def ChainType_add_alias(old_key, new_name):
8380 """ChainType_add_alias(ChainType old_key, std::string new_name) -> ChainType"""
8381 return _IMP_atom.ChainType_add_alias(old_key, new_name)
8383 def ChainType_get_number_of_keys():
8384 """ChainType_get_number_of_keys() -> unsigned int"""
8385 return _IMP_atom.ChainType_get_number_of_keys()
8387 def ChainType_show_all(out):
8388 """ChainType_show_all(_ostream out)"""
8389 return _IMP_atom.ChainType_show_all(out)
8391 def ChainType_get_all_strings():
8392 """ChainType_get_all_strings() -> IMP::Vector< std::string >"""
8393 return _IMP_atom.ChainType_get_all_strings()
8395 def ChainType_get_number_unique():
8396 """ChainType_get_number_unique() -> unsigned int"""
8397 return _IMP_atom.ChainType_get_number_unique()
8399 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8508 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8511 """hash_value(IMP::atom::Element e) -> size_t"""
8512 return _IMP_atom.hash_value(e)
8513 class ElementTable(object):
8514 """Proxy of C++ IMP::atom::ElementTable class."""
8516 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8517 __repr__ = _swig_repr
8520 """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8521 this = _IMP_atom.new_ElementTable()
8523 self.this.append(this)
8524 except __builtin__.Exception:
8527 def get_element(self, s):
8528 """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8529 return _IMP_atom.ElementTable_get_element(self, s)
8532 def get_name(self, e):
8533 """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8534 return _IMP_atom.ElementTable_get_name(self, e)
8538 """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8539 return _IMP_atom.ElementTable_get_mass(self, e)
8541 __swig_destroy__ = _IMP_atom.delete_ElementTable
8542 __del__ =
lambda self:
None
8543 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8544 ElementTable_swigregister(ElementTable)
8547 def get_element_table():
8548 """get_element_table() -> ElementTable"""
8549 return _IMP_atom.get_element_table()
8550 class Atom(Hierarchy):
8551 """Proxy of C++ IMP::atom::Atom class."""
8553 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8555 def __init__(self, *args):
8557 __init__(IMP::atom::Atom self) -> Atom
8558 __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8559 __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8561 this = _IMP_atom.new_Atom(*args)
8563 self.this.append(this)
8564 except __builtin__.Exception:
8567 def show(self, *args):
8569 show(Atom self, _ostream out)
8572 return _IMP_atom.Atom_show(self, *args)
8575 def setup_particle(*args):
8577 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8578 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8579 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8580 setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8582 return _IMP_atom.Atom_setup_particle(*args)
8584 setup_particle = staticmethod(setup_particle)
8586 def get_is_setup(*args):
8588 get_is_setup(_ParticleAdaptor p) -> bool
8589 get_is_setup(Model m, ParticleIndex pi) -> bool
8591 return _IMP_atom.Atom_get_is_setup(*args)
8593 get_is_setup = staticmethod(get_is_setup)
8595 def get_atom_type(self):
8596 """get_atom_type(Atom self) -> AtomType"""
8597 return _IMP_atom.Atom_get_atom_type(self)
8600 def set_atom_type(self, t):
8601 """set_atom_type(Atom self, AtomType t)"""
8602 return _IMP_atom.Atom_set_atom_type(self, t)
8605 def get_element(self):
8606 """get_element(Atom self) -> IMP::atom::Element"""
8607 return _IMP_atom.Atom_get_element(self)
8610 def set_element(self, e):
8611 """set_element(Atom self, IMP::atom::Element e)"""
8612 return _IMP_atom.Atom_set_element(self, e)
8615 def get_occupancy(self):
8616 """get_occupancy(Atom self) -> double"""
8617 return _IMP_atom.Atom_get_occupancy(self)
8620 def set_occupancy(self, occupancy):
8621 """set_occupancy(Atom self, double occupancy)"""
8622 return _IMP_atom.Atom_set_occupancy(self, occupancy)
8625 def get_temperature_factor(self):
8626 """get_temperature_factor(Atom self) -> double"""
8627 return _IMP_atom.Atom_get_temperature_factor(self)
8630 def set_temperature_factor(self, tempFactor):
8631 """set_temperature_factor(Atom self, double tempFactor)"""
8632 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8635 def get_input_index(self):
8636 """get_input_index(Atom self) -> IMP::Int"""
8637 return _IMP_atom.Atom_get_input_index(self)
8640 def set_input_index(self, t):
8641 """set_input_index(Atom self, IMP::Int t)"""
8642 return _IMP_atom.Atom_set_input_index(self, t)
8645 def get_atom_type_key():
8646 """get_atom_type_key() -> IntKey"""
8647 return _IMP_atom.Atom_get_atom_type_key()
8649 get_atom_type_key = staticmethod(get_atom_type_key)
8651 def get_element_key():
8652 """get_element_key() -> IntKey"""
8653 return _IMP_atom.Atom_get_element_key()
8655 get_element_key = staticmethod(get_element_key)
8657 def get_input_index_key():
8658 """get_input_index_key() -> IntKey"""
8659 return _IMP_atom.Atom_get_input_index_key()
8661 get_input_index_key = staticmethod(get_input_index_key)
8663 def get_occupancy_key():
8664 """get_occupancy_key() -> FloatKey"""
8665 return _IMP_atom.Atom_get_occupancy_key()
8667 get_occupancy_key = staticmethod(get_occupancy_key)
8669 def get_temperature_factor_key():
8670 """get_temperature_factor_key() -> FloatKey"""
8671 return _IMP_atom.Atom_get_temperature_factor_key()
8673 get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8675 def add_attribute(self, *args):
8677 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8678 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8679 add_attribute(Atom self, IntKey a0, IMP::Int a1)
8680 add_attribute(Atom self, FloatsKey a0, IMP::Floats a1)
8681 add_attribute(Atom self, IntsKey a0, IMP::Ints a1)
8682 add_attribute(Atom self, StringKey a0, IMP::String a1)
8683 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8684 add_attribute(Atom self, ObjectKey a0, Object a1)
8686 return _IMP_atom.Atom_add_attribute(self, *args)
8689 def get_value(self, *args):
8691 get_value(Atom self, FloatKey a0) -> IMP::Float
8692 get_value(Atom self, IntKey a0) -> IMP::Int
8693 get_value(Atom self, FloatsKey a0) -> IMP::Floats
8694 get_value(Atom self, IntsKey a0) -> IMP::Ints
8695 get_value(Atom self, StringKey a0) -> IMP::String
8696 get_value(Atom self, ParticleIndexKey a0) -> Particle
8697 get_value(Atom self, ObjectKey a0) -> Object
8699 return _IMP_atom.Atom_get_value(self, *args)
8702 def set_value(self, *args):
8704 set_value(Atom self, FloatKey a0, IMP::Float a1)
8705 set_value(Atom self, IntKey a0, IMP::Int a1)
8706 set_value(Atom self, FloatsKey a0, IMP::Floats a1)
8707 set_value(Atom self, IntsKey a0, IMP::Ints a1)
8708 set_value(Atom self, StringKey a0, IMP::String a1)
8709 set_value(Atom self, ParticleIndexKey a0, Particle a1)
8710 set_value(Atom self, ObjectKey a0, Object a1)
8712 return _IMP_atom.Atom_set_value(self, *args)
8715 def remove_attribute(self, *args):
8717 remove_attribute(Atom self, FloatKey a0)
8718 remove_attribute(Atom self, IntKey a0)
8719 remove_attribute(Atom self, FloatsKey a0)
8720 remove_attribute(Atom self, IntsKey a0)
8721 remove_attribute(Atom self, StringKey a0)
8722 remove_attribute(Atom self, ParticleIndexKey a0)
8723 remove_attribute(Atom self, ObjectKey a0)
8725 return _IMP_atom.Atom_remove_attribute(self, *args)
8728 def has_attribute(self, *args):
8730 has_attribute(Atom self, FloatKey a0) -> bool
8731 has_attribute(Atom self, IntKey a0) -> bool
8732 has_attribute(Atom self, FloatsKey a0) -> bool
8733 has_attribute(Atom self, IntsKey a0) -> bool
8734 has_attribute(Atom self, StringKey a0) -> bool
8735 has_attribute(Atom self, ParticleIndexKey a0) -> bool
8736 has_attribute(Atom self, ObjectKey a0) -> bool
8738 return _IMP_atom.Atom_has_attribute(self, *args)
8741 def get_derivative(self, a0):
8742 """get_derivative(Atom self, FloatKey a0) -> double"""
8743 return _IMP_atom.Atom_get_derivative(self, a0)
8747 """get_name(Atom self) -> std::string"""
8748 return _IMP_atom.Atom_get_name(self)
8751 def clear_caches(self):
8752 """clear_caches(Atom self)"""
8753 return _IMP_atom.Atom_clear_caches(self)
8756 def set_name(self, a0):
8757 """set_name(Atom self, std::string a0)"""
8758 return _IMP_atom.Atom_set_name(self, a0)
8762 """set_check_level(Atom self, IMP::CheckLevel a0)"""
8763 return _IMP_atom.Atom_set_check_level(self, a0)
8766 def add_to_derivative(self, a0, a1, a2):
8767 """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8768 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8771 def set_is_optimized(self, a0, a1):
8772 """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8773 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8776 def get_is_optimized(self, a0):
8777 """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8778 return _IMP_atom.Atom_get_is_optimized(self, a0)
8782 """get_check_level(Atom self) -> IMP::CheckLevel"""
8783 return _IMP_atom.Atom_get_check_level(self)
8786 def __eq__(self, *args):
8788 __eq__(Atom self, Atom o) -> bool
8789 __eq__(Atom self, Particle d) -> bool
8791 return _IMP_atom.Atom___eq__(self, *args)
8794 def __ne__(self, *args):
8796 __ne__(Atom self, Atom o) -> bool
8797 __ne__(Atom self, Particle d) -> bool
8799 return _IMP_atom.Atom___ne__(self, *args)
8802 def __le__(self, *args):
8804 __le__(Atom self, Atom o) -> bool
8805 __le__(Atom self, Particle d) -> bool
8807 return _IMP_atom.Atom___le__(self, *args)
8810 def __lt__(self, *args):
8812 __lt__(Atom self, Atom o) -> bool
8813 __lt__(Atom self, Particle d) -> bool
8815 return _IMP_atom.Atom___lt__(self, *args)
8818 def __ge__(self, *args):
8820 __ge__(Atom self, Atom o) -> bool
8821 __ge__(Atom self, Particle d) -> bool
8823 return _IMP_atom.Atom___ge__(self, *args)
8826 def __gt__(self, *args):
8828 __gt__(Atom self, Atom o) -> bool
8829 __gt__(Atom self, Particle d) -> bool
8831 return _IMP_atom.Atom___gt__(self, *args)
8835 """__hash__(Atom self) -> std::size_t"""
8836 return _IMP_atom.Atom___hash__(self)
8840 """__str__(Atom self) -> std::string"""
8841 return _IMP_atom.Atom___str__(self)
8845 """__repr__(Atom self) -> std::string"""
8846 return _IMP_atom.Atom___repr__(self)
8848 __swig_destroy__ = _IMP_atom.delete_Atom
8849 __del__ =
lambda self:
None
8850 Atom_swigregister = _IMP_atom.Atom_swigregister
8851 Atom_swigregister(Atom)
8852 AT_UNKNOWN = cvar.AT_UNKNOWN
8862 AT_HA1 = cvar.AT_HA1
8863 AT_HA2 = cvar.AT_HA2
8864 AT_HA3 = cvar.AT_HA3
8867 AT_HB1 = cvar.AT_HB1
8868 AT_HB2 = cvar.AT_HB2
8869 AT_HB3 = cvar.AT_HB3
8870 AT_OXT = cvar.AT_OXT
8871 AT_CH3 = cvar.AT_CH3
8874 AT_CG1 = cvar.AT_CG1
8875 AT_CG2 = cvar.AT_CG2
8877 AT_HG1 = cvar.AT_HG1
8878 AT_HG2 = cvar.AT_HG2
8879 AT_HG3 = cvar.AT_HG3
8880 AT_HG11 = cvar.AT_HG11
8881 AT_HG21 = cvar.AT_HG21
8882 AT_HG31 = cvar.AT_HG31
8883 AT_HG12 = cvar.AT_HG12
8884 AT_HG13 = cvar.AT_HG13
8885 AT_HG22 = cvar.AT_HG22
8886 AT_HG23 = cvar.AT_HG23
8887 AT_HG32 = cvar.AT_HG32
8889 AT_OG1 = cvar.AT_OG1
8892 AT_CD1 = cvar.AT_CD1
8893 AT_CD2 = cvar.AT_CD2
8895 AT_HD1 = cvar.AT_HD1
8896 AT_HD2 = cvar.AT_HD2
8897 AT_HD3 = cvar.AT_HD3
8898 AT_HD11 = cvar.AT_HD11
8899 AT_HD21 = cvar.AT_HD21
8900 AT_HD31 = cvar.AT_HD31
8901 AT_HD12 = cvar.AT_HD12
8902 AT_HD13 = cvar.AT_HD13
8903 AT_HD22 = cvar.AT_HD22
8904 AT_HD23 = cvar.AT_HD23
8905 AT_HD32 = cvar.AT_HD32
8907 AT_OD1 = cvar.AT_OD1
8908 AT_OD2 = cvar.AT_OD2
8909 AT_ND1 = cvar.AT_ND1
8910 AT_ND2 = cvar.AT_ND2
8912 AT_CE1 = cvar.AT_CE1
8913 AT_CE2 = cvar.AT_CE2
8914 AT_CE3 = cvar.AT_CE3
8916 AT_HE1 = cvar.AT_HE1
8917 AT_HE2 = cvar.AT_HE2
8918 AT_HE3 = cvar.AT_HE3
8919 AT_HE21 = cvar.AT_HE21
8920 AT_HE22 = cvar.AT_HE22
8921 AT_OE1 = cvar.AT_OE1
8922 AT_OE2 = cvar.AT_OE2
8924 AT_NE1 = cvar.AT_NE1
8925 AT_NE2 = cvar.AT_NE2
8927 AT_CZ2 = cvar.AT_CZ2
8928 AT_CZ3 = cvar.AT_CZ3
8931 AT_HZ1 = cvar.AT_HZ1
8932 AT_HZ2 = cvar.AT_HZ2
8933 AT_HZ3 = cvar.AT_HZ3
8934 AT_CH2 = cvar.AT_CH2
8935 AT_NH1 = cvar.AT_NH1
8936 AT_NH2 = cvar.AT_NH2
8939 AT_HH11 = cvar.AT_HH11
8940 AT_HH21 = cvar.AT_HH21
8941 AT_HH2 = cvar.AT_HH2
8942 AT_HH12 = cvar.AT_HH12
8943 AT_HH22 = cvar.AT_HH22
8944 AT_HH13 = cvar.AT_HH13
8945 AT_HH23 = cvar.AT_HH23
8946 AT_HH33 = cvar.AT_HH33
8948 AT_OP1 = cvar.AT_OP1
8949 AT_OP2 = cvar.AT_OP2
8950 AT_OP3 = cvar.AT_OP3
8951 AT_O5p = cvar.AT_O5p
8952 AT_C5p = cvar.AT_C5p
8953 AT_H5p = cvar.AT_H5p
8954 AT_H5pp = cvar.AT_H5pp
8955 AT_C4p = cvar.AT_C4p
8956 AT_H4p = cvar.AT_H4p
8957 AT_O4p = cvar.AT_O4p
8958 AT_C1p = cvar.AT_C1p
8959 AT_H1p = cvar.AT_H1p
8960 AT_C3p = cvar.AT_C3p
8961 AT_H3p = cvar.AT_H3p
8962 AT_O3p = cvar.AT_O3p
8963 AT_C2p = cvar.AT_C2p
8964 AT_H2p = cvar.AT_H2p
8965 AT_H2pp = cvar.AT_H2pp
8966 AT_O2p = cvar.AT_O2p
8967 AT_HO2p = cvar.AT_HO2p
8979 AT_H61 = cvar.AT_H61
8980 AT_H62 = cvar.AT_H62
8984 AT_H21 = cvar.AT_H21
8985 AT_H22 = cvar.AT_H22
8990 AT_H41 = cvar.AT_H41
8991 AT_H42 = cvar.AT_H42
8994 AT_H71 = cvar.AT_H71
8995 AT_H72 = cvar.AT_H72
8996 AT_H73 = cvar.AT_H73
8997 AT_O1A = cvar.AT_O1A
8998 AT_O2A = cvar.AT_O2A
8999 AT_O3A = cvar.AT_O3A
9000 AT_O1B = cvar.AT_O1B
9001 AT_O2B = cvar.AT_O2B
9002 AT_O3B = cvar.AT_O3B
9004 def Atom_setup_particle(*args):
9006 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
9007 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
9008 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
9009 Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
9011 return _IMP_atom.Atom_setup_particle(*args)
9013 def Atom_get_is_setup(*args):
9015 get_is_setup(_ParticleAdaptor p) -> bool
9016 Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
9018 return _IMP_atom.Atom_get_is_setup(*args)
9020 def Atom_get_atom_type_key():
9021 """Atom_get_atom_type_key() -> IntKey"""
9022 return _IMP_atom.Atom_get_atom_type_key()
9024 def Atom_get_element_key():
9025 """Atom_get_element_key() -> IntKey"""
9026 return _IMP_atom.Atom_get_element_key()
9028 def Atom_get_input_index_key():
9029 """Atom_get_input_index_key() -> IntKey"""
9030 return _IMP_atom.Atom_get_input_index_key()
9032 def Atom_get_occupancy_key():
9033 """Atom_get_occupancy_key() -> FloatKey"""
9034 return _IMP_atom.Atom_get_occupancy_key()
9036 def Atom_get_temperature_factor_key():
9037 """Atom_get_temperature_factor_key() -> FloatKey"""
9038 return _IMP_atom.Atom_get_temperature_factor_key()
9043 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
9044 get_residue(Atom d, bool nothrow=False) -> Residue
9045 get_residue(Atom d) -> Residue
9047 return _IMP_atom.get_residue(*args)
9050 """get_atom(Residue rd, AtomType at) -> Atom"""
9051 return _IMP_atom.get_atom(rd, at)
9054 """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
9055 return _IMP_atom.add_atom_type(name, e)
9057 def get_element_for_atom_type(at):
9058 """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
9059 return _IMP_atom.get_element_for_atom_type(at)
9062 """get_atom_type_exists(std::string name) -> bool"""
9063 return _IMP_atom.get_atom_type_exists(name)
9064 class Residue(Hierarchy):
9065 """Proxy of C++ IMP::atom::Residue class."""
9067 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9069 def __init__(self, *args):
9071 __init__(IMP::atom::Residue self) -> Residue
9072 __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
9073 __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
9075 this = _IMP_atom.new_Residue(*args)
9077 self.this.append(this)
9078 except __builtin__.Exception:
9081 def show(self, *args):
9083 show(Residue self, _ostream out)
9086 return _IMP_atom.Residue_show(self, *args)
9089 def setup_particle(*args):
9091 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9092 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9093 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9094 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9095 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9096 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9097 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9098 setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9100 return _IMP_atom.Residue_setup_particle(*args)
9102 setup_particle = staticmethod(setup_particle)
9104 def get_is_setup(*args):
9106 get_is_setup(_ParticleAdaptor p) -> bool
9107 get_is_setup(Model m, ParticleIndex pi) -> bool
9109 return _IMP_atom.Residue_get_is_setup(*args)
9111 get_is_setup = staticmethod(get_is_setup)
9113 def get_residue_type(self):
9114 """get_residue_type(Residue self) -> ResidueType"""
9115 return _IMP_atom.Residue_get_residue_type(self)
9118 def set_residue_type(self, t):
9119 """set_residue_type(Residue self, ResidueType t)"""
9120 return _IMP_atom.Residue_set_residue_type(self, t)
9123 def get_is_protein(self):
9124 """get_is_protein(Residue self) -> bool"""
9125 return _IMP_atom.Residue_get_is_protein(self)
9128 def get_is_dna(self):
9129 """get_is_dna(Residue self) -> bool"""
9130 return _IMP_atom.Residue_get_is_dna(self)
9133 def get_is_rna(self):
9134 """get_is_rna(Residue self) -> bool"""
9135 return _IMP_atom.Residue_get_is_rna(self)
9139 """get_index(Residue self) -> IMP::Int"""
9140 return _IMP_atom.Residue_get_index(self)
9143 def set_index(self, t):
9144 """set_index(Residue self, IMP::Int t)"""
9145 return _IMP_atom.Residue_set_index(self, t)
9148 def get_insertion_code(self):
9149 """get_insertion_code(Residue self) -> char"""
9150 return _IMP_atom.Residue_get_insertion_code(self)
9153 def set_insertion_code(self, insertion_code):
9154 """set_insertion_code(Residue self, char insertion_code)"""
9155 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
9158 def get_index_key():
9159 """get_index_key() -> IntKey"""
9160 return _IMP_atom.Residue_get_index_key()
9162 get_index_key = staticmethod(get_index_key)
9164 def get_residue_type_key():
9165 """get_residue_type_key() -> IntKey"""
9166 return _IMP_atom.Residue_get_residue_type_key()
9168 get_residue_type_key = staticmethod(get_residue_type_key)
9170 def get_insertion_code_key():
9171 """get_insertion_code_key() -> IntKey"""
9172 return _IMP_atom.Residue_get_insertion_code_key()
9174 get_insertion_code_key = staticmethod(get_insertion_code_key)
9176 def add_attribute(self, *args):
9178 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
9179 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
9180 add_attribute(Residue self, IntKey a0, IMP::Int a1)
9181 add_attribute(Residue self, FloatsKey a0, IMP::Floats a1)
9182 add_attribute(Residue self, IntsKey a0, IMP::Ints a1)
9183 add_attribute(Residue self, StringKey a0, IMP::String a1)
9184 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
9185 add_attribute(Residue self, ObjectKey a0, Object a1)
9187 return _IMP_atom.Residue_add_attribute(self, *args)
9190 def get_value(self, *args):
9192 get_value(Residue self, FloatKey a0) -> IMP::Float
9193 get_value(Residue self, IntKey a0) -> IMP::Int
9194 get_value(Residue self, FloatsKey a0) -> IMP::Floats
9195 get_value(Residue self, IntsKey a0) -> IMP::Ints
9196 get_value(Residue self, StringKey a0) -> IMP::String
9197 get_value(Residue self, ParticleIndexKey a0) -> Particle
9198 get_value(Residue self, ObjectKey a0) -> Object
9200 return _IMP_atom.Residue_get_value(self, *args)
9203 def set_value(self, *args):
9205 set_value(Residue self, FloatKey a0, IMP::Float a1)
9206 set_value(Residue self, IntKey a0, IMP::Int a1)
9207 set_value(Residue self, FloatsKey a0, IMP::Floats a1)
9208 set_value(Residue self, IntsKey a0, IMP::Ints a1)
9209 set_value(Residue self, StringKey a0, IMP::String a1)
9210 set_value(Residue self, ParticleIndexKey a0, Particle a1)
9211 set_value(Residue self, ObjectKey a0, Object a1)
9213 return _IMP_atom.Residue_set_value(self, *args)
9216 def remove_attribute(self, *args):
9218 remove_attribute(Residue self, FloatKey a0)
9219 remove_attribute(Residue self, IntKey a0)
9220 remove_attribute(Residue self, FloatsKey a0)
9221 remove_attribute(Residue self, IntsKey a0)
9222 remove_attribute(Residue self, StringKey a0)
9223 remove_attribute(Residue self, ParticleIndexKey a0)
9224 remove_attribute(Residue self, ObjectKey a0)
9226 return _IMP_atom.Residue_remove_attribute(self, *args)
9229 def has_attribute(self, *args):
9231 has_attribute(Residue self, FloatKey a0) -> bool
9232 has_attribute(Residue self, IntKey a0) -> bool
9233 has_attribute(Residue self, FloatsKey a0) -> bool
9234 has_attribute(Residue self, IntsKey a0) -> bool
9235 has_attribute(Residue self, StringKey a0) -> bool
9236 has_attribute(Residue self, ParticleIndexKey a0) -> bool
9237 has_attribute(Residue self, ObjectKey a0) -> bool
9239 return _IMP_atom.Residue_has_attribute(self, *args)
9242 def get_derivative(self, a0):
9243 """get_derivative(Residue self, FloatKey a0) -> double"""
9244 return _IMP_atom.Residue_get_derivative(self, a0)
9248 """get_name(Residue self) -> std::string"""
9249 return _IMP_atom.Residue_get_name(self)
9252 def clear_caches(self):
9253 """clear_caches(Residue self)"""
9254 return _IMP_atom.Residue_clear_caches(self)
9257 def set_name(self, a0):
9258 """set_name(Residue self, std::string a0)"""
9259 return _IMP_atom.Residue_set_name(self, a0)
9263 """set_check_level(Residue self, IMP::CheckLevel a0)"""
9264 return _IMP_atom.Residue_set_check_level(self, a0)
9267 def add_to_derivative(self, a0, a1, a2):
9268 """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9269 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
9272 def set_is_optimized(self, a0, a1):
9273 """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
9274 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
9277 def get_is_optimized(self, a0):
9278 """get_is_optimized(Residue self, FloatKey a0) -> bool"""
9279 return _IMP_atom.Residue_get_is_optimized(self, a0)
9283 """get_check_level(Residue self) -> IMP::CheckLevel"""
9284 return _IMP_atom.Residue_get_check_level(self)
9287 def __eq__(self, *args):
9289 __eq__(Residue self, Residue o) -> bool
9290 __eq__(Residue self, Particle d) -> bool
9292 return _IMP_atom.Residue___eq__(self, *args)
9295 def __ne__(self, *args):
9297 __ne__(Residue self, Residue o) -> bool
9298 __ne__(Residue self, Particle d) -> bool
9300 return _IMP_atom.Residue___ne__(self, *args)
9303 def __le__(self, *args):
9305 __le__(Residue self, Residue o) -> bool
9306 __le__(Residue self, Particle d) -> bool
9308 return _IMP_atom.Residue___le__(self, *args)
9311 def __lt__(self, *args):
9313 __lt__(Residue self, Residue o) -> bool
9314 __lt__(Residue self, Particle d) -> bool
9316 return _IMP_atom.Residue___lt__(self, *args)
9319 def __ge__(self, *args):
9321 __ge__(Residue self, Residue o) -> bool
9322 __ge__(Residue self, Particle d) -> bool
9324 return _IMP_atom.Residue___ge__(self, *args)
9327 def __gt__(self, *args):
9329 __gt__(Residue self, Residue o) -> bool
9330 __gt__(Residue self, Particle d) -> bool
9332 return _IMP_atom.Residue___gt__(self, *args)
9336 """__hash__(Residue self) -> std::size_t"""
9337 return _IMP_atom.Residue___hash__(self)
9341 """__str__(Residue self) -> std::string"""
9342 return _IMP_atom.Residue___str__(self)
9346 """__repr__(Residue self) -> std::string"""
9347 return _IMP_atom.Residue___repr__(self)
9349 __swig_destroy__ = _IMP_atom.delete_Residue
9350 __del__ =
lambda self:
None
9351 Residue_swigregister = _IMP_atom.Residue_swigregister
9352 Residue_swigregister(Residue)
9390 def Residue_setup_particle(*args):
9392 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9393 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9394 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9395 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9396 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9397 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9398 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9399 Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9401 return _IMP_atom.Residue_setup_particle(*args)
9403 def Residue_get_is_setup(*args):
9405 get_is_setup(_ParticleAdaptor p) -> bool
9406 Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
9408 return _IMP_atom.Residue_get_is_setup(*args)
9410 def Residue_get_index_key():
9411 """Residue_get_index_key() -> IntKey"""
9412 return _IMP_atom.Residue_get_index_key()
9414 def Residue_get_residue_type_key():
9415 """Residue_get_residue_type_key() -> IntKey"""
9416 return _IMP_atom.Residue_get_residue_type_key()
9418 def Residue_get_insertion_code_key():
9419 """Residue_get_insertion_code_key() -> IntKey"""
9420 return _IMP_atom.Residue_get_insertion_code_key()
9424 """get_next_residue(Residue rd) -> Hierarchy"""
9425 return _IMP_atom.get_next_residue(rd)
9428 """get_previous_residue(Residue rd) -> Hierarchy"""
9429 return _IMP_atom.get_previous_residue(rd)
9432 """get_one_letter_code(ResidueType c) -> char"""
9433 return _IMP_atom.get_one_letter_code(c)
9434 BALLS = _IMP_atom.BALLS
9435 DENSITIES = _IMP_atom.DENSITIES
9436 class Representation(Hierarchy):
9437 """Proxy of C++ IMP::atom::Representation class."""
9439 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9441 def setup_particle(*args):
9443 setup_particle(Model m, ParticleIndex pi) -> Representation
9444 setup_particle(_ParticleAdaptor decorator) -> Representation
9445 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9446 setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9447 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9448 setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9450 return _IMP_atom.Representation_setup_particle(*args)
9452 setup_particle = staticmethod(setup_particle)
9454 def __init__(self, *args):
9456 __init__(IMP::atom::Representation self) -> Representation
9457 __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
9458 __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
9460 this = _IMP_atom.new_Representation(*args)
9462 self.this.append(this)
9463 except __builtin__.Exception:
9466 def show(self, *args):
9468 show(Representation self, _ostream out)
9469 show(Representation self)
9471 return _IMP_atom.Representation_show(self, *args)
9474 def get_is_setup(*args):
9476 get_is_setup(_ParticleAdaptor p) -> bool
9477 get_is_setup(Model m, ParticleIndex pi) -> bool
9479 return _IMP_atom.Representation_get_is_setup(*args)
9481 get_is_setup = staticmethod(get_is_setup)
9485 get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
9486 get_representation(Representation self, double resolution) -> Hierarchy
9488 return _IMP_atom.Representation_get_representation(self, *args)
9491 def get_representations(self, *args):
9493 get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
9494 get_representations(Representation self) -> IMP::atom::Hierarchies
9496 return _IMP_atom.Representation_get_representations(self, *args)
9499 def add_representation(self, *args):
9501 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
9502 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
9503 add_representation(Representation self, _ParticleIndexAdaptor rep)
9505 return _IMP_atom.Representation_add_representation(self, *args)
9508 def get_resolutions(self, *args):
9510 get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9511 get_resolutions(Representation self) -> IMP::Floats
9513 return _IMP_atom.Representation_get_resolutions(self, *args)
9516 def remove_representation(self, rep):
9517 """remove_representation(Representation self, _ParticleIndexAdaptor rep)"""
9518 return _IMP_atom.Representation_remove_representation(self, rep)
9521 def update_parents(self):
9522 """update_parents(Representation self)"""
9523 return _IMP_atom.Representation_update_parents(self)
9526 def add_attribute(self, *args):
9528 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9529 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9530 add_attribute(Representation self, IntKey a0, IMP::Int a1)
9531 add_attribute(Representation self, FloatsKey a0, IMP::Floats a1)
9532 add_attribute(Representation self, IntsKey a0, IMP::Ints a1)
9533 add_attribute(Representation self, StringKey a0, IMP::String a1)
9534 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9535 add_attribute(Representation self, ObjectKey a0, Object a1)
9537 return _IMP_atom.Representation_add_attribute(self, *args)
9540 def get_value(self, *args):
9542 get_value(Representation self, FloatKey a0) -> IMP::Float
9543 get_value(Representation self, IntKey a0) -> IMP::Int
9544 get_value(Representation self, FloatsKey a0) -> IMP::Floats
9545 get_value(Representation self, IntsKey a0) -> IMP::Ints
9546 get_value(Representation self, StringKey a0) -> IMP::String
9547 get_value(Representation self, ParticleIndexKey a0) -> Particle
9548 get_value(Representation self, ObjectKey a0) -> Object
9550 return _IMP_atom.Representation_get_value(self, *args)
9553 def set_value(self, *args):
9555 set_value(Representation self, FloatKey a0, IMP::Float a1)
9556 set_value(Representation self, IntKey a0, IMP::Int a1)
9557 set_value(Representation self, FloatsKey a0, IMP::Floats a1)
9558 set_value(Representation self, IntsKey a0, IMP::Ints a1)
9559 set_value(Representation self, StringKey a0, IMP::String a1)
9560 set_value(Representation self, ParticleIndexKey a0, Particle a1)
9561 set_value(Representation self, ObjectKey a0, Object a1)
9563 return _IMP_atom.Representation_set_value(self, *args)
9566 def remove_attribute(self, *args):
9568 remove_attribute(Representation self, FloatKey a0)
9569 remove_attribute(Representation self, IntKey a0)
9570 remove_attribute(Representation self, FloatsKey a0)
9571 remove_attribute(Representation self, IntsKey a0)
9572 remove_attribute(Representation self, StringKey a0)
9573 remove_attribute(Representation self, ParticleIndexKey a0)
9574 remove_attribute(Representation self, ObjectKey a0)
9576 return _IMP_atom.Representation_remove_attribute(self, *args)
9579 def has_attribute(self, *args):
9581 has_attribute(Representation self, FloatKey a0) -> bool
9582 has_attribute(Representation self, IntKey a0) -> bool
9583 has_attribute(Representation self, FloatsKey a0) -> bool
9584 has_attribute(Representation self, IntsKey a0) -> bool
9585 has_attribute(Representation self, StringKey a0) -> bool
9586 has_attribute(Representation self, ParticleIndexKey a0) -> bool
9587 has_attribute(Representation self, ObjectKey a0) -> bool
9589 return _IMP_atom.Representation_has_attribute(self, *args)
9592 def get_derivative(self, a0):
9593 """get_derivative(Representation self, FloatKey a0) -> double"""
9594 return _IMP_atom.Representation_get_derivative(self, a0)
9598 """get_name(Representation self) -> std::string"""
9599 return _IMP_atom.Representation_get_name(self)
9602 def clear_caches(self):
9603 """clear_caches(Representation self)"""
9604 return _IMP_atom.Representation_clear_caches(self)
9607 def set_name(self, a0):
9608 """set_name(Representation self, std::string a0)"""
9609 return _IMP_atom.Representation_set_name(self, a0)
9613 """set_check_level(Representation self, IMP::CheckLevel a0)"""
9614 return _IMP_atom.Representation_set_check_level(self, a0)
9617 def add_to_derivative(self, a0, a1, a2):
9618 """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9619 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9622 def set_is_optimized(self, a0, a1):
9623 """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9624 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9627 def get_is_optimized(self, a0):
9628 """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9629 return _IMP_atom.Representation_get_is_optimized(self, a0)
9633 """get_check_level(Representation self) -> IMP::CheckLevel"""
9634 return _IMP_atom.Representation_get_check_level(self)
9637 def __eq__(self, *args):
9639 __eq__(Representation self, Representation o) -> bool
9640 __eq__(Representation self, Particle d) -> bool
9642 return _IMP_atom.Representation___eq__(self, *args)
9645 def __ne__(self, *args):
9647 __ne__(Representation self, Representation o) -> bool
9648 __ne__(Representation self, Particle d) -> bool
9650 return _IMP_atom.Representation___ne__(self, *args)
9653 def __le__(self, *args):
9655 __le__(Representation self, Representation o) -> bool
9656 __le__(Representation self, Particle d) -> bool
9658 return _IMP_atom.Representation___le__(self, *args)
9661 def __lt__(self, *args):
9663 __lt__(Representation self, Representation o) -> bool
9664 __lt__(Representation self, Particle d) -> bool
9666 return _IMP_atom.Representation___lt__(self, *args)
9669 def __ge__(self, *args):
9671 __ge__(Representation self, Representation o) -> bool
9672 __ge__(Representation self, Particle d) -> bool
9674 return _IMP_atom.Representation___ge__(self, *args)
9677 def __gt__(self, *args):
9679 __gt__(Representation self, Representation o) -> bool
9680 __gt__(Representation self, Particle d) -> bool
9682 return _IMP_atom.Representation___gt__(self, *args)
9686 """__hash__(Representation self) -> std::size_t"""
9687 return _IMP_atom.Representation___hash__(self)
9691 """__str__(Representation self) -> std::string"""
9692 return _IMP_atom.Representation___str__(self)
9696 """__repr__(Representation self) -> std::string"""
9697 return _IMP_atom.Representation___repr__(self)
9699 __swig_destroy__ = _IMP_atom.delete_Representation
9700 __del__ =
lambda self:
None
9701 Representation_swigregister = _IMP_atom.Representation_swigregister
9702 Representation_swigregister(Representation)
9703 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9705 def Representation_setup_particle(*args):
9707 setup_particle(Model m, ParticleIndex pi) -> Representation
9708 setup_particle(_ParticleAdaptor decorator) -> Representation
9709 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9710 setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9711 setup_particle(Model m, ParticleIndex pi, Representation other) -> Representation
9712 Representation_setup_particle(_ParticleAdaptor decorator, Representation other) -> Representation
9714 return _IMP_atom.Representation_setup_particle(*args)
9716 def Representation_get_is_setup(*args):
9718 get_is_setup(_ParticleAdaptor p) -> bool
9719 Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9721 return _IMP_atom.Representation_get_is_setup(*args)
9726 get_resolution(Model m, ParticleIndex pi) -> double
9727 get_resolution(Hierarchy h) -> double
9729 return _IMP_atom.get_resolution(*args)
9733 get_representation(Hierarchy h, bool nothrow=False) -> Representation
9734 get_representation(Hierarchy h) -> Representation
9736 return _IMP_atom.get_representation(h, nothrow)
9740 show_with_representations(Hierarchy h, _ostream out)
9741 show_with_representations(Hierarchy h)
9743 return _IMP_atom.show_with_representations(*args)
9744 class State(Hierarchy):
9745 """Proxy of C++ IMP::atom::State class."""
9747 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9749 def setup_particle(*args):
9751 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9752 setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9753 setup_particle(Model m, ParticleIndex pi, State other) -> State
9754 setup_particle(_ParticleAdaptor decorator, State other) -> State
9756 return _IMP_atom.State_setup_particle(*args)
9758 setup_particle = staticmethod(setup_particle)
9760 def __init__(self, *args):
9762 __init__(IMP::atom::State self) -> State
9763 __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9764 __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9766 this = _IMP_atom.new_State(*args)
9768 self.this.append(this)
9769 except __builtin__.Exception:
9772 def show(self, *args):
9774 show(State self, _ostream out)
9777 return _IMP_atom.State_show(self, *args)
9780 def get_is_setup(*args):
9782 get_is_setup(_ParticleAdaptor p) -> bool
9783 get_is_setup(Model m, ParticleIndex pi) -> bool
9785 return _IMP_atom.State_get_is_setup(*args)
9787 get_is_setup = staticmethod(get_is_setup)
9790 """get_state_index(State self) -> unsigned int"""
9791 return _IMP_atom.State_get_state_index(self)
9794 def add_attribute(self, *args):
9796 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9797 add_attribute(State self, FloatKey a0, IMP::Float a1)
9798 add_attribute(State self, IntKey a0, IMP::Int a1)
9799 add_attribute(State self, FloatsKey a0, IMP::Floats a1)
9800 add_attribute(State self, IntsKey a0, IMP::Ints a1)
9801 add_attribute(State self, StringKey a0, IMP::String a1)
9802 add_attribute(State self, ParticleIndexKey a0, Particle a1)
9803 add_attribute(State self, ObjectKey a0, Object a1)
9805 return _IMP_atom.State_add_attribute(self, *args)
9808 def get_value(self, *args):
9810 get_value(State self, FloatKey a0) -> IMP::Float
9811 get_value(State self, IntKey a0) -> IMP::Int
9812 get_value(State self, FloatsKey a0) -> IMP::Floats
9813 get_value(State self, IntsKey a0) -> IMP::Ints
9814 get_value(State self, StringKey a0) -> IMP::String
9815 get_value(State self, ParticleIndexKey a0) -> Particle
9816 get_value(State self, ObjectKey a0) -> Object
9818 return _IMP_atom.State_get_value(self, *args)
9821 def set_value(self, *args):
9823 set_value(State self, FloatKey a0, IMP::Float a1)
9824 set_value(State self, IntKey a0, IMP::Int a1)
9825 set_value(State self, FloatsKey a0, IMP::Floats a1)
9826 set_value(State self, IntsKey a0, IMP::Ints a1)
9827 set_value(State self, StringKey a0, IMP::String a1)
9828 set_value(State self, ParticleIndexKey a0, Particle a1)
9829 set_value(State self, ObjectKey a0, Object a1)
9831 return _IMP_atom.State_set_value(self, *args)
9834 def remove_attribute(self, *args):
9836 remove_attribute(State self, FloatKey a0)
9837 remove_attribute(State self, IntKey a0)
9838 remove_attribute(State self, FloatsKey a0)
9839 remove_attribute(State self, IntsKey a0)
9840 remove_attribute(State self, StringKey a0)
9841 remove_attribute(State self, ParticleIndexKey a0)
9842 remove_attribute(State self, ObjectKey a0)
9844 return _IMP_atom.State_remove_attribute(self, *args)
9847 def has_attribute(self, *args):
9849 has_attribute(State self, FloatKey a0) -> bool
9850 has_attribute(State self, IntKey a0) -> bool
9851 has_attribute(State self, FloatsKey a0) -> bool
9852 has_attribute(State self, IntsKey a0) -> bool
9853 has_attribute(State self, StringKey a0) -> bool
9854 has_attribute(State self, ParticleIndexKey a0) -> bool
9855 has_attribute(State self, ObjectKey a0) -> bool
9857 return _IMP_atom.State_has_attribute(self, *args)
9860 def get_derivative(self, a0):
9861 """get_derivative(State self, FloatKey a0) -> double"""
9862 return _IMP_atom.State_get_derivative(self, a0)
9866 """get_name(State self) -> std::string"""
9867 return _IMP_atom.State_get_name(self)
9870 def clear_caches(self):
9871 """clear_caches(State self)"""
9872 return _IMP_atom.State_clear_caches(self)
9875 def set_name(self, a0):
9876 """set_name(State self, std::string a0)"""
9877 return _IMP_atom.State_set_name(self, a0)
9881 """set_check_level(State self, IMP::CheckLevel a0)"""
9882 return _IMP_atom.State_set_check_level(self, a0)
9885 def add_to_derivative(self, a0, a1, a2):
9886 """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9887 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9890 def set_is_optimized(self, a0, a1):
9891 """set_is_optimized(State self, FloatKey a0, bool a1)"""
9892 return _IMP_atom.State_set_is_optimized(self, a0, a1)
9895 def get_is_optimized(self, a0):
9896 """get_is_optimized(State self, FloatKey a0) -> bool"""
9897 return _IMP_atom.State_get_is_optimized(self, a0)
9901 """get_check_level(State self) -> IMP::CheckLevel"""
9902 return _IMP_atom.State_get_check_level(self)
9905 def __eq__(self, *args):
9907 __eq__(State self, State o) -> bool
9908 __eq__(State self, Particle d) -> bool
9910 return _IMP_atom.State___eq__(self, *args)
9913 def __ne__(self, *args):
9915 __ne__(State self, State o) -> bool
9916 __ne__(State self, Particle d) -> bool
9918 return _IMP_atom.State___ne__(self, *args)
9921 def __le__(self, *args):
9923 __le__(State self, State o) -> bool
9924 __le__(State self, Particle d) -> bool
9926 return _IMP_atom.State___le__(self, *args)
9929 def __lt__(self, *args):
9931 __lt__(State self, State o) -> bool
9932 __lt__(State self, Particle d) -> bool
9934 return _IMP_atom.State___lt__(self, *args)
9937 def __ge__(self, *args):
9939 __ge__(State self, State o) -> bool
9940 __ge__(State self, Particle d) -> bool
9942 return _IMP_atom.State___ge__(self, *args)
9945 def __gt__(self, *args):
9947 __gt__(State self, State o) -> bool
9948 __gt__(State self, Particle d) -> bool
9950 return _IMP_atom.State___gt__(self, *args)
9954 """__hash__(State self) -> std::size_t"""
9955 return _IMP_atom.State___hash__(self)
9959 """__str__(State self) -> std::string"""
9960 return _IMP_atom.State___str__(self)
9964 """__repr__(State self) -> std::string"""
9965 return _IMP_atom.State___repr__(self)
9967 __swig_destroy__ = _IMP_atom.delete_State
9968 __del__ =
lambda self:
None
9969 State_swigregister = _IMP_atom.State_swigregister
9970 State_swigregister(State)
9972 def State_setup_particle(*args):
9974 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9975 setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9976 setup_particle(Model m, ParticleIndex pi, State other) -> State
9977 State_setup_particle(_ParticleAdaptor decorator, State other) -> State
9979 return _IMP_atom.State_setup_particle(*args)
9981 def State_get_is_setup(*args):
9983 get_is_setup(_ParticleAdaptor p) -> bool
9984 State_get_is_setup(Model m, ParticleIndex pi) -> bool
9986 return _IMP_atom.State_get_is_setup(*args)
9990 """get_state_index(Hierarchy h) -> int"""
9991 return _IMP_atom.get_state_index(h)
9994 """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9995 return _IMP_atom.get_phi_dihedral_atoms(rd)
9998 """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9999 return _IMP_atom.get_psi_dihedral_atoms(rd)
10002 """get_omega_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
10003 return _IMP_atom.get_omega_dihedral_atoms(rd)
10006 """get_chi_dihedral_atom_types(ResidueType rt) -> IMP::Vector< IMP::atom::AtomTypes >"""
10007 return _IMP_atom.get_chi_dihedral_atom_types(rt)
10010 """get_chi_dihedral_atoms(Residue rd) -> IMP::Vector< IMP::atom::Atoms >"""
10011 return _IMP_atom.get_chi_dihedral_atoms(rd)
10014 """get_chi_dihedral_particle_indexes(Residue rd) -> IMP::ParticleIndexQuads"""
10015 return _IMP_atom.get_chi_dihedral_particle_indexes(rd)
10016 class Molecule(Hierarchy):
10017 """Proxy of C++ IMP::atom::Molecule class."""
10019 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10021 def __init__(self, *args):
10023 __init__(IMP::atom::Molecule self) -> Molecule
10024 __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
10025 __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
10027 this = _IMP_atom.new_Molecule(*args)
10029 self.this.append(this)
10030 except __builtin__.Exception:
10033 def show(self, *args):
10035 show(Molecule self, _ostream out)
10036 show(Molecule self)
10038 return _IMP_atom.Molecule_show(self, *args)
10041 def setup_particle(*args):
10043 setup_particle(Model m, ParticleIndex pi) -> Molecule
10044 setup_particle(_ParticleAdaptor decorator) -> Molecule
10045 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10046 setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10048 return _IMP_atom.Molecule_setup_particle(*args)
10050 setup_particle = staticmethod(setup_particle)
10052 def get_is_setup(*args):
10054 get_is_setup(_ParticleAdaptor p) -> bool
10055 get_is_setup(Model m, ParticleIndex pi) -> bool
10057 return _IMP_atom.Molecule_get_is_setup(*args)
10059 get_is_setup = staticmethod(get_is_setup)
10061 def add_attribute(self, *args):
10063 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
10064 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
10065 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
10066 add_attribute(Molecule self, FloatsKey a0, IMP::Floats a1)
10067 add_attribute(Molecule self, IntsKey a0, IMP::Ints a1)
10068 add_attribute(Molecule self, StringKey a0, IMP::String a1)
10069 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
10070 add_attribute(Molecule self, ObjectKey a0, Object a1)
10072 return _IMP_atom.Molecule_add_attribute(self, *args)
10075 def get_value(self, *args):
10077 get_value(Molecule self, FloatKey a0) -> IMP::Float
10078 get_value(Molecule self, IntKey a0) -> IMP::Int
10079 get_value(Molecule self, FloatsKey a0) -> IMP::Floats
10080 get_value(Molecule self, IntsKey a0) -> IMP::Ints
10081 get_value(Molecule self, StringKey a0) -> IMP::String
10082 get_value(Molecule self, ParticleIndexKey a0) -> Particle
10083 get_value(Molecule self, ObjectKey a0) -> Object
10085 return _IMP_atom.Molecule_get_value(self, *args)
10088 def set_value(self, *args):
10090 set_value(Molecule self, FloatKey a0, IMP::Float a1)
10091 set_value(Molecule self, IntKey a0, IMP::Int a1)
10092 set_value(Molecule self, FloatsKey a0, IMP::Floats a1)
10093 set_value(Molecule self, IntsKey a0, IMP::Ints a1)
10094 set_value(Molecule self, StringKey a0, IMP::String a1)
10095 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
10096 set_value(Molecule self, ObjectKey a0, Object a1)
10098 return _IMP_atom.Molecule_set_value(self, *args)
10101 def remove_attribute(self, *args):
10103 remove_attribute(Molecule self, FloatKey a0)
10104 remove_attribute(Molecule self, IntKey a0)
10105 remove_attribute(Molecule self, FloatsKey a0)
10106 remove_attribute(Molecule self, IntsKey a0)
10107 remove_attribute(Molecule self, StringKey a0)
10108 remove_attribute(Molecule self, ParticleIndexKey a0)
10109 remove_attribute(Molecule self, ObjectKey a0)
10111 return _IMP_atom.Molecule_remove_attribute(self, *args)
10114 def has_attribute(self, *args):
10116 has_attribute(Molecule self, FloatKey a0) -> bool
10117 has_attribute(Molecule self, IntKey a0) -> bool
10118 has_attribute(Molecule self, FloatsKey a0) -> bool
10119 has_attribute(Molecule self, IntsKey a0) -> bool
10120 has_attribute(Molecule self, StringKey a0) -> bool
10121 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
10122 has_attribute(Molecule self, ObjectKey a0) -> bool
10124 return _IMP_atom.Molecule_has_attribute(self, *args)
10127 def get_derivative(self, a0):
10128 """get_derivative(Molecule self, FloatKey a0) -> double"""
10129 return _IMP_atom.Molecule_get_derivative(self, a0)
10132 def get_name(self):
10133 """get_name(Molecule self) -> std::string"""
10134 return _IMP_atom.Molecule_get_name(self)
10137 def clear_caches(self):
10138 """clear_caches(Molecule self)"""
10139 return _IMP_atom.Molecule_clear_caches(self)
10142 def set_name(self, a0):
10143 """set_name(Molecule self, std::string a0)"""
10144 return _IMP_atom.Molecule_set_name(self, a0)
10148 """set_check_level(Molecule self, IMP::CheckLevel a0)"""
10149 return _IMP_atom.Molecule_set_check_level(self, a0)
10152 def add_to_derivative(self, a0, a1, a2):
10153 """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10154 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
10157 def set_is_optimized(self, a0, a1):
10158 """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
10159 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
10162 def get_is_optimized(self, a0):
10163 """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
10164 return _IMP_atom.Molecule_get_is_optimized(self, a0)
10168 """get_check_level(Molecule self) -> IMP::CheckLevel"""
10169 return _IMP_atom.Molecule_get_check_level(self)
10172 def __eq__(self, *args):
10174 __eq__(Molecule self, Molecule o) -> bool
10175 __eq__(Molecule self, Particle d) -> bool
10177 return _IMP_atom.Molecule___eq__(self, *args)
10180 def __ne__(self, *args):
10182 __ne__(Molecule self, Molecule o) -> bool
10183 __ne__(Molecule self, Particle d) -> bool
10185 return _IMP_atom.Molecule___ne__(self, *args)
10188 def __le__(self, *args):
10190 __le__(Molecule self, Molecule o) -> bool
10191 __le__(Molecule self, Particle d) -> bool
10193 return _IMP_atom.Molecule___le__(self, *args)
10196 def __lt__(self, *args):
10198 __lt__(Molecule self, Molecule o) -> bool
10199 __lt__(Molecule self, Particle d) -> bool
10201 return _IMP_atom.Molecule___lt__(self, *args)
10204 def __ge__(self, *args):
10206 __ge__(Molecule self, Molecule o) -> bool
10207 __ge__(Molecule self, Particle d) -> bool
10209 return _IMP_atom.Molecule___ge__(self, *args)
10212 def __gt__(self, *args):
10214 __gt__(Molecule self, Molecule o) -> bool
10215 __gt__(Molecule self, Particle d) -> bool
10217 return _IMP_atom.Molecule___gt__(self, *args)
10220 def __hash__(self):
10221 """__hash__(Molecule self) -> std::size_t"""
10222 return _IMP_atom.Molecule___hash__(self)
10226 """__str__(Molecule self) -> std::string"""
10227 return _IMP_atom.Molecule___str__(self)
10230 def __repr__(self):
10231 """__repr__(Molecule self) -> std::string"""
10232 return _IMP_atom.Molecule___repr__(self)
10234 __swig_destroy__ = _IMP_atom.delete_Molecule
10235 __del__ =
lambda self:
None
10236 Molecule_swigregister = _IMP_atom.Molecule_swigregister
10237 Molecule_swigregister(Molecule)
10239 def Molecule_setup_particle(*args):
10241 setup_particle(Model m, ParticleIndex pi) -> Molecule
10242 setup_particle(_ParticleAdaptor decorator) -> Molecule
10243 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10244 Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10246 return _IMP_atom.Molecule_setup_particle(*args)
10248 def Molecule_get_is_setup(*args):
10250 get_is_setup(_ParticleAdaptor p) -> bool
10251 Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
10253 return _IMP_atom.Molecule_get_is_setup(*args)
10257 """get_molecule_name(Hierarchy h) -> std::string"""
10258 return _IMP_atom.get_molecule_name(h)
10259 class Copy(Molecule):
10260 """Proxy of C++ IMP::atom::Copy class."""
10262 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10264 def get_copy_index_key():
10265 """get_copy_index_key() -> IntKey"""
10266 return _IMP_atom.Copy_get_copy_index_key()
10268 get_copy_index_key = staticmethod(get_copy_index_key)
10270 def __init__(self, *args):
10272 __init__(IMP::atom::Copy self) -> Copy
10273 __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
10274 __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
10276 this = _IMP_atom.new_Copy(*args)
10278 self.this.append(this)
10279 except __builtin__.Exception:
10282 def show(self, *args):
10284 show(Copy self, _ostream out)
10287 return _IMP_atom.Copy_show(self, *args)
10290 def setup_particle(*args):
10292 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10293 setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10295 return _IMP_atom.Copy_setup_particle(*args)
10297 setup_particle = staticmethod(setup_particle)
10299 def get_is_setup(*args):
10301 get_is_setup(_ParticleAdaptor p) -> bool
10302 get_is_setup(Model m, ParticleIndex pi) -> bool
10304 return _IMP_atom.Copy_get_is_setup(*args)
10306 get_is_setup = staticmethod(get_is_setup)
10309 """get_copy_index(Copy self) -> int"""
10310 return _IMP_atom.Copy_get_copy_index(self)
10313 def add_attribute(self, *args):
10315 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
10316 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
10317 add_attribute(Copy self, IntKey a0, IMP::Int a1)
10318 add_attribute(Copy self, FloatsKey a0, IMP::Floats a1)
10319 add_attribute(Copy self, IntsKey a0, IMP::Ints a1)
10320 add_attribute(Copy self, StringKey a0, IMP::String a1)
10321 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
10322 add_attribute(Copy self, ObjectKey a0, Object a1)
10324 return _IMP_atom.Copy_add_attribute(self, *args)
10327 def get_value(self, *args):
10329 get_value(Copy self, FloatKey a0) -> IMP::Float
10330 get_value(Copy self, IntKey a0) -> IMP::Int
10331 get_value(Copy self, FloatsKey a0) -> IMP::Floats
10332 get_value(Copy self, IntsKey a0) -> IMP::Ints
10333 get_value(Copy self, StringKey a0) -> IMP::String
10334 get_value(Copy self, ParticleIndexKey a0) -> Particle
10335 get_value(Copy self, ObjectKey a0) -> Object
10337 return _IMP_atom.Copy_get_value(self, *args)
10340 def set_value(self, *args):
10342 set_value(Copy self, FloatKey a0, IMP::Float a1)
10343 set_value(Copy self, IntKey a0, IMP::Int a1)
10344 set_value(Copy self, FloatsKey a0, IMP::Floats a1)
10345 set_value(Copy self, IntsKey a0, IMP::Ints a1)
10346 set_value(Copy self, StringKey a0, IMP::String a1)
10347 set_value(Copy self, ParticleIndexKey a0, Particle a1)
10348 set_value(Copy self, ObjectKey a0, Object a1)
10350 return _IMP_atom.Copy_set_value(self, *args)
10353 def remove_attribute(self, *args):
10355 remove_attribute(Copy self, FloatKey a0)
10356 remove_attribute(Copy self, IntKey a0)
10357 remove_attribute(Copy self, FloatsKey a0)
10358 remove_attribute(Copy self, IntsKey a0)
10359 remove_attribute(Copy self, StringKey a0)
10360 remove_attribute(Copy self, ParticleIndexKey a0)
10361 remove_attribute(Copy self, ObjectKey a0)
10363 return _IMP_atom.Copy_remove_attribute(self, *args)
10366 def has_attribute(self, *args):
10368 has_attribute(Copy self, FloatKey a0) -> bool
10369 has_attribute(Copy self, IntKey a0) -> bool
10370 has_attribute(Copy self, FloatsKey a0) -> bool
10371 has_attribute(Copy self, IntsKey a0) -> bool
10372 has_attribute(Copy self, StringKey a0) -> bool
10373 has_attribute(Copy self, ParticleIndexKey a0) -> bool
10374 has_attribute(Copy self, ObjectKey a0) -> bool
10376 return _IMP_atom.Copy_has_attribute(self, *args)
10379 def get_derivative(self, a0):
10380 """get_derivative(Copy self, FloatKey a0) -> double"""
10381 return _IMP_atom.Copy_get_derivative(self, a0)
10384 def get_name(self):
10385 """get_name(Copy self) -> std::string"""
10386 return _IMP_atom.Copy_get_name(self)
10389 def clear_caches(self):
10390 """clear_caches(Copy self)"""
10391 return _IMP_atom.Copy_clear_caches(self)
10394 def set_name(self, a0):
10395 """set_name(Copy self, std::string a0)"""
10396 return _IMP_atom.Copy_set_name(self, a0)
10400 """set_check_level(Copy self, IMP::CheckLevel a0)"""
10401 return _IMP_atom.Copy_set_check_level(self, a0)
10404 def add_to_derivative(self, a0, a1, a2):
10405 """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10406 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
10409 def set_is_optimized(self, a0, a1):
10410 """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
10411 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
10414 def get_is_optimized(self, a0):
10415 """get_is_optimized(Copy self, FloatKey a0) -> bool"""
10416 return _IMP_atom.Copy_get_is_optimized(self, a0)
10420 """get_check_level(Copy self) -> IMP::CheckLevel"""
10421 return _IMP_atom.Copy_get_check_level(self)
10424 def __eq__(self, *args):
10426 __eq__(Copy self, Copy o) -> bool
10427 __eq__(Copy self, Particle d) -> bool
10429 return _IMP_atom.Copy___eq__(self, *args)
10432 def __ne__(self, *args):
10434 __ne__(Copy self, Copy o) -> bool
10435 __ne__(Copy self, Particle d) -> bool
10437 return _IMP_atom.Copy___ne__(self, *args)
10440 def __le__(self, *args):
10442 __le__(Copy self, Copy o) -> bool
10443 __le__(Copy self, Particle d) -> bool
10445 return _IMP_atom.Copy___le__(self, *args)
10448 def __lt__(self, *args):
10450 __lt__(Copy self, Copy o) -> bool
10451 __lt__(Copy self, Particle d) -> bool
10453 return _IMP_atom.Copy___lt__(self, *args)
10456 def __ge__(self, *args):
10458 __ge__(Copy self, Copy o) -> bool
10459 __ge__(Copy self, Particle d) -> bool
10461 return _IMP_atom.Copy___ge__(self, *args)
10464 def __gt__(self, *args):
10466 __gt__(Copy self, Copy o) -> bool
10467 __gt__(Copy self, Particle d) -> bool
10469 return _IMP_atom.Copy___gt__(self, *args)
10472 def __hash__(self):
10473 """__hash__(Copy self) -> std::size_t"""
10474 return _IMP_atom.Copy___hash__(self)
10478 """__str__(Copy self) -> std::string"""
10479 return _IMP_atom.Copy___str__(self)
10482 def __repr__(self):
10483 """__repr__(Copy self) -> std::string"""
10484 return _IMP_atom.Copy___repr__(self)
10486 __swig_destroy__ = _IMP_atom.delete_Copy
10487 __del__ =
lambda self:
None
10488 Copy_swigregister = _IMP_atom.Copy_swigregister
10489 Copy_swigregister(Copy)
10491 def Copy_get_copy_index_key():
10492 """Copy_get_copy_index_key() -> IntKey"""
10493 return _IMP_atom.Copy_get_copy_index_key()
10495 def Copy_setup_particle(*args):
10497 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10498 Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10500 return _IMP_atom.Copy_setup_particle(*args)
10502 def Copy_get_is_setup(*args):
10504 get_is_setup(_ParticleAdaptor p) -> bool
10505 Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
10507 return _IMP_atom.Copy_get_is_setup(*args)
10511 """get_copy_index(Hierarchy h) -> int"""
10512 return _IMP_atom.get_copy_index(h)
10513 class Selection(IMP._ParticleIndexesAdaptor):
10514 """Proxy of C++ IMP::atom::Selection class."""
10516 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10517 NONE = _IMP_atom.Selection_NONE
10518 C = _IMP_atom.Selection_C
10519 N = _IMP_atom.Selection_N
10521 def __init__(self, *args):
10523 __init__(IMP::atom::Selection self) -> Selection
10524 __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
10525 __init__(IMP::atom::Selection self, Particle h) -> Selection
10526 __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10527 __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
10529 this = _IMP_atom.new_Selection(*args)
10531 self.this.append(this)
10532 except __builtin__.Exception:
10536 """create_clone(Selection self) -> Selection"""
10537 return _IMP_atom.Selection_create_clone(self)
10540 def get_hierarchies(self):
10541 """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10542 return _IMP_atom.Selection_get_hierarchies(self)
10545 def set_molecules(self, mols):
10546 """set_molecules(Selection self, IMP::Strings mols)"""
10547 return _IMP_atom.Selection_set_molecules(self, mols)
10550 def set_resolution(self, r):
10551 """set_resolution(Selection self, double r)"""
10552 return _IMP_atom.Selection_set_resolution(self, r)
10555 def set_representation_type(self, t):
10556 """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10557 return _IMP_atom.Selection_set_representation_type(self, t)
10560 def set_state_index(self, state):
10561 """set_state_index(Selection self, int state)"""
10562 return _IMP_atom.Selection_set_state_index(self, state)
10565 def set_state_indexes(self, states):
10566 """set_state_indexes(Selection self, IMP::Ints states)"""
10567 return _IMP_atom.Selection_set_state_indexes(self, states)
10570 def set_terminus(self, t):
10571 """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10572 return _IMP_atom.Selection_set_terminus(self, t)
10575 def set_element(self, e):
10576 """set_element(Selection self, IMP::atom::Element e)"""
10577 return _IMP_atom.Selection_set_element(self, e)
10580 def set_chain_ids(self, chains):
10581 """set_chain_ids(Selection self, IMP::Strings chains)"""
10582 return _IMP_atom.Selection_set_chain_ids(self, chains)
10585 def set_chains(self, chains):
10586 """set_chains(Selection self, IMP::Strings chains)"""
10587 return _IMP_atom.Selection_set_chains(self, chains)
10590 def set_residue_indexes(self, indexes):
10591 """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10592 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10595 def set_atom_types(self, types):
10596 """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10597 return _IMP_atom.Selection_set_atom_types(self, types)
10600 def set_residue_types(self, types):
10601 """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10602 return _IMP_atom.Selection_set_residue_types(self, types)
10605 def set_domains(self, names):
10606 """set_domains(Selection self, IMP::Strings names)"""
10607 return _IMP_atom.Selection_set_domains(self, names)
10610 def set_molecule(self, mol):
10611 """set_molecule(Selection self, std::string mol)"""
10612 return _IMP_atom.Selection_set_molecule(self, mol)
10615 def set_chain_id(self, c):
10616 """set_chain_id(Selection self, std::string c)"""
10617 return _IMP_atom.Selection_set_chain_id(self, c)
10620 def set_chain(self, c):
10621 """set_chain(Selection self, std::string c)"""
10622 return _IMP_atom.Selection_set_chain(self, c)
10625 def set_residue_index(self, i):
10626 """set_residue_index(Selection self, int i)"""
10627 return _IMP_atom.Selection_set_residue_index(self, i)
10630 def set_atom_type(self, types):
10631 """set_atom_type(Selection self, AtomType types)"""
10632 return _IMP_atom.Selection_set_atom_type(self, types)
10635 def set_residue_type(self, type):
10636 """set_residue_type(Selection self, ResidueType type)"""
10637 return _IMP_atom.Selection_set_residue_type(self, type)
10640 def set_domain(self, name):
10641 """set_domain(Selection self, std::string name)"""
10642 return _IMP_atom.Selection_set_domain(self, name)
10645 def set_copy_index(self, copy):
10646 """set_copy_index(Selection self, unsigned int copy)"""
10647 return _IMP_atom.Selection_set_copy_index(self, copy)
10650 def set_copy_indexes(self, copies):
10651 """set_copy_indexes(Selection self, IMP::Ints copies)"""
10652 return _IMP_atom.Selection_set_copy_indexes(self, copies)
10655 def set_particle_type(self, t):
10656 """set_particle_type(Selection self, ParticleType t)"""
10657 return _IMP_atom.Selection_set_particle_type(self, t)
10660 def set_particle_types(self, t):
10661 """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10662 return _IMP_atom.Selection_set_particle_types(self, t)
10665 def set_hierarchy_types(self, types):
10666 """set_hierarchy_types(Selection self, IMP::Ints types)"""
10667 return _IMP_atom.Selection_set_hierarchy_types(self, types)
10670 def set_intersection(self, s):
10671 """set_intersection(Selection self, Selection s)"""
10672 return _IMP_atom.Selection_set_intersection(self, s)
10675 def set_union(self, s):
10676 """set_union(Selection self, Selection s)"""
10677 return _IMP_atom.Selection_set_union(self, s)
10680 def set_symmetric_difference(self, s):
10681 """set_symmetric_difference(Selection self, Selection s)"""
10682 return _IMP_atom.Selection_set_symmetric_difference(self, s)
10685 def set_difference(self, s):
10686 """set_difference(Selection self, Selection s)"""
10687 return _IMP_atom.Selection_set_difference(self, s)
10690 def get_selected_particles(self, with_representation=True):
10692 get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10693 get_selected_particles(Selection self) -> IMP::ParticlesTemp
10695 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10698 def get_selected_particle_indexes(self, with_representation=True):
10700 get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10701 get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10703 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10706 def show(self, *args):
10708 show(Selection self, _ostream out)
10709 show(Selection self)
10711 return _IMP_atom.Selection_show(self, *args)
10715 """__str__(Selection self) -> std::string"""
10716 return _IMP_atom.Selection___str__(self)
10719 def __repr__(self):
10720 """__repr__(Selection self) -> std::string"""
10721 return _IMP_atom.Selection___repr__(self)
10724 def __init__(self, hierarchy=None,
10725 hierarchies=
None, **params):
10726 if hierarchy
and hierarchies:
10727 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
10729 this = _IMP_atom.new_Selection(hierarchy)
10730 try: self.this.append(this)
10731 except: self.this = this
10733 this = _IMP_atom.new_Selection(hierarchies)
10734 try: self.this.append(this)
10735 except: self.this = this
10737 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
10738 for k
in params.keys():
10739 eval(
"self.set_%s(params[k])"%k)
10741 def union(self, s):
10742 news = self.create_clone()
10743 news.union_update(s)
10745 def intersection(self, s):
10746 news = self.create_clone()
10747 news.intersection_update(s)
10749 def symmetric_difference(self, s):
10750 news = self.create_clone()
10751 news.symmetric_difference_update(s)
10753 def difference(self, s):
10754 news = self.create_clone()
10755 news.difference_update(s)
10757 def union_update(self, s):
10760 def intersection_update(self, s):
10761 self.set_intersection(s)
10763 def symmetric_difference_update(self, s):
10764 self.set_symmetric_difference(s)
10766 def difference_update(self, s):
10767 self.set_difference(s)
10770 __and__ = intersection
10771 __xor__ = symmetric_difference
10772 __sub__ = difference
10773 __ior__ = union_update
10774 __iand__ = intersection_update
10775 __ixor__ = symmetric_difference_update
10776 __isub__ = difference_update
10778 __swig_destroy__ = _IMP_atom.delete_Selection
10779 __del__ =
lambda self:
None
10780 Selection_swigregister = _IMP_atom.Selection_swigregister
10781 Selection_swigregister(Selection)
10786 create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10787 create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10789 return _IMP_atom.create_distance_restraint(*args)
10793 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10794 create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10795 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10796 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10798 return _IMP_atom.create_connectivity_restraint(*args)
10802 create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10803 create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10804 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10805 create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10807 return _IMP_atom.create_internal_connectivity_restraint(*args)
10811 create_cover(Selection s, std::string name) -> XYZR
10812 create_cover(Selection s) -> XYZR
10814 return _IMP_atom.create_cover(*args)
10818 get_mass(ResidueType c) -> double
10819 get_mass(Selection s) -> double
10821 return _IMP_atom.get_mass(*args)
10824 """get_volume(Selection s) -> double"""
10825 return _IMP_atom.get_volume(s)
10828 """get_surface_area(Selection s) -> double"""
10829 return _IMP_atom.get_surface_area(s)
10833 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10834 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10835 get_leaves(Selection h) -> IMP::atom::Hierarchies
10837 return _IMP_atom.get_leaves(*args)
10839 """Proxy of C++ IMP::atom::SelectionGeometry class."""
10841 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10843 def __init__(self, *args):
10845 __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10846 __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10848 this = _IMP_atom.new_SelectionGeometry(*args)
10850 self.this.append(this)
10851 except __builtin__.Exception:
10854 def get_version_info(self):
10855 """get_version_info(SelectionGeometry self) -> VersionInfo"""
10856 return _IMP_atom.SelectionGeometry_get_version_info(self)
10860 """__str__(SelectionGeometry self) -> std::string"""
10861 return _IMP_atom.SelectionGeometry___str__(self)
10864 def __repr__(self):
10865 """__repr__(SelectionGeometry self) -> std::string"""
10866 return _IMP_atom.SelectionGeometry___repr__(self)
10871 return _object_cast_to_SelectionGeometry(o)
10873 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10874 SelectionGeometry_swigregister(SelectionGeometry)
10879 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10880 get_rmsd(Selection s0, Selection s1) -> double
10882 return _IMP_atom.get_rmsd(*args)
10886 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10887 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10889 return _IMP_atom.get_rmsd_transforming_first(*args)
10892 """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10893 return _IMP_atom.get_placement_score(source, target)
10896 """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"""
10897 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10900 """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"""
10901 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10905 get_radius_of_gyration(Selection s) -> double
10906 get_radius_of_gyration(IMP::ParticlesTemp const & ps, bool weighted=True) -> double
10907 get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10909 return _IMP_atom.get_radius_of_gyration(*args)
10911 """Proxy of C++ IMP::atom::ForceFieldParameters class."""
10913 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10915 def __init__(self):
10916 """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10917 this = _IMP_atom.new_ForceFieldParameters()
10919 self.this.append(this)
10920 except __builtin__.Exception:
10923 def get_radius(self, atom):
10924 """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10925 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10928 def get_epsilon(self, atom):
10929 """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10930 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10935 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10936 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10937 add_radii(ForceFieldParameters self, Hierarchy mhd)
10939 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10942 def add_well_depths(self, mhd):
10943 """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10944 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10948 """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10949 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10951 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10952 __del__ =
lambda self:
None
10955 """__str__(ForceFieldParameters self) -> std::string"""
10956 return _IMP_atom.ForceFieldParameters___str__(self)
10959 def __repr__(self):
10960 """__repr__(ForceFieldParameters self) -> std::string"""
10961 return _IMP_atom.ForceFieldParameters___repr__(self)
10966 return _object_cast_to_ForceFieldParameters(o)
10968 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10969 ForceFieldParameters_swigregister(ForceFieldParameters)
10971 class CHARMMAtomTopology(object):
10972 """Proxy of C++ IMP::atom::CHARMMAtomTopology class."""
10974 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10976 def __init__(self, *args):
10978 __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10979 __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10981 this = _IMP_atom.new_CHARMMAtomTopology(*args)
10983 self.this.append(this)
10984 except __builtin__.Exception:
10987 def get_name(self):
10988 """get_name(CHARMMAtomTopology self) -> std::string"""
10989 return _IMP_atom.CHARMMAtomTopology_get_name(self)
10992 def get_charmm_type(self):
10993 """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10994 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10997 def get_charge(self):
10998 """get_charge(CHARMMAtomTopology self) -> double"""
10999 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
11002 def set_charmm_type(self, charmm_type):
11003 """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
11004 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
11007 def set_charge(self, charge):
11008 """set_charge(CHARMMAtomTopology self, double charge)"""
11009 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
11012 def show(self, *args):
11014 show(CHARMMAtomTopology self, _ostream out)
11015 show(CHARMMAtomTopology self)
11017 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
11021 """__str__(CHARMMAtomTopology self) -> std::string"""
11022 return _IMP_atom.CHARMMAtomTopology___str__(self)
11025 def __repr__(self):
11026 """__repr__(CHARMMAtomTopology self) -> std::string"""
11027 return _IMP_atom.CHARMMAtomTopology___repr__(self)
11029 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
11030 __del__ =
lambda self:
None
11031 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
11032 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
11034 class CHARMMBondEndpoint(object):
11035 """Proxy of C++ IMP::atom::CHARMMBondEndpoint class."""
11037 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11039 def __init__(self, atom_name, residue=None):
11041 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
11042 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
11044 this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
11046 self.this.append(this)
11047 except __builtin__.Exception:
11050 def get_atom_name(self):
11051 """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
11052 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
11055 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
11056 """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"""
11057 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
11060 def show(self, *args):
11062 show(CHARMMBondEndpoint self, _ostream out)
11063 show(CHARMMBondEndpoint self)
11065 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
11069 """__str__(CHARMMBondEndpoint self) -> std::string"""
11070 return _IMP_atom.CHARMMBondEndpoint___str__(self)
11073 def __repr__(self):
11074 """__repr__(CHARMMBondEndpoint self) -> std::string"""
11075 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
11077 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
11078 __del__ =
lambda self:
None
11079 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
11080 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
11082 class CHARMMDihedral(object):
11083 """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class."""
11085 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11086 __repr__ = _swig_repr
11088 def __init__(self, atoms):
11089 """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
11090 this = _IMP_atom.new_CHARMMDihedral(atoms)
11092 self.this.append(this)
11093 except __builtin__.Exception:
11096 def get_endpoint(self, i):
11097 """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
11098 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
11101 def get_contains_atom(self, name):
11102 """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
11103 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
11106 def show(self, *args):
11108 show(CHARMMDihedral self, _ostream out)
11109 show(CHARMMDihedral self)
11111 return _IMP_atom.CHARMMDihedral_show(self, *args)
11113 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
11114 __del__ =
lambda self:
None
11115 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
11116 CHARMMDihedral_swigregister(CHARMMDihedral)
11118 class CHARMMInternalCoordinate(CHARMMDihedral):
11119 """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class."""
11121 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11123 def __init__(self, *args):
11125 __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
11126 __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
11128 this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
11130 self.this.append(this)
11131 except __builtin__.Exception:
11134 def get_first_distance(self):
11135 """get_first_distance(CHARMMInternalCoordinate self) -> float"""
11136 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
11139 def get_second_distance(self):
11140 """get_second_distance(CHARMMInternalCoordinate self) -> float"""
11141 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
11144 def get_first_angle(self):
11145 """get_first_angle(CHARMMInternalCoordinate self) -> float"""
11146 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
11149 def get_second_angle(self):
11150 """get_second_angle(CHARMMInternalCoordinate self) -> float"""
11151 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
11155 """get_dihedral(CHARMMInternalCoordinate self) -> float"""
11156 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
11159 def get_improper(self):
11160 """get_improper(CHARMMInternalCoordinate self) -> bool"""
11161 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
11164 def show(self, *args):
11166 show(CHARMMInternalCoordinate self, _ostream out)
11167 show(CHARMMInternalCoordinate self)
11169 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
11173 """__str__(CHARMMInternalCoordinate self) -> std::string"""
11174 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
11177 def __repr__(self):
11178 """__repr__(CHARMMInternalCoordinate self) -> std::string"""
11179 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
11181 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
11182 __del__ =
lambda self:
None
11183 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
11184 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
11186 class CHARMMResidueTopologyBase(
IMP.Object):
11187 """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class."""
11189 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11191 def __init__(self, *args, **kwargs):
11192 raise AttributeError(
"No constructor defined")
11194 def get_type(self):
11195 """get_type(CHARMMResidueTopologyBase self) -> std::string"""
11196 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
11199 def get_number_of_atoms(self):
11200 """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
11201 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
11204 def add_atom(self, atom):
11205 """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
11206 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
11211 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
11212 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
11213 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
11215 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
11218 def get_number_of_bonds(self):
11219 """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
11220 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
11223 def add_bond(self, bond):
11224 """add_bond(CHARMMResidueTopologyBase self, CHARMMBond bond)"""
11225 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
11228 def get_number_of_angles(self):
11229 """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
11230 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
11233 def add_angle(self, bond):
11234 """add_angle(CHARMMResidueTopologyBase self, CHARMMAngle bond)"""
11235 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
11238 def get_number_of_dihedrals(self):
11239 """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
11240 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
11243 def add_dihedral(self, bond):
11244 """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11245 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
11248 def get_number_of_impropers(self):
11249 """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
11250 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
11253 def add_improper(self, bond):
11254 """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11255 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
11258 def get_number_of_internal_coordinates(self):
11259 """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11260 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11263 def add_internal_coordinate(self, ic):
11264 """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11265 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11268 def get_internal_coordinate(self, index):
11269 """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11270 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11274 """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMBond"""
11275 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11279 """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMAngle"""
11280 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11284 """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11285 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11288 def get_improper(self, index):
11289 """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11290 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11293 def get_version_info(self):
11294 """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11295 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11299 """__str__(CHARMMResidueTopologyBase self) -> std::string"""
11300 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11303 def __repr__(self):
11304 """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11305 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11310 return _object_cast_to_CHARMMResidueTopologyBase(o)
11312 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
11313 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11315 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11316 """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class."""
11318 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11320 def __init__(self, *args):
11322 __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11323 __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11325 this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
11327 self.this.append(this)
11328 except __builtin__.Exception:
11331 def remove_atom(self, name):
11332 """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11333 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11336 def set_default_first_patch(self, patch):
11337 """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11338 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11341 def set_default_last_patch(self, patch):
11342 """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11343 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11346 def get_default_first_patch(self):
11347 """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11348 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11351 def get_default_last_patch(self):
11352 """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11353 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11357 """__str__(CHARMMIdealResidueTopology self) -> std::string"""
11358 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11361 def __repr__(self):
11362 """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11363 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11368 return _object_cast_to_CHARMMIdealResidueTopology(o)
11370 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
11371 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11373 class CHARMMPatch(CHARMMResidueTopologyBase):
11374 """Proxy of C++ IMP::atom::CHARMMPatch class."""
11376 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11378 def __init__(self, type):
11379 """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
11380 this = _IMP_atom.new_CHARMMPatch(type)
11382 self.this.append(this)
11383 except __builtin__.Exception:
11386 def add_removed_atom(self, name):
11387 """add_removed_atom(CHARMMPatch self, std::string name)"""
11388 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11391 def get_number_of_removed_atoms(self):
11392 """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11393 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11396 def get_removed_atom(self, i):
11397 """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11398 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11401 def apply(self, *args):
11403 apply(CHARMMPatch self, CHARMMResidueTopology res)
11404 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11406 return _IMP_atom.CHARMMPatch_apply(self, *args)
11410 """__str__(CHARMMPatch self) -> std::string"""
11411 return _IMP_atom.CHARMMPatch___str__(self)
11414 def __repr__(self):
11415 """__repr__(CHARMMPatch self) -> std::string"""
11416 return _IMP_atom.CHARMMPatch___repr__(self)
11421 return _object_cast_to_CHARMMPatch(o)
11423 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
11424 CHARMMPatch_swigregister(CHARMMPatch)
11426 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11427 """Proxy of C++ IMP::atom::CHARMMResidueTopology class."""
11429 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11431 def __init__(self, *args):
11433 __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11434 __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11436 this = _IMP_atom.new_CHARMMResidueTopology(*args)
11438 self.this.append(this)
11439 except __builtin__.Exception:
11442 def get_patched(self):
11443 """get_patched(CHARMMResidueTopology self) -> bool"""
11444 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11447 def set_patched(self, patched):
11448 """set_patched(CHARMMResidueTopology self, bool patched)"""
11449 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11453 """__str__(CHARMMResidueTopology self) -> std::string"""
11454 return _IMP_atom.CHARMMResidueTopology___str__(self)
11457 def __repr__(self):
11458 """__repr__(CHARMMResidueTopology self) -> std::string"""
11459 return _IMP_atom.CHARMMResidueTopology___repr__(self)
11464 return _object_cast_to_CHARMMResidueTopology(o)
11466 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
11467 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11469 class CHARMMAtom(Atom):
11470 """Proxy of C++ IMP::atom::CHARMMAtom class."""
11472 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11474 def __init__(self, *args):
11476 __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
11477 __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11478 __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11480 this = _IMP_atom.new_CHARMMAtom(*args)
11482 self.this.append(this)
11483 except __builtin__.Exception:
11486 def show(self, *args):
11488 show(CHARMMAtom self, _ostream out)
11489 show(CHARMMAtom self)
11491 return _IMP_atom.CHARMMAtom_show(self, *args)
11494 def setup_particle(*args):
11496 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11497 setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11499 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11501 setup_particle = staticmethod(setup_particle)
11503 def get_charmm_type(self):
11504 """get_charmm_type(CHARMMAtom self) -> IMP::String"""
11505 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11508 def set_charmm_type(self, t):
11509 """set_charmm_type(CHARMMAtom self, IMP::String t)"""
11510 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11513 def get_is_setup(*args):
11515 get_is_setup(_ParticleAdaptor p) -> bool
11516 get_is_setup(Model m, ParticleIndex pi) -> bool
11518 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11520 get_is_setup = staticmethod(get_is_setup)
11522 def get_charmm_type_key():
11523 """get_charmm_type_key() -> StringKey"""
11524 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11526 get_charmm_type_key = staticmethod(get_charmm_type_key)
11528 def add_attribute(self, *args):
11530 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11531 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11532 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11533 add_attribute(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11534 add_attribute(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11535 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11536 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11537 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11539 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11542 def get_value(self, *args):
11544 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11545 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11546 get_value(CHARMMAtom self, FloatsKey a0) -> IMP::Floats
11547 get_value(CHARMMAtom self, IntsKey a0) -> IMP::Ints
11548 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11549 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11550 get_value(CHARMMAtom self, ObjectKey a0) -> Object
11552 return _IMP_atom.CHARMMAtom_get_value(self, *args)
11555 def set_value(self, *args):
11557 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11558 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11559 set_value(CHARMMAtom self, FloatsKey a0, IMP::Floats a1)
11560 set_value(CHARMMAtom self, IntsKey a0, IMP::Ints a1)
11561 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11562 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11563 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11565 return _IMP_atom.CHARMMAtom_set_value(self, *args)
11568 def remove_attribute(self, *args):
11570 remove_attribute(CHARMMAtom self, FloatKey a0)
11571 remove_attribute(CHARMMAtom self, IntKey a0)
11572 remove_attribute(CHARMMAtom self, FloatsKey a0)
11573 remove_attribute(CHARMMAtom self, IntsKey a0)
11574 remove_attribute(CHARMMAtom self, StringKey a0)
11575 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11576 remove_attribute(CHARMMAtom self, ObjectKey a0)
11578 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11581 def has_attribute(self, *args):
11583 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11584 has_attribute(CHARMMAtom self, IntKey a0) -> bool
11585 has_attribute(CHARMMAtom self, FloatsKey a0) -> bool
11586 has_attribute(CHARMMAtom self, IntsKey a0) -> bool
11587 has_attribute(CHARMMAtom self, StringKey a0) -> bool
11588 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11589 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11591 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11594 def get_derivative(self, a0):
11595 """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11596 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11599 def get_name(self):
11600 """get_name(CHARMMAtom self) -> std::string"""
11601 return _IMP_atom.CHARMMAtom_get_name(self)
11604 def clear_caches(self):
11605 """clear_caches(CHARMMAtom self)"""
11606 return _IMP_atom.CHARMMAtom_clear_caches(self)
11609 def set_name(self, a0):
11610 """set_name(CHARMMAtom self, std::string a0)"""
11611 return _IMP_atom.CHARMMAtom_set_name(self, a0)
11615 """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11616 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11619 def add_to_derivative(self, a0, a1, a2):
11620 """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11621 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11624 def set_is_optimized(self, a0, a1):
11625 """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11626 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11629 def get_is_optimized(self, a0):
11630 """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11631 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11635 """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11636 return _IMP_atom.CHARMMAtom_get_check_level(self)
11639 def __eq__(self, *args):
11641 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11642 __eq__(CHARMMAtom self, Particle d) -> bool
11644 return _IMP_atom.CHARMMAtom___eq__(self, *args)
11647 def __ne__(self, *args):
11649 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11650 __ne__(CHARMMAtom self, Particle d) -> bool
11652 return _IMP_atom.CHARMMAtom___ne__(self, *args)
11655 def __le__(self, *args):
11657 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11658 __le__(CHARMMAtom self, Particle d) -> bool
11660 return _IMP_atom.CHARMMAtom___le__(self, *args)
11663 def __lt__(self, *args):
11665 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11666 __lt__(CHARMMAtom self, Particle d) -> bool
11668 return _IMP_atom.CHARMMAtom___lt__(self, *args)
11671 def __ge__(self, *args):
11673 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11674 __ge__(CHARMMAtom self, Particle d) -> bool
11676 return _IMP_atom.CHARMMAtom___ge__(self, *args)
11679 def __gt__(self, *args):
11681 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11682 __gt__(CHARMMAtom self, Particle d) -> bool
11684 return _IMP_atom.CHARMMAtom___gt__(self, *args)
11687 def __hash__(self):
11688 """__hash__(CHARMMAtom self) -> std::size_t"""
11689 return _IMP_atom.CHARMMAtom___hash__(self)
11693 """__str__(CHARMMAtom self) -> std::string"""
11694 return _IMP_atom.CHARMMAtom___str__(self)
11697 def __repr__(self):
11698 """__repr__(CHARMMAtom self) -> std::string"""
11699 return _IMP_atom.CHARMMAtom___repr__(self)
11701 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11702 __del__ =
lambda self:
None
11703 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11704 CHARMMAtom_swigregister(CHARMMAtom)
11706 def CHARMMAtom_setup_particle(*args):
11708 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11709 CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11711 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11713 def CHARMMAtom_get_is_setup(*args):
11715 get_is_setup(_ParticleAdaptor p) -> bool
11716 CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11718 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11720 def CHARMMAtom_get_charmm_type_key():
11721 """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11722 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11726 """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11727 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11730 """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11731 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11732 class CHARMMBondParameters(object):
11733 """Proxy of C++ IMP::atom::CHARMMBondParameters class."""
11735 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11736 force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11737 ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11739 def __init__(self):
11740 """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11741 this = _IMP_atom.new_CHARMMBondParameters()
11743 self.this.append(this)
11744 except __builtin__.Exception:
11747 def show(self, *args):
11749 show(CHARMMBondParameters self, _ostream out)
11750 show(CHARMMBondParameters self)
11752 return _IMP_atom.CHARMMBondParameters_show(self, *args)
11756 """__str__(CHARMMBondParameters self) -> std::string"""
11757 return _IMP_atom.CHARMMBondParameters___str__(self)
11760 def __repr__(self):
11761 """__repr__(CHARMMBondParameters self) -> std::string"""
11762 return _IMP_atom.CHARMMBondParameters___repr__(self)
11764 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11765 __del__ =
lambda self:
None
11766 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11767 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11769 class CHARMMDihedralParameters(object):
11770 """Proxy of C++ IMP::atom::CHARMMDihedralParameters class."""
11772 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11773 force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11774 multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11775 ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11777 def __init__(self):
11778 """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11779 this = _IMP_atom.new_CHARMMDihedralParameters()
11781 self.this.append(this)
11782 except __builtin__.Exception:
11785 def show(self, *args):
11787 show(CHARMMDihedralParameters self, _ostream out)
11788 show(CHARMMDihedralParameters self)
11790 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11794 """__str__(CHARMMDihedralParameters self) -> std::string"""
11795 return _IMP_atom.CHARMMDihedralParameters___str__(self)
11798 def __repr__(self):
11799 """__repr__(CHARMMDihedralParameters self) -> std::string"""
11800 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11802 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11803 __del__ =
lambda self:
None
11804 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11805 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11807 class CHARMMParameters(ForceFieldParameters):
11808 """Proxy of C++ IMP::atom::CHARMMParameters class."""
11810 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11812 def __init__(self, *args):
11814 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11815 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11816 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11818 this = _IMP_atom.new_CHARMMParameters(*args)
11820 self.this.append(this)
11821 except __builtin__.Exception:
11824 def add_residue_topology(self, res):
11825 """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11826 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11829 def get_residue_topology(self, type):
11830 """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11831 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11834 def add_patch(self, patch):
11835 """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11836 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11839 def get_patch(self, name):
11840 """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11841 return _IMP_atom.CHARMMParameters_get_patch(self, name)
11844 def create_topology(self, hierarchy):
11845 """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11846 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11849 def get_bond_parameters(self, type1, type2):
11850 """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11851 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11854 def get_angle_parameters(self, type1, type2, type3):
11855 """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11856 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11859 def get_dihedral_parameters(self, type1, type2, type3, type4):
11860 """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11861 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11864 def get_improper_parameters(self, type1, type2, type3, type4):
11865 """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11866 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11869 def create_angles(self, bonds):
11870 """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11871 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11874 def create_dihedrals(self, bonds):
11875 """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11876 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11879 def get_version_info(self):
11880 """get_version_info(CHARMMParameters self) -> VersionInfo"""
11881 return _IMP_atom.CHARMMParameters_get_version_info(self)
11885 """__str__(CHARMMParameters self) -> std::string"""
11886 return _IMP_atom.CHARMMParameters___str__(self)
11889 def __repr__(self):
11890 """__repr__(CHARMMParameters self) -> std::string"""
11891 return _IMP_atom.CHARMMParameters___repr__(self)
11896 return _object_cast_to_CHARMMParameters(o)
11898 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11899 CHARMMParameters_swigregister(CHARMMParameters)
11903 """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11904 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11907 """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11908 return _IMP_atom.get_all_atom_CHARMM_parameters()
11910 """Proxy of C++ IMP::atom::CHARMMSegmentTopology class."""
11912 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11914 def remove_residue(self, d):
11915 """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11916 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11919 def remove_residues(self, d):
11920 """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11921 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11924 def set_residues(self, ps):
11925 """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11926 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11929 def set_residues_order(self, objs):
11930 """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11931 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11934 def add_residue(self, obj):
11935 """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11936 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11939 def add_residues(self, objs):
11940 """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11941 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11944 def clear_residues(self):
11945 """clear_residues(CHARMMSegmentTopology self)"""
11946 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11949 def get_number_of_residues(self):
11950 """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11951 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11954 def get_has_residues(self):
11955 """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11956 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11960 """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11961 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11964 def get_residues(self):
11965 """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11966 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11969 def reserve_residues(self, sz):
11970 """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11971 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11974 def get_version_info(self):
11975 """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11976 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11979 def __init__(self, *args):
11981 __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11982 __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11984 this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11986 self.this.append(this)
11987 except __builtin__.Exception:
11990 def apply_default_patches(self, ff):
11991 """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11992 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11996 """__str__(CHARMMSegmentTopology self) -> std::string"""
11997 return _IMP_atom.CHARMMSegmentTopology___str__(self)
12000 def __repr__(self):
12001 """__repr__(CHARMMSegmentTopology self) -> std::string"""
12002 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
12007 return _object_cast_to_CHARMMSegmentTopology(o)
12009 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
12010 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
12013 """Proxy of C++ IMP::atom::CHARMMTopology class."""
12015 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12017 def __init__(self, *args):
12019 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
12020 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
12022 this = _IMP_atom.new_CHARMMTopology(*args)
12024 self.this.append(this)
12025 except __builtin__.Exception:
12028 def get_parameters(self):
12029 """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
12030 return _IMP_atom.CHARMMTopology_get_parameters(self)
12033 def add_sequence(self, sequence):
12034 """add_sequence(CHARMMTopology self, std::string sequence)"""
12035 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
12038 def apply_default_patches(self):
12039 """apply_default_patches(CHARMMTopology self)"""
12040 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
12043 def create_hierarchy(self, model):
12044 """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
12045 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
12048 def add_atom_types(self, hierarchy):
12049 """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
12050 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
12053 def add_coordinates(self, hierarchy):
12054 """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
12055 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
12058 def add_missing_atoms(self, hierarchy):
12059 """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
12060 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
12063 def setup_hierarchy(self, hierarchy):
12064 """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
12065 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
12068 def add_charges(self, hierarchy):
12069 """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
12070 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
12074 """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12075 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
12078 def add_dihedrals(self, hierarchy):
12079 """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12080 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
12083 def add_impropers(self, hierarchy):
12084 """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
12085 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
12088 def remove_segment(self, d):
12089 """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
12090 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
12093 def remove_segments(self, d):
12094 """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
12095 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
12098 def set_segments(self, ps):
12099 """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
12100 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
12103 def set_segments_order(self, objs):
12104 """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
12105 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
12108 def add_segment(self, obj):
12109 """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
12110 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
12113 def add_segments(self, objs):
12114 """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
12115 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
12118 def clear_segments(self):
12119 """clear_segments(CHARMMTopology self)"""
12120 return _IMP_atom.CHARMMTopology_clear_segments(self)
12123 def get_number_of_segments(self):
12124 """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
12125 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
12128 def get_has_segments(self):
12129 """get_has_segments(CHARMMTopology self) -> bool"""
12130 return _IMP_atom.CHARMMTopology_get_has_segments(self)
12134 """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
12135 return _IMP_atom.CHARMMTopology_get_segment(self, i)
12138 def get_segments(self):
12139 """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
12140 return _IMP_atom.CHARMMTopology_get_segments(self)
12143 def reserve_segments(self, sz):
12144 """reserve_segments(CHARMMTopology self, unsigned int sz)"""
12145 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
12148 def get_version_info(self):
12149 """get_version_info(CHARMMTopology self) -> VersionInfo"""
12150 return _IMP_atom.CHARMMTopology_get_version_info(self)
12154 """__str__(CHARMMTopology self) -> std::string"""
12155 return _IMP_atom.CHARMMTopology___str__(self)
12158 def __repr__(self):
12159 """__repr__(CHARMMTopology self) -> std::string"""
12160 return _IMP_atom.CHARMMTopology___repr__(self)
12165 return _object_cast_to_CHARMMTopology(o)
12167 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
12168 CHARMMTopology_swigregister(CHARMMTopology)
12171 """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class."""
12173 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12175 def __init__(self, *args):
12177 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
12178 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
12180 this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
12182 self.this.append(this)
12183 except __builtin__.Exception:
12186 def get_pair_filter(self):
12187 """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
12188 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
12191 def get_full_pair_filter(self):
12192 """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
12193 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
12196 def do_get_inputs(self):
12197 """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
12198 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
12201 def get_version_info(self):
12202 """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
12203 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
12207 """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
12208 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
12211 def __repr__(self):
12212 """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
12213 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
12218 return _object_cast_to_CHARMMStereochemistryRestraint(o)
12220 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
12221 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
12226 add_bonds(Hierarchy d, ForceFieldParameters ffp)
12227 add_bonds(Hierarchy d)
12229 return _IMP_atom.add_bonds(*args)
12233 add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
12234 add_radii(Hierarchy d, ForceFieldParameters ffp)
12235 add_radii(Hierarchy d)
12237 return _IMP_atom.add_radii(*args)
12238 ALBER = _IMP_atom.ALBER
12239 HARPAZ = _IMP_atom.HARPAZ
12240 ANDERSSON = _IMP_atom.ANDERSSON
12241 TSAI = _IMP_atom.TSAI
12242 QUILLIN = _IMP_atom.QUILLIN
12243 SQUIRE = _IMP_atom.SQUIRE
12246 """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
12247 return _IMP_atom.get_protein_density_from_reference(densityReference)
12251 get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
12252 get_volume_from_mass(double m) -> double
12254 return _IMP_atom.get_volume_from_mass(*args)
12258 get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
12259 get_mass_from_volume(double v) -> double
12261 return _IMP_atom.get_mass_from_volume(*args)
12264 """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
12265 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
12268 """get_volume_from_residue_type(ResidueType rt) -> double"""
12269 return _IMP_atom.get_volume_from_residue_type(rt)
12272 """get_molarity(double n, double volume) -> double"""
12273 return _IMP_atom.get_molarity(n, volume)
12275 def get_kd(na, nb, nab, volume):
12276 """get_kd(double na, double nb, double nab, double volume) -> double"""
12277 return _IMP_atom.get_kd(na, nb, nab, volume)
12281 get_einstein_diffusion_coefficient(double r, double temp=-1) -> double
12282 get_einstein_diffusion_coefficient(double r) -> double
12284 return _IMP_atom.get_einstein_diffusion_coefficient(r, temp)
12288 get_einstein_rotational_diffusion_coefficient(double r, double temp=-1) -> double
12289 get_einstein_rotational_diffusion_coefficient(double r) -> double
12291 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r, temp)
12295 get_diffusion_length(double D, double t) -> double
12296 get_diffusion_length(double D, double force, double t, double temp=-1) -> double
12297 get_diffusion_length(double D, double force, double t) -> double
12299 return _IMP_atom.get_diffusion_length(*args)
12302 """get_diffusion_angle(double D, double dtfs) -> double"""
12303 return _IMP_atom.get_diffusion_angle(D, dtfs)
12307 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double
12308 get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, IMP::Floats const & dts) -> double
12310 return _IMP_atom.get_diffusion_coefficient(*args)
12313 """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & orientations, double dt) -> double"""
12314 return _IMP_atom.get_rotational_diffusion_coefficient(orientations, dt)
12316 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
12317 """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
12318 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
12321 """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
12322 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
12325 """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
12326 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
12328 """Proxy of C++ IMP::atom::EzRestraint class."""
12330 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12332 def __init__(self, m, ps):
12333 """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
12334 this = _IMP_atom.new_EzRestraint(m, ps)
12336 self.this.append(this)
12337 except __builtin__.Exception:
12340 def get_version_info(self):
12341 """get_version_info(EzRestraint self) -> VersionInfo"""
12342 return _IMP_atom.EzRestraint_get_version_info(self)
12346 """__str__(EzRestraint self) -> std::string"""
12347 return _IMP_atom.EzRestraint___str__(self)
12350 def __repr__(self):
12351 """__repr__(EzRestraint self) -> std::string"""
12352 return _IMP_atom.EzRestraint___repr__(self)
12357 return _object_cast_to_EzRestraint(o)
12359 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
12360 EzRestraint_swigregister(EzRestraint)
12365 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
12366 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
12367 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
12368 create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
12369 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12371 return _IMP_atom.create_protein(*args)
12375 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12376 create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
12377 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12378 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
12380 return _IMP_atom.create_simplified_along_backbone(*args)
12383 """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12384 return _IMP_atom.create_simplified_from_volume(h, resolution)
12387 """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12388 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12390 def get_residue_indexes(h):
12391 """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12392 return _IMP_atom.get_residue_indexes(h)
12394 def get_residue_type(*args):
12396 get_residue_type(char c) -> ResidueType
12397 get_residue_type(Hierarchy h) -> ResidueType
12399 return _IMP_atom.get_residue_type(*args)
12401 def get_atom_type(h):
12402 """get_atom_type(Hierarchy h) -> AtomType"""
12403 return _IMP_atom.get_atom_type(h)
12405 def get_domain_name(h):
12406 """get_domain_name(Hierarchy h) -> std::string"""
12407 return _IMP_atom.get_domain_name(h)
12411 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12412 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12413 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
12415 return _IMP_atom.create_excluded_volume_restraint(*args)
12419 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12420 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
12421 setup_as_approximation(Hierarchy h, double resolution=-1)
12422 setup_as_approximation(Hierarchy h)
12424 return _IMP_atom.setup_as_approximation(*args)
12425 class _HierarchyTreeVertexIndex(object):
12426 """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class."""
12428 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12429 __repr__ = _swig_repr
12431 def __init__(self):
12432 """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12433 this = _IMP_atom.new__HierarchyTreeVertexIndex()
12435 self.this.append(this)
12436 except __builtin__.Exception:
12438 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12439 __del__ =
lambda self:
None
12440 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
12441 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12444 def show_as_graphviz(name, out):
12445 """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12446 return _IMP_atom.show_as_graphviz(name, out)
12448 def get_vertex_index(g):
12449 """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12450 return _IMP_atom.get_vertex_index(g)
12453 """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12454 return _IMP_atom.get_hierarchy_tree(h)
12456 """Proxy of C++ IMP::atom::HierarchyGeometry class."""
12458 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12460 def __init__(self, d, resolution=0):
12462 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
12463 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
12465 this = _IMP_atom.new_HierarchyGeometry(d, resolution)
12467 self.this.append(this)
12468 except __builtin__.Exception:
12471 def get_version_info(self):
12472 """get_version_info(HierarchyGeometry self) -> VersionInfo"""
12473 return _IMP_atom.HierarchyGeometry_get_version_info(self)
12477 """__str__(HierarchyGeometry self) -> std::string"""
12478 return _IMP_atom.HierarchyGeometry___str__(self)
12481 def __repr__(self):
12482 """__repr__(HierarchyGeometry self) -> std::string"""
12483 return _IMP_atom.HierarchyGeometry___repr__(self)
12488 return _object_cast_to_HierarchyGeometry(o)
12490 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
12491 HierarchyGeometry_swigregister(HierarchyGeometry)
12494 """Proxy of C++ IMP::atom::HierarchiesGeometry class."""
12496 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12498 def __init__(self, sc, resolution=-1):
12500 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
12501 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
12503 this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
12505 self.this.append(this)
12506 except __builtin__.Exception:
12509 def get_version_info(self):
12510 """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12511 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12515 """__str__(HierarchiesGeometry self) -> std::string"""
12516 return _IMP_atom.HierarchiesGeometry___str__(self)
12519 def __repr__(self):
12520 """__repr__(HierarchiesGeometry self) -> std::string"""
12521 return _IMP_atom.HierarchiesGeometry___repr__(self)
12526 return _object_cast_to_HierarchiesGeometry(o)
12528 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
12529 HierarchiesGeometry_swigregister(HierarchiesGeometry)
12534 transform(Hierarchy h, Transformation3D tr)
12535 transform(Hierarchy h, Transformation3D tr)
12537 return _IMP_atom.transform(*args)
12538 class DopePairScore(_ADopeBase):
12539 """Proxy of C++ IMP::atom::DopePairScore class."""
12541 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12543 def __init__(self, *args):
12545 __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
12546 __init__(IMP::atom::DopePairScore self) -> DopePairScore
12547 __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12549 this = _IMP_atom.new_DopePairScore(*args)
12551 self.this.append(this)
12552 except __builtin__.Exception:
12556 """__str__(DopePairScore self) -> std::string"""
12557 return _IMP_atom.DopePairScore___str__(self)
12560 def __repr__(self):
12561 """__repr__(DopePairScore self) -> std::string"""
12562 return _IMP_atom.DopePairScore___repr__(self)
12567 return _object_cast_to_DopePairScore(o)
12569 __swig_destroy__ = _IMP_atom.delete_DopePairScore
12570 __del__ =
lambda self:
None
12571 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
12572 DopePairScore_swigregister(DopePairScore)
12576 """add_dope_score_data(Hierarchy h)"""
12577 return _IMP_atom.add_dope_score_data(h)
12578 class LoopStatisticalPairScore(_ALoopStatisticalBase):
12579 """Proxy of C++ IMP::atom::LoopStatisticalPairScore class."""
12581 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12583 def __init__(self, *args):
12585 __init__(IMP::atom::LoopStatisticalPairScore self, double threshold) -> LoopStatisticalPairScore
12586 __init__(IMP::atom::LoopStatisticalPairScore self) -> LoopStatisticalPairScore
12587 __init__(IMP::atom::LoopStatisticalPairScore self, double threshold, TextInput data_file) -> LoopStatisticalPairScore
12589 this = _IMP_atom.new_LoopStatisticalPairScore(*args)
12591 self.this.append(this)
12592 except __builtin__.Exception:
12596 """__str__(LoopStatisticalPairScore self) -> std::string"""
12597 return _IMP_atom.LoopStatisticalPairScore___str__(self)
12600 def __repr__(self):
12601 """__repr__(LoopStatisticalPairScore self) -> std::string"""
12602 return _IMP_atom.LoopStatisticalPairScore___repr__(self)
12607 return _object_cast_to_LoopStatisticalPairScore(o)
12609 __swig_destroy__ = _IMP_atom.delete_LoopStatisticalPairScore
12610 __del__ =
lambda self:
None
12611 LoopStatisticalPairScore_swigregister = _IMP_atom.LoopStatisticalPairScore_swigregister
12612 LoopStatisticalPairScore_swigregister(LoopStatisticalPairScore)
12616 """add_loop_statistical_score_data(Hierarchy h)"""
12617 return _IMP_atom.add_loop_statistical_score_data(h)
12618 class OrientedSoapPairScore(_OrientedSoapBase):
12619 """Proxy of C++ IMP::atom::OrientedSoapPairScore class."""
12621 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12623 def __init__(self, library):
12624 """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12625 this = _IMP_atom.new_OrientedSoapPairScore(library)
12627 self.this.append(this)
12628 except __builtin__.Exception:
12631 def get_pair_filter(self):
12632 """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12633 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12637 """__str__(OrientedSoapPairScore self) -> std::string"""
12638 return _IMP_atom.OrientedSoapPairScore___str__(self)
12641 def __repr__(self):
12642 """__repr__(OrientedSoapPairScore self) -> std::string"""
12643 return _IMP_atom.OrientedSoapPairScore___repr__(self)
12648 return _object_cast_to_OrientedSoapPairScore(o)
12650 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12651 __del__ =
lambda self:
None
12652 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12653 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12656 """Proxy of C++ IMP::atom::SameResiduePairFilter class."""
12658 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12660 def __init__(self):
12661 """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12662 this = _IMP_atom.new_SameResiduePairFilter()
12664 self.this.append(this)
12665 except __builtin__.Exception:
12668 def do_get_inputs(self, m, pis):
12669 """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12670 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12673 def get_value(self, *args):
12675 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12676 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12678 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12681 def get_value_index(self, *args):
12683 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12684 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12686 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12689 def get_version_info(self):
12690 """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12691 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12695 """__str__(SameResiduePairFilter self) -> std::string"""
12696 return _IMP_atom.SameResiduePairFilter___str__(self)
12699 def __repr__(self):
12700 """__repr__(SameResiduePairFilter self) -> std::string"""
12701 return _IMP_atom.SameResiduePairFilter___repr__(self)
12706 return _object_cast_to_SameResiduePairFilter(o)
12708 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12709 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12712 """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class."""
12714 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12716 def __init__(self, m, pis):
12717 """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12718 this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12720 self.this.append(this)
12721 except __builtin__.Exception:
12724 def set_particles(self, pis):
12725 """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12726 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12729 def remove_rigid_motion(self):
12730 """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12731 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12734 def get_version_info(self):
12735 """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12736 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12740 """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12741 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12744 def __repr__(self):
12745 """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12746 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12751 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12753 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12754 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12757 """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class."""
12759 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12761 def __init__(self, pis, temperature, tau):
12762 """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12763 this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12765 self.this.append(this)
12766 except __builtin__.Exception:
12769 def set_particles(self, pis):
12770 """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12771 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12774 def get_temperature(self):
12775 """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12776 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12780 """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12781 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12784 def set_temperature(self, temperature):
12785 """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12786 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12789 def set_tau(self, tau):
12790 """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12791 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12794 def rescale_velocities(self):
12795 """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12796 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12799 def get_version_info(self):
12800 """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12801 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12805 """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12806 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12809 def __repr__(self):
12810 """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12811 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12816 return _object_cast_to_BerendsenThermostatOptimizerState(o)
12818 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12819 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12822 """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class."""
12824 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12826 def __init__(self, m, pis, temperature, gamma):
12827 """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12828 this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12830 self.this.append(this)
12831 except __builtin__.Exception:
12834 def set_particles(self, pis):
12835 """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12836 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12839 def get_temperature(self):
12840 """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12841 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12844 def get_gamma(self):
12845 """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12846 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12849 def set_temperature(self, temperature):
12850 """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12851 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12854 def set_gamma(self, gamma):
12855 """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12856 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12859 def rescale_velocities(self):
12860 """rescale_velocities(LangevinThermostatOptimizerState self)"""
12861 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12864 def get_version_info(self):
12865 """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12866 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12870 """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12871 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12874 def __repr__(self):
12875 """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12876 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12881 return _object_cast_to_LangevinThermostatOptimizerState(o)
12883 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12884 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12887 """Proxy of C++ IMP::atom::PDBSelector class."""
12889 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12891 def __init__(self, name):
12892 """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12893 if self.__class__ == PDBSelector:
12897 this = _IMP_atom.new_PDBSelector(_self, name)
12899 self.this.append(this)
12900 except __builtin__.Exception:
12903 if self.__class__ != PDBSelector:
12904 _director_objects.register(self)
12909 def get_is_selected(self, pdb_line):
12910 """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12911 return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12913 __swig_destroy__ = _IMP_atom.delete_PDBSelector
12914 __del__ =
lambda self:
None
12917 """__str__(PDBSelector self) -> std::string"""
12918 return _IMP_atom.PDBSelector___str__(self)
12921 def __repr__(self):
12922 """__repr__(PDBSelector self) -> std::string"""
12923 return _IMP_atom.PDBSelector___repr__(self)
12928 return _object_cast_to_PDBSelector(o)
12931 def get_type_name(self):
12932 return self.__class__.__name__
12933 def do_show(self, out):
12935 def get_version_info(self):
12936 if"IMP::atom" ==
"IMP":
12937 return VersionInfo(self.__module__,
12944 return _object_cast_to_PDBSelector(o)
12947 def __and__(self, s):
12948 return AndPDBSelector(self, s)
12949 def __or__(self, s):
12950 return OrPDBSelector(self, s)
12951 def __xor__(self, s):
12952 return XorPDBSelector(self, s)
12953 def __invert__(self):
12954 return NotPDBSelector(self)
12955 def __sub__(self, s):
12956 return AndPDBSelector(self, NotPDBSelector(s))
12958 def __disown__(self):
12960 _IMP_atom.disown_PDBSelector(self)
12961 return weakref_proxy(self)
12963 def do_destroy(self):
12964 """do_destroy(PDBSelector self)"""
12965 return _IMP_atom.PDBSelector_do_destroy(self)
12967 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12968 PDBSelector_swigregister(PDBSelector)
12970 class NonAlternativePDBSelector(PDBSelector):
12971 """Proxy of C++ IMP::atom::NonAlternativePDBSelector class."""
12973 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12975 def __init__(self, *args):
12977 __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12978 __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12980 this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12982 self.this.append(this)
12983 except __builtin__.Exception:
12986 def get_version_info(self):
12987 """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12988 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12992 """__str__(NonAlternativePDBSelector self) -> std::string"""
12993 return _IMP_atom.NonAlternativePDBSelector___str__(self)
12996 def __repr__(self):
12997 """__repr__(NonAlternativePDBSelector self) -> std::string"""
12998 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
13003 return _object_cast_to_NonAlternativePDBSelector(o)
13005 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
13006 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
13008 class ATOMPDBSelector(NonAlternativePDBSelector):
13009 """Proxy of C++ IMP::atom::ATOMPDBSelector class."""
13011 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13013 def __init__(self, *args):
13015 __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
13016 __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
13018 this = _IMP_atom.new_ATOMPDBSelector(*args)
13020 self.this.append(this)
13021 except __builtin__.Exception:
13025 """__str__(ATOMPDBSelector self) -> std::string"""
13026 return _IMP_atom.ATOMPDBSelector___str__(self)
13029 def __repr__(self):
13030 """__repr__(ATOMPDBSelector self) -> std::string"""
13031 return _IMP_atom.ATOMPDBSelector___repr__(self)
13036 return _object_cast_to_ATOMPDBSelector(o)
13038 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
13039 ATOMPDBSelector_swigregister(ATOMPDBSelector)
13041 class CAlphaPDBSelector(NonAlternativePDBSelector):
13042 """Proxy of C++ IMP::atom::CAlphaPDBSelector class."""
13044 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13046 def __init__(self, *args):
13048 __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
13049 __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
13051 this = _IMP_atom.new_CAlphaPDBSelector(*args)
13053 self.this.append(this)
13054 except __builtin__.Exception:
13058 """__str__(CAlphaPDBSelector self) -> std::string"""
13059 return _IMP_atom.CAlphaPDBSelector___str__(self)
13062 def __repr__(self):
13063 """__repr__(CAlphaPDBSelector self) -> std::string"""
13064 return _IMP_atom.CAlphaPDBSelector___repr__(self)
13069 return _object_cast_to_CAlphaPDBSelector(o)
13071 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
13072 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
13074 class CBetaPDBSelector(NonAlternativePDBSelector):
13075 """Proxy of C++ IMP::atom::CBetaPDBSelector class."""
13077 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13079 def __init__(self, *args):
13081 __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
13082 __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
13084 this = _IMP_atom.new_CBetaPDBSelector(*args)
13086 self.this.append(this)
13087 except __builtin__.Exception:
13091 """__str__(CBetaPDBSelector self) -> std::string"""
13092 return _IMP_atom.CBetaPDBSelector___str__(self)
13095 def __repr__(self):
13096 """__repr__(CBetaPDBSelector self) -> std::string"""
13097 return _IMP_atom.CBetaPDBSelector___repr__(self)
13102 return _object_cast_to_CBetaPDBSelector(o)
13104 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
13105 CBetaPDBSelector_swigregister(CBetaPDBSelector)
13107 class AtomTypePDBSelector(PDBSelector):
13108 """Proxy of C++ IMP::atom::AtomTypePDBSelector class."""
13110 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13112 def __init__(self, *args):
13114 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
13115 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
13117 this = _IMP_atom.new_AtomTypePDBSelector(*args)
13119 self.this.append(this)
13120 except __builtin__.Exception:
13123 def get_version_info(self):
13124 """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
13125 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
13129 """__str__(AtomTypePDBSelector self) -> std::string"""
13130 return _IMP_atom.AtomTypePDBSelector___str__(self)
13133 def __repr__(self):
13134 """__repr__(AtomTypePDBSelector self) -> std::string"""
13135 return _IMP_atom.AtomTypePDBSelector___repr__(self)
13140 return _object_cast_to_AtomTypePDBSelector(o)
13142 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
13143 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
13145 class ResidueTypePDBSelector(PDBSelector):
13146 """Proxy of C++ IMP::atom::ResidueTypePDBSelector class."""
13148 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13150 def __init__(self, *args):
13152 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
13153 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
13155 this = _IMP_atom.new_ResidueTypePDBSelector(*args)
13157 self.this.append(this)
13158 except __builtin__.Exception:
13161 def get_version_info(self):
13162 """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
13163 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
13167 """__str__(ResidueTypePDBSelector self) -> std::string"""
13168 return _IMP_atom.ResidueTypePDBSelector___str__(self)
13171 def __repr__(self):
13172 """__repr__(ResidueTypePDBSelector self) -> std::string"""
13173 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
13178 return _object_cast_to_ResidueTypePDBSelector(o)
13180 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
13181 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
13183 class CPDBSelector(NonAlternativePDBSelector):
13184 """Proxy of C++ IMP::atom::CPDBSelector class."""
13186 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13188 def __init__(self, *args):
13190 __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
13191 __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
13193 this = _IMP_atom.new_CPDBSelector(*args)
13195 self.this.append(this)
13196 except __builtin__.Exception:
13200 """__str__(CPDBSelector self) -> std::string"""
13201 return _IMP_atom.CPDBSelector___str__(self)
13204 def __repr__(self):
13205 """__repr__(CPDBSelector self) -> std::string"""
13206 return _IMP_atom.CPDBSelector___repr__(self)
13211 return _object_cast_to_CPDBSelector(o)
13213 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
13214 CPDBSelector_swigregister(CPDBSelector)
13216 class NPDBSelector(NonAlternativePDBSelector):
13217 """Proxy of C++ IMP::atom::NPDBSelector class."""
13219 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13221 def __init__(self, *args):
13223 __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
13224 __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
13226 this = _IMP_atom.new_NPDBSelector(*args)
13228 self.this.append(this)
13229 except __builtin__.Exception:
13233 """__str__(NPDBSelector self) -> std::string"""
13234 return _IMP_atom.NPDBSelector___str__(self)
13237 def __repr__(self):
13238 """__repr__(NPDBSelector self) -> std::string"""
13239 return _IMP_atom.NPDBSelector___repr__(self)
13244 return _object_cast_to_NPDBSelector(o)
13246 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
13247 NPDBSelector_swigregister(NPDBSelector)
13249 class AllPDBSelector(PDBSelector):
13250 """Proxy of C++ IMP::atom::AllPDBSelector class."""
13252 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13254 def __init__(self, *args):
13256 __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
13257 __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
13259 this = _IMP_atom.new_AllPDBSelector(*args)
13261 self.this.append(this)
13262 except __builtin__.Exception:
13265 def get_version_info(self):
13266 """get_version_info(AllPDBSelector self) -> VersionInfo"""
13267 return _IMP_atom.AllPDBSelector_get_version_info(self)
13271 """__str__(AllPDBSelector self) -> std::string"""
13272 return _IMP_atom.AllPDBSelector___str__(self)
13275 def __repr__(self):
13276 """__repr__(AllPDBSelector self) -> std::string"""
13277 return _IMP_atom.AllPDBSelector___repr__(self)
13282 return _object_cast_to_AllPDBSelector(o)
13284 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
13285 AllPDBSelector_swigregister(AllPDBSelector)
13287 class ChainPDBSelector(NonAlternativePDBSelector):
13288 """Proxy of C++ IMP::atom::ChainPDBSelector class."""
13290 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13292 def __init__(self, *args):
13294 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
13295 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
13297 this = _IMP_atom.new_ChainPDBSelector(*args)
13299 self.this.append(this)
13300 except __builtin__.Exception:
13304 """__str__(ChainPDBSelector self) -> std::string"""
13305 return _IMP_atom.ChainPDBSelector___str__(self)
13308 def __repr__(self):
13309 """__repr__(ChainPDBSelector self) -> std::string"""
13310 return _IMP_atom.ChainPDBSelector___repr__(self)
13315 return _object_cast_to_ChainPDBSelector(o)
13317 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
13318 ChainPDBSelector_swigregister(ChainPDBSelector)
13320 class WaterPDBSelector(NonAlternativePDBSelector):
13321 """Proxy of C++ IMP::atom::WaterPDBSelector class."""
13323 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13325 def __init__(self, *args):
13327 __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
13328 __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
13330 this = _IMP_atom.new_WaterPDBSelector(*args)
13332 self.this.append(this)
13333 except __builtin__.Exception:
13337 """__str__(WaterPDBSelector self) -> std::string"""
13338 return _IMP_atom.WaterPDBSelector___str__(self)
13341 def __repr__(self):
13342 """__repr__(WaterPDBSelector self) -> std::string"""
13343 return _IMP_atom.WaterPDBSelector___repr__(self)
13348 return _object_cast_to_WaterPDBSelector(o)
13350 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
13351 WaterPDBSelector_swigregister(WaterPDBSelector)
13353 class HydrogenPDBSelector(NonAlternativePDBSelector):
13354 """Proxy of C++ IMP::atom::HydrogenPDBSelector class."""
13356 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13358 def __init__(self, *args):
13360 __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
13361 __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
13363 this = _IMP_atom.new_HydrogenPDBSelector(*args)
13365 self.this.append(this)
13366 except __builtin__.Exception:
13370 """__str__(HydrogenPDBSelector self) -> std::string"""
13371 return _IMP_atom.HydrogenPDBSelector___str__(self)
13374 def __repr__(self):
13375 """__repr__(HydrogenPDBSelector self) -> std::string"""
13376 return _IMP_atom.HydrogenPDBSelector___repr__(self)
13381 return _object_cast_to_HydrogenPDBSelector(o)
13383 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
13384 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
13386 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
13387 """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class."""
13389 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13391 def __init__(self, *args):
13393 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
13394 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
13396 this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
13398 self.this.append(this)
13399 except __builtin__.Exception:
13403 """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13404 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
13407 def __repr__(self):
13408 """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13409 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
13414 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
13416 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
13417 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
13419 class NonHydrogenPDBSelector(NonAlternativePDBSelector):
13420 """Proxy of C++ IMP::atom::NonHydrogenPDBSelector class."""
13422 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13424 def __init__(self, *args):
13426 __init__(IMP::atom::NonHydrogenPDBSelector self, std::string name) -> NonHydrogenPDBSelector
13427 __init__(IMP::atom::NonHydrogenPDBSelector self) -> NonHydrogenPDBSelector
13429 this = _IMP_atom.new_NonHydrogenPDBSelector(*args)
13431 self.this.append(this)
13432 except __builtin__.Exception:
13436 """__str__(NonHydrogenPDBSelector self) -> std::string"""
13437 return _IMP_atom.NonHydrogenPDBSelector___str__(self)
13440 def __repr__(self):
13441 """__repr__(NonHydrogenPDBSelector self) -> std::string"""
13442 return _IMP_atom.NonHydrogenPDBSelector___repr__(self)
13447 return _object_cast_to_NonHydrogenPDBSelector(o)
13449 NonHydrogenPDBSelector_swigregister = _IMP_atom.NonHydrogenPDBSelector_swigregister
13450 NonHydrogenPDBSelector_swigregister(NonHydrogenPDBSelector)
13452 class NonWaterPDBSelector(NonAlternativePDBSelector):
13453 """Proxy of C++ IMP::atom::NonWaterPDBSelector class."""
13455 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13457 def __init__(self, *args):
13459 __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
13460 __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
13462 this = _IMP_atom.new_NonWaterPDBSelector(*args)
13464 self.this.append(this)
13465 except __builtin__.Exception:
13469 """__str__(NonWaterPDBSelector self) -> std::string"""
13470 return _IMP_atom.NonWaterPDBSelector___str__(self)
13473 def __repr__(self):
13474 """__repr__(NonWaterPDBSelector self) -> std::string"""
13475 return _IMP_atom.NonWaterPDBSelector___repr__(self)
13480 return _object_cast_to_NonWaterPDBSelector(o)
13482 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
13483 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
13485 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
13486 """Proxy of C++ IMP::atom::BackbonePDBSelector class."""
13488 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13490 def __init__(self, *args):
13492 __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
13493 __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
13495 this = _IMP_atom.new_BackbonePDBSelector(*args)
13497 self.this.append(this)
13498 except __builtin__.Exception:
13502 """__str__(BackbonePDBSelector self) -> std::string"""
13503 return _IMP_atom.BackbonePDBSelector___str__(self)
13506 def __repr__(self):
13507 """__repr__(BackbonePDBSelector self) -> std::string"""
13508 return _IMP_atom.BackbonePDBSelector___repr__(self)
13513 return _object_cast_to_BackbonePDBSelector(o)
13515 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
13516 BackbonePDBSelector_swigregister(BackbonePDBSelector)
13518 class PPDBSelector(NonAlternativePDBSelector):
13519 """Proxy of C++ IMP::atom::PPDBSelector 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, *args):
13525 __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
13526 __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
13528 this = _IMP_atom.new_PPDBSelector(*args)
13530 self.this.append(this)
13531 except __builtin__.Exception:
13535 """__str__(PPDBSelector self) -> std::string"""
13536 return _IMP_atom.PPDBSelector___str__(self)
13539 def __repr__(self):
13540 """__repr__(PPDBSelector self) -> std::string"""
13541 return _IMP_atom.PPDBSelector___repr__(self)
13546 return _object_cast_to_PPDBSelector(o)
13548 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
13549 PPDBSelector_swigregister(PPDBSelector)
13551 class AndPDBSelector(PDBSelector):
13552 """Proxy of C++ IMP::atom::AndPDBSelector class."""
13554 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13556 def get_version_info(self):
13557 """get_version_info(AndPDBSelector self) -> VersionInfo"""
13558 return _IMP_atom.AndPDBSelector_get_version_info(self)
13561 def __init__(self, a, b):
13562 """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13563 this = _IMP_atom.new_AndPDBSelector(a, b)
13565 self.this.append(this)
13566 except __builtin__.Exception:
13570 """__str__(AndPDBSelector self) -> std::string"""
13571 return _IMP_atom.AndPDBSelector___str__(self)
13574 def __repr__(self):
13575 """__repr__(AndPDBSelector self) -> std::string"""
13576 return _IMP_atom.AndPDBSelector___repr__(self)
13581 return _object_cast_to_AndPDBSelector(o)
13583 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
13584 AndPDBSelector_swigregister(AndPDBSelector)
13586 class OrPDBSelector(PDBSelector):
13587 """Proxy of C++ IMP::atom::OrPDBSelector class."""
13589 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13591 def get_version_info(self):
13592 """get_version_info(OrPDBSelector self) -> VersionInfo"""
13593 return _IMP_atom.OrPDBSelector_get_version_info(self)
13596 def __init__(self, a, b):
13597 """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13598 this = _IMP_atom.new_OrPDBSelector(a, b)
13600 self.this.append(this)
13601 except __builtin__.Exception:
13605 """__str__(OrPDBSelector self) -> std::string"""
13606 return _IMP_atom.OrPDBSelector___str__(self)
13609 def __repr__(self):
13610 """__repr__(OrPDBSelector self) -> std::string"""
13611 return _IMP_atom.OrPDBSelector___repr__(self)
13616 return _object_cast_to_OrPDBSelector(o)
13618 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
13619 OrPDBSelector_swigregister(OrPDBSelector)
13621 class XorPDBSelector(PDBSelector):
13622 """Proxy of C++ IMP::atom::XorPDBSelector class."""
13624 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13626 def get_version_info(self):
13627 """get_version_info(XorPDBSelector self) -> VersionInfo"""
13628 return _IMP_atom.XorPDBSelector_get_version_info(self)
13631 def __init__(self, a, b):
13632 """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13633 this = _IMP_atom.new_XorPDBSelector(a, b)
13635 self.this.append(this)
13636 except __builtin__.Exception:
13640 """__str__(XorPDBSelector self) -> std::string"""
13641 return _IMP_atom.XorPDBSelector___str__(self)
13644 def __repr__(self):
13645 """__repr__(XorPDBSelector self) -> std::string"""
13646 return _IMP_atom.XorPDBSelector___repr__(self)
13651 return _object_cast_to_XorPDBSelector(o)
13653 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13654 XorPDBSelector_swigregister(XorPDBSelector)
13656 class NotPDBSelector(PDBSelector):
13657 """Proxy of C++ IMP::atom::NotPDBSelector class."""
13659 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13661 def get_version_info(self):
13662 """get_version_info(NotPDBSelector self) -> VersionInfo"""
13663 return _IMP_atom.NotPDBSelector_get_version_info(self)
13666 def __init__(self, a):
13667 """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13668 this = _IMP_atom.new_NotPDBSelector(a)
13670 self.this.append(this)
13671 except __builtin__.Exception:
13675 """__str__(NotPDBSelector self) -> std::string"""
13676 return _IMP_atom.NotPDBSelector___str__(self)
13679 def __repr__(self):
13680 """__repr__(NotPDBSelector self) -> std::string"""
13681 return _IMP_atom.NotPDBSelector___repr__(self)
13686 return _object_cast_to_NotPDBSelector(o)
13688 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13689 NotPDBSelector_swigregister(NotPDBSelector)
13692 def get_default_pdb_selector():
13693 """get_default_pdb_selector() -> PDBSelector"""
13694 return _IMP_atom.get_default_pdb_selector()
13698 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13699 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13700 read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13701 read_pdb(TextInput input, Model model) -> Hierarchy
13702 read_pdb(TextInput input, int model, Hierarchy h)
13704 return _IMP_atom.read_pdb(*args)
13708 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13709 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13710 read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13712 return _IMP_atom.read_multimodel_pdb(*args)
13716 write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13717 write_pdb(Selection mhd, TextOutput out)
13719 return _IMP_atom.write_pdb(mhd, out, model)
13723 write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13724 write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13726 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13729 """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13730 return _IMP_atom.write_multimodel_pdb(mhd, out)
13732 def get_pdb_string(*args):
13734 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
13735 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
13736 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
13737 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13738 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13739 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13740 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13741 get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13742 get_pdb_string(Vector3D v, int index=-1) -> std::string
13743 get_pdb_string(Vector3D v) -> std::string
13745 return _IMP_atom.get_pdb_string(*args)
13747 def get_pdb_conect_record_string(arg1, arg2):
13748 """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13749 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13751 """Proxy of C++ IMP::atom::WritePDBOptimizerState class."""
13753 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13755 def __init__(self, *args):
13757 __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13758 __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13760 this = _IMP_atom.new_WritePDBOptimizerState(*args)
13762 self.this.append(this)
13763 except __builtin__.Exception:
13766 def get_version_info(self):
13767 """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13768 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13772 """__str__(WritePDBOptimizerState self) -> std::string"""
13773 return _IMP_atom.WritePDBOptimizerState___str__(self)
13776 def __repr__(self):
13777 """__repr__(WritePDBOptimizerState self) -> std::string"""
13778 return _IMP_atom.WritePDBOptimizerState___repr__(self)
13783 return _object_cast_to_WritePDBOptimizerState(o)
13785 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13786 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13791 read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13792 read_multimodel_mmcif(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13793 read_multimodel_mmcif(TextInput input, Model model) -> IMP::atom::Hierarchies
13795 return _IMP_atom.read_multimodel_mmcif(*args)
13799 read_mmcif(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> Hierarchy
13800 read_mmcif(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13801 read_mmcif(TextInput input, Model model) -> Hierarchy
13803 return _IMP_atom.read_mmcif(*args)
13806 """get_kt(double T) -> double"""
13807 return _IMP_atom.get_kt(T)
13809 """Proxy of C++ IMP::atom::CAAngleRestraint class."""
13811 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13813 def __init__(self, m, p1, p2, p3, phi0, score):
13814 """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13815 this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13817 self.this.append(this)
13818 except __builtin__.Exception:
13821 def do_get_inputs(self):
13822 """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13823 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13826 def get_version_info(self):
13827 """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13828 return _IMP_atom.CAAngleRestraint_get_version_info(self)
13832 """__str__(CAAngleRestraint self) -> std::string"""
13833 return _IMP_atom.CAAngleRestraint___str__(self)
13836 def __repr__(self):
13837 """__repr__(CAAngleRestraint self) -> std::string"""
13838 return _IMP_atom.CAAngleRestraint___repr__(self)
13843 return _object_cast_to_CAAngleRestraint(o)
13845 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13846 CAAngleRestraint_swigregister(CAAngleRestraint)
13849 """Proxy of C++ IMP::atom::CADihedralRestraint class."""
13851 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13853 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13854 """__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"""
13855 this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13857 self.this.append(this)
13858 except __builtin__.Exception:
13861 def do_get_inputs(self):
13862 """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13863 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13866 def get_version_info(self):
13867 """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13868 return _IMP_atom.CADihedralRestraint_get_version_info(self)
13872 """__str__(CADihedralRestraint self) -> std::string"""
13873 return _IMP_atom.CADihedralRestraint___str__(self)
13876 def __repr__(self):
13877 """__repr__(CADihedralRestraint self) -> std::string"""
13878 return _IMP_atom.CADihedralRestraint___repr__(self)
13883 return _object_cast_to_CADihedralRestraint(o)
13885 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13886 CADihedralRestraint_swigregister(CADihedralRestraint)
13889 """Proxy of C++ IMP::atom::StructureSource class."""
13891 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13893 def get_source_id(self):
13894 """get_source_id(StructureSource self) -> std::string"""
13895 return _IMP_atom.StructureSource_get_source_id(self)
13898 def get_source_chain_id(self):
13899 """get_source_chain_id(StructureSource self) -> std::string"""
13900 return _IMP_atom.StructureSource_get_source_chain_id(self)
13903 def set_source_id(self, source_id):
13904 """set_source_id(StructureSource self, std::string source_id)"""
13905 return _IMP_atom.StructureSource_set_source_id(self, source_id)
13908 def set_source_chain_id(self, source_chain_id):
13909 """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13910 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13913 def __init__(self, *args):
13915 __init__(IMP::atom::StructureSource self) -> StructureSource
13916 __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13917 __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13919 this = _IMP_atom.new_StructureSource(*args)
13921 self.this.append(this)
13922 except __builtin__.Exception:
13925 def get_is_setup(*args):
13927 get_is_setup(Model m, ParticleIndex pi) -> bool
13928 get_is_setup(_ParticleAdaptor p) -> bool
13930 return _IMP_atom.StructureSource_get_is_setup(*args)
13932 get_is_setup = staticmethod(get_is_setup)
13934 def show(self, *args):
13936 show(StructureSource self, _ostream out)
13937 show(StructureSource self)
13939 return _IMP_atom.StructureSource_show(self, *args)
13942 def setup_particle(*args):
13944 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13945 setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13947 return _IMP_atom.StructureSource_setup_particle(*args)
13949 setup_particle = staticmethod(setup_particle)
13951 def add_attribute(self, *args):
13953 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13954 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13955 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13956 add_attribute(StructureSource self, FloatsKey a0, IMP::Floats a1)
13957 add_attribute(StructureSource self, IntsKey a0, IMP::Ints a1)
13958 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13959 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13960 add_attribute(StructureSource self, ObjectKey a0, Object a1)
13962 return _IMP_atom.StructureSource_add_attribute(self, *args)
13965 def get_value(self, *args):
13967 get_value(StructureSource self, FloatKey a0) -> IMP::Float
13968 get_value(StructureSource self, IntKey a0) -> IMP::Int
13969 get_value(StructureSource self, FloatsKey a0) -> IMP::Floats
13970 get_value(StructureSource self, IntsKey a0) -> IMP::Ints
13971 get_value(StructureSource self, StringKey a0) -> IMP::String
13972 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13973 get_value(StructureSource self, ObjectKey a0) -> Object
13975 return _IMP_atom.StructureSource_get_value(self, *args)
13978 def set_value(self, *args):
13980 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13981 set_value(StructureSource self, IntKey a0, IMP::Int a1)
13982 set_value(StructureSource self, FloatsKey a0, IMP::Floats a1)
13983 set_value(StructureSource self, IntsKey a0, IMP::Ints a1)
13984 set_value(StructureSource self, StringKey a0, IMP::String a1)
13985 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13986 set_value(StructureSource self, ObjectKey a0, Object a1)
13988 return _IMP_atom.StructureSource_set_value(self, *args)
13991 def remove_attribute(self, *args):
13993 remove_attribute(StructureSource self, FloatKey a0)
13994 remove_attribute(StructureSource self, IntKey a0)
13995 remove_attribute(StructureSource self, FloatsKey a0)
13996 remove_attribute(StructureSource self, IntsKey a0)
13997 remove_attribute(StructureSource self, StringKey a0)
13998 remove_attribute(StructureSource self, ParticleIndexKey a0)
13999 remove_attribute(StructureSource self, ObjectKey a0)
14001 return _IMP_atom.StructureSource_remove_attribute(self, *args)
14004 def has_attribute(self, *args):
14006 has_attribute(StructureSource self, FloatKey a0) -> bool
14007 has_attribute(StructureSource self, IntKey a0) -> bool
14008 has_attribute(StructureSource self, FloatsKey a0) -> bool
14009 has_attribute(StructureSource self, IntsKey a0) -> bool
14010 has_attribute(StructureSource self, StringKey a0) -> bool
14011 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
14012 has_attribute(StructureSource self, ObjectKey a0) -> bool
14014 return _IMP_atom.StructureSource_has_attribute(self, *args)
14017 def get_derivative(self, a0):
14018 """get_derivative(StructureSource self, FloatKey a0) -> double"""
14019 return _IMP_atom.StructureSource_get_derivative(self, a0)
14022 def get_name(self):
14023 """get_name(StructureSource self) -> std::string"""
14024 return _IMP_atom.StructureSource_get_name(self)
14027 def clear_caches(self):
14028 """clear_caches(StructureSource self)"""
14029 return _IMP_atom.StructureSource_clear_caches(self)
14032 def set_name(self, a0):
14033 """set_name(StructureSource self, std::string a0)"""
14034 return _IMP_atom.StructureSource_set_name(self, a0)
14038 """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
14039 return _IMP_atom.StructureSource_set_check_level(self, a0)
14042 def add_to_derivative(self, a0, a1, a2):
14043 """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
14044 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
14047 def set_is_optimized(self, a0, a1):
14048 """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
14049 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
14052 def get_is_optimized(self, a0):
14053 """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
14054 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
14058 """get_check_level(StructureSource self) -> IMP::CheckLevel"""
14059 return _IMP_atom.StructureSource_get_check_level(self)
14062 def __eq__(self, *args):
14064 __eq__(StructureSource self, StructureSource o) -> bool
14065 __eq__(StructureSource self, Particle d) -> bool
14067 return _IMP_atom.StructureSource___eq__(self, *args)
14070 def __ne__(self, *args):
14072 __ne__(StructureSource self, StructureSource o) -> bool
14073 __ne__(StructureSource self, Particle d) -> bool
14075 return _IMP_atom.StructureSource___ne__(self, *args)
14078 def __le__(self, *args):
14080 __le__(StructureSource self, StructureSource o) -> bool
14081 __le__(StructureSource self, Particle d) -> bool
14083 return _IMP_atom.StructureSource___le__(self, *args)
14086 def __lt__(self, *args):
14088 __lt__(StructureSource self, StructureSource o) -> bool
14089 __lt__(StructureSource self, Particle d) -> bool
14091 return _IMP_atom.StructureSource___lt__(self, *args)
14094 def __ge__(self, *args):
14096 __ge__(StructureSource self, StructureSource o) -> bool
14097 __ge__(StructureSource self, Particle d) -> bool
14099 return _IMP_atom.StructureSource___ge__(self, *args)
14102 def __gt__(self, *args):
14104 __gt__(StructureSource self, StructureSource o) -> bool
14105 __gt__(StructureSource self, Particle d) -> bool
14107 return _IMP_atom.StructureSource___gt__(self, *args)
14110 def __hash__(self):
14111 """__hash__(StructureSource self) -> std::size_t"""
14112 return _IMP_atom.StructureSource___hash__(self)
14116 """__str__(StructureSource self) -> std::string"""
14117 return _IMP_atom.StructureSource___str__(self)
14120 def __repr__(self):
14121 """__repr__(StructureSource self) -> std::string"""
14122 return _IMP_atom.StructureSource___repr__(self)
14124 __swig_destroy__ = _IMP_atom.delete_StructureSource
14125 __del__ =
lambda self:
None
14126 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
14127 StructureSource_swigregister(StructureSource)
14129 def StructureSource_get_is_setup(*args):
14131 get_is_setup(Model m, ParticleIndex pi) -> bool
14132 StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
14134 return _IMP_atom.StructureSource_get_is_setup(*args)
14136 def StructureSource_setup_particle(*args):
14138 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
14139 StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
14141 return _IMP_atom.StructureSource_setup_particle(*args)
14144 def __lshift__(*args):
14146 __lshift__(_ostream out, Bonded n) -> _ostream
14147 __lshift__(_ostream out, Bond n) -> _ostream
14148 __lshift__(_ostream out, Hierarchy n) -> _ostream
14149 __lshift__(_ostream out, Angle n) -> _ostream
14150 __lshift__(_ostream out, Dihedral n) -> _ostream
14151 __lshift__(_ostream out, CenterOfMass n) -> _ostream
14152 __lshift__(_ostream out, Diffusion n) -> _ostream
14153 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
14154 __lshift__(_ostream out, TAMDParticle n) -> _ostream
14155 __lshift__(_ostream out, Chain n) -> _ostream
14156 __lshift__(_ostream out, Charged n) -> _ostream
14157 __lshift__(_ostream out, Domain n) -> _ostream
14158 __lshift__(_ostream out, LennardJones n) -> _ostream
14159 __lshift__(_ostream out, Fragment n) -> _ostream
14160 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
14161 __lshift__(_ostream out, Atom n) -> _ostream
14162 __lshift__(_ostream out, Residue n) -> _ostream
14163 __lshift__(_ostream out, Representation n) -> _ostream
14164 __lshift__(_ostream out, State n) -> _ostream
14165 __lshift__(_ostream out, Molecule n) -> _ostream
14166 __lshift__(_ostream out, Copy n) -> _ostream
14167 __lshift__(_ostream out, StructureSource n) -> _ostream
14169 return _IMP_atom.__lshift__(*args)
14171 """Proxy of C++ IMP::atom::HelixRestraint class."""
14173 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
14175 def __init__(self, rs, ideal=True):
14177 __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs, bool ideal=True) -> HelixRestraint
14178 __init__(IMP::atom::HelixRestraint self, IMP::atom::Residues rs) -> HelixRestraint
14180 this = _IMP_atom.new_HelixRestraint(rs, ideal)
14182 self.this.append(this)
14183 except __builtin__.Exception:
14186 def get_number_of_bonds(self):
14187 """get_number_of_bonds(HelixRestraint self) -> int"""
14188 return _IMP_atom.HelixRestraint_get_number_of_bonds(self)
14191 def get_number_of_dihedrals(self):
14192 """get_number_of_dihedrals(HelixRestraint self) -> int"""
14193 return _IMP_atom.HelixRestraint_get_number_of_dihedrals(self)
14196 def do_get_inputs(self):
14197 """do_get_inputs(HelixRestraint self) -> IMP::ModelObjectsTemp"""
14198 return _IMP_atom.HelixRestraint_do_get_inputs(self)
14201 def get_version_info(self):
14202 """get_version_info(HelixRestraint self) -> VersionInfo"""
14203 return _IMP_atom.HelixRestraint_get_version_info(self)
14207 """__str__(HelixRestraint self) -> std::string"""
14208 return _IMP_atom.HelixRestraint___str__(self)
14211 def __repr__(self):
14212 """__repr__(HelixRestraint self) -> std::string"""
14213 return _IMP_atom.HelixRestraint___repr__(self)
14218 return _object_cast_to_HelixRestraint(o)
14220 HelixRestraint_swigregister = _IMP_atom.HelixRestraint_swigregister
14221 HelixRestraint_swigregister(HelixRestraint)
14225 """get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
14226 return _IMP_atom.get_transformation_aligning_first_to_second(s1, s2)
14230 show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
14231 show_molecular_hierarchy(Hierarchy h) -> _ostream
14233 return _IMP_atom.show_molecular_hierarchy(*args)
14234 class CHARMMBond(object):
14235 """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class."""
14237 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
14238 __repr__ = _swig_repr
14240 def __init__(self, atoms):
14241 """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
14242 this = _IMP_atom.new_CHARMMBond(atoms)
14244 self.this.append(this)
14245 except __builtin__.Exception:
14248 def get_endpoint(self, i):
14249 """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
14250 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
14253 def get_contains_atom(self, name):
14254 """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
14255 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
14258 def show(self, *args):
14260 show(CHARMMBond self, _ostream out)
14261 show(CHARMMBond self)
14263 return _IMP_atom.CHARMMBond_show(self, *args)
14265 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
14266 __del__ =
lambda self:
None
14267 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
14268 CHARMMBond_swigregister(CHARMMBond)
14270 class CHARMMAngle(object):
14271 """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class."""
14273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
14274 __repr__ = _swig_repr
14276 def __init__(self, atoms):
14277 """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
14278 this = _IMP_atom.new_CHARMMAngle(atoms)
14280 self.this.append(this)
14281 except __builtin__.Exception:
14284 def get_endpoint(self, i):
14285 """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
14286 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
14289 def get_contains_atom(self, name):
14290 """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
14291 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
14294 def show(self, *args):
14296 show(CHARMMAngle self, _ostream out)
14297 show(CHARMMAngle self)
14299 return _IMP_atom.CHARMMAngle_show(self, *args)
14301 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
14302 __del__ =
lambda self:
None
14303 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
14304 CHARMMAngle_swigregister(CHARMMAngle)
14307 def _get_native_overlap_cpp(m1, m2, threshold):
14308 """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
14309 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
14311 def _get_drmsd_cpp(m0, m1):
14312 """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
14313 return _IMP_atom._get_drmsd_cpp(m0, m1)
14315 def _get_drmsd_Q_cpp(m0, m1, threshold):
14316 """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
14317 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
14319 def _get_drms_cpp(m1, m2):
14320 """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
14321 return _IMP_atom._get_drms_cpp(m1, m2)
14323 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
14324 """_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"""
14325 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
14328 va= [IMP.algebra.get_vector(x)
for x
in a]
14329 vb= [IMP.algebra.get_vector(x)
for x
in b]
14330 return _get_native_overlap_cpp(va, vb, d)
14333 va= [IMP.algebra.get_vector(x)
for x
in a]
14334 vb= [IMP.algebra.get_vector(x)
for x
in b]
14335 return _get_drmsd_cpp(va, vb)
14338 va= [IMP.algebra.get_vector(x)
for x
in a]
14339 vb= [IMP.algebra.get_vector(x)
for x
in b]
14340 return _get_drms_cpp(va, vb)
14343 va= [IMP.algebra.get_vector(x)
for x
in a]
14344 vb= [IMP.algebra.get_vector(x)
for x
in b]
14345 return _get_drmsd_Q_cpp(va, vb, t)
14348 va= [IMP.algebra.get_vector(x)
for x
in a]
14349 vb= [IMP.algebra.get_vector(x)
for x
in b]
14351 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
14356 """get_module_version() -> std::string const"""
14357 return _IMP_atom.get_module_version()
14360 """get_example_path(std::string fname) -> std::string"""
14361 return _IMP_atom.get_example_path(fname)
14364 """get_data_path(std::string fname) -> std::string"""
14365 return _IMP_atom.get_data_path(fname)
14367 from .
import _version_check
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature in units of [kcal/mol].
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
double get_einstein_rotational_diffusion_coefficient(double r, double temp=-1)
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
Get the containing chain or Chain() if there is none.
CheckLevel get_check_level()
Get the current audit mode.
Vector< AtomTypes > get_chi_dihedral_atom_types(ResidueType rt)
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square)
Convert spring constant from kcal/mol/A^2 to femtonewton/A.
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
Provenance create_clone(Provenance p)
Clone provenance (including previous provenance)
Atoms get_omega_dihedral_atoms(Residue rd)
Return the atoms comprising the omega dihedral.
ParticleIndexQuads get_chi_dihedral_particle_indexes(Residue rd)
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Composable functors to implement scores via compile-time composition.
double get_angle(const Line3D &a, const Line3D &b)
Get angle in radians between two lines around their closest points.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
Hierarchies read_multimodel_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all models from the mmCIF file.
double get_kd(double na, double nb, double nab, double volume)
double get_diffusion_angle(double D, double dtfs)
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &orientations, double dt)
Hierarchy read_mmcif(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
Read all the molecules in the first model of the mmCIF file.
Base class for all optimizers.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
A decorator for a particle with x,y,z coordinates.
void add_loop_statistical_score_data(atom::Hierarchy h)
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
Read all the molecules in the first model of the PDB file.
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Vector< Atoms > get_chi_dihedral_atoms(Residue rd)
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
double get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom)
Convert force from kcal/mol/A to femtonewtons.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
Walk up the hierarchy to determine the chain id.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_einstein_diffusion_coefficient(double r, double temp=-1)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
double get_diffusion_length(double D, double t)
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
A decorator for a particle with x,y,z coordinates and a radius.