11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 import _IMP_bayesianem
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_BAYESIANEM_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_BAYESIANEM_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_bayesianem.delete_IMP_BAYESIANEM_SwigPyIterator
78 r"""value(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
79 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_value(self)
82 r"""incr(IMP_BAYESIANEM_SwigPyIterator self, size_t n=1) -> IMP_BAYESIANEM_SwigPyIterator"""
83 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_BAYESIANEM_SwigPyIterator self, size_t n=1) -> IMP_BAYESIANEM_SwigPyIterator"""
87 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
95 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_BAYESIANEM_SwigPyIterator self) -> IMP_BAYESIANEM_SwigPyIterator"""
99 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_copy(self)
102 r"""next(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
103 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_next(self)
106 r"""__next__(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
107 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___next__(self)
110 r"""previous(IMP_BAYESIANEM_SwigPyIterator self) -> PyObject *"""
111 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
115 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
119 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> bool"""
123 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
127 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
131 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator"""
135 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_BAYESIANEM_SwigPyIterator self, ptrdiff_t n) -> IMP_BAYESIANEM_SwigPyIterator
140 __sub__(IMP_BAYESIANEM_SwigPyIterator self, IMP_BAYESIANEM_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator___sub__(self, *args)
147 _IMP_bayesianem.IMP_BAYESIANEM_SwigPyIterator_swigregister(IMP_BAYESIANEM_SwigPyIterator)
154 IMP_DEBUG = _IMP_bayesianem.IMP_DEBUG
156 IMP_RELEASE = _IMP_bayesianem.IMP_RELEASE
158 IMP_SILENT = _IMP_bayesianem.IMP_SILENT
160 IMP_PROGRESS = _IMP_bayesianem.IMP_PROGRESS
162 IMP_TERSE = _IMP_bayesianem.IMP_TERSE
164 IMP_VERBOSE = _IMP_bayesianem.IMP_VERBOSE
166 IMP_MEMORY = _IMP_bayesianem.IMP_MEMORY
168 IMP_NONE = _IMP_bayesianem.IMP_NONE
170 IMP_USAGE = _IMP_bayesianem.IMP_USAGE
172 IMP_INTERNAL = _IMP_bayesianem.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_bayesianem.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_bayesianem.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_bayesianem.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_bayesianem.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_bayesianem.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_bayesianem.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_bayesianem.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_bayesianem.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_bayesianem.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_bayesianem.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_bayesianem._ostream_write(self, osa_buf)
237 _IMP_bayesianem._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_bayesianem.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_bayesianem.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_bayesianem.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_bayesianem.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_bayesianem.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_bayesianem.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_bayesianem.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_bayesianem.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_bayesianem.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_bayesianem.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_bayesianem.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_bayesianem.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_bayesianem.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_bayesianem.IMP_STATISTICS_HAS_IMP_CGAL
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_RANDOM
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_STATISTICS_HAS_BOOST_SYSTEM
319 IMP_STATISTICS_HAS_CGAL = _IMP_bayesianem.IMP_STATISTICS_HAS_CGAL
321 IMP_STATISTICS_HAS_NUMPY = _IMP_bayesianem.IMP_STATISTICS_HAS_NUMPY
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_bayesianem.IMPSTATISTICS_SHOW_WARNINGS
326 IMP_CORE_HAS_IMP_CGAL = _IMP_bayesianem.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_CORE_HAS_IMP_KERNEL
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_RANDOM
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CORE_HAS_BOOST_SYSTEM
338 IMP_CORE_HAS_CGAL = _IMP_bayesianem.IMP_CORE_HAS_CGAL
340 IMP_CORE_HAS_HDF5 = _IMP_bayesianem.IMP_CORE_HAS_HDF5
342 IMP_CORE_HAS_NUMPY = _IMP_bayesianem.IMP_CORE_HAS_NUMPY
344 IMPCORE_SHOW_WARNINGS = _IMP_bayesianem.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_CGAL
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_DISPLAY
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_KERNEL
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_RANDOM
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_CONTAINER_HAS_BOOST_SYSTEM
365 IMP_CONTAINER_HAS_CGAL = _IMP_bayesianem.IMP_CONTAINER_HAS_CGAL
367 IMP_CONTAINER_HAS_HDF5 = _IMP_bayesianem.IMP_CONTAINER_HAS_HDF5
369 IMP_CONTAINER_HAS_NUMPY = _IMP_bayesianem.IMP_CONTAINER_HAS_NUMPY
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_CONTAINER_HAS_PYTHON_IHM
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_bayesianem.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_bayesianem.IMP_CONTAINER_HAS_ROBIN_MAP
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_bayesianem.IMPCONTAINER_SHOW_WARNINGS
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ATOM_HAS_IMP_CGAL
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_ATOM_HAS_IMP_KERNEL
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_RANDOM
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_REGEX
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ATOM_HAS_BOOST_SYSTEM
394 IMP_ATOM_HAS_CGAL = _IMP_bayesianem.IMP_ATOM_HAS_CGAL
396 IMP_ATOM_HAS_HDF5 = _IMP_bayesianem.IMP_ATOM_HAS_HDF5
398 IMP_ATOM_HAS_NUMPY = _IMP_bayesianem.IMP_ATOM_HAS_NUMPY
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_ATOM_HAS_PYTHON_IHM
402 IMPATOM_SHOW_WARNINGS = _IMP_bayesianem.IMPATOM_SHOW_WARNINGS
404 IMP_ATOM_TYPE_INDEX = _IMP_bayesianem.IMP_ATOM_TYPE_INDEX
406 IMP_RESIDUE_TYPE_INDEX = _IMP_bayesianem.IMP_RESIDUE_TYPE_INDEX
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_bayesianem.IMP_HIERARCHY_TYPE_INDEX
410 IMP_CHAIN_TYPE_INDEX = _IMP_bayesianem.IMP_CHAIN_TYPE_INDEX
413 IMP_EM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_EM_HAS_IMP_CGAL
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_bayesianem.IMP_EM_HAS_IMP_CONTAINER
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_EM_HAS_IMP_DISPLAY
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_EM_HAS_IMP_SCORE_FUNCTOR
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_EM_HAS_BOOST_FILESYSTEM
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_EM_HAS_BOOST_RANDOM
427 IMP_EM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_EM_HAS_BOOST_REGEX
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_EM_HAS_BOOST_SYSTEM
431 IMP_EM_HAS_CGAL = _IMP_bayesianem.IMP_EM_HAS_CGAL
433 IMP_EM_HAS_HDF5 = _IMP_bayesianem.IMP_EM_HAS_HDF5
435 IMP_EM_HAS_NUMPY = _IMP_bayesianem.IMP_EM_HAS_NUMPY
437 IMP_EM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_EM_HAS_PYTHON_IHM
439 IMPEM_SHOW_WARNINGS = _IMP_bayesianem.IMPEM_SHOW_WARNINGS
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_bayesianem.IMP_SAXS_HAS_IMP_CGAL
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_bayesianem.IMP_SAXS_HAS_IMP_CONTAINER
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_SAXS_HAS_IMP_DISPLAY
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_bayesianem.IMP_SAXS_HAS_IMP_KERNEL
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_FILESYSTEM
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_RANDOM
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_REGEX
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_SAXS_HAS_BOOST_SYSTEM
462 IMP_SAXS_HAS_CGAL = _IMP_bayesianem.IMP_SAXS_HAS_CGAL
464 IMP_SAXS_HAS_HDF5 = _IMP_bayesianem.IMP_SAXS_HAS_HDF5
466 IMP_SAXS_HAS_NUMPY = _IMP_bayesianem.IMP_SAXS_HAS_NUMPY
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_SAXS_HAS_PYTHON_IHM
470 IMPSAXS_SHOW_WARNINGS = _IMP_bayesianem.IMPSAXS_SHOW_WARNINGS
473 IMP_ISD_HAS_IMP_CGAL = _IMP_bayesianem.IMP_ISD_HAS_IMP_CGAL
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_ISD_HAS_IMP_DISPLAY
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_FILESYSTEM
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_RANDOM
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_ISD_HAS_BOOST_REGEX
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_ISD_HAS_BOOST_SYSTEM
489 IMP_ISD_HAS_CGAL = _IMP_bayesianem.IMP_ISD_HAS_CGAL
491 IMP_ISD_HAS_HDF5 = _IMP_bayesianem.IMP_ISD_HAS_HDF5
493 IMP_ISD_HAS_NUMPY = _IMP_bayesianem.IMP_ISD_HAS_NUMPY
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_ISD_HAS_PYTHON_IHM
497 IMPISD_SHOW_WARNINGS = _IMP_bayesianem.IMPISD_SHOW_WARNINGS
500 IMP_BAYESIANEM_HAS_IMP_CGAL = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_CGAL
502 IMP_BAYESIANEM_HAS_IMP_DISPLAY = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_DISPLAY
504 IMP_BAYESIANEM_HAS_IMP_SCORE_FUNCTOR = _IMP_bayesianem.IMP_BAYESIANEM_HAS_IMP_SCORE_FUNCTOR
506 IMP_BAYESIANEM_HAS_BOOST_FILESYSTEM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_FILESYSTEM
508 IMP_BAYESIANEM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_PROGRAMOPTIONS
510 IMP_BAYESIANEM_HAS_BOOST_RANDOM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_RANDOM
512 IMP_BAYESIANEM_HAS_BOOST_REGEX = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_REGEX
514 IMP_BAYESIANEM_HAS_BOOST_SYSTEM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_BOOST_SYSTEM
516 IMP_BAYESIANEM_HAS_CGAL = _IMP_bayesianem.IMP_BAYESIANEM_HAS_CGAL
518 IMP_BAYESIANEM_HAS_HDF5 = _IMP_bayesianem.IMP_BAYESIANEM_HAS_HDF5
520 IMP_BAYESIANEM_HAS_NUMPY = _IMP_bayesianem.IMP_BAYESIANEM_HAS_NUMPY
522 IMP_BAYESIANEM_HAS_PYTHON_IHM = _IMP_bayesianem.IMP_BAYESIANEM_HAS_PYTHON_IHM
524 IMPBAYESIANEM_SHOW_WARNINGS = _IMP_bayesianem.IMPBAYESIANEM_SHOW_WARNINGS
527 _object_types.append(
"GaussianEMRestraint")
530 r"""Proxy of C++ IMP::bayesianem::GaussianEMRestraint class."""
532 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
534 def __init__(self, *args):
535 r"""__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, std::string name="GaussianEMRestraint%1%") -> GaussianEMRestraint"""
536 _IMP_bayesianem.GaussianEMRestraint_swiginit(self, _IMP_bayesianem.new_GaussianEMRestraint(*args))
538 def get_probability(self):
539 r"""get_probability(GaussianEMRestraint self) -> double"""
540 return _IMP_bayesianem.GaussianEMRestraint_get_probability(self)
542 def set_density_filename(self, density_fn):
543 r"""set_density_filename(GaussianEMRestraint self, std::string density_fn)"""
544 return _IMP_bayesianem.GaussianEMRestraint_set_density_filename(self, density_fn)
546 def compute_initial_scores(self):
547 r"""compute_initial_scores(GaussianEMRestraint self)"""
548 return _IMP_bayesianem.GaussianEMRestraint_compute_initial_scores(self)
551 r"""get_indexes(GaussianEMRestraint self) -> IMP::ParticleIndexes const"""
552 return _IMP_bayesianem.GaussianEMRestraint_get_indexes(self)
555 r"""get_log2(GaussianEMRestraint self) -> IMP::Floats const"""
556 return _IMP_bayesianem.GaussianEMRestraint_get_log2(self)
559 r"""debug(GaussianEMRestraint self)"""
560 return _IMP_bayesianem.GaussianEMRestraint_debug(self)
562 def set_slope(self, s):
563 r"""set_slope(GaussianEMRestraint self, IMP::Float s)"""
564 return _IMP_bayesianem.GaussianEMRestraint_set_slope(self, s)
567 r"""get_slope(GaussianEMRestraint self) -> IMP::Float"""
568 return _IMP_bayesianem.GaussianEMRestraint_get_slope(self)
570 def do_get_inputs(self):
571 r"""do_get_inputs(GaussianEMRestraint self) -> IMP::ModelObjectsTemp"""
572 return _IMP_bayesianem.GaussianEMRestraint_do_get_inputs(self)
575 r"""show(GaussianEMRestraint self, _ostream out)"""
576 return _IMP_bayesianem.GaussianEMRestraint_show(self, out)
578 def get_version_info(self):
579 r"""get_version_info(GaussianEMRestraint self) -> VersionInfo"""
580 return _IMP_bayesianem.GaussianEMRestraint_get_version_info(self)
581 __swig_destroy__ = _IMP_bayesianem.delete_GaussianEMRestraint
584 r"""__str__(GaussianEMRestraint self) -> std::string"""
585 return _IMP_bayesianem.GaussianEMRestraint___str__(self)
588 r"""__repr__(GaussianEMRestraint self) -> std::string"""
589 return _IMP_bayesianem.GaussianEMRestraint___repr__(self)
593 return _object_cast_to_GaussianEMRestraint(o)
597 _IMP_bayesianem.GaussianEMRestraint_swigregister(GaussianEMRestraint)
599 def get_rmsd_excluding_higher_than(m1, m2, t):
600 r"""get_rmsd_excluding_higher_than(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const t) -> double"""
601 return _IMP_bayesianem.get_rmsd_excluding_higher_than(m1, m2, t)
603 def get_percentage_closer_than(m1, m2, t):
604 r"""get_percentage_closer_than(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const t) -> double"""
605 return _IMP_bayesianem.get_percentage_closer_than(m1, m2, t)
608 r"""get_transformation_aligning_first_to_second(Selection s1, Selection s2) -> Transformation3D"""
609 return _IMP_bayesianem.get_transformation_aligning_first_to_second(s1, s2)
611 def get_rmsd_of_best_population(*args):
613 get_rmsd_of_best_population(IMP::core::XYZs const & m1, IMP::core::XYZs const & m2, double const percentage) -> double
614 get_rmsd_of_best_population(Selection s1, Selection s2, double const percentage) -> double
615 get_rmsd_of_best_population(IMP::algebra::Vector3Ds const & m1, IMP::algebra::Vector3Ds const & m2, double const percentage) -> double
617 return _IMP_bayesianem.get_rmsd_of_best_population(*args)
619 def gem_score_cc(model_ps, density_ps):
620 r"""gem_score_cc(IMP::Particles model_ps, IMP::Particles density_ps) -> double"""
621 return _IMP_bayesianem.gem_score_cc(model_ps, density_ps)
624 r"""get_grid(DensityMap _in) -> DenseDoubleGrid3D"""
625 return _IMP_bayesianem.get_grid(_in)
627 def get_masked_map(gmm, weights, densitymap, threshold):
628 r"""get_masked_map(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap densitymap, double threshold) -> DensityMap"""
629 return _IMP_bayesianem.get_masked_map(gmm, weights, densitymap, threshold)
631 def get_sub_map(dm, sub_gmm, gmm):
632 r"""get_sub_map(DensityMap dm, DensityMap sub_gmm, DensityMap gmm) -> DensityMap"""
633 return _IMP_bayesianem.get_sub_map(dm, sub_gmm, gmm)
635 def get_overlap_fast(gmm, weights, dm, factor=2.5):
636 r"""get_overlap_fast(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap dm, double factor=2.5) -> double"""
637 return _IMP_bayesianem.get_overlap_fast(gmm, weights, dm, factor)
639 def get_overlap_binned(gmm, weights, dm, factor=2.5, Nbin=100):
640 r"""get_overlap_binned(IMP::algebra::Gaussian3Ds const & gmm, IMP::Floats const & weights, DensityMap dm, double factor=2.5, int Nbin=100) -> IMP::algebra::Vector3Ds"""
641 return _IMP_bayesianem.get_overlap_binned(gmm, weights, dm, factor, Nbin)
643 def get_rotation_matrix(x, y):
644 r"""get_rotation_matrix(Vector3D x, Vector3D y) -> Rotation3D"""
645 return _IMP_bayesianem.get_rotation_matrix(x, y)
648 r"""sgn(double v) -> float"""
649 return _IMP_bayesianem.sgn(v)
651 def NormalizePCA(pca, ps):
652 r"""NormalizePCA(PrincipalComponentAnalysis3D pca, IMP::Particles const & ps) -> PrincipalComponentAnalysis3D"""
653 return _IMP_bayesianem.NormalizePCA(pca, ps)
655 def PCAalign(pca1, pca2):
656 r"""PCAalign(PrincipalComponentAnalysis3D pca1, PrincipalComponentAnalysis3D pca2) -> IMP::algebra::Transformation3Ds"""
657 return _IMP_bayesianem.PCAalign(pca1, pca2)
660 r"""get_module_version() -> std::string const"""
661 return _IMP_bayesianem.get_module_version()
664 r"""get_example_path(std::string fname) -> std::string"""
665 return _IMP_bayesianem.get_example_path(fname)
668 r"""get_data_path(std::string fname) -> std::string"""
669 return _IMP_bayesianem.get_data_path(fname)
671 from .
import _version_check
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
IMP::algebra::Transformation3D get_transformation_aligning_first_to_second(const Vector3DsOrXYZs0 &source, const Vector3DsOrXYZs1 &target)
Compute the rigid transform bringing the first point set to the second.
Basic utilities for handling cryo-electron microscopy 3D density maps.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
DensityGrid get_grid(IMP::em::DensityMap *in)
Return a dense grid containing the voxels of the passed density map.
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_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.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
Support for small angle X-ray scattering (SAXS) data.
std::string get_module_version()
Return the version of this module, as a string.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.