10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_multifit')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_multifit')
25 _IMP_multifit = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_multifit', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_multifit', fp, pathname, description)
43 _IMP_multifit = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_MULTIFIT_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_MULTIFIT_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_multifit.delete_IMP_MULTIFIT_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
126 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_value(self)
131 incr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
132 incr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
134 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_incr(self, n)
139 decr(IMP_MULTIFIT_SwigPyIterator self, size_t n=1) -> IMP_MULTIFIT_SwigPyIterator
140 decr(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator
142 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_distance(self, x)
151 """equal(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
152 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_equal(self, x)
156 """copy(IMP_MULTIFIT_SwigPyIterator self) -> IMP_MULTIFIT_SwigPyIterator"""
157 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_copy(self)
161 """next(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
162 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_next(self)
166 """__next__(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
167 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___next__(self)
171 """previous(IMP_MULTIFIT_SwigPyIterator self) -> PyObject *"""
172 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
177 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
182 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> bool"""
187 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
192 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
197 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator"""
202 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_MULTIFIT_SwigPyIterator self, ptrdiff_t n) -> IMP_MULTIFIT_SwigPyIterator
208 __sub__(IMP_MULTIFIT_SwigPyIterator self, IMP_MULTIFIT_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_multifit.IMP_MULTIFIT_SwigPyIterator___sub__(self, *args)
214 IMP_MULTIFIT_SwigPyIterator_swigregister = _IMP_multifit.IMP_MULTIFIT_SwigPyIterator_swigregister
215 IMP_MULTIFIT_SwigPyIterator_swigregister(IMP_MULTIFIT_SwigPyIterator)
223 IMP_DEBUG = _IMP_multifit.IMP_DEBUG
224 IMP_RELEASE = _IMP_multifit.IMP_RELEASE
225 IMP_SILENT = _IMP_multifit.IMP_SILENT
226 IMP_PROGRESS = _IMP_multifit.IMP_PROGRESS
227 IMP_TERSE = _IMP_multifit.IMP_TERSE
228 IMP_VERBOSE = _IMP_multifit.IMP_VERBOSE
229 IMP_MEMORY = _IMP_multifit.IMP_MEMORY
230 IMP_NONE = _IMP_multifit.IMP_NONE
231 IMP_USAGE = _IMP_multifit.IMP_USAGE
232 IMP_INTERNAL = _IMP_multifit.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_multifit.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_multifit.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_multifit.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_multifit.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_multifit.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_multifit.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_multifit.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_multifit.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
250 def register(self, obj):
251 """Take a reference to a director object; will only work for
252 refcounted C++ classes"""
253 if hasattr(obj,
'get_ref_count'):
254 self._objects.append(obj)
256 """Only drop our reference and allow cleanup by Python if no other
257 Python references exist (we hold 3 references: one in self._objects,
258 one in x, and one in the argument list for getrefcount) *and* no
259 other C++ references exist (the Python object always holds one)"""
260 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
261 or x.get_ref_count() > 1]
265 def get_object_count(self):
266 """Get number of director objects (useful for testing only)"""
267 return len(self._objects)
268 _director_objects = _DirectorObjects()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_multifit._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_multifit._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_multifit.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_multifit.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_multifit.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_multifit.IMP_C_OPEN_BINARY
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_multifit.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_multifit.IMPCGAL_SHOW_WARNINGS
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_multifit.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_multifit.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_multifit.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_multifit.IMPALGEBRA_SHOW_WARNINGS
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_multifit.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_multifit.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_multifit.IMPDISPLAY_SHOW_WARNINGS
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_multifit.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_multifit.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_multifit.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_multifit.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_multifit.IMPSTATISTICS_SHOW_WARNINGS
336 IMP_CORE_HAS_IMP_CGAL = _IMP_multifit.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_multifit.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_multifit.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_multifit.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_multifit.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_multifit.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_multifit.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_multifit.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_multifit.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_multifit.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_multifit.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_multifit.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_multifit.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_multifit.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_multifit.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_multifit.IMPCONTAINER_SHOW_WARNINGS
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_multifit.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_multifit.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_multifit.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_multifit.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_multifit.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_multifit.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_multifit.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_multifit.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_multifit.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_multifit.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_multifit.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_multifit.IMP_CHAIN_TYPE_INDEX
381 IMP_EM_HAS_IMP_CGAL = _IMP_multifit.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_multifit.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_multifit.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_multifit.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_multifit.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_multifit.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_multifit.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_multifit.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_multifit.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_multifit.IMPEM_SHOW_WARNINGS
396 IMP_RMF_HAS_IMP_CGAL = _IMP_multifit.IMP_RMF_HAS_IMP_CGAL
397 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
398 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_FILESYSTEM
399 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
400 IMP_RMF_HAS_BOOST_RANDOM = _IMP_multifit.IMP_RMF_HAS_BOOST_RANDOM
401 IMP_RMF_HAS_BOOST_REGEX = _IMP_multifit.IMP_RMF_HAS_BOOST_REGEX
402 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_RMF_HAS_BOOST_SYSTEM
403 IMP_RMF_HAS_CGAL = _IMP_multifit.IMP_RMF_HAS_CGAL
404 IMP_RMF_HAS_HDF5 = _IMP_multifit.IMP_RMF_HAS_HDF5
405 IMP_RMF_HAS_NUMPY = _IMP_multifit.IMP_RMF_HAS_NUMPY
406 IMP_RMF_HAS_PYTHON_IHM = _IMP_multifit.IMP_RMF_HAS_PYTHON_IHM
407 IMPRMF_SHOW_WARNINGS = _IMP_multifit.IMPRMF_SHOW_WARNINGS
410 IMP_DOMINO_HAS_IMP_ATOM = _IMP_multifit.IMP_DOMINO_HAS_IMP_ATOM
411 IMP_DOMINO_HAS_IMP_CGAL = _IMP_multifit.IMP_DOMINO_HAS_IMP_CGAL
412 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_multifit.IMP_DOMINO_HAS_IMP_KERNEL
413 IMP_DOMINO_HAS_IMP_RMF = _IMP_multifit.IMP_DOMINO_HAS_IMP_RMF
414 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
415 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_FILESYSTEM
416 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_multifit.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
417 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_RANDOM
418 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_multifit.IMP_DOMINO_HAS_BOOST_REGEX
419 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_DOMINO_HAS_BOOST_SYSTEM
420 IMP_DOMINO_HAS_CGAL = _IMP_multifit.IMP_DOMINO_HAS_CGAL
421 IMP_DOMINO_HAS_HDF5 = _IMP_multifit.IMP_DOMINO_HAS_HDF5
422 IMP_DOMINO_HAS_NUMPY = _IMP_multifit.IMP_DOMINO_HAS_NUMPY
423 IMP_DOMINO_HAS_RMF = _IMP_multifit.IMP_DOMINO_HAS_RMF
424 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_multifit.IMP_DOMINO_HAS_PYTHON_IHM
425 IMPDOMINO_SHOW_WARNINGS = _IMP_multifit.IMPDOMINO_SHOW_WARNINGS
428 IMP_MULTIFIT_HAS_IMP_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CGAL
429 IMP_MULTIFIT_HAS_IMP_CONTAINER = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_CONTAINER
430 IMP_MULTIFIT_HAS_IMP_DISPLAY = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_DISPLAY
431 IMP_MULTIFIT_HAS_IMP_KERNEL = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_KERNEL
432 IMP_MULTIFIT_HAS_IMP_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_RMF
433 IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR = _IMP_multifit.IMP_MULTIFIT_HAS_IMP_SCORE_FUNCTOR
434 IMP_MULTIFIT_HAS_BOOST_GRAPH = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_GRAPH
435 IMP_MULTIFIT_HAS_BOOST_RANDOM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_RANDOM
436 IMP_MULTIFIT_HAS_BOOST_REGEX = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_REGEX
437 IMP_MULTIFIT_HAS_BOOST_SYSTEM = _IMP_multifit.IMP_MULTIFIT_HAS_BOOST_SYSTEM
438 IMP_MULTIFIT_HAS_CGAL = _IMP_multifit.IMP_MULTIFIT_HAS_CGAL
439 IMP_MULTIFIT_HAS_HDF5 = _IMP_multifit.IMP_MULTIFIT_HAS_HDF5
440 IMP_MULTIFIT_HAS_NUMPY = _IMP_multifit.IMP_MULTIFIT_HAS_NUMPY
441 IMP_MULTIFIT_HAS_RMF = _IMP_multifit.IMP_MULTIFIT_HAS_RMF
442 IMP_MULTIFIT_HAS_PYTHON_IHM = _IMP_multifit.IMP_MULTIFIT_HAS_PYTHON_IHM
443 IMPMULTIFIT_SHOW_WARNINGS = _IMP_multifit.IMPMULTIFIT_SHOW_WARNINGS
445 _object_types.append(
"RadiusOfGyrationRestraint")
448 def _object_cast_to_RadiusOfGyrationRestraint(o):
449 """_object_cast_to_RadiusOfGyrationRestraint(Object o) -> RadiusOfGyrationRestraint"""
450 return _IMP_multifit._object_cast_to_RadiusOfGyrationRestraint(o)
452 _object_types.append(
"ComponentHeader")
455 def _object_cast_to_ComponentHeader(o):
456 """_object_cast_to_ComponentHeader(Object o) -> ComponentHeader"""
457 return _IMP_multifit._object_cast_to_ComponentHeader(o)
459 _object_types.append(
"AssemblyHeader")
462 def _object_cast_to_AssemblyHeader(o):
463 """_object_cast_to_AssemblyHeader(Object o) -> AssemblyHeader"""
464 return _IMP_multifit._object_cast_to_AssemblyHeader(o)
466 _object_types.append(
"SettingsData")
469 def _object_cast_to_SettingsData(o):
470 """_object_cast_to_SettingsData(Object o) -> SettingsData"""
471 return _IMP_multifit._object_cast_to_SettingsData(o)
473 _object_types.append(
"WeightedExcludedVolumeRestraint")
476 def _object_cast_to_WeightedExcludedVolumeRestraint(o):
477 """_object_cast_to_WeightedExcludedVolumeRestraint(Object o) -> WeightedExcludedVolumeRestraint"""
478 return _IMP_multifit._object_cast_to_WeightedExcludedVolumeRestraint(o)
480 _object_types.append(
"ComplementarityRestraint")
483 def _object_cast_to_ComplementarityRestraint(o):
484 """_object_cast_to_ComplementarityRestraint(Object o) -> ComplementarityRestraint"""
485 return _IMP_multifit._object_cast_to_ComplementarityRestraint(o)
487 ProteinRecordDataList=list
488 _plural_types.append(
"ProteinRecordDataList")
489 _value_types.append(
"ProteinRecordData")
492 FittingSolutionRecords=list
493 _plural_types.append(
"FittingSolutionRecords")
494 _value_types.append(
"FittingSolutionRecord")
498 _plural_types.append(
"AnchorsDataList")
499 _value_types.append(
"AnchorsData")
502 DominoParamsList=list
503 _plural_types.append(
"DominoParamsList")
504 _value_types.append(
"DominoParams")
507 ComplementarityParamsList=list
508 _plural_types.append(
"ComplementarityParamsList")
509 _value_types.append(
"ComplementarityParams")
513 _plural_types.append(
"XlinkParamsList")
514 _value_types.append(
"XlinkParams")
517 ConnectivityParamsList=list
518 _plural_types.append(
"ConnectivityParamsList")
519 _value_types.append(
"ConnectivityParams")
522 FragmentsParamsList=list
523 _plural_types.append(
"FragmentsParamsList")
524 _value_types.append(
"FragmentsParams")
528 _plural_types.append(
"RogParamsList")
529 _value_types.append(
"RogParams")
533 _plural_types.append(
"EVParamsList")
534 _value_types.append(
"EVParams")
537 FiltersParamsList=list
538 _plural_types.append(
"FiltersParamsList")
539 _value_types.append(
"FiltersParams")
542 AlignmentParamsList=list
543 _plural_types.append(
"AlignmentParamsList")
544 _value_types.append(
"AlignmentParams")
547 FittingParamsList=list
548 _plural_types.append(
"FittingParamsList")
549 _value_types.append(
"FittingParams")
552 ProteinsAnchorsSamplingSpaces=list
553 _plural_types.append(
"ProteinsAnchorsSamplingSpaces")
554 _value_types.append(
"ProteinsAnchorsSamplingSpace")
557 _object_types.append(
"ProteomicsData")
560 def _object_cast_to_ProteomicsData(o):
561 """_object_cast_to_ProteomicsData(Object o) -> ProteomicsData"""
562 return _IMP_multifit._object_cast_to_ProteomicsData(o)
564 _object_types.append(
"FFTFitting")
567 def _object_cast_to_FFTFitting(o):
568 """_object_cast_to_FFTFitting(Object o) -> FFTFitting"""
569 return _IMP_multifit._object_cast_to_FFTFitting(o)
571 _object_types.append(
"FFTFittingOutput")
574 def _object_cast_to_FFTFittingOutput(o):
575 """_object_cast_to_FFTFittingOutput(Object o) -> FFTFittingOutput"""
576 return _IMP_multifit._object_cast_to_FFTFittingOutput(o)
578 _object_types.append(
"ProbabilisticAnchorGraph")
581 def _object_cast_to_ProbabilisticAnchorGraph(o):
582 """_object_cast_to_ProbabilisticAnchorGraph(Object o) -> ProbabilisticAnchorGraph"""
583 return _IMP_multifit._object_cast_to_ProbabilisticAnchorGraph(o)
585 _object_types.append(
"Ensemble")
588 def _object_cast_to_Ensemble(o):
589 """_object_cast_to_Ensemble(Object o) -> Ensemble"""
590 return _IMP_multifit._object_cast_to_Ensemble(o)
592 _object_types.append(
"ProteomicsEMAlignmentAtomic")
595 def _object_cast_to_ProteomicsEMAlignmentAtomic(o):
596 """_object_cast_to_ProteomicsEMAlignmentAtomic(Object o) -> ProteomicsEMAlignmentAtomic"""
597 return _IMP_multifit._object_cast_to_ProteomicsEMAlignmentAtomic(o)
599 _object_types.append(
"RigidLeavesRefiner")
602 def _object_cast_to_RigidLeavesRefiner(o):
603 """_object_cast_to_RigidLeavesRefiner(Object o) -> RigidLeavesRefiner"""
604 return _IMP_multifit._object_cast_to_RigidLeavesRefiner(o)
608 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key, FloatKey weight_key)
609 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key, FloatKey radius_key)
610 add_surface_index(Hierarchy mhd, IMP::Float apix, FloatKey shell_key)
611 add_surface_index(Hierarchy mhd, IMP::Float apix)
613 return _IMP_multifit.add_surface_index(*args)
617 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2, FloatKey shell_key) -> Restraint
618 create_weighted_excluded_volume_restraint(RigidBody rb1, RigidBody rb2) -> Restraint
620 return _IMP_multifit.create_weighted_excluded_volume_restraint(*args)
621 class FittingSolutionRecord(object):
622 """Proxy of C++ IMP::multifit::FittingSolutionRecord class."""
624 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
627 """__init__(IMP::multifit::FittingSolutionRecord self) -> FittingSolutionRecord"""
628 this = _IMP_multifit.new_FittingSolutionRecord()
630 self.this.append(this)
631 except __builtin__.Exception:
635 """get_index(FittingSolutionRecord self) -> unsigned int"""
636 return _IMP_multifit.FittingSolutionRecord_get_index(self)
639 def set_index(self, new_ind):
640 """set_index(FittingSolutionRecord self, unsigned int new_ind)"""
641 return _IMP_multifit.FittingSolutionRecord_set_index(self, new_ind)
644 def get_solution_filename(self):
645 """get_solution_filename(FittingSolutionRecord self) -> std::string"""
646 return _IMP_multifit.FittingSolutionRecord_get_solution_filename(self)
649 def set_solution_filename(self, sol_fn):
650 """set_solution_filename(FittingSolutionRecord self, std::string sol_fn)"""
651 return _IMP_multifit.FittingSolutionRecord_set_solution_filename(self, sol_fn)
654 def get_fit_transformation(self):
655 """get_fit_transformation(FittingSolutionRecord self) -> Transformation3D"""
656 return _IMP_multifit.FittingSolutionRecord_get_fit_transformation(self)
659 def set_fit_transformation(self, t):
660 """set_fit_transformation(FittingSolutionRecord self, Transformation3D t)"""
661 return _IMP_multifit.FittingSolutionRecord_set_fit_transformation(self, t)
664 def get_match_size(self):
665 """get_match_size(FittingSolutionRecord self) -> unsigned int"""
666 return _IMP_multifit.FittingSolutionRecord_get_match_size(self)
669 def set_match_size(self, match_size):
670 """set_match_size(FittingSolutionRecord self, unsigned int match_size)"""
671 return _IMP_multifit.FittingSolutionRecord_set_match_size(self, match_size)
674 def get_match_average_distance(self):
675 """get_match_average_distance(FittingSolutionRecord self) -> IMP::Float"""
676 return _IMP_multifit.FittingSolutionRecord_get_match_average_distance(self)
679 def set_match_average_distance(self, match_avg_dist):
680 """set_match_average_distance(FittingSolutionRecord self, IMP::Float match_avg_dist)"""
681 return _IMP_multifit.FittingSolutionRecord_set_match_average_distance(self, match_avg_dist)
684 def get_fitting_score(self):
685 """get_fitting_score(FittingSolutionRecord self) -> IMP::Float"""
686 return _IMP_multifit.FittingSolutionRecord_get_fitting_score(self)
689 def set_fitting_score(self, fit_score):
690 """set_fitting_score(FittingSolutionRecord self, IMP::Float fit_score)"""
691 return _IMP_multifit.FittingSolutionRecord_set_fitting_score(self, fit_score)
694 def get_rmsd_to_reference(self):
695 """get_rmsd_to_reference(FittingSolutionRecord self) -> IMP::Float"""
696 return _IMP_multifit.FittingSolutionRecord_get_rmsd_to_reference(self)
699 def set_rmsd_to_reference(self, rmsd_to_ref):
700 """set_rmsd_to_reference(FittingSolutionRecord self, IMP::Float rmsd_to_ref)"""
701 return _IMP_multifit.FittingSolutionRecord_set_rmsd_to_reference(self, rmsd_to_ref)
704 def get_dock_transformation(self):
705 """get_dock_transformation(FittingSolutionRecord self) -> Transformation3D"""
706 return _IMP_multifit.FittingSolutionRecord_get_dock_transformation(self)
709 def set_dock_transformation(self, t):
710 """set_dock_transformation(FittingSolutionRecord self, Transformation3D t)"""
711 return _IMP_multifit.FittingSolutionRecord_set_dock_transformation(self, t)
714 def get_envelope_penetration_score(self):
715 """get_envelope_penetration_score(FittingSolutionRecord self) -> IMP::Float"""
716 return _IMP_multifit.FittingSolutionRecord_get_envelope_penetration_score(self)
719 def set_envelope_penetration_score(self, s):
720 """set_envelope_penetration_score(FittingSolutionRecord self, IMP::Float s)"""
721 return _IMP_multifit.FittingSolutionRecord_set_envelope_penetration_score(self, s)
724 def show(self, *args):
726 show(FittingSolutionRecord self, _ostream out)
727 show(FittingSolutionRecord self)
729 return _IMP_multifit.FittingSolutionRecord_show(self, *args)
732 def get_record_header():
733 """get_record_header() -> std::string"""
734 return _IMP_multifit.FittingSolutionRecord_get_record_header()
736 get_record_header = staticmethod(get_record_header)
739 """__str__(FittingSolutionRecord self) -> std::string"""
740 return _IMP_multifit.FittingSolutionRecord___str__(self)
744 """__repr__(FittingSolutionRecord self) -> std::string"""
745 return _IMP_multifit.FittingSolutionRecord___repr__(self)
747 __swig_destroy__ = _IMP_multifit.delete_FittingSolutionRecord
748 __del__ =
lambda self:
None
749 FittingSolutionRecord_swigregister = _IMP_multifit.FittingSolutionRecord_swigregister
750 FittingSolutionRecord_swigregister(FittingSolutionRecord)
752 def FittingSolutionRecord_get_record_header():
753 """FittingSolutionRecord_get_record_header() -> std::string"""
754 return _IMP_multifit.FittingSolutionRecord_get_record_header()
759 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
760 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
761 pca_based_rigid_fitting(RigidBody rb, Refiner rb_refiner, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
762 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key, PrincipalComponentAnalysis3D dens_pca_input) -> FittingSolutions
763 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold, FloatKey wei_key) -> FittingSolutions
764 pca_based_rigid_fitting(IMP::ParticlesTemp ps, DensityMap em_map, IMP::Float threshold) -> FittingSolutions
766 return _IMP_multifit.pca_based_rigid_fitting(*args)
768 def write_markers(pca, out):
769 """write_markers(PrincipalComponentAnalysis3D pca, _ostream out)"""
770 return _IMP_multifit.write_markers(pca, out)
772 """Proxy of C++ IMP::multifit::ComponentHeader class."""
774 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
777 """__init__(IMP::multifit::ComponentHeader self) -> ComponentHeader"""
778 this = _IMP_multifit.new_ComponentHeader()
780 self.this.append(this)
781 except __builtin__.Exception:
784 def set_name(self, name):
785 """set_name(ComponentHeader self, std::string const & name)"""
786 return _IMP_multifit.ComponentHeader_set_name(self, name)
790 """get_name(ComponentHeader self) -> std::string"""
791 return _IMP_multifit.ComponentHeader_get_name(self)
794 def get_filename(self):
795 """get_filename(ComponentHeader self) -> std::string"""
796 return _IMP_multifit.ComponentHeader_get_filename(self)
799 def set_filename(self, filename):
800 """set_filename(ComponentHeader self, std::string const & filename)"""
801 return _IMP_multifit.ComponentHeader_set_filename(self, filename)
804 def get_surface_fn(self):
805 """get_surface_fn(ComponentHeader self) -> std::string"""
806 return _IMP_multifit.ComponentHeader_get_surface_fn(self)
809 def set_surface_fn(self, fn):
810 """set_surface_fn(ComponentHeader self, std::string const & fn)"""
811 return _IMP_multifit.ComponentHeader_set_surface_fn(self, fn)
814 def set_txt_ap_fn(self, pdb_ap_fn):
815 """set_txt_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
816 return _IMP_multifit.ComponentHeader_set_txt_ap_fn(self, pdb_ap_fn)
819 def get_txt_ap_fn(self):
820 """get_txt_ap_fn(ComponentHeader self) -> std::string"""
821 return _IMP_multifit.ComponentHeader_get_txt_ap_fn(self)
824 def set_txt_fine_ap_fn(self, pdb_ap_fn):
825 """set_txt_fine_ap_fn(ComponentHeader self, std::string const & pdb_ap_fn)"""
826 return _IMP_multifit.ComponentHeader_set_txt_fine_ap_fn(self, pdb_ap_fn)
829 def get_txt_fine_ap_fn(self):
830 """get_txt_fine_ap_fn(ComponentHeader self) -> std::string"""
831 return _IMP_multifit.ComponentHeader_get_txt_fine_ap_fn(self)
834 def set_num_ap(self, num_ap):
835 """set_num_ap(ComponentHeader self, int num_ap)"""
836 return _IMP_multifit.ComponentHeader_set_num_ap(self, num_ap)
839 def get_num_ap(self):
840 """get_num_ap(ComponentHeader self) -> int"""
841 return _IMP_multifit.ComponentHeader_get_num_ap(self)
844 def set_num_fine_ap(self, num_ap):
845 """set_num_fine_ap(ComponentHeader self, int num_ap)"""
846 return _IMP_multifit.ComponentHeader_set_num_fine_ap(self, num_ap)
849 def get_num_fine_ap(self):
850 """get_num_fine_ap(ComponentHeader self) -> int"""
851 return _IMP_multifit.ComponentHeader_get_num_fine_ap(self)
854 def set_transformations_fn(self, transformations_fn):
855 """set_transformations_fn(ComponentHeader self, std::string transformations_fn)"""
856 return _IMP_multifit.ComponentHeader_set_transformations_fn(self, transformations_fn)
859 def get_transformations_fn(self):
860 """get_transformations_fn(ComponentHeader self) -> std::string"""
861 return _IMP_multifit.ComponentHeader_get_transformations_fn(self)
864 def set_reference_fn(self, ref_fn):
865 """set_reference_fn(ComponentHeader self, std::string const & ref_fn)"""
866 return _IMP_multifit.ComponentHeader_set_reference_fn(self, ref_fn)
869 def get_reference_fn(self):
870 """get_reference_fn(ComponentHeader self) -> std::string"""
871 return _IMP_multifit.ComponentHeader_get_reference_fn(self)
874 def get_version_info(self):
875 """get_version_info(ComponentHeader self) -> VersionInfo"""
876 return _IMP_multifit.ComponentHeader_get_version_info(self)
880 """__str__(ComponentHeader self) -> std::string"""
881 return _IMP_multifit.ComponentHeader___str__(self)
885 """__repr__(ComponentHeader self) -> std::string"""
886 return _IMP_multifit.ComponentHeader___repr__(self)
891 return _object_cast_to_ComponentHeader(o)
893 ComponentHeader_swigregister = _IMP_multifit.ComponentHeader_swigregister
894 ComponentHeader_swigregister(ComponentHeader)
897 """Proxy of C++ IMP::multifit::AssemblyHeader class."""
899 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
902 """__init__(IMP::multifit::AssemblyHeader self) -> AssemblyHeader"""
903 this = _IMP_multifit.new_AssemblyHeader()
905 self.this.append(this)
906 except __builtin__.Exception:
909 def set_dens_fn(self, dens_fn):
910 """set_dens_fn(AssemblyHeader self, std::string const & dens_fn)"""
911 return _IMP_multifit.AssemblyHeader_set_dens_fn(self, dens_fn)
914 def get_dens_fn(self):
915 """get_dens_fn(AssemblyHeader self) -> std::string"""
916 return _IMP_multifit.AssemblyHeader_get_dens_fn(self)
919 def set_resolution(self, res):
920 """set_resolution(AssemblyHeader self, float res)"""
921 return _IMP_multifit.AssemblyHeader_set_resolution(self, res)
925 """get_resolution(AssemblyHeader self) -> float"""
926 return _IMP_multifit.AssemblyHeader_get_resolution(self)
929 def get_spacing(self):
930 """get_spacing(AssemblyHeader self) -> float"""
931 return _IMP_multifit.AssemblyHeader_get_spacing(self)
934 def set_spacing(self, spacing):
935 """set_spacing(AssemblyHeader self, float spacing)"""
936 return _IMP_multifit.AssemblyHeader_set_spacing(self, spacing)
939 def set_threshold(self, t):
940 """set_threshold(AssemblyHeader self, float t)"""
941 return _IMP_multifit.AssemblyHeader_set_threshold(self, t)
944 def get_threshold(self):
945 """get_threshold(AssemblyHeader self) -> float"""
946 return _IMP_multifit.AssemblyHeader_get_threshold(self)
949 def get_origin(self):
950 """get_origin(AssemblyHeader self) -> Vector3D"""
951 return _IMP_multifit.AssemblyHeader_get_origin(self)
954 def set_origin(self, origin):
955 """set_origin(AssemblyHeader self, Vector3D origin)"""
956 return _IMP_multifit.AssemblyHeader_set_origin(self, origin)
959 def get_coarse_ap_fn(self):
960 """get_coarse_ap_fn(AssemblyHeader self) -> std::string"""
961 return _IMP_multifit.AssemblyHeader_get_coarse_ap_fn(self)
964 def set_coarse_ap_fn(self, new_fn):
965 """set_coarse_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
966 return _IMP_multifit.AssemblyHeader_set_coarse_ap_fn(self, new_fn)
969 def get_coarse_over_sampled_ap_fn(self):
970 """get_coarse_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
971 return _IMP_multifit.AssemblyHeader_get_coarse_over_sampled_ap_fn(self)
974 def set_coarse_over_sampled_ap_fn(self, new_fn):
975 """set_coarse_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
976 return _IMP_multifit.AssemblyHeader_set_coarse_over_sampled_ap_fn(self, new_fn)
979 def get_fine_ap_fn(self):
980 """get_fine_ap_fn(AssemblyHeader self) -> std::string"""
981 return _IMP_multifit.AssemblyHeader_get_fine_ap_fn(self)
984 def set_fine_ap_fn(self, new_fn):
985 """set_fine_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
986 return _IMP_multifit.AssemblyHeader_set_fine_ap_fn(self, new_fn)
989 def get_fine_over_sampled_ap_fn(self):
990 """get_fine_over_sampled_ap_fn(AssemblyHeader self) -> std::string"""
991 return _IMP_multifit.AssemblyHeader_get_fine_over_sampled_ap_fn(self)
994 def set_fine_over_sampled_ap_fn(self, new_fn):
995 """set_fine_over_sampled_ap_fn(AssemblyHeader self, std::string const & new_fn)"""
996 return _IMP_multifit.AssemblyHeader_set_fine_over_sampled_ap_fn(self, new_fn)
999 def get_version_info(self):
1000 """get_version_info(AssemblyHeader self) -> VersionInfo"""
1001 return _IMP_multifit.AssemblyHeader_get_version_info(self)
1005 """__str__(AssemblyHeader self) -> std::string"""
1006 return _IMP_multifit.AssemblyHeader___str__(self)
1010 """__repr__(AssemblyHeader self) -> std::string"""
1011 return _IMP_multifit.AssemblyHeader___repr__(self)
1016 return _object_cast_to_AssemblyHeader(o)
1018 AssemblyHeader_swigregister = _IMP_multifit.AssemblyHeader_swigregister
1019 AssemblyHeader_swigregister(AssemblyHeader)
1022 """Proxy of C++ IMP::multifit::SettingsData class."""
1024 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1027 """__init__(IMP::multifit::SettingsData self) -> SettingsData"""
1028 this = _IMP_multifit.new_SettingsData()
1030 self.this.append(this)
1031 except __builtin__.Exception:
1034 def show_component_header_line(*args):
1036 show_component_header_line(_ostream out)
1037 show_component_header_line()
1039 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1041 show_component_header_line = staticmethod(show_component_header_line)
1043 def get_component_header_line():
1044 """get_component_header_line() -> std::string"""
1045 return _IMP_multifit.SettingsData_get_component_header_line()
1047 get_component_header_line = staticmethod(get_component_header_line)
1049 def show_density_header_line(*args):
1051 show_density_header_line(_ostream out)
1052 show_density_header_line()
1054 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1056 show_density_header_line = staticmethod(show_density_header_line)
1058 def get_density_header_line():
1059 """get_density_header_line() -> std::string"""
1060 return _IMP_multifit.SettingsData_get_density_header_line()
1062 get_density_header_line = staticmethod(get_density_header_line)
1064 def set_assembly_filename(self, fn):
1065 """set_assembly_filename(SettingsData self, std::string const & fn)"""
1066 return _IMP_multifit.SettingsData_set_assembly_filename(self, fn)
1069 def get_assembly_filename(self):
1070 """get_assembly_filename(SettingsData self) -> char const *"""
1071 return _IMP_multifit.SettingsData_get_assembly_filename(self)
1074 def set_assembly_header(self, h):
1075 """set_assembly_header(SettingsData self, AssemblyHeader h)"""
1076 return _IMP_multifit.SettingsData_set_assembly_header(self, h)
1079 def get_assembly_header(self):
1080 """get_assembly_header(SettingsData self) -> AssemblyHeader"""
1081 return _IMP_multifit.SettingsData_get_assembly_header(self)
1084 def set_data_path(self, fn):
1085 """set_data_path(SettingsData self, std::string const & fn)"""
1086 return _IMP_multifit.SettingsData_set_data_path(self, fn)
1090 """get_data_path(SettingsData self) -> std::string"""
1091 return _IMP_multifit.SettingsData_get_data_path(self)
1094 def get_version_info(self):
1095 """get_version_info(SettingsData self) -> VersionInfo"""
1096 return _IMP_multifit.SettingsData_get_version_info(self)
1099 def remove_component_header(self, d):
1100 """remove_component_header(SettingsData self, ComponentHeader d)"""
1101 return _IMP_multifit.SettingsData_remove_component_header(self, d)
1104 def remove_component_headers(self, d):
1105 """remove_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & d)"""
1106 return _IMP_multifit.SettingsData_remove_component_headers(self, d)
1109 def set_component_headers(self, ps):
1110 """set_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & ps)"""
1111 return _IMP_multifit.SettingsData_set_component_headers(self, ps)
1114 def set_component_headers_order(self, objs):
1115 """set_component_headers_order(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1116 return _IMP_multifit.SettingsData_set_component_headers_order(self, objs)
1119 def add_component_header(self, obj):
1120 """add_component_header(SettingsData self, ComponentHeader obj) -> unsigned int"""
1121 return _IMP_multifit.SettingsData_add_component_header(self, obj)
1124 def add_component_headers(self, objs):
1125 """add_component_headers(SettingsData self, IMP::multifit::ComponentHeaders const & objs)"""
1126 return _IMP_multifit.SettingsData_add_component_headers(self, objs)
1129 def clear_component_headers(self):
1130 """clear_component_headers(SettingsData self)"""
1131 return _IMP_multifit.SettingsData_clear_component_headers(self)
1134 def get_number_of_component_headers(self):
1135 """get_number_of_component_headers(SettingsData self) -> unsigned int"""
1136 return _IMP_multifit.SettingsData_get_number_of_component_headers(self)
1139 def get_has_component_headers(self):
1140 """get_has_component_headers(SettingsData self) -> bool"""
1141 return _IMP_multifit.SettingsData_get_has_component_headers(self)
1144 def get_component_header(self, i):
1145 """get_component_header(SettingsData self, unsigned int i) -> ComponentHeader"""
1146 return _IMP_multifit.SettingsData_get_component_header(self, i)
1149 def get_component_headers(self):
1150 """get_component_headers(SettingsData self) -> IMP::multifit::ComponentHeaders"""
1151 return _IMP_multifit.SettingsData_get_component_headers(self)
1154 def reserve_component_headers(self, sz):
1155 """reserve_component_headers(SettingsData self, unsigned int sz)"""
1156 return _IMP_multifit.SettingsData_reserve_component_headers(self, sz)
1160 """__str__(SettingsData self) -> std::string"""
1161 return _IMP_multifit.SettingsData___str__(self)
1165 """__repr__(SettingsData self) -> std::string"""
1166 return _IMP_multifit.SettingsData___repr__(self)
1171 return _object_cast_to_SettingsData(o)
1173 SettingsData_swigregister = _IMP_multifit.SettingsData_swigregister
1174 SettingsData_swigregister(SettingsData)
1176 def SettingsData_show_component_header_line(*args):
1178 show_component_header_line(_ostream out)
1179 SettingsData_show_component_header_line()
1181 return _IMP_multifit.SettingsData_show_component_header_line(*args)
1183 def SettingsData_get_component_header_line():
1184 """SettingsData_get_component_header_line() -> std::string"""
1185 return _IMP_multifit.SettingsData_get_component_header_line()
1187 def SettingsData_show_density_header_line(*args):
1189 show_density_header_line(_ostream out)
1190 SettingsData_show_density_header_line()
1192 return _IMP_multifit.SettingsData_show_density_header_line(*args)
1194 def SettingsData_get_density_header_line():
1195 """SettingsData_get_density_header_line() -> std::string"""
1196 return _IMP_multifit.SettingsData_get_density_header_line()
1199 def read_settings(filename):
1200 """read_settings(char const * filename) -> SettingsData"""
1201 return _IMP_multifit.read_settings(filename)
1203 def write_settings(filename, sd):
1204 """write_settings(char const * filename, SettingsData sd)"""
1205 return _IMP_multifit.write_settings(filename, sd)
1207 """Proxy of C++ IMP::multifit::WeightedExcludedVolumeRestraint class."""
1209 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1213 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner, FloatKey weight_key) -> WeightedExcludedVolumeRestraint
1214 __init__(IMP::multifit::WeightedExcludedVolumeRestraint self, IMP::core::RigidBodies rbs, Refiner refiner) -> WeightedExcludedVolumeRestraint
1216 this = _IMP_multifit.new_WeightedExcludedVolumeRestraint(*args)
1218 self.this.append(this)
1219 except __builtin__.Exception:
1222 def do_get_inputs(self):
1223 """do_get_inputs(WeightedExcludedVolumeRestraint self) -> IMP::ModelObjectsTemp"""
1224 return _IMP_multifit.WeightedExcludedVolumeRestraint_do_get_inputs(self)
1227 def get_version_info(self):
1228 """get_version_info(WeightedExcludedVolumeRestraint self) -> VersionInfo"""
1229 return _IMP_multifit.WeightedExcludedVolumeRestraint_get_version_info(self)
1233 """__str__(WeightedExcludedVolumeRestraint self) -> std::string"""
1234 return _IMP_multifit.WeightedExcludedVolumeRestraint___str__(self)
1238 """__repr__(WeightedExcludedVolumeRestraint self) -> std::string"""
1239 return _IMP_multifit.WeightedExcludedVolumeRestraint___repr__(self)
1244 return _object_cast_to_WeightedExcludedVolumeRestraint(o)
1246 WeightedExcludedVolumeRestraint_swigregister = _IMP_multifit.WeightedExcludedVolumeRestraint_swigregister
1247 WeightedExcludedVolumeRestraint_swigregister(WeightedExcludedVolumeRestraint)
1250 """Proxy of C++ IMP::multifit::FFTFittingOutput class."""
1252 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1255 """__init__(IMP::multifit::FFTFittingOutput self) -> FFTFittingOutput"""
1256 this = _IMP_multifit.new_FFTFittingOutput()
1258 self.this.append(this)
1259 except __builtin__.Exception:
1262 def get_version_info(self):
1263 """get_version_info(FFTFittingOutput self) -> VersionInfo"""
1264 return _IMP_multifit.FFTFittingOutput_get_version_info(self)
1266 best_fits_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_fits__get, _IMP_multifit.FFTFittingOutput_best_fits__set)
1267 best_trans_per_rot_ = _swig_property(_IMP_multifit.FFTFittingOutput_best_trans_per_rot__get, _IMP_multifit.FFTFittingOutput_best_trans_per_rot__set)
1270 """__str__(FFTFittingOutput self) -> std::string"""
1271 return _IMP_multifit.FFTFittingOutput___str__(self)
1275 """__repr__(FFTFittingOutput self) -> std::string"""
1276 return _IMP_multifit.FFTFittingOutput___repr__(self)
1281 return _object_cast_to_FFTFittingOutput(o)
1283 FFTFittingOutput_swigregister = _IMP_multifit.FFTFittingOutput_swigregister
1284 FFTFittingOutput_swigregister(FFTFittingOutput)
1287 """Proxy of C++ IMP::multifit::FFTFitting class."""
1289 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1291 def get_version_info(self):
1292 """get_version_info(FFTFitting self) -> VersionInfo"""
1293 return _IMP_multifit.FFTFitting_get_version_info(self)
1297 """__init__(IMP::multifit::FFTFitting self) -> FFTFitting"""
1298 this = _IMP_multifit.new_FFTFitting()
1300 self.this.append(this)
1301 except __builtin__.Exception:
1304 def do_global_fitting(self, *args):
1306 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
1307 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) -> FFTFittingOutput
1308 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) -> FFTFittingOutput
1309 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) -> FFTFittingOutput
1311 return _IMP_multifit.FFTFitting_do_global_fitting(self, *args)
1314 def do_local_fitting(self, *args):
1316 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
1317 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) -> FFTFittingOutput
1319 return _IMP_multifit.FFTFitting_do_local_fitting(self, *args)
1323 """__str__(FFTFitting self) -> std::string"""
1324 return _IMP_multifit.FFTFitting___str__(self)
1328 """__repr__(FFTFitting self) -> std::string"""
1329 return _IMP_multifit.FFTFitting___repr__(self)
1334 return _object_cast_to_FFTFitting(o)
1336 FFTFitting_swigregister = _IMP_multifit.FFTFitting_swigregister
1337 FFTFitting_swigregister(FFTFitting)
1341 """fft_based_rigid_fitting(Hierarchy mol2fit, DensityMap dmap, double density_threshold, double angle_sampling_interval_rad) -> IMP::multifit::FittingSolutionRecords"""
1342 return _IMP_multifit.fft_based_rigid_fitting(mol2fit, dmap, density_threshold, angle_sampling_interval_rad)
1345 """remove_background(DensityMap dmap, float threshold, float edge_threshold) -> DensityMap"""
1346 return _IMP_multifit.remove_background(dmap, threshold, edge_threshold)
1349 """get_connected_components(DensityMap dmap, float threshold, float edge_threshold) -> IMP::IntsList"""
1350 return _IMP_multifit.get_connected_components(dmap, threshold, edge_threshold)
1352 def get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename):
1353 """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)"""
1354 return _IMP_multifit.get_segmentation(dmap, apix, density_threshold, num_means, pdb_filename, cmm_filename, seg_filename, txt_filename)
1356 """Proxy of C++ IMP::multifit::ComplementarityRestraint class."""
1358 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1362 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b, std::string name) -> ComplementarityRestraint
1363 __init__(IMP::multifit::ComplementarityRestraint self, IMP::ParticlesTemp const & a, IMP::ParticlesTemp const & b) -> ComplementarityRestraint
1365 this = _IMP_multifit.new_ComplementarityRestraint(*args)
1367 self.this.append(this)
1368 except __builtin__.Exception:
1371 def set_maximum_penetration_score(self, s):
1372 """set_maximum_penetration_score(ComplementarityRestraint self, double s)"""
1373 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration_score(self, s)
1376 def set_maximum_penetration(self, d):
1377 """set_maximum_penetration(ComplementarityRestraint self, double d)"""
1378 return _IMP_multifit.ComplementarityRestraint_set_maximum_penetration(self, d)
1381 def set_maximum_separation(self, s):
1382 """set_maximum_separation(ComplementarityRestraint self, double s)"""
1383 return _IMP_multifit.ComplementarityRestraint_set_maximum_separation(self, s)
1386 def set_complementarity_thickness(self, th):
1387 """set_complementarity_thickness(ComplementarityRestraint self, double th)"""
1388 return _IMP_multifit.ComplementarityRestraint_set_complementarity_thickness(self, th)
1391 def set_complementarity_value(self, th):
1392 """set_complementarity_value(ComplementarityRestraint self, double th)"""
1393 return _IMP_multifit.ComplementarityRestraint_set_complementarity_value(self, th)
1396 def set_interior_layer_thickness(self, th):
1397 """set_interior_layer_thickness(ComplementarityRestraint self, double th)"""
1398 return _IMP_multifit.ComplementarityRestraint_set_interior_layer_thickness(self, th)
1401 def set_penetration_coefficient(self, pc):
1402 """set_penetration_coefficient(ComplementarityRestraint self, double pc)"""
1403 return _IMP_multifit.ComplementarityRestraint_set_penetration_coefficient(self, pc)
1406 def set_complementarity_coefficient(self, cc):
1407 """set_complementarity_coefficient(ComplementarityRestraint self, double cc)"""
1408 return _IMP_multifit.ComplementarityRestraint_set_complementarity_coefficient(self, cc)
1411 def set_boundary_coefficient(self, bc):
1412 """set_boundary_coefficient(ComplementarityRestraint self, double bc)"""
1413 return _IMP_multifit.ComplementarityRestraint_set_boundary_coefficient(self, bc)
1416 def get_voxel_size(self):
1417 """get_voxel_size(ComplementarityRestraint self) -> float"""
1418 return _IMP_multifit.ComplementarityRestraint_get_voxel_size(self)
1421 def do_get_inputs(self):
1422 """do_get_inputs(ComplementarityRestraint self) -> IMP::ModelObjectsTemp"""
1423 return _IMP_multifit.ComplementarityRestraint_do_get_inputs(self)
1426 def get_version_info(self):
1427 """get_version_info(ComplementarityRestraint self) -> VersionInfo"""
1428 return _IMP_multifit.ComplementarityRestraint_get_version_info(self)
1432 """__str__(ComplementarityRestraint self) -> std::string"""
1433 return _IMP_multifit.ComplementarityRestraint___str__(self)
1437 """__repr__(ComplementarityRestraint self) -> std::string"""
1438 return _IMP_multifit.ComplementarityRestraint___repr__(self)
1443 return _object_cast_to_ComplementarityRestraint(o)
1445 ComplementarityRestraint_swigregister = _IMP_multifit.ComplementarityRestraint_swigregister
1446 ComplementarityRestraint_swigregister(ComplementarityRestraint)
1450 """read_fitting_solutions(char const * fitting_fn) -> IMP::multifit::FittingSolutionRecords"""
1451 return _IMP_multifit.read_fitting_solutions(fitting_fn)
1455 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols, int num_sols=-1)
1456 write_fitting_solutions(char const * fitting_fn, IMP::multifit::FittingSolutionRecords const & fit_sols)
1458 return _IMP_multifit.write_fitting_solutions(fitting_fn, fit_sols, num_sols)
1460 def convert_em_to_multifit_format(em_fits):
1461 """convert_em_to_multifit_format(FittingSolutions em_fits) -> IMP::multifit::FittingSolutionRecords"""
1462 return _IMP_multifit.convert_em_to_multifit_format(em_fits)
1464 def convert_multifit_to_em_format(multifit_fits):
1465 """convert_multifit_to_em_format(IMP::multifit::FittingSolutionRecords const & multifit_fits) -> FittingSolutions"""
1466 return _IMP_multifit.convert_multifit_to_em_format(multifit_fits)
1468 def convert_transformations_to_multifit_format(trans):
1469 """convert_transformations_to_multifit_format(IMP::algebra::Transformation3Ds const & trans) -> IMP::multifit::FittingSolutionRecords"""
1470 return _IMP_multifit.convert_transformations_to_multifit_format(trans)
1472 def convert_multifit_format_to_transformations(recs):
1473 """convert_multifit_format_to_transformations(IMP::multifit::FittingSolutionRecords const & recs) -> IMP::algebra::Transformation3Ds"""
1474 return _IMP_multifit.convert_multifit_format_to_transformations(recs)
1477 """get_close_to_point(IMP::multifit::FittingSolutionRecords const & fit_sols, Hierarchy mh, Particle ap, IMP::Float dist) -> IMP::multifit::FittingSolutionRecords"""
1478 return _IMP_multifit.get_close_to_point(fit_sols, mh, ap, dist)
1480 """Proxy of C++ IMP::multifit::ProbabilisticAnchorGraph class."""
1482 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1484 def __init__(self, anchor_positions):
1485 """__init__(IMP::multifit::ProbabilisticAnchorGraph self, IMP::algebra::Vector3Ds anchor_positions) -> ProbabilisticAnchorGraph"""
1486 this = _IMP_multifit.new_ProbabilisticAnchorGraph(anchor_positions)
1488 self.this.append(this)
1489 except __builtin__.Exception:
1492 def add_edge(self, i, j):
1493 """add_edge(ProbabilisticAnchorGraph self, int i, int j)"""
1494 return _IMP_multifit.ProbabilisticAnchorGraph_add_edge(self, i, j)
1497 def set_particle_probabilities_on_anchors(self, p, sols):
1498 """set_particle_probabilities_on_anchors(ProbabilisticAnchorGraph self, Particle p, IMP::multifit::FittingSolutionRecords sols)"""
1499 return _IMP_multifit.ProbabilisticAnchorGraph_set_particle_probabilities_on_anchors(self, p, sols)
1502 def show(self, *args):
1504 show(ProbabilisticAnchorGraph self, _ostream out)
1505 show(ProbabilisticAnchorGraph self)
1507 return _IMP_multifit.ProbabilisticAnchorGraph_show(self, *args)
1510 def get_number_of_anchors(self):
1511 """get_number_of_anchors(ProbabilisticAnchorGraph self) -> unsigned int"""
1512 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_anchors(self)
1515 def get_number_of_edges(self):
1516 """get_number_of_edges(ProbabilisticAnchorGraph self) -> unsigned int"""
1517 return _IMP_multifit.ProbabilisticAnchorGraph_get_number_of_edges(self)
1520 def get_edge_list(self):
1521 """get_edge_list(ProbabilisticAnchorGraph self) -> IMP::IntRanges"""
1522 return _IMP_multifit.ProbabilisticAnchorGraph_get_edge_list(self)
1525 def get_anchors(self):
1526 """get_anchors(ProbabilisticAnchorGraph self) -> IMP::algebra::Vector3Ds"""
1527 return _IMP_multifit.ProbabilisticAnchorGraph_get_anchors(self)
1530 def get_particle_anchors(self, p, min_prob=0):
1532 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p, float min_prob=0) -> IMP::algebra::Vector3Ds
1533 get_particle_anchors(ProbabilisticAnchorGraph self, Particle p) -> IMP::algebra::Vector3Ds
1535 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_anchors(self, p, min_prob)
1538 def get_are_probabilities_for_particle_set(self, p):
1539 """get_are_probabilities_for_particle_set(ProbabilisticAnchorGraph self, Particle p) -> bool"""
1540 return _IMP_multifit.ProbabilisticAnchorGraph_get_are_probabilities_for_particle_set(self, p)
1543 def get_particle_probabilities(self, p):
1544 """get_particle_probabilities(ProbabilisticAnchorGraph self, Particle p) -> IMP::Floats"""
1545 return _IMP_multifit.ProbabilisticAnchorGraph_get_particle_probabilities(self, p)
1548 def get_version_info(self):
1549 """get_version_info(ProbabilisticAnchorGraph self) -> VersionInfo"""
1550 return _IMP_multifit.ProbabilisticAnchorGraph_get_version_info(self)
1554 """__str__(ProbabilisticAnchorGraph self) -> std::string"""
1555 return _IMP_multifit.ProbabilisticAnchorGraph___str__(self)
1559 """__repr__(ProbabilisticAnchorGraph self) -> std::string"""
1560 return _IMP_multifit.ProbabilisticAnchorGraph___repr__(self)
1565 return _object_cast_to_ProbabilisticAnchorGraph(o)
1567 ProbabilisticAnchorGraph_swigregister = _IMP_multifit.ProbabilisticAnchorGraph_swigregister
1568 ProbabilisticAnchorGraph_swigregister(ProbabilisticAnchorGraph)
1570 class ProteinRecordData(object):
1571 """Proxy of C++ IMP::multifit::ProteinRecordData class."""
1573 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1575 def reset_all(self):
1576 """reset_all(ProteinRecordData self)"""
1577 return _IMP_multifit.ProteinRecordData_reset_all(self)
1582 __init__(IMP::multifit::ProteinRecordData self) -> ProteinRecordData
1583 __init__(IMP::multifit::ProteinRecordData self, std::string const & name) -> ProteinRecordData
1584 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, std::string const fn) -> ProteinRecordData
1585 __init__(IMP::multifit::ProteinRecordData self, std::string const & name, int start_res, int end_res, std::string const fn) -> ProteinRecordData
1586 __init__(IMP::multifit::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
1588 this = _IMP_multifit.new_ProteinRecordData(*args)
1590 self.this.append(this)
1591 except __builtin__.Exception:
1594 def show(self, *args):
1596 show(ProteinRecordData self, _ostream out)
1597 show(ProteinRecordData self)
1599 return _IMP_multifit.ProteinRecordData_show(self, *args)
1601 name_ = _swig_property(_IMP_multifit.ProteinRecordData_name__get, _IMP_multifit.ProteinRecordData_name__set)
1602 start_res_ = _swig_property(_IMP_multifit.ProteinRecordData_start_res__get, _IMP_multifit.ProteinRecordData_start_res__set)
1603 end_res_ = _swig_property(_IMP_multifit.ProteinRecordData_end_res__get, _IMP_multifit.ProteinRecordData_end_res__set)
1604 filename_ = _swig_property(_IMP_multifit.ProteinRecordData_filename__get, _IMP_multifit.ProteinRecordData_filename__set)
1605 surface_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_surface_filename__get, _IMP_multifit.ProteinRecordData_surface_filename__set)
1606 ref_filename_ = _swig_property(_IMP_multifit.ProteinRecordData_ref_filename__get, _IMP_multifit.ProteinRecordData_ref_filename__set)
1609 """__str__(ProteinRecordData self) -> std::string"""
1610 return _IMP_multifit.ProteinRecordData___str__(self)
1614 """__repr__(ProteinRecordData self) -> std::string"""
1615 return _IMP_multifit.ProteinRecordData___repr__(self)
1617 __swig_destroy__ = _IMP_multifit.delete_ProteinRecordData
1618 __del__ =
lambda self:
None
1619 ProteinRecordData_swigregister = _IMP_multifit.ProteinRecordData_swigregister
1620 ProteinRecordData_swigregister(ProteinRecordData)
1623 """Proxy of C++ IMP::multifit::ProteomicsData class."""
1625 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1628 """__init__(IMP::multifit::ProteomicsData self) -> ProteomicsData"""
1629 this = _IMP_multifit.new_ProteomicsData()
1631 self.this.append(this)
1632 except __builtin__.Exception:
1635 def add_protein(self, *args):
1637 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
1638 add_protein(ProteomicsData self, ProteinRecordData rec) -> int
1640 return _IMP_multifit.ProteomicsData_add_protein(self, *args)
1643 def find(self, name):
1644 """find(ProteomicsData self, std::string const & name) -> int"""
1645 return _IMP_multifit.ProteomicsData_find(self, name)
1648 def add_interaction(self, ii, used_for_filter, linker_len):
1649 """add_interaction(ProteomicsData self, IMP::Ints const & ii, bool used_for_filter, float linker_len)"""
1650 return _IMP_multifit.ProteomicsData_add_interaction(self, ii, used_for_filter, linker_len)
1653 def add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len):
1654 """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)"""
1655 return _IMP_multifit.ProteomicsData_add_cross_link_interaction(self, prot1, res1, prot2, res2, used_in_filter, linker_len)
1658 def add_ev_pair(self, prot1, prot2):
1659 """add_ev_pair(ProteomicsData self, IMP::Int prot1, IMP::Int prot2)"""
1660 return _IMP_multifit.ProteomicsData_add_ev_pair(self, prot1, prot2)
1663 def get_number_of_proteins(self):
1664 """get_number_of_proteins(ProteomicsData self) -> int"""
1665 return _IMP_multifit.ProteomicsData_get_number_of_proteins(self)
1668 def get_number_of_interactions(self):
1669 """get_number_of_interactions(ProteomicsData self) -> int"""
1670 return _IMP_multifit.ProteomicsData_get_number_of_interactions(self)
1673 def get_interaction(self, interaction_ind):
1674 """get_interaction(ProteomicsData self, int interaction_ind) -> IMP::Ints"""
1675 return _IMP_multifit.ProteomicsData_get_interaction(self, interaction_ind)
1678 def get_interaction_part_of_filter(self, interaction_ind):
1679 """get_interaction_part_of_filter(ProteomicsData self, int interaction_ind) -> bool"""
1680 return _IMP_multifit.ProteomicsData_get_interaction_part_of_filter(self, interaction_ind)
1683 def get_interaction_linker_length(self, interaction_ind):
1684 """get_interaction_linker_length(ProteomicsData self, int interaction_ind) -> int"""
1685 return _IMP_multifit.ProteomicsData_get_interaction_linker_length(self, interaction_ind)
1688 def get_number_of_cross_links(self):
1689 """get_number_of_cross_links(ProteomicsData self) -> int"""
1690 return _IMP_multifit.ProteomicsData_get_number_of_cross_links(self)
1693 def get_cross_link(self, xlink_ind):
1694 """get_cross_link(ProteomicsData self, int xlink_ind) -> std::pair< IMP::IntPair,IMP::IntPair >"""
1695 return _IMP_multifit.ProteomicsData_get_cross_link(self, xlink_ind)
1698 def get_cross_link_part_of_filter(self, xlink_ind):
1699 """get_cross_link_part_of_filter(ProteomicsData self, int xlink_ind) -> bool"""
1700 return _IMP_multifit.ProteomicsData_get_cross_link_part_of_filter(self, xlink_ind)
1703 def get_cross_link_length(self, xlink_ind):
1704 """get_cross_link_length(ProteomicsData self, int xlink_ind) -> float"""
1705 return _IMP_multifit.ProteomicsData_get_cross_link_length(self, xlink_ind)
1708 def get_number_of_ev_pairs(self):
1709 """get_number_of_ev_pairs(ProteomicsData self) -> int"""
1710 return _IMP_multifit.ProteomicsData_get_number_of_ev_pairs(self)
1713 def get_ev_pair(self, ev_ind):
1714 """get_ev_pair(ProteomicsData self, int ev_ind) -> IMP::IntPair"""
1715 return _IMP_multifit.ProteomicsData_get_ev_pair(self, ev_ind)
1718 def get_protein_name(self, protein_ind):
1719 """get_protein_name(ProteomicsData self, int protein_ind) -> std::string"""
1720 return _IMP_multifit.ProteomicsData_get_protein_name(self, protein_ind)
1723 def get_end_res(self, protein_ind):
1724 """get_end_res(ProteomicsData self, int protein_ind) -> int"""
1725 return _IMP_multifit.ProteomicsData_get_end_res(self, protein_ind)
1728 def get_start_res(self, protein_ind):
1729 """get_start_res(ProteomicsData self, int protein_ind) -> int"""
1730 return _IMP_multifit.ProteomicsData_get_start_res(self, protein_ind)
1733 def get_protein_filename(self, protein_ind):
1734 """get_protein_filename(ProteomicsData self, int protein_ind) -> std::string"""
1735 return _IMP_multifit.ProteomicsData_get_protein_filename(self, protein_ind)
1738 def get_reference_filename(self, protein_ind):
1739 """get_reference_filename(ProteomicsData self, int protein_ind) -> std::string"""
1740 return _IMP_multifit.ProteomicsData_get_reference_filename(self, protein_ind)
1743 def get_surface_filename(self, protein_ind):
1744 """get_surface_filename(ProteomicsData self, int protein_ind) -> std::string"""
1745 return _IMP_multifit.ProteomicsData_get_surface_filename(self, protein_ind)
1748 def get_protein_data(self, protein_ind):
1749 """get_protein_data(ProteomicsData self, int protein_ind) -> ProteinRecordData"""
1750 return _IMP_multifit.ProteomicsData_get_protein_data(self, protein_ind)
1753 def get_version_info(self):
1754 """get_version_info(ProteomicsData self) -> VersionInfo"""
1755 return _IMP_multifit.ProteomicsData_get_version_info(self)
1758 def get_num_allowed_violated_interactions(self):
1759 """get_num_allowed_violated_interactions(ProteomicsData self) -> int"""
1760 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_interactions(self)
1763 def set_num_allowed_violated_interactions(self, n):
1764 """set_num_allowed_violated_interactions(ProteomicsData self, int n)"""
1765 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_interactions(self, n)
1768 def get_num_allowed_violated_cross_links(self):
1769 """get_num_allowed_violated_cross_links(ProteomicsData self) -> int"""
1770 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_cross_links(self)
1773 def set_num_allowed_violated_cross_links(self, n):
1774 """set_num_allowed_violated_cross_links(ProteomicsData self, int n)"""
1775 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_cross_links(self, n)
1778 def get_num_allowed_violated_ev(self):
1779 """get_num_allowed_violated_ev(ProteomicsData self) -> int"""
1780 return _IMP_multifit.ProteomicsData_get_num_allowed_violated_ev(self)
1783 def set_num_allowed_violated_ev(self, n):
1784 """set_num_allowed_violated_ev(ProteomicsData self, int n)"""
1785 return _IMP_multifit.ProteomicsData_set_num_allowed_violated_ev(self, n)
1789 """__str__(ProteomicsData self) -> std::string"""
1790 return _IMP_multifit.ProteomicsData___str__(self)
1794 """__repr__(ProteomicsData self) -> std::string"""
1795 return _IMP_multifit.ProteomicsData___repr__(self)
1800 return _object_cast_to_ProteomicsData(o)
1802 ProteomicsData_swigregister = _IMP_multifit.ProteomicsData_swigregister
1803 ProteomicsData_swigregister(ProteomicsData)
1807 """read_proteomics_data(char const * proteomics_fn) -> ProteomicsData"""
1808 return _IMP_multifit.read_proteomics_data(proteomics_fn)
1810 def get_partial_proteomics_data(pd, prot_names):
1811 """get_partial_proteomics_data(ProteomicsData pd, IMP::Strings const & prot_names) -> ProteomicsData"""
1812 return _IMP_multifit.get_partial_proteomics_data(pd, prot_names)
1813 class AnchorsData(object):
1814 """Proxy of C++ IMP::multifit::AnchorsData class."""
1816 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1820 __init__(IMP::multifit::AnchorsData self) -> AnchorsData
1821 __init__(IMP::multifit::AnchorsData self, IMP::algebra::Vector3Ds points, IMP::IntPairs edges) -> AnchorsData
1823 this = _IMP_multifit.new_AnchorsData(*args)
1825 self.this.append(this)
1826 except __builtin__.Exception:
1829 def remove_edges_for_node(self, node_ind):
1830 """remove_edges_for_node(AnchorsData self, int node_ind)"""
1831 return _IMP_multifit.AnchorsData_remove_edges_for_node(self, node_ind)
1834 def get_number_of_points(self):
1835 """get_number_of_points(AnchorsData self) -> int"""
1836 return _IMP_multifit.AnchorsData_get_number_of_points(self)
1839 def get_number_of_edges(self):
1840 """get_number_of_edges(AnchorsData self) -> int"""
1841 return _IMP_multifit.AnchorsData_get_number_of_edges(self)
1844 def get_is_point_considered(self, node_ind):
1845 """get_is_point_considered(AnchorsData self, int node_ind) -> bool"""
1846 return _IMP_multifit.AnchorsData_get_is_point_considered(self, node_ind)
1849 def show(self, *args):
1851 show(AnchorsData self, _ostream out)
1852 show(AnchorsData self)
1854 return _IMP_multifit.AnchorsData_show(self, *args)
1857 def get_secondary_structure_is_set(self):
1858 """get_secondary_structure_is_set(AnchorsData self) -> bool"""
1859 return _IMP_multifit.AnchorsData_get_secondary_structure_is_set(self)
1862 def setup_secondary_structure(self, mdl):
1863 """setup_secondary_structure(AnchorsData self, Model mdl)"""
1864 return _IMP_multifit.AnchorsData_setup_secondary_structure(self, mdl)
1867 def set_secondary_structure_probabilities(self, *args):
1869 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps, IMP::Ints const & indices)
1870 set_secondary_structure_probabilities(AnchorsData self, IMP::Particles const & ssres_ps)
1872 return _IMP_multifit.AnchorsData_set_secondary_structure_probabilities(self, *args)
1875 def get_secondary_structure_particles(self):
1876 """get_secondary_structure_particles(AnchorsData self) -> IMP::Particles"""
1877 return _IMP_multifit.AnchorsData_get_secondary_structure_particles(self)
1879 points_ = _swig_property(_IMP_multifit.AnchorsData_points__get, _IMP_multifit.AnchorsData_points__set)
1880 consider_point_ = _swig_property(_IMP_multifit.AnchorsData_consider_point__get, _IMP_multifit.AnchorsData_consider_point__set)
1881 edges_ = _swig_property(_IMP_multifit.AnchorsData_edges__get, _IMP_multifit.AnchorsData_edges__set)
1884 """__str__(AnchorsData self) -> std::string"""
1885 return _IMP_multifit.AnchorsData___str__(self)
1889 """__repr__(AnchorsData self) -> std::string"""
1890 return _IMP_multifit.AnchorsData___repr__(self)
1892 __swig_destroy__ = _IMP_multifit.delete_AnchorsData
1893 __del__ =
lambda self:
None
1894 AnchorsData_swigregister = _IMP_multifit.AnchorsData_swigregister
1895 AnchorsData_swigregister(AnchorsData)
1898 def read_anchors_data(txt_filename):
1899 """read_anchors_data(char const * txt_filename) -> AnchorsData"""
1900 return _IMP_multifit.read_anchors_data(txt_filename)
1902 def write_txt(txt_filename, ad):
1903 """write_txt(std::string const & txt_filename, AnchorsData ad)"""
1904 return _IMP_multifit.write_txt(txt_filename, ad)
1906 def write_cmm(cmm_filename, marker_set_name, dpa):
1907 """write_cmm(std::string const & cmm_filename, std::string const & marker_set_name, AnchorsData dpa)"""
1908 return _IMP_multifit.write_cmm(cmm_filename, marker_set_name, dpa)
1911 """create_coarse_molecule_from_density(DensityMap dmap, float dens_threshold, int num_beads, Model mdl, float bead_radius) -> Hierarchy"""
1912 return _IMP_multifit.create_coarse_molecule_from_density(dmap, dens_threshold, num_beads, mdl, bead_radius)
1914 def create_hit_map(rb, rb_ref, sols, damp):
1915 """create_hit_map(RigidBody rb, Refiner rb_ref, IMP::multifit::FittingSolutionRecords const & sols, DensityMap damp) -> DensityMap"""
1916 return _IMP_multifit.create_hit_map(rb, rb_ref, sols, damp)
1919 """get_points_close_to_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1920 return _IMP_multifit.get_points_close_to_molecule(mh, points, max_dist)
1922 def get_points_far_from_molecule(mh, points, max_dist):
1923 """get_points_far_from_molecule(Hierarchy mh, IMP::algebra::Vector3Ds const points, IMP::Float max_dist) -> IMP::algebra::Vector3Ds"""
1924 return _IMP_multifit.get_points_far_from_molecule(mh, points, max_dist)
1926 """Proxy of C++ IMP::multifit::RadiusOfGyrationRestraint class."""
1928 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1930 def __init__(self, ps, num_residues, scale=1.):
1932 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues, IMP::Float scale=1.) -> RadiusOfGyrationRestraint
1933 __init__(IMP::multifit::RadiusOfGyrationRestraint self, IMP::Particles ps, int num_residues) -> RadiusOfGyrationRestraint
1935 this = _IMP_multifit.new_RadiusOfGyrationRestraint(ps, num_residues, scale)
1937 self.this.append(this)
1938 except __builtin__.Exception:
1941 def do_get_inputs(self):
1942 """do_get_inputs(RadiusOfGyrationRestraint self) -> IMP::ModelObjectsTemp"""
1943 return _IMP_multifit.RadiusOfGyrationRestraint_do_get_inputs(self)
1946 def get_version_info(self):
1947 """get_version_info(RadiusOfGyrationRestraint self) -> VersionInfo"""
1948 return _IMP_multifit.RadiusOfGyrationRestraint_get_version_info(self)
1951 def set_radius_of_gyration(self, r):
1952 """set_radius_of_gyration(RadiusOfGyrationRestraint self, IMP::Float r)"""
1953 return _IMP_multifit.RadiusOfGyrationRestraint_set_radius_of_gyration(self, r)
1957 """get_radius_of_gyration(RadiusOfGyrationRestraint self) -> IMP::Float"""
1958 return _IMP_multifit.RadiusOfGyrationRestraint_get_radius_of_gyration(self)
1962 """__str__(RadiusOfGyrationRestraint self) -> std::string"""
1963 return _IMP_multifit.RadiusOfGyrationRestraint___str__(self)
1967 """__repr__(RadiusOfGyrationRestraint self) -> std::string"""
1968 return _IMP_multifit.RadiusOfGyrationRestraint___repr__(self)
1973 return _object_cast_to_RadiusOfGyrationRestraint(o)
1975 RadiusOfGyrationRestraint_swigregister = _IMP_multifit.RadiusOfGyrationRestraint_swigregister
1976 RadiusOfGyrationRestraint_swigregister(RadiusOfGyrationRestraint)
1979 def get_approximated_radius_of_gyration(len):
1980 """get_approximated_radius_of_gyration(int len) -> float"""
1981 return _IMP_multifit.get_approximated_radius_of_gyration(len)
1983 def get_actual_radius_of_gyration(ps):
1984 """get_actual_radius_of_gyration(IMP::ParticlesTemp ps) -> float"""
1985 return _IMP_multifit.get_actual_radius_of_gyration(ps)
1987 def get_approximated_radius(len):
1988 """get_approximated_radius(int len) -> float"""
1989 return _IMP_multifit.get_approximated_radius(len)
1990 class ProteinsAnchorsSamplingSpace(object):
1991 """Proxy of C++ IMP::multifit::ProteinsAnchorsSamplingSpace class."""
1993 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1997 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self, ProteomicsData prots=None) -> ProteinsAnchorsSamplingSpace
1998 __init__(IMP::multifit::ProteinsAnchorsSamplingSpace self) -> ProteinsAnchorsSamplingSpace
2000 this = _IMP_multifit.new_ProteinsAnchorsSamplingSpace(prots)
2002 self.this.append(this)
2003 except __builtin__.Exception:
2006 def set_anchors(self, data):
2007 """set_anchors(ProteinsAnchorsSamplingSpace self, AnchorsData data)"""
2008 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors(self, data)
2011 def get_anchors(self):
2012 """get_anchors(ProteinsAnchorsSamplingSpace self) -> AnchorsData"""
2013 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors(self)
2016 def get_anchors_filename(self):
2017 """get_anchors_filename(ProteinsAnchorsSamplingSpace self) -> std::string"""
2018 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_anchors_filename(self)
2021 def set_anchors_filename(self, fn):
2022 """set_anchors_filename(ProteinsAnchorsSamplingSpace self, std::string const & fn)"""
2023 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_anchors_filename(self, fn)
2026 def get_proteomics_data(self):
2027 """get_proteomics_data(ProteinsAnchorsSamplingSpace self) -> ProteomicsData"""
2028 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_proteomics_data(self)
2031 def add_protein(self, rec):
2032 """add_protein(ProteinsAnchorsSamplingSpace self, ProteinRecordData rec)"""
2033 return _IMP_multifit.ProteinsAnchorsSamplingSpace_add_protein(self, rec)
2036 def get_paths_for_protein(self, prot_name):
2037 """get_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> IMP::IntsList"""
2038 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_for_protein(self, prot_name)
2041 def set_paths_filename_for_protein(self, prot_name, paths_filename):
2042 """set_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, std::string const & paths_filename)"""
2043 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_filename_for_protein(self, prot_name, paths_filename)
2046 def get_paths_filename_for_protein(self, prot_name):
2047 """get_paths_filename_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name) -> std::string"""
2048 return _IMP_multifit.ProteinsAnchorsSamplingSpace_get_paths_filename_for_protein(self, prot_name)
2051 def set_paths_for_protein(self, prot_name, paths):
2052 """set_paths_for_protein(ProteinsAnchorsSamplingSpace self, std::string const & prot_name, IMP::IntsList paths)"""
2053 return _IMP_multifit.ProteinsAnchorsSamplingSpace_set_paths_for_protein(self, prot_name, paths)
2056 def show(self, *args):
2058 show(ProteinsAnchorsSamplingSpace self, _ostream s)
2059 show(ProteinsAnchorsSamplingSpace self)
2061 return _IMP_multifit.ProteinsAnchorsSamplingSpace_show(self, *args)
2065 """__str__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2066 return _IMP_multifit.ProteinsAnchorsSamplingSpace___str__(self)
2070 """__repr__(ProteinsAnchorsSamplingSpace self) -> std::string"""
2071 return _IMP_multifit.ProteinsAnchorsSamplingSpace___repr__(self)
2073 __swig_destroy__ = _IMP_multifit.delete_ProteinsAnchorsSamplingSpace
2074 __del__ =
lambda self:
None
2075 ProteinsAnchorsSamplingSpace_swigregister = _IMP_multifit.ProteinsAnchorsSamplingSpace_swigregister
2076 ProteinsAnchorsSamplingSpace_swigregister(ProteinsAnchorsSamplingSpace)
2079 def read_protein_anchors_mapping(*args):
2081 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn, int max_paths) -> ProteinsAnchorsSamplingSpace
2082 read_protein_anchors_mapping(ProteomicsData prots, std::string const & anchors_prot_map_fn) -> ProteinsAnchorsSamplingSpace
2084 return _IMP_multifit.read_protein_anchors_mapping(*args)
2086 def write_protein_anchors_mapping(*args):
2088 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)
2089 write_protein_anchors_mapping(std::string const & anchors_prot_map_fn, ProteinsAnchorsSamplingSpace pa, IMP::Strings const & prot_names)
2091 return _IMP_multifit.write_protein_anchors_mapping(*args)
2094 """get_part_of_sampling_space(ProteinsAnchorsSamplingSpace prots_ss, IMP::Strings const & prot_names) -> ProteinsAnchorsSamplingSpace"""
2095 return _IMP_multifit.get_part_of_sampling_space(prots_ss, prot_names)
2098 """get_partial_assembly_setting_data(SettingsData prots_sd, IMP::Strings const & prot_names) -> SettingsData"""
2099 return _IMP_multifit.get_partial_assembly_setting_data(prots_sd, prot_names)
2103 read_paths(char const * txt_filename, int max_paths) -> IMP::IntsList
2104 read_paths(char const * txt_filename) -> IMP::IntsList
2106 return _IMP_multifit.read_paths(*args)
2108 def write_paths(paths, txt_filename):
2109 """write_paths(IMP::IntsList const & paths, std::string const & txt_filename)"""
2110 return _IMP_multifit.write_paths(paths, txt_filename)
2112 def molecule2anchors(mh, k):
2113 """molecule2anchors(Hierarchy mh, int k) -> AnchorsData"""
2114 return _IMP_multifit.molecule2anchors(mh, k)
2116 def get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename):
2117 """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)"""
2118 return _IMP_multifit.get_anchors_for_density(dmap, number_of_means, density_threshold, pdb_filename, cmm_filename, seg_filename, txt_filename)
2122 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs, IMP::Float max_rmsd=0.7) -> IMP::IntsList
2123 get_anchor_indices_matching_secondary_structure(AnchorsData ad, IMP::atom::SecondaryStructureResidues const & ssrs) -> IMP::IntsList
2125 return _IMP_multifit.get_anchor_indices_matching_secondary_structure(ad, ssrs, max_rmsd)
2126 class DominoParams(object):
2127 """Proxy of C++ IMP::multifit::DominoParams class."""
2129 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2132 """__init__(IMP::multifit::DominoParams self) -> DominoParams"""
2133 this = _IMP_multifit.new_DominoParams()
2135 self.this.append(this)
2136 except __builtin__.Exception:
2140 """add(DominoParams self, boost::property_tree::ptree const & pt)"""
2141 return _IMP_multifit.DominoParams_add(self, pt)
2144 def show(self, *args):
2146 show(DominoParams self, _ostream s)
2147 show(DominoParams self)
2149 return _IMP_multifit.DominoParams_show(self, *args)
2151 max_value_threshold_ = _swig_property(_IMP_multifit.DominoParams_max_value_threshold__get, _IMP_multifit.DominoParams_max_value_threshold__set)
2152 max_num_states_for_subset_ = _swig_property(_IMP_multifit.DominoParams_max_num_states_for_subset__get, _IMP_multifit.DominoParams_max_num_states_for_subset__set)
2153 max_anchor_penetration_ = _swig_property(_IMP_multifit.DominoParams_max_anchor_penetration__get, _IMP_multifit.DominoParams_max_anchor_penetration__set)
2154 heap_size_ = _swig_property(_IMP_multifit.DominoParams_heap_size__get, _IMP_multifit.DominoParams_heap_size__set)
2155 cache_size_ = _swig_property(_IMP_multifit.DominoParams_cache_size__get, _IMP_multifit.DominoParams_cache_size__set)
2158 """__str__(DominoParams self) -> std::string"""
2159 return _IMP_multifit.DominoParams___str__(self)
2163 """__repr__(DominoParams self) -> std::string"""
2164 return _IMP_multifit.DominoParams___repr__(self)
2166 __swig_destroy__ = _IMP_multifit.delete_DominoParams
2167 __del__ =
lambda self:
None
2168 DominoParams_swigregister = _IMP_multifit.DominoParams_swigregister
2169 DominoParams_swigregister(DominoParams)
2171 class XlinkParams(object):
2172 """Proxy of C++ IMP::multifit::XlinkParams class."""
2174 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2177 """__init__(IMP::multifit::XlinkParams self) -> XlinkParams"""
2178 this = _IMP_multifit.new_XlinkParams()
2180 self.this.append(this)
2181 except __builtin__.Exception:
2185 """add(XlinkParams self, boost::property_tree::ptree const & pt)"""
2186 return _IMP_multifit.XlinkParams_add(self, pt)
2189 def show(self, *args):
2191 show(XlinkParams self, _ostream s)
2192 show(XlinkParams self)
2194 return _IMP_multifit.XlinkParams_show(self, *args)
2196 upper_bound_ = _swig_property(_IMP_multifit.XlinkParams_upper_bound__get, _IMP_multifit.XlinkParams_upper_bound__set)
2197 k_ = _swig_property(_IMP_multifit.XlinkParams_k__get, _IMP_multifit.XlinkParams_k__set)
2198 max_xlink_val_ = _swig_property(_IMP_multifit.XlinkParams_max_xlink_val__get, _IMP_multifit.XlinkParams_max_xlink_val__set)
2199 treat_between_residues_ = _swig_property(_IMP_multifit.XlinkParams_treat_between_residues__get, _IMP_multifit.XlinkParams_treat_between_residues__set)
2202 """__str__(XlinkParams self) -> std::string"""
2203 return _IMP_multifit.XlinkParams___str__(self)
2207 """__repr__(XlinkParams self) -> std::string"""
2208 return _IMP_multifit.XlinkParams___repr__(self)
2210 __swig_destroy__ = _IMP_multifit.delete_XlinkParams
2211 __del__ =
lambda self:
None
2212 XlinkParams_swigregister = _IMP_multifit.XlinkParams_swigregister
2213 XlinkParams_swigregister(XlinkParams)
2215 class ConnectivityParams(object):
2216 """Proxy of C++ IMP::multifit::ConnectivityParams class."""
2218 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2221 """__init__(IMP::multifit::ConnectivityParams self) -> ConnectivityParams"""
2222 this = _IMP_multifit.new_ConnectivityParams()
2224 self.this.append(this)
2225 except __builtin__.Exception:
2229 """add(ConnectivityParams self, boost::property_tree::ptree const & pt)"""
2230 return _IMP_multifit.ConnectivityParams_add(self, pt)
2233 def show(self, *args):
2235 show(ConnectivityParams self, _ostream s)
2236 show(ConnectivityParams self)
2238 return _IMP_multifit.ConnectivityParams_show(self, *args)
2240 upper_bound_ = _swig_property(_IMP_multifit.ConnectivityParams_upper_bound__get, _IMP_multifit.ConnectivityParams_upper_bound__set)
2241 k_ = _swig_property(_IMP_multifit.ConnectivityParams_k__get, _IMP_multifit.ConnectivityParams_k__set)
2242 max_conn_rest_val_ = _swig_property(_IMP_multifit.ConnectivityParams_max_conn_rest_val__get, _IMP_multifit.ConnectivityParams_max_conn_rest_val__set)
2245 """__str__(ConnectivityParams self) -> std::string"""
2246 return _IMP_multifit.ConnectivityParams___str__(self)
2250 """__repr__(ConnectivityParams self) -> std::string"""
2251 return _IMP_multifit.ConnectivityParams___repr__(self)
2253 __swig_destroy__ = _IMP_multifit.delete_ConnectivityParams
2254 __del__ =
lambda self:
None
2255 ConnectivityParams_swigregister = _IMP_multifit.ConnectivityParams_swigregister
2256 ConnectivityParams_swigregister(ConnectivityParams)
2258 class FragmentsParams(object):
2259 """Proxy of C++ IMP::multifit::FragmentsParams class."""
2261 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2264 """__init__(IMP::multifit::FragmentsParams self) -> FragmentsParams"""
2265 this = _IMP_multifit.new_FragmentsParams()
2267 self.this.append(this)
2268 except __builtin__.Exception:
2272 """add(FragmentsParams self, boost::property_tree::ptree const & pt)"""
2273 return _IMP_multifit.FragmentsParams_add(self, pt)
2276 def show(self, *args):
2278 show(FragmentsParams self, _ostream s)
2279 show(FragmentsParams self)
2281 return _IMP_multifit.FragmentsParams_show(self, *args)
2283 frag_len_ = _swig_property(_IMP_multifit.FragmentsParams_frag_len__get, _IMP_multifit.FragmentsParams_frag_len__set)
2284 bead_radius_scale_ = _swig_property(_IMP_multifit.FragmentsParams_bead_radius_scale__get, _IMP_multifit.FragmentsParams_bead_radius_scale__set)
2285 load_atomic_ = _swig_property(_IMP_multifit.FragmentsParams_load_atomic__get, _IMP_multifit.FragmentsParams_load_atomic__set)
2286 subunit_rigid_ = _swig_property(_IMP_multifit.FragmentsParams_subunit_rigid__get, _IMP_multifit.FragmentsParams_subunit_rigid__set)
2289 """__str__(FragmentsParams self) -> std::string"""
2290 return _IMP_multifit.FragmentsParams___str__(self)
2294 """__repr__(FragmentsParams self) -> std::string"""
2295 return _IMP_multifit.FragmentsParams___repr__(self)
2297 __swig_destroy__ = _IMP_multifit.delete_FragmentsParams
2298 __del__ =
lambda self:
None
2299 FragmentsParams_swigregister = _IMP_multifit.FragmentsParams_swigregister
2300 FragmentsParams_swigregister(FragmentsParams)
2302 class RogParams(object):
2303 """Proxy of C++ IMP::multifit::RogParams class."""
2305 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2308 """__init__(IMP::multifit::RogParams self) -> RogParams"""
2309 this = _IMP_multifit.new_RogParams()
2311 self.this.append(this)
2312 except __builtin__.Exception:
2316 """add(RogParams self, boost::property_tree::ptree const & pt)"""
2317 return _IMP_multifit.RogParams_add(self, pt)
2320 def get_max_score(self):
2321 """get_max_score(RogParams self) -> float"""
2322 return _IMP_multifit.RogParams_get_max_score(self)
2325 def get_scale(self):
2326 """get_scale(RogParams self) -> float"""
2327 return _IMP_multifit.RogParams_get_scale(self)
2330 def show(self, *args):
2332 show(RogParams self, _ostream s)
2333 show(RogParams self)
2335 return _IMP_multifit.RogParams_show(self, *args)
2339 """__str__(RogParams self) -> std::string"""
2340 return _IMP_multifit.RogParams___str__(self)
2344 """__repr__(RogParams self) -> std::string"""
2345 return _IMP_multifit.RogParams___repr__(self)
2347 __swig_destroy__ = _IMP_multifit.delete_RogParams
2348 __del__ =
lambda self:
None
2349 RogParams_swigregister = _IMP_multifit.RogParams_swigregister
2350 RogParams_swigregister(RogParams)
2352 class EVParams(object):
2353 """Proxy of C++ IMP::multifit::EVParams class."""
2355 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2358 """__init__(IMP::multifit::EVParams self) -> EVParams"""
2359 this = _IMP_multifit.new_EVParams()
2361 self.this.append(this)
2362 except __builtin__.Exception:
2366 """add(EVParams self, boost::property_tree::ptree const & pt)"""
2367 return _IMP_multifit.EVParams_add(self, pt)
2370 def show(self, *args):
2372 show(EVParams self, _ostream s)
2375 return _IMP_multifit.EVParams_show(self, *args)
2377 pair_distance_ = _swig_property(_IMP_multifit.EVParams_pair_distance__get, _IMP_multifit.EVParams_pair_distance__set)
2378 pair_slack_ = _swig_property(_IMP_multifit.EVParams_pair_slack__get, _IMP_multifit.EVParams_pair_slack__set)
2379 hlb_mean_ = _swig_property(_IMP_multifit.EVParams_hlb_mean__get, _IMP_multifit.EVParams_hlb_mean__set)
2380 hlb_k_ = _swig_property(_IMP_multifit.EVParams_hlb_k__get, _IMP_multifit.EVParams_hlb_k__set)
2381 maximum_ev_score_for_pair_ = _swig_property(_IMP_multifit.EVParams_maximum_ev_score_for_pair__get, _IMP_multifit.EVParams_maximum_ev_score_for_pair__set)
2382 allowed_percentage_of_bad_pairs_ = _swig_property(_IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__get, _IMP_multifit.EVParams_allowed_percentage_of_bad_pairs__set)
2383 scoring_mode_ = _swig_property(_IMP_multifit.EVParams_scoring_mode__get, _IMP_multifit.EVParams_scoring_mode__set)
2386 """__str__(EVParams self) -> std::string"""
2387 return _IMP_multifit.EVParams___str__(self)
2391 """__repr__(EVParams self) -> std::string"""
2392 return _IMP_multifit.EVParams___repr__(self)
2394 __swig_destroy__ = _IMP_multifit.delete_EVParams
2395 __del__ =
lambda self:
None
2396 EVParams_swigregister = _IMP_multifit.EVParams_swigregister
2397 EVParams_swigregister(EVParams)
2399 class FiltersParams(object):
2400 """Proxy of C++ IMP::multifit::FiltersParams class."""
2402 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2405 """__init__(IMP::multifit::FiltersParams self) -> FiltersParams"""
2406 this = _IMP_multifit.new_FiltersParams()
2408 self.this.append(this)
2409 except __builtin__.Exception:
2413 """add(FiltersParams self, boost::property_tree::ptree const & pt)"""
2414 return _IMP_multifit.FiltersParams_add(self, pt)
2417 def show(self, *args):
2419 show(FiltersParams self, _ostream s)
2420 show(FiltersParams self)
2422 return _IMP_multifit.FiltersParams_show(self, *args)
2424 max_num_violated_xlink_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_xlink__get, _IMP_multifit.FiltersParams_max_num_violated_xlink__set)
2425 max_num_violated_conn_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_conn__get, _IMP_multifit.FiltersParams_max_num_violated_conn__set)
2426 max_num_violated_ev_ = _swig_property(_IMP_multifit.FiltersParams_max_num_violated_ev__get, _IMP_multifit.FiltersParams_max_num_violated_ev__set)
2429 """__str__(FiltersParams self) -> std::string"""
2430 return _IMP_multifit.FiltersParams___str__(self)
2434 """__repr__(FiltersParams self) -> std::string"""
2435 return _IMP_multifit.FiltersParams___repr__(self)
2437 __swig_destroy__ = _IMP_multifit.delete_FiltersParams
2438 __del__ =
lambda self:
None
2439 FiltersParams_swigregister = _IMP_multifit.FiltersParams_swigregister
2440 FiltersParams_swigregister(FiltersParams)
2442 class FittingParams(object):
2443 """Proxy of C++ IMP::multifit::FittingParams class."""
2445 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2448 """__init__(IMP::multifit::FittingParams self) -> FittingParams"""
2449 this = _IMP_multifit.new_FittingParams()
2451 self.this.append(this)
2452 except __builtin__.Exception:
2456 """add(FittingParams self, boost::property_tree::ptree const & pt)"""
2457 return _IMP_multifit.FittingParams_add(self, pt)
2460 def show(self, *args):
2462 show(FittingParams self, _ostream s)
2463 show(FittingParams self)
2465 return _IMP_multifit.FittingParams_show(self, *args)
2467 pca_max_angle_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_angle_diff__get, _IMP_multifit.FittingParams_pca_max_angle_diff__set)
2468 pca_max_size_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_size_diff__get, _IMP_multifit.FittingParams_pca_max_size_diff__set)
2469 pca_max_cent_dist_diff_ = _swig_property(_IMP_multifit.FittingParams_pca_max_cent_dist_diff__get, _IMP_multifit.FittingParams_pca_max_cent_dist_diff__set)
2470 max_asmb_fit_score_ = _swig_property(_IMP_multifit.FittingParams_max_asmb_fit_score__get, _IMP_multifit.FittingParams_max_asmb_fit_score__set)
2473 """__str__(FittingParams self) -> std::string"""
2474 return _IMP_multifit.FittingParams___str__(self)
2478 """__repr__(FittingParams self) -> std::string"""
2479 return _IMP_multifit.FittingParams___repr__(self)
2481 __swig_destroy__ = _IMP_multifit.delete_FittingParams
2482 __del__ =
lambda self:
None
2483 FittingParams_swigregister = _IMP_multifit.FittingParams_swigregister
2484 FittingParams_swigregister(FittingParams)
2486 class ComplementarityParams(object):
2487 """Proxy of C++ IMP::multifit::ComplementarityParams class."""
2489 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2492 """__init__(IMP::multifit::ComplementarityParams self) -> ComplementarityParams"""
2493 this = _IMP_multifit.new_ComplementarityParams()
2495 self.this.append(this)
2496 except __builtin__.Exception:
2500 """add(ComplementarityParams self, boost::property_tree::ptree const & pt)"""
2501 return _IMP_multifit.ComplementarityParams_add(self, pt)
2504 def show(self, *args):
2506 show(ComplementarityParams self, _ostream s)
2507 show(ComplementarityParams self)
2509 return _IMP_multifit.ComplementarityParams_show(self, *args)
2511 max_score_ = _swig_property(_IMP_multifit.ComplementarityParams_max_score__get, _IMP_multifit.ComplementarityParams_max_score__set)
2512 max_penetration_ = _swig_property(_IMP_multifit.ComplementarityParams_max_penetration__get, _IMP_multifit.ComplementarityParams_max_penetration__set)
2513 interior_layer_thickness_ = _swig_property(_IMP_multifit.ComplementarityParams_interior_layer_thickness__get, _IMP_multifit.ComplementarityParams_interior_layer_thickness__set)
2514 boundary_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_boundary_coef__get, _IMP_multifit.ComplementarityParams_boundary_coef__set)
2515 comp_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_comp_coef__get, _IMP_multifit.ComplementarityParams_comp_coef__set)
2516 penetration_coef_ = _swig_property(_IMP_multifit.ComplementarityParams_penetration_coef__get, _IMP_multifit.ComplementarityParams_penetration_coef__set)
2519 """__str__(ComplementarityParams self) -> std::string"""
2520 return _IMP_multifit.ComplementarityParams___str__(self)
2524 """__repr__(ComplementarityParams self) -> std::string"""
2525 return _IMP_multifit.ComplementarityParams___repr__(self)
2527 __swig_destroy__ = _IMP_multifit.delete_ComplementarityParams
2528 __del__ =
lambda self:
None
2529 ComplementarityParams_swigregister = _IMP_multifit.ComplementarityParams_swigregister
2530 ComplementarityParams_swigregister(ComplementarityParams)
2532 class AlignmentParams(object):
2533 """Proxy of C++ IMP::multifit::AlignmentParams class."""
2535 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2537 def __init__(self, param_filename):
2538 """__init__(IMP::multifit::AlignmentParams self, char const * param_filename) -> AlignmentParams"""
2539 this = _IMP_multifit.new_AlignmentParams(param_filename)
2541 self.this.append(this)
2542 except __builtin__.Exception:
2545 def get_domino_params(self):
2546 """get_domino_params(AlignmentParams self) -> DominoParams"""
2547 return _IMP_multifit.AlignmentParams_get_domino_params(self)
2550 def get_fitting_params(self):
2551 """get_fitting_params(AlignmentParams self) -> FittingParams"""
2552 return _IMP_multifit.AlignmentParams_get_fitting_params(self)
2555 def get_complementarity_params(self):
2556 """get_complementarity_params(AlignmentParams self) -> ComplementarityParams"""
2557 return _IMP_multifit.AlignmentParams_get_complementarity_params(self)
2560 def get_xlink_params(self):
2561 """get_xlink_params(AlignmentParams self) -> XlinkParams"""
2562 return _IMP_multifit.AlignmentParams_get_xlink_params(self)
2565 def get_connectivity_params(self):
2566 """get_connectivity_params(AlignmentParams self) -> ConnectivityParams"""
2567 return _IMP_multifit.AlignmentParams_get_connectivity_params(self)
2570 def get_rog_params(self):
2571 """get_rog_params(AlignmentParams self) -> RogParams"""
2572 return _IMP_multifit.AlignmentParams_get_rog_params(self)
2575 def get_fragments_params(self):
2576 """get_fragments_params(AlignmentParams self) -> FragmentsParams"""
2577 return _IMP_multifit.AlignmentParams_get_fragments_params(self)
2580 def get_filters_params(self):
2581 """get_filters_params(AlignmentParams self) -> FiltersParams"""
2582 return _IMP_multifit.AlignmentParams_get_filters_params(self)
2585 def get_ev_params(self):
2586 """get_ev_params(AlignmentParams self) -> EVParams"""
2587 return _IMP_multifit.AlignmentParams_get_ev_params(self)
2590 def show(self, *args):
2592 show(AlignmentParams self, _ostream s)
2593 show(AlignmentParams self)
2595 return _IMP_multifit.AlignmentParams_show(self, *args)
2599 """__str__(AlignmentParams self) -> std::string"""
2600 return _IMP_multifit.AlignmentParams___str__(self)
2604 """__repr__(AlignmentParams self) -> std::string"""
2605 return _IMP_multifit.AlignmentParams___repr__(self)
2607 __swig_destroy__ = _IMP_multifit.delete_AlignmentParams
2608 __del__ =
lambda self:
None
2609 AlignmentParams_swigregister = _IMP_multifit.AlignmentParams_swigregister
2610 AlignmentParams_swigregister(AlignmentParams)
2612 class ProteomicsEMAlignmentAtomic(
IMP.Object):
2613 """Proxy of C++ IMP::multifit::ProteomicsEMAlignmentAtomic class."""
2615 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2617 def __init__(self, mapping_data, asmb_data, align_param):
2618 """__init__(IMP::multifit::ProteomicsEMAlignmentAtomic self, ProteinsAnchorsSamplingSpace mapping_data, SettingsData asmb_data, AlignmentParams align_param) -> ProteomicsEMAlignmentAtomic"""
2619 this = _IMP_multifit.new_ProteomicsEMAlignmentAtomic(mapping_data, asmb_data, align_param)
2621 self.this.append(this)
2622 except __builtin__.Exception:
2626 """align(ProteomicsEMAlignmentAtomic self)"""
2627 return _IMP_multifit.ProteomicsEMAlignmentAtomic_align(self)
2630 def add_all_restraints(self):
2631 """add_all_restraints(ProteomicsEMAlignmentAtomic self)"""
2632 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_all_restraints(self)
2635 def get_restraint_set(self):
2636 """get_restraint_set(ProteomicsEMAlignmentAtomic self) -> RestraintSet"""
2637 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_restraint_set(self)
2640 def add_states_and_filters(self):
2641 """add_states_and_filters(ProteomicsEMAlignmentAtomic self)"""
2642 return _IMP_multifit.ProteomicsEMAlignmentAtomic_add_states_and_filters(self)
2645 def show_domino_merge_tree(self):
2646 """show_domino_merge_tree(ProteomicsEMAlignmentAtomic self)"""
2647 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_domino_merge_tree(self)
2650 def get_combinations(self, uniques=False):
2652 get_combinations(ProteomicsEMAlignmentAtomic self, bool uniques=False) -> IMP::domino::Assignments
2653 get_combinations(ProteomicsEMAlignmentAtomic self) -> IMP::domino::Assignments
2655 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_combinations(self, uniques)
2658 def set_density_map(self, dmap, threshold):
2659 """set_density_map(ProteomicsEMAlignmentAtomic self, DensityMap dmap, float threshold)"""
2660 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_density_map(self, dmap, threshold)
2663 def get_molecules(self):
2664 """get_molecules(ProteomicsEMAlignmentAtomic self) -> IMP::atom::Hierarchies"""
2665 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_molecules(self)
2668 def get_rigid_bodies(self):
2669 """get_rigid_bodies(ProteomicsEMAlignmentAtomic self) -> IMP::core::RigidBodies"""
2670 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_rigid_bodies(self)
2673 def load_combination_of_states(self, state4particles):
2674 """load_combination_of_states(ProteomicsEMAlignmentAtomic self, IMP::Ints const & state4particles)"""
2675 return _IMP_multifit.ProteomicsEMAlignmentAtomic_load_combination_of_states(self, state4particles)
2678 def show_scores_header(self, *args):
2680 show_scores_header(ProteomicsEMAlignmentAtomic self, _ostream ous)
2681 show_scores_header(ProteomicsEMAlignmentAtomic self)
2683 return _IMP_multifit.ProteomicsEMAlignmentAtomic_show_scores_header(self, *args)
2686 def get_model(self):
2687 """get_model(ProteomicsEMAlignmentAtomic self) -> Model"""
2688 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_model(self)
2691 def set_fast_scoring(self, state):
2692 """set_fast_scoring(ProteomicsEMAlignmentAtomic self, bool state)"""
2693 return _IMP_multifit.ProteomicsEMAlignmentAtomic_set_fast_scoring(self, state)
2696 def get_version_info(self):
2697 """get_version_info(ProteomicsEMAlignmentAtomic self) -> VersionInfo"""
2698 return _IMP_multifit.ProteomicsEMAlignmentAtomic_get_version_info(self)
2702 """__str__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2703 return _IMP_multifit.ProteomicsEMAlignmentAtomic___str__(self)
2707 """__repr__(ProteomicsEMAlignmentAtomic self) -> std::string"""
2708 return _IMP_multifit.ProteomicsEMAlignmentAtomic___repr__(self)
2713 return _object_cast_to_ProteomicsEMAlignmentAtomic(o)
2715 ProteomicsEMAlignmentAtomic_swigregister = _IMP_multifit.ProteomicsEMAlignmentAtomic_swigregister
2716 ProteomicsEMAlignmentAtomic_swigregister(ProteomicsEMAlignmentAtomic)
2720 """write_connolly_surface(IMP::atom::Atoms atoms, TextOutput fn, float density, float probe_radius)"""
2721 return _IMP_multifit.write_connolly_surface(atoms, fn, density, probe_radius)
2723 """Proxy of C++ IMP::multifit::Ensemble class."""
2725 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2727 def load_combination(self, fit_comb):
2728 """load_combination(Ensemble self, IMP::Ints fit_comb)"""
2729 return _IMP_multifit.Ensemble_load_combination(self, fit_comb)
2732 def unload_combination(self, fit_comb):
2733 """unload_combination(Ensemble self, IMP::Ints fit_comb)"""
2734 return _IMP_multifit.Ensemble_unload_combination(self, fit_comb)
2737 def add_component_and_fits(self, mh, fits):
2738 """add_component_and_fits(Ensemble self, Hierarchy mh, IMP::multifit::FittingSolutionRecords const & fits)"""
2739 return _IMP_multifit.Ensemble_add_component_and_fits(self, mh, fits)
2742 def get_molecules(self):
2743 """get_molecules(Ensemble self) -> IMP::atom::Hierarchies"""
2744 return _IMP_multifit.Ensemble_get_molecules(self)
2747 def get_rigid_bodies(self):
2748 """get_rigid_bodies(Ensemble self) -> IMP::core::RigidBodies"""
2749 return _IMP_multifit.Ensemble_get_rigid_bodies(self)
2753 """get_rmsd(Ensemble self, IMP::core::XYZs const & second_xyz) -> float"""
2754 return _IMP_multifit.Ensemble_get_rmsd(self, second_xyz)
2757 def __init__(self, sd, mapping_data):
2758 """__init__(IMP::multifit::Ensemble self, SettingsData sd, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2759 this = _IMP_multifit.new_Ensemble(sd, mapping_data)
2761 self.this.append(this)
2762 except __builtin__.Exception:
2765 def score_by_restraints(self, rs, combinations):
2766 """score_by_restraints(Ensemble self, IMP::Restraints rs, IMP::IntsList const & combinations) -> std::vector< IMP::Floats,std::allocator< IMP::Floats > >"""
2767 return _IMP_multifit.Ensemble_score_by_restraints(self, rs, combinations)
2770 def get_version_info(self):
2771 """get_version_info(Ensemble self) -> VersionInfo"""
2772 return _IMP_multifit.Ensemble_get_version_info(self)
2776 """__str__(Ensemble self) -> std::string"""
2777 return _IMP_multifit.Ensemble___str__(self)
2781 """__repr__(Ensemble self) -> std::string"""
2782 return _IMP_multifit.Ensemble___repr__(self)
2787 return _object_cast_to_Ensemble(o)
2789 Ensemble_swigregister = _IMP_multifit.Ensemble_swigregister
2790 Ensemble_swigregister(Ensemble)
2793 def load_ensemble(sd, mdl, mapping_data):
2794 """load_ensemble(SettingsData sd, Model mdl, ProteinsAnchorsSamplingSpace mapping_data) -> Ensemble"""
2795 return _IMP_multifit.load_ensemble(sd, mdl, mapping_data)
2797 """Proxy of C++ IMP::multifit::RigidLeavesRefiner class."""
2799 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2803 __init__(IMP::multifit::RigidLeavesRefiner self, std::string name) -> RigidLeavesRefiner
2804 __init__(IMP::multifit::RigidLeavesRefiner self) -> RigidLeavesRefiner
2806 this = _IMP_multifit.new_RigidLeavesRefiner(*args)
2808 self.this.append(this)
2809 except __builtin__.Exception:
2812 def do_get_inputs(self, m, pis):
2813 """do_get_inputs(RigidLeavesRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
2814 return _IMP_multifit.RigidLeavesRefiner_do_get_inputs(self, m, pis)
2817 def get_version_info(self):
2818 """get_version_info(RigidLeavesRefiner self) -> VersionInfo"""
2819 return _IMP_multifit.RigidLeavesRefiner_get_version_info(self)
2823 """__str__(RigidLeavesRefiner self) -> std::string"""
2824 return _IMP_multifit.RigidLeavesRefiner___str__(self)
2828 """__repr__(RigidLeavesRefiner self) -> std::string"""
2829 return _IMP_multifit.RigidLeavesRefiner___repr__(self)
2834 return _object_cast_to_RigidLeavesRefiner(o)
2836 RigidLeavesRefiner_swigregister = _IMP_multifit.RigidLeavesRefiner_swigregister
2837 RigidLeavesRefiner_swigregister(RigidLeavesRefiner)
2840 _all_commands = [
"param",
"anchors",
"fit_fft",
"cluster",
"add_fit_rmsd",
2841 "indexes",
"proteomics",
"align",
"models",
"transforms",
2842 "score",
"merge_tree",
"reference",
"refine_fft",
"segment"]
2845 def get_module_version():
2846 """get_module_version() -> std::string const"""
2847 return _IMP_multifit.get_module_version()
2850 """get_example_path(std::string fname) -> std::string"""
2851 return _IMP_multifit.get_example_path(fname)
2854 """get_data_path(std::string fname) -> std::string"""
2855 return _IMP_multifit.get_data_path(fname)
2857 from .
import _version_check
2858 _version_check.check_version(get_module_version())
2859 __version__ = get_module_version()
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_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.
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.