11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_ISD_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_ISD_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
72 def __init__(self, *args, **kwargs):
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_isd.delete_IMP_ISD_SwigPyIterator
78 r"""value(IMP_ISD_SwigPyIterator self) -> PyObject *"""
79 return _IMP_isd.IMP_ISD_SwigPyIterator_value(self)
82 r"""incr(IMP_ISD_SwigPyIterator self, size_t n=1) -> IMP_ISD_SwigPyIterator"""
83 return _IMP_isd.IMP_ISD_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_ISD_SwigPyIterator self, size_t n=1) -> IMP_ISD_SwigPyIterator"""
87 return _IMP_isd.IMP_ISD_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_ISD_SwigPyIterator self, IMP_ISD_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_isd.IMP_ISD_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_ISD_SwigPyIterator self, IMP_ISD_SwigPyIterator x) -> bool"""
95 return _IMP_isd.IMP_ISD_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_ISD_SwigPyIterator self) -> IMP_ISD_SwigPyIterator"""
99 return _IMP_isd.IMP_ISD_SwigPyIterator_copy(self)
102 r"""next(IMP_ISD_SwigPyIterator self) -> PyObject *"""
103 return _IMP_isd.IMP_ISD_SwigPyIterator_next(self)
106 r"""__next__(IMP_ISD_SwigPyIterator self) -> PyObject *"""
107 return _IMP_isd.IMP_ISD_SwigPyIterator___next__(self)
110 r"""previous(IMP_ISD_SwigPyIterator self) -> PyObject *"""
111 return _IMP_isd.IMP_ISD_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_ISD_SwigPyIterator self, ptrdiff_t n) -> IMP_ISD_SwigPyIterator"""
115 return _IMP_isd.IMP_ISD_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_ISD_SwigPyIterator self, IMP_ISD_SwigPyIterator x) -> bool"""
119 return _IMP_isd.IMP_ISD_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_ISD_SwigPyIterator self, IMP_ISD_SwigPyIterator x) -> bool"""
123 return _IMP_isd.IMP_ISD_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_ISD_SwigPyIterator self, ptrdiff_t n) -> IMP_ISD_SwigPyIterator"""
127 return _IMP_isd.IMP_ISD_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_ISD_SwigPyIterator self, ptrdiff_t n) -> IMP_ISD_SwigPyIterator"""
131 return _IMP_isd.IMP_ISD_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_ISD_SwigPyIterator self, ptrdiff_t n) -> IMP_ISD_SwigPyIterator"""
135 return _IMP_isd.IMP_ISD_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_ISD_SwigPyIterator self, ptrdiff_t n) -> IMP_ISD_SwigPyIterator
140 __sub__(IMP_ISD_SwigPyIterator self, IMP_ISD_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_isd.IMP_ISD_SwigPyIterator___sub__(self, *args)
147 _IMP_isd.IMP_ISD_SwigPyIterator_swigregister(IMP_ISD_SwigPyIterator)
154 IMP_DEBUG = _IMP_isd.IMP_DEBUG
156 IMP_RELEASE = _IMP_isd.IMP_RELEASE
158 IMP_SILENT = _IMP_isd.IMP_SILENT
160 IMP_PROGRESS = _IMP_isd.IMP_PROGRESS
162 IMP_TERSE = _IMP_isd.IMP_TERSE
164 IMP_VERBOSE = _IMP_isd.IMP_VERBOSE
166 IMP_MEMORY = _IMP_isd.IMP_MEMORY
168 IMP_NONE = _IMP_isd.IMP_NONE
170 IMP_USAGE = _IMP_isd.IMP_USAGE
172 IMP_INTERNAL = _IMP_isd.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_isd.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_isd.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_isd.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_isd.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_isd.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_isd.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_isd.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_isd.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_isd.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_isd.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_isd.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_isd._ostream_write(self, osa_buf)
237 _IMP_isd._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_isd.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_isd.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_isd.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_isd.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_isd.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_isd.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_isd.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_isd.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_isd.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_isd.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_isd.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_isd.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_isd.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_isd.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_isd.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_isd.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_isd.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_isd.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_isd.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_isd.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_isd.IMP_STATISTICS_HAS_IMP_CGAL
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_isd.IMP_STATISTICS_HAS_BOOST_RANDOM
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_isd.IMP_STATISTICS_HAS_BOOST_SYSTEM
319 IMP_STATISTICS_HAS_CGAL = _IMP_isd.IMP_STATISTICS_HAS_CGAL
321 IMP_STATISTICS_HAS_NUMPY = _IMP_isd.IMP_STATISTICS_HAS_NUMPY
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_isd.IMPSTATISTICS_SHOW_WARNINGS
326 IMP_CORE_HAS_IMP_CGAL = _IMP_isd.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_isd.IMP_CORE_HAS_IMP_KERNEL
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_isd.IMP_CORE_HAS_BOOST_RANDOM
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_isd.IMP_CORE_HAS_BOOST_SYSTEM
338 IMP_CORE_HAS_CGAL = _IMP_isd.IMP_CORE_HAS_CGAL
340 IMP_CORE_HAS_HDF5 = _IMP_isd.IMP_CORE_HAS_HDF5
342 IMP_CORE_HAS_NUMPY = _IMP_isd.IMP_CORE_HAS_NUMPY
344 IMPCORE_SHOW_WARNINGS = _IMP_isd.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_isd.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_isd.IMP_CONTAINER_HAS_IMP_CGAL
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_isd.IMP_CONTAINER_HAS_IMP_DISPLAY
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_isd.IMP_CONTAINER_HAS_IMP_KERNEL
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_isd.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_isd.IMP_CONTAINER_HAS_BOOST_RANDOM
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_isd.IMP_CONTAINER_HAS_BOOST_SYSTEM
365 IMP_CONTAINER_HAS_CGAL = _IMP_isd.IMP_CONTAINER_HAS_CGAL
367 IMP_CONTAINER_HAS_HDF5 = _IMP_isd.IMP_CONTAINER_HAS_HDF5
369 IMP_CONTAINER_HAS_NUMPY = _IMP_isd.IMP_CONTAINER_HAS_NUMPY
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_isd.IMP_CONTAINER_HAS_PYTHON_IHM
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_isd.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_isd.IMP_CONTAINER_HAS_ROBIN_MAP
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_isd.IMPCONTAINER_SHOW_WARNINGS
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_isd.IMP_ATOM_HAS_IMP_CGAL
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_isd.IMP_ATOM_HAS_IMP_KERNEL
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_isd.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_isd.IMP_ATOM_HAS_BOOST_RANDOM
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_isd.IMP_ATOM_HAS_BOOST_REGEX
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_isd.IMP_ATOM_HAS_BOOST_SYSTEM
394 IMP_ATOM_HAS_CGAL = _IMP_isd.IMP_ATOM_HAS_CGAL
396 IMP_ATOM_HAS_HDF5 = _IMP_isd.IMP_ATOM_HAS_HDF5
398 IMP_ATOM_HAS_NUMPY = _IMP_isd.IMP_ATOM_HAS_NUMPY
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_isd.IMP_ATOM_HAS_PYTHON_IHM
402 IMPATOM_SHOW_WARNINGS = _IMP_isd.IMPATOM_SHOW_WARNINGS
404 IMP_ATOM_TYPE_INDEX = _IMP_isd.IMP_ATOM_TYPE_INDEX
406 IMP_RESIDUE_TYPE_INDEX = _IMP_isd.IMP_RESIDUE_TYPE_INDEX
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_isd.IMP_HIERARCHY_TYPE_INDEX
410 IMP_CHAIN_TYPE_INDEX = _IMP_isd.IMP_CHAIN_TYPE_INDEX
413 IMP_EM_HAS_IMP_CGAL = _IMP_isd.IMP_EM_HAS_IMP_CGAL
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_isd.IMP_EM_HAS_IMP_CONTAINER
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_isd.IMP_EM_HAS_IMP_DISPLAY
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_isd.IMP_EM_HAS_IMP_SCORE_FUNCTOR
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_EM_HAS_BOOST_FILESYSTEM
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_isd.IMP_EM_HAS_BOOST_RANDOM
427 IMP_EM_HAS_BOOST_REGEX = _IMP_isd.IMP_EM_HAS_BOOST_REGEX
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_isd.IMP_EM_HAS_BOOST_SYSTEM
431 IMP_EM_HAS_CGAL = _IMP_isd.IMP_EM_HAS_CGAL
433 IMP_EM_HAS_HDF5 = _IMP_isd.IMP_EM_HAS_HDF5
435 IMP_EM_HAS_NUMPY = _IMP_isd.IMP_EM_HAS_NUMPY
437 IMP_EM_HAS_PYTHON_IHM = _IMP_isd.IMP_EM_HAS_PYTHON_IHM
439 IMPEM_SHOW_WARNINGS = _IMP_isd.IMPEM_SHOW_WARNINGS
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_isd.IMP_SAXS_HAS_IMP_CGAL
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_isd.IMP_SAXS_HAS_IMP_CONTAINER
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_isd.IMP_SAXS_HAS_IMP_DISPLAY
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_isd.IMP_SAXS_HAS_IMP_KERNEL
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_isd.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_SAXS_HAS_BOOST_FILESYSTEM
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_isd.IMP_SAXS_HAS_BOOST_RANDOM
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_isd.IMP_SAXS_HAS_BOOST_REGEX
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_isd.IMP_SAXS_HAS_BOOST_SYSTEM
462 IMP_SAXS_HAS_CGAL = _IMP_isd.IMP_SAXS_HAS_CGAL
464 IMP_SAXS_HAS_HDF5 = _IMP_isd.IMP_SAXS_HAS_HDF5
466 IMP_SAXS_HAS_NUMPY = _IMP_isd.IMP_SAXS_HAS_NUMPY
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_isd.IMP_SAXS_HAS_PYTHON_IHM
470 IMPSAXS_SHOW_WARNINGS = _IMP_isd.IMPSAXS_SHOW_WARNINGS
473 IMP_ISD_HAS_IMP_CGAL = _IMP_isd.IMP_ISD_HAS_IMP_CGAL
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_isd.IMP_ISD_HAS_IMP_DISPLAY
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_isd.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_isd.IMP_ISD_HAS_BOOST_FILESYSTEM
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_isd.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_isd.IMP_ISD_HAS_BOOST_RANDOM
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_isd.IMP_ISD_HAS_BOOST_REGEX
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_isd.IMP_ISD_HAS_BOOST_SYSTEM
489 IMP_ISD_HAS_CGAL = _IMP_isd.IMP_ISD_HAS_CGAL
491 IMP_ISD_HAS_HDF5 = _IMP_isd.IMP_ISD_HAS_HDF5
493 IMP_ISD_HAS_NUMPY = _IMP_isd.IMP_ISD_HAS_NUMPY
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_isd.IMP_ISD_HAS_PYTHON_IHM
497 IMPISD_SHOW_WARNINGS = _IMP_isd.IMPISD_SHOW_WARNINGS
500 _object_types.append(
"ISDRestraint")
503 def _object_cast_to_ISDRestraint(o):
504 r"""_object_cast_to_ISDRestraint(Object o) -> ISDRestraint"""
505 return _IMP_isd._object_cast_to_ISDRestraint(o)
507 _object_types.append(
"CrossLinkMSRestraint")
510 def _object_cast_to_CrossLinkMSRestraint(o):
511 r"""_object_cast_to_CrossLinkMSRestraint(Object o) -> CrossLinkMSRestraint"""
512 return _IMP_isd._object_cast_to_CrossLinkMSRestraint(o)
514 _object_types.append(
"LogWrapper")
517 def _object_cast_to_LogWrapper(o):
518 r"""_object_cast_to_LogWrapper(Object o) -> LogWrapper"""
519 return _IMP_isd._object_cast_to_LogWrapper(o)
521 _object_types.append(
"UniformPrior")
524 def _object_cast_to_UniformPrior(o):
525 r"""_object_cast_to_UniformPrior(Object o) -> UniformPrior"""
526 return _IMP_isd._object_cast_to_UniformPrior(o)
528 _object_types.append(
"JeffreysRestraint")
531 def _object_cast_to_JeffreysRestraint(o):
532 r"""_object_cast_to_JeffreysRestraint(Object o) -> JeffreysRestraint"""
533 return _IMP_isd._object_cast_to_JeffreysRestraint(o)
535 _object_types.append(
"NormalSigmaPCRestraint")
538 def _object_cast_to_NormalSigmaPCRestraint(o):
539 r"""_object_cast_to_NormalSigmaPCRestraint(Object o) -> NormalSigmaPCRestraint"""
540 return _IMP_isd._object_cast_to_NormalSigmaPCRestraint(o)
542 _object_types.append(
"vonMisesKappaJeffreysRestraint")
545 def _object_cast_to_vonMisesKappaJeffreysRestraint(o):
546 r"""_object_cast_to_vonMisesKappaJeffreysRestraint(Object o) -> vonMisesKappaJeffreysRestraint"""
547 return _IMP_isd._object_cast_to_vonMisesKappaJeffreysRestraint(o)
549 _object_types.append(
"vonMisesKappaConjugateRestraint")
552 def _object_cast_to_vonMisesKappaConjugateRestraint(o):
553 r"""_object_cast_to_vonMisesKappaConjugateRestraint(Object o) -> vonMisesKappaConjugateRestraint"""
554 return _IMP_isd._object_cast_to_vonMisesKappaConjugateRestraint(o)
556 _object_types.append(
"Distribution")
559 def _object_cast_to_Distribution(o):
560 r"""_object_cast_to_Distribution(Object o) -> Distribution"""
561 return _IMP_isd._object_cast_to_Distribution(o)
563 _object_types.append(
"OneDimensionalDistribution")
566 def _object_cast_to_OneDimensionalDistribution(o):
567 r"""_object_cast_to_OneDimensionalDistribution(Object o) -> OneDimensionalDistribution"""
568 return _IMP_isd._object_cast_to_OneDimensionalDistribution(o)
570 _object_types.append(
"OneDimensionalSufficientDistribution")
573 def _object_cast_to_OneDimensionalSufficientDistribution(o):
574 r"""_object_cast_to_OneDimensionalSufficientDistribution(Object o) -> OneDimensionalSufficientDistribution"""
575 return _IMP_isd._object_cast_to_OneDimensionalSufficientDistribution(o)
577 _object_types.append(
"FNormal")
580 def _object_cast_to_FNormal(o):
581 r"""_object_cast_to_FNormal(Object o) -> FNormal"""
582 return _IMP_isd._object_cast_to_FNormal(o)
584 _object_types.append(
"FStudentT")
587 def _object_cast_to_FStudentT(o):
588 r"""_object_cast_to_FStudentT(Object o) -> FStudentT"""
589 return _IMP_isd._object_cast_to_FStudentT(o)
591 _object_types.append(
"vonMises")
594 def _object_cast_to_vonMises(o):
595 r"""_object_cast_to_vonMises(Object o) -> vonMises"""
596 return _IMP_isd._object_cast_to_vonMises(o)
598 _object_types.append(
"vonMisesSufficient")
601 def _object_cast_to_vonMisesSufficient(o):
602 r"""_object_cast_to_vonMisesSufficient(Object o) -> vonMisesSufficient"""
603 return _IMP_isd._object_cast_to_vonMisesSufficient(o)
605 _object_types.append(
"PenalizedComplexityPrior")
608 def _object_cast_to_PenalizedComplexityPrior(o):
609 r"""_object_cast_to_PenalizedComplexityPrior(Object o) -> PenalizedComplexityPrior"""
610 return _IMP_isd._object_cast_to_PenalizedComplexityPrior(o)
613 return [Nuisance(x)
for x
in l]
614 _plural_types.append(
"Nuisances")
617 _value_types.append(
"Nuisance")
621 return [Scale(x)
for x
in l]
622 _plural_types.append(
"Scales")
625 _value_types.append(
"Scale")
628 def Switchings(l=[]):
629 return [Switching(x)
for x
in l]
630 _plural_types.append(
"Switchings")
633 _value_types.append(
"Switching")
636 _object_types.append(
"NOERestraint")
639 def _object_cast_to_NOERestraint(o):
640 r"""_object_cast_to_NOERestraint(Object o) -> NOERestraint"""
641 return _IMP_isd._object_cast_to_NOERestraint(o)
644 return [Weight(x)
for x
in l]
645 _plural_types.append(
"Weights")
648 _value_types.append(
"Weight")
651 _object_types.append(
"GaussianRestraint")
654 def _object_cast_to_GaussianRestraint(o):
655 r"""_object_cast_to_GaussianRestraint(Object o) -> GaussianRestraint"""
656 return _IMP_isd._object_cast_to_GaussianRestraint(o)
658 _object_types.append(
"StudentTRestraint")
661 def _object_cast_to_StudentTRestraint(o):
662 r"""_object_cast_to_StudentTRestraint(Object o) -> StudentTRestraint"""
663 return _IMP_isd._object_cast_to_StudentTRestraint(o)
665 _object_types.append(
"LognormalRestraint")
668 def _object_cast_to_LognormalRestraint(o):
669 r"""_object_cast_to_LognormalRestraint(Object o) -> LognormalRestraint"""
670 return _IMP_isd._object_cast_to_LognormalRestraint(o)
672 _object_types.append(
"LognormalAmbiguousRestraint")
675 def _object_cast_to_LognormalAmbiguousRestraint(o):
676 r"""_object_cast_to_LognormalAmbiguousRestraint(Object o) -> LognormalAmbiguousRestraint"""
677 return _IMP_isd._object_cast_to_LognormalAmbiguousRestraint(o)
679 _object_types.append(
"AmbiguousNOERestraint")
682 def _object_cast_to_AmbiguousNOERestraint(o):
683 r"""_object_cast_to_AmbiguousNOERestraint(Object o) -> AmbiguousNOERestraint"""
684 return _IMP_isd._object_cast_to_AmbiguousNOERestraint(o)
686 _object_types.append(
"MarginalNOERestraint")
689 def _object_cast_to_MarginalNOERestraint(o):
690 r"""_object_cast_to_MarginalNOERestraint(Object o) -> MarginalNOERestraint"""
691 return _IMP_isd._object_cast_to_MarginalNOERestraint(o)
693 _object_types.append(
"MarginalHBondRestraint")
696 def _object_cast_to_MarginalHBondRestraint(o):
697 r"""_object_cast_to_MarginalHBondRestraint(Object o) -> MarginalHBondRestraint"""
698 return _IMP_isd._object_cast_to_MarginalHBondRestraint(o)
700 _object_types.append(
"TALOSRestraint")
703 def _object_cast_to_TALOSRestraint(o):
704 r"""_object_cast_to_TALOSRestraint(Object o) -> TALOSRestraint"""
705 return _IMP_isd._object_cast_to_TALOSRestraint(o)
707 _object_types.append(
"RepulsiveDistancePairScore")
710 def _object_cast_to_RepulsiveDistancePairScore(o):
711 r"""_object_cast_to_RepulsiveDistancePairScore(Object o) -> RepulsiveDistancePairScore"""
712 return _IMP_isd._object_cast_to_RepulsiveDistancePairScore(o)
714 _object_types.append(
"AmbiguousRestraint")
717 def _object_cast_to_AmbiguousRestraint(o):
718 r"""_object_cast_to_AmbiguousRestraint(Object o) -> AmbiguousRestraint"""
719 return _IMP_isd._object_cast_to_AmbiguousRestraint(o)
721 _object_types.append(
"UnivariateFunction")
724 def _object_cast_to_UnivariateFunction(o):
725 r"""_object_cast_to_UnivariateFunction(Object o) -> UnivariateFunction"""
726 return _IMP_isd._object_cast_to_UnivariateFunction(o)
728 _object_types.append(
"Linear1DFunction")
731 def _object_cast_to_Linear1DFunction(o):
732 r"""_object_cast_to_Linear1DFunction(Object o) -> Linear1DFunction"""
733 return _IMP_isd._object_cast_to_Linear1DFunction(o)
735 _object_types.append(
"GeneralizedGuinierPorodFunction")
738 def _object_cast_to_GeneralizedGuinierPorodFunction(o):
739 r"""_object_cast_to_GeneralizedGuinierPorodFunction(Object o) -> GeneralizedGuinierPorodFunction"""
740 return _IMP_isd._object_cast_to_GeneralizedGuinierPorodFunction(o)
742 _object_types.append(
"BivariateFunction")
745 def _object_cast_to_BivariateFunction(o):
746 r"""_object_cast_to_BivariateFunction(Object o) -> BivariateFunction"""
747 return _IMP_isd._object_cast_to_BivariateFunction(o)
749 _object_types.append(
"Covariance1DFunction")
752 def _object_cast_to_Covariance1DFunction(o):
753 r"""_object_cast_to_Covariance1DFunction(Object o) -> Covariance1DFunction"""
754 return _IMP_isd._object_cast_to_Covariance1DFunction(o)
756 _object_types.append(
"GaussianProcessInterpolation")
759 def _object_cast_to_GaussianProcessInterpolation(o):
760 r"""_object_cast_to_GaussianProcessInterpolation(Object o) -> GaussianProcessInterpolation"""
761 return _IMP_isd._object_cast_to_GaussianProcessInterpolation(o)
763 _object_types.append(
"GaussianProcessInterpolationRestraint")
766 def _object_cast_to_GaussianProcessInterpolationRestraint(o):
767 r"""_object_cast_to_GaussianProcessInterpolationRestraint(Object o) -> GaussianProcessInterpolationRestraint"""
768 return _IMP_isd._object_cast_to_GaussianProcessInterpolationRestraint(o)
770 _object_types.append(
"MolecularDynamics")
773 _object_types.append(
"MolecularDynamicsMover")
776 def _object_cast_to_MolecularDynamicsMover(o):
777 r"""_object_cast_to_MolecularDynamicsMover(Object o) -> MolecularDynamicsMover"""
778 return _IMP_isd._object_cast_to_MolecularDynamicsMover(o)
780 _object_types.append(
"HybridMonteCarlo")
783 def _object_cast_to_HybridMonteCarlo(o):
784 r"""_object_cast_to_HybridMonteCarlo(Object o) -> HybridMonteCarlo"""
785 return _IMP_isd._object_cast_to_HybridMonteCarlo(o)
787 _object_types.append(
"FretData")
790 def _object_cast_to_FretData(o):
791 r"""_object_cast_to_FretData(Object o) -> FretData"""
792 return _IMP_isd._object_cast_to_FretData(o)
794 _object_types.append(
"FretRestraint")
797 def _object_cast_to_FretRestraint(o):
798 r"""_object_cast_to_FretRestraint(Object o) -> FretRestraint"""
799 return _IMP_isd._object_cast_to_FretRestraint(o)
801 _object_types.append(
"CrossLinkData")
804 def _object_cast_to_CrossLinkData(o):
805 r"""_object_cast_to_CrossLinkData(Object o) -> CrossLinkData"""
806 return _IMP_isd._object_cast_to_CrossLinkData(o)
808 _object_types.append(
"CysteineCrossLinkData")
811 def _object_cast_to_CysteineCrossLinkData(o):
812 r"""_object_cast_to_CysteineCrossLinkData(Object o) -> CysteineCrossLinkData"""
813 return _IMP_isd._object_cast_to_CysteineCrossLinkData(o)
815 _object_types.append(
"CysteineCrossLinkRestraint")
818 def _object_cast_to_CysteineCrossLinkRestraint(o):
819 r"""_object_cast_to_CysteineCrossLinkRestraint(Object o) -> CysteineCrossLinkRestraint"""
820 return _IMP_isd._object_cast_to_CysteineCrossLinkRestraint(o)
822 _object_types.append(
"WeightMover")
825 def _object_cast_to_WeightMover(o):
826 r"""_object_cast_to_WeightMover(Object o) -> WeightMover"""
827 return _IMP_isd._object_cast_to_WeightMover(o)
829 _object_types.append(
"WeightRestraint")
832 def _object_cast_to_WeightRestraint(o):
833 r"""_object_cast_to_WeightRestraint(Object o) -> WeightRestraint"""
834 return _IMP_isd._object_cast_to_WeightRestraint(o)
836 _object_types.append(
"AtomicCrossLinkMSRestraint")
839 def _object_cast_to_AtomicCrossLinkMSRestraint(o):
840 r"""_object_cast_to_AtomicCrossLinkMSRestraint(Object o) -> AtomicCrossLinkMSRestraint"""
841 return _IMP_isd._object_cast_to_AtomicCrossLinkMSRestraint(o)
843 _object_types.append(
"GaussianEMRestraint")
846 def _object_cast_to_GaussianEMRestraint(o):
847 r"""_object_cast_to_GaussianEMRestraint(Object o) -> GaussianEMRestraint"""
848 return _IMP_isd._object_cast_to_GaussianEMRestraint(o)
850 _object_types.append(
"GaussianAnchorEMRestraint")
853 def _object_cast_to_GaussianAnchorEMRestraint(o):
854 r"""_object_cast_to_GaussianAnchorEMRestraint(Object o) -> GaussianAnchorEMRestraint"""
855 return _IMP_isd._object_cast_to_GaussianAnchorEMRestraint(o)
857 _object_types.append(
"GammaPrior")
860 def _object_cast_to_GammaPrior(o):
861 r"""_object_cast_to_GammaPrior(Object o) -> GammaPrior"""
862 return _IMP_isd._object_cast_to_GammaPrior(o)
864 _object_types.append(
"ResidueProteinProximityRestraint")
867 def _object_cast_to_ResidueProteinProximityRestraint(o):
868 r"""_object_cast_to_ResidueProteinProximityRestraint(Object o) -> ResidueProteinProximityRestraint"""
869 return _IMP_isd._object_cast_to_ResidueProteinProximityRestraint(o)
871 def create_model_and_particles():
876 for i
in range(0,100):
880 d.set_coordinates_are_optimized(
True)
884 r"""Proxy of C++ IMP::isd::ISDRestraint class."""
886 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
888 def __init__(self, m, name):
889 r"""__init__(ISDRestraint self, Model m, std::string name) -> ISDRestraint"""
890 if self.__class__ == ISDRestraint:
894 _IMP_isd.ISDRestraint_swiginit(self, _IMP_isd.new_ISDRestraint(_self, m, name))
896 if self.__class__ != ISDRestraint:
897 _director_objects.register(self)
902 def get_probability(self):
903 r"""get_probability(ISDRestraint self) -> double"""
904 return _IMP_isd.ISDRestraint_get_probability(self)
906 def unprotected_evaluate(self, accum):
907 r"""unprotected_evaluate(ISDRestraint self, DerivativeAccumulator accum) -> double"""
908 return _IMP_isd.ISDRestraint_unprotected_evaluate(self, accum)
911 r"""do_get_inputs(ISDRestraint self) -> IMP::ModelObjectsTemp"""
912 return _IMP_isd.ISDRestraint_do_get_inputs(self)
914 def get_type_name(self):
915 r"""get_type_name(ISDRestraint self) -> std::string"""
916 return _IMP_isd.ISDRestraint_get_type_name(self)
919 r"""get_version_info(ISDRestraint self) -> VersionInfo"""
920 return _IMP_isd.ISDRestraint_get_version_info(self)
921 __swig_destroy__ = _IMP_isd.delete_ISDRestraint
924 r"""__str__(ISDRestraint self) -> std::string"""
925 return _IMP_isd.ISDRestraint___str__(self)
928 r"""__repr__(ISDRestraint self) -> std::string"""
929 return _IMP_isd.ISDRestraint___repr__(self)
933 return _object_cast_to_ISDRestraint(o)
936 def get_type_name(self):
937 return self.__class__.__name__
938 def do_show(self, out):
941 if"IMP::isd" ==
"IMP":
942 return VersionInfo(self.__module__,
949 return _object_cast_to_ISDRestraint(o)
951 def __disown__(self):
953 _IMP_isd.disown_ISDRestraint(self)
954 return weakref.proxy(self)
957 r"""do_destroy(ISDRestraint self)"""
958 return _IMP_isd.ISDRestraint_do_destroy(self)
960 def handle_set_has_required_score_states(self, arg0):
961 r"""handle_set_has_required_score_states(ISDRestraint self, bool arg0)"""
962 return _IMP_isd.ISDRestraint_handle_set_has_required_score_states(self, arg0)
965 r"""do_get_outputs(ISDRestraint self) -> IMP::ModelObjectsTemp"""
966 return _IMP_isd.ISDRestraint_do_get_outputs(self)
968 def do_get_interactions(self):
969 r"""do_get_interactions(ISDRestraint self) -> IMP::ModelObjectsTemps"""
970 return _IMP_isd.ISDRestraint_do_get_interactions(self)
972 def do_create_decomposition(self):
973 r"""do_create_decomposition(ISDRestraint self) -> IMP::Restraints"""
974 return _IMP_isd.ISDRestraint_do_create_decomposition(self)
976 def do_create_current_decomposition(self):
977 r"""do_create_current_decomposition(ISDRestraint self) -> IMP::Restraints"""
978 return _IMP_isd.ISDRestraint_do_create_current_decomposition(self)
980 def do_add_score_and_derivatives(self, sa):
981 r"""do_add_score_and_derivatives(ISDRestraint self, ScoreAccumulator sa)"""
982 return _IMP_isd.ISDRestraint_do_add_score_and_derivatives(self, sa)
984 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
985 r"""do_add_score_and_derivatives_moved(ISDRestraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
986 return _IMP_isd.ISDRestraint_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
989 _IMP_isd.ISDRestraint_swigregister(ISDRestraint)
991 r"""Proxy of C++ IMP::isd::CrossLinkMSRestraint class."""
993 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
995 def __init__(self, *args):
997 __init__(CrossLinkMSRestraint self, Model m, double length, bool get_log_prob=False, std::string name="CrossLinkMSRestraint%1%") -> CrossLinkMSRestraint
998 __init__(CrossLinkMSRestraint self, Model m, _ParticleIndexAdaptor lengthi, bool get_log_prob=False, std::string name="CrossLinkMSRestraint%1%") -> CrossLinkMSRestraint
999 __init__(CrossLinkMSRestraint self, Model m, double length, double slope, bool get_log_prob=False, std::string name="CrossLinkMSRestraint%1%") -> CrossLinkMSRestraint
1000 __init__(CrossLinkMSRestraint self) -> CrossLinkMSRestraint
1002 _IMP_isd.CrossLinkMSRestraint_swiginit(self, _IMP_isd.new_CrossLinkMSRestraint(*args))
1004 def set_source_protein1(self, protein1):
1005 r"""set_source_protein1(CrossLinkMSRestraint self, std::string protein1)"""
1006 return _IMP_isd.CrossLinkMSRestraint_set_source_protein1(self, protein1)
1008 def get_source_protein1(self):
1009 r"""get_source_protein1(CrossLinkMSRestraint self) -> std::string"""
1010 return _IMP_isd.CrossLinkMSRestraint_get_source_protein1(self)
1012 def set_source_protein2(self, protein2):
1013 r"""set_source_protein2(CrossLinkMSRestraint self, std::string protein2)"""
1014 return _IMP_isd.CrossLinkMSRestraint_set_source_protein2(self, protein2)
1016 def get_source_protein2(self):
1017 r"""get_source_protein2(CrossLinkMSRestraint self) -> std::string"""
1018 return _IMP_isd.CrossLinkMSRestraint_get_source_protein2(self)
1020 def set_source_residue1(self, residue1):
1021 r"""set_source_residue1(CrossLinkMSRestraint self, int residue1)"""
1022 return _IMP_isd.CrossLinkMSRestraint_set_source_residue1(self, residue1)
1024 def get_source_residue1(self):
1025 r"""get_source_residue1(CrossLinkMSRestraint self) -> int"""
1026 return _IMP_isd.CrossLinkMSRestraint_get_source_residue1(self)
1028 def set_source_residue2(self, residue2):
1029 r"""set_source_residue2(CrossLinkMSRestraint self, int residue2)"""
1030 return _IMP_isd.CrossLinkMSRestraint_set_source_residue2(self, residue2)
1032 def get_source_residue2(self):
1033 r"""get_source_residue2(CrossLinkMSRestraint self) -> int"""
1034 return _IMP_isd.CrossLinkMSRestraint_get_source_residue2(self)
1036 def add_contribution(self, pps, sigmas, psi):
1037 r"""add_contribution(CrossLinkMSRestraint self, IMP::ParticleIndexPair const & pps, IMP::ParticleIndexPair const & sigmas, ParticleIndex psi)"""
1038 return _IMP_isd.CrossLinkMSRestraint_add_contribution(self, pps, sigmas, psi)
1040 def get_probability(self):
1041 r"""get_probability(CrossLinkMSRestraint self) -> double"""
1042 return _IMP_isd.CrossLinkMSRestraint_get_probability(self)
1044 def get_length(self):
1045 r"""get_length(CrossLinkMSRestraint self) -> double"""
1046 return _IMP_isd.CrossLinkMSRestraint_get_length(self)
1048 def get_is_length_variable(self):
1049 r"""get_is_length_variable(CrossLinkMSRestraint self) -> bool"""
1050 return _IMP_isd.CrossLinkMSRestraint_get_is_length_variable(self)
1052 def get_has_slope(self):
1053 r"""get_has_slope(CrossLinkMSRestraint self) -> bool"""
1054 return _IMP_isd.CrossLinkMSRestraint_get_has_slope(self)
1056 def get_slope(self):
1057 r"""get_slope(CrossLinkMSRestraint self) -> double"""
1058 return _IMP_isd.CrossLinkMSRestraint_get_slope(self)
1060 def get_log_prob(self):
1061 r"""get_log_prob(CrossLinkMSRestraint self) -> bool"""
1062 return _IMP_isd.CrossLinkMSRestraint_get_log_prob(self)
1064 def get_contribution_sigma_indexes(self, i):
1065 r"""get_contribution_sigma_indexes(CrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
1066 return _IMP_isd.CrossLinkMSRestraint_get_contribution_sigma_indexes(self, i)
1068 def get_contribution_psi_index(self, i):
1069 r"""get_contribution_psi_index(CrossLinkMSRestraint self, int i) -> ParticleIndex"""
1070 return _IMP_isd.CrossLinkMSRestraint_get_contribution_psi_index(self, i)
1072 def get_contribution_particle_indexes(self, i):
1073 r"""get_contribution_particle_indexes(CrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
1074 return _IMP_isd.CrossLinkMSRestraint_get_contribution_particle_indexes(self, i)
1076 def get_number_of_contributions(self):
1077 r"""get_number_of_contributions(CrossLinkMSRestraint self) -> unsigned int"""
1078 return _IMP_isd.CrossLinkMSRestraint_get_number_of_contributions(self)
1081 r"""do_get_inputs(CrossLinkMSRestraint self) -> IMP::ModelObjectsTemp"""
1082 return _IMP_isd.CrossLinkMSRestraint_do_get_inputs(self)
1085 r"""get_version_info(CrossLinkMSRestraint self) -> VersionInfo"""
1086 return _IMP_isd.CrossLinkMSRestraint_get_version_info(self)
1087 __swig_destroy__ = _IMP_isd.delete_CrossLinkMSRestraint
1090 r"""__str__(CrossLinkMSRestraint self) -> std::string"""
1091 return _IMP_isd.CrossLinkMSRestraint___str__(self)
1094 r"""__repr__(CrossLinkMSRestraint self) -> std::string"""
1095 return _IMP_isd.CrossLinkMSRestraint___repr__(self)
1099 return _object_cast_to_CrossLinkMSRestraint(o)
1102 def _get_as_binary(self):
1103 r"""_get_as_binary(CrossLinkMSRestraint self) -> PyObject *"""
1104 return _IMP_isd.CrossLinkMSRestraint__get_as_binary(self)
1106 def _set_from_binary(self, p):
1107 r"""_set_from_binary(CrossLinkMSRestraint self, PyObject * p)"""
1108 return _IMP_isd.CrossLinkMSRestraint__set_from_binary(self, p)
1110 def __getstate__(self):
1111 p = self._get_as_binary()
1112 if len(self.__dict__) > 1:
1113 d = self.__dict__.copy()
1118 def __setstate__(self, p):
1119 if not hasattr(self,
'this'):
1121 if isinstance(p, tuple):
1123 self.__dict__.update(d)
1124 return self._set_from_binary(p)
1127 def _get_contributions_sigma_numpy(self):
1129 n = self.get_number_of_contributions()
1130 ret = numpy.empty((n, 2), int)
1132 ret[i] = self.get_contribution_sigma_indexes(i)
1135 def _get_contributions_psi_numpy(self):
1137 n = self.get_number_of_contributions()
1138 ret = numpy.empty(n, int)
1140 ret[i] = self.get_contribution_psi_index(i)
1143 def _get_contributions_particles_numpy(self):
1145 n = self.get_number_of_contributions()
1146 ret = numpy.empty((n, 2), int)
1148 ret[i] = self.get_contribution_particle_indexes(i)
1151 def _get_python_evaluate(self):
1152 from numba
import njit
1157 def sphere_cap(r1, r2, d):
1159 if d <= max(r1, r2) - min(r1, r2):
1160 sc = min(4.0 / 3.0 * math.pi * r1 * r1 * r1,
1161 4.0 / 3.0 * math.pi * r2 * r2 * r2)
1165 sc = ((math.pi / 12 / d * (r1 + r2 - d) * (r1 + r2 - d)) *
1166 (d * d + 2 * d * r1 - 3 * r1 * r1 + 2 * d * r2
1167 + 6 * r1 * r2 - 3 * r2 * r2))
1171 def get_probability(xyz, scale, ps, ncontrib, sigma, psi, length,
1174 for k
in range(ncontrib):
1175 dist = numpy.linalg.norm(xyz[ps[k, 0]] - xyz[ps[k, 1]])
1178 psik = scale[psi[k]]
1179 sigmai = scale[sigma[k, 0]]
1180 sigmaj = scale[sigma[k, 1]]
1182 voli = 4.0 / 3.0 * math.pi * sigmai * sigmai * sigmai
1183 volj = 4.0 / 3.0 * math.pi * sigmaj * sigmaj * sigmaj
1185 if dist < sigmai + sigmaj:
1186 xlvol = (4.0 / 3.0 * math.pi * (length / 2.)
1187 * (length / 2.) * (length / 2))
1188 fi = min(voli, xlvol)
1189 fj = min(volj, xlvol)
1191 di = dist - sigmaj - length / 2.
1192 dj = dist - sigmai - length / 2.
1193 fi = sphere_cap(sigmai, length / 2., abs(di))
1194 fj = sphere_cap(sigmaj, length / 2., abs(dj))
1196 pofr = fi * fj / voli / volj
1197 if slope
is not None:
1198 prior = math.exp(slope * dist)
1199 onemprob = onemprob * (1.0 - (psik * (1.0 - pofr)
1200 + pofr * (1 - psik)) * prior)
1202 onemprob = onemprob * (1.0 - (psik * (1.0 - pofr)
1203 + pofr * (1 - psik)))
1204 return 1.0 - onemprob
1206 if self.get_is_length_variable():
1207 raise NotImplementedError(
"Only implemented for fixed-length")
1208 m = self.get_model()
1209 xyz, radius = m.get_spheres_numpy()
1211 sigma = self._get_contributions_sigma_numpy()
1212 psi = self._get_contributions_psi_numpy()
1213 pis = self._get_contributions_particles_numpy()
1214 get_log_prob = self.get_log_prob()
1215 length = self.get_length()
1216 ncontrib = len(sigma)
1217 slope = self.get_slope()
if self.get_has_slope()
else None
1221 prob = get_probability(xyz, scale, pis, ncontrib, sigma, psi,
1224 return -math.log(prob)
1232 _IMP_isd.CrossLinkMSRestraint_swigregister(CrossLinkMSRestraint)
1234 r"""Proxy of C++ IMP::isd::LogWrapper class."""
1236 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1238 def __init__(self, *args):
1240 __init__(LogWrapper self, Model m, double weight, std::string const & name="LogWrapper %1%") -> LogWrapper
1241 __init__(LogWrapper self, Model m, std::string const & name="LogWrapper %1%") -> LogWrapper
1242 __init__(LogWrapper self, IMP::RestraintsTemp const & rs, double weight, std::string const & name="LogWrapper %1%") -> LogWrapper
1243 __init__(LogWrapper self) -> LogWrapper
1245 _IMP_isd.LogWrapper_swiginit(self, _IMP_isd.new_LogWrapper(*args))
1247 def do_add_score_and_derivatives(self, sa):
1248 r"""do_add_score_and_derivatives(LogWrapper self, ScoreAccumulator sa)"""
1249 return _IMP_isd.LogWrapper_do_add_score_and_derivatives(self, sa)
1251 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
1252 r"""do_add_score_and_derivatives_moved(LogWrapper self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
1253 return _IMP_isd.LogWrapper_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
1254 __swig_destroy__ = _IMP_isd.delete_LogWrapper
1257 r"""__str__(LogWrapper self) -> std::string"""
1258 return _IMP_isd.LogWrapper___str__(self)
1261 r"""__repr__(LogWrapper self) -> std::string"""
1262 return _IMP_isd.LogWrapper___repr__(self)
1266 return _object_cast_to_LogWrapper(o)
1269 def _get_as_binary(self):
1270 r"""_get_as_binary(LogWrapper self) -> PyObject *"""
1271 return _IMP_isd.LogWrapper__get_as_binary(self)
1273 def _set_from_binary(self, p):
1274 r"""_set_from_binary(LogWrapper self, PyObject * p)"""
1275 return _IMP_isd.LogWrapper__set_from_binary(self, p)
1277 def __getstate__(self):
1278 p = self._get_as_binary()
1279 if len(self.__dict__) > 1:
1280 d = self.__dict__.copy()
1285 def __setstate__(self, p):
1286 if not hasattr(self,
'this'):
1288 if isinstance(p, tuple):
1290 self.__dict__.update(d)
1291 return self._set_from_binary(p)
1295 _IMP_isd.LogWrapper_swigregister(LogWrapper)
1297 r"""Proxy of C++ IMP::isd::UniformPrior class."""
1299 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1301 def __init__(self, *args):
1303 __init__(UniformPrior self, Model m, Particle p, double k, double upperb, double lowerb, std::string name="UniformPrior%1%") -> UniformPrior
1304 __init__(UniformPrior self) -> UniformPrior
1306 _IMP_isd.UniformPrior_swiginit(self, _IMP_isd.new_UniformPrior(*args))
1309 r"""do_get_inputs(UniformPrior self) -> IMP::ModelObjectsTemp"""
1310 return _IMP_isd.UniformPrior_do_get_inputs(self)
1313 r"""get_version_info(UniformPrior self) -> VersionInfo"""
1314 return _IMP_isd.UniformPrior_get_version_info(self)
1315 __swig_destroy__ = _IMP_isd.delete_UniformPrior
1317 def get_probability(self):
1318 r"""get_probability(UniformPrior self) -> double"""
1319 return _IMP_isd.UniformPrior_get_probability(self)
1322 r"""__str__(UniformPrior self) -> std::string"""
1323 return _IMP_isd.UniformPrior___str__(self)
1326 r"""__repr__(UniformPrior self) -> std::string"""
1327 return _IMP_isd.UniformPrior___repr__(self)
1331 return _object_cast_to_UniformPrior(o)
1334 def _get_as_binary(self):
1335 r"""_get_as_binary(UniformPrior self) -> PyObject *"""
1336 return _IMP_isd.UniformPrior__get_as_binary(self)
1338 def _set_from_binary(self, p):
1339 r"""_set_from_binary(UniformPrior self, PyObject * p)"""
1340 return _IMP_isd.UniformPrior__set_from_binary(self, p)
1342 def __getstate__(self):
1343 p = self._get_as_binary()
1344 if len(self.__dict__) > 1:
1345 d = self.__dict__.copy()
1350 def __setstate__(self, p):
1351 if not hasattr(self,
'this'):
1353 if isinstance(p, tuple):
1355 self.__dict__.update(d)
1356 return self._set_from_binary(p)
1360 _IMP_isd.UniformPrior_swigregister(UniformPrior)
1362 r"""Proxy of C++ IMP::isd::Nuisance class."""
1364 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1366 def __init__(self, *args):
1368 __init__(Nuisance self) -> Nuisance
1369 __init__(Nuisance self, Model m, ParticleIndex id) -> Nuisance
1370 __init__(Nuisance self, _ParticleAdaptor d) -> Nuisance
1372 _IMP_isd.Nuisance_swiginit(self, _IMP_isd.new_Nuisance(*args))
1374 def show(self, *args):
1375 r"""show(Nuisance self, _ostream out=std::cout)"""
1376 return _IMP_isd.Nuisance_show(self, *args)
1379 def setup_particle(*args):
1381 setup_particle(Model m, ParticleIndex pi) -> Nuisance
1382 setup_particle(_ParticleAdaptor pa) -> Nuisance
1383 setup_particle(Model m, ParticleIndex pi, double nuisance) -> Nuisance
1384 setup_particle(_ParticleAdaptor pa, double nuisance) -> Nuisance
1386 return _IMP_isd.Nuisance_setup_particle(*args)
1389 def get_is_setup(*args):
1391 get_is_setup(_ParticleAdaptor p) -> bool
1392 get_is_setup(Model m, ParticleIndex pi) -> bool
1394 return _IMP_isd.Nuisance_get_is_setup(*args)
1397 def get_nuisance_key():
1398 r"""get_nuisance_key() -> FloatKey"""
1399 return _IMP_isd.Nuisance_get_nuisance_key()
1401 def get_nuisance(self):
1402 r"""get_nuisance(Nuisance self) -> IMP::Float"""
1403 return _IMP_isd.Nuisance_get_nuisance(self)
1405 def set_nuisance(self, d):
1406 r"""set_nuisance(Nuisance self, IMP::Float d)"""
1407 return _IMP_isd.Nuisance_set_nuisance(self, d)
1409 def get_has_lower(self):
1410 r"""get_has_lower(Nuisance self) -> bool"""
1411 return _IMP_isd.Nuisance_get_has_lower(self)
1413 def get_lower(self):
1414 r"""get_lower(Nuisance self) -> IMP::Float"""
1415 return _IMP_isd.Nuisance_get_lower(self)
1418 def get_lower_key():
1419 r"""get_lower_key() -> FloatKey"""
1420 return _IMP_isd.Nuisance_get_lower_key()
1423 def get_lower_particle_key():
1424 r"""get_lower_particle_key() -> ParticleIndexKey"""
1425 return _IMP_isd.Nuisance_get_lower_particle_key()
1427 def set_lower(self, *args):
1429 set_lower(Nuisance self, IMP::Float d)
1430 set_lower(Nuisance self, Particle d)
1432 return _IMP_isd.Nuisance_set_lower(self, *args)
1434 def remove_lower(self):
1435 r"""remove_lower(Nuisance self)"""
1436 return _IMP_isd.Nuisance_remove_lower(self)
1438 def get_has_upper(self):
1439 r"""get_has_upper(Nuisance self) -> bool"""
1440 return _IMP_isd.Nuisance_get_has_upper(self)
1442 def get_upper(self):
1443 r"""get_upper(Nuisance self) -> IMP::Float"""
1444 return _IMP_isd.Nuisance_get_upper(self)
1447 def get_upper_key():
1448 r"""get_upper_key() -> FloatKey"""
1449 return _IMP_isd.Nuisance_get_upper_key()
1452 def get_upper_particle_key():
1453 r"""get_upper_particle_key() -> ParticleIndexKey"""
1454 return _IMP_isd.Nuisance_get_upper_particle_key()
1456 def set_upper(self, *args):
1458 set_upper(Nuisance self, IMP::Float d)
1459 set_upper(Nuisance self, Particle d)
1461 return _IMP_isd.Nuisance_set_upper(self, *args)
1463 def remove_upper(self):
1464 r"""remove_upper(Nuisance self)"""
1465 return _IMP_isd.Nuisance_remove_upper(self)
1467 def get_nuisance_derivative(self):
1468 r"""get_nuisance_derivative(Nuisance self) -> IMP::Float"""
1469 return _IMP_isd.Nuisance_get_nuisance_derivative(self)
1471 def add_to_nuisance_derivative(self, d, accum):
1472 r"""add_to_nuisance_derivative(Nuisance self, IMP::Float d, DerivativeAccumulator accum)"""
1473 return _IMP_isd.Nuisance_add_to_nuisance_derivative(self, d, accum)
1475 def get_nuisance_is_optimized(self):
1476 r"""get_nuisance_is_optimized(Nuisance self) -> bool"""
1477 return _IMP_isd.Nuisance_get_nuisance_is_optimized(self)
1479 def set_nuisance_is_optimized(self, val):
1480 r"""set_nuisance_is_optimized(Nuisance self, bool val)"""
1481 return _IMP_isd.Nuisance_set_nuisance_is_optimized(self, val)
1483 def add_attribute(self, *args):
1485 add_attribute(Nuisance self, FloatKey k, IMP::Float v, bool opt)
1486 add_attribute(Nuisance self, FloatKey a0, IMP::Float a1)
1487 add_attribute(Nuisance self, IntKey a0, IMP::Int a1)
1488 add_attribute(Nuisance self, FloatsKey a0, IMP::Floats a1)
1489 add_attribute(Nuisance self, IntsKey a0, IMP::Ints a1)
1490 add_attribute(Nuisance self, StringKey a0, IMP::String a1)
1491 add_attribute(Nuisance self, ParticleIndexKey a0, Particle a1)
1492 add_attribute(Nuisance self, ObjectKey a0, Object a1)
1494 return _IMP_isd.Nuisance_add_attribute(self, *args)
1496 def get_value(self, *args):
1498 get_value(Nuisance self, FloatKey a0) -> IMP::Float
1499 get_value(Nuisance self, IntKey a0) -> IMP::Int
1500 get_value(Nuisance self, FloatsKey a0) -> IMP::Floats
1501 get_value(Nuisance self, IntsKey a0) -> IMP::Ints
1502 get_value(Nuisance self, StringKey a0) -> IMP::String
1503 get_value(Nuisance self, ParticleIndexKey a0) -> Particle
1504 get_value(Nuisance self, ObjectKey a0) -> Object
1506 return _IMP_isd.Nuisance_get_value(self, *args)
1508 def set_value(self, *args):
1510 set_value(Nuisance self, FloatKey a0, IMP::Float a1)
1511 set_value(Nuisance self, IntKey a0, IMP::Int a1)
1512 set_value(Nuisance self, FloatsKey a0, IMP::Floats a1)
1513 set_value(Nuisance self, IntsKey a0, IMP::Ints a1)
1514 set_value(Nuisance self, StringKey a0, IMP::String a1)
1515 set_value(Nuisance self, ParticleIndexKey a0, Particle a1)
1516 set_value(Nuisance self, ObjectKey a0, Object a1)
1518 return _IMP_isd.Nuisance_set_value(self, *args)
1520 def remove_attribute(self, *args):
1522 remove_attribute(Nuisance self, FloatKey a0)
1523 remove_attribute(Nuisance self, IntKey a0)
1524 remove_attribute(Nuisance self, FloatsKey a0)
1525 remove_attribute(Nuisance self, IntsKey a0)
1526 remove_attribute(Nuisance self, StringKey a0)
1527 remove_attribute(Nuisance self, ParticleIndexKey a0)
1528 remove_attribute(Nuisance self, ObjectKey a0)
1530 return _IMP_isd.Nuisance_remove_attribute(self, *args)
1532 def has_attribute(self, *args):
1534 has_attribute(Nuisance self, FloatKey a0) -> bool
1535 has_attribute(Nuisance self, IntKey a0) -> bool
1536 has_attribute(Nuisance self, FloatsKey a0) -> bool
1537 has_attribute(Nuisance self, IntsKey a0) -> bool
1538 has_attribute(Nuisance self, StringKey a0) -> bool
1539 has_attribute(Nuisance self, ParticleIndexKey a0) -> bool
1540 has_attribute(Nuisance self, ObjectKey a0) -> bool
1542 return _IMP_isd.Nuisance_has_attribute(self, *args)
1544 def get_derivative(self, a0):
1545 r"""get_derivative(Nuisance self, FloatKey a0) -> double"""
1546 return _IMP_isd.Nuisance_get_derivative(self, a0)
1549 r"""get_name(Nuisance self) -> std::string"""
1550 return _IMP_isd.Nuisance_get_name(self)
1553 r"""clear_caches(Nuisance self)"""
1554 return _IMP_isd.Nuisance_clear_caches(self)
1556 def set_name(self, a0):
1557 r"""set_name(Nuisance self, std::string a0)"""
1558 return _IMP_isd.Nuisance_set_name(self, a0)
1561 r"""set_check_level(Nuisance self, IMP::CheckLevel a0)"""
1562 return _IMP_isd.Nuisance_set_check_level(self, a0)
1564 def add_to_derivative(self, a0, a1, a2):
1565 r"""add_to_derivative(Nuisance self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1566 return _IMP_isd.Nuisance_add_to_derivative(self, a0, a1, a2)
1568 def set_is_optimized(self, a0, a1):
1569 r"""set_is_optimized(Nuisance self, FloatKey a0, bool a1)"""
1570 return _IMP_isd.Nuisance_set_is_optimized(self, a0, a1)
1572 def get_is_optimized(self, a0):
1573 r"""get_is_optimized(Nuisance self, FloatKey a0) -> bool"""
1574 return _IMP_isd.Nuisance_get_is_optimized(self, a0)
1576 def get_check_level(self):
1577 r"""get_check_level(Nuisance self) -> IMP::CheckLevel"""
1578 return _IMP_isd.Nuisance_get_check_level(self)
1580 def __eq__(self, *args):
1582 __eq__(Nuisance self, Nuisance o) -> bool
1583 __eq__(Nuisance self, Particle d) -> bool
1585 return _IMP_isd.Nuisance___eq__(self, *args)
1587 def __ne__(self, *args):
1589 __ne__(Nuisance self, Nuisance o) -> bool
1590 __ne__(Nuisance self, Particle d) -> bool
1592 return _IMP_isd.Nuisance___ne__(self, *args)
1594 def __le__(self, *args):
1596 __le__(Nuisance self, Nuisance o) -> bool
1597 __le__(Nuisance self, Particle d) -> bool
1599 return _IMP_isd.Nuisance___le__(self, *args)
1601 def __lt__(self, *args):
1603 __lt__(Nuisance self, Nuisance o) -> bool
1604 __lt__(Nuisance self, Particle d) -> bool
1606 return _IMP_isd.Nuisance___lt__(self, *args)
1608 def __ge__(self, *args):
1610 __ge__(Nuisance self, Nuisance o) -> bool
1611 __ge__(Nuisance self, Particle d) -> bool
1613 return _IMP_isd.Nuisance___ge__(self, *args)
1615 def __gt__(self, *args):
1617 __gt__(Nuisance self, Nuisance o) -> bool
1618 __gt__(Nuisance self, Particle d) -> bool
1620 return _IMP_isd.Nuisance___gt__(self, *args)
1623 r"""__hash__(Nuisance self) -> std::size_t"""
1624 return _IMP_isd.Nuisance___hash__(self)
1627 r"""__str__(Nuisance self) -> std::string"""
1628 return _IMP_isd.Nuisance___str__(self)
1631 r"""__repr__(Nuisance self) -> std::string"""
1632 return _IMP_isd.Nuisance___repr__(self)
1634 def _get_as_binary(self):
1635 r"""_get_as_binary(Nuisance self) -> PyObject *"""
1636 return _IMP_isd.Nuisance__get_as_binary(self)
1638 def _set_from_binary(self, p):
1639 r"""_set_from_binary(Nuisance self, PyObject * p)"""
1640 return _IMP_isd.Nuisance__set_from_binary(self, p)
1642 def __getstate__(self):
1643 p = self._get_as_binary()
1644 if len(self.__dict__) > 1:
1645 d = self.__dict__.copy()
1650 def __setstate__(self, p):
1651 if not hasattr(self,
'this'):
1653 if isinstance(p, tuple):
1655 self.__dict__.update(d)
1656 return self._set_from_binary(p)
1658 __swig_destroy__ = _IMP_isd.delete_Nuisance
1661 _IMP_isd.Nuisance_swigregister(Nuisance)
1662 class Scale(Nuisance):
1663 r"""Proxy of C++ IMP::isd::Scale class."""
1665 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1667 def __init__(self, *args):
1669 __init__(Scale self) -> Scale
1670 __init__(Scale self, Model m, ParticleIndex id) -> Scale
1671 __init__(Scale self, _ParticleAdaptor d) -> Scale
1673 _IMP_isd.Scale_swiginit(self, _IMP_isd.new_Scale(*args))
1675 def show(self, *args):
1676 r"""show(Scale self, _ostream out=std::cout)"""
1677 return _IMP_isd.Scale_show(self, *args)
1680 def setup_particle(*args):
1682 setup_particle(Model m, ParticleIndex pi) -> Scale
1683 setup_particle(_ParticleAdaptor pa) -> Scale
1684 setup_particle(Model m, ParticleIndex pi, double scale) -> Scale
1685 setup_particle(_ParticleAdaptor pa, double scale) -> Scale
1687 return _IMP_isd.Scale_setup_particle(*args)
1690 def get_is_setup(*args):
1692 get_is_setup(_ParticleAdaptor p) -> bool
1693 get_is_setup(Model m, ParticleIndex pi) -> bool
1695 return _IMP_isd.Scale_get_is_setup(*args)
1697 def get_scale(self):
1698 r"""get_scale(Scale self) -> IMP::Float"""
1699 return _IMP_isd.Scale_get_scale(self)
1701 def set_scale(self, d):
1702 r"""set_scale(Scale self, IMP::Float d)"""
1703 return _IMP_isd.Scale_set_scale(self, d)
1705 def add_to_scale_derivative(self, d, accum):
1706 r"""add_to_scale_derivative(Scale self, IMP::Float d, DerivativeAccumulator accum)"""
1707 return _IMP_isd.Scale_add_to_scale_derivative(self, d, accum)
1709 def get_scale_derivative(self):
1710 r"""get_scale_derivative(Scale self) -> IMP::Float"""
1711 return _IMP_isd.Scale_get_scale_derivative(self)
1714 def get_scale_key():
1715 r"""get_scale_key() -> FloatKey"""
1716 return _IMP_isd.Scale_get_scale_key()
1718 def get_scale_is_optimized(self):
1719 r"""get_scale_is_optimized(Scale self) -> bool"""
1720 return _IMP_isd.Scale_get_scale_is_optimized(self)
1722 def set_scale_is_optimized(self, val):
1723 r"""set_scale_is_optimized(Scale self, bool val)"""
1724 return _IMP_isd.Scale_set_scale_is_optimized(self, val)
1726 def add_attribute(self, *args):
1728 add_attribute(Scale self, FloatKey k, IMP::Float v, bool opt)
1729 add_attribute(Scale self, FloatKey a0, IMP::Float a1)
1730 add_attribute(Scale self, IntKey a0, IMP::Int a1)
1731 add_attribute(Scale self, FloatsKey a0, IMP::Floats a1)
1732 add_attribute(Scale self, IntsKey a0, IMP::Ints a1)
1733 add_attribute(Scale self, StringKey a0, IMP::String a1)
1734 add_attribute(Scale self, ParticleIndexKey a0, Particle a1)
1735 add_attribute(Scale self, ObjectKey a0, Object a1)
1737 return _IMP_isd.Scale_add_attribute(self, *args)
1739 def get_value(self, *args):
1741 get_value(Scale self, FloatKey a0) -> IMP::Float
1742 get_value(Scale self, IntKey a0) -> IMP::Int
1743 get_value(Scale self, FloatsKey a0) -> IMP::Floats
1744 get_value(Scale self, IntsKey a0) -> IMP::Ints
1745 get_value(Scale self, StringKey a0) -> IMP::String
1746 get_value(Scale self, ParticleIndexKey a0) -> Particle
1747 get_value(Scale self, ObjectKey a0) -> Object
1749 return _IMP_isd.Scale_get_value(self, *args)
1751 def set_value(self, *args):
1753 set_value(Scale self, FloatKey a0, IMP::Float a1)
1754 set_value(Scale self, IntKey a0, IMP::Int a1)
1755 set_value(Scale self, FloatsKey a0, IMP::Floats a1)
1756 set_value(Scale self, IntsKey a0, IMP::Ints a1)
1757 set_value(Scale self, StringKey a0, IMP::String a1)
1758 set_value(Scale self, ParticleIndexKey a0, Particle a1)
1759 set_value(Scale self, ObjectKey a0, Object a1)
1761 return _IMP_isd.Scale_set_value(self, *args)
1763 def remove_attribute(self, *args):
1765 remove_attribute(Scale self, FloatKey a0)
1766 remove_attribute(Scale self, IntKey a0)
1767 remove_attribute(Scale self, FloatsKey a0)
1768 remove_attribute(Scale self, IntsKey a0)
1769 remove_attribute(Scale self, StringKey a0)
1770 remove_attribute(Scale self, ParticleIndexKey a0)
1771 remove_attribute(Scale self, ObjectKey a0)
1773 return _IMP_isd.Scale_remove_attribute(self, *args)
1775 def has_attribute(self, *args):
1777 has_attribute(Scale self, FloatKey a0) -> bool
1778 has_attribute(Scale self, IntKey a0) -> bool
1779 has_attribute(Scale self, FloatsKey a0) -> bool
1780 has_attribute(Scale self, IntsKey a0) -> bool
1781 has_attribute(Scale self, StringKey a0) -> bool
1782 has_attribute(Scale self, ParticleIndexKey a0) -> bool
1783 has_attribute(Scale self, ObjectKey a0) -> bool
1785 return _IMP_isd.Scale_has_attribute(self, *args)
1787 def get_derivative(self, a0):
1788 r"""get_derivative(Scale self, FloatKey a0) -> double"""
1789 return _IMP_isd.Scale_get_derivative(self, a0)
1792 r"""get_name(Scale self) -> std::string"""
1793 return _IMP_isd.Scale_get_name(self)
1796 r"""clear_caches(Scale self)"""
1797 return _IMP_isd.Scale_clear_caches(self)
1799 def set_name(self, a0):
1800 r"""set_name(Scale self, std::string a0)"""
1801 return _IMP_isd.Scale_set_name(self, a0)
1804 r"""set_check_level(Scale self, IMP::CheckLevel a0)"""
1805 return _IMP_isd.Scale_set_check_level(self, a0)
1807 def add_to_derivative(self, a0, a1, a2):
1808 r"""add_to_derivative(Scale self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1809 return _IMP_isd.Scale_add_to_derivative(self, a0, a1, a2)
1811 def set_is_optimized(self, a0, a1):
1812 r"""set_is_optimized(Scale self, FloatKey a0, bool a1)"""
1813 return _IMP_isd.Scale_set_is_optimized(self, a0, a1)
1815 def get_is_optimized(self, a0):
1816 r"""get_is_optimized(Scale self, FloatKey a0) -> bool"""
1817 return _IMP_isd.Scale_get_is_optimized(self, a0)
1819 def get_check_level(self):
1820 r"""get_check_level(Scale self) -> IMP::CheckLevel"""
1821 return _IMP_isd.Scale_get_check_level(self)
1823 def __eq__(self, *args):
1825 __eq__(Scale self, Scale o) -> bool
1826 __eq__(Scale self, Particle d) -> bool
1828 return _IMP_isd.Scale___eq__(self, *args)
1830 def __ne__(self, *args):
1832 __ne__(Scale self, Scale o) -> bool
1833 __ne__(Scale self, Particle d) -> bool
1835 return _IMP_isd.Scale___ne__(self, *args)
1837 def __le__(self, *args):
1839 __le__(Scale self, Scale o) -> bool
1840 __le__(Scale self, Particle d) -> bool
1842 return _IMP_isd.Scale___le__(self, *args)
1844 def __lt__(self, *args):
1846 __lt__(Scale self, Scale o) -> bool
1847 __lt__(Scale self, Particle d) -> bool
1849 return _IMP_isd.Scale___lt__(self, *args)
1851 def __ge__(self, *args):
1853 __ge__(Scale self, Scale o) -> bool
1854 __ge__(Scale self, Particle d) -> bool
1856 return _IMP_isd.Scale___ge__(self, *args)
1858 def __gt__(self, *args):
1860 __gt__(Scale self, Scale o) -> bool
1861 __gt__(Scale self, Particle d) -> bool
1863 return _IMP_isd.Scale___gt__(self, *args)
1866 r"""__hash__(Scale self) -> std::size_t"""
1867 return _IMP_isd.Scale___hash__(self)
1870 r"""__str__(Scale self) -> std::string"""
1871 return _IMP_isd.Scale___str__(self)
1874 r"""__repr__(Scale self) -> std::string"""
1875 return _IMP_isd.Scale___repr__(self)
1877 def _get_as_binary(self):
1878 r"""_get_as_binary(Scale self) -> PyObject *"""
1879 return _IMP_isd.Scale__get_as_binary(self)
1881 def _set_from_binary(self, p):
1882 r"""_set_from_binary(Scale self, PyObject * p)"""
1883 return _IMP_isd.Scale__set_from_binary(self, p)
1885 def __getstate__(self):
1886 p = self._get_as_binary()
1887 if len(self.__dict__) > 1:
1888 d = self.__dict__.copy()
1893 def __setstate__(self, p):
1894 if not hasattr(self,
'this'):
1896 if isinstance(p, tuple):
1898 self.__dict__.update(d)
1899 return self._set_from_binary(p)
1901 __swig_destroy__ = _IMP_isd.delete_Scale
1904 _IMP_isd.Scale_swigregister(Scale)
1905 class Switching(Nuisance):
1906 r"""Proxy of C++ IMP::isd::Switching class."""
1908 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1910 def __init__(self, *args):
1912 __init__(Switching self) -> Switching
1913 __init__(Switching self, Model m, ParticleIndex id) -> Switching
1914 __init__(Switching self, _ParticleAdaptor d) -> Switching
1916 _IMP_isd.Switching_swiginit(self, _IMP_isd.new_Switching(*args))
1918 def show(self, *args):
1919 r"""show(Switching self, _ostream out=std::cout)"""
1920 return _IMP_isd.Switching_show(self, *args)
1923 def setup_particle(*args):
1925 setup_particle(Model m, ParticleIndex pi) -> Switching
1926 setup_particle(_ParticleAdaptor pa) -> Switching
1927 setup_particle(Model m, ParticleIndex pi, double switching) -> Switching
1928 setup_particle(_ParticleAdaptor pa, double switching) -> Switching
1930 return _IMP_isd.Switching_setup_particle(*args)
1933 def get_is_setup(*args):
1935 get_is_setup(_ParticleAdaptor p) -> bool
1936 get_is_setup(Model m, ParticleIndex pi) -> bool
1938 return _IMP_isd.Switching_get_is_setup(*args)
1940 def get_switching(self):
1941 r"""get_switching(Switching self) -> IMP::Float"""
1942 return _IMP_isd.Switching_get_switching(self)
1944 def set_switching(self, d):
1945 r"""set_switching(Switching self, IMP::Float d)"""
1946 return _IMP_isd.Switching_set_switching(self, d)
1948 def add_to_switching_derivative(self, d, accum):
1949 r"""add_to_switching_derivative(Switching self, IMP::Float d, DerivativeAccumulator accum)"""
1950 return _IMP_isd.Switching_add_to_switching_derivative(self, d, accum)
1952 def get_switching_derivative(self):
1953 r"""get_switching_derivative(Switching self) -> IMP::Float"""
1954 return _IMP_isd.Switching_get_switching_derivative(self)
1957 def get_switching_key():
1958 r"""get_switching_key() -> FloatKey"""
1959 return _IMP_isd.Switching_get_switching_key()
1961 def get_switching_is_optimized(self):
1962 r"""get_switching_is_optimized(Switching self) -> bool"""
1963 return _IMP_isd.Switching_get_switching_is_optimized(self)
1965 def set_switching_is_optimized(self, val):
1966 r"""set_switching_is_optimized(Switching self, bool val)"""
1967 return _IMP_isd.Switching_set_switching_is_optimized(self, val)
1969 def add_attribute(self, *args):
1971 add_attribute(Switching self, FloatKey k, IMP::Float v, bool opt)
1972 add_attribute(Switching self, FloatKey a0, IMP::Float a1)
1973 add_attribute(Switching self, IntKey a0, IMP::Int a1)
1974 add_attribute(Switching self, FloatsKey a0, IMP::Floats a1)
1975 add_attribute(Switching self, IntsKey a0, IMP::Ints a1)
1976 add_attribute(Switching self, StringKey a0, IMP::String a1)
1977 add_attribute(Switching self, ParticleIndexKey a0, Particle a1)
1978 add_attribute(Switching self, ObjectKey a0, Object a1)
1980 return _IMP_isd.Switching_add_attribute(self, *args)
1982 def get_value(self, *args):
1984 get_value(Switching self, FloatKey a0) -> IMP::Float
1985 get_value(Switching self, IntKey a0) -> IMP::Int
1986 get_value(Switching self, FloatsKey a0) -> IMP::Floats
1987 get_value(Switching self, IntsKey a0) -> IMP::Ints
1988 get_value(Switching self, StringKey a0) -> IMP::String
1989 get_value(Switching self, ParticleIndexKey a0) -> Particle
1990 get_value(Switching self, ObjectKey a0) -> Object
1992 return _IMP_isd.Switching_get_value(self, *args)
1994 def set_value(self, *args):
1996 set_value(Switching self, FloatKey a0, IMP::Float a1)
1997 set_value(Switching self, IntKey a0, IMP::Int a1)
1998 set_value(Switching self, FloatsKey a0, IMP::Floats a1)
1999 set_value(Switching self, IntsKey a0, IMP::Ints a1)
2000 set_value(Switching self, StringKey a0, IMP::String a1)
2001 set_value(Switching self, ParticleIndexKey a0, Particle a1)
2002 set_value(Switching self, ObjectKey a0, Object a1)
2004 return _IMP_isd.Switching_set_value(self, *args)
2006 def remove_attribute(self, *args):
2008 remove_attribute(Switching self, FloatKey a0)
2009 remove_attribute(Switching self, IntKey a0)
2010 remove_attribute(Switching self, FloatsKey a0)
2011 remove_attribute(Switching self, IntsKey a0)
2012 remove_attribute(Switching self, StringKey a0)
2013 remove_attribute(Switching self, ParticleIndexKey a0)
2014 remove_attribute(Switching self, ObjectKey a0)
2016 return _IMP_isd.Switching_remove_attribute(self, *args)
2018 def has_attribute(self, *args):
2020 has_attribute(Switching self, FloatKey a0) -> bool
2021 has_attribute(Switching self, IntKey a0) -> bool
2022 has_attribute(Switching self, FloatsKey a0) -> bool
2023 has_attribute(Switching self, IntsKey a0) -> bool
2024 has_attribute(Switching self, StringKey a0) -> bool
2025 has_attribute(Switching self, ParticleIndexKey a0) -> bool
2026 has_attribute(Switching self, ObjectKey a0) -> bool
2028 return _IMP_isd.Switching_has_attribute(self, *args)
2030 def get_derivative(self, a0):
2031 r"""get_derivative(Switching self, FloatKey a0) -> double"""
2032 return _IMP_isd.Switching_get_derivative(self, a0)
2035 r"""get_name(Switching self) -> std::string"""
2036 return _IMP_isd.Switching_get_name(self)
2039 r"""clear_caches(Switching self)"""
2040 return _IMP_isd.Switching_clear_caches(self)
2042 def set_name(self, a0):
2043 r"""set_name(Switching self, std::string a0)"""
2044 return _IMP_isd.Switching_set_name(self, a0)
2047 r"""set_check_level(Switching self, IMP::CheckLevel a0)"""
2048 return _IMP_isd.Switching_set_check_level(self, a0)
2050 def add_to_derivative(self, a0, a1, a2):
2051 r"""add_to_derivative(Switching self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2052 return _IMP_isd.Switching_add_to_derivative(self, a0, a1, a2)
2054 def set_is_optimized(self, a0, a1):
2055 r"""set_is_optimized(Switching self, FloatKey a0, bool a1)"""
2056 return _IMP_isd.Switching_set_is_optimized(self, a0, a1)
2058 def get_is_optimized(self, a0):
2059 r"""get_is_optimized(Switching self, FloatKey a0) -> bool"""
2060 return _IMP_isd.Switching_get_is_optimized(self, a0)
2062 def get_check_level(self):
2063 r"""get_check_level(Switching self) -> IMP::CheckLevel"""
2064 return _IMP_isd.Switching_get_check_level(self)
2066 def __eq__(self, *args):
2068 __eq__(Switching self, Switching o) -> bool
2069 __eq__(Switching self, Particle d) -> bool
2071 return _IMP_isd.Switching___eq__(self, *args)
2073 def __ne__(self, *args):
2075 __ne__(Switching self, Switching o) -> bool
2076 __ne__(Switching self, Particle d) -> bool
2078 return _IMP_isd.Switching___ne__(self, *args)
2080 def __le__(self, *args):
2082 __le__(Switching self, Switching o) -> bool
2083 __le__(Switching self, Particle d) -> bool
2085 return _IMP_isd.Switching___le__(self, *args)
2087 def __lt__(self, *args):
2089 __lt__(Switching self, Switching o) -> bool
2090 __lt__(Switching self, Particle d) -> bool
2092 return _IMP_isd.Switching___lt__(self, *args)
2094 def __ge__(self, *args):
2096 __ge__(Switching self, Switching o) -> bool
2097 __ge__(Switching self, Particle d) -> bool
2099 return _IMP_isd.Switching___ge__(self, *args)
2101 def __gt__(self, *args):
2103 __gt__(Switching self, Switching o) -> bool
2104 __gt__(Switching self, Particle d) -> bool
2106 return _IMP_isd.Switching___gt__(self, *args)
2109 r"""__hash__(Switching self) -> std::size_t"""
2110 return _IMP_isd.Switching___hash__(self)
2113 r"""__str__(Switching self) -> std::string"""
2114 return _IMP_isd.Switching___str__(self)
2117 r"""__repr__(Switching self) -> std::string"""
2118 return _IMP_isd.Switching___repr__(self)
2120 def _get_as_binary(self):
2121 r"""_get_as_binary(Switching self) -> PyObject *"""
2122 return _IMP_isd.Switching__get_as_binary(self)
2124 def _set_from_binary(self, p):
2125 r"""_set_from_binary(Switching self, PyObject * p)"""
2126 return _IMP_isd.Switching__set_from_binary(self, p)
2128 def __getstate__(self):
2129 p = self._get_as_binary()
2130 if len(self.__dict__) > 1:
2131 d = self.__dict__.copy()
2136 def __setstate__(self, p):
2137 if not hasattr(self,
'this'):
2139 if isinstance(p, tuple):
2141 self.__dict__.update(d)
2142 return self._set_from_binary(p)
2144 __swig_destroy__ = _IMP_isd.delete_Switching
2147 _IMP_isd.Switching_swigregister(Switching)
2149 r"""Proxy of C++ IMP::isd::Weight class."""
2151 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2153 def __init__(self, *args):
2155 __init__(Weight self) -> Weight
2156 __init__(Weight self, Model m, ParticleIndex id) -> Weight
2157 __init__(Weight self, _ParticleAdaptor d) -> Weight
2159 _IMP_isd.Weight_swiginit(self, _IMP_isd.new_Weight(*args))
2161 def show(self, *args):
2162 r"""show(Weight self, _ostream out=std::cout)"""
2163 return _IMP_isd.Weight_show(self, *args)
2166 def setup_particle(*args):
2168 setup_particle(Model m, ParticleIndex pi) -> Weight
2169 setup_particle(_ParticleAdaptor pa) -> Weight
2170 setup_particle(Model m, ParticleIndex pi, IMP::Int nweights) -> Weight
2171 setup_particle(_ParticleAdaptor pa, IMP::Int nweights) -> Weight
2172 setup_particle(Model m, ParticleIndex pi, VectorKD w) -> Weight
2173 setup_particle(_ParticleAdaptor pa, VectorKD w) -> Weight
2175 return _IMP_isd.Weight_setup_particle(*args)
2178 def get_number_of_weights_key():
2179 r"""get_number_of_weights_key() -> IntKey"""
2180 return _IMP_isd.Weight_get_number_of_weights_key()
2183 def get_weight_key(i):
2184 r"""get_weight_key(int i) -> FloatKey"""
2185 return _IMP_isd.Weight_get_weight_key(i)
2187 def get_weight_keys(self):
2188 r"""get_weight_keys(Weight self) -> IMP::FloatKeys"""
2189 return _IMP_isd.Weight_get_weight_keys(self)
2191 def get_weight(self, i):
2192 r"""get_weight(Weight self, int i) -> IMP::Float"""
2193 return _IMP_isd.Weight_get_weight(self, i)
2195 def get_weights(self):
2196 r"""get_weights(Weight self) -> VectorKD"""
2197 return _IMP_isd.Weight_get_weights(self)
2199 def set_weight_lazy(self, i, wi):
2200 r"""set_weight_lazy(Weight self, int i, IMP::Float wi)"""
2201 return _IMP_isd.Weight_set_weight_lazy(self, i, wi)
2203 def set_weights_lazy(self, w):
2204 r"""set_weights_lazy(Weight self, VectorKD w)"""
2205 return _IMP_isd.Weight_set_weights_lazy(self, w)
2207 def set_weights(self, w):
2208 r"""set_weights(Weight self, VectorKD w)"""
2209 return _IMP_isd.Weight_set_weights(self, w)
2211 def get_weights_are_optimized(self):
2212 r"""get_weights_are_optimized(Weight self) -> bool"""
2213 return _IMP_isd.Weight_get_weights_are_optimized(self)
2215 def set_weights_are_optimized(self, tf):
2216 r"""set_weights_are_optimized(Weight self, bool tf)"""
2217 return _IMP_isd.Weight_set_weights_are_optimized(self, tf)
2219 def get_weight_derivative(self, i):
2220 r"""get_weight_derivative(Weight self, int i) -> IMP::Float"""
2221 return _IMP_isd.Weight_get_weight_derivative(self, i)
2223 def get_weights_derivatives(self):
2224 r"""get_weights_derivatives(Weight self) -> VectorKD"""
2225 return _IMP_isd.Weight_get_weights_derivatives(self)
2227 def add_to_weight_derivative(self, i, dwi, da):
2228 r"""add_to_weight_derivative(Weight self, int i, IMP::Float dwi, DerivativeAccumulator da)"""
2229 return _IMP_isd.Weight_add_to_weight_derivative(self, i, dwi, da)
2231 def add_to_weights_derivatives(self, dw, da):
2232 r"""add_to_weights_derivatives(Weight self, VectorKD dw, DerivativeAccumulator da)"""
2233 return _IMP_isd.Weight_add_to_weights_derivatives(self, dw, da)
2235 def add_weight_lazy(self, wi=0):
2236 r"""add_weight_lazy(Weight self, IMP::Float wi=0)"""
2237 return _IMP_isd.Weight_add_weight_lazy(self, wi)
2239 def add_weight(self, wi=0):
2240 r"""add_weight(Weight self, IMP::Float wi=0)"""
2241 return _IMP_isd.Weight_add_weight(self, wi)
2243 def get_number_of_weights(self):
2244 r"""get_number_of_weights(Weight self) -> IMP::Int"""
2245 return _IMP_isd.Weight_get_number_of_weights(self)
2247 def get_unit_simplex(self):
2248 r"""get_unit_simplex(Weight self) -> UnitSimplexKD"""
2249 return _IMP_isd.Weight_get_unit_simplex(self)
2251 def set_number_of_weights_lazy(self, nweights):
2252 r"""set_number_of_weights_lazy(Weight self, IMP::Int nweights)"""
2253 return _IMP_isd.Weight_set_number_of_weights_lazy(self, nweights)
2255 def set_number_of_weights(self, nweights):
2256 r"""set_number_of_weights(Weight self, IMP::Int nweights)"""
2257 return _IMP_isd.Weight_set_number_of_weights(self, nweights)
2260 def get_is_setup(*args):
2262 get_is_setup(_ParticleAdaptor p) -> bool
2263 get_is_setup(Model m, ParticleIndex pi) -> bool
2265 return _IMP_isd.Weight_get_is_setup(*args)
2267 def add_attribute(self, *args):
2269 add_attribute(Weight self, FloatKey k, IMP::Float v, bool opt)
2270 add_attribute(Weight self, FloatKey a0, IMP::Float a1)
2271 add_attribute(Weight self, IntKey a0, IMP::Int a1)
2272 add_attribute(Weight self, FloatsKey a0, IMP::Floats a1)
2273 add_attribute(Weight self, IntsKey a0, IMP::Ints a1)
2274 add_attribute(Weight self, StringKey a0, IMP::String a1)
2275 add_attribute(Weight self, ParticleIndexKey a0, Particle a1)
2276 add_attribute(Weight self, ObjectKey a0, Object a1)
2278 return _IMP_isd.Weight_add_attribute(self, *args)
2280 def get_value(self, *args):
2282 get_value(Weight self, FloatKey a0) -> IMP::Float
2283 get_value(Weight self, IntKey a0) -> IMP::Int
2284 get_value(Weight self, FloatsKey a0) -> IMP::Floats
2285 get_value(Weight self, IntsKey a0) -> IMP::Ints
2286 get_value(Weight self, StringKey a0) -> IMP::String
2287 get_value(Weight self, ParticleIndexKey a0) -> Particle
2288 get_value(Weight self, ObjectKey a0) -> Object
2290 return _IMP_isd.Weight_get_value(self, *args)
2292 def set_value(self, *args):
2294 set_value(Weight self, FloatKey a0, IMP::Float a1)
2295 set_value(Weight self, IntKey a0, IMP::Int a1)
2296 set_value(Weight self, FloatsKey a0, IMP::Floats a1)
2297 set_value(Weight self, IntsKey a0, IMP::Ints a1)
2298 set_value(Weight self, StringKey a0, IMP::String a1)
2299 set_value(Weight self, ParticleIndexKey a0, Particle a1)
2300 set_value(Weight self, ObjectKey a0, Object a1)
2302 return _IMP_isd.Weight_set_value(self, *args)
2304 def remove_attribute(self, *args):
2306 remove_attribute(Weight self, FloatKey a0)
2307 remove_attribute(Weight self, IntKey a0)
2308 remove_attribute(Weight self, FloatsKey a0)
2309 remove_attribute(Weight self, IntsKey a0)
2310 remove_attribute(Weight self, StringKey a0)
2311 remove_attribute(Weight self, ParticleIndexKey a0)
2312 remove_attribute(Weight self, ObjectKey a0)
2314 return _IMP_isd.Weight_remove_attribute(self, *args)
2316 def has_attribute(self, *args):
2318 has_attribute(Weight self, FloatKey a0) -> bool
2319 has_attribute(Weight self, IntKey a0) -> bool
2320 has_attribute(Weight self, FloatsKey a0) -> bool
2321 has_attribute(Weight self, IntsKey a0) -> bool
2322 has_attribute(Weight self, StringKey a0) -> bool
2323 has_attribute(Weight self, ParticleIndexKey a0) -> bool
2324 has_attribute(Weight self, ObjectKey a0) -> bool
2326 return _IMP_isd.Weight_has_attribute(self, *args)
2328 def get_derivative(self, a0):
2329 r"""get_derivative(Weight self, FloatKey a0) -> double"""
2330 return _IMP_isd.Weight_get_derivative(self, a0)
2333 r"""get_name(Weight self) -> std::string"""
2334 return _IMP_isd.Weight_get_name(self)
2337 r"""clear_caches(Weight self)"""
2338 return _IMP_isd.Weight_clear_caches(self)
2340 def set_name(self, a0):
2341 r"""set_name(Weight self, std::string a0)"""
2342 return _IMP_isd.Weight_set_name(self, a0)
2345 r"""set_check_level(Weight self, IMP::CheckLevel a0)"""
2346 return _IMP_isd.Weight_set_check_level(self, a0)
2348 def add_to_derivative(self, a0, a1, a2):
2349 r"""add_to_derivative(Weight self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2350 return _IMP_isd.Weight_add_to_derivative(self, a0, a1, a2)
2352 def set_is_optimized(self, a0, a1):
2353 r"""set_is_optimized(Weight self, FloatKey a0, bool a1)"""
2354 return _IMP_isd.Weight_set_is_optimized(self, a0, a1)
2356 def get_is_optimized(self, a0):
2357 r"""get_is_optimized(Weight self, FloatKey a0) -> bool"""
2358 return _IMP_isd.Weight_get_is_optimized(self, a0)
2360 def get_check_level(self):
2361 r"""get_check_level(Weight self) -> IMP::CheckLevel"""
2362 return _IMP_isd.Weight_get_check_level(self)
2364 def __eq__(self, *args):
2366 __eq__(Weight self, Weight o) -> bool
2367 __eq__(Weight self, Particle d) -> bool
2369 return _IMP_isd.Weight___eq__(self, *args)
2371 def __ne__(self, *args):
2373 __ne__(Weight self, Weight o) -> bool
2374 __ne__(Weight self, Particle d) -> bool
2376 return _IMP_isd.Weight___ne__(self, *args)
2378 def __le__(self, *args):
2380 __le__(Weight self, Weight o) -> bool
2381 __le__(Weight self, Particle d) -> bool
2383 return _IMP_isd.Weight___le__(self, *args)
2385 def __lt__(self, *args):
2387 __lt__(Weight self, Weight o) -> bool
2388 __lt__(Weight self, Particle d) -> bool
2390 return _IMP_isd.Weight___lt__(self, *args)
2392 def __ge__(self, *args):
2394 __ge__(Weight self, Weight o) -> bool
2395 __ge__(Weight self, Particle d) -> bool
2397 return _IMP_isd.Weight___ge__(self, *args)
2399 def __gt__(self, *args):
2401 __gt__(Weight self, Weight o) -> bool
2402 __gt__(Weight self, Particle d) -> bool
2404 return _IMP_isd.Weight___gt__(self, *args)
2407 r"""__hash__(Weight self) -> std::size_t"""
2408 return _IMP_isd.Weight___hash__(self)
2411 r"""__str__(Weight self) -> std::string"""
2412 return _IMP_isd.Weight___str__(self)
2415 r"""__repr__(Weight self) -> std::string"""
2416 return _IMP_isd.Weight___repr__(self)
2418 def _get_as_binary(self):
2419 r"""_get_as_binary(Weight self) -> PyObject *"""
2420 return _IMP_isd.Weight__get_as_binary(self)
2422 def _set_from_binary(self, p):
2423 r"""_set_from_binary(Weight self, PyObject * p)"""
2424 return _IMP_isd.Weight__set_from_binary(self, p)
2426 def __getstate__(self):
2427 p = self._get_as_binary()
2428 if len(self.__dict__) > 1:
2429 d = self.__dict__.copy()
2434 def __setstate__(self, p):
2435 if not hasattr(self,
'this'):
2437 if isinstance(p, tuple):
2439 self.__dict__.update(d)
2440 return self._set_from_binary(p)
2442 __swig_destroy__ = _IMP_isd.delete_Weight
2445 _IMP_isd.Weight_swigregister(Weight)
2446 cvar = _IMP_isd.cvar
2447 IMPISD_MAX_WEIGHTS = cvar.IMPISD_MAX_WEIGHTS
2450 def __lshift__(*args):
2452 __lshift__(_ostream out, Nuisance n) -> _ostream
2453 __lshift__(_ostream out, Scale n) -> _ostream
2454 __lshift__(_ostream out, Switching n) -> _ostream
2455 __lshift__(_ostream out, Weight n) -> _ostream
2457 return _IMP_isd.__lshift__(*args)
2459 r"""Proxy of C++ IMP::isd::JeffreysRestraint class."""
2461 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2463 def __init__(self, *args):
2465 __init__(JeffreysRestraint self, Model m, Particle p) -> JeffreysRestraint
2466 __init__(JeffreysRestraint self) -> JeffreysRestraint
2468 _IMP_isd.JeffreysRestraint_swiginit(self, _IMP_isd.new_JeffreysRestraint(*args))
2471 r"""do_get_inputs(JeffreysRestraint self) -> IMP::ModelObjectsTemp"""
2472 return _IMP_isd.JeffreysRestraint_do_get_inputs(self)
2475 r"""get_version_info(JeffreysRestraint self) -> VersionInfo"""
2476 return _IMP_isd.JeffreysRestraint_get_version_info(self)
2477 __swig_destroy__ = _IMP_isd.delete_JeffreysRestraint
2479 def get_probability(self):
2480 r"""get_probability(JeffreysRestraint self) -> double"""
2481 return _IMP_isd.JeffreysRestraint_get_probability(self)
2484 r"""__str__(JeffreysRestraint self) -> std::string"""
2485 return _IMP_isd.JeffreysRestraint___str__(self)
2488 r"""__repr__(JeffreysRestraint self) -> std::string"""
2489 return _IMP_isd.JeffreysRestraint___repr__(self)
2493 return _object_cast_to_JeffreysRestraint(o)
2496 def _get_as_binary(self):
2497 r"""_get_as_binary(JeffreysRestraint self) -> PyObject *"""
2498 return _IMP_isd.JeffreysRestraint__get_as_binary(self)
2500 def _set_from_binary(self, p):
2501 r"""_set_from_binary(JeffreysRestraint self, PyObject * p)"""
2502 return _IMP_isd.JeffreysRestraint__set_from_binary(self, p)
2504 def __getstate__(self):
2505 p = self._get_as_binary()
2506 if len(self.__dict__) > 1:
2507 d = self.__dict__.copy()
2512 def __setstate__(self, p):
2513 if not hasattr(self,
'this'):
2515 if isinstance(p, tuple):
2517 self.__dict__.update(d)
2518 return self._set_from_binary(p)
2522 _IMP_isd.JeffreysRestraint_swigregister(JeffreysRestraint)
2524 r"""Proxy of C++ IMP::isd::NormalSigmaPCRestraint class."""
2526 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2528 def __init__(self, *args):
2530 __init__(NormalSigmaPCRestraint self, Model m, ParticleIndex spi, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%") -> NormalSigmaPCRestraint
2531 __init__(NormalSigmaPCRestraint self, Scale s, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%") -> NormalSigmaPCRestraint
2533 _IMP_isd.NormalSigmaPCRestraint_swiginit(self, _IMP_isd.new_NormalSigmaPCRestraint(*args))
2535 def get_sigma(self):
2536 r"""get_sigma(NormalSigmaPCRestraint self) -> Scale"""
2537 return _IMP_isd.NormalSigmaPCRestraint_get_sigma(self)
2539 def get_alpha(self):
2540 r"""get_alpha(NormalSigmaPCRestraint self) -> double"""
2541 return _IMP_isd.NormalSigmaPCRestraint_get_alpha(self)
2543 def get_sigma_upper(self):
2544 r"""get_sigma_upper(NormalSigmaPCRestraint self) -> double"""
2545 return _IMP_isd.NormalSigmaPCRestraint_get_sigma_upper(self)
2547 def get_probability(self):
2548 r"""get_probability(NormalSigmaPCRestraint self) -> double"""
2549 return _IMP_isd.NormalSigmaPCRestraint_get_probability(self)
2552 r"""do_get_inputs(NormalSigmaPCRestraint self) -> IMP::ModelObjectsTemp"""
2553 return _IMP_isd.NormalSigmaPCRestraint_do_get_inputs(self)
2556 r"""get_version_info(NormalSigmaPCRestraint self) -> VersionInfo"""
2557 return _IMP_isd.NormalSigmaPCRestraint_get_version_info(self)
2558 __swig_destroy__ = _IMP_isd.delete_NormalSigmaPCRestraint
2561 r"""__str__(NormalSigmaPCRestraint self) -> std::string"""
2562 return _IMP_isd.NormalSigmaPCRestraint___str__(self)
2565 r"""__repr__(NormalSigmaPCRestraint self) -> std::string"""
2566 return _IMP_isd.NormalSigmaPCRestraint___repr__(self)
2570 return _object_cast_to_NormalSigmaPCRestraint(o)
2574 _IMP_isd.NormalSigmaPCRestraint_swigregister(NormalSigmaPCRestraint)
2576 r"""Proxy of C++ IMP::isd::Distribution class."""
2578 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2580 def __init__(self, *args):
2581 r"""__init__(Distribution self, std::string name="Distribution %1%") -> Distribution"""
2582 if self.__class__ == Distribution:
2586 _IMP_isd.Distribution_swiginit(self, _IMP_isd.new_Distribution(_self, *args))
2588 if self.__class__ != Distribution:
2589 _director_objects.register(self)
2594 def get_type_name(self):
2595 r"""get_type_name(Distribution self) -> std::string"""
2596 return _IMP_isd.Distribution_get_type_name(self)
2599 r"""get_version_info(Distribution self) -> VersionInfo"""
2600 return _IMP_isd.Distribution_get_version_info(self)
2601 __swig_destroy__ = _IMP_isd.delete_Distribution
2604 r"""__str__(Distribution self) -> std::string"""
2605 return _IMP_isd.Distribution___str__(self)
2608 r"""__repr__(Distribution self) -> std::string"""
2609 return _IMP_isd.Distribution___repr__(self)
2613 return _object_cast_to_Distribution(o)
2616 def get_type_name(self):
2617 return self.__class__.__name__
2618 def do_show(self, out):
2621 if"IMP::isd" ==
"IMP":
2622 return VersionInfo(self.__module__,
2629 return _object_cast_to_Distribution(o)
2631 def __disown__(self):
2633 _IMP_isd.disown_Distribution(self)
2634 return weakref.proxy(self)
2637 r"""do_destroy(Distribution self)"""
2638 return _IMP_isd.Distribution_do_destroy(self)
2641 _IMP_isd.Distribution_swigregister(Distribution)
2642 class OneDimensionalDistribution(Distribution):
2643 r"""Proxy of C++ IMP::isd::OneDimensionalDistribution class."""
2645 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2647 def do_evaluate(self, *args):
2649 do_evaluate(OneDimensionalDistribution self, double v) -> double
2650 do_evaluate(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2652 return _IMP_isd.OneDimensionalDistribution_do_evaluate(self, *args)
2654 def do_get_density(self, *args):
2656 do_get_density(OneDimensionalDistribution self, double v) -> double
2657 do_get_density(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2659 return _IMP_isd.OneDimensionalDistribution_do_get_density(self, *args)
2661 def __init__(self, *args):
2662 r"""__init__(OneDimensionalDistribution self, std::string name="OneDimensionalDistribution %1%") -> OneDimensionalDistribution"""
2663 if self.__class__ == OneDimensionalDistribution:
2667 _IMP_isd.OneDimensionalDistribution_swiginit(self, _IMP_isd.new_OneDimensionalDistribution(_self, *args))
2669 if self.__class__ != OneDimensionalDistribution:
2670 _director_objects.register(self)
2675 def evaluate(self, *args):
2677 evaluate(OneDimensionalDistribution self, double v) -> double
2678 evaluate(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2680 return _IMP_isd.OneDimensionalDistribution_evaluate(self, *args)
2682 def get_density(self, *args):
2684 get_density(OneDimensionalDistribution self, double v) -> double
2685 get_density(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2687 return _IMP_isd.OneDimensionalDistribution_get_density(self, *args)
2689 def get_type_name(self):
2690 r"""get_type_name(OneDimensionalDistribution self) -> std::string"""
2691 return _IMP_isd.OneDimensionalDistribution_get_type_name(self)
2694 r"""get_version_info(OneDimensionalDistribution self) -> VersionInfo"""
2695 return _IMP_isd.OneDimensionalDistribution_get_version_info(self)
2696 __swig_destroy__ = _IMP_isd.delete_OneDimensionalDistribution
2699 r"""__str__(OneDimensionalDistribution self) -> std::string"""
2700 return _IMP_isd.OneDimensionalDistribution___str__(self)
2703 r"""__repr__(OneDimensionalDistribution self) -> std::string"""
2704 return _IMP_isd.OneDimensionalDistribution___repr__(self)
2708 return _object_cast_to_OneDimensionalDistribution(o)
2711 def get_type_name(self):
2712 return self.__class__.__name__
2713 def do_show(self, out):
2716 if"IMP::isd" ==
"IMP":
2717 return VersionInfo(self.__module__,
2724 return _object_cast_to_OneDimensionalDistribution(o)
2726 def __disown__(self):
2728 _IMP_isd.disown_OneDimensionalDistribution(self)
2729 return weakref.proxy(self)
2732 r"""do_destroy(OneDimensionalDistribution self)"""
2733 return _IMP_isd.OneDimensionalDistribution_do_destroy(self)
2736 _IMP_isd.OneDimensionalDistribution_swigregister(OneDimensionalDistribution)
2737 class OneDimensionalSufficientDistribution(Distribution):
2738 r"""Proxy of C++ IMP::isd::OneDimensionalSufficientDistribution class."""
2740 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2742 def do_update_sufficient_statistics(self, vs):
2743 r"""do_update_sufficient_statistics(OneDimensionalSufficientDistribution self, IMP::Floats vs)"""
2744 return _IMP_isd.OneDimensionalSufficientDistribution_do_update_sufficient_statistics(self, vs)
2746 def do_get_sufficient_statistics(self):
2747 r"""do_get_sufficient_statistics(OneDimensionalSufficientDistribution self) -> IMP::Floats"""
2748 return _IMP_isd.OneDimensionalSufficientDistribution_do_get_sufficient_statistics(self)
2750 def do_evaluate(self):
2751 r"""do_evaluate(OneDimensionalSufficientDistribution self) -> double"""
2752 return _IMP_isd.OneDimensionalSufficientDistribution_do_evaluate(self)
2754 def do_get_density(self):
2755 r"""do_get_density(OneDimensionalSufficientDistribution self) -> double"""
2756 return _IMP_isd.OneDimensionalSufficientDistribution_do_get_density(self)
2758 def __init__(self, *args):
2759 r"""__init__(OneDimensionalSufficientDistribution self, std::string name="OneDimensionalSufficientDistribution %1%") -> OneDimensionalSufficientDistribution"""
2760 if self.__class__ == OneDimensionalSufficientDistribution:
2764 _IMP_isd.OneDimensionalSufficientDistribution_swiginit(self, _IMP_isd.new_OneDimensionalSufficientDistribution(_self, *args))
2766 if self.__class__ != OneDimensionalSufficientDistribution:
2767 _director_objects.register(self)
2772 def update_sufficient_statistics(self, vs):
2773 r"""update_sufficient_statistics(OneDimensionalSufficientDistribution self, IMP::Floats vs)"""
2774 return _IMP_isd.OneDimensionalSufficientDistribution_update_sufficient_statistics(self, vs)
2776 def get_sufficient_statistics(self):
2777 r"""get_sufficient_statistics(OneDimensionalSufficientDistribution self) -> IMP::Floats"""
2778 return _IMP_isd.OneDimensionalSufficientDistribution_get_sufficient_statistics(self)
2781 r"""evaluate(OneDimensionalSufficientDistribution self) -> double"""
2782 return _IMP_isd.OneDimensionalSufficientDistribution_evaluate(self)
2784 def get_density(self):
2785 r"""get_density(OneDimensionalSufficientDistribution self) -> double"""
2786 return _IMP_isd.OneDimensionalSufficientDistribution_get_density(self)
2788 def get_type_name(self):
2789 r"""get_type_name(OneDimensionalSufficientDistribution self) -> std::string"""
2790 return _IMP_isd.OneDimensionalSufficientDistribution_get_type_name(self)
2793 r"""get_version_info(OneDimensionalSufficientDistribution self) -> VersionInfo"""
2794 return _IMP_isd.OneDimensionalSufficientDistribution_get_version_info(self)
2795 __swig_destroy__ = _IMP_isd.delete_OneDimensionalSufficientDistribution
2798 r"""__str__(OneDimensionalSufficientDistribution self) -> std::string"""
2799 return _IMP_isd.OneDimensionalSufficientDistribution___str__(self)
2802 r"""__repr__(OneDimensionalSufficientDistribution self) -> std::string"""
2803 return _IMP_isd.OneDimensionalSufficientDistribution___repr__(self)
2807 return _object_cast_to_OneDimensionalSufficientDistribution(o)
2810 def get_type_name(self):
2811 return self.__class__.__name__
2812 def do_show(self, out):
2815 if"IMP::isd" ==
"IMP":
2816 return VersionInfo(self.__module__,
2823 return _object_cast_to_OneDimensionalSufficientDistribution(o)
2825 def __disown__(self):
2827 _IMP_isd.disown_OneDimensionalSufficientDistribution(self)
2828 return weakref.proxy(self)
2831 r"""do_destroy(OneDimensionalSufficientDistribution self)"""
2832 return _IMP_isd.OneDimensionalSufficientDistribution_do_destroy(self)
2835 _IMP_isd.OneDimensionalSufficientDistribution_swigregister(OneDimensionalSufficientDistribution)
2836 class FNormal(OneDimensionalSufficientDistribution):
2837 r"""Proxy of C++ IMP::isd::FNormal class."""
2839 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2841 def __init__(self, FA, JA, FM, sigma):
2842 r"""__init__(FNormal self, double FA, double JA, double FM, double sigma) -> FNormal"""
2843 _IMP_isd.FNormal_swiginit(self, _IMP_isd.new_FNormal(FA, JA, FM, sigma))
2845 def update_sufficient_statistics(self, FA):
2846 r"""update_sufficient_statistics(FNormal self, double FA)"""
2847 return _IMP_isd.FNormal_update_sufficient_statistics(self, FA)
2849 def do_update_sufficient_statistics(self, data):
2850 r"""do_update_sufficient_statistics(FNormal self, IMP::Floats data)"""
2851 return _IMP_isd.FNormal_do_update_sufficient_statistics(self, data)
2853 def do_get_sufficient_statistics(self):
2854 r"""do_get_sufficient_statistics(FNormal self) -> IMP::Floats"""
2855 return _IMP_isd.FNormal_do_get_sufficient_statistics(self)
2857 def do_evaluate(self):
2858 r"""do_evaluate(FNormal self) -> double"""
2859 return _IMP_isd.FNormal_do_evaluate(self)
2861 def evaluate_derivative_FA(self):
2862 r"""evaluate_derivative_FA(FNormal self) -> double"""
2863 return _IMP_isd.FNormal_evaluate_derivative_FA(self)
2865 def evaluate_derivative_JA(self):
2866 r"""evaluate_derivative_JA(FNormal self) -> double"""
2867 return _IMP_isd.FNormal_evaluate_derivative_JA(self)
2869 def evaluate_derivative_FM(self):
2870 r"""evaluate_derivative_FM(FNormal self) -> double"""
2871 return _IMP_isd.FNormal_evaluate_derivative_FM(self)
2873 def evaluate_derivative_sigma(self):
2874 r"""evaluate_derivative_sigma(FNormal self) -> double"""
2875 return _IMP_isd.FNormal_evaluate_derivative_sigma(self)
2877 def do_get_density(self):
2878 r"""do_get_density(FNormal self) -> double"""
2879 return _IMP_isd.FNormal_do_get_density(self)
2881 def set_FA(self, f):
2882 r"""set_FA(FNormal self, double f)"""
2883 return _IMP_isd.FNormal_set_FA(self, f)
2885 def set_JA(self, f):
2886 r"""set_JA(FNormal self, double f)"""
2887 return _IMP_isd.FNormal_set_JA(self, f)
2889 def set_FM(self, f):
2890 r"""set_FM(FNormal self, double f)"""
2891 return _IMP_isd.FNormal_set_FM(self, f)
2893 def set_sigma(self, f):
2894 r"""set_sigma(FNormal self, double f)"""
2895 return _IMP_isd.FNormal_set_sigma(self, f)
2896 __swig_destroy__ = _IMP_isd.delete_FNormal
2899 r"""__str__(FNormal self) -> std::string"""
2900 return _IMP_isd.FNormal___str__(self)
2903 r"""__repr__(FNormal self) -> std::string"""
2904 return _IMP_isd.FNormal___repr__(self)
2908 return _object_cast_to_FNormal(o)
2912 _IMP_isd.FNormal_swigregister(FNormal)
2913 class FStudentT(OneDimensionalSufficientDistribution):
2914 r"""Proxy of C++ IMP::isd::FStudentT class."""
2916 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2918 def __init__(self, *args):
2920 __init__(FStudentT self, IMP::Floats FXs, IMP::Floats JXs, double FM, double sigma, double nu, std::string name="FStudentT %1%") -> FStudentT
2921 __init__(FStudentT self, double sumFX, double sumFX2, unsigned int N, double LogJX, double FM, double sigma, double nu, std::string name="FStudentT %1%") -> FStudentT
2923 _IMP_isd.FStudentT_swiginit(self, _IMP_isd.new_FStudentT(*args))
2925 def update_sufficient_statistics(self, FXs, JXs):
2926 r"""update_sufficient_statistics(FStudentT self, IMP::Floats FXs, IMP::Floats JXs)"""
2927 return _IMP_isd.FStudentT_update_sufficient_statistics(self, FXs, JXs)
2929 def evaluate_derivative_Fx(self, Fx):
2930 r"""evaluate_derivative_Fx(FStudentT self, double Fx) -> double"""
2931 return _IMP_isd.FStudentT_evaluate_derivative_Fx(self, Fx)
2933 def evaluate_derivative_FX(self, FXs):
2934 r"""evaluate_derivative_FX(FStudentT self, IMP::Floats const FXs) -> IMP::Floats"""
2935 return _IMP_isd.FStudentT_evaluate_derivative_FX(self, FXs)
2937 def evaluate_derivative_LogJX(self):
2938 r"""evaluate_derivative_LogJX(FStudentT self) -> double"""
2939 return _IMP_isd.FStudentT_evaluate_derivative_LogJX(self)
2941 def evaluate_derivative_FM(self):
2942 r"""evaluate_derivative_FM(FStudentT self) -> double"""
2943 return _IMP_isd.FStudentT_evaluate_derivative_FM(self)
2945 def evaluate_derivative_sigma(self):
2946 r"""evaluate_derivative_sigma(FStudentT self) -> double"""
2947 return _IMP_isd.FStudentT_evaluate_derivative_sigma(self)
2949 def evaluate_derivative_nu(self):
2950 r"""evaluate_derivative_nu(FStudentT self) -> double"""
2951 return _IMP_isd.FStudentT_evaluate_derivative_nu(self)
2953 def update_cached_values(self):
2954 r"""update_cached_values(FStudentT self)"""
2955 return _IMP_isd.FStudentT_update_cached_values(self)
2957 def set_sumFX(self, v):
2958 r"""set_sumFX(FStudentT self, double v)"""
2959 return _IMP_isd.FStudentT_set_sumFX(self, v)
2961 def set_sumFX2(self, v):
2962 r"""set_sumFX2(FStudentT self, double v)"""
2963 return _IMP_isd.FStudentT_set_sumFX2(self, v)
2966 r"""set_N(FStudentT self, unsigned int v)"""
2967 return _IMP_isd.FStudentT_set_N(self, v)
2969 def set_LogJX(self, v):
2970 r"""set_LogJX(FStudentT self, double v)"""
2971 return _IMP_isd.FStudentT_set_LogJX(self, v)
2973 def set_FM(self, v):
2974 r"""set_FM(FStudentT self, double v)"""
2975 return _IMP_isd.FStudentT_set_FM(self, v)
2977 def set_sigma(self, v):
2978 r"""set_sigma(FStudentT self, double v)"""
2979 return _IMP_isd.FStudentT_set_sigma(self, v)
2981 def set_nu(self, v):
2982 r"""set_nu(FStudentT self, double v)"""
2983 return _IMP_isd.FStudentT_set_nu(self, v)
2985 def get_sumFX(self):
2986 r"""get_sumFX(FStudentT self) -> double"""
2987 return _IMP_isd.FStudentT_get_sumFX(self)
2989 def get_sumFX2(self):
2990 r"""get_sumFX2(FStudentT self) -> double"""
2991 return _IMP_isd.FStudentT_get_sumFX2(self)
2994 r"""get_N(FStudentT self) -> unsigned int"""
2995 return _IMP_isd.FStudentT_get_N(self)
2997 def get_LogJX(self):
2998 r"""get_LogJX(FStudentT self) -> double"""
2999 return _IMP_isd.FStudentT_get_LogJX(self)
3002 r"""get_FM(FStudentT self) -> double"""
3003 return _IMP_isd.FStudentT_get_FM(self)
3005 def get_sigma(self):
3006 r"""get_sigma(FStudentT self) -> double"""
3007 return _IMP_isd.FStudentT_get_sigma(self)
3010 r"""get_nu(FStudentT self) -> double"""
3011 return _IMP_isd.FStudentT_get_nu(self)
3012 __swig_destroy__ = _IMP_isd.delete_FStudentT
3015 r"""__str__(FStudentT self) -> std::string"""
3016 return _IMP_isd.FStudentT___str__(self)
3019 r"""__repr__(FStudentT self) -> std::string"""
3020 return _IMP_isd.FStudentT___repr__(self)
3024 return _object_cast_to_FStudentT(o)
3028 _IMP_isd.FStudentT_swigregister(FStudentT)
3030 r"""Proxy of C++ IMP::isd::vonMises class."""
3032 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3034 def __init__(self, x, mu, kappa):
3035 r"""__init__(vonMises self, double x, double mu, double kappa) -> vonMises"""
3036 _IMP_isd.vonMises_swiginit(self, _IMP_isd.new_vonMises(x, mu, kappa))
3039 r"""evaluate(vonMises self) -> double"""
3040 return _IMP_isd.vonMises_evaluate(self)
3042 def evaluate_derivative_x(self):
3043 r"""evaluate_derivative_x(vonMises self) -> double"""
3044 return _IMP_isd.vonMises_evaluate_derivative_x(self)
3046 def evaluate_derivative_mu(self):
3047 r"""evaluate_derivative_mu(vonMises self) -> double"""
3048 return _IMP_isd.vonMises_evaluate_derivative_mu(self)
3050 def evaluate_derivative_kappa(self):
3051 r"""evaluate_derivative_kappa(vonMises self) -> double"""
3052 return _IMP_isd.vonMises_evaluate_derivative_kappa(self)
3055 r"""density(vonMises self) -> double"""
3056 return _IMP_isd.vonMises_density(self)
3059 r"""set_x(vonMises self, double x)"""
3060 return _IMP_isd.vonMises_set_x(self, x)
3062 def set_mu(self, mu):
3063 r"""set_mu(vonMises self, double mu)"""
3064 return _IMP_isd.vonMises_set_mu(self, mu)
3066 def set_kappa(self, kappa):
3067 r"""set_kappa(vonMises self, double kappa)"""
3068 return _IMP_isd.vonMises_set_kappa(self, kappa)
3071 r"""get_version_info(vonMises self) -> VersionInfo"""
3072 return _IMP_isd.vonMises_get_version_info(self)
3073 __swig_destroy__ = _IMP_isd.delete_vonMises
3076 r"""__str__(vonMises self) -> std::string"""
3077 return _IMP_isd.vonMises___str__(self)
3080 r"""__repr__(vonMises self) -> std::string"""
3081 return _IMP_isd.vonMises___repr__(self)
3085 return _object_cast_to_vonMises(o)
3089 _IMP_isd.vonMises_swigregister(vonMises)
3091 r"""Proxy of C++ IMP::isd::vonMisesSufficient class."""
3093 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3095 def __init__(self, *args):
3097 __init__(vonMisesSufficient self, double chi, unsigned int N, double R0, double chiexp, double kappa) -> vonMisesSufficient
3098 __init__(vonMisesSufficient self, double chi, IMP::Floats obs, double kappa) -> vonMisesSufficient
3100 _IMP_isd.vonMisesSufficient_swiginit(self, _IMP_isd.new_vonMisesSufficient(*args))
3103 r"""evaluate(vonMisesSufficient self) -> double"""
3104 return _IMP_isd.vonMisesSufficient_evaluate(self)
3106 def evaluate_derivative_x(self):
3107 r"""evaluate_derivative_x(vonMisesSufficient self) -> double"""
3108 return _IMP_isd.vonMisesSufficient_evaluate_derivative_x(self)
3110 def evaluate_derivative_kappa(self):
3111 r"""evaluate_derivative_kappa(vonMisesSufficient self) -> double"""
3112 return _IMP_isd.vonMisesSufficient_evaluate_derivative_kappa(self)
3115 r"""density(vonMisesSufficient self) -> double"""
3116 return _IMP_isd.vonMisesSufficient_density(self)
3119 r"""get_x(vonMisesSufficient self) -> double"""
3120 return _IMP_isd.vonMisesSufficient_get_x(self)
3123 r"""get_R0(vonMisesSufficient self) -> double"""
3124 return _IMP_isd.vonMisesSufficient_get_R0(self)
3126 def get_chiexp(self):
3127 r"""get_chiexp(vonMisesSufficient self) -> double"""
3128 return _IMP_isd.vonMisesSufficient_get_chiexp(self)
3131 r"""get_N(vonMisesSufficient self) -> double"""
3132 return _IMP_isd.vonMisesSufficient_get_N(self)
3134 def get_kappa(self):
3135 r"""get_kappa(vonMisesSufficient self) -> double"""
3136 return _IMP_isd.vonMisesSufficient_get_kappa(self)
3139 r"""set_x(vonMisesSufficient self, double x)"""
3140 return _IMP_isd.vonMisesSufficient_set_x(self, x)
3142 def set_R0(self, R0):
3143 r"""set_R0(vonMisesSufficient self, double R0)"""
3144 return _IMP_isd.vonMisesSufficient_set_R0(self, R0)
3146 def set_chiexp(self, chiexp):
3147 r"""set_chiexp(vonMisesSufficient self, double chiexp)"""
3148 return _IMP_isd.vonMisesSufficient_set_chiexp(self, chiexp)
3151 r"""set_N(vonMisesSufficient self, unsigned int N)"""
3152 return _IMP_isd.vonMisesSufficient_set_N(self, N)
3154 def set_kappa(self, kappa):
3155 r"""set_kappa(vonMisesSufficient self, double kappa)"""
3156 return _IMP_isd.vonMisesSufficient_set_kappa(self, kappa)
3159 def get_sufficient_statistics(data):
3160 r"""get_sufficient_statistics(IMP::Floats data) -> IMP::Floats"""
3161 return _IMP_isd.vonMisesSufficient_get_sufficient_statistics(data)
3164 r"""get_version_info(vonMisesSufficient self) -> VersionInfo"""
3165 return _IMP_isd.vonMisesSufficient_get_version_info(self)
3166 __swig_destroy__ = _IMP_isd.delete_vonMisesSufficient
3169 r"""__str__(vonMisesSufficient self) -> std::string"""
3170 return _IMP_isd.vonMisesSufficient___str__(self)
3173 r"""__repr__(vonMisesSufficient self) -> std::string"""
3174 return _IMP_isd.vonMisesSufficient___repr__(self)
3178 return _object_cast_to_vonMisesSufficient(o)
3182 _IMP_isd.vonMisesSufficient_swigregister(vonMisesSufficient)
3183 class PenalizedComplexityPrior(OneDimensionalSufficientDistribution):
3184 r"""Proxy of C++ IMP::isd::PenalizedComplexityPrior class."""
3186 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3188 def __init__(self, *args):
3189 r"""__init__(PenalizedComplexityPrior self, double Dxi, double Jxi, double alpha, std::string name="PenalizedComplexityPrior %1%") -> PenalizedComplexityPrior"""
3190 _IMP_isd.PenalizedComplexityPrior_swiginit(self, _IMP_isd.new_PenalizedComplexityPrior(*args))
3192 def update_sufficient_statistics(self, Dxis, Jxis):
3193 r"""update_sufficient_statistics(PenalizedComplexityPrior self, IMP::Floats Dxis, IMP::Floats Jxis)"""
3194 return _IMP_isd.PenalizedComplexityPrior_update_sufficient_statistics(self, Dxis, Jxis)
3196 def evaluate_derivative_Dxi(self):
3197 r"""evaluate_derivative_Dxi(PenalizedComplexityPrior self) -> double"""
3198 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_Dxi(self)
3200 def evaluate_derivative_Jxi(self):
3201 r"""evaluate_derivative_Jxi(PenalizedComplexityPrior self) -> double"""
3202 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_Jxi(self)
3204 def evaluate_derivative_alpha(self):
3205 r"""evaluate_derivative_alpha(PenalizedComplexityPrior self) -> double"""
3206 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_alpha(self)
3208 def evaluate_derivative_xi(self, JJxi):
3209 r"""evaluate_derivative_xi(PenalizedComplexityPrior self, double JJxi) -> double"""
3210 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_xi(self, JJxi)
3212 def set_Dxi(self, v):
3213 r"""set_Dxi(PenalizedComplexityPrior self, double v)"""
3214 return _IMP_isd.PenalizedComplexityPrior_set_Dxi(self, v)
3216 def set_Jxi(self, v):
3217 r"""set_Jxi(PenalizedComplexityPrior self, double v)"""
3218 return _IMP_isd.PenalizedComplexityPrior_set_Jxi(self, v)
3220 def set_alpha(self, v):
3221 r"""set_alpha(PenalizedComplexityPrior self, double v)"""
3222 return _IMP_isd.PenalizedComplexityPrior_set_alpha(self, v)
3225 r"""get_Dxi(PenalizedComplexityPrior self) -> double"""
3226 return _IMP_isd.PenalizedComplexityPrior_get_Dxi(self)
3229 r"""get_Jxi(PenalizedComplexityPrior self) -> double"""
3230 return _IMP_isd.PenalizedComplexityPrior_get_Jxi(self)
3232 def get_alpha(self):
3233 r"""get_alpha(PenalizedComplexityPrior self) -> double"""
3234 return _IMP_isd.PenalizedComplexityPrior_get_alpha(self)
3235 __swig_destroy__ = _IMP_isd.delete_PenalizedComplexityPrior
3238 r"""__str__(PenalizedComplexityPrior self) -> std::string"""
3239 return _IMP_isd.PenalizedComplexityPrior___str__(self)
3242 r"""__repr__(PenalizedComplexityPrior self) -> std::string"""
3243 return _IMP_isd.PenalizedComplexityPrior___repr__(self)
3247 return _object_cast_to_PenalizedComplexityPrior(o)
3251 _IMP_isd.PenalizedComplexityPrior_swigregister(PenalizedComplexityPrior)
3253 r"""Proxy of C++ IMP::isd::vonMisesKappaJeffreysRestraint class."""
3255 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3257 def __init__(self, m, kappa):
3258 r"""__init__(vonMisesKappaJeffreysRestraint self, Model m, Particle kappa) -> vonMisesKappaJeffreysRestraint"""
3259 _IMP_isd.vonMisesKappaJeffreysRestraint_swiginit(self, _IMP_isd.new_vonMisesKappaJeffreysRestraint(m, kappa))
3262 r"""do_get_inputs(vonMisesKappaJeffreysRestraint self) -> IMP::ModelObjectsTemp"""
3263 return _IMP_isd.vonMisesKappaJeffreysRestraint_do_get_inputs(self)
3266 r"""get_version_info(vonMisesKappaJeffreysRestraint self) -> VersionInfo"""
3267 return _IMP_isd.vonMisesKappaJeffreysRestraint_get_version_info(self)
3268 __swig_destroy__ = _IMP_isd.delete_vonMisesKappaJeffreysRestraint
3270 def get_probability(self):
3271 r"""get_probability(vonMisesKappaJeffreysRestraint self) -> double"""
3272 return _IMP_isd.vonMisesKappaJeffreysRestraint_get_probability(self)
3275 r"""__str__(vonMisesKappaJeffreysRestraint self) -> std::string"""
3276 return _IMP_isd.vonMisesKappaJeffreysRestraint___str__(self)
3279 r"""__repr__(vonMisesKappaJeffreysRestraint self) -> std::string"""
3280 return _IMP_isd.vonMisesKappaJeffreysRestraint___repr__(self)
3284 return _object_cast_to_vonMisesKappaJeffreysRestraint(o)
3288 _IMP_isd.vonMisesKappaJeffreysRestraint_swigregister(vonMisesKappaJeffreysRestraint)
3290 r"""Proxy of C++ IMP::isd::vonMisesKappaConjugateRestraint class."""
3292 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3294 def __init__(self, m, kappa, c=10.0, R0=0.0):
3295 r"""__init__(vonMisesKappaConjugateRestraint self, Model m, Particle kappa, double c=10.0, double R0=0.0) -> vonMisesKappaConjugateRestraint"""
3296 _IMP_isd.vonMisesKappaConjugateRestraint_swiginit(self, _IMP_isd.new_vonMisesKappaConjugateRestraint(m, kappa, c, R0))
3299 r"""do_get_inputs(vonMisesKappaConjugateRestraint self) -> IMP::ModelObjectsTemp"""
3300 return _IMP_isd.vonMisesKappaConjugateRestraint_do_get_inputs(self)
3303 r"""get_version_info(vonMisesKappaConjugateRestraint self) -> VersionInfo"""
3304 return _IMP_isd.vonMisesKappaConjugateRestraint_get_version_info(self)
3305 __swig_destroy__ = _IMP_isd.delete_vonMisesKappaConjugateRestraint
3307 def get_probability(self):
3308 r"""get_probability(vonMisesKappaConjugateRestraint self) -> double"""
3309 return _IMP_isd.vonMisesKappaConjugateRestraint_get_probability(self)
3312 r"""__str__(vonMisesKappaConjugateRestraint self) -> std::string"""
3313 return _IMP_isd.vonMisesKappaConjugateRestraint___str__(self)
3316 r"""__repr__(vonMisesKappaConjugateRestraint self) -> std::string"""
3317 return _IMP_isd.vonMisesKappaConjugateRestraint___repr__(self)
3321 return _object_cast_to_vonMisesKappaConjugateRestraint(o)
3325 _IMP_isd.vonMisesKappaConjugateRestraint_swigregister(vonMisesKappaConjugateRestraint)
3327 r"""Proxy of C++ IMP::isd::NOERestraint class."""
3329 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3331 def __init__(self, m, p0, p1, sigma, gamma, Iexp):
3332 r"""__init__(NOERestraint self, Model m, Particle p0, Particle p1, Particle sigma, Particle gamma, double Iexp) -> NOERestraint"""
3333 _IMP_isd.NOERestraint_swiginit(self, _IMP_isd.new_NOERestraint(m, p0, p1, sigma, gamma, Iexp))
3335 def get_probability(self):
3336 r"""get_probability(NOERestraint self) -> double"""
3337 return _IMP_isd.NOERestraint_get_probability(self)
3340 r"""get_chi(NOERestraint self) -> double"""
3341 return _IMP_isd.NOERestraint_get_chi(self)
3344 r"""do_get_inputs(NOERestraint self) -> IMP::ModelObjectsTemp"""
3345 return _IMP_isd.NOERestraint_do_get_inputs(self)
3348 r"""get_version_info(NOERestraint self) -> VersionInfo"""
3349 return _IMP_isd.NOERestraint_get_version_info(self)
3350 __swig_destroy__ = _IMP_isd.delete_NOERestraint
3353 r"""__str__(NOERestraint self) -> std::string"""
3354 return _IMP_isd.NOERestraint___str__(self)
3357 r"""__repr__(NOERestraint self) -> std::string"""
3358 return _IMP_isd.NOERestraint___repr__(self)
3362 return _object_cast_to_NOERestraint(o)
3366 _IMP_isd.NOERestraint_swigregister(NOERestraint)
3368 r"""Proxy of C++ IMP::isd::GaussianRestraint class."""
3370 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3372 def __init__(self, *args):
3374 __init__(GaussianRestraint self, Particle x, Particle mu, Particle sigma) -> GaussianRestraint
3375 __init__(GaussianRestraint self, double x, Particle mu, Particle sigma) -> GaussianRestraint
3376 __init__(GaussianRestraint self, Particle x, double mu, Particle sigma) -> GaussianRestraint
3377 __init__(GaussianRestraint self, Particle x, Particle mu, double sigma) -> GaussianRestraint
3378 __init__(GaussianRestraint self, double x, double mu, Particle sigma) -> GaussianRestraint
3379 __init__(GaussianRestraint self, Particle x, double mu, double sigma) -> GaussianRestraint
3380 __init__(GaussianRestraint self, double x, Particle mu, double sigma) -> GaussianRestraint
3382 _IMP_isd.GaussianRestraint_swiginit(self, _IMP_isd.new_GaussianRestraint(*args))
3384 def get_probability(self):
3385 r"""get_probability(GaussianRestraint self) -> double"""
3386 return _IMP_isd.GaussianRestraint_get_probability(self)
3389 r"""get_chi(GaussianRestraint self) -> double"""
3390 return _IMP_isd.GaussianRestraint_get_chi(self)
3393 r"""do_get_inputs(GaussianRestraint self) -> IMP::ModelObjectsTemp"""
3394 return _IMP_isd.GaussianRestraint_do_get_inputs(self)
3397 r"""get_version_info(GaussianRestraint self) -> VersionInfo"""
3398 return _IMP_isd.GaussianRestraint_get_version_info(self)
3399 __swig_destroy__ = _IMP_isd.delete_GaussianRestraint
3402 r"""__str__(GaussianRestraint self) -> std::string"""
3403 return _IMP_isd.GaussianRestraint___str__(self)
3406 r"""__repr__(GaussianRestraint self) -> std::string"""
3407 return _IMP_isd.GaussianRestraint___repr__(self)
3411 return _object_cast_to_GaussianRestraint(o)
3415 _IMP_isd.GaussianRestraint_swigregister(GaussianRestraint)
3417 r"""Proxy of C++ IMP::isd::StudentTRestraint class."""
3419 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3421 def __init__(self, *args):
3423 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3424 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3425 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3426 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3427 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3428 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3429 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, double sigma, double nu) -> StudentTRestraint
3430 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, double sigma, double nu) -> StudentTRestraint
3431 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3432 __init__(StudentTRestraint self, Model m, double x, double mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3433 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3434 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3435 __init__(StudentTRestraint self, Model m, double x, double mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3436 __init__(StudentTRestraint self, Model m, double x, double mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3437 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, double sigma, double nu) -> StudentTRestraint
3439 _IMP_isd.StudentTRestraint_swiginit(self, _IMP_isd.new_StudentTRestraint(*args))
3441 def get_probability(self):
3442 r"""get_probability(StudentTRestraint self) -> double"""
3443 return _IMP_isd.StudentTRestraint_get_probability(self)
3446 r"""do_get_inputs(StudentTRestraint self) -> IMP::ModelObjectsTemp"""
3447 return _IMP_isd.StudentTRestraint_do_get_inputs(self)
3450 r"""get_version_info(StudentTRestraint self) -> VersionInfo"""
3451 return _IMP_isd.StudentTRestraint_get_version_info(self)
3452 __swig_destroy__ = _IMP_isd.delete_StudentTRestraint
3455 r"""__str__(StudentTRestraint self) -> std::string"""
3456 return _IMP_isd.StudentTRestraint___str__(self)
3459 r"""__repr__(StudentTRestraint self) -> std::string"""
3460 return _IMP_isd.StudentTRestraint___repr__(self)
3464 return _object_cast_to_StudentTRestraint(o)
3468 _IMP_isd.StudentTRestraint_swigregister(StudentTRestraint)
3470 r"""Proxy of C++ IMP::isd::LognormalRestraint class."""
3472 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3474 def __init__(self, *args):
3476 __init__(LognormalRestraint self, Particle x, Particle mu, Particle sigma) -> LognormalRestraint
3477 __init__(LognormalRestraint self, double x, Particle mu, Particle sigma) -> LognormalRestraint
3478 __init__(LognormalRestraint self, Particle x, double mu, Particle sigma) -> LognormalRestraint
3479 __init__(LognormalRestraint self, Particle x, Particle mu, double sigma) -> LognormalRestraint
3480 __init__(LognormalRestraint self, double x, double mu, Particle sigma) -> LognormalRestraint
3481 __init__(LognormalRestraint self, Particle x, double mu, double sigma) -> LognormalRestraint
3482 __init__(LognormalRestraint self, double x, Particle mu, double sigma) -> LognormalRestraint
3484 _IMP_isd.LognormalRestraint_swiginit(self, _IMP_isd.new_LognormalRestraint(*args))
3486 def get_probability(self):
3487 r"""get_probability(LognormalRestraint self) -> double"""
3488 return _IMP_isd.LognormalRestraint_get_probability(self)
3491 r"""get_chi(LognormalRestraint self) -> double"""
3492 return _IMP_isd.LognormalRestraint_get_chi(self)
3495 r"""do_get_inputs(LognormalRestraint self) -> IMP::ModelObjectsTemp"""
3496 return _IMP_isd.LognormalRestraint_do_get_inputs(self)
3499 r"""get_version_info(LognormalRestraint self) -> VersionInfo"""
3500 return _IMP_isd.LognormalRestraint_get_version_info(self)
3501 __swig_destroy__ = _IMP_isd.delete_LognormalRestraint
3504 r"""__str__(LognormalRestraint self) -> std::string"""
3505 return _IMP_isd.LognormalRestraint___str__(self)
3508 r"""__repr__(LognormalRestraint self) -> std::string"""
3509 return _IMP_isd.LognormalRestraint___repr__(self)
3513 return _object_cast_to_LognormalRestraint(o)
3517 _IMP_isd.LognormalRestraint_swigregister(LognormalRestraint)
3519 r"""Proxy of C++ IMP::isd::LognormalAmbiguousRestraint class."""
3521 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3523 def __init__(self, p1, p2, ki, sigmaG):
3524 r"""__init__(LognormalAmbiguousRestraint self, Particle p1, Particle p2, Particle ki, Particle sigmaG) -> LognormalAmbiguousRestraint"""
3525 _IMP_isd.LognormalAmbiguousRestraint_swiginit(self, _IMP_isd.new_LognormalAmbiguousRestraint(p1, p2, ki, sigmaG))
3527 def add_contribution(self, lexp, omega):
3528 r"""add_contribution(LognormalAmbiguousRestraint self, double lexp, Particle omega)"""
3529 return _IMP_isd.LognormalAmbiguousRestraint_add_contribution(self, lexp, omega)
3531 def get_number_of_contributions(self):
3532 r"""get_number_of_contributions(LognormalAmbiguousRestraint self) -> unsigned int"""
3533 return _IMP_isd.LognormalAmbiguousRestraint_get_number_of_contributions(self)
3535 def draw_k_from_posterior(self, kt):
3536 r"""draw_k_from_posterior(LognormalAmbiguousRestraint self, double kt)"""
3537 return _IMP_isd.LognormalAmbiguousRestraint_draw_k_from_posterior(self, kt)
3539 def get_probability(self):
3540 r"""get_probability(LognormalAmbiguousRestraint self) -> double"""
3541 return _IMP_isd.LognormalAmbiguousRestraint_get_probability(self)
3544 r"""do_get_inputs(LognormalAmbiguousRestraint self) -> IMP::ModelObjectsTemp"""
3545 return _IMP_isd.LognormalAmbiguousRestraint_do_get_inputs(self)
3548 r"""get_version_info(LognormalAmbiguousRestraint self) -> VersionInfo"""
3549 return _IMP_isd.LognormalAmbiguousRestraint_get_version_info(self)
3550 __swig_destroy__ = _IMP_isd.delete_LognormalAmbiguousRestraint
3553 r"""__str__(LognormalAmbiguousRestraint self) -> std::string"""
3554 return _IMP_isd.LognormalAmbiguousRestraint___str__(self)
3557 r"""__repr__(LognormalAmbiguousRestraint self) -> std::string"""
3558 return _IMP_isd.LognormalAmbiguousRestraint___repr__(self)
3562 return _object_cast_to_LognormalAmbiguousRestraint(o)
3566 _IMP_isd.LognormalAmbiguousRestraint_swigregister(LognormalAmbiguousRestraint)
3568 r"""Proxy of C++ IMP::isd::AmbiguousNOERestraint class."""
3570 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3572 def __init__(self, *args):
3574 __init__(AmbiguousNOERestraint self, Model m, PairContainer pc, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor gamma, double Iexp) -> AmbiguousNOERestraint
3575 __init__(AmbiguousNOERestraint self) -> AmbiguousNOERestraint
3577 _IMP_isd.AmbiguousNOERestraint_swiginit(self, _IMP_isd.new_AmbiguousNOERestraint(*args))
3579 def get_probability(self):
3580 r"""get_probability(AmbiguousNOERestraint self) -> double"""
3581 return _IMP_isd.AmbiguousNOERestraint_get_probability(self)
3584 r"""get_chi(AmbiguousNOERestraint self) -> double"""
3585 return _IMP_isd.AmbiguousNOERestraint_get_chi(self)
3588 r"""do_get_inputs(AmbiguousNOERestraint self) -> IMP::ModelObjectsTemp"""
3589 return _IMP_isd.AmbiguousNOERestraint_do_get_inputs(self)
3592 r"""get_version_info(AmbiguousNOERestraint self) -> VersionInfo"""
3593 return _IMP_isd.AmbiguousNOERestraint_get_version_info(self)
3594 __swig_destroy__ = _IMP_isd.delete_AmbiguousNOERestraint
3597 r"""__str__(AmbiguousNOERestraint self) -> std::string"""
3598 return _IMP_isd.AmbiguousNOERestraint___str__(self)
3601 r"""__repr__(AmbiguousNOERestraint self) -> std::string"""
3602 return _IMP_isd.AmbiguousNOERestraint___repr__(self)
3606 return _object_cast_to_AmbiguousNOERestraint(o)
3609 def _get_as_binary(self):
3610 r"""_get_as_binary(AmbiguousNOERestraint self) -> PyObject *"""
3611 return _IMP_isd.AmbiguousNOERestraint__get_as_binary(self)
3613 def _set_from_binary(self, p):
3614 r"""_set_from_binary(AmbiguousNOERestraint self, PyObject * p)"""
3615 return _IMP_isd.AmbiguousNOERestraint__set_from_binary(self, p)
3617 def __getstate__(self):
3618 p = self._get_as_binary()
3619 if len(self.__dict__) > 1:
3620 d = self.__dict__.copy()
3625 def __setstate__(self, p):
3626 if not hasattr(self,
'this'):
3628 if isinstance(p, tuple):
3630 self.__dict__.update(d)
3631 return self._set_from_binary(p)
3635 _IMP_isd.AmbiguousNOERestraint_swigregister(AmbiguousNOERestraint)
3637 r"""Proxy of C++ IMP::isd::MarginalNOERestraint class."""
3639 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3641 def __init__(self, m):
3642 r"""__init__(MarginalNOERestraint self, Model m) -> MarginalNOERestraint"""
3643 _IMP_isd.MarginalNOERestraint_swiginit(self, _IMP_isd.new_MarginalNOERestraint(m))
3645 def add_contribution(self, *args):
3647 add_contribution(MarginalNOERestraint self, Particle p1, Particle p2, double Iexp)
3648 add_contribution(MarginalNOERestraint self, PairContainer pc, double Iexp)
3650 return _IMP_isd.MarginalNOERestraint_add_contribution(self, *args)
3652 def get_log_gammahat(self):
3653 r"""get_log_gammahat(MarginalNOERestraint self) -> double"""
3654 return _IMP_isd.MarginalNOERestraint_get_log_gammahat(self)
3657 r"""get_SS(MarginalNOERestraint self) -> double"""
3658 return _IMP_isd.MarginalNOERestraint_get_SS(self)
3660 def get_number_of_contributions(self):
3661 r"""get_number_of_contributions(MarginalNOERestraint self) -> unsigned int"""
3662 return _IMP_isd.MarginalNOERestraint_get_number_of_contributions(self)
3664 def get_probability(self):
3665 r"""get_probability(MarginalNOERestraint self) -> double"""
3666 return _IMP_isd.MarginalNOERestraint_get_probability(self)
3669 r"""do_get_inputs(MarginalNOERestraint self) -> IMP::ModelObjectsTemp"""
3670 return _IMP_isd.MarginalNOERestraint_do_get_inputs(self)
3673 r"""get_version_info(MarginalNOERestraint self) -> VersionInfo"""
3674 return _IMP_isd.MarginalNOERestraint_get_version_info(self)
3675 __swig_destroy__ = _IMP_isd.delete_MarginalNOERestraint
3678 r"""__str__(MarginalNOERestraint self) -> std::string"""
3679 return _IMP_isd.MarginalNOERestraint___str__(self)
3682 r"""__repr__(MarginalNOERestraint self) -> std::string"""
3683 return _IMP_isd.MarginalNOERestraint___repr__(self)
3687 return _object_cast_to_MarginalNOERestraint(o)
3691 _IMP_isd.MarginalNOERestraint_swigregister(MarginalNOERestraint)
3693 r"""Proxy of C++ IMP::isd::MarginalHBondRestraint class."""
3695 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3697 def __init__(self, m):
3698 r"""__init__(MarginalHBondRestraint self, Model m) -> MarginalHBondRestraint"""
3699 _IMP_isd.MarginalHBondRestraint_swiginit(self, _IMP_isd.new_MarginalHBondRestraint(m))
3701 def add_contribution(self, *args):
3703 add_contribution(MarginalHBondRestraint self, Particle p1, Particle p2, double Iexp)
3704 add_contribution(MarginalHBondRestraint self, PairContainer pc, double Iexp)
3706 return _IMP_isd.MarginalHBondRestraint_add_contribution(self, *args)
3708 def get_logsquares(self):
3709 r"""get_logsquares(MarginalHBondRestraint self) -> double"""
3710 return _IMP_isd.MarginalHBondRestraint_get_logsquares(self)
3712 def get_number_of_contributions(self):
3713 r"""get_number_of_contributions(MarginalHBondRestraint self) -> unsigned int"""
3714 return _IMP_isd.MarginalHBondRestraint_get_number_of_contributions(self)
3716 def get_probability(self):
3717 r"""get_probability(MarginalHBondRestraint self) -> double"""
3718 return _IMP_isd.MarginalHBondRestraint_get_probability(self)
3721 r"""do_get_inputs(MarginalHBondRestraint self) -> IMP::ModelObjectsTemp"""
3722 return _IMP_isd.MarginalHBondRestraint_do_get_inputs(self)
3725 r"""get_version_info(MarginalHBondRestraint self) -> VersionInfo"""
3726 return _IMP_isd.MarginalHBondRestraint_get_version_info(self)
3727 __swig_destroy__ = _IMP_isd.delete_MarginalHBondRestraint
3730 r"""__str__(MarginalHBondRestraint self) -> std::string"""
3731 return _IMP_isd.MarginalHBondRestraint___str__(self)
3734 r"""__repr__(MarginalHBondRestraint self) -> std::string"""
3735 return _IMP_isd.MarginalHBondRestraint___repr__(self)
3739 return _object_cast_to_MarginalHBondRestraint(o)
3743 _IMP_isd.MarginalHBondRestraint_swigregister(MarginalHBondRestraint)
3745 r"""Proxy of C++ IMP::isd::TALOSRestraint class."""
3747 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3749 def __init__(self, *args):
3751 __init__(TALOSRestraint self, Model m, IMP::Particles p, IMP::Floats data, Particle kappa) -> TALOSRestraint
3752 __init__(TALOSRestraint self, Model m, Particle p1, Particle p2, Particle p3, Particle p4, IMP::Floats data, Particle kappa) -> TALOSRestraint
3753 __init__(TALOSRestraint self, Model m, IMP::Particles p, unsigned int N, double R0, double chiexp, Particle kappa) -> TALOSRestraint
3754 __init__(TALOSRestraint self, Model m, Particle p1, Particle p2, Particle p3, Particle p4, unsigned int N, double R0, double chiexp, Particle kappa) -> TALOSRestraint
3756 _IMP_isd.TALOSRestraint_swiginit(self, _IMP_isd.new_TALOSRestraint(*args))
3758 def get_probability(self):
3759 r"""get_probability(TALOSRestraint self) -> double"""
3760 return _IMP_isd.TALOSRestraint_get_probability(self)
3763 r"""get_R0(TALOSRestraint self) -> double"""
3764 return _IMP_isd.TALOSRestraint_get_R0(self)
3766 def get_chiexp(self):
3767 r"""get_chiexp(TALOSRestraint self) -> double"""
3768 return _IMP_isd.TALOSRestraint_get_chiexp(self)
3771 r"""do_get_inputs(TALOSRestraint self) -> IMP::ModelObjectsTemp"""
3772 return _IMP_isd.TALOSRestraint_do_get_inputs(self)
3775 r"""get_version_info(TALOSRestraint self) -> VersionInfo"""
3776 return _IMP_isd.TALOSRestraint_get_version_info(self)
3777 __swig_destroy__ = _IMP_isd.delete_TALOSRestraint
3780 r"""__str__(TALOSRestraint self) -> std::string"""
3781 return _IMP_isd.TALOSRestraint___str__(self)
3784 r"""__repr__(TALOSRestraint self) -> std::string"""
3785 return _IMP_isd.TALOSRestraint___repr__(self)
3789 return _object_cast_to_TALOSRestraint(o)
3793 _IMP_isd.TALOSRestraint_swigregister(TALOSRestraint)
3795 r"""Proxy of C++ IMP::isd::RepulsiveDistancePairScore class."""
3797 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3799 def __init__(self, d0, k):
3800 r"""__init__(RepulsiveDistancePairScore self, double d0, double k) -> RepulsiveDistancePairScore"""
3801 _IMP_isd.RepulsiveDistancePairScore_swiginit(self, _IMP_isd.new_RepulsiveDistancePairScore(d0, k))
3803 def get_rest_length(self):
3804 r"""get_rest_length(RepulsiveDistancePairScore self) -> double"""
3805 return _IMP_isd.RepulsiveDistancePairScore_get_rest_length(self)
3807 def get_stiffness(self):
3808 r"""get_stiffness(RepulsiveDistancePairScore self) -> double"""
3809 return _IMP_isd.RepulsiveDistancePairScore_get_stiffness(self)
3812 r"""do_get_inputs(RepulsiveDistancePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3813 return _IMP_isd.RepulsiveDistancePairScore_do_get_inputs(self, m, pis)
3816 r"""get_version_info(RepulsiveDistancePairScore self) -> VersionInfo"""
3817 return _IMP_isd.RepulsiveDistancePairScore_get_version_info(self)
3818 __swig_destroy__ = _IMP_isd.delete_RepulsiveDistancePairScore
3821 r"""__str__(RepulsiveDistancePairScore self) -> std::string"""
3822 return _IMP_isd.RepulsiveDistancePairScore___str__(self)
3825 r"""__repr__(RepulsiveDistancePairScore self) -> std::string"""
3826 return _IMP_isd.RepulsiveDistancePairScore___repr__(self)
3830 return _object_cast_to_RepulsiveDistancePairScore(o)
3834 _IMP_isd.RepulsiveDistancePairScore_swigregister(RepulsiveDistancePairScore)
3836 r"""Proxy of C++ IMP::isd::AmbiguousRestraint class."""
3838 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3840 def __init__(self, *args):
3842 __init__(AmbiguousRestraint self, Model m, int d, Restraint r0, Restraint r1) -> AmbiguousRestraint
3843 __init__(AmbiguousRestraint self, Model m, int d, IMP::Restraints rs) -> AmbiguousRestraint
3844 __init__(AmbiguousRestraint self) -> AmbiguousRestraint
3846 _IMP_isd.AmbiguousRestraint_swiginit(self, _IMP_isd.new_AmbiguousRestraint(*args))
3848 def get_probability(self):
3849 r"""get_probability(AmbiguousRestraint self) -> double"""
3850 return _IMP_isd.AmbiguousRestraint_get_probability(self)
3853 r"""do_get_inputs(AmbiguousRestraint self) -> IMP::ModelObjectsTemp"""
3854 return _IMP_isd.AmbiguousRestraint_do_get_inputs(self)
3857 r"""get_version_info(AmbiguousRestraint self) -> VersionInfo"""
3858 return _IMP_isd.AmbiguousRestraint_get_version_info(self)
3859 __swig_destroy__ = _IMP_isd.delete_AmbiguousRestraint
3862 r"""__str__(AmbiguousRestraint self) -> std::string"""
3863 return _IMP_isd.AmbiguousRestraint___str__(self)
3866 r"""__repr__(AmbiguousRestraint self) -> std::string"""
3867 return _IMP_isd.AmbiguousRestraint___repr__(self)
3871 return _object_cast_to_AmbiguousRestraint(o)
3874 def _get_as_binary(self):
3875 r"""_get_as_binary(AmbiguousRestraint self) -> PyObject *"""
3876 return _IMP_isd.AmbiguousRestraint__get_as_binary(self)
3878 def _set_from_binary(self, p):
3879 r"""_set_from_binary(AmbiguousRestraint self, PyObject * p)"""
3880 return _IMP_isd.AmbiguousRestraint__set_from_binary(self, p)
3882 def __getstate__(self):
3883 p = self._get_as_binary()
3884 if len(self.__dict__) > 1:
3885 d = self.__dict__.copy()
3890 def __setstate__(self, p):
3891 if not hasattr(self,
'this'):
3893 if isinstance(p, tuple):
3895 self.__dict__.update(d)
3896 return self._set_from_binary(p)
3900 _IMP_isd.AmbiguousRestraint_swigregister(AmbiguousRestraint)
3901 IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM = _IMP_isd.IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM
3904 r"""Proxy of C++ IMP::isd::UnivariateFunction class."""
3906 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3908 def __init__(self, *args, **kwargs):
3909 raise AttributeError(
"No constructor defined - class is abstract")
3911 def __call__(self, *args):
3913 __call__(UnivariateFunction self, IMP::Floats const & x) -> IMP::Floats
3914 __call__(UnivariateFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
3915 __call__(UnivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
3917 return _IMP_isd.UnivariateFunction___call__(self, *args)
3919 def has_changed(self):
3920 r"""has_changed(UnivariateFunction self) -> bool"""
3921 return _IMP_isd.UnivariateFunction_has_changed(self)
3924 r"""update(UnivariateFunction self)"""
3925 return _IMP_isd.UnivariateFunction_update(self)
3927 def add_to_derivatives(self, x, accum):
3928 r"""add_to_derivatives(UnivariateFunction self, IMP::Floats const & x, DerivativeAccumulator accum)"""
3929 return _IMP_isd.UnivariateFunction_add_to_derivatives(self, x, accum)
3931 def add_to_particle_derivative(self, particle_no, value, accum):
3932 r"""add_to_particle_derivative(UnivariateFunction self, unsigned int particle_no, double value, DerivativeAccumulator accum)"""
3933 return _IMP_isd.UnivariateFunction_add_to_particle_derivative(self, particle_no, value, accum)
3935 def get_derivative_vector(self, particle_no, xlist):
3936 r"""get_derivative_vector(UnivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::VectorXd"""
3937 return _IMP_isd.UnivariateFunction_get_derivative_vector(self, particle_no, xlist)
3939 def get_derivative_matrix(self, xlist, stupid):
3940 r"""get_derivative_matrix(UnivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList"""
3941 return _IMP_isd.UnivariateFunction_get_derivative_matrix(self, xlist, stupid)
3943 def get_second_derivative_vector(self, *args):
3945 get_second_derivative_vector(UnivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::VectorXd
3946 get_second_derivative_vector(UnivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
3948 return _IMP_isd.UnivariateFunction_get_second_derivative_vector(self, *args)
3950 def get_ndims_x(self):
3951 r"""get_ndims_x(UnivariateFunction self) -> unsigned int"""
3952 return _IMP_isd.UnivariateFunction_get_ndims_x(self)
3954 def get_ndims_y(self):
3955 r"""get_ndims_y(UnivariateFunction self) -> unsigned int"""
3956 return _IMP_isd.UnivariateFunction_get_ndims_y(self)
3958 def get_number_of_particles(self):
3959 r"""get_number_of_particles(UnivariateFunction self) -> unsigned int"""
3960 return _IMP_isd.UnivariateFunction_get_number_of_particles(self)
3962 def get_particle_is_optimized(self, particle_no):
3963 r"""get_particle_is_optimized(UnivariateFunction self, unsigned int particle_no) -> bool"""
3964 return _IMP_isd.UnivariateFunction_get_particle_is_optimized(self, particle_no)
3966 def get_number_of_optimized_particles(self):
3967 r"""get_number_of_optimized_particles(UnivariateFunction self) -> unsigned int"""
3968 return _IMP_isd.UnivariateFunction_get_number_of_optimized_particles(self)
3971 r"""get_inputs(UnivariateFunction self) -> IMP::ModelObjectsTemp"""
3972 return _IMP_isd.UnivariateFunction_get_inputs(self)
3973 __swig_destroy__ = _IMP_isd.delete_UnivariateFunction
3976 r"""__str__(UnivariateFunction self) -> std::string"""
3977 return _IMP_isd.UnivariateFunction___str__(self)
3980 r"""__repr__(UnivariateFunction self) -> std::string"""
3981 return _IMP_isd.UnivariateFunction___repr__(self)
3985 return _object_cast_to_UnivariateFunction(o)
3989 _IMP_isd.UnivariateFunction_swigregister(UnivariateFunction)
3990 class Linear1DFunction(UnivariateFunction):
3991 r"""Proxy of C++ IMP::isd::Linear1DFunction class."""
3993 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3995 def __init__(self, a, b):
3996 r"""__init__(Linear1DFunction self, Particle a, Particle b) -> Linear1DFunction"""
3997 _IMP_isd.Linear1DFunction_swiginit(self, _IMP_isd.new_Linear1DFunction(a, b))
3999 def __call__(self, *args):
4001 __call__(Linear1DFunction self, IMP::Floats const & x) -> IMP::Floats
4002 __call__(Linear1DFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4003 __call__(Linear1DFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4005 return _IMP_isd.Linear1DFunction___call__(self, *args)
4007 def get_second_derivative_vector(self, *args):
4009 get_second_derivative_vector(Linear1DFunction self, unsigned int arg2, unsigned int arg3, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4010 get_second_derivative_vector(Linear1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4012 return _IMP_isd.Linear1DFunction_get_second_derivative_vector(self, *args)
4015 r"""get_version_info(Linear1DFunction self) -> VersionInfo"""
4016 return _IMP_isd.Linear1DFunction_get_version_info(self)
4017 __swig_destroy__ = _IMP_isd.delete_Linear1DFunction
4020 r"""__str__(Linear1DFunction self) -> std::string"""
4021 return _IMP_isd.Linear1DFunction___str__(self)
4024 r"""__repr__(Linear1DFunction self) -> std::string"""
4025 return _IMP_isd.Linear1DFunction___repr__(self)
4029 return _object_cast_to_Linear1DFunction(o)
4033 _IMP_isd.Linear1DFunction_swigregister(Linear1DFunction)
4034 class GeneralizedGuinierPorodFunction(UnivariateFunction):
4035 r"""Proxy of C++ IMP::isd::GeneralizedGuinierPorodFunction class."""
4037 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4039 def __init__(self, G, Rg, d, s, A):
4040 r"""__init__(GeneralizedGuinierPorodFunction self, Particle G, Particle Rg, Particle d, Particle s, Particle A) -> GeneralizedGuinierPorodFunction"""
4041 _IMP_isd.GeneralizedGuinierPorodFunction_swiginit(self, _IMP_isd.new_GeneralizedGuinierPorodFunction(G, Rg, d, s, A))
4043 def __call__(self, *args):
4045 __call__(GeneralizedGuinierPorodFunction self, IMP::Floats const & x) -> IMP::Floats
4046 __call__(GeneralizedGuinierPorodFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4047 __call__(GeneralizedGuinierPorodFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4049 return _IMP_isd.GeneralizedGuinierPorodFunction___call__(self, *args)
4051 def get_second_derivative_vector(self, *args):
4053 get_second_derivative_vector(GeneralizedGuinierPorodFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4054 get_second_derivative_vector(GeneralizedGuinierPorodFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4056 return _IMP_isd.GeneralizedGuinierPorodFunction_get_second_derivative_vector(self, *args)
4059 r"""get_version_info(GeneralizedGuinierPorodFunction self) -> VersionInfo"""
4060 return _IMP_isd.GeneralizedGuinierPorodFunction_get_version_info(self)
4061 __swig_destroy__ = _IMP_isd.delete_GeneralizedGuinierPorodFunction
4064 r"""__str__(GeneralizedGuinierPorodFunction self) -> std::string"""
4065 return _IMP_isd.GeneralizedGuinierPorodFunction___str__(self)
4068 r"""__repr__(GeneralizedGuinierPorodFunction self) -> std::string"""
4069 return _IMP_isd.GeneralizedGuinierPorodFunction___repr__(self)
4073 return _object_cast_to_GeneralizedGuinierPorodFunction(o)
4077 _IMP_isd.GeneralizedGuinierPorodFunction_swigregister(GeneralizedGuinierPorodFunction)
4078 IMP_ISD_BIVARIATE_FUNCTIONS_MINIMUM = _IMP_isd.IMP_ISD_BIVARIATE_FUNCTIONS_MINIMUM
4081 r"""Proxy of C++ IMP::isd::BivariateFunction class."""
4083 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4085 def __init__(self, *args, **kwargs):
4086 raise AttributeError(
"No constructor defined - class is abstract")
4088 def __call__(self, *args):
4090 __call__(BivariateFunction self, IMP::Floats const & x1, IMP::Floats const & x2) -> IMP::Floats
4091 __call__(BivariateFunction self, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4092 __call__(BivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4094 return _IMP_isd.BivariateFunction___call__(self, *args)
4096 def has_changed(self):
4097 r"""has_changed(BivariateFunction self) -> bool"""
4098 return _IMP_isd.BivariateFunction_has_changed(self)
4101 r"""update(BivariateFunction self)"""
4102 return _IMP_isd.BivariateFunction_update(self)
4104 def add_to_derivatives(self, x1, x2, accum):
4105 r"""add_to_derivatives(BivariateFunction self, IMP::Floats const & x1, IMP::Floats const & x2, DerivativeAccumulator accum)"""
4106 return _IMP_isd.BivariateFunction_add_to_derivatives(self, x1, x2, accum)
4108 def add_to_particle_derivative(self, particle_no, value, accum):
4109 r"""add_to_particle_derivative(BivariateFunction self, unsigned int particle_no, double value, DerivativeAccumulator accum)"""
4110 return _IMP_isd.BivariateFunction_add_to_particle_derivative(self, particle_no, value, accum)
4112 def get_derivative_matrix(self, *args):
4114 get_derivative_matrix(BivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4115 get_derivative_matrix(BivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4117 return _IMP_isd.BivariateFunction_get_derivative_matrix(self, *args)
4119 def get_second_derivative_matrix(self, *args):
4121 get_second_derivative_matrix(BivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4122 get_second_derivative_matrix(BivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4124 return _IMP_isd.BivariateFunction_get_second_derivative_matrix(self, *args)
4126 def get_ndims_x1(self):
4127 r"""get_ndims_x1(BivariateFunction self) -> unsigned int"""
4128 return _IMP_isd.BivariateFunction_get_ndims_x1(self)
4130 def get_ndims_x2(self):
4131 r"""get_ndims_x2(BivariateFunction self) -> unsigned int"""
4132 return _IMP_isd.BivariateFunction_get_ndims_x2(self)
4134 def get_ndims_y(self):
4135 r"""get_ndims_y(BivariateFunction self) -> unsigned int"""
4136 return _IMP_isd.BivariateFunction_get_ndims_y(self)
4138 def get_number_of_particles(self):
4139 r"""get_number_of_particles(BivariateFunction self) -> unsigned int"""
4140 return _IMP_isd.BivariateFunction_get_number_of_particles(self)
4142 def get_particle_is_optimized(self, particle_no):
4143 r"""get_particle_is_optimized(BivariateFunction self, unsigned int particle_no) -> bool"""
4144 return _IMP_isd.BivariateFunction_get_particle_is_optimized(self, particle_no)
4146 def get_number_of_optimized_particles(self):
4147 r"""get_number_of_optimized_particles(BivariateFunction self) -> unsigned int"""
4148 return _IMP_isd.BivariateFunction_get_number_of_optimized_particles(self)
4151 r"""get_inputs(BivariateFunction self) -> IMP::ModelObjectsTemp"""
4152 return _IMP_isd.BivariateFunction_get_inputs(self)
4153 __swig_destroy__ = _IMP_isd.delete_BivariateFunction
4156 r"""__str__(BivariateFunction self) -> std::string"""
4157 return _IMP_isd.BivariateFunction___str__(self)
4160 r"""__repr__(BivariateFunction self) -> std::string"""
4161 return _IMP_isd.BivariateFunction___repr__(self)
4165 return _object_cast_to_BivariateFunction(o)
4169 _IMP_isd.BivariateFunction_swigregister(BivariateFunction)
4170 class Covariance1DFunction(BivariateFunction):
4171 r"""Proxy of C++ IMP::isd::Covariance1DFunction class."""
4173 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4175 def __init__(self, tau, ilambda, alpha=2.0, jitter=0.0, cutoff=1e-7):
4176 r"""__init__(Covariance1DFunction self, Particle tau, Particle ilambda, double alpha=2.0, double jitter=0.0, double cutoff=1e-7) -> Covariance1DFunction"""
4177 _IMP_isd.Covariance1DFunction_swiginit(self, _IMP_isd.new_Covariance1DFunction(tau, ilambda, alpha, jitter, cutoff))
4179 def __call__(self, *args):
4181 __call__(Covariance1DFunction self, IMP::Floats const & x1, IMP::Floats const & x2) -> IMP::Floats
4182 __call__(Covariance1DFunction self, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4183 __call__(Covariance1DFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4185 return _IMP_isd.Covariance1DFunction___call__(self, *args)
4187 def get_derivative_matrix(self, *args):
4189 get_derivative_matrix(Covariance1DFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4190 get_derivative_matrix(Covariance1DFunction self, unsigned int particle_no, IMP::FloatsList const & xlist, bool arg4) -> IMP::FloatsList
4192 return _IMP_isd.Covariance1DFunction_get_derivative_matrix(self, *args)
4194 def get_second_derivative_matrix(self, *args):
4196 get_second_derivative_matrix(Covariance1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4197 get_second_derivative_matrix(Covariance1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4199 return _IMP_isd.Covariance1DFunction_get_second_derivative_matrix(self, *args)
4202 r"""get_version_info(Covariance1DFunction self) -> VersionInfo"""
4203 return _IMP_isd.Covariance1DFunction_get_version_info(self)
4204 __swig_destroy__ = _IMP_isd.delete_Covariance1DFunction
4207 r"""__str__(Covariance1DFunction self) -> std::string"""
4208 return _IMP_isd.Covariance1DFunction___str__(self)
4211 r"""__repr__(Covariance1DFunction self) -> std::string"""
4212 return _IMP_isd.Covariance1DFunction___repr__(self)
4216 return _object_cast_to_Covariance1DFunction(o)
4220 _IMP_isd.Covariance1DFunction_swigregister(Covariance1DFunction)
4221 class GaussianProcessInterpolation(
IMP.Object):
4222 r"""Proxy of C++ IMP::isd::GaussianProcessInterpolation class."""
4224 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4226 def __init__(self, x, sample_mean, sample_std, n_obs, mean_function, covariance_function, sigma, sparse_cutoff=1e-7):
4227 r"""__init__(GaussianProcessInterpolation self, IMP::FloatsList x, IMP::Floats sample_mean, IMP::Floats sample_std, unsigned int n_obs, UnivariateFunction mean_function, BivariateFunction covariance_function, Particle sigma, double sparse_cutoff=1e-7) -> GaussianProcessInterpolation"""
4228 _IMP_isd.GaussianProcessInterpolation_swiginit(self, _IMP_isd.new_GaussianProcessInterpolation(x, sample_mean, sample_std, n_obs, mean_function, covariance_function, sigma, sparse_cutoff))
4230 def get_posterior_mean(self, x):
4231 r"""get_posterior_mean(GaussianProcessInterpolation self, IMP::Floats x) -> double"""
4232 return _IMP_isd.GaussianProcessInterpolation_get_posterior_mean(self, x)
4234 def get_posterior_covariance(self, x1, x2):
4235 r"""get_posterior_covariance(GaussianProcessInterpolation self, IMP::Floats x1, IMP::Floats x2) -> double"""
4236 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance(self, x1, x2)
4238 def get_posterior_covariance_matrix(self, x, arg3):
4239 r"""get_posterior_covariance_matrix(GaussianProcessInterpolation self, IMP::FloatsList x, bool arg3) -> IMP::FloatsList"""
4240 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_matrix(self, x, arg3)
4242 def get_posterior_covariance_derivative(self, x, arg3):
4243 r"""get_posterior_covariance_derivative(GaussianProcessInterpolation self, IMP::Floats x, bool arg3) -> IMP::Floats"""
4244 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_derivative(self, x, arg3)
4246 def get_posterior_covariance_hessian(self, x, arg3):
4247 r"""get_posterior_covariance_hessian(GaussianProcessInterpolation self, IMP::Floats x, bool arg3) -> IMP::FloatsList"""
4248 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_hessian(self, x, arg3)
4251 r"""get_inputs(GaussianProcessInterpolation self) -> IMP::ModelObjectsTemp"""
4252 return _IMP_isd.GaussianProcessInterpolation_get_inputs(self)
4254 def force_mean_update(self):
4255 r"""force_mean_update(GaussianProcessInterpolation self)"""
4256 return _IMP_isd.GaussianProcessInterpolation_force_mean_update(self)
4258 def force_covariance_update(self):
4259 r"""force_covariance_update(GaussianProcessInterpolation self)"""
4260 return _IMP_isd.GaussianProcessInterpolation_force_covariance_update(self)
4262 def get_number_of_m_particles(self):
4263 r"""get_number_of_m_particles(GaussianProcessInterpolation self) -> unsigned int"""
4264 return _IMP_isd.GaussianProcessInterpolation_get_number_of_m_particles(self)
4266 def get_m_particle_is_optimized(self, i):
4267 r"""get_m_particle_is_optimized(GaussianProcessInterpolation self, unsigned int i) -> bool"""
4268 return _IMP_isd.GaussianProcessInterpolation_get_m_particle_is_optimized(self, i)
4270 def get_number_of_Omega_particles(self):
4271 r"""get_number_of_Omega_particles(GaussianProcessInterpolation self) -> unsigned int"""
4272 return _IMP_isd.GaussianProcessInterpolation_get_number_of_Omega_particles(self)
4274 def get_Omega_particle_is_optimized(self, i):
4275 r"""get_Omega_particle_is_optimized(GaussianProcessInterpolation self, unsigned int i) -> bool"""
4276 return _IMP_isd.GaussianProcessInterpolation_get_Omega_particle_is_optimized(self, i)
4278 def get_data_abscissa(self):
4279 r"""get_data_abscissa(GaussianProcessInterpolation self) -> IMP::FloatsList"""
4280 return _IMP_isd.GaussianProcessInterpolation_get_data_abscissa(self)
4282 def get_data_mean(self):
4283 r"""get_data_mean(GaussianProcessInterpolation self) -> IMP::Floats"""
4284 return _IMP_isd.GaussianProcessInterpolation_get_data_mean(self)
4286 def get_data_variance(self):
4287 r"""get_data_variance(GaussianProcessInterpolation self) -> IMP::FloatsList"""
4288 return _IMP_isd.GaussianProcessInterpolation_get_data_variance(self)
4291 r"""get_version_info(GaussianProcessInterpolation self) -> VersionInfo"""
4292 return _IMP_isd.GaussianProcessInterpolation_get_version_info(self)
4293 __swig_destroy__ = _IMP_isd.delete_GaussianProcessInterpolation
4296 r"""__str__(GaussianProcessInterpolation self) -> std::string"""
4297 return _IMP_isd.GaussianProcessInterpolation___str__(self)
4300 r"""__repr__(GaussianProcessInterpolation self) -> std::string"""
4301 return _IMP_isd.GaussianProcessInterpolation___repr__(self)
4305 return _object_cast_to_GaussianProcessInterpolation(o)
4309 _IMP_isd.GaussianProcessInterpolation_swigregister(GaussianProcessInterpolation)
4311 r"""Proxy of C++ IMP::isd::GaussianProcessInterpolationRestraint class."""
4313 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4315 def __init__(self, m, gpi):
4316 r"""__init__(GaussianProcessInterpolationRestraint self, Model m, GaussianProcessInterpolation gpi) -> GaussianProcessInterpolationRestraint"""
4317 _IMP_isd.GaussianProcessInterpolationRestraint_swiginit(self, _IMP_isd.new_GaussianProcessInterpolationRestraint(m, gpi))
4319 def get_probability(self):
4320 r"""get_probability(GaussianProcessInterpolationRestraint self) -> double"""
4321 return _IMP_isd.GaussianProcessInterpolationRestraint_get_probability(self)
4323 def set_use_cg(self, use, tol):
4324 r"""set_use_cg(GaussianProcessInterpolationRestraint self, bool use, double tol)"""
4325 return _IMP_isd.GaussianProcessInterpolationRestraint_set_use_cg(self, use, tol)
4327 def get_minus_log_normalization(self):
4328 r"""get_minus_log_normalization(GaussianProcessInterpolationRestraint self) -> double"""
4329 return _IMP_isd.GaussianProcessInterpolationRestraint_get_minus_log_normalization(self)
4331 def get_minus_exponent(self):
4332 r"""get_minus_exponent(GaussianProcessInterpolationRestraint self) -> double"""
4333 return _IMP_isd.GaussianProcessInterpolationRestraint_get_minus_exponent(self)
4335 def get_logdet_hessian(self):
4336 r"""get_logdet_hessian(GaussianProcessInterpolationRestraint self) -> double"""
4337 return _IMP_isd.GaussianProcessInterpolationRestraint_get_logdet_hessian(self)
4339 def get_hessian(self, *args):
4341 get_hessian(GaussianProcessInterpolationRestraint self) -> Eigen::MatrixXd
4342 get_hessian(GaussianProcessInterpolationRestraint self, bool unused) -> IMP::FloatsList
4344 return _IMP_isd.GaussianProcessInterpolationRestraint_get_hessian(self, *args)
4347 r"""do_get_inputs(GaussianProcessInterpolationRestraint self) -> IMP::ModelObjectsTemp"""
4348 return _IMP_isd.GaussianProcessInterpolationRestraint_do_get_inputs(self)
4351 r"""get_version_info(GaussianProcessInterpolationRestraint self) -> VersionInfo"""
4352 return _IMP_isd.GaussianProcessInterpolationRestraint_get_version_info(self)
4353 __swig_destroy__ = _IMP_isd.delete_GaussianProcessInterpolationRestraint
4356 r"""__str__(GaussianProcessInterpolationRestraint self) -> std::string"""
4357 return _IMP_isd.GaussianProcessInterpolationRestraint___str__(self)
4360 r"""__repr__(GaussianProcessInterpolationRestraint self) -> std::string"""
4361 return _IMP_isd.GaussianProcessInterpolationRestraint___repr__(self)
4365 return _object_cast_to_GaussianProcessInterpolationRestraint(o)
4369 _IMP_isd.GaussianProcessInterpolationRestraint_swigregister(GaussianProcessInterpolationRestraint)
4371 r"""Proxy of C++ IMP::isd::MolecularDynamics class."""
4373 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4375 def __init__(self, m=None):
4376 r"""__init__(MolecularDynamics self, Model m=None) -> MolecularDynamics"""
4377 _IMP_isd.MolecularDynamics_swiginit(self, _IMP_isd.new_MolecularDynamics(m))
4380 r"""__str__(MolecularDynamics self) -> std::string"""
4381 return _IMP_isd.MolecularDynamics___str__(self)
4384 r"""__repr__(MolecularDynamics self) -> std::string"""
4385 return _IMP_isd.MolecularDynamics___repr__(self)
4389 return _object_cast_to_MolecularDynamics(o)
4391 __swig_destroy__ = _IMP_isd.delete_MolecularDynamics
4394 _IMP_isd.MolecularDynamics_swigregister(MolecularDynamics)
4396 r"""Proxy of C++ IMP::isd::MolecularDynamicsMover class."""
4398 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4400 def __init__(self, m, nsteps=100, timestep=1.):
4401 r"""__init__(MolecularDynamicsMover self, Model m, unsigned int nsteps=100, IMP::Float timestep=1.) -> MolecularDynamicsMover"""
4402 _IMP_isd.MolecularDynamicsMover_swiginit(self, _IMP_isd.new_MolecularDynamicsMover(m, nsteps, timestep))
4405 r"""get_md(MolecularDynamicsMover self) -> MolecularDynamics"""
4406 return _IMP_isd.MolecularDynamicsMover_get_md(self)
4408 def get_number_of_md_steps(self):
4409 r"""get_number_of_md_steps(MolecularDynamicsMover self) -> unsigned int"""
4410 return _IMP_isd.MolecularDynamicsMover_get_number_of_md_steps(self)
4412 def set_number_of_md_steps(self, nsteps):
4413 r"""set_number_of_md_steps(MolecularDynamicsMover self, unsigned int nsteps)"""
4414 return _IMP_isd.MolecularDynamicsMover_set_number_of_md_steps(self, nsteps)
4417 r"""get_version_info(MolecularDynamicsMover self) -> VersionInfo"""
4418 return _IMP_isd.MolecularDynamicsMover_get_version_info(self)
4419 __swig_destroy__ = _IMP_isd.delete_MolecularDynamicsMover
4422 r"""__str__(MolecularDynamicsMover self) -> std::string"""
4423 return _IMP_isd.MolecularDynamicsMover___str__(self)
4426 r"""__repr__(MolecularDynamicsMover self) -> std::string"""
4427 return _IMP_isd.MolecularDynamicsMover___repr__(self)
4431 return _object_cast_to_MolecularDynamicsMover(o)
4435 _IMP_isd.MolecularDynamicsMover_swigregister(MolecularDynamicsMover)
4437 r"""Proxy of C++ IMP::isd::HybridMonteCarlo class."""
4439 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4441 def __init__(self, m, kT=1.0, steps=100, timestep=1.0, persistence=1):
4442 r"""__init__(HybridMonteCarlo self, Model m, IMP::Float kT=1.0, unsigned int steps=100, IMP::Float timestep=1.0, unsigned int persistence=1) -> HybridMonteCarlo"""
4443 _IMP_isd.HybridMonteCarlo_swiginit(self, _IMP_isd.new_HybridMonteCarlo(m, kT, steps, timestep, persistence))
4445 def get_kinetic_energy(self):
4446 r"""get_kinetic_energy(HybridMonteCarlo self) -> IMP::Float"""
4447 return _IMP_isd.HybridMonteCarlo_get_kinetic_energy(self)
4449 def get_potential_energy(self):
4450 r"""get_potential_energy(HybridMonteCarlo self) -> IMP::Float"""
4451 return _IMP_isd.HybridMonteCarlo_get_potential_energy(self)
4453 def get_total_energy(self):
4454 r"""get_total_energy(HybridMonteCarlo self) -> IMP::Float"""
4455 return _IMP_isd.HybridMonteCarlo_get_total_energy(self)
4457 def set_timestep(self, ts):
4458 r"""set_timestep(HybridMonteCarlo self, IMP::Float ts)"""
4459 return _IMP_isd.HybridMonteCarlo_set_timestep(self, ts)
4461 def get_timestep(self):
4462 r"""get_timestep(HybridMonteCarlo self) -> double"""
4463 return _IMP_isd.HybridMonteCarlo_get_timestep(self)
4465 def set_number_of_md_steps(self, nsteps):
4466 r"""set_number_of_md_steps(HybridMonteCarlo self, unsigned int nsteps)"""
4467 return _IMP_isd.HybridMonteCarlo_set_number_of_md_steps(self, nsteps)
4469 def get_number_of_md_steps(self):
4470 r"""get_number_of_md_steps(HybridMonteCarlo self) -> unsigned int"""
4471 return _IMP_isd.HybridMonteCarlo_get_number_of_md_steps(self)
4473 def set_persistence(self, persistence=1):
4474 r"""set_persistence(HybridMonteCarlo self, unsigned int persistence=1)"""
4475 return _IMP_isd.HybridMonteCarlo_set_persistence(self, persistence)
4477 def get_persistence(self):
4478 r"""get_persistence(HybridMonteCarlo self) -> unsigned int"""
4479 return _IMP_isd.HybridMonteCarlo_get_persistence(self)
4482 r"""get_md(HybridMonteCarlo self) -> MolecularDynamics"""
4483 return _IMP_isd.HybridMonteCarlo_get_md(self)
4485 def do_evaluate(self, arg2, arg3):
4486 r"""do_evaluate(HybridMonteCarlo self, IMP::ParticleIndexes const & arg2, bool arg3) -> double"""
4487 return _IMP_isd.HybridMonteCarlo_do_evaluate(self, arg2, arg3)
4490 r"""do_step(HybridMonteCarlo self)"""
4491 return _IMP_isd.HybridMonteCarlo_do_step(self)
4492 __swig_destroy__ = _IMP_isd.delete_HybridMonteCarlo
4495 r"""__str__(HybridMonteCarlo self) -> std::string"""
4496 return _IMP_isd.HybridMonteCarlo___str__(self)
4499 r"""__repr__(HybridMonteCarlo self) -> std::string"""
4500 return _IMP_isd.HybridMonteCarlo___repr__(self)
4504 return _object_cast_to_HybridMonteCarlo(o)
4508 _IMP_isd.HybridMonteCarlo_swigregister(HybridMonteCarlo)
4510 r"""Proxy of C++ IMP::isd::FretData class."""
4512 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4514 def __init__(self, *args):
4516 __init__(FretData self, IMP::Floats d_term, IMP::Floats d_center, IMP::Floats d_int, IMP::Floats s_grid, IMP::Float R0, IMP::Float Rmin, IMP::Float Rmax, bool do_limit=True) -> FretData
4517 __init__(FretData self) -> FretData
4519 _IMP_isd.FretData_swiginit(self, _IMP_isd.new_FretData(*args))
4521 def get_closest(self, vec, value):
4522 r"""get_closest(FretData self, DistBase vec, double value) -> int"""
4523 return _IMP_isd.FretData_get_closest(self, vec, value)
4525 def get_probability(self, distn, dist, sigma):
4526 r"""get_probability(FretData self, IMP::Float distn, IMP::Float dist, IMP::Float sigma) -> IMP::Float"""
4527 return _IMP_isd.FretData_get_probability(self, distn, dist, sigma)
4529 def get_kernel(self, dist, R0):
4530 r"""get_kernel(FretData self, IMP::Float dist, IMP::Float R0) -> IMP::Float"""
4531 return _IMP_isd.FretData_get_kernel(self, dist, R0)
4533 def get_marginal_element(self, d_term, d_center, sigma):
4534 r"""get_marginal_element(FretData self, IMP::Float d_term, IMP::Float d_center, IMP::Float sigma) -> IMP::FloatPair"""
4535 return _IMP_isd.FretData_get_marginal_element(self, d_term, d_center, sigma)
4538 r"""get_version_info(FretData self) -> VersionInfo"""
4539 return _IMP_isd.FretData_get_version_info(self)
4540 __swig_destroy__ = _IMP_isd.delete_FretData
4543 r"""__str__(FretData self) -> std::string"""
4544 return _IMP_isd.FretData___str__(self)
4547 r"""__repr__(FretData self) -> std::string"""
4548 return _IMP_isd.FretData___repr__(self)
4552 return _object_cast_to_FretData(o)
4555 def _get_as_binary(self):
4556 r"""_get_as_binary(FretData self) -> PyObject *"""
4557 return _IMP_isd.FretData__get_as_binary(self)
4559 def _set_from_binary(self, p):
4560 r"""_set_from_binary(FretData self, PyObject * p)"""
4561 return _IMP_isd.FretData__set_from_binary(self, p)
4563 def __getstate__(self):
4564 p = self._get_as_binary()
4565 if len(self.__dict__) > 1:
4566 d = self.__dict__.copy()
4571 def __setstate__(self, p):
4572 if not hasattr(self,
'this'):
4574 if isinstance(p, tuple):
4576 self.__dict__.update(d)
4577 return self._set_from_binary(p)
4581 _IMP_isd.FretData_swigregister(FretData)
4583 r"""Proxy of C++ IMP::isd::FretRestraint class."""
4585 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4587 def __init__(self, *args):
4589 __init__(FretRestraint self, IMP::ParticlesTemp pd, IMP::ParticlesTemp pa, Particle kda, Particle Ida, Particle R0, Particle sigma0, Particle Pbl, double fexp, double m_d=1.0, double m_a=1.0) -> FretRestraint
4590 __init__(FretRestraint self, Particle kda, Particle Ida, Particle sumFi, Particle sigma0, Particle Pbl, double fexp) -> FretRestraint
4591 __init__(FretRestraint self, Particle prd, Vector3D GMMterd, IMP::algebra::Vector3Ds GMMctrd, IMP::Floats GMMwd, IMP::Floats GMMsigd, Particle pra, Vector3D GMMtera, IMP::algebra::Vector3Ds GMMctra, IMP::Floats GMMwa, IMP::Floats GMMsiga, Particle kda, Particle Ida, Particle sigma0, Particle Pbl, FretData data, double fexp) -> FretRestraint
4592 __init__(FretRestraint self) -> FretRestraint
4594 _IMP_isd.FretRestraint_swiginit(self, _IMP_isd.new_FretRestraint(*args))
4596 def get_sumFi(self):
4597 r"""get_sumFi(FretRestraint self) -> double"""
4598 return _IMP_isd.FretRestraint_get_sumFi(self)
4600 def get_average_sigma(self, fmod):
4601 r"""get_average_sigma(FretRestraint self, double fmod) -> double"""
4602 return _IMP_isd.FretRestraint_get_average_sigma(self, fmod)
4604 def get_standard_error(self):
4605 r"""get_standard_error(FretRestraint self) -> double"""
4606 return _IMP_isd.FretRestraint_get_standard_error(self)
4608 def get_model_fretr(self):
4609 r"""get_model_fretr(FretRestraint self) -> double"""
4610 return _IMP_isd.FretRestraint_get_model_fretr(self)
4612 def get_probability(self):
4613 r"""get_probability(FretRestraint self) -> double"""
4614 return _IMP_isd.FretRestraint_get_probability(self)
4616 def get_experimental_value(self):
4617 r"""get_experimental_value(FretRestraint self) -> double"""
4618 return _IMP_isd.FretRestraint_get_experimental_value(self)
4620 def set_experimental_value(self, fexp):
4621 r"""set_experimental_value(FretRestraint self, double fexp)"""
4622 return _IMP_isd.FretRestraint_set_experimental_value(self, fexp)
4625 r"""do_get_inputs(FretRestraint self) -> IMP::ModelObjectsTemp"""
4626 return _IMP_isd.FretRestraint_do_get_inputs(self)
4629 r"""get_version_info(FretRestraint self) -> VersionInfo"""
4630 return _IMP_isd.FretRestraint_get_version_info(self)
4631 __swig_destroy__ = _IMP_isd.delete_FretRestraint
4634 r"""__str__(FretRestraint self) -> std::string"""
4635 return _IMP_isd.FretRestraint___str__(self)
4638 r"""__repr__(FretRestraint self) -> std::string"""
4639 return _IMP_isd.FretRestraint___repr__(self)
4643 return _object_cast_to_FretRestraint(o)
4646 def _get_as_binary(self):
4647 r"""_get_as_binary(FretRestraint self) -> PyObject *"""
4648 return _IMP_isd.FretRestraint__get_as_binary(self)
4650 def _set_from_binary(self, p):
4651 r"""_set_from_binary(FretRestraint self, PyObject * p)"""
4652 return _IMP_isd.FretRestraint__set_from_binary(self, p)
4654 def __getstate__(self):
4655 p = self._get_as_binary()
4656 if len(self.__dict__) > 1:
4657 d = self.__dict__.copy()
4662 def __setstate__(self, p):
4663 if not hasattr(self,
'this'):
4665 if isinstance(p, tuple):
4667 self.__dict__.update(d)
4668 return self._set_from_binary(p)
4672 _IMP_isd.FretRestraint_swigregister(FretRestraint)
4674 r"""Proxy of C++ IMP::isd::CysteineCrossLinkData class."""
4676 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4678 def __init__(self, *args):
4680 __init__(CysteineCrossLinkData self, double fexp, IMP::Floats fmod_grid, IMP::Floats omega_grid, IMP::Floats omega0_grid, int prior_type=3) -> CysteineCrossLinkData
4681 __init__(CysteineCrossLinkData self) -> CysteineCrossLinkData
4683 _IMP_isd.CysteineCrossLinkData_swiginit(self, _IMP_isd.new_CysteineCrossLinkData(*args))
4685 def get_closest(self, vec, value):
4686 r"""get_closest(CysteineCrossLinkData self, DistBase vec, double value) -> int"""
4687 return _IMP_isd.CysteineCrossLinkData_get_closest(self, vec, value)
4689 def get_omegas(self, fmods, omega0):
4690 r"""get_omegas(CysteineCrossLinkData self, IMP::Floats fmods, double omega0) -> IMP::Floats"""
4691 return _IMP_isd.CysteineCrossLinkData_get_omegas(self, fmods, omega0)
4693 def get_nonmarginal_elements(self, fexp, fmods, omega):
4694 r"""get_nonmarginal_elements(CysteineCrossLinkData self, double fexp, IMP::Floats fmods, double omega) -> IMP::Floats"""
4695 return _IMP_isd.CysteineCrossLinkData_get_nonmarginal_elements(self, fexp, fmods, omega)
4697 def get_marginal_elements(self, fmods, omega0):
4698 r"""get_marginal_elements(CysteineCrossLinkData self, IMP::Floats fmods, double omega0) -> IMP::Floats"""
4699 return _IMP_isd.CysteineCrossLinkData_get_marginal_elements(self, fmods, omega0)
4701 def get_omega(self, fmod, omega0):
4702 r"""get_omega(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4703 return _IMP_isd.CysteineCrossLinkData_get_omega(self, fmod, omega0)
4705 def get_standard_deviation(self, fmod, omega0):
4706 r"""get_standard_deviation(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4707 return _IMP_isd.CysteineCrossLinkData_get_standard_deviation(self, fmod, omega0)
4709 def get_nonmarginal_element(self, fexp, fmod, omega):
4710 r"""get_nonmarginal_element(CysteineCrossLinkData self, double fexp, double fmod, double omega) -> double"""
4711 return _IMP_isd.CysteineCrossLinkData_get_nonmarginal_element(self, fexp, fmod, omega)
4713 def get_marginal_element(self, fmod, omega0):
4714 r"""get_marginal_element(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4715 return _IMP_isd.CysteineCrossLinkData_get_marginal_element(self, fmod, omega0)
4718 r"""get_version_info(CysteineCrossLinkData self) -> VersionInfo"""
4719 return _IMP_isd.CysteineCrossLinkData_get_version_info(self)
4720 __swig_destroy__ = _IMP_isd.delete_CysteineCrossLinkData
4723 r"""__str__(CysteineCrossLinkData self) -> std::string"""
4724 return _IMP_isd.CysteineCrossLinkData___str__(self)
4727 r"""__repr__(CysteineCrossLinkData self) -> std::string"""
4728 return _IMP_isd.CysteineCrossLinkData___repr__(self)
4732 return _object_cast_to_CysteineCrossLinkData(o)
4735 def _get_as_binary(self):
4736 r"""_get_as_binary(CysteineCrossLinkData self) -> PyObject *"""
4737 return _IMP_isd.CysteineCrossLinkData__get_as_binary(self)
4739 def _set_from_binary(self, p):
4740 r"""_set_from_binary(CysteineCrossLinkData self, PyObject * p)"""
4741 return _IMP_isd.CysteineCrossLinkData__set_from_binary(self, p)
4743 def __getstate__(self):
4744 p = self._get_as_binary()
4745 if len(self.__dict__) > 1:
4746 d = self.__dict__.copy()
4751 def __setstate__(self, p):
4752 if not hasattr(self,
'this'):
4754 if isinstance(p, tuple):
4756 self.__dict__.update(d)
4757 return self._set_from_binary(p)
4761 _IMP_isd.CysteineCrossLinkData_swigregister(CysteineCrossLinkData)
4763 r"""Proxy of C++ IMP::isd::CrossLinkData class."""
4765 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4767 def __init__(self, *args):
4769 __init__(CrossLinkData self, IMP::Floats dist_grid, IMP::Floats omega_grid, IMP::Floats sigma_grid, double lexp_, double don=std::numeric_limits< double >::max(), double doff=std::numeric_limits< double >::max(), int prior_type=0) -> CrossLinkData
4770 __init__(CrossLinkData self, IMP::Floats dist_grid, IMP::Floats omega_grid, IMP::Floats sigma_grid, IMP::Floats pot_x_grid, IMP::Floats pot_value_grid, double don=std::numeric_limits< double >::max(), double doff=std::numeric_limits< double >::max(), int prior_type=0) -> CrossLinkData
4771 __init__(CrossLinkData self) -> CrossLinkData
4773 _IMP_isd.CrossLinkData_swiginit(self, _IMP_isd.new_CrossLinkData(*args))
4775 def get_closest(self, vec, value):
4776 r"""get_closest(CrossLinkData self, DistBase vec, double value) -> int"""
4777 return _IMP_isd.CrossLinkData_get_closest(self, vec, value)
4779 def get_omegas(self, sigma, dists):
4780 r"""get_omegas(CrossLinkData self, double sigma, IMP::Floats dists) -> IMP::Floats"""
4781 return _IMP_isd.CrossLinkData_get_omegas(self, sigma, dists)
4783 def get_omega_prior(self, omega, omega0):
4784 r"""get_omega_prior(CrossLinkData self, double omega, double omega0) -> double"""
4785 return _IMP_isd.CrossLinkData_get_omega_prior(self, omega, omega0)
4787 def get_nonmarginal_elements(self, sigmai, dists):
4788 r"""get_nonmarginal_elements(CrossLinkData self, double sigmai, IMP::Floats dists) -> IMP::Floats"""
4789 return _IMP_isd.CrossLinkData_get_nonmarginal_elements(self, sigmai, dists)
4791 def get_marginal_elements(self, sigma, dists):
4792 r"""get_marginal_elements(CrossLinkData self, double sigma, IMP::Floats dists) -> IMP::Floats"""
4793 return _IMP_isd.CrossLinkData_get_marginal_elements(self, sigma, dists)
4795 def get_marginal_maximum(self, *args):
4797 get_marginal_maximum(CrossLinkData self, double sigma) -> double
4798 get_marginal_maximum(CrossLinkData self) -> double
4800 return _IMP_isd.CrossLinkData_get_marginal_maximum(self, *args)
4803 r"""get_version_info(CrossLinkData self) -> VersionInfo"""
4804 return _IMP_isd.CrossLinkData_get_version_info(self)
4805 __swig_destroy__ = _IMP_isd.delete_CrossLinkData
4808 r"""__str__(CrossLinkData self) -> std::string"""
4809 return _IMP_isd.CrossLinkData___str__(self)
4812 r"""__repr__(CrossLinkData self) -> std::string"""
4813 return _IMP_isd.CrossLinkData___repr__(self)
4817 return _object_cast_to_CrossLinkData(o)
4820 def _get_as_binary(self):
4821 r"""_get_as_binary(CrossLinkData self) -> PyObject *"""
4822 return _IMP_isd.CrossLinkData__get_as_binary(self)
4824 def _set_from_binary(self, p):
4825 r"""_set_from_binary(CrossLinkData self, PyObject * p)"""
4826 return _IMP_isd.CrossLinkData__set_from_binary(self, p)
4828 def __getstate__(self):
4829 p = self._get_as_binary()
4830 if len(self.__dict__) > 1:
4831 d = self.__dict__.copy()
4836 def __setstate__(self, p):
4837 if not hasattr(self,
'this'):
4839 if isinstance(p, tuple):
4841 self.__dict__.update(d)
4842 return self._set_from_binary(p)
4846 _IMP_isd.CrossLinkData_swigregister(CrossLinkData)
4848 r"""Proxy of C++ IMP::isd::CysteineCrossLinkRestraint class."""
4850 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4852 def __init__(self, *args):
4854 __init__(CysteineCrossLinkRestraint self, Model m, _ParticleIndexAdaptor beta, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor epsilon, _ParticleIndexAdaptor weight, CrossLinkData data, double fexp) -> CysteineCrossLinkRestraint
4855 __init__(CysteineCrossLinkRestraint self, Model m, _ParticleIndexAdaptor beta, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor epsilon, _ParticleIndexAdaptor weight, CrossLinkData data, CysteineCrossLinkData ccldata) -> CysteineCrossLinkRestraint
4856 __init__(CysteineCrossLinkRestraint self) -> CysteineCrossLinkRestraint
4858 _IMP_isd.CysteineCrossLinkRestraint_swiginit(self, _IMP_isd.new_CysteineCrossLinkRestraint(*args))
4860 def get_probability(self):
4861 r"""get_probability(CysteineCrossLinkRestraint self) -> double"""
4862 return _IMP_isd.CysteineCrossLinkRestraint_get_probability(self)
4864 def get_standard_error(self):
4865 r"""get_standard_error(CysteineCrossLinkRestraint self) -> double"""
4866 return _IMP_isd.CysteineCrossLinkRestraint_get_standard_error(self)
4868 def get_frequencies(self):
4869 r"""get_frequencies(CysteineCrossLinkRestraint self) -> IMP::Floats"""
4870 return _IMP_isd.CysteineCrossLinkRestraint_get_frequencies(self)
4872 def get_model_frequency(self):
4873 r"""get_model_frequency(CysteineCrossLinkRestraint self) -> double"""
4874 return _IMP_isd.CysteineCrossLinkRestraint_get_model_frequency(self)
4876 def get_distances(self):
4877 r"""get_distances(CysteineCrossLinkRestraint self) -> IMP::Floats"""
4878 return _IMP_isd.CysteineCrossLinkRestraint_get_distances(self)
4880 def get_truncated_normalization(self, mean, sigma):
4881 r"""get_truncated_normalization(CysteineCrossLinkRestraint self, double mean, double sigma) -> double"""
4882 return _IMP_isd.CysteineCrossLinkRestraint_get_truncated_normalization(self, mean, sigma)
4884 def get_normal_pdf(self, mean, sigma, x):
4885 r"""get_normal_pdf(CysteineCrossLinkRestraint self, double mean, double sigma, double x) -> double"""
4886 return _IMP_isd.CysteineCrossLinkRestraint_get_normal_pdf(self, mean, sigma, x)
4888 def add_contribution(self, *args):
4890 add_contribution(CysteineCrossLinkRestraint self, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2)
4891 add_contribution(CysteineCrossLinkRestraint self, IMP::ParticleIndexes p1, IMP::ParticleIndexes p2)
4893 return _IMP_isd.CysteineCrossLinkRestraint_add_contribution(self, *args)
4895 def get_CB_coordinates(self, ps):
4896 r"""get_CB_coordinates(CysteineCrossLinkRestraint self, IMP::ParticleIndexes const & ps) -> Vector3D"""
4897 return _IMP_isd.CysteineCrossLinkRestraint_get_CB_coordinates(self, ps)
4899 def get_number_of_contributions(self):
4900 r"""get_number_of_contributions(CysteineCrossLinkRestraint self) -> unsigned int"""
4901 return _IMP_isd.CysteineCrossLinkRestraint_get_number_of_contributions(self)
4904 r"""do_get_inputs(CysteineCrossLinkRestraint self) -> IMP::ModelObjectsTemp"""
4905 return _IMP_isd.CysteineCrossLinkRestraint_do_get_inputs(self)
4908 r"""get_version_info(CysteineCrossLinkRestraint self) -> VersionInfo"""
4909 return _IMP_isd.CysteineCrossLinkRestraint_get_version_info(self)
4910 __swig_destroy__ = _IMP_isd.delete_CysteineCrossLinkRestraint
4913 r"""__str__(CysteineCrossLinkRestraint self) -> std::string"""
4914 return _IMP_isd.CysteineCrossLinkRestraint___str__(self)
4917 r"""__repr__(CysteineCrossLinkRestraint self) -> std::string"""
4918 return _IMP_isd.CysteineCrossLinkRestraint___repr__(self)
4922 return _object_cast_to_CysteineCrossLinkRestraint(o)
4925 def _get_as_binary(self):
4926 r"""_get_as_binary(CysteineCrossLinkRestraint self) -> PyObject *"""
4927 return _IMP_isd.CysteineCrossLinkRestraint__get_as_binary(self)
4929 def _set_from_binary(self, p):
4930 r"""_set_from_binary(CysteineCrossLinkRestraint self, PyObject * p)"""
4931 return _IMP_isd.CysteineCrossLinkRestraint__set_from_binary(self, p)
4933 def __getstate__(self):
4934 p = self._get_as_binary()
4935 if len(self.__dict__) > 1:
4936 d = self.__dict__.copy()
4941 def __setstate__(self, p):
4942 if not hasattr(self,
'this'):
4944 if isinstance(p, tuple):
4946 self.__dict__.update(d)
4947 return self._set_from_binary(p)
4951 _IMP_isd.CysteineCrossLinkRestraint_swigregister(CysteineCrossLinkRestraint)
4953 r"""Proxy of C++ IMP::isd::WeightMover class."""
4955 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4957 def __init__(self, w, radius):
4958 r"""__init__(WeightMover self, Particle w, IMP::Float radius) -> WeightMover"""
4959 _IMP_isd.WeightMover_swiginit(self, _IMP_isd.new_WeightMover(w, radius))
4961 def set_radius(self, radius):
4962 r"""set_radius(WeightMover self, IMP::Float radius)"""
4963 return _IMP_isd.WeightMover_set_radius(self, radius)
4965 def get_radius(self):
4966 r"""get_radius(WeightMover self) -> IMP::Float"""
4967 return _IMP_isd.WeightMover_get_radius(self)
4970 r"""get_version_info(WeightMover self) -> VersionInfo"""
4971 return _IMP_isd.WeightMover_get_version_info(self)
4972 __swig_destroy__ = _IMP_isd.delete_WeightMover
4975 r"""__str__(WeightMover self) -> std::string"""
4976 return _IMP_isd.WeightMover___str__(self)
4979 r"""__repr__(WeightMover self) -> std::string"""
4980 return _IMP_isd.WeightMover___repr__(self)
4984 return _object_cast_to_WeightMover(o)
4988 _IMP_isd.WeightMover_swigregister(WeightMover)
4990 r"""Proxy of C++ IMP::isd::WeightRestraint class."""
4992 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4994 def __init__(self, w, wmin, wmax, kappa):
4995 r"""__init__(WeightRestraint self, Particle w, IMP::Float wmin, IMP::Float wmax, IMP::Float kappa) -> WeightRestraint"""
4996 _IMP_isd.WeightRestraint_swiginit(self, _IMP_isd.new_WeightRestraint(w, wmin, wmax, kappa))
4999 r"""do_get_inputs(WeightRestraint self) -> IMP::ModelObjectsTemp"""
5000 return _IMP_isd.WeightRestraint_do_get_inputs(self)
5003 r"""get_version_info(WeightRestraint self) -> VersionInfo"""
5004 return _IMP_isd.WeightRestraint_get_version_info(self)
5005 __swig_destroy__ = _IMP_isd.delete_WeightRestraint
5008 r"""__str__(WeightRestraint self) -> std::string"""
5009 return _IMP_isd.WeightRestraint___str__(self)
5012 r"""__repr__(WeightRestraint self) -> std::string"""
5013 return _IMP_isd.WeightRestraint___repr__(self)
5017 return _object_cast_to_WeightRestraint(o)
5021 _IMP_isd.WeightRestraint_swigregister(WeightRestraint)
5023 r"""Proxy of C++ IMP::isd::AtomicCrossLinkMSRestraint class."""
5025 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5027 def __init__(self, *args):
5029 __init__(AtomicCrossLinkMSRestraint self, Model m, double length, ParticleIndex psi, IMP::Float slope=0.0, bool part_of_log_score=False, std::string name="AtomicCrossLinkMSRestraint%1%") -> AtomicCrossLinkMSRestraint
5030 __init__(AtomicCrossLinkMSRestraint self) -> AtomicCrossLinkMSRestraint
5032 _IMP_isd.AtomicCrossLinkMSRestraint_swiginit(self, _IMP_isd.new_AtomicCrossLinkMSRestraint(*args))
5034 def add_contribution(self, ppi, sigmas):
5035 r"""add_contribution(AtomicCrossLinkMSRestraint self, IMP::ParticleIndexPair const & ppi, IMP::ParticleIndexPair const & sigmas)"""
5036 return _IMP_isd.AtomicCrossLinkMSRestraint_add_contribution(self, ppi, sigmas)
5038 def evaluate_for_contributions(self, c, accum):
5039 r"""evaluate_for_contributions(AtomicCrossLinkMSRestraint self, IMP::Ints c, DerivativeAccumulator accum) -> IMP::Float"""
5040 return _IMP_isd.AtomicCrossLinkMSRestraint_evaluate_for_contributions(self, c, accum)
5042 def get_number_of_contributions(self):
5043 r"""get_number_of_contributions(AtomicCrossLinkMSRestraint self) -> unsigned int"""
5044 return _IMP_isd.AtomicCrossLinkMSRestraint_get_number_of_contributions(self)
5046 def get_contribution(self, i):
5047 r"""get_contribution(AtomicCrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
5048 return _IMP_isd.AtomicCrossLinkMSRestraint_get_contribution(self, i)
5050 def get_contribution_sigmas(self, i):
5051 r"""get_contribution_sigmas(AtomicCrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
5052 return _IMP_isd.AtomicCrossLinkMSRestraint_get_contribution_sigmas(self, i)
5055 r"""get_psi(AtomicCrossLinkMSRestraint self) -> ParticleIndex"""
5056 return _IMP_isd.AtomicCrossLinkMSRestraint_get_psi(self)
5059 r"""do_get_inputs(AtomicCrossLinkMSRestraint self) -> IMP::ModelObjectsTemp"""
5060 return _IMP_isd.AtomicCrossLinkMSRestraint_do_get_inputs(self)
5062 def show(self, out):
5063 r"""show(AtomicCrossLinkMSRestraint self, _ostream out)"""
5064 return _IMP_isd.AtomicCrossLinkMSRestraint_show(self, out)
5066 def set_slope(self, slope):
5067 r"""set_slope(AtomicCrossLinkMSRestraint self, IMP::Float slope)"""
5068 return _IMP_isd.AtomicCrossLinkMSRestraint_set_slope(self, slope)
5070 def set_part_of_log_score(self, hey):
5071 r"""set_part_of_log_score(AtomicCrossLinkMSRestraint self, bool hey)"""
5072 return _IMP_isd.AtomicCrossLinkMSRestraint_set_part_of_log_score(self, hey)
5075 r"""get_version_info(AtomicCrossLinkMSRestraint self) -> VersionInfo"""
5076 return _IMP_isd.AtomicCrossLinkMSRestraint_get_version_info(self)
5077 __swig_destroy__ = _IMP_isd.delete_AtomicCrossLinkMSRestraint
5080 r"""__str__(AtomicCrossLinkMSRestraint self) -> std::string"""
5081 return _IMP_isd.AtomicCrossLinkMSRestraint___str__(self)
5084 r"""__repr__(AtomicCrossLinkMSRestraint self) -> std::string"""
5085 return _IMP_isd.AtomicCrossLinkMSRestraint___repr__(self)
5089 return _object_cast_to_AtomicCrossLinkMSRestraint(o)
5092 def _get_as_binary(self):
5093 r"""_get_as_binary(AtomicCrossLinkMSRestraint self) -> PyObject *"""
5094 return _IMP_isd.AtomicCrossLinkMSRestraint__get_as_binary(self)
5096 def _set_from_binary(self, p):
5097 r"""_set_from_binary(AtomicCrossLinkMSRestraint self, PyObject * p)"""
5098 return _IMP_isd.AtomicCrossLinkMSRestraint__set_from_binary(self, p)
5100 def __getstate__(self):
5101 p = self._get_as_binary()
5102 if len(self.__dict__) > 1:
5103 d = self.__dict__.copy()
5108 def __setstate__(self, p):
5109 if not hasattr(self,
'this'):
5111 if isinstance(p, tuple):
5113 self.__dict__.update(d)
5114 return self._set_from_binary(p)
5118 _IMP_isd.AtomicCrossLinkMSRestraint_swigregister(AtomicCrossLinkMSRestraint)
5120 r"""Proxy of C++ IMP::isd::GaussianEMRestraint class."""
5122 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5124 def __init__(self, *args):
5126 __init__(GaussianEMRestraint self, Model mdl, IMP::ParticleIndexes model_ps, IMP::ParticleIndexes density_ps, ParticleIndex global_sigma, IMP::Float model_cutoff_dist, IMP::Float density_cutoff_dist, IMP::Float slope, bool update_model=True, bool backbone_slope=False, bool local=False, std::string name="GaussianEMRestraint%1%") -> GaussianEMRestraint
5127 __init__(GaussianEMRestraint self) -> GaussianEMRestraint
5129 _IMP_isd.GaussianEMRestraint_swiginit(self, _IMP_isd.new_GaussianEMRestraint(*args))
5131 def get_probability(self):
5132 r"""get_probability(GaussianEMRestraint self) -> double"""
5133 return _IMP_isd.GaussianEMRestraint_get_probability(self)
5136 r"""get_cross_correlation_coefficient(GaussianEMRestraint self) -> double"""
5137 return _IMP_isd.GaussianEMRestraint_get_cross_correlation_coefficient(self)
5139 def set_density_filename(self, density_fn):
5140 r"""set_density_filename(GaussianEMRestraint self, std::string density_fn)"""
5141 return _IMP_isd.GaussianEMRestraint_set_density_filename(self, density_fn)
5143 def compute_initial_scores(self):
5144 r"""compute_initial_scores(GaussianEMRestraint self)"""
5145 return _IMP_isd.GaussianEMRestraint_compute_initial_scores(self)
5147 def set_slope(self, s):
5148 r"""set_slope(GaussianEMRestraint self, IMP::Float s)"""
5149 return _IMP_isd.GaussianEMRestraint_set_slope(self, s)
5151 def get_slope(self):
5152 r"""get_slope(GaussianEMRestraint self) -> IMP::Float"""
5153 return _IMP_isd.GaussianEMRestraint_get_slope(self)
5156 r"""do_get_inputs(GaussianEMRestraint self) -> IMP::ModelObjectsTemp"""
5157 return _IMP_isd.GaussianEMRestraint_do_get_inputs(self)
5159 def show(self, out):
5160 r"""show(GaussianEMRestraint self, _ostream out)"""
5161 return _IMP_isd.GaussianEMRestraint_show(self, out)
5164 r"""get_version_info(GaussianEMRestraint self) -> VersionInfo"""
5165 return _IMP_isd.GaussianEMRestraint_get_version_info(self)
5166 __swig_destroy__ = _IMP_isd.delete_GaussianEMRestraint
5169 r"""__str__(GaussianEMRestraint self) -> std::string"""
5170 return _IMP_isd.GaussianEMRestraint___str__(self)
5173 r"""__repr__(GaussianEMRestraint self) -> std::string"""
5174 return _IMP_isd.GaussianEMRestraint___repr__(self)
5178 return _object_cast_to_GaussianEMRestraint(o)
5181 def _get_as_binary(self):
5182 r"""_get_as_binary(GaussianEMRestraint self) -> PyObject *"""
5183 return _IMP_isd.GaussianEMRestraint__get_as_binary(self)
5185 def _set_from_binary(self, p):
5186 r"""_set_from_binary(GaussianEMRestraint self, PyObject * p)"""
5187 return _IMP_isd.GaussianEMRestraint__set_from_binary(self, p)
5189 def __getstate__(self):
5190 p = self._get_as_binary()
5191 if len(self.__dict__) > 1:
5192 d = self.__dict__.copy()
5197 def __setstate__(self, p):
5198 if not hasattr(self,
'this'):
5200 if isinstance(p, tuple):
5202 self.__dict__.update(d)
5203 return self._set_from_binary(p)
5207 _IMP_isd.GaussianEMRestraint_swigregister(GaussianEMRestraint)
5208 class GaussianAnchorEMRestraint(ISDRestraint):
5209 r"""Proxy of C++ IMP::isd::GaussianAnchorEMRestraint class."""
5211 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5213 def __init__(self, *args):
5214 r"""__init__(GaussianAnchorEMRestraint self, IMP::ParticlesTemp model_ps, IMP::Floats model_sigs, IMP::Floats model_weights, IMP::ParticlesTemp density_ps, IMP::Floats density_sigs, IMP::Floats density_weights, Particle global_sigma, IMP::Float cutoff_dist, bool rigid, bool tabexp, std::string name="GaussianAnchorEMRestraint%1%") -> GaussianAnchorEMRestraint"""
5215 _IMP_isd.GaussianAnchorEMRestraint_swiginit(self, _IMP_isd.new_GaussianAnchorEMRestraint(*args))
5217 def get_density_particles(self):
5218 r"""get_density_particles(GaussianAnchorEMRestraint self) -> IMP::ParticlesTemp"""
5219 return _IMP_isd.GaussianAnchorEMRestraint_get_density_particles(self)
5220 __swig_destroy__ = _IMP_isd.delete_GaussianAnchorEMRestraint
5223 r"""__str__(GaussianAnchorEMRestraint self) -> std::string"""
5224 return _IMP_isd.GaussianAnchorEMRestraint___str__(self)
5227 r"""__repr__(GaussianAnchorEMRestraint self) -> std::string"""
5228 return _IMP_isd.GaussianAnchorEMRestraint___repr__(self)
5232 return _object_cast_to_GaussianAnchorEMRestraint(o)
5236 _IMP_isd.GaussianAnchorEMRestraint_swigregister(GaussianAnchorEMRestraint)
5238 r"""Proxy of C++ IMP::isd::GammaPrior class."""
5240 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5242 def __init__(self, *args):
5243 r"""__init__(GammaPrior self, Model m, Particle p, IMP::Float k, IMP::Float theta, std::string name="GammaPrior%1%") -> GammaPrior"""
5244 _IMP_isd.GammaPrior_swiginit(self, _IMP_isd.new_GammaPrior(*args))
5246 def evaluate_at(self, val):
5247 r"""evaluate_at(GammaPrior self, IMP::Float val) -> double"""
5248 return _IMP_isd.GammaPrior_evaluate_at(self, val)
5251 r"""do_get_inputs(GammaPrior self) -> IMP::ModelObjectsTemp"""
5252 return _IMP_isd.GammaPrior_do_get_inputs(self)
5255 r"""get_version_info(GammaPrior self) -> VersionInfo"""
5256 return _IMP_isd.GammaPrior_get_version_info(self)
5257 __swig_destroy__ = _IMP_isd.delete_GammaPrior
5259 def get_probability(self):
5260 r"""get_probability(GammaPrior self) -> double"""
5261 return _IMP_isd.GammaPrior_get_probability(self)
5264 r"""__str__(GammaPrior self) -> std::string"""
5265 return _IMP_isd.GammaPrior___str__(self)
5268 r"""__repr__(GammaPrior self) -> std::string"""
5269 return _IMP_isd.GammaPrior___repr__(self)
5273 return _object_cast_to_GammaPrior(o)
5277 _IMP_isd.GammaPrior_swigregister(GammaPrior)
5279 def sample_points_from_density(dmap_orig, npoints, threshold=0.0):
5280 r"""sample_points_from_density(DensityMap dmap_orig, int npoints, IMP::Float threshold=0.0) -> IMP::FloatsList"""
5281 return _IMP_isd.sample_points_from_density(dmap_orig, npoints, threshold)
5283 r"""Proxy of C++ IMP::isd::ResidueProteinProximityRestraint class."""
5285 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5287 def __init__(self, *args):
5288 r"""__init__(ResidueProteinProximityRestraint self, Model m, double cutoff=6.0, double sigma=3.0, double xi=0.5, bool part_of_log_score=False, std::string name="ResidueProteinProximityRestraint_%1%") -> ResidueProteinProximityRestraint"""
5289 _IMP_isd.ResidueProteinProximityRestraint_swiginit(self, _IMP_isd.new_ResidueProteinProximityRestraint(*args))
5291 def add_pairs_container(self, pc):
5292 r"""add_pairs_container(ResidueProteinProximityRestraint self, PairContainer pc)"""
5293 return _IMP_isd.ResidueProteinProximityRestraint_add_pairs_container(self, pc)
5295 def add_contribution_particles(self, ppis1, ppis2):
5296 r"""add_contribution_particles(ResidueProteinProximityRestraint self, IMP::ParticleIndexes const ppis1, IMP::ParticleIndexes const ppis2)"""
5297 return _IMP_isd.ResidueProteinProximityRestraint_add_contribution_particles(self, ppis1, ppis2)
5299 def evaluate_for_contributions(self, c):
5300 r"""evaluate_for_contributions(ResidueProteinProximityRestraint self, IMP::Ints c) -> double"""
5301 return _IMP_isd.ResidueProteinProximityRestraint_evaluate_for_contributions(self, c)
5303 def get_number_of_contributions(self):
5304 r"""get_number_of_contributions(ResidueProteinProximityRestraint self) -> unsigned int"""
5305 return _IMP_isd.ResidueProteinProximityRestraint_get_number_of_contributions(self)
5307 def set_sigma(self, sigma):
5308 r"""set_sigma(ResidueProteinProximityRestraint self, double sigma)"""
5309 return _IMP_isd.ResidueProteinProximityRestraint_set_sigma(self, sigma)
5311 def set_cutoff(self, cutoff):
5312 r"""set_cutoff(ResidueProteinProximityRestraint self, double cutoff)"""
5313 return _IMP_isd.ResidueProteinProximityRestraint_set_cutoff(self, cutoff)
5315 def set_max_score(self, max_score):
5316 r"""set_max_score(ResidueProteinProximityRestraint self, double max_score)"""
5317 return _IMP_isd.ResidueProteinProximityRestraint_set_max_score(self, max_score)
5319 def set_yi(self, yi):
5320 r"""set_yi(ResidueProteinProximityRestraint self, double yi)"""
5321 return _IMP_isd.ResidueProteinProximityRestraint_set_yi(self, yi)
5323 def set_interpolation_factor(self, interpolation_factor):
5324 r"""set_interpolation_factor(ResidueProteinProximityRestraint self, double interpolation_factor)"""
5325 return _IMP_isd.ResidueProteinProximityRestraint_set_interpolation_factor(self, interpolation_factor)
5327 def set_part_of_log_score(self, hey):
5328 r"""set_part_of_log_score(ResidueProteinProximityRestraint self, bool hey)"""
5329 return _IMP_isd.ResidueProteinProximityRestraint_set_part_of_log_score(self, hey)
5332 r"""do_get_inputs(ResidueProteinProximityRestraint self) -> IMP::ModelObjectsTemp"""
5333 return _IMP_isd.ResidueProteinProximityRestraint_do_get_inputs(self)
5336 r"""get_version_info(ResidueProteinProximityRestraint self) -> VersionInfo"""
5337 return _IMP_isd.ResidueProteinProximityRestraint_get_version_info(self)
5338 __swig_destroy__ = _IMP_isd.delete_ResidueProteinProximityRestraint
5341 r"""__str__(ResidueProteinProximityRestraint self) -> std::string"""
5342 return _IMP_isd.ResidueProteinProximityRestraint___str__(self)
5345 r"""__repr__(ResidueProteinProximityRestraint self) -> std::string"""
5346 return _IMP_isd.ResidueProteinProximityRestraint___repr__(self)
5350 return _object_cast_to_ResidueProteinProximityRestraint(o)
5354 _IMP_isd.ResidueProteinProximityRestraint_swigregister(ResidueProteinProximityRestraint)
5357 r"""get_module_version() -> std::string const"""
5358 return _IMP_isd.get_module_version()
5361 r"""get_example_path(std::string fname) -> std::string"""
5362 return _IMP_isd.get_example_path(fname)
5365 r"""get_data_path(std::string fname) -> std::string"""
5366 return _IMP_isd.get_data_path(fname)
5368 from .
import _version_check
Abstract class for scoring object(s) of type ParticleIndexPair.
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
static FloatKey get_scale_key()
Make CGAL functionality available to IMP.
virtual void clear_caches()
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
Composable functors to implement scores via compile-time composition.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
Code to compute statistical measures.
Object used to hold a set of restraints.
Class for storing model, its restraints, constraints, and particles.
ModelObjectsTemp get_inputs(Model *m, const ParticleIndexes &pis) const
Get the ModelObjects read when the given list of particles is used.
virtual void do_destroy()
Common base class for heavy weight IMP objects.
Simple molecular dynamics simulator.
Store a list of ParticleIndexes.
A base class for classes which perturb particles.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
Version and module information for Objects.
Basic utilities for handling cryo-electron microscopy 3D density maps.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
Interface to specialized Particle types (e.g. atoms)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
std::string get_module_version()
Return the version of this module, as a string.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Class to handle individual particles of a Model object.
void set_check_level(CheckLevel l)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Support for small angle X-ray scattering (SAXS) data.
A restraint is a term in an IMP ScoringFunction.