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_MULTIFIT_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_MULTIFIT_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_multifit.delete_IMP_MULTIFIT_SwigPyIterator
78 r"""value(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
79 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_value(self)
82 r"""incr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator"""
83 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator"""
87 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
95 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator"""
99 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_copy(self)
102 r"""next(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
103 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_next(self)
106 r"""__next__(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
107 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___next__(self)
110 r"""previous(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
111 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
115 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
119 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
123 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
127 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
131 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
135 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator
140 __sub__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___sub__(self, *args)
147 _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_swigregister(IMP_MULTIFIT_SwigPyIterator)
154 IMP_DEBUG = _IMP_multifit.IMP_DEBUG
156 IMP_RELEASE = _IMP_multifit.IMP_RELEASE
158 IMP_SILENT = _IMP_multifit.IMP_SILENT
160 IMP_PROGRESS = _IMP_multifit.IMP_PROGRESS
162 IMP_TERSE = _IMP_multifit.IMP_TERSE
164 IMP_VERBOSE = _IMP_multifit.IMP_VERBOSE
166 IMP_MEMORY = _IMP_multifit.IMP_MEMORY
168 IMP_NONE = _IMP_multifit.IMP_NONE
170 IMP_USAGE = _IMP_multifit.IMP_USAGE
172 IMP_INTERNAL = _IMP_multifit.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_multifit.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_multifit.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_multifit.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_multifit.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_multifit.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_multifit.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.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_multifit._ostream_write(self, osa_buf)
237 _IMP_multifit._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_multifit.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_multifit.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_multifit.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
319 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
321 IMP_STATISTICS_HAS_NUMPY = _IMP_multifit.IMP_STATISTICS_HAS_NUMPY
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
326 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
338 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
340 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
342 IMP_CORE_HAS_NUMPY = _IMP_multifit.IMP_CORE_HAS_NUMPY
344 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
365 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
367 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
369 IMP_CONTAINER_HAS_NUMPY = _IMP_multifit.IMP_CONTAINER_HAS_NUMPY
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
394 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
396 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
398 IMP_ATOM_HAS_NUMPY = _IMP_multifit.IMP_ATOM_HAS_NUMPY
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
402 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
404 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
406 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
410 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
413 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
427 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
431 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
433 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
435 IMP_EM_HAS_NUMPY = _IMP_multifit.IMP_EM_HAS_NUMPY
437 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
439 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_multifit.IMP_SAXS_HAS_IMP_CGAL
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_multifit.IMP_SAXS_HAS_IMP_CONTAINER
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_multifit.IMP_SAXS_HAS_IMP_DISPLAY
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_multifit.IMP_SAXS_HAS_IMP_KERNEL
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SAXS_HAS_BOOST_FILESYSTEM
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SAXS_HAS_BOOST_RANDOM
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_multifit.IMP_SAXS_HAS_BOOST_REGEX
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SAXS_HAS_BOOST_SYSTEM
462 IMP_SAXS_HAS_CGAL = _IMP_multifit.IMP_SAXS_HAS_CGAL
464 IMP_SAXS_HAS_HDF5 = _IMP_multifit.IMP_SAXS_HAS_HDF5
466 IMP_SAXS_HAS_NUMPY = _IMP_multifit.IMP_SAXS_HAS_NUMPY
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_multifit.IMP_SAXS_HAS_PYTHON_IHM
470 IMPSAXS_SHOW_WARNINGS = _IMP_multifit.IMPSAXS_SHOW_WARNINGS
473 IMP_ISD_HAS_IMP_CGAL = _IMP_multifit.IMP_ISD_HAS_IMP_CGAL
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_multifit.IMP_ISD_HAS_IMP_DISPLAY
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ISD_HAS_BOOST_FILESYSTEM
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ISD_HAS_BOOST_RANDOM
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_multifit.IMP_ISD_HAS_BOOST_REGEX
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ISD_HAS_BOOST_SYSTEM
489 IMP_ISD_HAS_CGAL = _IMP_multifit.IMP_ISD_HAS_CGAL
491 IMP_ISD_HAS_HDF5 = _IMP_multifit.IMP_ISD_HAS_HDF5
493 IMP_ISD_HAS_NUMPY = _IMP_multifit.IMP_ISD_HAS_NUMPY
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_multifit.IMP_ISD_HAS_PYTHON_IHM
497 IMPISD_SHOW_WARNINGS = _IMP_multifit.IMPISD_SHOW_WARNINGS
500 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
502 IMP_RMF_HAS_IMP_EM = _IMP_multifit.IMP_RMF_HAS_IMP_EM
504 IMP_RMF_HAS_IMP_SAXS = _IMP_multifit.IMP_RMF_HAS_IMP_SAXS
506 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
508 IMP_RMF_HAS_IMP_STATISTICS = _IMP_multifit.IMP_RMF_HAS_IMP_STATISTICS
510 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
512 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
514 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
516 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
518 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
520 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
522 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
524 IMP_RMF_HAS_NUMPY = _IMP_multifit.IMP_RMF_HAS_NUMPY
526 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
528 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
532 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
534 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
536 IMP_DOMINO_HAS_IMP_EM = _IMP_multifit.IMP_DOMINO_HAS_IMP_EM
538 IMP_DOMINO_HAS_IMP_ISD = _IMP_multifit.IMP_DOMINO_HAS_IMP_ISD
540 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
542 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
544 IMP_DOMINO_HAS_IMP_SAXS = _IMP_multifit.IMP_DOMINO_HAS_IMP_SAXS
546 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
548 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
550 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
552 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
554 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
556 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
558 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
560 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
562 IMP_DOMINO_HAS_NUMPY = _IMP_multifit.IMP_DOMINO_HAS_NUMPY
564 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
566 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
568 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
572 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
574 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
576 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
578 IMP_MULTIFIT_HAS_IMP_ISD = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_ISD
580 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
582 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
584 IMP_MULTIFIT_HAS_IMP_SAXS = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SAXS
586 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
588 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
590 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
592 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
594 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
596 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
598 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
600 IMP_MULTIFIT_HAS_NUMPY = _IMP_multifit.IMP_MULTIFIT_HAS_NUMPY
602 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
604 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
606 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
609 _object_types.append(
"RadiusOfGyrationRestraint")
612 def _object_cast_to_RadiusOfGyrationRestraint(o):
613 r"""_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
614 return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
616 _object_types.append(
"ComponentHeader")
619 def _object_cast_to_ComponentHeader(o):
620 r"""_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
621 return _IMP_multifit._object_cast_to_ComponentHeader(o)
623 _object_types.append(
"AssemblyHeader")
626 def _object_cast_to_AssemblyHeader(o):
627 r"""_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
628 return _IMP_multifit._object_cast_to_AssemblyHeader(o)
630 _object_types.append(
"SettingsData")
633 def _object_cast_to_SettingsData(o):
634 r"""_object_cast_to_SettingsData(Object o) -> SettingsData"""
635 return _IMP_multifit._object_cast_to_SettingsData(o)
637 _object_types.append(
"WeightedExcludedVolumeRestraint")
640 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
641 r"""_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
642 return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
644 _object_types.append(
"ComplementarityRestraint")
647 def _object_cast_to_ComplementarityRestraint(o):
648 r"""_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
649 return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
651 ProteinRecordDataList=list
652 _plural_types.append(
"ProteinRecordDataList")
653 _value_types.append(
"ProteinRecordData")
656 FittingSolutionRecords=list
657 _plural_types.append(
"FittingSolutionRecords")
658 _value_types.append(
"FittingSolutionRecord")
662 _plural_types.append(
"AnchorsDataList")
663 _value_types.append(
"AnchorsData")
666 DominoParamsList=list
667 _plural_types.append(
"DominoParamsList")
668 _value_types.append(
"DominoParams")
671 ComplementarityParamsList=list
672 _plural_types.append(
"ComplementarityParamsList")
673 _value_types.append(
"ComplementarityParams")
677 _plural_types.append(
"XlinkParamsList")
678 _value_types.append(
"XlinkParams")
681 ConnectivityParamsList=list
682 _plural_types.append(
"ConnectivityParamsList")
683 _value_types.append(
"ConnectivityParams")
686 FragmentsParamsList=list
687 _plural_types.append(
"FragmentsParamsList")
688 _value_types.append(
"FragmentsParams")
692 _plural_types.append(
"RogParamsList")
693 _value_types.append(
"RogParams")
697 _plural_types.append(
"EVParamsList")
698 _value_types.append(
"EVParams")
701 FiltersParamsList=list
702 _plural_types.append(
"FiltersParamsList")
703 _value_types.append(
"FiltersParams")
706 AlignmentParamsList=list
707 _plural_types.append(
"AlignmentParamsList")
708 _value_types.append(
"AlignmentParams")
711 FittingParamsList=list
712 _plural_types.append(
"FittingParamsList")
713 _value_types.append(
"FittingParams")
716 ProteinsAnchorsSamplingSpaces=list
717 _plural_types.append(
"ProteinsAnchorsSamplingSpaces")
718 _value_types.append(
"ProteinsAnchorsSamplingSpace")
721 _object_types.append(
"ProteomicsData")
724 def _object_cast_to_ProteomicsData(o):
725 r"""_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
726 return _IMP_multifit._object_cast_to_ProteomicsData(o)
728 _object_types.append(
"FFTFitting")
731 def _object_cast_to_FFTFitting(o):
732 r"""_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
733 return _IMP_multifit._object_cast_to_FFTFitting(o)
735 _object_types.append(
"FFTFittingOutput")
738 def _object_cast_to_FFTFittingOutput(o):
739 r"""_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
740 return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
742 _object_types.append(
"ProbabilisticAnchorGraph")
745 def _object_cast_to_ProbabilisticAnchorGraph(o):
746 r"""_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
747 return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
749 _object_types.append(
"Ensemble")
752 def _object_cast_to_Ensemble(o):
753 r"""_object_cast_to_Ensemble(Object o) -> Ensemble"""
754 return _IMP_multifit._object_cast_to_Ensemble(o)
756 _object_types.append(
"ProteomicsEMAlignmentAtomic")
759 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
760 r"""_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
761 return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
763 _object_types.append(
"RigidLeavesRefiner")
766 def _object_cast_to_RigidLeavesRefiner(o):
767 r"""_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
768 return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
771 r"""add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key=IMP::FloatKey("surf_ind"), FloatKey radius_key=IMP::core::XYZR::get_radius_key(), FloatKey weight_key=IMP::atom::Mass::get_mass_key())"""
772 return _IMP_multifit.add_surface_index(*args)
775 r"""create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key=IMP::FloatKey("surf_ind")) -> Restraint"""
776 return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
777 class FittingSolutionRecord(object):
778 r"""Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
780 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
783 r"""__init__(FittingSolutionRecord self) -> FittingSolutionRecord"""
784 _IMP_multifit.FittingSolutionRecord_swiginit(self, _IMP_multifit.new_FittingSolutionRecord())
787 r"""get_index(FittingSolutionRecord self) -> unsigned int"""
788 return _IMP_multifit.FittingSolutionRecord_get_index(self)
790 def set_index(self, new_ind):
791 r"""set_index(FittingSolutionRecord self, unsigned int new_ind)"""
792 return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
794 def get_solution_filename(self):
795 r"""get_solution_filename(FittingSolutionRecord self) -> std::string"""
796 return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
798 def set_solution_filename(self, sol_fn):
799 r"""set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
800 return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
802 def get_fit_transformation(self):
803 r"""get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
804 return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
806 def set_fit_transformation(self, t):
807 r"""set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
808 return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
810 def get_match_size(self):
811 r"""get_match_size(FittingSolutionRecord self) -> unsigned int"""
812 return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
814 def set_match_size(self, match_size):
815 r"""set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
816 return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
818 def get_match_average_distance(self):
819 r"""get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
820 return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
822 def set_match_average_distance(self, match_avg_dist):
823 r"""set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
824 return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
826 def get_fitting_score(self):
827 r"""get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
828 return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
830 def set_fitting_score(self, fit_score):
831 r"""set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
832 return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
834 def get_rmsd_to_reference(self):
835 r"""get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
836 return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
838 def set_rmsd_to_reference(self, rmsd_to_ref):
839 r"""set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
840 return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
842 def get_dock_transformation(self):
843 r"""get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
844 return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
846 def set_dock_transformation(self, t):
847 r"""set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
848 return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
850 def get_envelope_penetration_score(self):
851 r"""get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
852 return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
854 def set_envelope_penetration_score(self, s):
855 r"""set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
856 return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
858 def show(self, *args):
859 r"""show(FittingSolutionRecord self, _ostream out=std::cout)"""
860 return _IMP_multifit.FittingSolutionRecord_show(self, *args)
863 def get_record_header():
864 r"""get_record_header() -> std::string"""
865 return _IMP_multifit.FittingSolutionRecord_get_record_header()
868 r"""__str__(FittingSolutionRecord self) -> std::string"""
869 return _IMP_multifit.FittingSolutionRecord___str__(self)
872 r"""__repr__(FittingSolutionRecord self) -> std::string"""
873 return _IMP_multifit.FittingSolutionRecord___repr__(self)
875 def _get_as_binary(self):
876 r"""_get_as_binary(FittingSolutionRecord self) -> PyObject *"""
877 return _IMP_multifit.FittingSolutionRecord__get_as_binary(self)
879 def _set_from_binary(self, p):
880 r"""_set_from_binary(FittingSolutionRecord self, PyObject * p)"""
881 return _IMP_multifit.FittingSolutionRecord__set_from_binary(self, p)
883 def __getstate__(self):
884 p = self._get_as_binary()
885 if len(self.__dict__) > 1:
886 d = self.__dict__.copy()
891 def __setstate__(self, p):
892 if not hasattr(self,
'this'):
894 if isinstance(p, tuple):
896 self.__dict__.update(d)
897 return self._set_from_binary(p)
899 __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
902 _IMP_multifit.FittingSolutionRecord_swigregister(FittingSolutionRecord)
906 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key(), PrincipalComponentAnalysis3D dens_pca_input=IMP::algebra::PrincipalComponentAnalysis()) -> FittingSolutions
907 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key=IMP::atom::Mass::get_mass_key(), PrincipalComponentAnalysis3D dens_pca_input=IMP::algebra::PrincipalComponentAnalysis()) -> FittingSolutions
909 return _IMP_multifit.pca_based_rigid_fitting(*args)
911 def write_markers(pca, out):
912 r"""write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
913 return _IMP_multifit.write_markers(pca, out)
915 r"""Proxy of C++ IMP::multifit::ComponentHeader class."""
917 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
920 r"""__init__(ComponentHeader self) -> ComponentHeader"""
921 _IMP_multifit.ComponentHeader_swiginit(self, _IMP_multifit.new_ComponentHeader())
923 def set_name(self, name):
924 r"""set_name(ComponentHeader self, std::string const & name)"""
925 return _IMP_multifit.ComponentHeader_set_name(self, name)
928 r"""get_name(ComponentHeader self) -> std::string"""
929 return _IMP_multifit.ComponentHeader_get_name(self)
931 def get_filename(self):
932 r"""get_filename(ComponentHeader self) -> std::string"""
933 return _IMP_multifit.ComponentHeader_get_filename(self)
935 def set_filename(self, filename):
936 r"""set_filename(ComponentHeader self, std::string const & filename)"""
937 return _IMP_multifit.ComponentHeader_set_filename(self, filename)
939 def get_surface_fn(self):
940 r"""get_surface_fn(ComponentHeader self) -> std::string"""
941 return _IMP_multifit.ComponentHeader_get_surface_fn(self)
943 def set_surface_fn(self, fn):
944 r"""set_surface_fn(ComponentHeader self, std::string const & fn)"""
945 return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
947 def set_txt_ap_fn(self, pdb_ap_fn):
948 r"""set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
949 return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
951 def get_txt_ap_fn(self):
952 r"""get_txt_ap_fn(ComponentHeader self) -> std::string"""
953 return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
955 def set_txt_fine_ap_fn(self, pdb_ap_fn):
956 r"""set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
957 return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
959 def get_txt_fine_ap_fn(self):
960 r"""get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
961 return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
963 def set_num_ap(self, num_ap):
964 r"""set_num_ap(ComponentHeader self, int num_ap)"""
965 return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
967 def get_num_ap(self):
968 r"""get_num_ap(ComponentHeader self) -> int"""
969 return _IMP_multifit.ComponentHeader_get_num_ap(self)
971 def set_num_fine_ap(self, num_ap):
972 r"""set_num_fine_ap(ComponentHeader self, int num_ap)"""
973 return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
975 def get_num_fine_ap(self):
976 r"""get_num_fine_ap(ComponentHeader self) -> int"""
977 return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
979 def set_transformations_fn(self, transformations_fn):
980 r"""set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
981 return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
983 def get_transformations_fn(self):
984 r"""get_transformations_fn(ComponentHeader self) -> std::string"""
985 return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
987 def set_reference_fn(self, ref_fn):
988 r"""set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
989 return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
991 def get_reference_fn(self):
992 r"""get_reference_fn(ComponentHeader self) -> std::string"""
993 return _IMP_multifit.ComponentHeader_get_reference_fn(self)
995 def get_version_info(self):
996 r"""get_version_info(ComponentHeader self) -> VersionInfo"""
997 return _IMP_multifit.ComponentHeader_get_version_info(self)
998 __swig_destroy__ = _IMP_multifit.delete_ComponentHeader
1001 r"""__str__(ComponentHeader self) -> std::string"""
1002 return _IMP_multifit.ComponentHeader___str__(self)
1005 r"""__repr__(ComponentHeader self) -> std::string"""
1006 return _IMP_multifit.ComponentHeader___repr__(self)
1010 return _object_cast_to_ComponentHeader(o)
1014 _IMP_multifit.ComponentHeader_swigregister(ComponentHeader)
1016 r"""Proxy of C++ IMP::multifit::AssemblyHeader class."""
1018 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1021 r"""__init__(AssemblyHeader self) -> AssemblyHeader"""
1022 _IMP_multifit.AssemblyHeader_swiginit(self, _IMP_multifit.new_AssemblyHeader())
1024 def set_dens_fn(self, dens_fn):
1025 r"""set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
1026 return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
1028 def get_dens_fn(self):
1029 r"""get_dens_fn(AssemblyHeader self) -> std::string"""
1030 return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
1032 def set_resolution(self, res):
1033 r"""set_resolution(AssemblyHeader self, float res)"""
1034 return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
1037 r"""get_resolution(AssemblyHeader self) -> float"""
1038 return _IMP_multifit.AssemblyHeader_get_resolution(self)
1040 def get_spacing(self):
1041 r"""get_spacing(AssemblyHeader self) -> float"""
1042 return _IMP_multifit.AssemblyHeader_get_spacing(self)
1044 def set_spacing(self, spacing):
1045 r"""set_spacing(AssemblyHeader self, float spacing)"""
1046 return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
1048 def set_threshold(self, t):
1049 r"""set_threshold(AssemblyHeader self, float t)"""
1050 return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
1052 def get_threshold(self):
1053 r"""get_threshold(AssemblyHeader self) -> float"""
1054 return _IMP_multifit.AssemblyHeader_get_threshold(self)
1056 def get_origin(self):
1057 r"""get_origin(AssemblyHeader self) -> Vector3D"""
1058 return _IMP_multifit.AssemblyHeader_get_origin(self)
1060 def set_origin(self, origin):
1061 r"""set_origin(AssemblyHeader self, Vector3D origin)"""
1062 return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
1064 def get_coarse_ap_fn(self):
1065 r"""get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
1066 return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
1068 def set_coarse_ap_fn(self, new_fn):
1069 r"""set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1070 return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
1072 def get_coarse_over_sampled_ap_fn(self):
1073 r"""get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
1074 return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
1076 def set_coarse_over_sampled_ap_fn(self, new_fn):
1077 r"""set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1078 return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
1080 def get_fine_ap_fn(self):
1081 r"""get_fine_ap_fn(AssemblyHeader self) -> std::string"""
1082 return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
1084 def set_fine_ap_fn(self, new_fn):
1085 r"""set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1086 return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
1088 def get_fine_over_sampled_ap_fn(self):
1089 r"""get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
1090 return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
1092 def set_fine_over_sampled_ap_fn(self, new_fn):
1093 r"""set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
1094 return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
1096 def get_version_info(self):
1097 r"""get_version_info(AssemblyHeader self) -> VersionInfo"""
1098 return _IMP_multifit.AssemblyHeader_get_version_info(self)
1099 __swig_destroy__ = _IMP_multifit.delete_AssemblyHeader
1102 r"""__str__(AssemblyHeader self) -> std::string"""
1103 return _IMP_multifit.AssemblyHeader___str__(self)
1106 r"""__repr__(AssemblyHeader self) -> std::string"""
1107 return _IMP_multifit.AssemblyHeader___repr__(self)
1111 return _object_cast_to_AssemblyHeader(o)
1115 _IMP_multifit.AssemblyHeader_swigregister(AssemblyHeader)
1117 r"""Proxy of C++ IMP::multifit::SettingsData class."""
1119 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1122 r"""__init__(SettingsData self) -> SettingsData"""
1123 _IMP_multifit.SettingsData_swiginit(self, _IMP_multifit.new_SettingsData())
1126 def show_component_header_line(*args):
1127 r"""show_component_header_line(_ostream out=std::cout)"""
1128 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1131 def get_component_header_line():
1132 r"""get_component_header_line() -> std::string"""
1133 return _IMP_multifit.SettingsData_get_component_header_line()
1136 def show_density_header_line(*args):
1137 r"""show_density_header_line(_ostream out=std::cout)"""
1138 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1141 def get_density_header_line():
1142 r"""get_density_header_line() -> std::string"""
1143 return _IMP_multifit.SettingsData_get_density_header_line()
1145 def set_assembly_filename(self, fn):
1146 r"""set_assembly_filename(SettingsData self, std::string const & fn)"""
1147 return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1149 def get_assembly_filename(self):
1150 r"""get_assembly_filename(SettingsData self) -> char const *"""
1151 return _IMP_multifit.SettingsData_get_assembly_filename(self)
1153 def set_assembly_header(self, h):
1154 r"""set_assembly_header(SettingsData self, AssemblyHeader h)"""
1155 return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1157 def get_assembly_header(self):
1158 r"""get_assembly_header(SettingsData self) -> AssemblyHeader"""
1159 return _IMP_multifit.SettingsData_get_assembly_header(self)
1161 def set_data_path(self, fn):
1162 r"""set_data_path(SettingsData self, std::string const & fn)"""
1163 return _IMP_multifit.SettingsData_set_data_path(self, fn)
1166 r"""get_data_path(SettingsData self) -> std::string"""
1167 return _IMP_multifit.SettingsData_get_data_path(self)
1169 def get_version_info(self):
1170 r"""get_version_info(SettingsData self) -> VersionInfo"""
1171 return _IMP_multifit.SettingsData_get_version_info(self)
1172 __swig_destroy__ = _IMP_multifit.delete_SettingsData
1173 def __get_component_headers(self):
return IMP._list_util.VarList(getdimfunc=self.get_number_of_component_headers, getfunc=self.get_component_header, erasefunc=self.erase_component_header, appendfunc=self.add_component_header, extendfunc=self.add_component_headers, clearfunc=self.clear_component_headers, indexfunc=self._python_index_component_header)
1174 def __set_component_headers(self, obj): IMP._list_util.set_varlist(self.component_headers, obj)
1175 def __del_component_headers(self): IMP._list_util.del_varlist(self.component_headers)
1176 component_headers = property(__get_component_headers, __set_component_headers, __del_component_headers, doc=
"List of ##ucnames")
1178 def remove_component_header(self, d):
1179 r"""remove_component_header(SettingsData self, ComponentHeader d)"""
1180 return _IMP_multifit.SettingsData_remove_component_header(self, d)
1182 def _python_index_component_header(self, d, start, stop):
1183 r"""_python_index_component_header(SettingsData self, ComponentHeader d, unsigned int start, unsigned int stop) -> unsigned int"""
1184 return _IMP_multifit.SettingsData__python_index_component_header(self, d, start, stop)
1186 def remove_component_headers(self, d):
1187 r"""remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1188 return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1190 def set_component_headers(self, ps):
1191 r"""set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1192 return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1194 def set_component_headers_order(self, objs):
1195 r"""set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1196 return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1198 def add_component_header(self, obj):
1199 r"""add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1200 return _IMP_multifit.SettingsData_add_component_header(self, obj)
1202 def add_component_headers(self, objs):
1203 r"""add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1204 return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1206 def clear_component_headers(self):
1207 r"""clear_component_headers(SettingsData self)"""
1208 return _IMP_multifit.SettingsData_clear_component_headers(self)
1210 def get_number_of_component_headers(self):
1211 r"""get_number_of_component_headers(SettingsData self) -> unsigned int"""
1212 return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1214 def get_has_component_headers(self):
1215 r"""get_has_component_headers(SettingsData self) -> bool"""
1216 return _IMP_multifit.SettingsData_get_has_component_headers(self)
1218 def get_component_header(self, i):
1219 r"""get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1220 return _IMP_multifit.SettingsData_get_component_header(self, i)
1222 def get_component_headers(self):
1223 r"""get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1224 return _IMP_multifit.SettingsData_get_component_headers(self)
1226 def erase_component_header(self, i):
1227 r"""erase_component_header(SettingsData self, unsigned int i)"""
1228 return _IMP_multifit.SettingsData_erase_component_header(self, i)
1230 def reserve_component_headers(self, sz):
1231 r"""reserve_component_headers(SettingsData self, unsigned int sz)"""
1232 return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1235 r"""__str__(SettingsData self) -> std::string"""
1236 return _IMP_multifit.SettingsData___str__(self)
1239 r"""__repr__(SettingsData self) -> std::string"""
1240 return _IMP_multifit.SettingsData___repr__(self)
1244 return _object_cast_to_SettingsData(o)
1248 _IMP_multifit.SettingsData_swigregister(SettingsData)
1250 def read_settings(filename):
1251 r"""read_settings(char const * filename) -> SettingsData"""
1252 return _IMP_multifit.read_settings(filename)
1254 def write_settings(filename, sd):
1255 r"""write_settings(char const * filename, SettingsData sd)"""
1256 return _IMP_multifit.write_settings(filename, sd)
1258 r"""Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1260 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1263 r"""__init__(WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key=IMP::atom::Mass::get_mass_key()) -> WeightedExcludedVolumeRestraint"""
1264 _IMP_multifit.WeightedExcludedVolumeRestraint_swiginit(self, _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args))
1266 def do_get_inputs(self):
1267 r"""do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1268 return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1270 def get_version_info(self):
1271 r"""get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1272 return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1273 __swig_destroy__ = _IMP_multifit.delete_WeightedExcludedVolumeRestraint
1276 r"""__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1277 return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1280 r"""__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1281 return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1285 return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1289 _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1291 r"""Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1293 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1296 r"""__init__(FFTFittingOutput self) -> FFTFittingOutput"""
1297 _IMP_multifit.FFTFittingOutput_swiginit(self, _IMP_multifit.new_FFTFittingOutput())
1299 def get_version_info(self):
1300 r"""get_version_info(FFTFittingOutput self) -> VersionInfo"""
1301 return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1302 __swig_destroy__ = _IMP_multifit.delete_FFTFittingOutput
1303 best_fits_ = property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set, doc=
r"""best_fits_ : IMP::multifit::FittingSolutionRecords""")
1304 best_trans_per_rot_ = property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set, doc=
r"""best_trans_per_rot_ : IMP::multifit::FittingSolutionRecords""")
1307 r"""__str__(FFTFittingOutput self) -> std::string"""
1308 return _IMP_multifit.FFTFittingOutput___str__(self)
1311 r"""__repr__(FFTFittingOutput self) -> std::string"""
1312 return _IMP_multifit.FFTFittingOutput___repr__(self)
1316 return _object_cast_to_FFTFittingOutput(o)
1320 _IMP_multifit.FFTFittingOutput_swigregister(FFTFittingOutput)
1322 r"""Proxy of C++ IMP::multifit::FFTFitting class."""
1324 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1326 def get_version_info(self):
1327 r"""get_version_info(FFTFitting self) -> VersionInfo"""
1328 return _IMP_multifit.FFTFitting_get_version_info(self)
1329 __swig_destroy__ = _IMP_multifit.delete_FFTFitting
1332 r"""__init__(FFTFitting self) -> FFTFitting"""
1333 _IMP_multifit.FFTFitting_swiginit(self, _IMP_multifit.new_FFTFitting())
1335 def do_global_fitting(self, *args):
1336 r"""do_global_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=True, int num_angle_per_voxel=1, std::string const & angles_filename="") -> FFTFittingOutput"""
1337 return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1339 def do_local_fitting(self, *args):
1340 r"""do_local_fitting(FFTFitting self, DensityMap dmap, double density_threshold, Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation, std::string const & angles_filename="") -> FFTFittingOutput"""
1341 return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1344 r"""__str__(FFTFitting self) -> std::string"""
1345 return _IMP_multifit.FFTFitting___str__(self)
1348 r"""__repr__(FFTFitting self) -> std::string"""
1349 return _IMP_multifit.FFTFitting___repr__(self)
1353 return _object_cast_to_FFTFitting(o)
1357 _IMP_multifit.FFTFitting_swigregister(FFTFitting)
1360 r"""fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1361 return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1364 r"""remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1365 return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1368 r"""get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1369 return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1371 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1372 r"""get_segmentation(DensityMap dmap, double apix, double density_threshold, int num_means, std::string const pdb_filename, std::string const cmm_filename, std::string const seg_filename, std::string const txt_filename)"""
1373 return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1375 r"""Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1377 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1380 r"""__init__(ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name="ComplementarityRestraint %1%") -> ComplementarityRestraint"""
1381 _IMP_multifit.ComplementarityRestraint_swiginit(self, _IMP_multifit.new_ComplementarityRestraint(*args))
1383 def set_maximum_penetration_score(self, s):
1384 r"""set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1385 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1387 def set_maximum_penetration(self, d):
1388 r"""set_maximum_penetration(ComplementarityRestraint self, double d)"""
1389 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1391 def set_maximum_separation(self, s):
1392 r"""set_maximum_separation(ComplementarityRestraint self, double s)"""
1393 return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1395 def set_complementarity_thickness(self, th):
1396 r"""set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1397 return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1399 def set_complementarity_value(self, th):
1400 r"""set_complementarity_value(ComplementarityRestraint self, double th)"""
1401 return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1403 def set_interior_layer_thickness(self, th):
1404 r"""set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1405 return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1407 def set_penetration_coefficient(self, pc):
1408 r"""set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1409 return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1411 def set_complementarity_coefficient(self, cc):
1412 r"""set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1413 return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1415 def set_boundary_coefficient(self, bc):
1416 r"""set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1417 return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1419 def get_voxel_size(self):
1420 r"""get_voxel_size(ComplementarityRestraint self) -> float"""
1421 return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1423 def do_get_inputs(self):
1424 r"""do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1425 return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1427 def get_version_info(self):
1428 r"""get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1429 return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1430 __swig_destroy__ = _IMP_multifit.delete_ComplementarityRestraint
1433 r"""__str__(ComplementarityRestraint self) -> std::string"""
1434 return _IMP_multifit.ComplementarityRestraint___str__(self)
1437 r"""__repr__(ComplementarityRestraint self) -> std::string"""
1438 return _IMP_multifit.ComplementarityRestraint___repr__(self)
1442 return _object_cast_to_ComplementarityRestraint(o)
1446 _IMP_multifit.ComplementarityRestraint_swigregister(ComplementarityRestraint)
1449 r"""read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1450 return _IMP_multifit.read_fitting_solutions(fitting_fn)
1453 r"""write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)"""
1454 return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1456 def convert_em_to_multifit_format(em_fits):
1457 r"""convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1458 return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1460 def convert_multifit_to_em_format(multifit_fits):
1461 r"""convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1462 return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1464 def convert_transformations_to_multifit_format(trans):
1465 r"""convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1466 return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1468 def convert_multifit_format_to_transformations(recs):
1469 r"""convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1470 return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1473 r"""get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1474 return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1476 r"""Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1478 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1480 def __init__(self, anchor_positions):
1481 r"""__init__(ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1482 _IMP_multifit.ProbabilisticAnchorGraph_swiginit(self, _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions))
1484 def add_edge(self, i, j):
1485 r"""add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1486 return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1488 def set_particle_probabilities_on_anchors(self, p, sols):
1489 r"""set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1490 return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1492 def show(self, *args):
1493 r"""show(ProbabilisticAnchorGraph self, _ostream out=std::cout)"""
1494 return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1496 def get_number_of_anchors(self):
1497 r"""get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1498 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1500 def get_number_of_edges(self):
1501 r"""get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1502 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1504 def get_edge_list(self):
1505 r"""get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1506 return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1508 def get_anchors(self):
1509 r"""get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1510 return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1512 def get_particle_anchors(self, p, min_prob=0):
1513 r"""get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds"""
1514 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1516 def get_are_probabilities_for_particle_set(self, p):
1517 r"""get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1518 return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1520 def get_particle_probabilities(self, p):
1521 r"""get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1522 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1524 def get_version_info(self):
1525 r"""get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1526 return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1527 __swig_destroy__ = _IMP_multifit.delete_ProbabilisticAnchorGraph
1530 r"""__str__(ProbabilisticAnchorGraph self) -> std::string"""
1531 return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1534 r"""__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1535 return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1539 return _object_cast_to_ProbabilisticAnchorGraph(o)
1543 _IMP_multifit.ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1544 class ProteinRecordData(object):
1545 r"""Proxy of C++ IMP::multifit::ProteinRecordData class."""
1547 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1549 def reset_all(self):
1550 r"""reset_all(ProteinRecordData self)"""
1551 return _IMP_multifit.ProteinRecordData_reset_all(self)
1555 __init__(ProteinRecordData self) -> ProteinRecordData
1556 __init__(ProteinRecordData self, std::string const & name) -> ProteinRecordData
1557 __init__(ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1558 __init__(ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1559 __init__(ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const & fn, std::string const & surface_fn, std::string const & ref_fn) -> ProteinRecordData
1561 _IMP_multifit.ProteinRecordData_swiginit(self, _IMP_multifit.new_ProteinRecordData(*args))
1563 def show(self, *args):
1564 r"""show(ProteinRecordData self, _ostream out=std::cout)"""
1565 return _IMP_multifit.ProteinRecordData_show(self, *args)
1566 name_ = property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set, doc=
r"""name_ : std::string""")
1567 start_res_ = property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set, doc=
r"""start_res_ : int""")
1568 end_res_ = property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set, doc=
r"""end_res_ : int""")
1569 filename_ = property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set, doc=
r"""filename_ : std::string""")
1570 surface_filename_ = property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set, doc=
r"""surface_filename_ : std::string""")
1571 ref_filename_ = property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set, doc=
r"""ref_filename_ : std::string""")
1574 r"""__str__(ProteinRecordData self) -> std::string"""
1575 return _IMP_multifit.ProteinRecordData___str__(self)
1578 r"""__repr__(ProteinRecordData self) -> std::string"""
1579 return _IMP_multifit.ProteinRecordData___repr__(self)
1581 def _get_as_binary(self):
1582 r"""_get_as_binary(ProteinRecordData self) -> PyObject *"""
1583 return _IMP_multifit.ProteinRecordData__get_as_binary(self)
1585 def _set_from_binary(self, p):
1586 r"""_set_from_binary(ProteinRecordData self, PyObject * p)"""
1587 return _IMP_multifit.ProteinRecordData__set_from_binary(self, p)
1589 def __getstate__(self):
1590 p = self._get_as_binary()
1591 if len(self.__dict__) > 1:
1592 d = self.__dict__.copy()
1597 def __setstate__(self, p):
1598 if not hasattr(self,
'this'):
1600 if isinstance(p, tuple):
1602 self.__dict__.update(d)
1603 return self._set_from_binary(p)
1605 __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1608 _IMP_multifit.ProteinRecordData_swigregister(ProteinRecordData)
1610 r"""Proxy of C++ IMP::multifit::ProteomicsData class."""
1612 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1615 r"""__init__(ProteomicsData self) -> ProteomicsData"""
1616 _IMP_multifit.ProteomicsData_swiginit(self, _IMP_multifit.new_ProteomicsData())
1618 def add_protein(self, *args):
1620 add_protein(ProteomicsData self, std::string name, int start_res, int end_res, std::string const & mol_fn, std::string const & surface_fn, std::string const & ref_fn) -> int
1621 add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1623 return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1625 def find(self, name):
1626 r"""find(ProteomicsData self, std::string const & name) -> int"""
1627 return _IMP_multifit.ProteomicsData_find(self, name)
1629 def add_interaction(self, ii, used_for_filter, linker_len):
1630 r"""add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1631 return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1633 def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1634 r"""add_cross_link_interaction(ProteomicsData self, IMP::Int prot1, IMP::Int res1, IMP::Int prot2, IMP::Int res2, bool used_in_filter, IMP::Float linker_len)"""
1635 return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1637 def add_ev_pair(self, prot1, prot2):
1638 r"""add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1639 return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1641 def get_number_of_proteins(self):
1642 r"""get_number_of_proteins(ProteomicsData self) -> int"""
1643 return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1645 def get_number_of_interactions(self):
1646 r"""get_number_of_interactions(ProteomicsData self) -> int"""
1647 return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1649 def get_interaction(self, interaction_ind):
1650 r"""get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1651 return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1653 def get_interaction_part_of_filter(self, interaction_ind):
1654 r"""get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1655 return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1657 def get_interaction_linker_length(self, interaction_ind):
1658 r"""get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1659 return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1661 def get_number_of_cross_links(self):
1662 r"""get_number_of_cross_links(ProteomicsData self) -> int"""
1663 return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1665 def get_cross_link(self, xlink_ind):
1666 r"""get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1667 return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1669 def get_cross_link_part_of_filter(self, xlink_ind):
1670 r"""get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1671 return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1673 def get_cross_link_length(self, xlink_ind):
1674 r"""get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1675 return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1677 def get_number_of_ev_pairs(self):
1678 r"""get_number_of_ev_pairs(ProteomicsData self) -> int"""
1679 return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1681 def get_ev_pair(self, ev_ind):
1682 r"""get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1683 return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1685 def get_protein_name(self, protein_ind):
1686 r"""get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1687 return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1689 def get_end_res(self, protein_ind):
1690 r"""get_end_res(ProteomicsData self, int protein_ind) -> int"""
1691 return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1693 def get_start_res(self, protein_ind):
1694 r"""get_start_res(ProteomicsData self, int protein_ind) -> int"""
1695 return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1697 def get_protein_filename(self, protein_ind):
1698 r"""get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1699 return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1701 def get_reference_filename(self, protein_ind):
1702 r"""get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1703 return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1705 def get_surface_filename(self, protein_ind):
1706 r"""get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1707 return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1709 def get_protein_data(self, protein_ind):
1710 r"""get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1711 return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1713 def get_version_info(self):
1714 r"""get_version_info(ProteomicsData self) -> VersionInfo"""
1715 return _IMP_multifit.ProteomicsData_get_version_info(self)
1716 __swig_destroy__ = _IMP_multifit.delete_ProteomicsData
1718 def get_num_allowed_violated_interactions(self):
1719 r"""get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1720 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1722 def set_num_allowed_violated_interactions(self, n):
1723 r"""set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1724 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1726 def get_num_allowed_violated_cross_links(self):
1727 r"""get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1728 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1730 def set_num_allowed_violated_cross_links(self, n):
1731 r"""set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1732 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1734 def get_num_allowed_violated_ev(self):
1735 r"""get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1736 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1738 def set_num_allowed_violated_ev(self, n):
1739 r"""set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1740 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1743 r"""__str__(ProteomicsData self) -> std::string"""
1744 return _IMP_multifit.ProteomicsData___str__(self)
1747 r"""__repr__(ProteomicsData self) -> std::string"""
1748 return _IMP_multifit.ProteomicsData___repr__(self)
1752 return _object_cast_to_ProteomicsData(o)
1756 _IMP_multifit.ProteomicsData_swigregister(ProteomicsData)
1759 r"""read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1760 return _IMP_multifit.read_proteomics_data(proteomics_fn)
1762 def get_partial_proteomics_data(pd, prot_names):
1763 r"""get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1764 return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1765 class AnchorsData(object):
1766 r"""Proxy of C++ IMP::multifit::AnchorsData class."""
1768 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1772 __init__(AnchorsData self) -> AnchorsData
1773 __init__(AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1775 _IMP_multifit.AnchorsData_swiginit(self, _IMP_multifit.new_AnchorsData(*args))
1777 def remove_edges_for_node(self, node_ind):
1778 r"""remove_edges_for_node(AnchorsData self, int node_ind)"""
1779 return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1781 def get_number_of_points(self):
1782 r"""get_number_of_points(AnchorsData self) -> int"""
1783 return _IMP_multifit.AnchorsData_get_number_of_points(self)
1785 def get_number_of_edges(self):
1786 r"""get_number_of_edges(AnchorsData self) -> int"""
1787 return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1789 def get_is_point_considered(self, node_ind):
1790 r"""get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1791 return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1793 def show(self, *args):
1794 r"""show(AnchorsData self, _ostream out=std::cout)"""
1795 return _IMP_multifit.AnchorsData_show(self, *args)
1797 def get_secondary_structure_is_set(self):
1798 r"""get_secondary_structure_is_set(AnchorsData self) -> bool"""
1799 return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1801 def setup_secondary_structure(self, mdl):
1802 r"""setup_secondary_structure(AnchorsData self, Model mdl)"""
1803 return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1805 def set_secondary_structure_probabilities(self, *args):
1806 r"""set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices=IMP::Ints())"""
1807 return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1809 def get_secondary_structure_particles(self):
1810 r"""get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1811 return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1812 points_ = property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set, doc=
r"""points_ : IMP::algebra::Vector3Ds""")
1813 consider_point_ = property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set, doc=
r"""consider_point_ : std::vector<(bool,std::allocator<(bool)>)>""")
1814 edges_ = property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set, doc=
r"""edges_ : IMP::IntPairs""")
1817 r"""__str__(AnchorsData self) -> std::string"""
1818 return _IMP_multifit.AnchorsData___str__(self)
1821 r"""__repr__(AnchorsData self) -> std::string"""
1822 return _IMP_multifit.AnchorsData___repr__(self)
1823 __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1826 _IMP_multifit.AnchorsData_swigregister(AnchorsData)
1828 def read_anchors_data(txt_filename):
1829 r"""read_anchors_data(char const * txt_filename) -> AnchorsData"""
1830 return _IMP_multifit.read_anchors_data(txt_filename)
1832 def write_txt(txt_filename, ad):
1833 r"""write_txt(std::string const & txt_filename, AnchorsData ad)"""
1834 return _IMP_multifit.write_txt(txt_filename, ad)
1836 def write_cmm(cmm_filename, marker_set_name, dpa):
1837 r"""write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1838 return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1841 r"""create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1842 return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1844 def create_hit_map(rb, rb_ref, sols, damp):
1845 r"""create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1846 return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1849 r"""get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1850 return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1852 def get_points_far_from_molecule(mh, points, max_dist):
1853 r"""get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1854 return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1856 r"""Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1858 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1860 def __init__(self, ps, num_residues, scale=1.):
1861 r"""__init__(RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint"""
1862 _IMP_multifit.RadiusOfGyrationRestraint_swiginit(self, _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale))
1864 def do_get_inputs(self):
1865 r"""do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1866 return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1868 def get_version_info(self):
1869 r"""get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1870 return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1871 __swig_destroy__ = _IMP_multifit.delete_RadiusOfGyrationRestraint
1873 def set_radius_of_gyration(self, r):
1874 r"""set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1875 return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1878 r"""get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1879 return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1882 r"""__str__(RadiusOfGyrationRestraint self) -> std::string"""
1883 return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1886 r"""__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1887 return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1891 return _object_cast_to_RadiusOfGyrationRestraint(o)
1895 _IMP_multifit.RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1897 def get_approximated_radius_of_gyration(len):
1898 r"""get_approximated_radius_of_gyration(int len) -> float"""
1899 return _IMP_multifit.get_approximated_radius_of_gyration(len)
1901 def get_actual_radius_of_gyration(ps):
1902 r"""get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1903 return _IMP_multifit.get_actual_radius_of_gyration(ps)
1905 def get_approximated_radius(len):
1906 r"""get_approximated_radius(int len) -> float"""
1907 return _IMP_multifit.get_approximated_radius(len)
1908 class ProteinsAnchorsSamplingSpace(object):
1909 r"""Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1911 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1914 r"""__init__(ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace"""
1915 _IMP_multifit.ProteinsAnchorsSamplingSpace_swiginit(self, _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots))
1917 def set_anchors(self, data):
1918 r"""set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
1919 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
1921 def get_anchors(self):
1922 r"""get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
1923 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
1925 def get_anchors_filename(self):
1926 r"""get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
1927 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
1929 def set_anchors_filename(self, fn):
1930 r"""set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
1931 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
1933 def get_proteomics_data(self):
1934 r"""get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
1935 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
1937 def add_protein(self, rec):
1938 r"""add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
1939 return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
1941 def get_paths_for_protein(self, prot_name):
1942 r"""get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
1943 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
1945 def set_paths_filename_for_protein(self, prot_name, paths_filename):
1946 r"""set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
1947 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
1949 def get_paths_filename_for_protein(self, prot_name):
1950 r"""get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
1951 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
1953 def set_paths_for_protein(self, prot_name, paths):
1954 r"""set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
1955 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
1957 def show(self, *args):
1958 r"""show(ProteinsAnchorsSamplingSpace self, _ostream s=std::cout)"""
1959 return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
1962 r"""__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
1963 return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
1966 r"""__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
1967 return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
1968 __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
1971 _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
1973 def read_protein_anchors_mapping(*args):
1974 r"""read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths=INT_MAX) -> ProteinsAnchorsSamplingSpace"""
1975 return _IMP_multifit.read_protein_anchors_mapping(*args)
1977 def write_protein_anchors_mapping(*args):
1979 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, std::string const & anchors_fn, std::vector< std::pair< IMP::String,IMP::String >,std::allocator< std::pair< IMP::String,IMP::String > > > const & prot_paths)
1980 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
1982 return _IMP_multifit.write_protein_anchors_mapping(*args)
1985 r"""get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
1986 return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
1989 r"""get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
1990 return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
1993 r"""read_paths(char const * txt_filename, int max_paths=INT_MAX) -> IMP::IntsList"""
1994 return _IMP_multifit.read_paths(*args)
1996 def write_paths(paths, txt_filename):
1997 r"""write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
1998 return _IMP_multifit.write_paths(paths, txt_filename)
2000 def molecule2anchors(mh, k):
2001 r"""molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2002 return _IMP_multifit.molecule2anchors(mh, k)
2004 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2005 r"""get_anchors_for_density(DensityMap dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)"""
2006 return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2009 r"""get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList"""
2010 return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2011 class DominoParams(object):
2012 r"""Proxy of C++ IMP::multifit::DominoParams class."""
2014 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2017 r"""__init__(DominoParams self) -> DominoParams"""
2018 _IMP_multifit.DominoParams_swiginit(self, _IMP_multifit.new_DominoParams())
2021 r"""add(DominoParams self, boost::property_tree::ptree const & pt)"""
2022 return _IMP_multifit.DominoParams_add(self, pt)
2024 def show(self, *args):
2025 r"""show(DominoParams self, _ostream s=std::cout)"""
2026 return _IMP_multifit.DominoParams_show(self, *args)
2027 max_value_threshold_ = property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set, doc=
r"""max_value_threshold_ : float""")
2028 max_num_states_for_subset_ = property(_IMP_multifit.DominoParams_max_num_states_for_subset__get, _IMP_multifit.DominoParams_max_num_states_for_subset__set, doc=
r"""max_num_states_for_subset_ : int""")
2029 max_anchor_penetration_ = property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set, doc=
r"""max_anchor_penetration_ : float""")
2030 heap_size_ = property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set, doc=
r"""heap_size_ : int""")
2031 cache_size_ = property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set, doc=
r"""cache_size_ : int""")
2034 r"""__str__(DominoParams self) -> std::string"""
2035 return _IMP_multifit.DominoParams___str__(self)
2038 r"""__repr__(DominoParams self) -> std::string"""
2039 return _IMP_multifit.DominoParams___repr__(self)
2041 def _get_as_binary(self):
2042 r"""_get_as_binary(DominoParams self) -> PyObject *"""
2043 return _IMP_multifit.DominoParams__get_as_binary(self)
2045 def _set_from_binary(self, p):
2046 r"""_set_from_binary(DominoParams self, PyObject * p)"""
2047 return _IMP_multifit.DominoParams__set_from_binary(self, p)
2049 def __getstate__(self):
2050 p = self._get_as_binary()
2051 if len(self.__dict__) > 1:
2052 d = self.__dict__.copy()
2057 def __setstate__(self, p):
2058 if not hasattr(self,
'this'):
2060 if isinstance(p, tuple):
2062 self.__dict__.update(d)
2063 return self._set_from_binary(p)
2065 __swig_destroy__ = _IMP_multifit.delete_DominoParams
2068 _IMP_multifit.DominoParams_swigregister(DominoParams)
2069 class XlinkParams(object):
2070 r"""Proxy of C++ IMP::multifit::XlinkParams class."""
2072 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2075 r"""__init__(XlinkParams self) -> XlinkParams"""
2076 _IMP_multifit.XlinkParams_swiginit(self, _IMP_multifit.new_XlinkParams())
2079 r"""add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2080 return _IMP_multifit.XlinkParams_add(self, pt)
2082 def show(self, *args):
2083 r"""show(XlinkParams self, _ostream s=std::cout)"""
2084 return _IMP_multifit.XlinkParams_show(self, *args)
2085 upper_bound_ = property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set, doc=
r"""upper_bound_ : float""")
2086 k_ = property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set, doc=
r"""k_ : float""")
2087 max_xlink_val_ = property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set, doc=
r"""max_xlink_val_ : float""")
2088 treat_between_residues_ = property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set, doc=
r"""treat_between_residues_ : bool""")
2091 r"""__str__(XlinkParams self) -> std::string"""
2092 return _IMP_multifit.XlinkParams___str__(self)
2095 r"""__repr__(XlinkParams self) -> std::string"""
2096 return _IMP_multifit.XlinkParams___repr__(self)
2098 def _get_as_binary(self):
2099 r"""_get_as_binary(XlinkParams self) -> PyObject *"""
2100 return _IMP_multifit.XlinkParams__get_as_binary(self)
2102 def _set_from_binary(self, p):
2103 r"""_set_from_binary(XlinkParams self, PyObject * p)"""
2104 return _IMP_multifit.XlinkParams__set_from_binary(self, p)
2106 def __getstate__(self):
2107 p = self._get_as_binary()
2108 if len(self.__dict__) > 1:
2109 d = self.__dict__.copy()
2114 def __setstate__(self, p):
2115 if not hasattr(self,
'this'):
2117 if isinstance(p, tuple):
2119 self.__dict__.update(d)
2120 return self._set_from_binary(p)
2122 __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2125 _IMP_multifit.XlinkParams_swigregister(XlinkParams)
2126 class ConnectivityParams(object):
2127 r"""Proxy of C++ IMP::multifit::ConnectivityParams class."""
2129 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2132 r"""__init__(ConnectivityParams self) -> ConnectivityParams"""
2133 _IMP_multifit.ConnectivityParams_swiginit(self, _IMP_multifit.new_ConnectivityParams())
2136 r"""add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2137 return _IMP_multifit.ConnectivityParams_add(self, pt)
2139 def show(self, *args):
2140 r"""show(ConnectivityParams self, _ostream s=std::cout)"""
2141 return _IMP_multifit.ConnectivityParams_show(self, *args)
2142 upper_bound_ = property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set, doc=
r"""upper_bound_ : float""")
2143 k_ = property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set, doc=
r"""k_ : float""")
2144 max_conn_rest_val_ = property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set, doc=
r"""max_conn_rest_val_ : float""")
2147 r"""__str__(ConnectivityParams self) -> std::string"""
2148 return _IMP_multifit.ConnectivityParams___str__(self)
2151 r"""__repr__(ConnectivityParams self) -> std::string"""
2152 return _IMP_multifit.ConnectivityParams___repr__(self)
2154 def _get_as_binary(self):
2155 r"""_get_as_binary(ConnectivityParams self) -> PyObject *"""
2156 return _IMP_multifit.ConnectivityParams__get_as_binary(self)
2158 def _set_from_binary(self, p):
2159 r"""_set_from_binary(ConnectivityParams self, PyObject * p)"""
2160 return _IMP_multifit.ConnectivityParams__set_from_binary(self, p)
2162 def __getstate__(self):
2163 p = self._get_as_binary()
2164 if len(self.__dict__) > 1:
2165 d = self.__dict__.copy()
2170 def __setstate__(self, p):
2171 if not hasattr(self,
'this'):
2173 if isinstance(p, tuple):
2175 self.__dict__.update(d)
2176 return self._set_from_binary(p)
2178 __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2181 _IMP_multifit.ConnectivityParams_swigregister(ConnectivityParams)
2182 class FragmentsParams(object):
2183 r"""Proxy of C++ IMP::multifit::FragmentsParams class."""
2185 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2188 r"""__init__(FragmentsParams self) -> FragmentsParams"""
2189 _IMP_multifit.FragmentsParams_swiginit(self, _IMP_multifit.new_FragmentsParams())
2192 r"""add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2193 return _IMP_multifit.FragmentsParams_add(self, pt)
2195 def show(self, *args):
2196 r"""show(FragmentsParams self, _ostream s=std::cout)"""
2197 return _IMP_multifit.FragmentsParams_show(self, *args)
2198 frag_len_ = property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set, doc=
r"""frag_len_ : int""")
2199 bead_radius_scale_ = property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set, doc=
r"""bead_radius_scale_ : float""")
2200 load_atomic_ = property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set, doc=
r"""load_atomic_ : bool""")
2201 subunit_rigid_ = property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set, doc=
r"""subunit_rigid_ : bool""")
2204 r"""__str__(FragmentsParams self) -> std::string"""
2205 return _IMP_multifit.FragmentsParams___str__(self)
2208 r"""__repr__(FragmentsParams self) -> std::string"""
2209 return _IMP_multifit.FragmentsParams___repr__(self)
2211 def _get_as_binary(self):
2212 r"""_get_as_binary(FragmentsParams self) -> PyObject *"""
2213 return _IMP_multifit.FragmentsParams__get_as_binary(self)
2215 def _set_from_binary(self, p):
2216 r"""_set_from_binary(FragmentsParams self, PyObject * p)"""
2217 return _IMP_multifit.FragmentsParams__set_from_binary(self, p)
2219 def __getstate__(self):
2220 p = self._get_as_binary()
2221 if len(self.__dict__) > 1:
2222 d = self.__dict__.copy()
2227 def __setstate__(self, p):
2228 if not hasattr(self,
'this'):
2230 if isinstance(p, tuple):
2232 self.__dict__.update(d)
2233 return self._set_from_binary(p)
2235 __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2238 _IMP_multifit.FragmentsParams_swigregister(FragmentsParams)
2239 class RogParams(object):
2240 r"""Proxy of C++ IMP::multifit::RogParams class."""
2242 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2245 r"""__init__(RogParams self) -> RogParams"""
2246 _IMP_multifit.RogParams_swiginit(self, _IMP_multifit.new_RogParams())
2249 r"""add(RogParams self, boost::property_tree::ptree const & pt)"""
2250 return _IMP_multifit.RogParams_add(self, pt)
2252 def get_max_score(self):
2253 r"""get_max_score(RogParams self) -> float"""
2254 return _IMP_multifit.RogParams_get_max_score(self)
2256 def get_scale(self):
2257 r"""get_scale(RogParams self) -> float"""
2258 return _IMP_multifit.RogParams_get_scale(self)
2260 def show(self, *args):
2261 r"""show(RogParams self, _ostream s=std::cout)"""
2262 return _IMP_multifit.RogParams_show(self, *args)
2265 r"""__str__(RogParams self) -> std::string"""
2266 return _IMP_multifit.RogParams___str__(self)
2269 r"""__repr__(RogParams self) -> std::string"""
2270 return _IMP_multifit.RogParams___repr__(self)
2272 def _get_as_binary(self):
2273 r"""_get_as_binary(RogParams self) -> PyObject *"""
2274 return _IMP_multifit.RogParams__get_as_binary(self)
2276 def _set_from_binary(self, p):
2277 r"""_set_from_binary(RogParams self, PyObject * p)"""
2278 return _IMP_multifit.RogParams__set_from_binary(self, p)
2280 def __getstate__(self):
2281 p = self._get_as_binary()
2282 if len(self.__dict__) > 1:
2283 d = self.__dict__.copy()
2288 def __setstate__(self, p):
2289 if not hasattr(self,
'this'):
2291 if isinstance(p, tuple):
2293 self.__dict__.update(d)
2294 return self._set_from_binary(p)
2296 __swig_destroy__ = _IMP_multifit.delete_RogParams
2299 _IMP_multifit.RogParams_swigregister(RogParams)
2300 class EVParams(object):
2301 r"""Proxy of C++ IMP::multifit::EVParams class."""
2303 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2306 r"""__init__(EVParams self) -> EVParams"""
2307 _IMP_multifit.EVParams_swiginit(self, _IMP_multifit.new_EVParams())
2310 r"""add(EVParams self, boost::property_tree::ptree const & pt)"""
2311 return _IMP_multifit.EVParams_add(self, pt)
2313 def show(self, *args):
2314 r"""show(EVParams self, _ostream s=std::cout)"""
2315 return _IMP_multifit.EVParams_show(self, *args)
2316 pair_distance_ = property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set, doc=
r"""pair_distance_ : float""")
2317 pair_slack_ = property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set, doc=
r"""pair_slack_ : float""")
2318 hlb_mean_ = property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set, doc=
r"""hlb_mean_ : float""")
2319 hlb_k_ = property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set, doc=
r"""hlb_k_ : float""")
2320 maximum_ev_score_for_pair_ = property(_IMP_multifit.EVParams_maximum_ev_score_for_pair__get, _IMP_multifit.EVParams_maximum_ev_score_for_pair__set, doc=
r"""maximum_ev_score_for_pair_ : float""")
2321 allowed_percentage_of_bad_pairs_ = property(_IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__get, _IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__set, doc=
r"""allowed_percentage_of_bad_pairs_ : float""")
2322 scoring_mode_ = property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set, doc=
r"""scoring_mode_ : int""")
2325 r"""__str__(EVParams self) -> std::string"""
2326 return _IMP_multifit.EVParams___str__(self)
2329 r"""__repr__(EVParams self) -> std::string"""
2330 return _IMP_multifit.EVParams___repr__(self)
2332 def _get_as_binary(self):
2333 r"""_get_as_binary(EVParams self) -> PyObject *"""
2334 return _IMP_multifit.EVParams__get_as_binary(self)
2336 def _set_from_binary(self, p):
2337 r"""_set_from_binary(EVParams self, PyObject * p)"""
2338 return _IMP_multifit.EVParams__set_from_binary(self, p)
2340 def __getstate__(self):
2341 p = self._get_as_binary()
2342 if len(self.__dict__) > 1:
2343 d = self.__dict__.copy()
2348 def __setstate__(self, p):
2349 if not hasattr(self,
'this'):
2351 if isinstance(p, tuple):
2353 self.__dict__.update(d)
2354 return self._set_from_binary(p)
2356 __swig_destroy__ = _IMP_multifit.delete_EVParams
2359 _IMP_multifit.EVParams_swigregister(EVParams)
2360 class FiltersParams(object):
2361 r"""Proxy of C++ IMP::multifit::FiltersParams class."""
2363 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2366 r"""__init__(FiltersParams self) -> FiltersParams"""
2367 _IMP_multifit.FiltersParams_swiginit(self, _IMP_multifit.new_FiltersParams())
2370 r"""add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2371 return _IMP_multifit.FiltersParams_add(self, pt)
2373 def show(self, *args):
2374 r"""show(FiltersParams self, _ostream s=std::cout)"""
2375 return _IMP_multifit.FiltersParams_show(self, *args)
2376 max_num_violated_xlink_ = property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set, doc=
r"""max_num_violated_xlink_ : int""")
2377 max_num_violated_conn_ = property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set, doc=
r"""max_num_violated_conn_ : int""")
2378 max_num_violated_ev_ = property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set, doc=
r"""max_num_violated_ev_ : int""")
2381 r"""__str__(FiltersParams self) -> std::string"""
2382 return _IMP_multifit.FiltersParams___str__(self)
2385 r"""__repr__(FiltersParams self) -> std::string"""
2386 return _IMP_multifit.FiltersParams___repr__(self)
2388 def _get_as_binary(self):
2389 r"""_get_as_binary(FiltersParams self) -> PyObject *"""
2390 return _IMP_multifit.FiltersParams__get_as_binary(self)
2392 def _set_from_binary(self, p):
2393 r"""_set_from_binary(FiltersParams self, PyObject * p)"""
2394 return _IMP_multifit.FiltersParams__set_from_binary(self, p)
2396 def __getstate__(self):
2397 p = self._get_as_binary()
2398 if len(self.__dict__) > 1:
2399 d = self.__dict__.copy()
2404 def __setstate__(self, p):
2405 if not hasattr(self,
'this'):
2407 if isinstance(p, tuple):
2409 self.__dict__.update(d)
2410 return self._set_from_binary(p)
2412 __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2415 _IMP_multifit.FiltersParams_swigregister(FiltersParams)
2416 class FittingParams(object):
2417 r"""Proxy of C++ IMP::multifit::FittingParams class."""
2419 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2422 r"""__init__(FittingParams self) -> FittingParams"""
2423 _IMP_multifit.FittingParams_swiginit(self, _IMP_multifit.new_FittingParams())
2426 r"""add(FittingParams self, boost::property_tree::ptree const & pt)"""
2427 return _IMP_multifit.FittingParams_add(self, pt)
2429 def show(self, *args):
2430 r"""show(FittingParams self, _ostream s=std::cout)"""
2431 return _IMP_multifit.FittingParams_show(self, *args)
2432 pca_max_angle_diff_ = property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set, doc=
r"""pca_max_angle_diff_ : float""")
2433 pca_max_size_diff_ = property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set, doc=
r"""pca_max_size_diff_ : float""")
2434 pca_max_cent_dist_diff_ = property(_IMP_multifit.FittingParams_pca_max_cent_dist_diff__get, _IMP_multifit.FittingParams_pca_max_cent_dist_diff__set, doc=
r"""pca_max_cent_dist_diff_ : float""")
2435 max_asmb_fit_score_ = property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set, doc=
r"""max_asmb_fit_score_ : float""")
2438 r"""__str__(FittingParams self) -> std::string"""
2439 return _IMP_multifit.FittingParams___str__(self)
2442 r"""__repr__(FittingParams self) -> std::string"""
2443 return _IMP_multifit.FittingParams___repr__(self)
2445 def _get_as_binary(self):
2446 r"""_get_as_binary(FittingParams self) -> PyObject *"""
2447 return _IMP_multifit.FittingParams__get_as_binary(self)
2449 def _set_from_binary(self, p):
2450 r"""_set_from_binary(FittingParams self, PyObject * p)"""
2451 return _IMP_multifit.FittingParams__set_from_binary(self, p)
2453 def __getstate__(self):
2454 p = self._get_as_binary()
2455 if len(self.__dict__) > 1:
2456 d = self.__dict__.copy()
2461 def __setstate__(self, p):
2462 if not hasattr(self,
'this'):
2464 if isinstance(p, tuple):
2466 self.__dict__.update(d)
2467 return self._set_from_binary(p)
2469 __swig_destroy__ = _IMP_multifit.delete_FittingParams
2472 _IMP_multifit.FittingParams_swigregister(FittingParams)
2473 class ComplementarityParams(object):
2474 r"""Proxy of C++ IMP::multifit::ComplementarityParams class."""
2476 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2479 r"""__init__(ComplementarityParams self) -> ComplementarityParams"""
2480 _IMP_multifit.ComplementarityParams_swiginit(self, _IMP_multifit.new_ComplementarityParams())
2483 r"""add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2484 return _IMP_multifit.ComplementarityParams_add(self, pt)
2486 def show(self, *args):
2487 r"""show(ComplementarityParams self, _ostream s=std::cout)"""
2488 return _IMP_multifit.ComplementarityParams_show(self, *args)
2489 max_score_ = property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set, doc=
r"""max_score_ : float""")
2490 max_penetration_ = property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set, doc=
r"""max_penetration_ : float""")
2491 interior_layer_thickness_ = property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set, doc=
r"""interior_layer_thickness_ : float""")
2492 boundary_coef_ = property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set, doc=
r"""boundary_coef_ : float""")
2493 comp_coef_ = property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set, doc=
r"""comp_coef_ : float""")
2494 penetration_coef_ = property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set, doc=
r"""penetration_coef_ : float""")
2497 r"""__str__(ComplementarityParams self) -> std::string"""
2498 return _IMP_multifit.ComplementarityParams___str__(self)
2501 r"""__repr__(ComplementarityParams self) -> std::string"""
2502 return _IMP_multifit.ComplementarityParams___repr__(self)
2504 def _get_as_binary(self):
2505 r"""_get_as_binary(ComplementarityParams self) -> PyObject *"""
2506 return _IMP_multifit.ComplementarityParams__get_as_binary(self)
2508 def _set_from_binary(self, p):
2509 r"""_set_from_binary(ComplementarityParams self, PyObject * p)"""
2510 return _IMP_multifit.ComplementarityParams__set_from_binary(self, p)
2512 def __getstate__(self):
2513 p = self._get_as_binary()
2514 if len(self.__dict__) > 1:
2515 d = self.__dict__.copy()
2520 def __setstate__(self, p):
2521 if not hasattr(self,
'this'):
2523 if isinstance(p, tuple):
2525 self.__dict__.update(d)
2526 return self._set_from_binary(p)
2528 __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2531 _IMP_multifit.ComplementarityParams_swigregister(ComplementarityParams)
2532 class AlignmentParams(object):
2533 r"""Proxy of C++ IMP::multifit::AlignmentParams class."""
2535 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2539 __init__(AlignmentParams self) -> AlignmentParams
2540 __init__(AlignmentParams self, char const * param_filename) -> AlignmentParams
2542 _IMP_multifit.AlignmentParams_swiginit(self, _IMP_multifit.new_AlignmentParams(*args))
2544 def get_domino_params(self):
2545 r"""get_domino_params(AlignmentParams self) -> DominoParams"""
2546 return _IMP_multifit.AlignmentParams_get_domino_params(self)
2548 def get_fitting_params(self):
2549 r"""get_fitting_params(AlignmentParams self) -> FittingParams"""
2550 return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2552 def get_complementarity_params(self):
2553 r"""get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2554 return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2556 def get_xlink_params(self):
2557 r"""get_xlink_params(AlignmentParams self) -> XlinkParams"""
2558 return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2560 def get_connectivity_params(self):
2561 r"""get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2562 return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2564 def get_rog_params(self):
2565 r"""get_rog_params(AlignmentParams self) -> RogParams"""
2566 return _IMP_multifit.AlignmentParams_get_rog_params(self)
2568 def get_fragments_params(self):
2569 r"""get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2570 return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2572 def get_filters_params(self):
2573 r"""get_filters_params(AlignmentParams self) -> FiltersParams"""
2574 return _IMP_multifit.AlignmentParams_get_filters_params(self)
2576 def get_ev_params(self):
2577 r"""get_ev_params(AlignmentParams self) -> EVParams"""
2578 return _IMP_multifit.AlignmentParams_get_ev_params(self)
2580 def show(self, *args):
2581 r"""show(AlignmentParams self, _ostream s=std::cout)"""
2582 return _IMP_multifit.AlignmentParams_show(self, *args)
2585 r"""__str__(AlignmentParams self) -> std::string"""
2586 return _IMP_multifit.AlignmentParams___str__(self)
2589 r"""__repr__(AlignmentParams self) -> std::string"""
2590 return _IMP_multifit.AlignmentParams___repr__(self)
2592 def _get_as_binary(self):
2593 r"""_get_as_binary(AlignmentParams self) -> PyObject *"""
2594 return _IMP_multifit.AlignmentParams__get_as_binary(self)
2596 def _set_from_binary(self, p):
2597 r"""_set_from_binary(AlignmentParams self, PyObject * p)"""
2598 return _IMP_multifit.AlignmentParams__set_from_binary(self, p)
2600 def __getstate__(self):
2601 p = self._get_as_binary()
2602 if len(self.__dict__) > 1:
2603 d = self.__dict__.copy()
2608 def __setstate__(self, p):
2609 if not hasattr(self,
'this'):
2611 if isinstance(p, tuple):
2613 self.__dict__.update(d)
2614 return self._set_from_binary(p)
2616 __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2619 _IMP_multifit.AlignmentParams_swigregister(AlignmentParams)
2620 class ProteomicsEMAlignmentAtomic(
IMP.Object):
2621 r"""Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2623 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2625 def __init__(self, mapping_data, asmb_data, align_param):
2626 r"""__init__(ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2627 _IMP_multifit.ProteomicsEMAlignmentAtomic_swiginit(self, _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param))
2630 r"""align(ProteomicsEMAlignmentAtomic self)"""
2631 return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2633 def add_all_restraints(self):
2634 r"""add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2635 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2637 def get_restraint_set(self):
2638 r"""get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2639 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2641 def add_states_and_filters(self):
2642 r"""add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2643 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2645 def show_domino_merge_tree(self):
2646 r"""show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2647 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2649 def get_combinations(self, uniques=False):
2650 r"""get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments"""
2651 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2653 def set_density_map(self, dmap, threshold):
2654 r"""set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2655 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2657 def get_molecules(self):
2658 r"""get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2659 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2661 def get_rigid_bodies(self):
2662 r"""get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2663 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2665 def load_combination_of_states(self, state4particles):
2666 r"""load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2667 return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2669 def show_scores_header(self, *args):
2670 r"""show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous=std::cout)"""
2671 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2673 def get_model(self):
2674 r"""get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2675 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2677 def set_fast_scoring(self, state):
2678 r"""set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2679 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2681 def get_version_info(self):
2682 r"""get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2683 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2684 __swig_destroy__ = _IMP_multifit.delete_ProteomicsEMAlignmentAtomic
2687 r"""__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2688 return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2691 r"""__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2692 return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2696 return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2700 _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2703 r"""write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2704 return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2706 r"""Proxy of C++ IMP::multifit::Ensemble class."""
2708 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2710 def load_combination(self, fit_comb):
2711 r"""load_combination(Ensemble self, IMP::Ints fit_comb)"""
2712 return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2714 def unload_combination(self, fit_comb):
2715 r"""unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2716 return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2718 def add_component_and_fits(self, mh, fits):
2719 r"""add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2720 return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2722 def get_molecules(self):
2723 r"""get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2724 return _IMP_multifit.Ensemble_get_molecules(self)
2726 def get_rigid_bodies(self):
2727 r"""get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2728 return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2731 r"""get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2732 return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2734 def __init__(self, sd, mapping_data):
2735 r"""__init__(Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2736 _IMP_multifit.Ensemble_swiginit(self, _IMP_multifit.new_Ensemble(sd, mapping_data))
2738 def score_by_restraints(self, rs, combinations):
2739 r"""score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2740 return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2742 def get_version_info(self):
2743 r"""get_version_info(Ensemble self) -> VersionInfo"""
2744 return _IMP_multifit.Ensemble_get_version_info(self)
2745 __swig_destroy__ = _IMP_multifit.delete_Ensemble
2748 r"""__str__(Ensemble self) -> std::string"""
2749 return _IMP_multifit.Ensemble___str__(self)
2752 r"""__repr__(Ensemble self) -> std::string"""
2753 return _IMP_multifit.Ensemble___repr__(self)
2757 return _object_cast_to_Ensemble(o)
2761 _IMP_multifit.Ensemble_swigregister(Ensemble)
2763 def load_ensemble(sd, mdl, mapping_data):
2764 r"""load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2765 return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2767 r"""Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2769 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2772 r"""__init__(RigidLeavesRefiner self, std::string name="RigidLeavesRefiner%d") -> RigidLeavesRefiner"""
2773 _IMP_multifit.RigidLeavesRefiner_swiginit(self, _IMP_multifit.new_RigidLeavesRefiner(*args))
2775 def do_get_inputs(self, m, pis):
2776 r"""do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2777 return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2779 def get_version_info(self):
2780 r"""get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2781 return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2782 __swig_destroy__ = _IMP_multifit.delete_RigidLeavesRefiner
2785 r"""__str__(RigidLeavesRefiner self) -> std::string"""
2786 return _IMP_multifit.RigidLeavesRefiner___str__(self)
2789 r"""__repr__(RigidLeavesRefiner self) -> std::string"""
2790 return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2794 return _object_cast_to_RigidLeavesRefiner(o)
2798 _IMP_multifit.RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2800 _all_commands = [
"param",
"anchors",
"fit_fft",
"cluster",
"add_fit_rmsd",
2801 "indexes",
"proteomics",
"align",
"models",
"transforms",
2802 "score",
"merge_tree",
"reference",
"refine_fft",
"segment"]
2806 r"""get_module_version() -> std::string const"""
2807 return _IMP_multifit.get_module_version()
2810 r"""get_example_path(std::string fname) -> std::string"""
2811 return _IMP_multifit.get_example_path(fname)
2814 r"""get_data_path(std::string fname) -> std::string"""
2815 return _IMP_multifit.get_data_path(fname)
2817 from .
import _version_check
IntsList get_anchor_indices_matching_secondary_structure(const AnchorsData &ad, const atom::SecondaryStructureResidues &ssrs, Float max_rmsd=0.7)
Get lists of anchors that match a sequence of secondary structures.
FittingSolutionRecords get_close_to_point(const FittingSolutionRecords &fit_sols, atom::Hierarchy mh, IMP::Particle *ap, Float dist)
prune solutions by distance to an anchor point
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IntsList get_connected_components(em::DensityMap *dmap, float threshold, float edge_threshold)
Return connected components based on density values.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
em::DensityMap * remove_background(em::DensityMap *dmap, float threshold, float edge_threshold)
Returns a map containing all density without the background.
ProteinsAnchorsSamplingSpace get_part_of_sampling_space(const ProteinsAnchorsSamplingSpace &prots_ss, const Strings &prot_names)
Get the sampling space of few of the proteins.
std::string get_module_version()
Return the version of this module, as a string.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
multifit::SettingsData * get_partial_assembly_setting_data(multifit::SettingsData *prots_sd, const Strings &prot_names)
Get the assembly data for a few of the proteins.
Composable functors to implement scores via compile-time composition.
em::FittingSolutions pca_based_rigid_fitting(core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
Code to compute statistical measures.
void add_surface_index(core::Hierarchy mhd, Float apix, FloatKey shell_key=FloatKey("surf_ind"), FloatKey radius_key=core::XYZR::get_radius_key(), FloatKey weight_key=atom::Mass::get_mass_key())
Add shell index to leaves.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
void get_anchors_for_density(em::DensityMap *dmap, int number_of_means, float density_threshold, std::string pdb_filename, std::string cmm_filename, std::string seg_filename, std::string txt_filename)
Generate anchors in several formats for a given density map.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void write_fitting_solutions(const char *fitting_fn, const FittingSolutionRecords &fit_sols, int num_sols=-1)
Write fitting solutions to a file.
ProteomicsData * read_proteomics_data(const char *proteomics_fn)
Proteomics reader.
IMP::Restraint * create_weighted_excluded_volume_restraint(core::RigidBody rb1, core::RigidBody rb2, FloatKey shell_key=FloatKey("surf_ind"))
Create a weighted excluded volume restraint between two rigid bodies.
algebra::Vector3Ds get_points_close_to_molecule(const atom::Hierarchy &mh, const algebra::Vector3Ds points, Float max_dist)
void get_segmentation(em::DensityMap *dmap, double apix, double density_threshold, int num_means, const std::string pdb_filename, const std::string cmm_filename, const std::string seg_filename, const std::string txt_filename)
Segment a density map using the anchor graph.
void write_connolly_surface(atom::Atoms atoms, TextOutput fn, float density, float probe_radius)
Write the Connolly surface for a set of atoms to a file.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
multifit::FittingSolutionRecords fft_based_rigid_fitting(atom::Hierarchy mol2fit, em::DensityMap *dmap, double density_threshold, double angle_sampling_interval_rad)
FFT fit of a molecule in the density.
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...
IntsList read_paths(const char *txt_filename, int max_paths=INT_MAX)
Read paths.
FittingSolutionRecords read_fitting_solutions(const char *fitting_fn)
Fitting solutions reader.
Abstract class to implement hierarchical methods.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap, float dens_threshold, int num_beads, Model *mdl, float bead_radius)
Coarsen a density map based on voxels clustering.