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)
1493 add_attribute(Nuisance self, SparseFloatKey a0, IMP::Float a1)
1494 add_attribute(Nuisance self, SparseIntKey a0, IMP::Int a1)
1495 add_attribute(Nuisance self, SparseStringKey a0, IMP::String a1)
1496 add_attribute(Nuisance self, SparseParticleIndexKey a0, ParticleIndex a1)
1498 return _IMP_isd.Nuisance_add_attribute(self, *args)
1500 def get_value(self, *args):
1502 get_value(Nuisance self, FloatKey a0) -> IMP::Float
1503 get_value(Nuisance self, IntKey a0) -> IMP::Int
1504 get_value(Nuisance self, FloatsKey a0) -> IMP::Floats
1505 get_value(Nuisance self, IntsKey a0) -> IMP::Ints
1506 get_value(Nuisance self, StringKey a0) -> IMP::String
1507 get_value(Nuisance self, ParticleIndexKey a0) -> Particle
1508 get_value(Nuisance self, ObjectKey a0) -> Object
1509 get_value(Nuisance self, SparseFloatKey a0) -> IMP::Float
1510 get_value(Nuisance self, SparseIntKey a0) -> IMP::Int
1511 get_value(Nuisance self, SparseStringKey a0) -> IMP::String
1512 get_value(Nuisance self, SparseParticleIndexKey a0) -> ParticleIndex
1514 return _IMP_isd.Nuisance_get_value(self, *args)
1516 def set_value(self, *args):
1518 set_value(Nuisance self, FloatKey a0, IMP::Float a1)
1519 set_value(Nuisance self, IntKey a0, IMP::Int a1)
1520 set_value(Nuisance self, FloatsKey a0, IMP::Floats a1)
1521 set_value(Nuisance self, IntsKey a0, IMP::Ints a1)
1522 set_value(Nuisance self, StringKey a0, IMP::String a1)
1523 set_value(Nuisance self, ParticleIndexKey a0, Particle a1)
1524 set_value(Nuisance self, ObjectKey a0, Object a1)
1525 set_value(Nuisance self, SparseFloatKey a0, IMP::Float a1)
1526 set_value(Nuisance self, SparseIntKey a0, IMP::Int a1)
1527 set_value(Nuisance self, SparseStringKey a0, IMP::String a1)
1528 set_value(Nuisance self, SparseParticleIndexKey a0, ParticleIndex a1)
1530 return _IMP_isd.Nuisance_set_value(self, *args)
1532 def remove_attribute(self, *args):
1534 remove_attribute(Nuisance self, FloatKey a0)
1535 remove_attribute(Nuisance self, IntKey a0)
1536 remove_attribute(Nuisance self, FloatsKey a0)
1537 remove_attribute(Nuisance self, IntsKey a0)
1538 remove_attribute(Nuisance self, StringKey a0)
1539 remove_attribute(Nuisance self, ParticleIndexKey a0)
1540 remove_attribute(Nuisance self, ObjectKey a0)
1541 remove_attribute(Nuisance self, SparseFloatKey a0)
1542 remove_attribute(Nuisance self, SparseIntKey a0)
1543 remove_attribute(Nuisance self, SparseStringKey a0)
1544 remove_attribute(Nuisance self, SparseParticleIndexKey a0)
1546 return _IMP_isd.Nuisance_remove_attribute(self, *args)
1548 def has_attribute(self, *args):
1550 has_attribute(Nuisance self, FloatKey a0) -> bool
1551 has_attribute(Nuisance self, IntKey a0) -> bool
1552 has_attribute(Nuisance self, FloatsKey a0) -> bool
1553 has_attribute(Nuisance self, IntsKey a0) -> bool
1554 has_attribute(Nuisance self, StringKey a0) -> bool
1555 has_attribute(Nuisance self, ParticleIndexKey a0) -> bool
1556 has_attribute(Nuisance self, ObjectKey a0) -> bool
1557 has_attribute(Nuisance self, SparseFloatKey a0) -> bool
1558 has_attribute(Nuisance self, SparseIntKey a0) -> bool
1559 has_attribute(Nuisance self, SparseStringKey a0) -> bool
1560 has_attribute(Nuisance self, SparseParticleIndexKey a0) -> bool
1562 return _IMP_isd.Nuisance_has_attribute(self, *args)
1564 def get_derivative(self, a0):
1565 r"""get_derivative(Nuisance self, FloatKey a0) -> double"""
1566 return _IMP_isd.Nuisance_get_derivative(self, a0)
1569 r"""get_name(Nuisance self) -> std::string"""
1570 return _IMP_isd.Nuisance_get_name(self)
1573 r"""clear_caches(Nuisance self)"""
1574 return _IMP_isd.Nuisance_clear_caches(self)
1576 def set_name(self, a0):
1577 r"""set_name(Nuisance self, std::string a0)"""
1578 return _IMP_isd.Nuisance_set_name(self, a0)
1581 r"""set_check_level(Nuisance self, IMP::CheckLevel a0)"""
1582 return _IMP_isd.Nuisance_set_check_level(self, a0)
1584 def add_to_derivative(self, a0, a1, a2):
1585 r"""add_to_derivative(Nuisance self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1586 return _IMP_isd.Nuisance_add_to_derivative(self, a0, a1, a2)
1588 def set_is_optimized(self, a0, a1):
1589 r"""set_is_optimized(Nuisance self, FloatKey a0, bool a1)"""
1590 return _IMP_isd.Nuisance_set_is_optimized(self, a0, a1)
1592 def get_is_optimized(self, a0):
1593 r"""get_is_optimized(Nuisance self, FloatKey a0) -> bool"""
1594 return _IMP_isd.Nuisance_get_is_optimized(self, a0)
1596 def get_check_level(self):
1597 r"""get_check_level(Nuisance self) -> IMP::CheckLevel"""
1598 return _IMP_isd.Nuisance_get_check_level(self)
1600 def __eq__(self, *args):
1602 __eq__(Nuisance self, Nuisance o) -> bool
1603 __eq__(Nuisance self, Particle d) -> bool
1605 return _IMP_isd.Nuisance___eq__(self, *args)
1607 def __ne__(self, *args):
1609 __ne__(Nuisance self, Nuisance o) -> bool
1610 __ne__(Nuisance self, Particle d) -> bool
1612 return _IMP_isd.Nuisance___ne__(self, *args)
1614 def __le__(self, *args):
1616 __le__(Nuisance self, Nuisance o) -> bool
1617 __le__(Nuisance self, Particle d) -> bool
1619 return _IMP_isd.Nuisance___le__(self, *args)
1621 def __lt__(self, *args):
1623 __lt__(Nuisance self, Nuisance o) -> bool
1624 __lt__(Nuisance self, Particle d) -> bool
1626 return _IMP_isd.Nuisance___lt__(self, *args)
1628 def __ge__(self, *args):
1630 __ge__(Nuisance self, Nuisance o) -> bool
1631 __ge__(Nuisance self, Particle d) -> bool
1633 return _IMP_isd.Nuisance___ge__(self, *args)
1635 def __gt__(self, *args):
1637 __gt__(Nuisance self, Nuisance o) -> bool
1638 __gt__(Nuisance self, Particle d) -> bool
1640 return _IMP_isd.Nuisance___gt__(self, *args)
1643 r"""__hash__(Nuisance self) -> std::size_t"""
1644 return _IMP_isd.Nuisance___hash__(self)
1647 r"""__str__(Nuisance self) -> std::string"""
1648 return _IMP_isd.Nuisance___str__(self)
1651 r"""__repr__(Nuisance self) -> std::string"""
1652 return _IMP_isd.Nuisance___repr__(self)
1654 def _get_as_binary(self):
1655 r"""_get_as_binary(Nuisance self) -> PyObject *"""
1656 return _IMP_isd.Nuisance__get_as_binary(self)
1658 def _set_from_binary(self, p):
1659 r"""_set_from_binary(Nuisance self, PyObject * p)"""
1660 return _IMP_isd.Nuisance__set_from_binary(self, p)
1662 def __getstate__(self):
1663 p = self._get_as_binary()
1664 if len(self.__dict__) > 1:
1665 d = self.__dict__.copy()
1670 def __setstate__(self, p):
1671 if not hasattr(self,
'this'):
1673 if isinstance(p, tuple):
1675 self.__dict__.update(d)
1676 return self._set_from_binary(p)
1678 __swig_destroy__ = _IMP_isd.delete_Nuisance
1681 _IMP_isd.Nuisance_swigregister(Nuisance)
1682 class Scale(Nuisance):
1683 r"""Proxy of C++ IMP::isd::Scale class."""
1685 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1687 def __init__(self, *args):
1689 __init__(Scale self) -> Scale
1690 __init__(Scale self, Model m, ParticleIndex id) -> Scale
1691 __init__(Scale self, _ParticleAdaptor d) -> Scale
1693 _IMP_isd.Scale_swiginit(self, _IMP_isd.new_Scale(*args))
1695 def show(self, *args):
1696 r"""show(Scale self, _ostream out=std::cout)"""
1697 return _IMP_isd.Scale_show(self, *args)
1700 def setup_particle(*args):
1702 setup_particle(Model m, ParticleIndex pi) -> Scale
1703 setup_particle(_ParticleAdaptor pa) -> Scale
1704 setup_particle(Model m, ParticleIndex pi, double scale) -> Scale
1705 setup_particle(_ParticleAdaptor pa, double scale) -> Scale
1707 return _IMP_isd.Scale_setup_particle(*args)
1710 def get_is_setup(*args):
1712 get_is_setup(_ParticleAdaptor p) -> bool
1713 get_is_setup(Model m, ParticleIndex pi) -> bool
1715 return _IMP_isd.Scale_get_is_setup(*args)
1717 def get_scale(self):
1718 r"""get_scale(Scale self) -> IMP::Float"""
1719 return _IMP_isd.Scale_get_scale(self)
1721 def set_scale(self, d):
1722 r"""set_scale(Scale self, IMP::Float d)"""
1723 return _IMP_isd.Scale_set_scale(self, d)
1725 def add_to_scale_derivative(self, d, accum):
1726 r"""add_to_scale_derivative(Scale self, IMP::Float d, DerivativeAccumulator accum)"""
1727 return _IMP_isd.Scale_add_to_scale_derivative(self, d, accum)
1729 def get_scale_derivative(self):
1730 r"""get_scale_derivative(Scale self) -> IMP::Float"""
1731 return _IMP_isd.Scale_get_scale_derivative(self)
1734 def get_scale_key():
1735 r"""get_scale_key() -> FloatKey"""
1736 return _IMP_isd.Scale_get_scale_key()
1738 def get_scale_is_optimized(self):
1739 r"""get_scale_is_optimized(Scale self) -> bool"""
1740 return _IMP_isd.Scale_get_scale_is_optimized(self)
1742 def set_scale_is_optimized(self, val):
1743 r"""set_scale_is_optimized(Scale self, bool val)"""
1744 return _IMP_isd.Scale_set_scale_is_optimized(self, val)
1746 def add_attribute(self, *args):
1748 add_attribute(Scale self, FloatKey k, IMP::Float v, bool opt)
1749 add_attribute(Scale self, FloatKey a0, IMP::Float a1)
1750 add_attribute(Scale self, IntKey a0, IMP::Int a1)
1751 add_attribute(Scale self, FloatsKey a0, IMP::Floats a1)
1752 add_attribute(Scale self, IntsKey a0, IMP::Ints a1)
1753 add_attribute(Scale self, StringKey a0, IMP::String a1)
1754 add_attribute(Scale self, ParticleIndexKey a0, Particle a1)
1755 add_attribute(Scale self, ObjectKey a0, Object a1)
1756 add_attribute(Scale self, SparseFloatKey a0, IMP::Float a1)
1757 add_attribute(Scale self, SparseIntKey a0, IMP::Int a1)
1758 add_attribute(Scale self, SparseStringKey a0, IMP::String a1)
1759 add_attribute(Scale self, SparseParticleIndexKey a0, ParticleIndex a1)
1761 return _IMP_isd.Scale_add_attribute(self, *args)
1763 def get_value(self, *args):
1765 get_value(Scale self, FloatKey a0) -> IMP::Float
1766 get_value(Scale self, IntKey a0) -> IMP::Int
1767 get_value(Scale self, FloatsKey a0) -> IMP::Floats
1768 get_value(Scale self, IntsKey a0) -> IMP::Ints
1769 get_value(Scale self, StringKey a0) -> IMP::String
1770 get_value(Scale self, ParticleIndexKey a0) -> Particle
1771 get_value(Scale self, ObjectKey a0) -> Object
1772 get_value(Scale self, SparseFloatKey a0) -> IMP::Float
1773 get_value(Scale self, SparseIntKey a0) -> IMP::Int
1774 get_value(Scale self, SparseStringKey a0) -> IMP::String
1775 get_value(Scale self, SparseParticleIndexKey a0) -> ParticleIndex
1777 return _IMP_isd.Scale_get_value(self, *args)
1779 def set_value(self, *args):
1781 set_value(Scale self, FloatKey a0, IMP::Float a1)
1782 set_value(Scale self, IntKey a0, IMP::Int a1)
1783 set_value(Scale self, FloatsKey a0, IMP::Floats a1)
1784 set_value(Scale self, IntsKey a0, IMP::Ints a1)
1785 set_value(Scale self, StringKey a0, IMP::String a1)
1786 set_value(Scale self, ParticleIndexKey a0, Particle a1)
1787 set_value(Scale self, ObjectKey a0, Object a1)
1788 set_value(Scale self, SparseFloatKey a0, IMP::Float a1)
1789 set_value(Scale self, SparseIntKey a0, IMP::Int a1)
1790 set_value(Scale self, SparseStringKey a0, IMP::String a1)
1791 set_value(Scale self, SparseParticleIndexKey a0, ParticleIndex a1)
1793 return _IMP_isd.Scale_set_value(self, *args)
1795 def remove_attribute(self, *args):
1797 remove_attribute(Scale self, FloatKey a0)
1798 remove_attribute(Scale self, IntKey a0)
1799 remove_attribute(Scale self, FloatsKey a0)
1800 remove_attribute(Scale self, IntsKey a0)
1801 remove_attribute(Scale self, StringKey a0)
1802 remove_attribute(Scale self, ParticleIndexKey a0)
1803 remove_attribute(Scale self, ObjectKey a0)
1804 remove_attribute(Scale self, SparseFloatKey a0)
1805 remove_attribute(Scale self, SparseIntKey a0)
1806 remove_attribute(Scale self, SparseStringKey a0)
1807 remove_attribute(Scale self, SparseParticleIndexKey a0)
1809 return _IMP_isd.Scale_remove_attribute(self, *args)
1811 def has_attribute(self, *args):
1813 has_attribute(Scale self, FloatKey a0) -> bool
1814 has_attribute(Scale self, IntKey a0) -> bool
1815 has_attribute(Scale self, FloatsKey a0) -> bool
1816 has_attribute(Scale self, IntsKey a0) -> bool
1817 has_attribute(Scale self, StringKey a0) -> bool
1818 has_attribute(Scale self, ParticleIndexKey a0) -> bool
1819 has_attribute(Scale self, ObjectKey a0) -> bool
1820 has_attribute(Scale self, SparseFloatKey a0) -> bool
1821 has_attribute(Scale self, SparseIntKey a0) -> bool
1822 has_attribute(Scale self, SparseStringKey a0) -> bool
1823 has_attribute(Scale self, SparseParticleIndexKey a0) -> bool
1825 return _IMP_isd.Scale_has_attribute(self, *args)
1827 def get_derivative(self, a0):
1828 r"""get_derivative(Scale self, FloatKey a0) -> double"""
1829 return _IMP_isd.Scale_get_derivative(self, a0)
1832 r"""get_name(Scale self) -> std::string"""
1833 return _IMP_isd.Scale_get_name(self)
1836 r"""clear_caches(Scale self)"""
1837 return _IMP_isd.Scale_clear_caches(self)
1839 def set_name(self, a0):
1840 r"""set_name(Scale self, std::string a0)"""
1841 return _IMP_isd.Scale_set_name(self, a0)
1844 r"""set_check_level(Scale self, IMP::CheckLevel a0)"""
1845 return _IMP_isd.Scale_set_check_level(self, a0)
1847 def add_to_derivative(self, a0, a1, a2):
1848 r"""add_to_derivative(Scale self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1849 return _IMP_isd.Scale_add_to_derivative(self, a0, a1, a2)
1851 def set_is_optimized(self, a0, a1):
1852 r"""set_is_optimized(Scale self, FloatKey a0, bool a1)"""
1853 return _IMP_isd.Scale_set_is_optimized(self, a0, a1)
1855 def get_is_optimized(self, a0):
1856 r"""get_is_optimized(Scale self, FloatKey a0) -> bool"""
1857 return _IMP_isd.Scale_get_is_optimized(self, a0)
1859 def get_check_level(self):
1860 r"""get_check_level(Scale self) -> IMP::CheckLevel"""
1861 return _IMP_isd.Scale_get_check_level(self)
1863 def __eq__(self, *args):
1865 __eq__(Scale self, Scale o) -> bool
1866 __eq__(Scale self, Particle d) -> bool
1868 return _IMP_isd.Scale___eq__(self, *args)
1870 def __ne__(self, *args):
1872 __ne__(Scale self, Scale o) -> bool
1873 __ne__(Scale self, Particle d) -> bool
1875 return _IMP_isd.Scale___ne__(self, *args)
1877 def __le__(self, *args):
1879 __le__(Scale self, Scale o) -> bool
1880 __le__(Scale self, Particle d) -> bool
1882 return _IMP_isd.Scale___le__(self, *args)
1884 def __lt__(self, *args):
1886 __lt__(Scale self, Scale o) -> bool
1887 __lt__(Scale self, Particle d) -> bool
1889 return _IMP_isd.Scale___lt__(self, *args)
1891 def __ge__(self, *args):
1893 __ge__(Scale self, Scale o) -> bool
1894 __ge__(Scale self, Particle d) -> bool
1896 return _IMP_isd.Scale___ge__(self, *args)
1898 def __gt__(self, *args):
1900 __gt__(Scale self, Scale o) -> bool
1901 __gt__(Scale self, Particle d) -> bool
1903 return _IMP_isd.Scale___gt__(self, *args)
1906 r"""__hash__(Scale self) -> std::size_t"""
1907 return _IMP_isd.Scale___hash__(self)
1910 r"""__str__(Scale self) -> std::string"""
1911 return _IMP_isd.Scale___str__(self)
1914 r"""__repr__(Scale self) -> std::string"""
1915 return _IMP_isd.Scale___repr__(self)
1917 def _get_as_binary(self):
1918 r"""_get_as_binary(Scale self) -> PyObject *"""
1919 return _IMP_isd.Scale__get_as_binary(self)
1921 def _set_from_binary(self, p):
1922 r"""_set_from_binary(Scale self, PyObject * p)"""
1923 return _IMP_isd.Scale__set_from_binary(self, p)
1925 def __getstate__(self):
1926 p = self._get_as_binary()
1927 if len(self.__dict__) > 1:
1928 d = self.__dict__.copy()
1933 def __setstate__(self, p):
1934 if not hasattr(self,
'this'):
1936 if isinstance(p, tuple):
1938 self.__dict__.update(d)
1939 return self._set_from_binary(p)
1941 __swig_destroy__ = _IMP_isd.delete_Scale
1944 _IMP_isd.Scale_swigregister(Scale)
1945 class Switching(Nuisance):
1946 r"""Proxy of C++ IMP::isd::Switching class."""
1948 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1950 def __init__(self, *args):
1952 __init__(Switching self) -> Switching
1953 __init__(Switching self, Model m, ParticleIndex id) -> Switching
1954 __init__(Switching self, _ParticleAdaptor d) -> Switching
1956 _IMP_isd.Switching_swiginit(self, _IMP_isd.new_Switching(*args))
1958 def show(self, *args):
1959 r"""show(Switching self, _ostream out=std::cout)"""
1960 return _IMP_isd.Switching_show(self, *args)
1963 def setup_particle(*args):
1965 setup_particle(Model m, ParticleIndex pi) -> Switching
1966 setup_particle(_ParticleAdaptor pa) -> Switching
1967 setup_particle(Model m, ParticleIndex pi, double switching) -> Switching
1968 setup_particle(_ParticleAdaptor pa, double switching) -> Switching
1970 return _IMP_isd.Switching_setup_particle(*args)
1973 def get_is_setup(*args):
1975 get_is_setup(_ParticleAdaptor p) -> bool
1976 get_is_setup(Model m, ParticleIndex pi) -> bool
1978 return _IMP_isd.Switching_get_is_setup(*args)
1980 def get_switching(self):
1981 r"""get_switching(Switching self) -> IMP::Float"""
1982 return _IMP_isd.Switching_get_switching(self)
1984 def set_switching(self, d):
1985 r"""set_switching(Switching self, IMP::Float d)"""
1986 return _IMP_isd.Switching_set_switching(self, d)
1988 def add_to_switching_derivative(self, d, accum):
1989 r"""add_to_switching_derivative(Switching self, IMP::Float d, DerivativeAccumulator accum)"""
1990 return _IMP_isd.Switching_add_to_switching_derivative(self, d, accum)
1992 def get_switching_derivative(self):
1993 r"""get_switching_derivative(Switching self) -> IMP::Float"""
1994 return _IMP_isd.Switching_get_switching_derivative(self)
1997 def get_switching_key():
1998 r"""get_switching_key() -> FloatKey"""
1999 return _IMP_isd.Switching_get_switching_key()
2001 def get_switching_is_optimized(self):
2002 r"""get_switching_is_optimized(Switching self) -> bool"""
2003 return _IMP_isd.Switching_get_switching_is_optimized(self)
2005 def set_switching_is_optimized(self, val):
2006 r"""set_switching_is_optimized(Switching self, bool val)"""
2007 return _IMP_isd.Switching_set_switching_is_optimized(self, val)
2009 def add_attribute(self, *args):
2011 add_attribute(Switching self, FloatKey k, IMP::Float v, bool opt)
2012 add_attribute(Switching self, FloatKey a0, IMP::Float a1)
2013 add_attribute(Switching self, IntKey a0, IMP::Int a1)
2014 add_attribute(Switching self, FloatsKey a0, IMP::Floats a1)
2015 add_attribute(Switching self, IntsKey a0, IMP::Ints a1)
2016 add_attribute(Switching self, StringKey a0, IMP::String a1)
2017 add_attribute(Switching self, ParticleIndexKey a0, Particle a1)
2018 add_attribute(Switching self, ObjectKey a0, Object a1)
2019 add_attribute(Switching self, SparseFloatKey a0, IMP::Float a1)
2020 add_attribute(Switching self, SparseIntKey a0, IMP::Int a1)
2021 add_attribute(Switching self, SparseStringKey a0, IMP::String a1)
2022 add_attribute(Switching self, SparseParticleIndexKey a0, ParticleIndex a1)
2024 return _IMP_isd.Switching_add_attribute(self, *args)
2026 def get_value(self, *args):
2028 get_value(Switching self, FloatKey a0) -> IMP::Float
2029 get_value(Switching self, IntKey a0) -> IMP::Int
2030 get_value(Switching self, FloatsKey a0) -> IMP::Floats
2031 get_value(Switching self, IntsKey a0) -> IMP::Ints
2032 get_value(Switching self, StringKey a0) -> IMP::String
2033 get_value(Switching self, ParticleIndexKey a0) -> Particle
2034 get_value(Switching self, ObjectKey a0) -> Object
2035 get_value(Switching self, SparseFloatKey a0) -> IMP::Float
2036 get_value(Switching self, SparseIntKey a0) -> IMP::Int
2037 get_value(Switching self, SparseStringKey a0) -> IMP::String
2038 get_value(Switching self, SparseParticleIndexKey a0) -> ParticleIndex
2040 return _IMP_isd.Switching_get_value(self, *args)
2042 def set_value(self, *args):
2044 set_value(Switching self, FloatKey a0, IMP::Float a1)
2045 set_value(Switching self, IntKey a0, IMP::Int a1)
2046 set_value(Switching self, FloatsKey a0, IMP::Floats a1)
2047 set_value(Switching self, IntsKey a0, IMP::Ints a1)
2048 set_value(Switching self, StringKey a0, IMP::String a1)
2049 set_value(Switching self, ParticleIndexKey a0, Particle a1)
2050 set_value(Switching self, ObjectKey a0, Object a1)
2051 set_value(Switching self, SparseFloatKey a0, IMP::Float a1)
2052 set_value(Switching self, SparseIntKey a0, IMP::Int a1)
2053 set_value(Switching self, SparseStringKey a0, IMP::String a1)
2054 set_value(Switching self, SparseParticleIndexKey a0, ParticleIndex a1)
2056 return _IMP_isd.Switching_set_value(self, *args)
2058 def remove_attribute(self, *args):
2060 remove_attribute(Switching self, FloatKey a0)
2061 remove_attribute(Switching self, IntKey a0)
2062 remove_attribute(Switching self, FloatsKey a0)
2063 remove_attribute(Switching self, IntsKey a0)
2064 remove_attribute(Switching self, StringKey a0)
2065 remove_attribute(Switching self, ParticleIndexKey a0)
2066 remove_attribute(Switching self, ObjectKey a0)
2067 remove_attribute(Switching self, SparseFloatKey a0)
2068 remove_attribute(Switching self, SparseIntKey a0)
2069 remove_attribute(Switching self, SparseStringKey a0)
2070 remove_attribute(Switching self, SparseParticleIndexKey a0)
2072 return _IMP_isd.Switching_remove_attribute(self, *args)
2074 def has_attribute(self, *args):
2076 has_attribute(Switching self, FloatKey a0) -> bool
2077 has_attribute(Switching self, IntKey a0) -> bool
2078 has_attribute(Switching self, FloatsKey a0) -> bool
2079 has_attribute(Switching self, IntsKey a0) -> bool
2080 has_attribute(Switching self, StringKey a0) -> bool
2081 has_attribute(Switching self, ParticleIndexKey a0) -> bool
2082 has_attribute(Switching self, ObjectKey a0) -> bool
2083 has_attribute(Switching self, SparseFloatKey a0) -> bool
2084 has_attribute(Switching self, SparseIntKey a0) -> bool
2085 has_attribute(Switching self, SparseStringKey a0) -> bool
2086 has_attribute(Switching self, SparseParticleIndexKey a0) -> bool
2088 return _IMP_isd.Switching_has_attribute(self, *args)
2090 def get_derivative(self, a0):
2091 r"""get_derivative(Switching self, FloatKey a0) -> double"""
2092 return _IMP_isd.Switching_get_derivative(self, a0)
2095 r"""get_name(Switching self) -> std::string"""
2096 return _IMP_isd.Switching_get_name(self)
2099 r"""clear_caches(Switching self)"""
2100 return _IMP_isd.Switching_clear_caches(self)
2102 def set_name(self, a0):
2103 r"""set_name(Switching self, std::string a0)"""
2104 return _IMP_isd.Switching_set_name(self, a0)
2107 r"""set_check_level(Switching self, IMP::CheckLevel a0)"""
2108 return _IMP_isd.Switching_set_check_level(self, a0)
2110 def add_to_derivative(self, a0, a1, a2):
2111 r"""add_to_derivative(Switching self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2112 return _IMP_isd.Switching_add_to_derivative(self, a0, a1, a2)
2114 def set_is_optimized(self, a0, a1):
2115 r"""set_is_optimized(Switching self, FloatKey a0, bool a1)"""
2116 return _IMP_isd.Switching_set_is_optimized(self, a0, a1)
2118 def get_is_optimized(self, a0):
2119 r"""get_is_optimized(Switching self, FloatKey a0) -> bool"""
2120 return _IMP_isd.Switching_get_is_optimized(self, a0)
2122 def get_check_level(self):
2123 r"""get_check_level(Switching self) -> IMP::CheckLevel"""
2124 return _IMP_isd.Switching_get_check_level(self)
2126 def __eq__(self, *args):
2128 __eq__(Switching self, Switching o) -> bool
2129 __eq__(Switching self, Particle d) -> bool
2131 return _IMP_isd.Switching___eq__(self, *args)
2133 def __ne__(self, *args):
2135 __ne__(Switching self, Switching o) -> bool
2136 __ne__(Switching self, Particle d) -> bool
2138 return _IMP_isd.Switching___ne__(self, *args)
2140 def __le__(self, *args):
2142 __le__(Switching self, Switching o) -> bool
2143 __le__(Switching self, Particle d) -> bool
2145 return _IMP_isd.Switching___le__(self, *args)
2147 def __lt__(self, *args):
2149 __lt__(Switching self, Switching o) -> bool
2150 __lt__(Switching self, Particle d) -> bool
2152 return _IMP_isd.Switching___lt__(self, *args)
2154 def __ge__(self, *args):
2156 __ge__(Switching self, Switching o) -> bool
2157 __ge__(Switching self, Particle d) -> bool
2159 return _IMP_isd.Switching___ge__(self, *args)
2161 def __gt__(self, *args):
2163 __gt__(Switching self, Switching o) -> bool
2164 __gt__(Switching self, Particle d) -> bool
2166 return _IMP_isd.Switching___gt__(self, *args)
2169 r"""__hash__(Switching self) -> std::size_t"""
2170 return _IMP_isd.Switching___hash__(self)
2173 r"""__str__(Switching self) -> std::string"""
2174 return _IMP_isd.Switching___str__(self)
2177 r"""__repr__(Switching self) -> std::string"""
2178 return _IMP_isd.Switching___repr__(self)
2180 def _get_as_binary(self):
2181 r"""_get_as_binary(Switching self) -> PyObject *"""
2182 return _IMP_isd.Switching__get_as_binary(self)
2184 def _set_from_binary(self, p):
2185 r"""_set_from_binary(Switching self, PyObject * p)"""
2186 return _IMP_isd.Switching__set_from_binary(self, p)
2188 def __getstate__(self):
2189 p = self._get_as_binary()
2190 if len(self.__dict__) > 1:
2191 d = self.__dict__.copy()
2196 def __setstate__(self, p):
2197 if not hasattr(self,
'this'):
2199 if isinstance(p, tuple):
2201 self.__dict__.update(d)
2202 return self._set_from_binary(p)
2204 __swig_destroy__ = _IMP_isd.delete_Switching
2207 _IMP_isd.Switching_swigregister(Switching)
2209 r"""Proxy of C++ IMP::isd::Weight class."""
2211 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2213 def __init__(self, *args):
2215 __init__(Weight self) -> Weight
2216 __init__(Weight self, Model m, ParticleIndex id) -> Weight
2217 __init__(Weight self, _ParticleAdaptor d) -> Weight
2219 _IMP_isd.Weight_swiginit(self, _IMP_isd.new_Weight(*args))
2221 def show(self, *args):
2222 r"""show(Weight self, _ostream out=std::cout)"""
2223 return _IMP_isd.Weight_show(self, *args)
2226 def setup_particle(*args):
2228 setup_particle(Model m, ParticleIndex pi) -> Weight
2229 setup_particle(_ParticleAdaptor pa) -> Weight
2230 setup_particle(Model m, ParticleIndex pi, IMP::Int nweights) -> Weight
2231 setup_particle(_ParticleAdaptor pa, IMP::Int nweights) -> Weight
2232 setup_particle(Model m, ParticleIndex pi, VectorKD w) -> Weight
2233 setup_particle(_ParticleAdaptor pa, VectorKD w) -> Weight
2235 return _IMP_isd.Weight_setup_particle(*args)
2238 def get_number_of_weights_key():
2239 r"""get_number_of_weights_key() -> IntKey"""
2240 return _IMP_isd.Weight_get_number_of_weights_key()
2243 def get_weight_key(i):
2244 r"""get_weight_key(int i) -> FloatKey"""
2245 return _IMP_isd.Weight_get_weight_key(i)
2247 def get_weight_keys(self):
2248 r"""get_weight_keys(Weight self) -> IMP::FloatKeys"""
2249 return _IMP_isd.Weight_get_weight_keys(self)
2251 def get_weight(self, i):
2252 r"""get_weight(Weight self, int i) -> IMP::Float"""
2253 return _IMP_isd.Weight_get_weight(self, i)
2255 def get_weights(self):
2256 r"""get_weights(Weight self) -> VectorKD"""
2257 return _IMP_isd.Weight_get_weights(self)
2259 def set_weight_lazy(self, i, wi):
2260 r"""set_weight_lazy(Weight self, int i, IMP::Float wi)"""
2261 return _IMP_isd.Weight_set_weight_lazy(self, i, wi)
2263 def set_weights_lazy(self, w):
2264 r"""set_weights_lazy(Weight self, VectorKD w)"""
2265 return _IMP_isd.Weight_set_weights_lazy(self, w)
2267 def set_weights(self, w):
2268 r"""set_weights(Weight self, VectorKD w)"""
2269 return _IMP_isd.Weight_set_weights(self, w)
2271 def get_weights_are_optimized(self):
2272 r"""get_weights_are_optimized(Weight self) -> bool"""
2273 return _IMP_isd.Weight_get_weights_are_optimized(self)
2275 def set_weights_are_optimized(self, tf):
2276 r"""set_weights_are_optimized(Weight self, bool tf)"""
2277 return _IMP_isd.Weight_set_weights_are_optimized(self, tf)
2279 def get_weight_derivative(self, i):
2280 r"""get_weight_derivative(Weight self, int i) -> IMP::Float"""
2281 return _IMP_isd.Weight_get_weight_derivative(self, i)
2283 def get_weights_derivatives(self):
2284 r"""get_weights_derivatives(Weight self) -> VectorKD"""
2285 return _IMP_isd.Weight_get_weights_derivatives(self)
2287 def add_to_weight_derivative(self, i, dwi, da):
2288 r"""add_to_weight_derivative(Weight self, int i, IMP::Float dwi, DerivativeAccumulator da)"""
2289 return _IMP_isd.Weight_add_to_weight_derivative(self, i, dwi, da)
2291 def add_to_weights_derivatives(self, dw, da):
2292 r"""add_to_weights_derivatives(Weight self, VectorKD dw, DerivativeAccumulator da)"""
2293 return _IMP_isd.Weight_add_to_weights_derivatives(self, dw, da)
2295 def add_weight_lazy(self, wi=0):
2296 r"""add_weight_lazy(Weight self, IMP::Float wi=0)"""
2297 return _IMP_isd.Weight_add_weight_lazy(self, wi)
2299 def add_weight(self, wi=0):
2300 r"""add_weight(Weight self, IMP::Float wi=0)"""
2301 return _IMP_isd.Weight_add_weight(self, wi)
2303 def get_number_of_weights(self):
2304 r"""get_number_of_weights(Weight self) -> IMP::Int"""
2305 return _IMP_isd.Weight_get_number_of_weights(self)
2307 def get_unit_simplex(self):
2308 r"""get_unit_simplex(Weight self) -> UnitSimplexKD"""
2309 return _IMP_isd.Weight_get_unit_simplex(self)
2311 def set_number_of_weights_lazy(self, nweights):
2312 r"""set_number_of_weights_lazy(Weight self, IMP::Int nweights)"""
2313 return _IMP_isd.Weight_set_number_of_weights_lazy(self, nweights)
2315 def set_number_of_weights(self, nweights):
2316 r"""set_number_of_weights(Weight self, IMP::Int nweights)"""
2317 return _IMP_isd.Weight_set_number_of_weights(self, nweights)
2320 def get_is_setup(*args):
2322 get_is_setup(_ParticleAdaptor p) -> bool
2323 get_is_setup(Model m, ParticleIndex pi) -> bool
2325 return _IMP_isd.Weight_get_is_setup(*args)
2327 def add_attribute(self, *args):
2329 add_attribute(Weight self, FloatKey k, IMP::Float v, bool opt)
2330 add_attribute(Weight self, FloatKey a0, IMP::Float a1)
2331 add_attribute(Weight self, IntKey a0, IMP::Int a1)
2332 add_attribute(Weight self, FloatsKey a0, IMP::Floats a1)
2333 add_attribute(Weight self, IntsKey a0, IMP::Ints a1)
2334 add_attribute(Weight self, StringKey a0, IMP::String a1)
2335 add_attribute(Weight self, ParticleIndexKey a0, Particle a1)
2336 add_attribute(Weight self, ObjectKey a0, Object a1)
2337 add_attribute(Weight self, SparseFloatKey a0, IMP::Float a1)
2338 add_attribute(Weight self, SparseIntKey a0, IMP::Int a1)
2339 add_attribute(Weight self, SparseStringKey a0, IMP::String a1)
2340 add_attribute(Weight self, SparseParticleIndexKey a0, ParticleIndex a1)
2342 return _IMP_isd.Weight_add_attribute(self, *args)
2344 def get_value(self, *args):
2346 get_value(Weight self, FloatKey a0) -> IMP::Float
2347 get_value(Weight self, IntKey a0) -> IMP::Int
2348 get_value(Weight self, FloatsKey a0) -> IMP::Floats
2349 get_value(Weight self, IntsKey a0) -> IMP::Ints
2350 get_value(Weight self, StringKey a0) -> IMP::String
2351 get_value(Weight self, ParticleIndexKey a0) -> Particle
2352 get_value(Weight self, ObjectKey a0) -> Object
2353 get_value(Weight self, SparseFloatKey a0) -> IMP::Float
2354 get_value(Weight self, SparseIntKey a0) -> IMP::Int
2355 get_value(Weight self, SparseStringKey a0) -> IMP::String
2356 get_value(Weight self, SparseParticleIndexKey a0) -> ParticleIndex
2358 return _IMP_isd.Weight_get_value(self, *args)
2360 def set_value(self, *args):
2362 set_value(Weight self, FloatKey a0, IMP::Float a1)
2363 set_value(Weight self, IntKey a0, IMP::Int a1)
2364 set_value(Weight self, FloatsKey a0, IMP::Floats a1)
2365 set_value(Weight self, IntsKey a0, IMP::Ints a1)
2366 set_value(Weight self, StringKey a0, IMP::String a1)
2367 set_value(Weight self, ParticleIndexKey a0, Particle a1)
2368 set_value(Weight self, ObjectKey a0, Object a1)
2369 set_value(Weight self, SparseFloatKey a0, IMP::Float a1)
2370 set_value(Weight self, SparseIntKey a0, IMP::Int a1)
2371 set_value(Weight self, SparseStringKey a0, IMP::String a1)
2372 set_value(Weight self, SparseParticleIndexKey a0, ParticleIndex a1)
2374 return _IMP_isd.Weight_set_value(self, *args)
2376 def remove_attribute(self, *args):
2378 remove_attribute(Weight self, FloatKey a0)
2379 remove_attribute(Weight self, IntKey a0)
2380 remove_attribute(Weight self, FloatsKey a0)
2381 remove_attribute(Weight self, IntsKey a0)
2382 remove_attribute(Weight self, StringKey a0)
2383 remove_attribute(Weight self, ParticleIndexKey a0)
2384 remove_attribute(Weight self, ObjectKey a0)
2385 remove_attribute(Weight self, SparseFloatKey a0)
2386 remove_attribute(Weight self, SparseIntKey a0)
2387 remove_attribute(Weight self, SparseStringKey a0)
2388 remove_attribute(Weight self, SparseParticleIndexKey a0)
2390 return _IMP_isd.Weight_remove_attribute(self, *args)
2392 def has_attribute(self, *args):
2394 has_attribute(Weight self, FloatKey a0) -> bool
2395 has_attribute(Weight self, IntKey a0) -> bool
2396 has_attribute(Weight self, FloatsKey a0) -> bool
2397 has_attribute(Weight self, IntsKey a0) -> bool
2398 has_attribute(Weight self, StringKey a0) -> bool
2399 has_attribute(Weight self, ParticleIndexKey a0) -> bool
2400 has_attribute(Weight self, ObjectKey a0) -> bool
2401 has_attribute(Weight self, SparseFloatKey a0) -> bool
2402 has_attribute(Weight self, SparseIntKey a0) -> bool
2403 has_attribute(Weight self, SparseStringKey a0) -> bool
2404 has_attribute(Weight self, SparseParticleIndexKey a0) -> bool
2406 return _IMP_isd.Weight_has_attribute(self, *args)
2408 def get_derivative(self, a0):
2409 r"""get_derivative(Weight self, FloatKey a0) -> double"""
2410 return _IMP_isd.Weight_get_derivative(self, a0)
2413 r"""get_name(Weight self) -> std::string"""
2414 return _IMP_isd.Weight_get_name(self)
2417 r"""clear_caches(Weight self)"""
2418 return _IMP_isd.Weight_clear_caches(self)
2420 def set_name(self, a0):
2421 r"""set_name(Weight self, std::string a0)"""
2422 return _IMP_isd.Weight_set_name(self, a0)
2425 r"""set_check_level(Weight self, IMP::CheckLevel a0)"""
2426 return _IMP_isd.Weight_set_check_level(self, a0)
2428 def add_to_derivative(self, a0, a1, a2):
2429 r"""add_to_derivative(Weight self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2430 return _IMP_isd.Weight_add_to_derivative(self, a0, a1, a2)
2432 def set_is_optimized(self, a0, a1):
2433 r"""set_is_optimized(Weight self, FloatKey a0, bool a1)"""
2434 return _IMP_isd.Weight_set_is_optimized(self, a0, a1)
2436 def get_is_optimized(self, a0):
2437 r"""get_is_optimized(Weight self, FloatKey a0) -> bool"""
2438 return _IMP_isd.Weight_get_is_optimized(self, a0)
2440 def get_check_level(self):
2441 r"""get_check_level(Weight self) -> IMP::CheckLevel"""
2442 return _IMP_isd.Weight_get_check_level(self)
2444 def __eq__(self, *args):
2446 __eq__(Weight self, Weight o) -> bool
2447 __eq__(Weight self, Particle d) -> bool
2449 return _IMP_isd.Weight___eq__(self, *args)
2451 def __ne__(self, *args):
2453 __ne__(Weight self, Weight o) -> bool
2454 __ne__(Weight self, Particle d) -> bool
2456 return _IMP_isd.Weight___ne__(self, *args)
2458 def __le__(self, *args):
2460 __le__(Weight self, Weight o) -> bool
2461 __le__(Weight self, Particle d) -> bool
2463 return _IMP_isd.Weight___le__(self, *args)
2465 def __lt__(self, *args):
2467 __lt__(Weight self, Weight o) -> bool
2468 __lt__(Weight self, Particle d) -> bool
2470 return _IMP_isd.Weight___lt__(self, *args)
2472 def __ge__(self, *args):
2474 __ge__(Weight self, Weight o) -> bool
2475 __ge__(Weight self, Particle d) -> bool
2477 return _IMP_isd.Weight___ge__(self, *args)
2479 def __gt__(self, *args):
2481 __gt__(Weight self, Weight o) -> bool
2482 __gt__(Weight self, Particle d) -> bool
2484 return _IMP_isd.Weight___gt__(self, *args)
2487 r"""__hash__(Weight self) -> std::size_t"""
2488 return _IMP_isd.Weight___hash__(self)
2491 r"""__str__(Weight self) -> std::string"""
2492 return _IMP_isd.Weight___str__(self)
2495 r"""__repr__(Weight self) -> std::string"""
2496 return _IMP_isd.Weight___repr__(self)
2498 def _get_as_binary(self):
2499 r"""_get_as_binary(Weight self) -> PyObject *"""
2500 return _IMP_isd.Weight__get_as_binary(self)
2502 def _set_from_binary(self, p):
2503 r"""_set_from_binary(Weight self, PyObject * p)"""
2504 return _IMP_isd.Weight__set_from_binary(self, p)
2506 def __getstate__(self):
2507 p = self._get_as_binary()
2508 if len(self.__dict__) > 1:
2509 d = self.__dict__.copy()
2514 def __setstate__(self, p):
2515 if not hasattr(self,
'this'):
2517 if isinstance(p, tuple):
2519 self.__dict__.update(d)
2520 return self._set_from_binary(p)
2522 __swig_destroy__ = _IMP_isd.delete_Weight
2525 _IMP_isd.Weight_swigregister(Weight)
2526 cvar = _IMP_isd.cvar
2527 IMPISD_MAX_WEIGHTS = cvar.IMPISD_MAX_WEIGHTS
2530 def __lshift__(*args):
2532 __lshift__(_ostream out, Nuisance n) -> _ostream
2533 __lshift__(_ostream out, Scale n) -> _ostream
2534 __lshift__(_ostream out, Switching n) -> _ostream
2535 __lshift__(_ostream out, Weight n) -> _ostream
2537 return _IMP_isd.__lshift__(*args)
2539 r"""Proxy of C++ IMP::isd::JeffreysRestraint class."""
2541 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2543 def __init__(self, *args):
2545 __init__(JeffreysRestraint self, Model m, Particle p) -> JeffreysRestraint
2546 __init__(JeffreysRestraint self) -> JeffreysRestraint
2548 _IMP_isd.JeffreysRestraint_swiginit(self, _IMP_isd.new_JeffreysRestraint(*args))
2551 r"""do_get_inputs(JeffreysRestraint self) -> IMP::ModelObjectsTemp"""
2552 return _IMP_isd.JeffreysRestraint_do_get_inputs(self)
2555 r"""get_version_info(JeffreysRestraint self) -> VersionInfo"""
2556 return _IMP_isd.JeffreysRestraint_get_version_info(self)
2557 __swig_destroy__ = _IMP_isd.delete_JeffreysRestraint
2559 def get_probability(self):
2560 r"""get_probability(JeffreysRestraint self) -> double"""
2561 return _IMP_isd.JeffreysRestraint_get_probability(self)
2564 r"""__str__(JeffreysRestraint self) -> std::string"""
2565 return _IMP_isd.JeffreysRestraint___str__(self)
2568 r"""__repr__(JeffreysRestraint self) -> std::string"""
2569 return _IMP_isd.JeffreysRestraint___repr__(self)
2573 return _object_cast_to_JeffreysRestraint(o)
2576 def _get_as_binary(self):
2577 r"""_get_as_binary(JeffreysRestraint self) -> PyObject *"""
2578 return _IMP_isd.JeffreysRestraint__get_as_binary(self)
2580 def _set_from_binary(self, p):
2581 r"""_set_from_binary(JeffreysRestraint self, PyObject * p)"""
2582 return _IMP_isd.JeffreysRestraint__set_from_binary(self, p)
2584 def __getstate__(self):
2585 p = self._get_as_binary()
2586 if len(self.__dict__) > 1:
2587 d = self.__dict__.copy()
2592 def __setstate__(self, p):
2593 if not hasattr(self,
'this'):
2595 if isinstance(p, tuple):
2597 self.__dict__.update(d)
2598 return self._set_from_binary(p)
2602 _IMP_isd.JeffreysRestraint_swigregister(JeffreysRestraint)
2604 r"""Proxy of C++ IMP::isd::NormalSigmaPCRestraint class."""
2606 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2608 def __init__(self, *args):
2610 __init__(NormalSigmaPCRestraint self, Model m, ParticleIndex spi, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%") -> NormalSigmaPCRestraint
2611 __init__(NormalSigmaPCRestraint self, Scale s, double su, double alpha, std::string name="NormalSigmaPCRestraint%1%") -> NormalSigmaPCRestraint
2613 _IMP_isd.NormalSigmaPCRestraint_swiginit(self, _IMP_isd.new_NormalSigmaPCRestraint(*args))
2615 def get_sigma(self):
2616 r"""get_sigma(NormalSigmaPCRestraint self) -> Scale"""
2617 return _IMP_isd.NormalSigmaPCRestraint_get_sigma(self)
2619 def get_alpha(self):
2620 r"""get_alpha(NormalSigmaPCRestraint self) -> double"""
2621 return _IMP_isd.NormalSigmaPCRestraint_get_alpha(self)
2623 def get_sigma_upper(self):
2624 r"""get_sigma_upper(NormalSigmaPCRestraint self) -> double"""
2625 return _IMP_isd.NormalSigmaPCRestraint_get_sigma_upper(self)
2627 def get_probability(self):
2628 r"""get_probability(NormalSigmaPCRestraint self) -> double"""
2629 return _IMP_isd.NormalSigmaPCRestraint_get_probability(self)
2632 r"""do_get_inputs(NormalSigmaPCRestraint self) -> IMP::ModelObjectsTemp"""
2633 return _IMP_isd.NormalSigmaPCRestraint_do_get_inputs(self)
2636 r"""get_version_info(NormalSigmaPCRestraint self) -> VersionInfo"""
2637 return _IMP_isd.NormalSigmaPCRestraint_get_version_info(self)
2638 __swig_destroy__ = _IMP_isd.delete_NormalSigmaPCRestraint
2641 r"""__str__(NormalSigmaPCRestraint self) -> std::string"""
2642 return _IMP_isd.NormalSigmaPCRestraint___str__(self)
2645 r"""__repr__(NormalSigmaPCRestraint self) -> std::string"""
2646 return _IMP_isd.NormalSigmaPCRestraint___repr__(self)
2650 return _object_cast_to_NormalSigmaPCRestraint(o)
2654 _IMP_isd.NormalSigmaPCRestraint_swigregister(NormalSigmaPCRestraint)
2656 r"""Proxy of C++ IMP::isd::Distribution class."""
2658 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2660 def __init__(self, *args):
2661 r"""__init__(Distribution self, std::string name="Distribution %1%") -> Distribution"""
2662 if self.__class__ == Distribution:
2666 _IMP_isd.Distribution_swiginit(self, _IMP_isd.new_Distribution(_self, *args))
2668 if self.__class__ != Distribution:
2669 _director_objects.register(self)
2674 def get_type_name(self):
2675 r"""get_type_name(Distribution self) -> std::string"""
2676 return _IMP_isd.Distribution_get_type_name(self)
2679 r"""get_version_info(Distribution self) -> VersionInfo"""
2680 return _IMP_isd.Distribution_get_version_info(self)
2681 __swig_destroy__ = _IMP_isd.delete_Distribution
2684 r"""__str__(Distribution self) -> std::string"""
2685 return _IMP_isd.Distribution___str__(self)
2688 r"""__repr__(Distribution self) -> std::string"""
2689 return _IMP_isd.Distribution___repr__(self)
2693 return _object_cast_to_Distribution(o)
2696 def get_type_name(self):
2697 return self.__class__.__name__
2698 def do_show(self, out):
2701 if"IMP::isd" ==
"IMP":
2702 return VersionInfo(self.__module__,
2709 return _object_cast_to_Distribution(o)
2711 def __disown__(self):
2713 _IMP_isd.disown_Distribution(self)
2714 return weakref.proxy(self)
2717 r"""do_destroy(Distribution self)"""
2718 return _IMP_isd.Distribution_do_destroy(self)
2721 _IMP_isd.Distribution_swigregister(Distribution)
2722 class OneDimensionalDistribution(Distribution):
2723 r"""Proxy of C++ IMP::isd::OneDimensionalDistribution class."""
2725 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2727 def do_evaluate(self, *args):
2729 do_evaluate(OneDimensionalDistribution self, double v) -> double
2730 do_evaluate(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2732 return _IMP_isd.OneDimensionalDistribution_do_evaluate(self, *args)
2734 def do_get_density(self, *args):
2736 do_get_density(OneDimensionalDistribution self, double v) -> double
2737 do_get_density(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2739 return _IMP_isd.OneDimensionalDistribution_do_get_density(self, *args)
2741 def __init__(self, *args):
2742 r"""__init__(OneDimensionalDistribution self, std::string name="OneDimensionalDistribution %1%") -> OneDimensionalDistribution"""
2743 if self.__class__ == OneDimensionalDistribution:
2747 _IMP_isd.OneDimensionalDistribution_swiginit(self, _IMP_isd.new_OneDimensionalDistribution(_self, *args))
2749 if self.__class__ != OneDimensionalDistribution:
2750 _director_objects.register(self)
2755 def evaluate(self, *args):
2757 evaluate(OneDimensionalDistribution self, double v) -> double
2758 evaluate(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2760 return _IMP_isd.OneDimensionalDistribution_evaluate(self, *args)
2762 def get_density(self, *args):
2764 get_density(OneDimensionalDistribution self, double v) -> double
2765 get_density(OneDimensionalDistribution self, IMP::Floats const & vs) -> IMP::Floats
2767 return _IMP_isd.OneDimensionalDistribution_get_density(self, *args)
2769 def get_type_name(self):
2770 r"""get_type_name(OneDimensionalDistribution self) -> std::string"""
2771 return _IMP_isd.OneDimensionalDistribution_get_type_name(self)
2774 r"""get_version_info(OneDimensionalDistribution self) -> VersionInfo"""
2775 return _IMP_isd.OneDimensionalDistribution_get_version_info(self)
2776 __swig_destroy__ = _IMP_isd.delete_OneDimensionalDistribution
2779 r"""__str__(OneDimensionalDistribution self) -> std::string"""
2780 return _IMP_isd.OneDimensionalDistribution___str__(self)
2783 r"""__repr__(OneDimensionalDistribution self) -> std::string"""
2784 return _IMP_isd.OneDimensionalDistribution___repr__(self)
2788 return _object_cast_to_OneDimensionalDistribution(o)
2791 def get_type_name(self):
2792 return self.__class__.__name__
2793 def do_show(self, out):
2796 if"IMP::isd" ==
"IMP":
2797 return VersionInfo(self.__module__,
2804 return _object_cast_to_OneDimensionalDistribution(o)
2806 def __disown__(self):
2808 _IMP_isd.disown_OneDimensionalDistribution(self)
2809 return weakref.proxy(self)
2812 r"""do_destroy(OneDimensionalDistribution self)"""
2813 return _IMP_isd.OneDimensionalDistribution_do_destroy(self)
2816 _IMP_isd.OneDimensionalDistribution_swigregister(OneDimensionalDistribution)
2817 class OneDimensionalSufficientDistribution(Distribution):
2818 r"""Proxy of C++ IMP::isd::OneDimensionalSufficientDistribution class."""
2820 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2822 def do_update_sufficient_statistics(self, vs):
2823 r"""do_update_sufficient_statistics(OneDimensionalSufficientDistribution self, IMP::Floats vs)"""
2824 return _IMP_isd.OneDimensionalSufficientDistribution_do_update_sufficient_statistics(self, vs)
2826 def do_get_sufficient_statistics(self):
2827 r"""do_get_sufficient_statistics(OneDimensionalSufficientDistribution self) -> IMP::Floats"""
2828 return _IMP_isd.OneDimensionalSufficientDistribution_do_get_sufficient_statistics(self)
2830 def do_evaluate(self):
2831 r"""do_evaluate(OneDimensionalSufficientDistribution self) -> double"""
2832 return _IMP_isd.OneDimensionalSufficientDistribution_do_evaluate(self)
2834 def do_get_density(self):
2835 r"""do_get_density(OneDimensionalSufficientDistribution self) -> double"""
2836 return _IMP_isd.OneDimensionalSufficientDistribution_do_get_density(self)
2838 def __init__(self, *args):
2839 r"""__init__(OneDimensionalSufficientDistribution self, std::string name="OneDimensionalSufficientDistribution %1%") -> OneDimensionalSufficientDistribution"""
2840 if self.__class__ == OneDimensionalSufficientDistribution:
2844 _IMP_isd.OneDimensionalSufficientDistribution_swiginit(self, _IMP_isd.new_OneDimensionalSufficientDistribution(_self, *args))
2846 if self.__class__ != OneDimensionalSufficientDistribution:
2847 _director_objects.register(self)
2852 def update_sufficient_statistics(self, vs):
2853 r"""update_sufficient_statistics(OneDimensionalSufficientDistribution self, IMP::Floats vs)"""
2854 return _IMP_isd.OneDimensionalSufficientDistribution_update_sufficient_statistics(self, vs)
2856 def get_sufficient_statistics(self):
2857 r"""get_sufficient_statistics(OneDimensionalSufficientDistribution self) -> IMP::Floats"""
2858 return _IMP_isd.OneDimensionalSufficientDistribution_get_sufficient_statistics(self)
2861 r"""evaluate(OneDimensionalSufficientDistribution self) -> double"""
2862 return _IMP_isd.OneDimensionalSufficientDistribution_evaluate(self)
2864 def get_density(self):
2865 r"""get_density(OneDimensionalSufficientDistribution self) -> double"""
2866 return _IMP_isd.OneDimensionalSufficientDistribution_get_density(self)
2868 def get_type_name(self):
2869 r"""get_type_name(OneDimensionalSufficientDistribution self) -> std::string"""
2870 return _IMP_isd.OneDimensionalSufficientDistribution_get_type_name(self)
2873 r"""get_version_info(OneDimensionalSufficientDistribution self) -> VersionInfo"""
2874 return _IMP_isd.OneDimensionalSufficientDistribution_get_version_info(self)
2875 __swig_destroy__ = _IMP_isd.delete_OneDimensionalSufficientDistribution
2878 r"""__str__(OneDimensionalSufficientDistribution self) -> std::string"""
2879 return _IMP_isd.OneDimensionalSufficientDistribution___str__(self)
2882 r"""__repr__(OneDimensionalSufficientDistribution self) -> std::string"""
2883 return _IMP_isd.OneDimensionalSufficientDistribution___repr__(self)
2887 return _object_cast_to_OneDimensionalSufficientDistribution(o)
2890 def get_type_name(self):
2891 return self.__class__.__name__
2892 def do_show(self, out):
2895 if"IMP::isd" ==
"IMP":
2896 return VersionInfo(self.__module__,
2903 return _object_cast_to_OneDimensionalSufficientDistribution(o)
2905 def __disown__(self):
2907 _IMP_isd.disown_OneDimensionalSufficientDistribution(self)
2908 return weakref.proxy(self)
2911 r"""do_destroy(OneDimensionalSufficientDistribution self)"""
2912 return _IMP_isd.OneDimensionalSufficientDistribution_do_destroy(self)
2915 _IMP_isd.OneDimensionalSufficientDistribution_swigregister(OneDimensionalSufficientDistribution)
2916 class FNormal(OneDimensionalSufficientDistribution):
2917 r"""Proxy of C++ IMP::isd::FNormal class."""
2919 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2921 def __init__(self, FA, JA, FM, sigma):
2922 r"""__init__(FNormal self, double FA, double JA, double FM, double sigma) -> FNormal"""
2923 _IMP_isd.FNormal_swiginit(self, _IMP_isd.new_FNormal(FA, JA, FM, sigma))
2925 def update_sufficient_statistics(self, FA):
2926 r"""update_sufficient_statistics(FNormal self, double FA)"""
2927 return _IMP_isd.FNormal_update_sufficient_statistics(self, FA)
2929 def do_update_sufficient_statistics(self, data):
2930 r"""do_update_sufficient_statistics(FNormal self, IMP::Floats data)"""
2931 return _IMP_isd.FNormal_do_update_sufficient_statistics(self, data)
2933 def do_get_sufficient_statistics(self):
2934 r"""do_get_sufficient_statistics(FNormal self) -> IMP::Floats"""
2935 return _IMP_isd.FNormal_do_get_sufficient_statistics(self)
2937 def do_evaluate(self):
2938 r"""do_evaluate(FNormal self) -> double"""
2939 return _IMP_isd.FNormal_do_evaluate(self)
2941 def evaluate_derivative_FA(self):
2942 r"""evaluate_derivative_FA(FNormal self) -> double"""
2943 return _IMP_isd.FNormal_evaluate_derivative_FA(self)
2945 def evaluate_derivative_JA(self):
2946 r"""evaluate_derivative_JA(FNormal self) -> double"""
2947 return _IMP_isd.FNormal_evaluate_derivative_JA(self)
2949 def evaluate_derivative_FM(self):
2950 r"""evaluate_derivative_FM(FNormal self) -> double"""
2951 return _IMP_isd.FNormal_evaluate_derivative_FM(self)
2953 def evaluate_derivative_sigma(self):
2954 r"""evaluate_derivative_sigma(FNormal self) -> double"""
2955 return _IMP_isd.FNormal_evaluate_derivative_sigma(self)
2957 def do_get_density(self):
2958 r"""do_get_density(FNormal self) -> double"""
2959 return _IMP_isd.FNormal_do_get_density(self)
2961 def set_FA(self, f):
2962 r"""set_FA(FNormal self, double f)"""
2963 return _IMP_isd.FNormal_set_FA(self, f)
2965 def set_JA(self, f):
2966 r"""set_JA(FNormal self, double f)"""
2967 return _IMP_isd.FNormal_set_JA(self, f)
2969 def set_FM(self, f):
2970 r"""set_FM(FNormal self, double f)"""
2971 return _IMP_isd.FNormal_set_FM(self, f)
2973 def set_sigma(self, f):
2974 r"""set_sigma(FNormal self, double f)"""
2975 return _IMP_isd.FNormal_set_sigma(self, f)
2976 __swig_destroy__ = _IMP_isd.delete_FNormal
2979 r"""__str__(FNormal self) -> std::string"""
2980 return _IMP_isd.FNormal___str__(self)
2983 r"""__repr__(FNormal self) -> std::string"""
2984 return _IMP_isd.FNormal___repr__(self)
2988 return _object_cast_to_FNormal(o)
2992 _IMP_isd.FNormal_swigregister(FNormal)
2993 class FStudentT(OneDimensionalSufficientDistribution):
2994 r"""Proxy of C++ IMP::isd::FStudentT class."""
2996 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2998 def __init__(self, *args):
3000 __init__(FStudentT self, IMP::Floats FXs, IMP::Floats JXs, double FM, double sigma, double nu, std::string name="FStudentT %1%") -> FStudentT
3001 __init__(FStudentT self, double sumFX, double sumFX2, unsigned int N, double LogJX, double FM, double sigma, double nu, std::string name="FStudentT %1%") -> FStudentT
3003 _IMP_isd.FStudentT_swiginit(self, _IMP_isd.new_FStudentT(*args))
3005 def update_sufficient_statistics(self, FXs, JXs):
3006 r"""update_sufficient_statistics(FStudentT self, IMP::Floats FXs, IMP::Floats JXs)"""
3007 return _IMP_isd.FStudentT_update_sufficient_statistics(self, FXs, JXs)
3009 def evaluate_derivative_Fx(self, Fx):
3010 r"""evaluate_derivative_Fx(FStudentT self, double Fx) -> double"""
3011 return _IMP_isd.FStudentT_evaluate_derivative_Fx(self, Fx)
3013 def evaluate_derivative_FX(self, FXs):
3014 r"""evaluate_derivative_FX(FStudentT self, IMP::Floats const FXs) -> IMP::Floats"""
3015 return _IMP_isd.FStudentT_evaluate_derivative_FX(self, FXs)
3017 def evaluate_derivative_LogJX(self):
3018 r"""evaluate_derivative_LogJX(FStudentT self) -> double"""
3019 return _IMP_isd.FStudentT_evaluate_derivative_LogJX(self)
3021 def evaluate_derivative_FM(self):
3022 r"""evaluate_derivative_FM(FStudentT self) -> double"""
3023 return _IMP_isd.FStudentT_evaluate_derivative_FM(self)
3025 def evaluate_derivative_sigma(self):
3026 r"""evaluate_derivative_sigma(FStudentT self) -> double"""
3027 return _IMP_isd.FStudentT_evaluate_derivative_sigma(self)
3029 def evaluate_derivative_nu(self):
3030 r"""evaluate_derivative_nu(FStudentT self) -> double"""
3031 return _IMP_isd.FStudentT_evaluate_derivative_nu(self)
3033 def update_cached_values(self):
3034 r"""update_cached_values(FStudentT self)"""
3035 return _IMP_isd.FStudentT_update_cached_values(self)
3037 def set_sumFX(self, v):
3038 r"""set_sumFX(FStudentT self, double v)"""
3039 return _IMP_isd.FStudentT_set_sumFX(self, v)
3041 def set_sumFX2(self, v):
3042 r"""set_sumFX2(FStudentT self, double v)"""
3043 return _IMP_isd.FStudentT_set_sumFX2(self, v)
3046 r"""set_N(FStudentT self, unsigned int v)"""
3047 return _IMP_isd.FStudentT_set_N(self, v)
3049 def set_LogJX(self, v):
3050 r"""set_LogJX(FStudentT self, double v)"""
3051 return _IMP_isd.FStudentT_set_LogJX(self, v)
3053 def set_FM(self, v):
3054 r"""set_FM(FStudentT self, double v)"""
3055 return _IMP_isd.FStudentT_set_FM(self, v)
3057 def set_sigma(self, v):
3058 r"""set_sigma(FStudentT self, double v)"""
3059 return _IMP_isd.FStudentT_set_sigma(self, v)
3061 def set_nu(self, v):
3062 r"""set_nu(FStudentT self, double v)"""
3063 return _IMP_isd.FStudentT_set_nu(self, v)
3065 def get_sumFX(self):
3066 r"""get_sumFX(FStudentT self) -> double"""
3067 return _IMP_isd.FStudentT_get_sumFX(self)
3069 def get_sumFX2(self):
3070 r"""get_sumFX2(FStudentT self) -> double"""
3071 return _IMP_isd.FStudentT_get_sumFX2(self)
3074 r"""get_N(FStudentT self) -> unsigned int"""
3075 return _IMP_isd.FStudentT_get_N(self)
3077 def get_LogJX(self):
3078 r"""get_LogJX(FStudentT self) -> double"""
3079 return _IMP_isd.FStudentT_get_LogJX(self)
3082 r"""get_FM(FStudentT self) -> double"""
3083 return _IMP_isd.FStudentT_get_FM(self)
3085 def get_sigma(self):
3086 r"""get_sigma(FStudentT self) -> double"""
3087 return _IMP_isd.FStudentT_get_sigma(self)
3090 r"""get_nu(FStudentT self) -> double"""
3091 return _IMP_isd.FStudentT_get_nu(self)
3092 __swig_destroy__ = _IMP_isd.delete_FStudentT
3095 r"""__str__(FStudentT self) -> std::string"""
3096 return _IMP_isd.FStudentT___str__(self)
3099 r"""__repr__(FStudentT self) -> std::string"""
3100 return _IMP_isd.FStudentT___repr__(self)
3104 return _object_cast_to_FStudentT(o)
3108 _IMP_isd.FStudentT_swigregister(FStudentT)
3110 r"""Proxy of C++ IMP::isd::vonMises class."""
3112 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3114 def __init__(self, x, mu, kappa):
3115 r"""__init__(vonMises self, double x, double mu, double kappa) -> vonMises"""
3116 _IMP_isd.vonMises_swiginit(self, _IMP_isd.new_vonMises(x, mu, kappa))
3119 r"""evaluate(vonMises self) -> double"""
3120 return _IMP_isd.vonMises_evaluate(self)
3122 def evaluate_derivative_x(self):
3123 r"""evaluate_derivative_x(vonMises self) -> double"""
3124 return _IMP_isd.vonMises_evaluate_derivative_x(self)
3126 def evaluate_derivative_mu(self):
3127 r"""evaluate_derivative_mu(vonMises self) -> double"""
3128 return _IMP_isd.vonMises_evaluate_derivative_mu(self)
3130 def evaluate_derivative_kappa(self):
3131 r"""evaluate_derivative_kappa(vonMises self) -> double"""
3132 return _IMP_isd.vonMises_evaluate_derivative_kappa(self)
3135 r"""density(vonMises self) -> double"""
3136 return _IMP_isd.vonMises_density(self)
3139 r"""set_x(vonMises self, double x)"""
3140 return _IMP_isd.vonMises_set_x(self, x)
3142 def set_mu(self, mu):
3143 r"""set_mu(vonMises self, double mu)"""
3144 return _IMP_isd.vonMises_set_mu(self, mu)
3146 def set_kappa(self, kappa):
3147 r"""set_kappa(vonMises self, double kappa)"""
3148 return _IMP_isd.vonMises_set_kappa(self, kappa)
3151 r"""get_version_info(vonMises self) -> VersionInfo"""
3152 return _IMP_isd.vonMises_get_version_info(self)
3153 __swig_destroy__ = _IMP_isd.delete_vonMises
3156 r"""__str__(vonMises self) -> std::string"""
3157 return _IMP_isd.vonMises___str__(self)
3160 r"""__repr__(vonMises self) -> std::string"""
3161 return _IMP_isd.vonMises___repr__(self)
3165 return _object_cast_to_vonMises(o)
3169 _IMP_isd.vonMises_swigregister(vonMises)
3171 r"""Proxy of C++ IMP::isd::vonMisesSufficient class."""
3173 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3175 def __init__(self, *args):
3177 __init__(vonMisesSufficient self, double chi, unsigned int N, double R0, double chiexp, double kappa) -> vonMisesSufficient
3178 __init__(vonMisesSufficient self, double chi, IMP::Floats obs, double kappa) -> vonMisesSufficient
3180 _IMP_isd.vonMisesSufficient_swiginit(self, _IMP_isd.new_vonMisesSufficient(*args))
3183 r"""evaluate(vonMisesSufficient self) -> double"""
3184 return _IMP_isd.vonMisesSufficient_evaluate(self)
3186 def evaluate_derivative_x(self):
3187 r"""evaluate_derivative_x(vonMisesSufficient self) -> double"""
3188 return _IMP_isd.vonMisesSufficient_evaluate_derivative_x(self)
3190 def evaluate_derivative_kappa(self):
3191 r"""evaluate_derivative_kappa(vonMisesSufficient self) -> double"""
3192 return _IMP_isd.vonMisesSufficient_evaluate_derivative_kappa(self)
3195 r"""density(vonMisesSufficient self) -> double"""
3196 return _IMP_isd.vonMisesSufficient_density(self)
3199 r"""get_x(vonMisesSufficient self) -> double"""
3200 return _IMP_isd.vonMisesSufficient_get_x(self)
3203 r"""get_R0(vonMisesSufficient self) -> double"""
3204 return _IMP_isd.vonMisesSufficient_get_R0(self)
3206 def get_chiexp(self):
3207 r"""get_chiexp(vonMisesSufficient self) -> double"""
3208 return _IMP_isd.vonMisesSufficient_get_chiexp(self)
3211 r"""get_N(vonMisesSufficient self) -> double"""
3212 return _IMP_isd.vonMisesSufficient_get_N(self)
3214 def get_kappa(self):
3215 r"""get_kappa(vonMisesSufficient self) -> double"""
3216 return _IMP_isd.vonMisesSufficient_get_kappa(self)
3219 r"""set_x(vonMisesSufficient self, double x)"""
3220 return _IMP_isd.vonMisesSufficient_set_x(self, x)
3222 def set_R0(self, R0):
3223 r"""set_R0(vonMisesSufficient self, double R0)"""
3224 return _IMP_isd.vonMisesSufficient_set_R0(self, R0)
3226 def set_chiexp(self, chiexp):
3227 r"""set_chiexp(vonMisesSufficient self, double chiexp)"""
3228 return _IMP_isd.vonMisesSufficient_set_chiexp(self, chiexp)
3231 r"""set_N(vonMisesSufficient self, unsigned int N)"""
3232 return _IMP_isd.vonMisesSufficient_set_N(self, N)
3234 def set_kappa(self, kappa):
3235 r"""set_kappa(vonMisesSufficient self, double kappa)"""
3236 return _IMP_isd.vonMisesSufficient_set_kappa(self, kappa)
3239 def get_sufficient_statistics(data):
3240 r"""get_sufficient_statistics(IMP::Floats data) -> IMP::Floats"""
3241 return _IMP_isd.vonMisesSufficient_get_sufficient_statistics(data)
3244 r"""get_version_info(vonMisesSufficient self) -> VersionInfo"""
3245 return _IMP_isd.vonMisesSufficient_get_version_info(self)
3246 __swig_destroy__ = _IMP_isd.delete_vonMisesSufficient
3249 r"""__str__(vonMisesSufficient self) -> std::string"""
3250 return _IMP_isd.vonMisesSufficient___str__(self)
3253 r"""__repr__(vonMisesSufficient self) -> std::string"""
3254 return _IMP_isd.vonMisesSufficient___repr__(self)
3258 return _object_cast_to_vonMisesSufficient(o)
3262 _IMP_isd.vonMisesSufficient_swigregister(vonMisesSufficient)
3263 class PenalizedComplexityPrior(OneDimensionalSufficientDistribution):
3264 r"""Proxy of C++ IMP::isd::PenalizedComplexityPrior class."""
3266 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3268 def __init__(self, *args):
3269 r"""__init__(PenalizedComplexityPrior self, double Dxi, double Jxi, double alpha, std::string name="PenalizedComplexityPrior %1%") -> PenalizedComplexityPrior"""
3270 _IMP_isd.PenalizedComplexityPrior_swiginit(self, _IMP_isd.new_PenalizedComplexityPrior(*args))
3272 def update_sufficient_statistics(self, Dxis, Jxis):
3273 r"""update_sufficient_statistics(PenalizedComplexityPrior self, IMP::Floats Dxis, IMP::Floats Jxis)"""
3274 return _IMP_isd.PenalizedComplexityPrior_update_sufficient_statistics(self, Dxis, Jxis)
3276 def evaluate_derivative_Dxi(self):
3277 r"""evaluate_derivative_Dxi(PenalizedComplexityPrior self) -> double"""
3278 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_Dxi(self)
3280 def evaluate_derivative_Jxi(self):
3281 r"""evaluate_derivative_Jxi(PenalizedComplexityPrior self) -> double"""
3282 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_Jxi(self)
3284 def evaluate_derivative_alpha(self):
3285 r"""evaluate_derivative_alpha(PenalizedComplexityPrior self) -> double"""
3286 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_alpha(self)
3288 def evaluate_derivative_xi(self, JJxi):
3289 r"""evaluate_derivative_xi(PenalizedComplexityPrior self, double JJxi) -> double"""
3290 return _IMP_isd.PenalizedComplexityPrior_evaluate_derivative_xi(self, JJxi)
3292 def set_Dxi(self, v):
3293 r"""set_Dxi(PenalizedComplexityPrior self, double v)"""
3294 return _IMP_isd.PenalizedComplexityPrior_set_Dxi(self, v)
3296 def set_Jxi(self, v):
3297 r"""set_Jxi(PenalizedComplexityPrior self, double v)"""
3298 return _IMP_isd.PenalizedComplexityPrior_set_Jxi(self, v)
3300 def set_alpha(self, v):
3301 r"""set_alpha(PenalizedComplexityPrior self, double v)"""
3302 return _IMP_isd.PenalizedComplexityPrior_set_alpha(self, v)
3305 r"""get_Dxi(PenalizedComplexityPrior self) -> double"""
3306 return _IMP_isd.PenalizedComplexityPrior_get_Dxi(self)
3309 r"""get_Jxi(PenalizedComplexityPrior self) -> double"""
3310 return _IMP_isd.PenalizedComplexityPrior_get_Jxi(self)
3312 def get_alpha(self):
3313 r"""get_alpha(PenalizedComplexityPrior self) -> double"""
3314 return _IMP_isd.PenalizedComplexityPrior_get_alpha(self)
3315 __swig_destroy__ = _IMP_isd.delete_PenalizedComplexityPrior
3318 r"""__str__(PenalizedComplexityPrior self) -> std::string"""
3319 return _IMP_isd.PenalizedComplexityPrior___str__(self)
3322 r"""__repr__(PenalizedComplexityPrior self) -> std::string"""
3323 return _IMP_isd.PenalizedComplexityPrior___repr__(self)
3327 return _object_cast_to_PenalizedComplexityPrior(o)
3331 _IMP_isd.PenalizedComplexityPrior_swigregister(PenalizedComplexityPrior)
3333 r"""Proxy of C++ IMP::isd::vonMisesKappaJeffreysRestraint class."""
3335 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3337 def __init__(self, m, kappa):
3338 r"""__init__(vonMisesKappaJeffreysRestraint self, Model m, Particle kappa) -> vonMisesKappaJeffreysRestraint"""
3339 _IMP_isd.vonMisesKappaJeffreysRestraint_swiginit(self, _IMP_isd.new_vonMisesKappaJeffreysRestraint(m, kappa))
3342 r"""do_get_inputs(vonMisesKappaJeffreysRestraint self) -> IMP::ModelObjectsTemp"""
3343 return _IMP_isd.vonMisesKappaJeffreysRestraint_do_get_inputs(self)
3346 r"""get_version_info(vonMisesKappaJeffreysRestraint self) -> VersionInfo"""
3347 return _IMP_isd.vonMisesKappaJeffreysRestraint_get_version_info(self)
3348 __swig_destroy__ = _IMP_isd.delete_vonMisesKappaJeffreysRestraint
3350 def get_probability(self):
3351 r"""get_probability(vonMisesKappaJeffreysRestraint self) -> double"""
3352 return _IMP_isd.vonMisesKappaJeffreysRestraint_get_probability(self)
3355 r"""__str__(vonMisesKappaJeffreysRestraint self) -> std::string"""
3356 return _IMP_isd.vonMisesKappaJeffreysRestraint___str__(self)
3359 r"""__repr__(vonMisesKappaJeffreysRestraint self) -> std::string"""
3360 return _IMP_isd.vonMisesKappaJeffreysRestraint___repr__(self)
3364 return _object_cast_to_vonMisesKappaJeffreysRestraint(o)
3368 _IMP_isd.vonMisesKappaJeffreysRestraint_swigregister(vonMisesKappaJeffreysRestraint)
3370 r"""Proxy of C++ IMP::isd::vonMisesKappaConjugateRestraint class."""
3372 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3374 def __init__(self, m, kappa, c=10.0, R0=0.0):
3375 r"""__init__(vonMisesKappaConjugateRestraint self, Model m, Particle kappa, double c=10.0, double R0=0.0) -> vonMisesKappaConjugateRestraint"""
3376 _IMP_isd.vonMisesKappaConjugateRestraint_swiginit(self, _IMP_isd.new_vonMisesKappaConjugateRestraint(m, kappa, c, R0))
3379 r"""do_get_inputs(vonMisesKappaConjugateRestraint self) -> IMP::ModelObjectsTemp"""
3380 return _IMP_isd.vonMisesKappaConjugateRestraint_do_get_inputs(self)
3383 r"""get_version_info(vonMisesKappaConjugateRestraint self) -> VersionInfo"""
3384 return _IMP_isd.vonMisesKappaConjugateRestraint_get_version_info(self)
3385 __swig_destroy__ = _IMP_isd.delete_vonMisesKappaConjugateRestraint
3387 def get_probability(self):
3388 r"""get_probability(vonMisesKappaConjugateRestraint self) -> double"""
3389 return _IMP_isd.vonMisesKappaConjugateRestraint_get_probability(self)
3392 r"""__str__(vonMisesKappaConjugateRestraint self) -> std::string"""
3393 return _IMP_isd.vonMisesKappaConjugateRestraint___str__(self)
3396 r"""__repr__(vonMisesKappaConjugateRestraint self) -> std::string"""
3397 return _IMP_isd.vonMisesKappaConjugateRestraint___repr__(self)
3401 return _object_cast_to_vonMisesKappaConjugateRestraint(o)
3405 _IMP_isd.vonMisesKappaConjugateRestraint_swigregister(vonMisesKappaConjugateRestraint)
3407 r"""Proxy of C++ IMP::isd::NOERestraint class."""
3409 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3411 def __init__(self, m, p0, p1, sigma, gamma, Iexp):
3412 r"""__init__(NOERestraint self, Model m, Particle p0, Particle p1, Particle sigma, Particle gamma, double Iexp) -> NOERestraint"""
3413 _IMP_isd.NOERestraint_swiginit(self, _IMP_isd.new_NOERestraint(m, p0, p1, sigma, gamma, Iexp))
3415 def get_probability(self):
3416 r"""get_probability(NOERestraint self) -> double"""
3417 return _IMP_isd.NOERestraint_get_probability(self)
3420 r"""get_chi(NOERestraint self) -> double"""
3421 return _IMP_isd.NOERestraint_get_chi(self)
3424 r"""do_get_inputs(NOERestraint self) -> IMP::ModelObjectsTemp"""
3425 return _IMP_isd.NOERestraint_do_get_inputs(self)
3428 r"""get_version_info(NOERestraint self) -> VersionInfo"""
3429 return _IMP_isd.NOERestraint_get_version_info(self)
3430 __swig_destroy__ = _IMP_isd.delete_NOERestraint
3433 r"""__str__(NOERestraint self) -> std::string"""
3434 return _IMP_isd.NOERestraint___str__(self)
3437 r"""__repr__(NOERestraint self) -> std::string"""
3438 return _IMP_isd.NOERestraint___repr__(self)
3442 return _object_cast_to_NOERestraint(o)
3446 _IMP_isd.NOERestraint_swigregister(NOERestraint)
3448 r"""Proxy of C++ IMP::isd::GaussianRestraint class."""
3450 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3452 def __init__(self, *args):
3454 __init__(GaussianRestraint self, Particle x, Particle mu, Particle sigma) -> GaussianRestraint
3455 __init__(GaussianRestraint self, double x, Particle mu, Particle sigma) -> GaussianRestraint
3456 __init__(GaussianRestraint self, Particle x, double mu, Particle sigma) -> GaussianRestraint
3457 __init__(GaussianRestraint self, Particle x, Particle mu, double sigma) -> GaussianRestraint
3458 __init__(GaussianRestraint self, double x, double mu, Particle sigma) -> GaussianRestraint
3459 __init__(GaussianRestraint self, Particle x, double mu, double sigma) -> GaussianRestraint
3460 __init__(GaussianRestraint self, double x, Particle mu, double sigma) -> GaussianRestraint
3462 _IMP_isd.GaussianRestraint_swiginit(self, _IMP_isd.new_GaussianRestraint(*args))
3464 def get_probability(self):
3465 r"""get_probability(GaussianRestraint self) -> double"""
3466 return _IMP_isd.GaussianRestraint_get_probability(self)
3469 r"""get_chi(GaussianRestraint self) -> double"""
3470 return _IMP_isd.GaussianRestraint_get_chi(self)
3473 r"""do_get_inputs(GaussianRestraint self) -> IMP::ModelObjectsTemp"""
3474 return _IMP_isd.GaussianRestraint_do_get_inputs(self)
3477 r"""get_version_info(GaussianRestraint self) -> VersionInfo"""
3478 return _IMP_isd.GaussianRestraint_get_version_info(self)
3479 __swig_destroy__ = _IMP_isd.delete_GaussianRestraint
3482 r"""__str__(GaussianRestraint self) -> std::string"""
3483 return _IMP_isd.GaussianRestraint___str__(self)
3486 r"""__repr__(GaussianRestraint self) -> std::string"""
3487 return _IMP_isd.GaussianRestraint___repr__(self)
3491 return _object_cast_to_GaussianRestraint(o)
3495 _IMP_isd.GaussianRestraint_swigregister(GaussianRestraint)
3497 r"""Proxy of C++ IMP::isd::StudentTRestraint class."""
3499 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3501 def __init__(self, *args):
3503 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3504 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3505 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3506 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3507 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3508 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3509 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, _ParticleIndexAdaptor mu, double sigma, double nu) -> StudentTRestraint
3510 __init__(StudentTRestraint self, Model m, _ParticleIndexAdaptor x, double mu, double sigma, double nu) -> StudentTRestraint
3511 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3512 __init__(StudentTRestraint self, Model m, double x, double mu, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3513 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3514 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3515 __init__(StudentTRestraint self, Model m, double x, double mu, double sigma, _ParticleIndexAdaptor nu) -> StudentTRestraint
3516 __init__(StudentTRestraint self, Model m, double x, double mu, _ParticleIndexAdaptor sigma, double nu) -> StudentTRestraint
3517 __init__(StudentTRestraint self, Model m, double x, _ParticleIndexAdaptor mu, double sigma, double nu) -> StudentTRestraint
3519 _IMP_isd.StudentTRestraint_swiginit(self, _IMP_isd.new_StudentTRestraint(*args))
3521 def get_probability(self):
3522 r"""get_probability(StudentTRestraint self) -> double"""
3523 return _IMP_isd.StudentTRestraint_get_probability(self)
3526 r"""do_get_inputs(StudentTRestraint self) -> IMP::ModelObjectsTemp"""
3527 return _IMP_isd.StudentTRestraint_do_get_inputs(self)
3530 r"""get_version_info(StudentTRestraint self) -> VersionInfo"""
3531 return _IMP_isd.StudentTRestraint_get_version_info(self)
3532 __swig_destroy__ = _IMP_isd.delete_StudentTRestraint
3535 r"""__str__(StudentTRestraint self) -> std::string"""
3536 return _IMP_isd.StudentTRestraint___str__(self)
3539 r"""__repr__(StudentTRestraint self) -> std::string"""
3540 return _IMP_isd.StudentTRestraint___repr__(self)
3544 return _object_cast_to_StudentTRestraint(o)
3548 _IMP_isd.StudentTRestraint_swigregister(StudentTRestraint)
3550 r"""Proxy of C++ IMP::isd::LognormalRestraint class."""
3552 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3554 def __init__(self, *args):
3556 __init__(LognormalRestraint self, Particle x, Particle mu, Particle sigma) -> LognormalRestraint
3557 __init__(LognormalRestraint self, double x, Particle mu, Particle sigma) -> LognormalRestraint
3558 __init__(LognormalRestraint self, Particle x, double mu, Particle sigma) -> LognormalRestraint
3559 __init__(LognormalRestraint self, Particle x, Particle mu, double sigma) -> LognormalRestraint
3560 __init__(LognormalRestraint self, double x, double mu, Particle sigma) -> LognormalRestraint
3561 __init__(LognormalRestraint self, Particle x, double mu, double sigma) -> LognormalRestraint
3562 __init__(LognormalRestraint self, double x, Particle mu, double sigma) -> LognormalRestraint
3564 _IMP_isd.LognormalRestraint_swiginit(self, _IMP_isd.new_LognormalRestraint(*args))
3566 def get_probability(self):
3567 r"""get_probability(LognormalRestraint self) -> double"""
3568 return _IMP_isd.LognormalRestraint_get_probability(self)
3571 r"""get_chi(LognormalRestraint self) -> double"""
3572 return _IMP_isd.LognormalRestraint_get_chi(self)
3575 r"""do_get_inputs(LognormalRestraint self) -> IMP::ModelObjectsTemp"""
3576 return _IMP_isd.LognormalRestraint_do_get_inputs(self)
3579 r"""get_version_info(LognormalRestraint self) -> VersionInfo"""
3580 return _IMP_isd.LognormalRestraint_get_version_info(self)
3581 __swig_destroy__ = _IMP_isd.delete_LognormalRestraint
3584 r"""__str__(LognormalRestraint self) -> std::string"""
3585 return _IMP_isd.LognormalRestraint___str__(self)
3588 r"""__repr__(LognormalRestraint self) -> std::string"""
3589 return _IMP_isd.LognormalRestraint___repr__(self)
3593 return _object_cast_to_LognormalRestraint(o)
3597 _IMP_isd.LognormalRestraint_swigregister(LognormalRestraint)
3599 r"""Proxy of C++ IMP::isd::LognormalAmbiguousRestraint class."""
3601 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3603 def __init__(self, p1, p2, ki, sigmaG):
3604 r"""__init__(LognormalAmbiguousRestraint self, Particle p1, Particle p2, Particle ki, Particle sigmaG) -> LognormalAmbiguousRestraint"""
3605 _IMP_isd.LognormalAmbiguousRestraint_swiginit(self, _IMP_isd.new_LognormalAmbiguousRestraint(p1, p2, ki, sigmaG))
3607 def add_contribution(self, lexp, omega):
3608 r"""add_contribution(LognormalAmbiguousRestraint self, double lexp, Particle omega)"""
3609 return _IMP_isd.LognormalAmbiguousRestraint_add_contribution(self, lexp, omega)
3611 def get_number_of_contributions(self):
3612 r"""get_number_of_contributions(LognormalAmbiguousRestraint self) -> unsigned int"""
3613 return _IMP_isd.LognormalAmbiguousRestraint_get_number_of_contributions(self)
3615 def draw_k_from_posterior(self, kt):
3616 r"""draw_k_from_posterior(LognormalAmbiguousRestraint self, double kt)"""
3617 return _IMP_isd.LognormalAmbiguousRestraint_draw_k_from_posterior(self, kt)
3619 def get_probability(self):
3620 r"""get_probability(LognormalAmbiguousRestraint self) -> double"""
3621 return _IMP_isd.LognormalAmbiguousRestraint_get_probability(self)
3624 r"""do_get_inputs(LognormalAmbiguousRestraint self) -> IMP::ModelObjectsTemp"""
3625 return _IMP_isd.LognormalAmbiguousRestraint_do_get_inputs(self)
3628 r"""get_version_info(LognormalAmbiguousRestraint self) -> VersionInfo"""
3629 return _IMP_isd.LognormalAmbiguousRestraint_get_version_info(self)
3630 __swig_destroy__ = _IMP_isd.delete_LognormalAmbiguousRestraint
3633 r"""__str__(LognormalAmbiguousRestraint self) -> std::string"""
3634 return _IMP_isd.LognormalAmbiguousRestraint___str__(self)
3637 r"""__repr__(LognormalAmbiguousRestraint self) -> std::string"""
3638 return _IMP_isd.LognormalAmbiguousRestraint___repr__(self)
3642 return _object_cast_to_LognormalAmbiguousRestraint(o)
3646 _IMP_isd.LognormalAmbiguousRestraint_swigregister(LognormalAmbiguousRestraint)
3648 r"""Proxy of C++ IMP::isd::AmbiguousNOERestraint class."""
3650 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3652 def __init__(self, *args):
3654 __init__(AmbiguousNOERestraint self, Model m, PairContainer pc, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor gamma, double Iexp) -> AmbiguousNOERestraint
3655 __init__(AmbiguousNOERestraint self) -> AmbiguousNOERestraint
3657 _IMP_isd.AmbiguousNOERestraint_swiginit(self, _IMP_isd.new_AmbiguousNOERestraint(*args))
3659 def get_probability(self):
3660 r"""get_probability(AmbiguousNOERestraint self) -> double"""
3661 return _IMP_isd.AmbiguousNOERestraint_get_probability(self)
3664 r"""get_chi(AmbiguousNOERestraint self) -> double"""
3665 return _IMP_isd.AmbiguousNOERestraint_get_chi(self)
3668 r"""do_get_inputs(AmbiguousNOERestraint self) -> IMP::ModelObjectsTemp"""
3669 return _IMP_isd.AmbiguousNOERestraint_do_get_inputs(self)
3672 r"""get_version_info(AmbiguousNOERestraint self) -> VersionInfo"""
3673 return _IMP_isd.AmbiguousNOERestraint_get_version_info(self)
3674 __swig_destroy__ = _IMP_isd.delete_AmbiguousNOERestraint
3677 r"""__str__(AmbiguousNOERestraint self) -> std::string"""
3678 return _IMP_isd.AmbiguousNOERestraint___str__(self)
3681 r"""__repr__(AmbiguousNOERestraint self) -> std::string"""
3682 return _IMP_isd.AmbiguousNOERestraint___repr__(self)
3686 return _object_cast_to_AmbiguousNOERestraint(o)
3689 def _get_as_binary(self):
3690 r"""_get_as_binary(AmbiguousNOERestraint self) -> PyObject *"""
3691 return _IMP_isd.AmbiguousNOERestraint__get_as_binary(self)
3693 def _set_from_binary(self, p):
3694 r"""_set_from_binary(AmbiguousNOERestraint self, PyObject * p)"""
3695 return _IMP_isd.AmbiguousNOERestraint__set_from_binary(self, p)
3697 def __getstate__(self):
3698 p = self._get_as_binary()
3699 if len(self.__dict__) > 1:
3700 d = self.__dict__.copy()
3705 def __setstate__(self, p):
3706 if not hasattr(self,
'this'):
3708 if isinstance(p, tuple):
3710 self.__dict__.update(d)
3711 return self._set_from_binary(p)
3715 _IMP_isd.AmbiguousNOERestraint_swigregister(AmbiguousNOERestraint)
3717 r"""Proxy of C++ IMP::isd::MarginalNOERestraint class."""
3719 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3721 def __init__(self, m):
3722 r"""__init__(MarginalNOERestraint self, Model m) -> MarginalNOERestraint"""
3723 _IMP_isd.MarginalNOERestraint_swiginit(self, _IMP_isd.new_MarginalNOERestraint(m))
3725 def add_contribution(self, *args):
3727 add_contribution(MarginalNOERestraint self, Particle p1, Particle p2, double Iexp)
3728 add_contribution(MarginalNOERestraint self, PairContainer pc, double Iexp)
3730 return _IMP_isd.MarginalNOERestraint_add_contribution(self, *args)
3732 def get_log_gammahat(self):
3733 r"""get_log_gammahat(MarginalNOERestraint self) -> double"""
3734 return _IMP_isd.MarginalNOERestraint_get_log_gammahat(self)
3737 r"""get_SS(MarginalNOERestraint self) -> double"""
3738 return _IMP_isd.MarginalNOERestraint_get_SS(self)
3740 def get_number_of_contributions(self):
3741 r"""get_number_of_contributions(MarginalNOERestraint self) -> unsigned int"""
3742 return _IMP_isd.MarginalNOERestraint_get_number_of_contributions(self)
3744 def get_probability(self):
3745 r"""get_probability(MarginalNOERestraint self) -> double"""
3746 return _IMP_isd.MarginalNOERestraint_get_probability(self)
3749 r"""do_get_inputs(MarginalNOERestraint self) -> IMP::ModelObjectsTemp"""
3750 return _IMP_isd.MarginalNOERestraint_do_get_inputs(self)
3753 r"""get_version_info(MarginalNOERestraint self) -> VersionInfo"""
3754 return _IMP_isd.MarginalNOERestraint_get_version_info(self)
3755 __swig_destroy__ = _IMP_isd.delete_MarginalNOERestraint
3758 r"""__str__(MarginalNOERestraint self) -> std::string"""
3759 return _IMP_isd.MarginalNOERestraint___str__(self)
3762 r"""__repr__(MarginalNOERestraint self) -> std::string"""
3763 return _IMP_isd.MarginalNOERestraint___repr__(self)
3767 return _object_cast_to_MarginalNOERestraint(o)
3771 _IMP_isd.MarginalNOERestraint_swigregister(MarginalNOERestraint)
3773 r"""Proxy of C++ IMP::isd::MarginalHBondRestraint class."""
3775 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3777 def __init__(self, m):
3778 r"""__init__(MarginalHBondRestraint self, Model m) -> MarginalHBondRestraint"""
3779 _IMP_isd.MarginalHBondRestraint_swiginit(self, _IMP_isd.new_MarginalHBondRestraint(m))
3781 def add_contribution(self, *args):
3783 add_contribution(MarginalHBondRestraint self, Particle p1, Particle p2, double Iexp)
3784 add_contribution(MarginalHBondRestraint self, PairContainer pc, double Iexp)
3786 return _IMP_isd.MarginalHBondRestraint_add_contribution(self, *args)
3788 def get_logsquares(self):
3789 r"""get_logsquares(MarginalHBondRestraint self) -> double"""
3790 return _IMP_isd.MarginalHBondRestraint_get_logsquares(self)
3792 def get_number_of_contributions(self):
3793 r"""get_number_of_contributions(MarginalHBondRestraint self) -> unsigned int"""
3794 return _IMP_isd.MarginalHBondRestraint_get_number_of_contributions(self)
3796 def get_probability(self):
3797 r"""get_probability(MarginalHBondRestraint self) -> double"""
3798 return _IMP_isd.MarginalHBondRestraint_get_probability(self)
3801 r"""do_get_inputs(MarginalHBondRestraint self) -> IMP::ModelObjectsTemp"""
3802 return _IMP_isd.MarginalHBondRestraint_do_get_inputs(self)
3805 r"""get_version_info(MarginalHBondRestraint self) -> VersionInfo"""
3806 return _IMP_isd.MarginalHBondRestraint_get_version_info(self)
3807 __swig_destroy__ = _IMP_isd.delete_MarginalHBondRestraint
3810 r"""__str__(MarginalHBondRestraint self) -> std::string"""
3811 return _IMP_isd.MarginalHBondRestraint___str__(self)
3814 r"""__repr__(MarginalHBondRestraint self) -> std::string"""
3815 return _IMP_isd.MarginalHBondRestraint___repr__(self)
3819 return _object_cast_to_MarginalHBondRestraint(o)
3823 _IMP_isd.MarginalHBondRestraint_swigregister(MarginalHBondRestraint)
3825 r"""Proxy of C++ IMP::isd::TALOSRestraint class."""
3827 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3829 def __init__(self, *args):
3831 __init__(TALOSRestraint self, Model m, IMP::Particles p, IMP::Floats data, Particle kappa) -> TALOSRestraint
3832 __init__(TALOSRestraint self, Model m, Particle p1, Particle p2, Particle p3, Particle p4, IMP::Floats data, Particle kappa) -> TALOSRestraint
3833 __init__(TALOSRestraint self, Model m, IMP::Particles p, unsigned int N, double R0, double chiexp, Particle kappa) -> TALOSRestraint
3834 __init__(TALOSRestraint self, Model m, Particle p1, Particle p2, Particle p3, Particle p4, unsigned int N, double R0, double chiexp, Particle kappa) -> TALOSRestraint
3836 _IMP_isd.TALOSRestraint_swiginit(self, _IMP_isd.new_TALOSRestraint(*args))
3838 def get_probability(self):
3839 r"""get_probability(TALOSRestraint self) -> double"""
3840 return _IMP_isd.TALOSRestraint_get_probability(self)
3843 r"""get_R0(TALOSRestraint self) -> double"""
3844 return _IMP_isd.TALOSRestraint_get_R0(self)
3846 def get_chiexp(self):
3847 r"""get_chiexp(TALOSRestraint self) -> double"""
3848 return _IMP_isd.TALOSRestraint_get_chiexp(self)
3851 r"""do_get_inputs(TALOSRestraint self) -> IMP::ModelObjectsTemp"""
3852 return _IMP_isd.TALOSRestraint_do_get_inputs(self)
3855 r"""get_version_info(TALOSRestraint self) -> VersionInfo"""
3856 return _IMP_isd.TALOSRestraint_get_version_info(self)
3857 __swig_destroy__ = _IMP_isd.delete_TALOSRestraint
3860 r"""__str__(TALOSRestraint self) -> std::string"""
3861 return _IMP_isd.TALOSRestraint___str__(self)
3864 r"""__repr__(TALOSRestraint self) -> std::string"""
3865 return _IMP_isd.TALOSRestraint___repr__(self)
3869 return _object_cast_to_TALOSRestraint(o)
3873 _IMP_isd.TALOSRestraint_swigregister(TALOSRestraint)
3875 r"""Proxy of C++ IMP::isd::RepulsiveDistancePairScore class."""
3877 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3879 def __init__(self, d0, k):
3880 r"""__init__(RepulsiveDistancePairScore self, double d0, double k) -> RepulsiveDistancePairScore"""
3881 _IMP_isd.RepulsiveDistancePairScore_swiginit(self, _IMP_isd.new_RepulsiveDistancePairScore(d0, k))
3883 def get_rest_length(self):
3884 r"""get_rest_length(RepulsiveDistancePairScore self) -> double"""
3885 return _IMP_isd.RepulsiveDistancePairScore_get_rest_length(self)
3887 def get_stiffness(self):
3888 r"""get_stiffness(RepulsiveDistancePairScore self) -> double"""
3889 return _IMP_isd.RepulsiveDistancePairScore_get_stiffness(self)
3892 r"""do_get_inputs(RepulsiveDistancePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3893 return _IMP_isd.RepulsiveDistancePairScore_do_get_inputs(self, m, pis)
3896 r"""get_version_info(RepulsiveDistancePairScore self) -> VersionInfo"""
3897 return _IMP_isd.RepulsiveDistancePairScore_get_version_info(self)
3898 __swig_destroy__ = _IMP_isd.delete_RepulsiveDistancePairScore
3901 r"""__str__(RepulsiveDistancePairScore self) -> std::string"""
3902 return _IMP_isd.RepulsiveDistancePairScore___str__(self)
3905 r"""__repr__(RepulsiveDistancePairScore self) -> std::string"""
3906 return _IMP_isd.RepulsiveDistancePairScore___repr__(self)
3910 return _object_cast_to_RepulsiveDistancePairScore(o)
3914 _IMP_isd.RepulsiveDistancePairScore_swigregister(RepulsiveDistancePairScore)
3916 r"""Proxy of C++ IMP::isd::AmbiguousRestraint class."""
3918 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3920 def __init__(self, *args):
3922 __init__(AmbiguousRestraint self, Model m, int d, Restraint r0, Restraint r1) -> AmbiguousRestraint
3923 __init__(AmbiguousRestraint self, Model m, int d, IMP::Restraints rs) -> AmbiguousRestraint
3924 __init__(AmbiguousRestraint self) -> AmbiguousRestraint
3926 _IMP_isd.AmbiguousRestraint_swiginit(self, _IMP_isd.new_AmbiguousRestraint(*args))
3928 def get_probability(self):
3929 r"""get_probability(AmbiguousRestraint self) -> double"""
3930 return _IMP_isd.AmbiguousRestraint_get_probability(self)
3933 r"""do_get_inputs(AmbiguousRestraint self) -> IMP::ModelObjectsTemp"""
3934 return _IMP_isd.AmbiguousRestraint_do_get_inputs(self)
3937 r"""get_version_info(AmbiguousRestraint self) -> VersionInfo"""
3938 return _IMP_isd.AmbiguousRestraint_get_version_info(self)
3939 __swig_destroy__ = _IMP_isd.delete_AmbiguousRestraint
3942 r"""__str__(AmbiguousRestraint self) -> std::string"""
3943 return _IMP_isd.AmbiguousRestraint___str__(self)
3946 r"""__repr__(AmbiguousRestraint self) -> std::string"""
3947 return _IMP_isd.AmbiguousRestraint___repr__(self)
3951 return _object_cast_to_AmbiguousRestraint(o)
3954 def _get_as_binary(self):
3955 r"""_get_as_binary(AmbiguousRestraint self) -> PyObject *"""
3956 return _IMP_isd.AmbiguousRestraint__get_as_binary(self)
3958 def _set_from_binary(self, p):
3959 r"""_set_from_binary(AmbiguousRestraint self, PyObject * p)"""
3960 return _IMP_isd.AmbiguousRestraint__set_from_binary(self, p)
3962 def __getstate__(self):
3963 p = self._get_as_binary()
3964 if len(self.__dict__) > 1:
3965 d = self.__dict__.copy()
3970 def __setstate__(self, p):
3971 if not hasattr(self,
'this'):
3973 if isinstance(p, tuple):
3975 self.__dict__.update(d)
3976 return self._set_from_binary(p)
3980 _IMP_isd.AmbiguousRestraint_swigregister(AmbiguousRestraint)
3981 IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM = _IMP_isd.IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM
3984 r"""Proxy of C++ IMP::isd::UnivariateFunction class."""
3986 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3988 def __init__(self, *args, **kwargs):
3989 raise AttributeError(
"No constructor defined - class is abstract")
3991 def __call__(self, *args):
3993 __call__(UnivariateFunction self, IMP::Floats const & x) -> IMP::Floats
3994 __call__(UnivariateFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
3995 __call__(UnivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
3997 return _IMP_isd.UnivariateFunction___call__(self, *args)
3999 def has_changed(self):
4000 r"""has_changed(UnivariateFunction self) -> bool"""
4001 return _IMP_isd.UnivariateFunction_has_changed(self)
4004 r"""update(UnivariateFunction self)"""
4005 return _IMP_isd.UnivariateFunction_update(self)
4007 def add_to_derivatives(self, x, accum):
4008 r"""add_to_derivatives(UnivariateFunction self, IMP::Floats const & x, DerivativeAccumulator accum)"""
4009 return _IMP_isd.UnivariateFunction_add_to_derivatives(self, x, accum)
4011 def add_to_particle_derivative(self, particle_no, value, accum):
4012 r"""add_to_particle_derivative(UnivariateFunction self, unsigned int particle_no, double value, DerivativeAccumulator accum)"""
4013 return _IMP_isd.UnivariateFunction_add_to_particle_derivative(self, particle_no, value, accum)
4015 def get_derivative_vector(self, particle_no, xlist):
4016 r"""get_derivative_vector(UnivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::VectorXd"""
4017 return _IMP_isd.UnivariateFunction_get_derivative_vector(self, particle_no, xlist)
4019 def get_derivative_matrix(self, xlist, stupid):
4020 r"""get_derivative_matrix(UnivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList"""
4021 return _IMP_isd.UnivariateFunction_get_derivative_matrix(self, xlist, stupid)
4023 def get_second_derivative_vector(self, *args):
4025 get_second_derivative_vector(UnivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4026 get_second_derivative_vector(UnivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4028 return _IMP_isd.UnivariateFunction_get_second_derivative_vector(self, *args)
4030 def get_ndims_x(self):
4031 r"""get_ndims_x(UnivariateFunction self) -> unsigned int"""
4032 return _IMP_isd.UnivariateFunction_get_ndims_x(self)
4034 def get_ndims_y(self):
4035 r"""get_ndims_y(UnivariateFunction self) -> unsigned int"""
4036 return _IMP_isd.UnivariateFunction_get_ndims_y(self)
4038 def get_number_of_particles(self):
4039 r"""get_number_of_particles(UnivariateFunction self) -> unsigned int"""
4040 return _IMP_isd.UnivariateFunction_get_number_of_particles(self)
4042 def get_particle_is_optimized(self, particle_no):
4043 r"""get_particle_is_optimized(UnivariateFunction self, unsigned int particle_no) -> bool"""
4044 return _IMP_isd.UnivariateFunction_get_particle_is_optimized(self, particle_no)
4046 def get_number_of_optimized_particles(self):
4047 r"""get_number_of_optimized_particles(UnivariateFunction self) -> unsigned int"""
4048 return _IMP_isd.UnivariateFunction_get_number_of_optimized_particles(self)
4051 r"""get_inputs(UnivariateFunction self) -> IMP::ModelObjectsTemp"""
4052 return _IMP_isd.UnivariateFunction_get_inputs(self)
4053 __swig_destroy__ = _IMP_isd.delete_UnivariateFunction
4056 r"""__str__(UnivariateFunction self) -> std::string"""
4057 return _IMP_isd.UnivariateFunction___str__(self)
4060 r"""__repr__(UnivariateFunction self) -> std::string"""
4061 return _IMP_isd.UnivariateFunction___repr__(self)
4065 return _object_cast_to_UnivariateFunction(o)
4069 _IMP_isd.UnivariateFunction_swigregister(UnivariateFunction)
4070 class Linear1DFunction(UnivariateFunction):
4071 r"""Proxy of C++ IMP::isd::Linear1DFunction class."""
4073 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4075 def __init__(self, a, b):
4076 r"""__init__(Linear1DFunction self, Particle a, Particle b) -> Linear1DFunction"""
4077 _IMP_isd.Linear1DFunction_swiginit(self, _IMP_isd.new_Linear1DFunction(a, b))
4079 def __call__(self, *args):
4081 __call__(Linear1DFunction self, IMP::Floats const & x) -> IMP::Floats
4082 __call__(Linear1DFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4083 __call__(Linear1DFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4085 return _IMP_isd.Linear1DFunction___call__(self, *args)
4087 def get_second_derivative_vector(self, *args):
4089 get_second_derivative_vector(Linear1DFunction self, unsigned int arg2, unsigned int arg3, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4090 get_second_derivative_vector(Linear1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4092 return _IMP_isd.Linear1DFunction_get_second_derivative_vector(self, *args)
4095 r"""get_version_info(Linear1DFunction self) -> VersionInfo"""
4096 return _IMP_isd.Linear1DFunction_get_version_info(self)
4097 __swig_destroy__ = _IMP_isd.delete_Linear1DFunction
4100 r"""__str__(Linear1DFunction self) -> std::string"""
4101 return _IMP_isd.Linear1DFunction___str__(self)
4104 r"""__repr__(Linear1DFunction self) -> std::string"""
4105 return _IMP_isd.Linear1DFunction___repr__(self)
4109 return _object_cast_to_Linear1DFunction(o)
4113 _IMP_isd.Linear1DFunction_swigregister(Linear1DFunction)
4114 class GeneralizedGuinierPorodFunction(UnivariateFunction):
4115 r"""Proxy of C++ IMP::isd::GeneralizedGuinierPorodFunction class."""
4117 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4119 def __init__(self, G, Rg, d, s, A):
4120 r"""__init__(GeneralizedGuinierPorodFunction self, Particle G, Particle Rg, Particle d, Particle s, Particle A) -> GeneralizedGuinierPorodFunction"""
4121 _IMP_isd.GeneralizedGuinierPorodFunction_swiginit(self, _IMP_isd.new_GeneralizedGuinierPorodFunction(G, Rg, d, s, A))
4123 def __call__(self, *args):
4125 __call__(GeneralizedGuinierPorodFunction self, IMP::Floats const & x) -> IMP::Floats
4126 __call__(GeneralizedGuinierPorodFunction self, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4127 __call__(GeneralizedGuinierPorodFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4129 return _IMP_isd.GeneralizedGuinierPorodFunction___call__(self, *args)
4131 def get_second_derivative_vector(self, *args):
4133 get_second_derivative_vector(GeneralizedGuinierPorodFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::VectorXd
4134 get_second_derivative_vector(GeneralizedGuinierPorodFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4136 return _IMP_isd.GeneralizedGuinierPorodFunction_get_second_derivative_vector(self, *args)
4139 r"""get_version_info(GeneralizedGuinierPorodFunction self) -> VersionInfo"""
4140 return _IMP_isd.GeneralizedGuinierPorodFunction_get_version_info(self)
4141 __swig_destroy__ = _IMP_isd.delete_GeneralizedGuinierPorodFunction
4144 r"""__str__(GeneralizedGuinierPorodFunction self) -> std::string"""
4145 return _IMP_isd.GeneralizedGuinierPorodFunction___str__(self)
4148 r"""__repr__(GeneralizedGuinierPorodFunction self) -> std::string"""
4149 return _IMP_isd.GeneralizedGuinierPorodFunction___repr__(self)
4153 return _object_cast_to_GeneralizedGuinierPorodFunction(o)
4157 _IMP_isd.GeneralizedGuinierPorodFunction_swigregister(GeneralizedGuinierPorodFunction)
4158 IMP_ISD_BIVARIATE_FUNCTIONS_MINIMUM = _IMP_isd.IMP_ISD_BIVARIATE_FUNCTIONS_MINIMUM
4161 r"""Proxy of C++ IMP::isd::BivariateFunction class."""
4163 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4165 def __init__(self, *args, **kwargs):
4166 raise AttributeError(
"No constructor defined - class is abstract")
4168 def __call__(self, *args):
4170 __call__(BivariateFunction self, IMP::Floats const & x1, IMP::Floats const & x2) -> IMP::Floats
4171 __call__(BivariateFunction self, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4172 __call__(BivariateFunction self, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4174 return _IMP_isd.BivariateFunction___call__(self, *args)
4176 def has_changed(self):
4177 r"""has_changed(BivariateFunction self) -> bool"""
4178 return _IMP_isd.BivariateFunction_has_changed(self)
4181 r"""update(BivariateFunction self)"""
4182 return _IMP_isd.BivariateFunction_update(self)
4184 def add_to_derivatives(self, x1, x2, accum):
4185 r"""add_to_derivatives(BivariateFunction self, IMP::Floats const & x1, IMP::Floats const & x2, DerivativeAccumulator accum)"""
4186 return _IMP_isd.BivariateFunction_add_to_derivatives(self, x1, x2, accum)
4188 def add_to_particle_derivative(self, particle_no, value, accum):
4189 r"""add_to_particle_derivative(BivariateFunction self, unsigned int particle_no, double value, DerivativeAccumulator accum)"""
4190 return _IMP_isd.BivariateFunction_add_to_particle_derivative(self, particle_no, value, accum)
4192 def get_derivative_matrix(self, *args):
4194 get_derivative_matrix(BivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4195 get_derivative_matrix(BivariateFunction self, unsigned int particle_no, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4197 return _IMP_isd.BivariateFunction_get_derivative_matrix(self, *args)
4199 def get_second_derivative_matrix(self, *args):
4201 get_second_derivative_matrix(BivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4202 get_second_derivative_matrix(BivariateFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool stupid) -> IMP::FloatsList
4204 return _IMP_isd.BivariateFunction_get_second_derivative_matrix(self, *args)
4206 def get_ndims_x1(self):
4207 r"""get_ndims_x1(BivariateFunction self) -> unsigned int"""
4208 return _IMP_isd.BivariateFunction_get_ndims_x1(self)
4210 def get_ndims_x2(self):
4211 r"""get_ndims_x2(BivariateFunction self) -> unsigned int"""
4212 return _IMP_isd.BivariateFunction_get_ndims_x2(self)
4214 def get_ndims_y(self):
4215 r"""get_ndims_y(BivariateFunction self) -> unsigned int"""
4216 return _IMP_isd.BivariateFunction_get_ndims_y(self)
4218 def get_number_of_particles(self):
4219 r"""get_number_of_particles(BivariateFunction self) -> unsigned int"""
4220 return _IMP_isd.BivariateFunction_get_number_of_particles(self)
4222 def get_particle_is_optimized(self, particle_no):
4223 r"""get_particle_is_optimized(BivariateFunction self, unsigned int particle_no) -> bool"""
4224 return _IMP_isd.BivariateFunction_get_particle_is_optimized(self, particle_no)
4226 def get_number_of_optimized_particles(self):
4227 r"""get_number_of_optimized_particles(BivariateFunction self) -> unsigned int"""
4228 return _IMP_isd.BivariateFunction_get_number_of_optimized_particles(self)
4231 r"""get_inputs(BivariateFunction self) -> IMP::ModelObjectsTemp"""
4232 return _IMP_isd.BivariateFunction_get_inputs(self)
4233 __swig_destroy__ = _IMP_isd.delete_BivariateFunction
4236 r"""__str__(BivariateFunction self) -> std::string"""
4237 return _IMP_isd.BivariateFunction___str__(self)
4240 r"""__repr__(BivariateFunction self) -> std::string"""
4241 return _IMP_isd.BivariateFunction___repr__(self)
4245 return _object_cast_to_BivariateFunction(o)
4249 _IMP_isd.BivariateFunction_swigregister(BivariateFunction)
4250 class Covariance1DFunction(BivariateFunction):
4251 r"""Proxy of C++ IMP::isd::Covariance1DFunction class."""
4253 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4255 def __init__(self, tau, ilambda, alpha=2.0, jitter=0.0, cutoff=1e-7):
4256 r"""__init__(Covariance1DFunction self, Particle tau, Particle ilambda, double alpha=2.0, double jitter=0.0, double cutoff=1e-7) -> Covariance1DFunction"""
4257 _IMP_isd.Covariance1DFunction_swiginit(self, _IMP_isd.new_Covariance1DFunction(tau, ilambda, alpha, jitter, cutoff))
4259 def __call__(self, *args):
4261 __call__(Covariance1DFunction self, IMP::Floats const & x1, IMP::Floats const & x2) -> IMP::Floats
4262 __call__(Covariance1DFunction self, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4263 __call__(Covariance1DFunction self, IMP::FloatsList const & xlist, bool arg3) -> IMP::FloatsList
4265 return _IMP_isd.Covariance1DFunction___call__(self, *args)
4267 def get_derivative_matrix(self, *args):
4269 get_derivative_matrix(Covariance1DFunction self, unsigned int particle_no, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4270 get_derivative_matrix(Covariance1DFunction self, unsigned int particle_no, IMP::FloatsList const & xlist, bool arg4) -> IMP::FloatsList
4272 return _IMP_isd.Covariance1DFunction_get_derivative_matrix(self, *args)
4274 def get_second_derivative_matrix(self, *args):
4276 get_second_derivative_matrix(Covariance1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist) -> Eigen::MatrixXd
4277 get_second_derivative_matrix(Covariance1DFunction self, unsigned int particle_a, unsigned int particle_b, IMP::FloatsList const & xlist, bool arg5) -> IMP::FloatsList
4279 return _IMP_isd.Covariance1DFunction_get_second_derivative_matrix(self, *args)
4282 r"""get_version_info(Covariance1DFunction self) -> VersionInfo"""
4283 return _IMP_isd.Covariance1DFunction_get_version_info(self)
4284 __swig_destroy__ = _IMP_isd.delete_Covariance1DFunction
4287 r"""__str__(Covariance1DFunction self) -> std::string"""
4288 return _IMP_isd.Covariance1DFunction___str__(self)
4291 r"""__repr__(Covariance1DFunction self) -> std::string"""
4292 return _IMP_isd.Covariance1DFunction___repr__(self)
4296 return _object_cast_to_Covariance1DFunction(o)
4300 _IMP_isd.Covariance1DFunction_swigregister(Covariance1DFunction)
4301 class GaussianProcessInterpolation(
IMP.Object):
4302 r"""Proxy of C++ IMP::isd::GaussianProcessInterpolation class."""
4304 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4306 def __init__(self, x, sample_mean, sample_std, n_obs, mean_function, covariance_function, sigma, sparse_cutoff=1e-7):
4307 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"""
4308 _IMP_isd.GaussianProcessInterpolation_swiginit(self, _IMP_isd.new_GaussianProcessInterpolation(x, sample_mean, sample_std, n_obs, mean_function, covariance_function, sigma, sparse_cutoff))
4310 def get_posterior_mean(self, x):
4311 r"""get_posterior_mean(GaussianProcessInterpolation self, IMP::Floats x) -> double"""
4312 return _IMP_isd.GaussianProcessInterpolation_get_posterior_mean(self, x)
4314 def get_posterior_covariance(self, x1, x2):
4315 r"""get_posterior_covariance(GaussianProcessInterpolation self, IMP::Floats x1, IMP::Floats x2) -> double"""
4316 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance(self, x1, x2)
4318 def get_posterior_covariance_matrix(self, x, arg3):
4319 r"""get_posterior_covariance_matrix(GaussianProcessInterpolation self, IMP::FloatsList x, bool arg3) -> IMP::FloatsList"""
4320 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_matrix(self, x, arg3)
4322 def get_posterior_covariance_derivative(self, x, arg3):
4323 r"""get_posterior_covariance_derivative(GaussianProcessInterpolation self, IMP::Floats x, bool arg3) -> IMP::Floats"""
4324 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_derivative(self, x, arg3)
4326 def get_posterior_covariance_hessian(self, x, arg3):
4327 r"""get_posterior_covariance_hessian(GaussianProcessInterpolation self, IMP::Floats x, bool arg3) -> IMP::FloatsList"""
4328 return _IMP_isd.GaussianProcessInterpolation_get_posterior_covariance_hessian(self, x, arg3)
4331 r"""get_inputs(GaussianProcessInterpolation self) -> IMP::ModelObjectsTemp"""
4332 return _IMP_isd.GaussianProcessInterpolation_get_inputs(self)
4334 def force_mean_update(self):
4335 r"""force_mean_update(GaussianProcessInterpolation self)"""
4336 return _IMP_isd.GaussianProcessInterpolation_force_mean_update(self)
4338 def force_covariance_update(self):
4339 r"""force_covariance_update(GaussianProcessInterpolation self)"""
4340 return _IMP_isd.GaussianProcessInterpolation_force_covariance_update(self)
4342 def get_number_of_m_particles(self):
4343 r"""get_number_of_m_particles(GaussianProcessInterpolation self) -> unsigned int"""
4344 return _IMP_isd.GaussianProcessInterpolation_get_number_of_m_particles(self)
4346 def get_m_particle_is_optimized(self, i):
4347 r"""get_m_particle_is_optimized(GaussianProcessInterpolation self, unsigned int i) -> bool"""
4348 return _IMP_isd.GaussianProcessInterpolation_get_m_particle_is_optimized(self, i)
4350 def get_number_of_Omega_particles(self):
4351 r"""get_number_of_Omega_particles(GaussianProcessInterpolation self) -> unsigned int"""
4352 return _IMP_isd.GaussianProcessInterpolation_get_number_of_Omega_particles(self)
4354 def get_Omega_particle_is_optimized(self, i):
4355 r"""get_Omega_particle_is_optimized(GaussianProcessInterpolation self, unsigned int i) -> bool"""
4356 return _IMP_isd.GaussianProcessInterpolation_get_Omega_particle_is_optimized(self, i)
4358 def get_data_abscissa(self):
4359 r"""get_data_abscissa(GaussianProcessInterpolation self) -> IMP::FloatsList"""
4360 return _IMP_isd.GaussianProcessInterpolation_get_data_abscissa(self)
4362 def get_data_mean(self):
4363 r"""get_data_mean(GaussianProcessInterpolation self) -> IMP::Floats"""
4364 return _IMP_isd.GaussianProcessInterpolation_get_data_mean(self)
4366 def get_data_variance(self):
4367 r"""get_data_variance(GaussianProcessInterpolation self) -> IMP::FloatsList"""
4368 return _IMP_isd.GaussianProcessInterpolation_get_data_variance(self)
4371 r"""get_version_info(GaussianProcessInterpolation self) -> VersionInfo"""
4372 return _IMP_isd.GaussianProcessInterpolation_get_version_info(self)
4373 __swig_destroy__ = _IMP_isd.delete_GaussianProcessInterpolation
4376 r"""__str__(GaussianProcessInterpolation self) -> std::string"""
4377 return _IMP_isd.GaussianProcessInterpolation___str__(self)
4380 r"""__repr__(GaussianProcessInterpolation self) -> std::string"""
4381 return _IMP_isd.GaussianProcessInterpolation___repr__(self)
4385 return _object_cast_to_GaussianProcessInterpolation(o)
4389 _IMP_isd.GaussianProcessInterpolation_swigregister(GaussianProcessInterpolation)
4391 r"""Proxy of C++ IMP::isd::GaussianProcessInterpolationRestraint class."""
4393 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4395 def __init__(self, m, gpi):
4396 r"""__init__(GaussianProcessInterpolationRestraint self, Model m, GaussianProcessInterpolation gpi) -> GaussianProcessInterpolationRestraint"""
4397 _IMP_isd.GaussianProcessInterpolationRestraint_swiginit(self, _IMP_isd.new_GaussianProcessInterpolationRestraint(m, gpi))
4399 def get_probability(self):
4400 r"""get_probability(GaussianProcessInterpolationRestraint self) -> double"""
4401 return _IMP_isd.GaussianProcessInterpolationRestraint_get_probability(self)
4403 def set_use_cg(self, use, tol):
4404 r"""set_use_cg(GaussianProcessInterpolationRestraint self, bool use, double tol)"""
4405 return _IMP_isd.GaussianProcessInterpolationRestraint_set_use_cg(self, use, tol)
4407 def get_minus_log_normalization(self):
4408 r"""get_minus_log_normalization(GaussianProcessInterpolationRestraint self) -> double"""
4409 return _IMP_isd.GaussianProcessInterpolationRestraint_get_minus_log_normalization(self)
4411 def get_minus_exponent(self):
4412 r"""get_minus_exponent(GaussianProcessInterpolationRestraint self) -> double"""
4413 return _IMP_isd.GaussianProcessInterpolationRestraint_get_minus_exponent(self)
4415 def get_logdet_hessian(self):
4416 r"""get_logdet_hessian(GaussianProcessInterpolationRestraint self) -> double"""
4417 return _IMP_isd.GaussianProcessInterpolationRestraint_get_logdet_hessian(self)
4419 def get_hessian(self, *args):
4421 get_hessian(GaussianProcessInterpolationRestraint self) -> Eigen::MatrixXd
4422 get_hessian(GaussianProcessInterpolationRestraint self, bool unused) -> IMP::FloatsList
4424 return _IMP_isd.GaussianProcessInterpolationRestraint_get_hessian(self, *args)
4427 r"""do_get_inputs(GaussianProcessInterpolationRestraint self) -> IMP::ModelObjectsTemp"""
4428 return _IMP_isd.GaussianProcessInterpolationRestraint_do_get_inputs(self)
4431 r"""get_version_info(GaussianProcessInterpolationRestraint self) -> VersionInfo"""
4432 return _IMP_isd.GaussianProcessInterpolationRestraint_get_version_info(self)
4433 __swig_destroy__ = _IMP_isd.delete_GaussianProcessInterpolationRestraint
4436 r"""__str__(GaussianProcessInterpolationRestraint self) -> std::string"""
4437 return _IMP_isd.GaussianProcessInterpolationRestraint___str__(self)
4440 r"""__repr__(GaussianProcessInterpolationRestraint self) -> std::string"""
4441 return _IMP_isd.GaussianProcessInterpolationRestraint___repr__(self)
4445 return _object_cast_to_GaussianProcessInterpolationRestraint(o)
4449 _IMP_isd.GaussianProcessInterpolationRestraint_swigregister(GaussianProcessInterpolationRestraint)
4451 r"""Proxy of C++ IMP::isd::MolecularDynamics class."""
4453 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4455 def __init__(self, m=None):
4456 r"""__init__(MolecularDynamics self, Model m=None) -> MolecularDynamics"""
4457 _IMP_isd.MolecularDynamics_swiginit(self, _IMP_isd.new_MolecularDynamics(m))
4460 r"""__str__(MolecularDynamics self) -> std::string"""
4461 return _IMP_isd.MolecularDynamics___str__(self)
4464 r"""__repr__(MolecularDynamics self) -> std::string"""
4465 return _IMP_isd.MolecularDynamics___repr__(self)
4469 return _object_cast_to_MolecularDynamics(o)
4471 __swig_destroy__ = _IMP_isd.delete_MolecularDynamics
4474 _IMP_isd.MolecularDynamics_swigregister(MolecularDynamics)
4476 r"""Proxy of C++ IMP::isd::MolecularDynamicsMover class."""
4478 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4480 def __init__(self, m, nsteps=100, timestep=1.):
4481 r"""__init__(MolecularDynamicsMover self, Model m, unsigned int nsteps=100, IMP::Float timestep=1.) -> MolecularDynamicsMover"""
4482 _IMP_isd.MolecularDynamicsMover_swiginit(self, _IMP_isd.new_MolecularDynamicsMover(m, nsteps, timestep))
4485 r"""get_md(MolecularDynamicsMover self) -> MolecularDynamics"""
4486 return _IMP_isd.MolecularDynamicsMover_get_md(self)
4488 def get_number_of_md_steps(self):
4489 r"""get_number_of_md_steps(MolecularDynamicsMover self) -> unsigned int"""
4490 return _IMP_isd.MolecularDynamicsMover_get_number_of_md_steps(self)
4492 def set_number_of_md_steps(self, nsteps):
4493 r"""set_number_of_md_steps(MolecularDynamicsMover self, unsigned int nsteps)"""
4494 return _IMP_isd.MolecularDynamicsMover_set_number_of_md_steps(self, nsteps)
4497 r"""get_version_info(MolecularDynamicsMover self) -> VersionInfo"""
4498 return _IMP_isd.MolecularDynamicsMover_get_version_info(self)
4499 __swig_destroy__ = _IMP_isd.delete_MolecularDynamicsMover
4502 r"""__str__(MolecularDynamicsMover self) -> std::string"""
4503 return _IMP_isd.MolecularDynamicsMover___str__(self)
4506 r"""__repr__(MolecularDynamicsMover self) -> std::string"""
4507 return _IMP_isd.MolecularDynamicsMover___repr__(self)
4511 return _object_cast_to_MolecularDynamicsMover(o)
4515 _IMP_isd.MolecularDynamicsMover_swigregister(MolecularDynamicsMover)
4517 r"""Proxy of C++ IMP::isd::HybridMonteCarlo class."""
4519 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4521 def __init__(self, m, kT=1.0, steps=100, timestep=1.0, persistence=1):
4522 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"""
4523 _IMP_isd.HybridMonteCarlo_swiginit(self, _IMP_isd.new_HybridMonteCarlo(m, kT, steps, timestep, persistence))
4525 def get_kinetic_energy(self):
4526 r"""get_kinetic_energy(HybridMonteCarlo self) -> IMP::Float"""
4527 return _IMP_isd.HybridMonteCarlo_get_kinetic_energy(self)
4529 def get_potential_energy(self):
4530 r"""get_potential_energy(HybridMonteCarlo self) -> IMP::Float"""
4531 return _IMP_isd.HybridMonteCarlo_get_potential_energy(self)
4533 def get_total_energy(self):
4534 r"""get_total_energy(HybridMonteCarlo self) -> IMP::Float"""
4535 return _IMP_isd.HybridMonteCarlo_get_total_energy(self)
4537 def set_timestep(self, ts):
4538 r"""set_timestep(HybridMonteCarlo self, IMP::Float ts)"""
4539 return _IMP_isd.HybridMonteCarlo_set_timestep(self, ts)
4541 def get_timestep(self):
4542 r"""get_timestep(HybridMonteCarlo self) -> double"""
4543 return _IMP_isd.HybridMonteCarlo_get_timestep(self)
4545 def set_number_of_md_steps(self, nsteps):
4546 r"""set_number_of_md_steps(HybridMonteCarlo self, unsigned int nsteps)"""
4547 return _IMP_isd.HybridMonteCarlo_set_number_of_md_steps(self, nsteps)
4549 def get_number_of_md_steps(self):
4550 r"""get_number_of_md_steps(HybridMonteCarlo self) -> unsigned int"""
4551 return _IMP_isd.HybridMonteCarlo_get_number_of_md_steps(self)
4553 def set_persistence(self, persistence=1):
4554 r"""set_persistence(HybridMonteCarlo self, unsigned int persistence=1)"""
4555 return _IMP_isd.HybridMonteCarlo_set_persistence(self, persistence)
4557 def get_persistence(self):
4558 r"""get_persistence(HybridMonteCarlo self) -> unsigned int"""
4559 return _IMP_isd.HybridMonteCarlo_get_persistence(self)
4562 r"""get_md(HybridMonteCarlo self) -> MolecularDynamics"""
4563 return _IMP_isd.HybridMonteCarlo_get_md(self)
4565 def do_evaluate(self, arg2, arg3):
4566 r"""do_evaluate(HybridMonteCarlo self, IMP::ParticleIndexes const & arg2, bool arg3) -> double"""
4567 return _IMP_isd.HybridMonteCarlo_do_evaluate(self, arg2, arg3)
4570 r"""do_step(HybridMonteCarlo self)"""
4571 return _IMP_isd.HybridMonteCarlo_do_step(self)
4572 __swig_destroy__ = _IMP_isd.delete_HybridMonteCarlo
4575 r"""__str__(HybridMonteCarlo self) -> std::string"""
4576 return _IMP_isd.HybridMonteCarlo___str__(self)
4579 r"""__repr__(HybridMonteCarlo self) -> std::string"""
4580 return _IMP_isd.HybridMonteCarlo___repr__(self)
4584 return _object_cast_to_HybridMonteCarlo(o)
4588 _IMP_isd.HybridMonteCarlo_swigregister(HybridMonteCarlo)
4590 r"""Proxy of C++ IMP::isd::FretData class."""
4592 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4594 def __init__(self, *args):
4596 __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
4597 __init__(FretData self) -> FretData
4599 _IMP_isd.FretData_swiginit(self, _IMP_isd.new_FretData(*args))
4601 def get_closest(self, vec, value):
4602 r"""get_closest(FretData self, DistBase vec, double value) -> int"""
4603 return _IMP_isd.FretData_get_closest(self, vec, value)
4605 def get_probability(self, distn, dist, sigma):
4606 r"""get_probability(FretData self, IMP::Float distn, IMP::Float dist, IMP::Float sigma) -> IMP::Float"""
4607 return _IMP_isd.FretData_get_probability(self, distn, dist, sigma)
4609 def get_kernel(self, dist, R0):
4610 r"""get_kernel(FretData self, IMP::Float dist, IMP::Float R0) -> IMP::Float"""
4611 return _IMP_isd.FretData_get_kernel(self, dist, R0)
4613 def get_marginal_element(self, d_term, d_center, sigma):
4614 r"""get_marginal_element(FretData self, IMP::Float d_term, IMP::Float d_center, IMP::Float sigma) -> IMP::FloatPair"""
4615 return _IMP_isd.FretData_get_marginal_element(self, d_term, d_center, sigma)
4618 r"""get_version_info(FretData self) -> VersionInfo"""
4619 return _IMP_isd.FretData_get_version_info(self)
4620 __swig_destroy__ = _IMP_isd.delete_FretData
4623 r"""__str__(FretData self) -> std::string"""
4624 return _IMP_isd.FretData___str__(self)
4627 r"""__repr__(FretData self) -> std::string"""
4628 return _IMP_isd.FretData___repr__(self)
4632 return _object_cast_to_FretData(o)
4635 def _get_as_binary(self):
4636 r"""_get_as_binary(FretData self) -> PyObject *"""
4637 return _IMP_isd.FretData__get_as_binary(self)
4639 def _set_from_binary(self, p):
4640 r"""_set_from_binary(FretData self, PyObject * p)"""
4641 return _IMP_isd.FretData__set_from_binary(self, p)
4643 def __getstate__(self):
4644 p = self._get_as_binary()
4645 if len(self.__dict__) > 1:
4646 d = self.__dict__.copy()
4651 def __setstate__(self, p):
4652 if not hasattr(self,
'this'):
4654 if isinstance(p, tuple):
4656 self.__dict__.update(d)
4657 return self._set_from_binary(p)
4661 _IMP_isd.FretData_swigregister(FretData)
4663 r"""Proxy of C++ IMP::isd::FretRestraint class."""
4665 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4667 def __init__(self, *args):
4669 __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
4670 __init__(FretRestraint self, Particle kda, Particle Ida, Particle sumFi, Particle sigma0, Particle Pbl, double fexp) -> FretRestraint
4671 __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
4672 __init__(FretRestraint self) -> FretRestraint
4674 _IMP_isd.FretRestraint_swiginit(self, _IMP_isd.new_FretRestraint(*args))
4676 def get_sumFi(self):
4677 r"""get_sumFi(FretRestraint self) -> double"""
4678 return _IMP_isd.FretRestraint_get_sumFi(self)
4680 def get_average_sigma(self, fmod):
4681 r"""get_average_sigma(FretRestraint self, double fmod) -> double"""
4682 return _IMP_isd.FretRestraint_get_average_sigma(self, fmod)
4684 def get_standard_error(self):
4685 r"""get_standard_error(FretRestraint self) -> double"""
4686 return _IMP_isd.FretRestraint_get_standard_error(self)
4688 def get_model_fretr(self):
4689 r"""get_model_fretr(FretRestraint self) -> double"""
4690 return _IMP_isd.FretRestraint_get_model_fretr(self)
4692 def get_probability(self):
4693 r"""get_probability(FretRestraint self) -> double"""
4694 return _IMP_isd.FretRestraint_get_probability(self)
4696 def get_experimental_value(self):
4697 r"""get_experimental_value(FretRestraint self) -> double"""
4698 return _IMP_isd.FretRestraint_get_experimental_value(self)
4700 def set_experimental_value(self, fexp):
4701 r"""set_experimental_value(FretRestraint self, double fexp)"""
4702 return _IMP_isd.FretRestraint_set_experimental_value(self, fexp)
4705 r"""do_get_inputs(FretRestraint self) -> IMP::ModelObjectsTemp"""
4706 return _IMP_isd.FretRestraint_do_get_inputs(self)
4709 r"""get_version_info(FretRestraint self) -> VersionInfo"""
4710 return _IMP_isd.FretRestraint_get_version_info(self)
4711 __swig_destroy__ = _IMP_isd.delete_FretRestraint
4714 r"""__str__(FretRestraint self) -> std::string"""
4715 return _IMP_isd.FretRestraint___str__(self)
4718 r"""__repr__(FretRestraint self) -> std::string"""
4719 return _IMP_isd.FretRestraint___repr__(self)
4723 return _object_cast_to_FretRestraint(o)
4726 def _get_as_binary(self):
4727 r"""_get_as_binary(FretRestraint self) -> PyObject *"""
4728 return _IMP_isd.FretRestraint__get_as_binary(self)
4730 def _set_from_binary(self, p):
4731 r"""_set_from_binary(FretRestraint self, PyObject * p)"""
4732 return _IMP_isd.FretRestraint__set_from_binary(self, p)
4734 def __getstate__(self):
4735 p = self._get_as_binary()
4736 if len(self.__dict__) > 1:
4737 d = self.__dict__.copy()
4742 def __setstate__(self, p):
4743 if not hasattr(self,
'this'):
4745 if isinstance(p, tuple):
4747 self.__dict__.update(d)
4748 return self._set_from_binary(p)
4752 _IMP_isd.FretRestraint_swigregister(FretRestraint)
4754 r"""Proxy of C++ IMP::isd::CysteineCrossLinkData class."""
4756 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4758 def __init__(self, *args):
4760 __init__(CysteineCrossLinkData self, double fexp, IMP::Floats fmod_grid, IMP::Floats omega_grid, IMP::Floats omega0_grid, int prior_type=3) -> CysteineCrossLinkData
4761 __init__(CysteineCrossLinkData self) -> CysteineCrossLinkData
4763 _IMP_isd.CysteineCrossLinkData_swiginit(self, _IMP_isd.new_CysteineCrossLinkData(*args))
4765 def get_closest(self, vec, value):
4766 r"""get_closest(CysteineCrossLinkData self, DistBase vec, double value) -> int"""
4767 return _IMP_isd.CysteineCrossLinkData_get_closest(self, vec, value)
4769 def get_omegas(self, fmods, omega0):
4770 r"""get_omegas(CysteineCrossLinkData self, IMP::Floats fmods, double omega0) -> IMP::Floats"""
4771 return _IMP_isd.CysteineCrossLinkData_get_omegas(self, fmods, omega0)
4773 def get_nonmarginal_elements(self, fexp, fmods, omega):
4774 r"""get_nonmarginal_elements(CysteineCrossLinkData self, double fexp, IMP::Floats fmods, double omega) -> IMP::Floats"""
4775 return _IMP_isd.CysteineCrossLinkData_get_nonmarginal_elements(self, fexp, fmods, omega)
4777 def get_marginal_elements(self, fmods, omega0):
4778 r"""get_marginal_elements(CysteineCrossLinkData self, IMP::Floats fmods, double omega0) -> IMP::Floats"""
4779 return _IMP_isd.CysteineCrossLinkData_get_marginal_elements(self, fmods, omega0)
4781 def get_omega(self, fmod, omega0):
4782 r"""get_omega(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4783 return _IMP_isd.CysteineCrossLinkData_get_omega(self, fmod, omega0)
4785 def get_standard_deviation(self, fmod, omega0):
4786 r"""get_standard_deviation(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4787 return _IMP_isd.CysteineCrossLinkData_get_standard_deviation(self, fmod, omega0)
4789 def get_nonmarginal_element(self, fexp, fmod, omega):
4790 r"""get_nonmarginal_element(CysteineCrossLinkData self, double fexp, double fmod, double omega) -> double"""
4791 return _IMP_isd.CysteineCrossLinkData_get_nonmarginal_element(self, fexp, fmod, omega)
4793 def get_marginal_element(self, fmod, omega0):
4794 r"""get_marginal_element(CysteineCrossLinkData self, double fmod, double omega0) -> double"""
4795 return _IMP_isd.CysteineCrossLinkData_get_marginal_element(self, fmod, omega0)
4798 r"""get_version_info(CysteineCrossLinkData self) -> VersionInfo"""
4799 return _IMP_isd.CysteineCrossLinkData_get_version_info(self)
4800 __swig_destroy__ = _IMP_isd.delete_CysteineCrossLinkData
4803 r"""__str__(CysteineCrossLinkData self) -> std::string"""
4804 return _IMP_isd.CysteineCrossLinkData___str__(self)
4807 r"""__repr__(CysteineCrossLinkData self) -> std::string"""
4808 return _IMP_isd.CysteineCrossLinkData___repr__(self)
4812 return _object_cast_to_CysteineCrossLinkData(o)
4815 def _get_as_binary(self):
4816 r"""_get_as_binary(CysteineCrossLinkData self) -> PyObject *"""
4817 return _IMP_isd.CysteineCrossLinkData__get_as_binary(self)
4819 def _set_from_binary(self, p):
4820 r"""_set_from_binary(CysteineCrossLinkData self, PyObject * p)"""
4821 return _IMP_isd.CysteineCrossLinkData__set_from_binary(self, p)
4823 def __getstate__(self):
4824 p = self._get_as_binary()
4825 if len(self.__dict__) > 1:
4826 d = self.__dict__.copy()
4831 def __setstate__(self, p):
4832 if not hasattr(self,
'this'):
4834 if isinstance(p, tuple):
4836 self.__dict__.update(d)
4837 return self._set_from_binary(p)
4841 _IMP_isd.CysteineCrossLinkData_swigregister(CysteineCrossLinkData)
4843 r"""Proxy of C++ IMP::isd::CrossLinkData class."""
4845 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4847 def __init__(self, *args):
4849 __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
4850 __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
4851 __init__(CrossLinkData self) -> CrossLinkData
4853 _IMP_isd.CrossLinkData_swiginit(self, _IMP_isd.new_CrossLinkData(*args))
4855 def get_closest(self, vec, value):
4856 r"""get_closest(CrossLinkData self, DistBase vec, double value) -> int"""
4857 return _IMP_isd.CrossLinkData_get_closest(self, vec, value)
4859 def get_omegas(self, sigma, dists):
4860 r"""get_omegas(CrossLinkData self, double sigma, IMP::Floats dists) -> IMP::Floats"""
4861 return _IMP_isd.CrossLinkData_get_omegas(self, sigma, dists)
4863 def get_omega_prior(self, omega, omega0):
4864 r"""get_omega_prior(CrossLinkData self, double omega, double omega0) -> double"""
4865 return _IMP_isd.CrossLinkData_get_omega_prior(self, omega, omega0)
4867 def get_nonmarginal_elements(self, sigmai, dists):
4868 r"""get_nonmarginal_elements(CrossLinkData self, double sigmai, IMP::Floats dists) -> IMP::Floats"""
4869 return _IMP_isd.CrossLinkData_get_nonmarginal_elements(self, sigmai, dists)
4871 def get_marginal_elements(self, sigma, dists):
4872 r"""get_marginal_elements(CrossLinkData self, double sigma, IMP::Floats dists) -> IMP::Floats"""
4873 return _IMP_isd.CrossLinkData_get_marginal_elements(self, sigma, dists)
4875 def get_marginal_maximum(self, *args):
4877 get_marginal_maximum(CrossLinkData self, double sigma) -> double
4878 get_marginal_maximum(CrossLinkData self) -> double
4880 return _IMP_isd.CrossLinkData_get_marginal_maximum(self, *args)
4883 r"""get_version_info(CrossLinkData self) -> VersionInfo"""
4884 return _IMP_isd.CrossLinkData_get_version_info(self)
4885 __swig_destroy__ = _IMP_isd.delete_CrossLinkData
4888 r"""__str__(CrossLinkData self) -> std::string"""
4889 return _IMP_isd.CrossLinkData___str__(self)
4892 r"""__repr__(CrossLinkData self) -> std::string"""
4893 return _IMP_isd.CrossLinkData___repr__(self)
4897 return _object_cast_to_CrossLinkData(o)
4900 def _get_as_binary(self):
4901 r"""_get_as_binary(CrossLinkData self) -> PyObject *"""
4902 return _IMP_isd.CrossLinkData__get_as_binary(self)
4904 def _set_from_binary(self, p):
4905 r"""_set_from_binary(CrossLinkData self, PyObject * p)"""
4906 return _IMP_isd.CrossLinkData__set_from_binary(self, p)
4908 def __getstate__(self):
4909 p = self._get_as_binary()
4910 if len(self.__dict__) > 1:
4911 d = self.__dict__.copy()
4916 def __setstate__(self, p):
4917 if not hasattr(self,
'this'):
4919 if isinstance(p, tuple):
4921 self.__dict__.update(d)
4922 return self._set_from_binary(p)
4926 _IMP_isd.CrossLinkData_swigregister(CrossLinkData)
4928 r"""Proxy of C++ IMP::isd::CysteineCrossLinkRestraint class."""
4930 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4932 def __init__(self, *args):
4934 __init__(CysteineCrossLinkRestraint self, Model m, _ParticleIndexAdaptor beta, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor epsilon, _ParticleIndexAdaptor weight, CrossLinkData data, double fexp) -> CysteineCrossLinkRestraint
4935 __init__(CysteineCrossLinkRestraint self, Model m, _ParticleIndexAdaptor beta, _ParticleIndexAdaptor sigma, _ParticleIndexAdaptor epsilon, _ParticleIndexAdaptor weight, CrossLinkData data, CysteineCrossLinkData ccldata) -> CysteineCrossLinkRestraint
4936 __init__(CysteineCrossLinkRestraint self) -> CysteineCrossLinkRestraint
4938 _IMP_isd.CysteineCrossLinkRestraint_swiginit(self, _IMP_isd.new_CysteineCrossLinkRestraint(*args))
4940 def get_probability(self):
4941 r"""get_probability(CysteineCrossLinkRestraint self) -> double"""
4942 return _IMP_isd.CysteineCrossLinkRestraint_get_probability(self)
4944 def get_standard_error(self):
4945 r"""get_standard_error(CysteineCrossLinkRestraint self) -> double"""
4946 return _IMP_isd.CysteineCrossLinkRestraint_get_standard_error(self)
4948 def get_frequencies(self):
4949 r"""get_frequencies(CysteineCrossLinkRestraint self) -> IMP::Floats"""
4950 return _IMP_isd.CysteineCrossLinkRestraint_get_frequencies(self)
4952 def get_model_frequency(self):
4953 r"""get_model_frequency(CysteineCrossLinkRestraint self) -> double"""
4954 return _IMP_isd.CysteineCrossLinkRestraint_get_model_frequency(self)
4956 def get_distances(self):
4957 r"""get_distances(CysteineCrossLinkRestraint self) -> IMP::Floats"""
4958 return _IMP_isd.CysteineCrossLinkRestraint_get_distances(self)
4960 def get_truncated_normalization(self, mean, sigma):
4961 r"""get_truncated_normalization(CysteineCrossLinkRestraint self, double mean, double sigma) -> double"""
4962 return _IMP_isd.CysteineCrossLinkRestraint_get_truncated_normalization(self, mean, sigma)
4964 def get_normal_pdf(self, mean, sigma, x):
4965 r"""get_normal_pdf(CysteineCrossLinkRestraint self, double mean, double sigma, double x) -> double"""
4966 return _IMP_isd.CysteineCrossLinkRestraint_get_normal_pdf(self, mean, sigma, x)
4968 def add_contribution(self, *args):
4970 add_contribution(CysteineCrossLinkRestraint self, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2)
4971 add_contribution(CysteineCrossLinkRestraint self, IMP::ParticleIndexes p1, IMP::ParticleIndexes p2)
4973 return _IMP_isd.CysteineCrossLinkRestraint_add_contribution(self, *args)
4975 def get_CB_coordinates(self, ps):
4976 r"""get_CB_coordinates(CysteineCrossLinkRestraint self, IMP::ParticleIndexes const & ps) -> Vector3D"""
4977 return _IMP_isd.CysteineCrossLinkRestraint_get_CB_coordinates(self, ps)
4979 def get_number_of_contributions(self):
4980 r"""get_number_of_contributions(CysteineCrossLinkRestraint self) -> unsigned int"""
4981 return _IMP_isd.CysteineCrossLinkRestraint_get_number_of_contributions(self)
4984 r"""do_get_inputs(CysteineCrossLinkRestraint self) -> IMP::ModelObjectsTemp"""
4985 return _IMP_isd.CysteineCrossLinkRestraint_do_get_inputs(self)
4988 r"""get_version_info(CysteineCrossLinkRestraint self) -> VersionInfo"""
4989 return _IMP_isd.CysteineCrossLinkRestraint_get_version_info(self)
4990 __swig_destroy__ = _IMP_isd.delete_CysteineCrossLinkRestraint
4993 r"""__str__(CysteineCrossLinkRestraint self) -> std::string"""
4994 return _IMP_isd.CysteineCrossLinkRestraint___str__(self)
4997 r"""__repr__(CysteineCrossLinkRestraint self) -> std::string"""
4998 return _IMP_isd.CysteineCrossLinkRestraint___repr__(self)
5002 return _object_cast_to_CysteineCrossLinkRestraint(o)
5005 def _get_as_binary(self):
5006 r"""_get_as_binary(CysteineCrossLinkRestraint self) -> PyObject *"""
5007 return _IMP_isd.CysteineCrossLinkRestraint__get_as_binary(self)
5009 def _set_from_binary(self, p):
5010 r"""_set_from_binary(CysteineCrossLinkRestraint self, PyObject * p)"""
5011 return _IMP_isd.CysteineCrossLinkRestraint__set_from_binary(self, p)
5013 def __getstate__(self):
5014 p = self._get_as_binary()
5015 if len(self.__dict__) > 1:
5016 d = self.__dict__.copy()
5021 def __setstate__(self, p):
5022 if not hasattr(self,
'this'):
5024 if isinstance(p, tuple):
5026 self.__dict__.update(d)
5027 return self._set_from_binary(p)
5031 _IMP_isd.CysteineCrossLinkRestraint_swigregister(CysteineCrossLinkRestraint)
5033 r"""Proxy of C++ IMP::isd::WeightMover class."""
5035 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5037 def __init__(self, w, radius):
5038 r"""__init__(WeightMover self, Particle w, IMP::Float radius) -> WeightMover"""
5039 _IMP_isd.WeightMover_swiginit(self, _IMP_isd.new_WeightMover(w, radius))
5041 def set_radius(self, radius):
5042 r"""set_radius(WeightMover self, IMP::Float radius)"""
5043 return _IMP_isd.WeightMover_set_radius(self, radius)
5045 def get_radius(self):
5046 r"""get_radius(WeightMover self) -> IMP::Float"""
5047 return _IMP_isd.WeightMover_get_radius(self)
5050 r"""get_version_info(WeightMover self) -> VersionInfo"""
5051 return _IMP_isd.WeightMover_get_version_info(self)
5052 __swig_destroy__ = _IMP_isd.delete_WeightMover
5055 r"""__str__(WeightMover self) -> std::string"""
5056 return _IMP_isd.WeightMover___str__(self)
5059 r"""__repr__(WeightMover self) -> std::string"""
5060 return _IMP_isd.WeightMover___repr__(self)
5064 return _object_cast_to_WeightMover(o)
5068 _IMP_isd.WeightMover_swigregister(WeightMover)
5070 r"""Proxy of C++ IMP::isd::WeightRestraint class."""
5072 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5074 def __init__(self, w, wmin, wmax, kappa):
5075 r"""__init__(WeightRestraint self, Particle w, IMP::Float wmin, IMP::Float wmax, IMP::Float kappa) -> WeightRestraint"""
5076 _IMP_isd.WeightRestraint_swiginit(self, _IMP_isd.new_WeightRestraint(w, wmin, wmax, kappa))
5079 r"""do_get_inputs(WeightRestraint self) -> IMP::ModelObjectsTemp"""
5080 return _IMP_isd.WeightRestraint_do_get_inputs(self)
5083 r"""get_version_info(WeightRestraint self) -> VersionInfo"""
5084 return _IMP_isd.WeightRestraint_get_version_info(self)
5085 __swig_destroy__ = _IMP_isd.delete_WeightRestraint
5088 r"""__str__(WeightRestraint self) -> std::string"""
5089 return _IMP_isd.WeightRestraint___str__(self)
5092 r"""__repr__(WeightRestraint self) -> std::string"""
5093 return _IMP_isd.WeightRestraint___repr__(self)
5097 return _object_cast_to_WeightRestraint(o)
5101 _IMP_isd.WeightRestraint_swigregister(WeightRestraint)
5103 r"""Proxy of C++ IMP::isd::AtomicCrossLinkMSRestraint class."""
5105 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5107 def __init__(self, *args):
5109 __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
5110 __init__(AtomicCrossLinkMSRestraint self) -> AtomicCrossLinkMSRestraint
5112 _IMP_isd.AtomicCrossLinkMSRestraint_swiginit(self, _IMP_isd.new_AtomicCrossLinkMSRestraint(*args))
5114 def add_contribution(self, ppi, sigmas):
5115 r"""add_contribution(AtomicCrossLinkMSRestraint self, IMP::ParticleIndexPair const & ppi, IMP::ParticleIndexPair const & sigmas)"""
5116 return _IMP_isd.AtomicCrossLinkMSRestraint_add_contribution(self, ppi, sigmas)
5118 def evaluate_for_contributions(self, c, accum):
5119 r"""evaluate_for_contributions(AtomicCrossLinkMSRestraint self, IMP::Ints c, DerivativeAccumulator accum) -> IMP::Float"""
5120 return _IMP_isd.AtomicCrossLinkMSRestraint_evaluate_for_contributions(self, c, accum)
5122 def get_number_of_contributions(self):
5123 r"""get_number_of_contributions(AtomicCrossLinkMSRestraint self) -> unsigned int"""
5124 return _IMP_isd.AtomicCrossLinkMSRestraint_get_number_of_contributions(self)
5126 def get_contribution(self, i):
5127 r"""get_contribution(AtomicCrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
5128 return _IMP_isd.AtomicCrossLinkMSRestraint_get_contribution(self, i)
5130 def get_contribution_sigmas(self, i):
5131 r"""get_contribution_sigmas(AtomicCrossLinkMSRestraint self, int i) -> IMP::ParticleIndexPair"""
5132 return _IMP_isd.AtomicCrossLinkMSRestraint_get_contribution_sigmas(self, i)
5135 r"""get_psi(AtomicCrossLinkMSRestraint self) -> ParticleIndex"""
5136 return _IMP_isd.AtomicCrossLinkMSRestraint_get_psi(self)
5139 r"""do_get_inputs(AtomicCrossLinkMSRestraint self) -> IMP::ModelObjectsTemp"""
5140 return _IMP_isd.AtomicCrossLinkMSRestraint_do_get_inputs(self)
5142 def show(self, out):
5143 r"""show(AtomicCrossLinkMSRestraint self, _ostream out)"""
5144 return _IMP_isd.AtomicCrossLinkMSRestraint_show(self, out)
5146 def set_slope(self, slope):
5147 r"""set_slope(AtomicCrossLinkMSRestraint self, IMP::Float slope)"""
5148 return _IMP_isd.AtomicCrossLinkMSRestraint_set_slope(self, slope)
5150 def set_part_of_log_score(self, hey):
5151 r"""set_part_of_log_score(AtomicCrossLinkMSRestraint self, bool hey)"""
5152 return _IMP_isd.AtomicCrossLinkMSRestraint_set_part_of_log_score(self, hey)
5155 r"""get_version_info(AtomicCrossLinkMSRestraint self) -> VersionInfo"""
5156 return _IMP_isd.AtomicCrossLinkMSRestraint_get_version_info(self)
5157 __swig_destroy__ = _IMP_isd.delete_AtomicCrossLinkMSRestraint
5160 r"""__str__(AtomicCrossLinkMSRestraint self) -> std::string"""
5161 return _IMP_isd.AtomicCrossLinkMSRestraint___str__(self)
5164 r"""__repr__(AtomicCrossLinkMSRestraint self) -> std::string"""
5165 return _IMP_isd.AtomicCrossLinkMSRestraint___repr__(self)
5169 return _object_cast_to_AtomicCrossLinkMSRestraint(o)
5172 def _get_as_binary(self):
5173 r"""_get_as_binary(AtomicCrossLinkMSRestraint self) -> PyObject *"""
5174 return _IMP_isd.AtomicCrossLinkMSRestraint__get_as_binary(self)
5176 def _set_from_binary(self, p):
5177 r"""_set_from_binary(AtomicCrossLinkMSRestraint self, PyObject * p)"""
5178 return _IMP_isd.AtomicCrossLinkMSRestraint__set_from_binary(self, p)
5180 def __getstate__(self):
5181 p = self._get_as_binary()
5182 if len(self.__dict__) > 1:
5183 d = self.__dict__.copy()
5188 def __setstate__(self, p):
5189 if not hasattr(self,
'this'):
5191 if isinstance(p, tuple):
5193 self.__dict__.update(d)
5194 return self._set_from_binary(p)
5198 _IMP_isd.AtomicCrossLinkMSRestraint_swigregister(AtomicCrossLinkMSRestraint)
5200 r"""Proxy of C++ IMP::isd::GaussianEMRestraint class."""
5202 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5204 def __init__(self, *args):
5206 __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
5207 __init__(GaussianEMRestraint self) -> GaussianEMRestraint
5209 _IMP_isd.GaussianEMRestraint_swiginit(self, _IMP_isd.new_GaussianEMRestraint(*args))
5211 def get_probability(self):
5212 r"""get_probability(GaussianEMRestraint self) -> double"""
5213 return _IMP_isd.GaussianEMRestraint_get_probability(self)
5216 r"""get_cross_correlation_coefficient(GaussianEMRestraint self) -> double"""
5217 return _IMP_isd.GaussianEMRestraint_get_cross_correlation_coefficient(self)
5219 def set_density_filename(self, density_fn):
5220 r"""set_density_filename(GaussianEMRestraint self, std::string density_fn)"""
5221 return _IMP_isd.GaussianEMRestraint_set_density_filename(self, density_fn)
5223 def compute_initial_scores(self):
5224 r"""compute_initial_scores(GaussianEMRestraint self)"""
5225 return _IMP_isd.GaussianEMRestraint_compute_initial_scores(self)
5227 def set_slope(self, s):
5228 r"""set_slope(GaussianEMRestraint self, IMP::Float s)"""
5229 return _IMP_isd.GaussianEMRestraint_set_slope(self, s)
5231 def get_slope(self):
5232 r"""get_slope(GaussianEMRestraint self) -> IMP::Float"""
5233 return _IMP_isd.GaussianEMRestraint_get_slope(self)
5236 r"""do_get_inputs(GaussianEMRestraint self) -> IMP::ModelObjectsTemp"""
5237 return _IMP_isd.GaussianEMRestraint_do_get_inputs(self)
5239 def show(self, out):
5240 r"""show(GaussianEMRestraint self, _ostream out)"""
5241 return _IMP_isd.GaussianEMRestraint_show(self, out)
5244 r"""get_version_info(GaussianEMRestraint self) -> VersionInfo"""
5245 return _IMP_isd.GaussianEMRestraint_get_version_info(self)
5246 __swig_destroy__ = _IMP_isd.delete_GaussianEMRestraint
5249 r"""__str__(GaussianEMRestraint self) -> std::string"""
5250 return _IMP_isd.GaussianEMRestraint___str__(self)
5253 r"""__repr__(GaussianEMRestraint self) -> std::string"""
5254 return _IMP_isd.GaussianEMRestraint___repr__(self)
5258 return _object_cast_to_GaussianEMRestraint(o)
5261 def _get_as_binary(self):
5262 r"""_get_as_binary(GaussianEMRestraint self) -> PyObject *"""
5263 return _IMP_isd.GaussianEMRestraint__get_as_binary(self)
5265 def _set_from_binary(self, p):
5266 r"""_set_from_binary(GaussianEMRestraint self, PyObject * p)"""
5267 return _IMP_isd.GaussianEMRestraint__set_from_binary(self, p)
5269 def __getstate__(self):
5270 p = self._get_as_binary()
5271 if len(self.__dict__) > 1:
5272 d = self.__dict__.copy()
5277 def __setstate__(self, p):
5278 if not hasattr(self,
'this'):
5280 if isinstance(p, tuple):
5282 self.__dict__.update(d)
5283 return self._set_from_binary(p)
5287 _IMP_isd.GaussianEMRestraint_swigregister(GaussianEMRestraint)
5288 class GaussianAnchorEMRestraint(ISDRestraint):
5289 r"""Proxy of C++ IMP::isd::GaussianAnchorEMRestraint class."""
5291 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5293 def __init__(self, *args):
5294 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"""
5295 _IMP_isd.GaussianAnchorEMRestraint_swiginit(self, _IMP_isd.new_GaussianAnchorEMRestraint(*args))
5297 def get_density_particles(self):
5298 r"""get_density_particles(GaussianAnchorEMRestraint self) -> IMP::ParticlesTemp"""
5299 return _IMP_isd.GaussianAnchorEMRestraint_get_density_particles(self)
5300 __swig_destroy__ = _IMP_isd.delete_GaussianAnchorEMRestraint
5303 r"""__str__(GaussianAnchorEMRestraint self) -> std::string"""
5304 return _IMP_isd.GaussianAnchorEMRestraint___str__(self)
5307 r"""__repr__(GaussianAnchorEMRestraint self) -> std::string"""
5308 return _IMP_isd.GaussianAnchorEMRestraint___repr__(self)
5312 return _object_cast_to_GaussianAnchorEMRestraint(o)
5316 _IMP_isd.GaussianAnchorEMRestraint_swigregister(GaussianAnchorEMRestraint)
5318 r"""Proxy of C++ IMP::isd::GammaPrior class."""
5320 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5322 def __init__(self, *args):
5323 r"""__init__(GammaPrior self, Model m, Particle p, IMP::Float k, IMP::Float theta, std::string name="GammaPrior%1%") -> GammaPrior"""
5324 _IMP_isd.GammaPrior_swiginit(self, _IMP_isd.new_GammaPrior(*args))
5326 def evaluate_at(self, val):
5327 r"""evaluate_at(GammaPrior self, IMP::Float val) -> double"""
5328 return _IMP_isd.GammaPrior_evaluate_at(self, val)
5331 r"""do_get_inputs(GammaPrior self) -> IMP::ModelObjectsTemp"""
5332 return _IMP_isd.GammaPrior_do_get_inputs(self)
5335 r"""get_version_info(GammaPrior self) -> VersionInfo"""
5336 return _IMP_isd.GammaPrior_get_version_info(self)
5337 __swig_destroy__ = _IMP_isd.delete_GammaPrior
5339 def get_probability(self):
5340 r"""get_probability(GammaPrior self) -> double"""
5341 return _IMP_isd.GammaPrior_get_probability(self)
5344 r"""__str__(GammaPrior self) -> std::string"""
5345 return _IMP_isd.GammaPrior___str__(self)
5348 r"""__repr__(GammaPrior self) -> std::string"""
5349 return _IMP_isd.GammaPrior___repr__(self)
5353 return _object_cast_to_GammaPrior(o)
5357 _IMP_isd.GammaPrior_swigregister(GammaPrior)
5359 def sample_points_from_density(dmap_orig, npoints, threshold=0.0):
5360 r"""sample_points_from_density(DensityMap dmap_orig, int npoints, IMP::Float threshold=0.0) -> IMP::FloatsList"""
5361 return _IMP_isd.sample_points_from_density(dmap_orig, npoints, threshold)
5363 r"""Proxy of C++ IMP::isd::ResidueProteinProximityRestraint class."""
5365 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5367 def __init__(self, *args):
5368 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"""
5369 _IMP_isd.ResidueProteinProximityRestraint_swiginit(self, _IMP_isd.new_ResidueProteinProximityRestraint(*args))
5371 def add_pairs_container(self, pc):
5372 r"""add_pairs_container(ResidueProteinProximityRestraint self, PairContainer pc)"""
5373 return _IMP_isd.ResidueProteinProximityRestraint_add_pairs_container(self, pc)
5375 def add_contribution_particles(self, ppis1, ppis2):
5376 r"""add_contribution_particles(ResidueProteinProximityRestraint self, IMP::ParticleIndexes const ppis1, IMP::ParticleIndexes const ppis2)"""
5377 return _IMP_isd.ResidueProteinProximityRestraint_add_contribution_particles(self, ppis1, ppis2)
5379 def evaluate_for_contributions(self, c):
5380 r"""evaluate_for_contributions(ResidueProteinProximityRestraint self, IMP::Ints c) -> double"""
5381 return _IMP_isd.ResidueProteinProximityRestraint_evaluate_for_contributions(self, c)
5383 def get_number_of_contributions(self):
5384 r"""get_number_of_contributions(ResidueProteinProximityRestraint self) -> unsigned int"""
5385 return _IMP_isd.ResidueProteinProximityRestraint_get_number_of_contributions(self)
5387 def set_sigma(self, sigma):
5388 r"""set_sigma(ResidueProteinProximityRestraint self, double sigma)"""
5389 return _IMP_isd.ResidueProteinProximityRestraint_set_sigma(self, sigma)
5391 def set_cutoff(self, cutoff):
5392 r"""set_cutoff(ResidueProteinProximityRestraint self, double cutoff)"""
5393 return _IMP_isd.ResidueProteinProximityRestraint_set_cutoff(self, cutoff)
5395 def set_max_score(self, max_score):
5396 r"""set_max_score(ResidueProteinProximityRestraint self, double max_score)"""
5397 return _IMP_isd.ResidueProteinProximityRestraint_set_max_score(self, max_score)
5399 def set_yi(self, yi):
5400 r"""set_yi(ResidueProteinProximityRestraint self, double yi)"""
5401 return _IMP_isd.ResidueProteinProximityRestraint_set_yi(self, yi)
5403 def set_interpolation_factor(self, interpolation_factor):
5404 r"""set_interpolation_factor(ResidueProteinProximityRestraint self, double interpolation_factor)"""
5405 return _IMP_isd.ResidueProteinProximityRestraint_set_interpolation_factor(self, interpolation_factor)
5407 def set_part_of_log_score(self, hey):
5408 r"""set_part_of_log_score(ResidueProteinProximityRestraint self, bool hey)"""
5409 return _IMP_isd.ResidueProteinProximityRestraint_set_part_of_log_score(self, hey)
5412 r"""do_get_inputs(ResidueProteinProximityRestraint self) -> IMP::ModelObjectsTemp"""
5413 return _IMP_isd.ResidueProteinProximityRestraint_do_get_inputs(self)
5416 r"""get_version_info(ResidueProteinProximityRestraint self) -> VersionInfo"""
5417 return _IMP_isd.ResidueProteinProximityRestraint_get_version_info(self)
5418 __swig_destroy__ = _IMP_isd.delete_ResidueProteinProximityRestraint
5421 r"""__str__(ResidueProteinProximityRestraint self) -> std::string"""
5422 return _IMP_isd.ResidueProteinProximityRestraint___str__(self)
5425 r"""__repr__(ResidueProteinProximityRestraint self) -> std::string"""
5426 return _IMP_isd.ResidueProteinProximityRestraint___repr__(self)
5430 return _object_cast_to_ResidueProteinProximityRestraint(o)
5434 _IMP_isd.ResidueProteinProximityRestraint_swigregister(ResidueProteinProximityRestraint)
5437 r"""get_module_version() -> std::string const"""
5438 return _IMP_isd.get_module_version()
5441 r"""get_example_path(std::string fname) -> std::string"""
5442 return _IMP_isd.get_example_path(fname)
5445 r"""get_data_path(std::string fname) -> std::string"""
5446 return _IMP_isd.get_data_path(fname)
5448 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.